|
Score: 15.00 |
|---|
| Title: Purification and characterization of a high molecular mass serine carboxypeptidase from Monascus pilosus .
| | Author: Liu F Tachibana S Taira T Ishihara M Kato F Yasuda M | | Journal: J Ind . Microbiol . Biotechnol . Citation: V : 31 ( 12 ) P : 572-80 Year: 2004 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub15592905 Accession (PMID): 15592905 | | Abstract: Two serine carboxypeptidases , MpiCP-1 and MpiCP-2 , were purified to homogeneity from Monascus pilosus IFO 4480 .
MpiCP-1 is a homodimer with a native molecular mass of 125 kDa composed of two identical subunits of 61 kDa , while MpiCP-2 is a high mass homooligomer with a native molecular mass of 2 , 263 kDa composed of about 38 identical subunits of 59 kDa .
This is unique among carboxypeptidases and distinguishes MpiCP-2 as the largest known carboxypeptidase .
The two purified enzymes were both acidic glycoproteins .
MpiCP-1 has an isoelectric point of 3 . 7 and a carbohydrate content of 11% , while for MpiCP-2 these values were 4 . 0 and 33% , respectively .
The optimum pH and temperature were around 4 . 0 and 50 degrees C for MpiCP-1 , and 3 . 5 and 50 degrees C for MpiCP-2 .
MpiCP-1 was stable over a broad range of pH between 2 . 0 and 8 . 0 at 37 degrees C for 1 h , and up to 55 degrees C for 15 min at pH 6 . 0 , but MpiCP-2 was stable in a narrow range of pH between 5 . 5 and 6 . 5 , and up to 50 degrees C for 15 min at pH 6 . 0 .
Phenylmethylsulfonylfluoride strongly inhibited MpiCP-1 and completely inhibited MpiCP-2 , suggesting that they are both serine carboxypeptidases .
Of the substrates tested , benzyloxycarbonyl-L : -tyrosyl-L : -glutamic acid ( Z-Tyr-Glu ) was the best for both enzymes .
The Km , Vmax , Kcat and Kcat/Km values of MpiCP-1 for Z-Tyr-Glu at pH 4 . 0 and 37 degrees C were 1 . 33 mM , 1 . 49 mM min ( -1 ) , 723 s ( -1 ) and 545 mM ( -1 ) s ( -1 ) , and those of MpiCP-2 at pH 3 . 5 and 37 degrees C were 1 . 55 mM , 1 . 54 mM min ( -1 ) , 2 , 039 s ( -1 ) and 1 , 318 mM ( -1 ) s ( -1 ) , respectively . | Matching Sentences:
[ Sen. 1, subscore: 2.00 ]: Two serine carboxypeptidases , MpiCP-1 and MpiCP-2 , were purified to homogeneity from Monascus pilosus IFO 4480 .
[ Sen. 2, subscore: 2.00 ]: MpiCP-1 is a homodimer with a native molecular mass of 125 kDa composed of two identical subunits of 61 kDa , while MpiCP-2 is a high mass homooligomer with a native molecular mass of 2 , 263 kDa composed of about 38 identical subunits of 59 kDa .
[ Sen. 5, subscore: 2.00 ]: MpiCP-1 has an isoelectric point of 3 . 7 and a carbohydrate content of 11% , while for MpiCP-2 these values were 4 . 0 and 33% , respectively .
[ Sen. 6, subscore: 2.00 ]: The optimum pH and temperature were around 4 . 0 and 50 degrees C for MpiCP-1 , and 3 . 5 and 50 degrees C for MpiCP-2 .
[ Sen. 7, subscore: 2.00 ]: MpiCP-1 was stable over a broad range of pH between 2 . 0 and 8 . 0 at 37 degrees C for 1 h , and up to 55 degrees C for 15 min at pH 6 . 0 , but MpiCP-2 was stable in a narrow range of pH between 5 . 5 and 6 . 5 , and up to 50 degrees C for 15 min at pH 6 . 0 .
[ Sen. 8, subscore: 2.00 ]: Phenylmethylsulfonylfluoride strongly inhibited MpiCP-1 and completely inhibited MpiCP-2 , suggesting that they are both serine carboxypeptidases .
[ Sen. 10, subscore: 2.00 ]: The Km , Vmax , Kcat and Kcat/Km values of MpiCP-1 for Z-Tyr-Glu at pH 4 . 0 and 37 degrees C were 1 . 33 mM , 1 . 49 mM min ( -1 ) , 723 s ( -1 ) and 545 mM ( -1 ) s ( -1 ) , and those of MpiCP-2 at pH 3 . 5 and 37 degrees C were 1 . 55 mM , 1 . 54 mM min ( -1 ) , 2 , 039 s ( -1 ) and 1 , 318 mM ( -1 ) s ( -1 ) , respectively .
[ Sen. 3, subscore: 1.00 ]: This is unique among carboxypeptidases and distinguishes MpiCP-2 as the largest known carboxypeptidase .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 15.00 |
|---|
| Title: Tissue culture-induced transpositional activity of mPing is correlated with cytosine methylation in rice .
| | Author: Ngezahayo F Xu C Wang H Jiang L Pang J Liu B | | Journal: BMC Plant Biol Citation: V : 9 P : 91 Year: 2009 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub19604382 Accession (PMID): 19604382 | | Abstract: BACKGROUND : mPing is an endogenous MITE in the rice genome , which is quiescent under normal conditions but can be induced towards mobilization under various stresses .
The cellular mechanism responsible for modulating the activity of mPing remains unknown .
Cytosine methylation is a major epigenetic modification in most eukaryotes , and the primary function of which is to serve as a genome defense system including taming activity of transposable elements ( TEs ) .
Given that it issue-culture is capable of inducing both methylation alteration and mPing transposition in certain rice genotypes , it provides a tractable system to investigate the possible relationship between the two phenomena .
RESULTS : mPing transposition and cytosine methylation alteration were measured in callus and regenerated plants in three rice ( ssp . indica ) genotypes , V14 , V27 and R09 .
All three genotypes showed transposition of mPing , though at various frequencies .
Cytosine methylation alteration occurred both at the mPing-flanks and at random loci sampled globally in callus and regenerated plants of all three genotypes .
However , a sharp difference in the changing patterns was noted between the mPing-flanks and random genomic loci , with a particular type of methylation modification , ie , CNG hypermethylation , occurred predominantly at the mPing-flanks .
Pearsons test on pairwise correlations indicated that mPing activity is positively correlated with specific patterns of methylation alteration at random genomic loci , while the elements immobility is positively correlated with methylation levels of the mPings 5-flanks .
Bisulfite sequencing of two mPing-containing loci showed that whereas for the immobile locus loss of CG methylation in the 5-flank was accompanied by an increase in CHG methylation , together with an overall increase in methylation of all three types ( CG , CHG and CHH ) in the mPing-body region , for the active locus erasure of CG methylation in the 5-flank was not followed by such a change .
CONCLUSION : Our results documented that it issue culture-induced mPing activity in rice ssp . indica is correlated with alteration in cytosine methylation patterns at both random genomic loci and the elements flanks , while the stability of mPing positively correlates with enhanced methylation levels of both the flanks and probably the elements per se .
Thus , our results implicate a possible role of cytosine methylation in maintaining mPing stability under normal conditions , and in releasing the elements activity as a consequence of epigenetic perturbation in a locus-specific manner under certain stress conditions .
| Matching Sentences:
[ Sen. 8, subscore: 2.00 ]: However , a sharp difference in the changing patterns was noted between the mPing-flanks and random genomic loci , with a particular type of methylation modification , ie , CNG hypermethylation , occurred predominantly at the mPing-flanks .
[ Sen. 9, subscore: 2.00 ]: Pearsons test on pairwise correlations indicated that mPing activity is positively correlated with specific patterns of methylation alteration at random genomic loci , while the elements immobility is positively correlated with methylation levels of the mPings 5-flanks .
[ Sen. 10, subscore: 2.00 ]: Bisulfite sequencing of two mPing-containing loci showed that whereas for the immobile locus loss of CG methylation in the 5-flank was accompanied by an increase in CHG methylation , together with an overall increase in methylation of all three types ( CG , CHG and CHH ) in the mPing-body region , for the active locus erasure of CG methylation in the 5-flank was not followed by such a change .
[ Sen. 11, subscore: 2.00 ]: CONCLUSION : Our results documented that it issue culture-induced mPing activity in rice ssp . indica is correlated with alteration in cytosine methylation patterns at both random genomic loci and the elements flanks , while the stability of mPing positively correlates with enhanced methylation levels of both the flanks and probably the elements per se .
[ Sen. 1, subscore: 1.00 ]: BACKGROUND : mPing is an endogenous MITE in the rice genome , which is quiescent under normal conditions but can be induced towards mobilization under various stresses .
[ Sen. 2, subscore: 1.00 ]: The cellular mechanism responsible for modulating the activity of mPing remains unknown .
[ Sen. 4, subscore: 1.00 ]: Given that it issue-culture is capable of inducing both methylation alteration and mPing transposition in certain rice genotypes , it provides a tractable system to investigate the possible relationship between the two phenomena .
[ Sen. 5, subscore: 1.00 ]: RESULTS : mPing transposition and cytosine methylation alteration were measured in callus and regenerated plants in three rice ( ssp . indica ) genotypes , V14 , V27 and R09 .
[ Sen. 6, subscore: 1.00 ]: All three genotypes showed transposition of mPing , though at various frequencies .
[ Sen. 7, subscore: 1.00 ]: Cytosine methylation alteration occurred both at the mPing-flanks and at random loci sampled globally in callus and regenerated plants of all three genotypes .
[ Sen. 12, subscore: 1.00 ]: Thus , our results implicate a possible role of cytosine methylation in maintaining mPing stability under normal conditions , and in releasing the elements activity as a consequence of epigenetic perturbation in a locus-specific manner under certain stress conditions .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 13.00 |
|---|
| Title: In planta mobilization of mPing and its putative autonomous element Pong in rice by hydrostatic pressurization .
| | Author: Lin X Long L Shan X Zhang S Shen S Liu B | | Journal: J Exp . Bot . Citation: V : 57 ( 10 ) P : 2313-23 Year: Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub16818484 Accession (PMID): 16818484 | | Abstract: The miniature Ping ( mPing ) is a recently discovered endogenous miniature inverted repeat transposable element ( MITE ) in rice , which can be mobilized by it issue culture or irradiation .
It is reported here that mPing , together with one of its putative transposase-encoding partners , Pong , was efficiently mobilized in somatic cells of intact rice plants of two distinct cultivars derived from germinating seeds subjected to high hydrostatic pressure , whereas the other autonomous element of mPing , Ping , remained static in the plants studied . mPing excision was detected in several plants of both cultivars in the treated generation ( P0 ) , which were selected based on their novel phenotypes .
Southern blot analysis and transposon-display assay on selfed progenies ( P1 generation ) of two selected P0 plants , one from each of the cultivars , revealed polymorphic banding patterns consistent with mobilization of mPing and Pong .
Various mPing excisions and de novo insertions , as detected by element-bracketing , locus-specific PCR assays , occurred in the different P1 plants of both cultivars .
Pong excision at one locus for each cultivar was also detected by using a Pong internal primer together with locus-specific flanking primers in the P1 plants .
In contrast to the pressurized plants , immobility of both mPing and Pong in control plants , and the absence of within-cultivar heterozygosity at the analysed loci were verified by Southern blotting and/or locus-assay .
Sequencing at 18 mPing empty donor sites isolated from the pressurized plants indicated properties characteristic of the element excision .
Sequence-based mapping of 10 identified mPing de novo insertions from P1 progenies of pressurized plants indicated that all were in unique or low-copy regions , conforming with the targeting propensity of mPing .
No evidence for further mPing activity was detected in the P2 plants tested .
In spite of the high activity of mPing and Pong in the pressurized plants , amplified fragment length polymorphism ( AFLP ) analysis denoted their general genomic stability , and several potentially active retrotransposons also remained largely immobile .
Further investigation showed that the same hydrostatic pressure treatments also caused mobilization of mPing in the standard laboratory cultivar for japonica rice , Nipponbare .
Thus , a simple and robust approach for in planta MITE-mobilization in rice has been established by using high hydrostatic pressure treatment , which may be useful as an alternative for gene-tagging in this important crop plant . | Matching Sentences:
[ Sen. 2, subscore: 3.00 ]: It is reported here that mPing , together with one of its putative transposase-encoding partners , Pong , was efficiently mobilized in somatic cells of intact rice plants of two distinct cultivars derived from germinating seeds subjected to high hydrostatic pressure , whereas the other autonomous element of mPing , Ping , remained static in the plants studied . mPing excision was detected in several plants of both cultivars in the treated generation ( P0 ) , which were selected based on their novel phenotypes .
[ Sen. 8, subscore: 2.00 ]: Sequence-based mapping of 10 identified mPing de novo insertions from P1 progenies of pressurized plants indicated that all were in unique or low-copy regions , conforming with the targeting propensity of mPing .
[ Sen. 1, subscore: 1.00 ]: The miniature Ping ( mPing ) is a recently discovered endogenous miniature inverted repeat transposable element ( MITE ) in rice , which can be mobilized by it issue culture or irradiation .
[ Sen. 3, subscore: 1.00 ]: Southern blot analysis and transposon-display assay on selfed progenies ( P1 generation ) of two selected P0 plants , one from each of the cultivars , revealed polymorphic banding patterns consistent with mobilization of mPing and Pong .
[ Sen. 4, subscore: 1.00 ]: Various mPing excisions and de novo insertions , as detected by element-bracketing , locus-specific PCR assays , occurred in the different P1 plants of both cultivars .
[ Sen. 6, subscore: 1.00 ]: In contrast to the pressurized plants , immobility of both mPing and Pong in control plants , and the absence of within-cultivar heterozygosity at the analysed loci were verified by Southern blotting and/or locus-assay .
[ Sen. 7, subscore: 1.00 ]: Sequencing at 18 mPing empty donor sites isolated from the pressurized plants indicated properties characteristic of the element excision .
[ Sen. 9, subscore: 1.00 ]: No evidence for further mPing activity was detected in the P2 plants tested .
[ Sen. 10, subscore: 1.00 ]: In spite of the high activity of mPing and Pong in the pressurized plants , amplified fragment length polymorphism ( AFLP ) analysis denoted their general genomic stability , and several potentially active retrotransposons also remained largely immobile .
[ Sen. 11, subscore: 1.00 ]: Further investigation showed that the same hydrostatic pressure treatments also caused mobilization of mPing in the standard laboratory cultivar for japonica rice , Nipponbare .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 13.00 |
|---|
| Title: Expression of the maize proteinase inhibitor ( mpi ) gene in rice plants enhances resistance against the striped stem borer ( Chilo suppressalis ) : effects on larval growth and insect gut proteinases .
| | Author: Vila L Quilis J Meynard D Breitler JC MarfEV Murillo I Vassal JM Messeguer J Guiderdoni E San Segundo B | | Journal: Plant Biotechnol .
J Citation: V : 3 ( 2 ) P : 187-202 Year: 2005 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub17173619 Accession (PMID): 17173619 | | Abstract: The maize proteinase inhibitor ( mpi ) gene was introduced into two elite japonica rice varieties .
Both constitutive expression of the mpi gene driven by the maize ubiquitin 1 promoter and wound-inducible expression of the mpi gene driven by its own promoter resulted in the accumulation of MPI protein in the transgenic plants .
No effect on plant phenotype was observed in mpi-expressing lines .
The stability of transgene expression through successive generations of mpi rice lines ( up to the T ( 4 ) generation ) and the production of functional MPI protein were confirmed .
Expression of the mpi gene in rice enhanced resistance to the striped stem borer ( Chilo suppressalis ) , one of the most important pests of rice .
In addition , transgenic mpi plants were evaluated in terms of their effects on the growth of C suppressalis larvae and the insect digestive proteolytic system .
An important dose-dependent reduction of larval weight of C suppressalis larvae fed on mpi rice , compared with larvae fed on untransformed rice plants , was observed .
Analysis of the digestive proteolytic activity from the gut of C suppressalis demonstrated that larvae adapted to mpi transgene expression by increasing the complement of digestive proteolytic activity : the serine and cysteine endoproteinases as well as the exopeptidases leucine aminopeptidase and carboxypeptidases A and B However , the induction of such proteolytic activity did not prevent the deleterious effects of MPI on larval growth .
The introduction of the mpi gene into rice plants can thus be considered as a promising strategy to protect rice plants against striped stem borer .
| Matching Sentences:
[ Sen. 2, subscore: 3.00 ]: Both constitutive expression of the mpi gene driven by the maize ubiquitin 1 promoter and wound-inducible expression of the mpi gene driven by its own promoter resulted in the accumulation of MPI protein in the transgenic plants .
[ Sen. 4, subscore: 2.00 ]: The stability of transgene expression through successive generations of mpi rice lines ( up to the T ( 4 ) generation ) and the production of functional MPI protein were confirmed .
[ Sen. 8, subscore: 2.00 ]: Analysis of the digestive proteolytic activity from the gut of C suppressalis demonstrated that larvae adapted to mpi transgene expression by increasing the complement of digestive proteolytic activity : the serine and cysteine endoproteinases as well as the exopeptidases leucine aminopeptidase and carboxypeptidases A and B However , the induction of such proteolytic activity did not prevent the deleterious effects of MPI on larval growth .
[ Sen. 1, subscore: 1.00 ]: The maize proteinase inhibitor ( mpi ) gene was introduced into two elite japonica rice varieties .
[ Sen. 3, subscore: 1.00 ]: No effect on plant phenotype was observed in mpi-expressing lines .
[ Sen. 5, subscore: 1.00 ]: Expression of the mpi gene in rice enhanced resistance to the striped stem borer ( Chilo suppressalis ) , one of the most important pests of rice .
[ Sen. 6, subscore: 1.00 ]: In addition , transgenic mpi plants were evaluated in terms of their effects on the growth of C suppressalis larvae and the insect digestive proteolytic system .
[ Sen. 7, subscore: 1.00 ]: An important dose-dependent reduction of larval weight of C suppressalis larvae fed on mpi rice , compared with larvae fed on untransformed rice plants , was observed .
[ Sen. 9, subscore: 1.00 ]: The introduction of the mpi gene into rice plants can thus be considered as a promising strategy to protect rice plants against striped stem borer .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 7.00 |
|---|
| Title: Transpositional activation of mPing in an asymmetric nuclear somatic cell hybrid of rice and Zizania latifolia was accompanied by massive element loss .
| | Author: Shan XH Ou XF Liu ZL Dong YZ Lin XY Li XW Liu B | | Journal: Theor Appl Genet Citation: V : 119 P : 1325-33 Year: 2009 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub19711051 Accession (PMID): 19711051 | | Abstract: We have reported previously that the most active miniature inverted terminal repeat transposable element ( MITE ) of rice , mPing , was transpositionally mobilized in several rice recombinant inbred lines ( RILs ) derived from an introgressive hybridization between rice and wild rice ( Zizania latifolia Griseb . ) .
To further study the phenomenon of hybridization-induced mPing activity , we undertook the present study to investigate the elements behavior in a highly asymmetric somatic nuclear hybrid ( SH6 ) of rice and Z latifolia , which is similar in genomic composition to that of the RILs , though probably contains more introgressed alien chromatins from the donor species than the RILs .
We found that mPing , together with its transposase-donor , Pong , underwent rampant transpositional activation in the somatic hybrid ( SH6 ) .
Because possible effects of protoplast isolation and cell culture can be ruled out , we attribute the transpositional activation of mPing and Pong in SH6 to the process of asymmetric somatic hybridization , namely , one-step introgression of multiple chromatin segments of the donor species Z latifolia into the recipient rice genome .
A salient feature of mPing transposition in the somatic hybrid is that the elements activation was accompanied by massive loss of its original copies , ie , abortive transpositions , which was not observed in previously reported cases of mPing activity .
These data not only corroborated our earlier finding that wide hybridization and introgression may trigger transpositional activation of otherwise quiescent transposable elements , but also suggest that transpositional mobilization of a MITE like mPing can be accompanied by dramatic reduction of its original copy numbers under certain conditions , thus provide novel insights into the dynamics of MITEs in the course of genome evolution .
| Matching Sentences:
[ Sen. 5, subscore: 2.00 ]: A salient feature of mPing transposition in the somatic hybrid is that the elements activation was accompanied by massive loss of its original copies , ie , abortive transpositions , which was not observed in previously reported cases of mPing activity .
[ Sen. 1, subscore: 1.00 ]: We have reported previously that the most active miniature inverted terminal repeat transposable element ( MITE ) of rice , mPing , was transpositionally mobilized in several rice recombinant inbred lines ( RILs ) derived from an introgressive hybridization between rice and wild rice ( Zizania latifolia Griseb . ) .
[ Sen. 2, subscore: 1.00 ]: To further study the phenomenon of hybridization-induced mPing activity , we undertook the present study to investigate the elements behavior in a highly asymmetric somatic nuclear hybrid ( SH6 ) of rice and Z latifolia , which is similar in genomic composition to that of the RILs , though probably contains more introgressed alien chromatins from the donor species than the RILs .
[ Sen. 3, subscore: 1.00 ]: We found that mPing , together with its transposase-donor , Pong , underwent rampant transpositional activation in the somatic hybrid ( SH6 ) .
[ Sen. 4, subscore: 1.00 ]: Because possible effects of protoplast isolation and cell culture can be ruled out , we attribute the transpositional activation of mPing and Pong in SH6 to the process of asymmetric somatic hybridization , namely , one-step introgression of multiple chromatin segments of the donor species Z latifolia into the recipient rice genome .
[ Sen. 6, subscore: 1.00 ]: These data not only corroborated our earlier finding that wide hybridization and introgression may trigger transpositional activation of otherwise quiescent transposable elements , but also suggest that transpositional mobilization of a MITE like mPing can be accompanied by dramatic reduction of its original copy numbers under certain conditions , thus provide novel insights into the dynamics of MITEs in the course of genome evolution .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 6.00 |
|---|
| Title: Mobilization of a transposon in the rice genome .
| | Author: Nakazaki T Okumoto Y Horibata A Yamahira S Teraishi M Nishida H Inoue H Tanisaka T | | Journal: Nature Citation: V : 421 ( 6919 ) P : 170-2 Year: 2003 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub12520304 Accession (PMID): 12520304 | | Abstract: Rice ( Oryza sativa L ) is an important crop worldwide and , with the availability of the draft sequence , a useful model for analysing the genome structure of grasses .
To practice efficient rice breeding through genetic engineering techniques , it is important to identify the economically important genes in this crop .
The use of mobile transposons as gene tags in intact plants is a powerful tool for functional analysis because transposon insertions often inactivate genes .
Here we identify an active rice transposon named miniature Ping ( mPing ) through analysis of the mutability of a slender mutation of the glume-the seed structure that encloses and determines the shape of the grain .
The mPing transposon is inserted in the slender glume ( slg ) mutant allele but not in the wild-type allele .
Search of the O sativa variety Nipponbare genome identified 34 sequences with high nucleotide similarity to mPing , indicating that mPing constitutes a family of transposon elements .
Excision of mPing from slg plants results in reversion to a wild-type phenotype .
The mobility of the transposon mPing in intact rice plants represents a useful alternative tool for the functional analysis of rice genes . | Matching Sentences:
[ Sen. 6, subscore: 2.00 ]: Search of the O sativa variety Nipponbare genome identified 34 sequences with high nucleotide similarity to mPing , indicating that mPing constitutes a family of transposon elements .
[ Sen. 4, subscore: 1.00 ]: Here we identify an active rice transposon named miniature Ping ( mPing ) through analysis of the mutability of a slender mutation of the glume-the seed structure that encloses and determines the shape of the grain .
[ Sen. 5, subscore: 1.00 ]: The mPing transposon is inserted in the slender glume ( slg ) mutant allele but not in the wild-type allele .
[ Sen. 7, subscore: 1.00 ]: Excision of mPing from slg plants results in reversion to a wild-type phenotype .
[ Sen. 8, subscore: 1.00 ]: The mobility of the transposon mPing in intact rice plants represents a useful alternative tool for the functional analysis of rice genes .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 6.00 |
|---|
| Title: Transposition of the rice miniature inverted repeat transposable element mPing in Arabidopsis thaliana .
| | Author: Yang G Zhang F Hancock CN Wessler SR | | Journal: Proc Natl Acad Sci U S A Citation: V : 104 P : 10962-7 Year: 2007 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub17578919 Accession (PMID): 17578919 | | Abstract: An active miniature inverted repeat transposable element ( MITE ) , mPing , was discovered by computer-assisted analysis of rice genome sequence .
The mPing element is mobile in rice cell culture and in a few rice strains where it has been amplified to >1 , 000 copies during recent domestication .
However , determination of the transposase source and characterization of the mechanism of transposition have been hampered by the high copy number of mPing and the presence of several candidate autonomous elements in the rice genome .
Here , we report that mPing is active in Arabidopsis thaliana , where its transposition is catalyzed by three sources of transposase from rice : the autonomous Ping and Pong elements and by a cDNA derived from a Ping transcript .
In addition to transposase , the product of a second element-encoded ORF of unknown function is also required for mPing transposition .
Excision of mPing in A thaliana is usually precise , and transposed copies usually insert into unlinked sites in the genome that are preferentially in or near genes .
As such , this will be a valuable assay system for the dissection of MITE transposition and a potentially powerful tagging system for gene discovery in eukaryotes .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: An active miniature inverted repeat transposable element ( MITE ) , mPing , was discovered by computer-assisted analysis of rice genome sequence .
[ Sen. 2, subscore: 1.00 ]: The mPing element is mobile in rice cell culture and in a few rice strains where it has been amplified to >1 , 000 copies during recent domestication .
[ Sen. 3, subscore: 1.00 ]: However , determination of the transposase source and characterization of the mechanism of transposition have been hampered by the high copy number of mPing and the presence of several candidate autonomous elements in the rice genome .
[ Sen. 4, subscore: 1.00 ]: Here , we report that mPing is active in Arabidopsis thaliana , where its transposition is catalyzed by three sources of transposase from rice : the autonomous Ping and Pong elements and by a cDNA derived from a Ping transcript .
[ Sen. 5, subscore: 1.00 ]: In addition to transposase , the product of a second element-encoded ORF of unknown function is also required for mPing transposition .
[ Sen. 6, subscore: 1.00 ]: Excision of mPing in A thaliana is usually precise , and transposed copies usually insert into unlinked sites in the genome that are preferentially in or near genes .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 6.00 |
|---|
| Title: Transposition of the Tourist-MITE mPing in yeast : an assay that retains key features of catalysis by the class 2 PIF/Harbinger superfamily .
| | Author: Hancock CN Zhang F Wessler SR | | Journal: Mob DNA Citation: V : 1 P : 5 Year: 2010 Type: PubMed-not-MEDLINE | | Literature: oryza Field: abstract Doc ID: pub20226077 Accession (PMID): 20226077 | | Abstract: BACKGROUND : PIF/Harbinger is the most recently discovered DNA transposon superfamily and is now known to populate genomes from fungi to plants to animals .
Mobilization of superfamily members requires two separate element-encoded proteins ( ORF1 and TPase ) .
Members of this superfamily also mobilize Tourist-like miniature inverted repeat transposable elements ( MITEs ) , which are the most abundant transposable elements associated with the genes of plants , especially the cereal grasses .
The phylogenetic analysis of many plant genomes indicates that MITEs can amplify rapidly from one or a few elements to hundreds or thousands . The most active DNA transposon identified to date in plants or animals is mPing , a rice Tourist-like MITE that is a deletion derivative of the autonomous Ping element .
Ping and the closely related Pong are the only known naturally active PIF/Harbinger elements .
Some rice strains accumulate 40 new mPing insertions per plant per generation .
In this study we report the development of a yeast transposition assay as a first step in deciphering the mechanism underlying the amplification of Tourist-MITEs .
RESULTS : The ORF1 and TPase proteins encoded by Ping and Pong have been shown to mobilize mPing in rice and in transgenic Arabidopsis .
Initial tests of the native proteins in a yeast assay resulted in very low transposition .
Significantly higher activities were obtained by mutation of a putative nuclear export signal ( NES ) in the TPase that increased the amount of TPase in the nucleus .
When introduced into Arabidopsis , the NES mutant protein also catalyzed higher frequencies of mPing excision from the gfp reporter gene .
Our yeast assay retains key features of excision and insertion of mPing including precise excision , extended insertion sequence preference , and a requirement for two proteins that can come from either Ping or Pong or both elements .
CONCLUSIONS : The yeast transposition assay provides a robust platform for analysis of the mechanism underlying transposition catalyzed by the two proteins of PIF/Harbinger elements .
It recapitulates all of the features of excision and reinsertion of mPing as seen in plant systems .
Furthermore , a mutation of a putative NES in the TPase increased transposition both in yeast and plants .
| Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: The phylogenetic analysis of many plant genomes indicates that MITEs can amplify rapidly from one or a few elements to hundreds or thousands . The most active DNA transposon identified to date in plants or animals is mPing , a rice Tourist-like MITE that is a deletion derivative of the autonomous Ping element .
[ Sen. 6, subscore: 1.00 ]: Some rice strains accumulate 40 new mPing insertions per plant per generation .
[ Sen. 8, subscore: 1.00 ]: RESULTS : The ORF1 and TPase proteins encoded by Ping and Pong have been shown to mobilize mPing in rice and in transgenic Arabidopsis .
[ Sen. 11, subscore: 1.00 ]: When introduced into Arabidopsis , the NES mutant protein also catalyzed higher frequencies of mPing excision from the gfp reporter gene .
[ Sen. 12, subscore: 1.00 ]: Our yeast assay retains key features of excision and insertion of mPing including precise excision , extended insertion sequence preference , and a requirement for two proteins that can come from either Ping or Pong or both elements .
[ Sen. 14, subscore: 1.00 ]: It recapitulates all of the features of excision and reinsertion of mPing as seen in plant systems .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 6.00 |
|---|
| Title: The rice miniature inverted repeat transposable element mPing is an effective insertional mutagen in soybean .
| | Author: Hancock CN Zhang F Floyd K Richardson AO Lafayette P Tucker D Wessler SR Parrott WA | | Journal: Plant Physiol Citation: V : 157 P : 552-62 Year: 2011 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub21844309 Accession (PMID): 21844309 | | Abstract: Insertional mutagenesis of legume genomes such as soybean ( Glycine max ) should aid in identifying genes responsible for key traits such as nitrogen fixation and seed quality .
The relatively low throughput of soybean transformation necessitates the use of a transposon-tagging strategy where a single transformation event will produce many mutations over a number of generations .
However , existing transposon-tagging tools being used in legumes are of limited utility because of restricted transposition ( Ac/Ds : soybean ) or the requirement for it issue culture activation ( Tnt1 : Medicago truncatula ) .
A recently discovered transposable element from rice ( Oryza sativa ) , mPing , and the genes required for its mobilization , were transferred to soybean to determine if it will be an improvement over the other available transposon-tagging tools .
Stable transformation events in soybean were tested for mPing transposition .
Analysis of mPing excision at early and late embryo developmental stages revealed increased excision during late development in most transgenic lines , suggesting that transposition is developmentally regulated .
Transgenic lines that produced heritable mPing insertions were identified , with the plants from the highest activity line producing at least one new insertion per generation .
Analysis of the mPing insertion sites in the soybean genome revealed that features displayed in rice were retained including transposition to unlinked sites and a preference for insertion within 2 . 5 kb of a gene .
Taken together these findings indicate that mPing has the characteristics necessary for an effective transposon-tagging resource .
| Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: A recently discovered transposable element from rice ( Oryza sativa ) , mPing , and the genes required for its mobilization , were transferred to soybean to determine if it will be an improvement over the other available transposon-tagging tools .
[ Sen. 5, subscore: 1.00 ]: Stable transformation events in soybean were tested for mPing transposition .
[ Sen. 6, subscore: 1.00 ]: Analysis of mPing excision at early and late embryo developmental stages revealed increased excision during late development in most transgenic lines , suggesting that transposition is developmentally regulated .
[ Sen. 7, subscore: 1.00 ]: Transgenic lines that produced heritable mPing insertions were identified , with the plants from the highest activity line producing at least one new insertion per generation .
[ Sen. 8, subscore: 1.00 ]: Analysis of the mPing insertion sites in the soybean genome revealed that features displayed in rice were retained including transposition to unlinked sites and a preference for insertion within 2 . 5 kb of a gene .
[ Sen. 9, subscore: 1.00 ]: Taken together these findings indicate that mPing has the characteristics necessary for an effective transposon-tagging resource .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 6.00 |
|---|
| Title: Analysis of copy-number variation , insertional polymorphism , and methylation status of the tiniest class I ( TRIM ) and class II ( MITE ) transposable element families in various rice strains .
| | Author: Baruch O Kashkush K | | Journal: Plant Cell Rep Citation: V : 31 P : 885-93 Year: 2012 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub22183295 Accession (PMID): 22183295 | | Abstract: Transposable elements ( TEs ) dominate the genetic capacity of most eukaryotes , especially plants , where they may compose up to 90% of the genome .
Many studies , both in plants and animals reported that in fact non-autonomous elements that have lost their protein-coding sequences and became miniature elements were highly associated with genes , and showed a high level of transpositional activity such as mPing family in rice .
In this study , we have investigated in detail the copy number , insertional polymorphism and the methylation status of the tiniest LTR retrotransposon family , termed TRIM , in nine rice strains , in comparison with mPing .
While TRIM showed similar copy numbers ( average of 79 insertions ) in all the nine rice strains , the copy number of mPing varied dramatically ( ranging from 6 to 203 insertions ) in the same strains .
Site-specific PCR analysis revealed that 58% of the TRIM elements have identical insertion sites among the nine rice strains , while none of the mPing elements ( 100% polymorphism ) have identical insertion sites in the same strains .
Finally , over 65% of the TRIM insertion sites were cytosine methylated in all nine rice strains , while the level of the methylated mPing insertion sites ranged between 43 and 81 . 5% .
The findings of this study indicate that unlike mPing , TRIM is most probably a fossil TE family in rice .
In addition , the data shows that there might be a strong correlation between TE methylation and copy number .
| Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: Many studies , both in plants and animals reported that in fact non-autonomous elements that have lost their protein-coding sequences and became miniature elements were highly associated with genes , and showed a high level of transpositional activity such as mPing family in rice .
[ Sen. 3, subscore: 1.00 ]: In this study , we have investigated in detail the copy number , insertional polymorphism and the methylation status of the tiniest LTR retrotransposon family , termed TRIM , in nine rice strains , in comparison with mPing .
[ Sen. 4, subscore: 1.00 ]: While TRIM showed similar copy numbers ( average of 79 insertions ) in all the nine rice strains , the copy number of mPing varied dramatically ( ranging from 6 to 203 insertions ) in the same strains .
[ Sen. 5, subscore: 1.00 ]: Site-specific PCR analysis revealed that 58% of the TRIM elements have identical insertion sites among the nine rice strains , while none of the mPing elements ( 100% polymorphism ) have identical insertion sites in the same strains .
[ Sen. 6, subscore: 1.00 ]: Finally , over 65% of the TRIM insertion sites were cytosine methylated in all nine rice strains , while the level of the methylated mPing insertion sites ranged between 43 and 81 . 5% .
[ Sen. 7, subscore: 1.00 ]: The findings of this study indicate that unlike mPing , TRIM is most probably a fossil TE family in rice .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 5.00 |
|---|
| Title: Transposon display for active DNA transposons in rice .
| | Author: Takagi K Ishikawa N Maekawa M Tsugane K Iida S | | Journal: Genes Genet Syst Citation: V : 82 P : 109-22 Year: 2007 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub17507777 Accession (PMID): 17507777 | | Abstract: Transposon display ( TD ) is a powerful technique to identify the integration site of transposons in gene tagging as a functional genomic tool for elucidating gene function .
Although active endogenous DNA transposons have been used extensively for gene tagging in maize , only two active endogenous DNA transposons in rice have been identified , the 0 . 43-kb element mPing of the MITE family and the 0 . 6-kb nDart element of the hAT family .
The nDart transposition was shown to be induced by crossing with a line containing its autonomous element aDart and stabilized by segregating aDart under natural growth conditions , while mPing-related elements were shown to transpose in cultured cells , plants regenerated from an anther culture , and gamma-ray-irradiated plants .
No somaclonal variation should occur in nDart-promoted gene tagging because no it issue culture was involved in nDart activation .
As an initial step to develop an effective tagging system using nDart in rice , we tried to visualize GC-rich nDart-related elements comprising 18 nDart-related sequences of 0 . 6-kb and 63 nDart-related elements longer than 2 kb in Nipponbare by TD .
Comparing the observed bands in TD with the anticipated virtual bands of the nDart-related elements based upon the available rice genome sequence , we have improved our TD protocol by optimizing the PCR amplification conditions and are able to visualize approximately 87% of the anticipated bands produced from the nDart-related elements .
To compare the visualization efficiency of these nDart-related elements with that of 50 mPing elements and a unique Ping sequence in Nipponbare , we also tried to visualize the mPing-related elements ; all mPing-related elements are easily visualized .
Based on these results , we discuss the parameters affecting the visualization efficiencies of these rice DNA transposons .
We also discuss the utilization of nDart elements in gene tagging for functional genomics in rice .
| Matching Sentences:
[ Sen. 7, subscore: 3.00 ]: To compare the visualization efficiency of these nDart-related elements with that of 50 mPing elements and a unique Ping sequence in Nipponbare , we also tried to visualize the mPing-related elements ; all mPing-related elements are easily visualized .
[ Sen. 2, subscore: 1.00 ]: Although active endogenous DNA transposons have been used extensively for gene tagging in maize , only two active endogenous DNA transposons in rice have been identified , the 0 . 43-kb element mPing of the MITE family and the 0 . 6-kb nDart element of the hAT family .
[ Sen. 3, subscore: 1.00 ]: The nDart transposition was shown to be induced by crossing with a line containing its autonomous element aDart and stabilized by segregating aDart under natural growth conditions , while mPing-related elements were shown to transpose in cultured cells , plants regenerated from an anther culture , and gamma-ray-irradiated plants .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 4.00 |
|---|
| Title: An active DNA transposon family in rice .
| | Author: Jiang N Bao Z Zhang X Hirochika H Eddy SR McCouch SR Wessler SR .
| | Journal: Nature Citation: V : 421 ( 6919 ) P : 163-7 Year: 2003 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub12520302 Accession (PMID): 12520302 | | Abstract: The publication of draft sequences for the two subspecies of Oryza sativa ( rice ) , japonica ( cv .
Nipponbare ) and indica ( cv .
93-11 ) , provides a unique opportunity to study the dynamics of transposable elements in this important crop plant .
Here we report the use of these sequences in a computational approach to identify the first active DNA transposons from rice and the first active miniature inverted-repeat transposable element ( MITE ) from any organism .
A sequence classified as a Tourist-like MITE of 430 base pairs , called miniature Ping ( mPing ) , was present in about 70 copies in Nipponbare and in about 14 copies in 93-11 .
These mPing elements , which are all nearly identical , transpose actively in an indica cell-culture line .
Database searches identified a family of related transposase-encoding elements ( called Pong ) , which also transpose actively in the same cells .
Virtually all new insertions of mPing and Pong elements were into low-copy regions of the rice genome .
Since the domestication of rice mPing MITEs have been amplified preferentially in cultivars adapted to environmental extremes-a situation that is reminiscent of the genomic shock theory for transposon activation . | Matching Sentences:
[ Sen. 5, subscore: 1.00 ]: A sequence classified as a Tourist-like MITE of 430 base pairs , called miniature Ping ( mPing ) , was present in about 70 copies in Nipponbare and in about 14 copies in 93-11 .
[ Sen. 6, subscore: 1.00 ]: These mPing elements , which are all nearly identical , transpose actively in an indica cell-culture line .
[ Sen. 8, subscore: 1.00 ]: Virtually all new insertions of mPing and Pong elements were into low-copy regions of the rice genome .
[ Sen. 9, subscore: 1.00 ]: Since the domestication of rice mPing MITEs have been amplified preferentially in cultivars adapted to environmental extremes-a situation that is reminiscent of the genomic shock theory for transposon activation .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 4.00 |
|---|
| Title: Dramatic amplification of a rice transposable element during recent domestication .
| | Author: Naito K Cho E Yang G Campbell MA Yano K Okumoto Y Tanisaka T Wessler SR .
| | Journal: Proc . Natl . Acad . Sci . USA Citation: V : 103 ( 47 ) P : 17620-5 Year: 2006 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub17101970 Accession (PMID): 17101970 | | Abstract: Despite the prevalence of transposable elements in the genomes of higher eukaryotes , what is virtually unknown is how they amplify to very high copy numbers without killing their host Here , we report the discovery of rice strains where a miniature inverted-repeat transposable element ( mPing ) has amplified from approximately 50 to approximately 1 , 000 copies in four rice strains .
We characterized 280 of the insertions and found that 70% were within 5 kb of coding regions but that insertions into exons and introns were significantly underrepresented .
Further analyses of gene expression and transposable-element activity demonstrate that the ability of mPing to attain high copy numbers is because of three factors : ( i ) the rapid selection against detrimental insertions , ( ii ) the neutral or minimal effect of the remaining insertions on gene transcription , and ( iii ) the continued mobility of mPingelements in strains that already have > 1 , 000 copies .
The rapid increase in mPing copy number documented in this study represents a potentially valuable source of population diversity in self-fertilizing plants like rice .
| Matching Sentences:
[ Sen. 3, subscore: 2.00 ]: Further analyses of gene expression and transposable-element activity demonstrate that the ability of mPing to attain high copy numbers is because of three factors : ( i ) the rapid selection against detrimental insertions , ( ii ) the neutral or minimal effect of the remaining insertions on gene transcription , and ( iii ) the continued mobility of mPingelements in strains that already have > 1 , 000 copies .
[ Sen. 1, subscore: 1.00 ]: Despite the prevalence of transposable elements in the genomes of higher eukaryotes , what is virtually unknown is how they amplify to very high copy numbers without killing their host Here , we report the discovery of rice strains where a miniature inverted-repeat transposable element ( mPing ) has amplified from approximately 50 to approximately 1 , 000 copies in four rice strains .
[ Sen. 4, subscore: 1.00 ]: The rapid increase in mPing copy number documented in this study represents a potentially valuable source of population diversity in self-fertilizing plants like rice .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 3.00 |
|---|
| Title: The plant MITE mPing is mobilized in anther culture .
| | Author: Kikuchi K Terauchi K Wada M Hirano HY .
| | Journal: Nature Citation: V : 421 ( 6919 ) P : 167-70 Year: 2003 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub12520303 Accession (PMID): 12520303 | | Abstract: Transposable elements constitute a large portion of eukaryotic genomes and contribute to their evolution and diversification .
Miniature inverted-repeat transposable elements ( MITEs ) constitute one of the main groups of transposable elements and are distributed ubiquitously in the genomes of plants and animals such as maize , rice , Arabidopsis , human , insect and nematode .
Because active MITEs have not been identified , the transposition mechanism of MITEs and their accumulation in eukaryotic genomes remain poorly understood .
Here we describe a new class of MITE , called miniature Ping ( mPing ) , in the genome of Oryza sativa ( rice ) . mPing elements are activated in cells derived from anther culture , where they are excised efficiently from original sites and reinserted into new loci .
An mPing-associated Ping element , which has a putative PIF family transposase , is implicated in the recent proliferation of this MITE family in a subspecies of rice . | Matching Sentences:
[ Sen. 4, subscore: 2.00 ]: Here we describe a new class of MITE , called miniature Ping ( mPing ) , in the genome of Oryza sativa ( rice ) . mPing elements are activated in cells derived from anther culture , where they are excised efficiently from original sites and reinserted into new loci .
[ Sen. 5, subscore: 1.00 ]: An mPing-associated Ping element , which has a putative PIF family transposase , is implicated in the recent proliferation of this MITE family in a subspecies of rice .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 3.00 |
|---|
| Title: The prediction of protein-protein interaction networks in rice blast fungus .
| | Author: He F Zhang Y Chen H Zhang Z Peng YL | | Journal: BMC Genomics Citation: V : 9 P : 519 Year: 2008 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub18976500 Accession (PMID): 18976500 | | Abstract: BACKGROUND : Protein-protein interaction ( PPI ) maps are useful tools for investigating the cellular functions of genes .
Thus far , large-scale PPI mapping projects have not been implemented for the rice blast fungus Magnaporthe grisea , which is responsible for the most severe rice disease .
Inspired by recent advances in PPI prediction , we constructed a PPI map of this important fungus .
RESULTS : Using a well-recognized interolog approach , we have predicted 11 , 674 interactions among 3 , 017 M grisea proteins .
Although the scale of the constructed map covers approximately only one-fourth of the M griseas proteome , it is the first PPI map for this crucial organism and will therefore provide new insights into the functional genomics of the rice blast fungus .
Focusing on the network topology of proteins encoded by known pathogenicity genes , we have found that pathogenicity proteins tend to interact with higher numbers of proteins .
The pathogenicity proteins and their interacting partners in the entire network were then used to construct a subnet called a pathogenicity network .
These data may provide further clues for the study of these pathogenicity proteins .
Finally , it has been established that secreted proteins in M grisea interact with fewer proteins .
These secreted proteins and their interacting partners were also compiled into a network of secreted proteins , which may be helpful in constructing an interactome between the rice blast fungus and rice .
CONCLUSION : We predicted the PPIs of M grisea and compiled them into a database server called MPID .
It is hoped that MPID will provide new hints as to the functional genomics of this fungus .
MPID is available at http : //bioinformatics . cau . edu . cn/zzd_lab/MPID . html .
| Matching Sentences:
[ Sen. 11, subscore: 1.00 ]: CONCLUSION : We predicted the PPIs of M grisea and compiled them into a database server called MPID .
[ Sen. 12, subscore: 1.00 ]: It is hoped that MPID will provide new hints as to the functional genomics of this fungus .
[ Sen. 13, subscore: 1.00 ]: MPID is available at http : //bioinformatics . cau . edu . cn/zzd_lab/MPID . html .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 3.00 |
|---|
| Title: High potential of a transposon mPing as a marker system in japonica x japonica cross in rice .
| | Author: Monden Y Naito K Okumoto Y Saito H Oki N Tsukiyama T Ideta O Nakazaki T Wessler SR Tanisaka T | | Journal: DNA Res Citation: V : 16 P : 131-40 Year: 2009 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub19270311 Accession (PMID): 19270311 | | Abstract: Although quantitative traits loci ( QTL ) analysis has been widely performed to isolate agronomically important genes , it has been difficult to obtain molecular markers between individuals with similar phenotypes ( assortative mating ) .
Recently , the miniature inverted-repeat transposable element mPing was shown to be active in the japonica strain Gimbozu EG4 where it had accumulated more than 1000 copies .
In contrast , most other japonicas , including Nipponbare , have 50 or fewer mPing insertions in their genome .
In this study we have exploited the polymorphism of mPing insertion sites to generate 150 PCR markers in a cross between the closely related japonicas , Nipponbare x Gimbozu ( EG4 ) .
These new markers were distributed in genic regions of the whole genome and showed significantly higher polymorphism ( 150 of 183 ) than all other molecular markers tested including short sequence repeat markers ( 46 of 661 ) .
In addition , we performed QTL analysis with these markers using recombinant inbred lines derived from Nipponbare x Gimbozu EG4 , and successfully mapped a locus involved in heading date on the short arm of chromosome 6 .
Moreover , we could easily map two novel loci involved in the culm length on the short arms of chromosomes 3 and 10 .
| Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: Recently , the miniature inverted-repeat transposable element mPing was shown to be active in the japonica strain Gimbozu EG4 where it had accumulated more than 1000 copies .
[ Sen. 3, subscore: 1.00 ]: In contrast , most other japonicas , including Nipponbare , have 50 or fewer mPing insertions in their genome .
[ Sen. 4, subscore: 1.00 ]: In this study we have exploited the polymorphism of mPing insertion sites to generate 150 PCR markers in a cross between the closely related japonicas , Nipponbare x Gimbozu ( EG4 ) .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 3.00 |
|---|
| Title: Unexpected consequences of a sudden and massive transposon amplification on rice gene expression .
| | Author: Naito K Zhang F Tsukiyama T Saito H Hancock CN Richardson AO Okumoto Y Tanisaka T Wessler SR | | Journal: Nature Citation: V : 461 P : 1130-4 Year: 2009 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub19847266 Accession (PMID): 19847266 | | Abstract: High-copy-number transposable elements comprise the majority of eukaryotic genomes where they are major contributors to gene and genome evolution .
However , it remains unclear how a host genome can survive a rapid burst of hundreds or thousands of insertions because such bursts are exceedingly rare in nature and therefore difficult to observe in real time .
In a previous study we reported that in a few rice strains the DNA transposon mPing was increasing its copy number by approximately 40 per plant per generation .
Here we exploit the completely sequenced rice genome to determine 1 , 664 insertion sites using high-throughput sequencing of 24 individual rice plants and assess the impact of insertion on the expression of 710 genes by comparative microarray analysis .
We find that the vast majority of transposable element insertions either upregulate or have no detectable effect on gene transcription .
This modest impact reflects a surprising avoidance of exon insertions by mPing and a preference for insertion into 5 flanking sequences of genes .
Furthermore , we document the generation of new regulatory networks by a subset of mPing insertions that render adjacent genes stress inducible .
As such , this study provides evidence for models first proposed previously for the involvement of transposable elements and other repetitive sequences in genome restructuring and gene regulation .
| Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: In a previous study we reported that in a few rice strains the DNA transposon mPing was increasing its copy number by approximately 40 per plant per generation .
[ Sen. 6, subscore: 1.00 ]: This modest impact reflects a surprising avoidance of exon insertions by mPing and a preference for insertion into 5 flanking sequences of genes .
[ Sen. 7, subscore: 1.00 ]: Furthermore , we document the generation of new regulatory networks by a subset of mPing insertions that render adjacent genes stress inducible .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 2.00 |
|---|
| Title: P instability factor : an active maize transposon system associated with the amplification of Tourist-like MITEs and a new superfamily of transposases .
| | Author: Zhang X Feschotte C Zhang Q Jiang N Eggleston WB Wessler SR .
| | Journal: Proc . Natl . Acad . Sci . USA Citation: V : 98 ( 22 ) P : 12572-7 Year: 2001 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11675493 Accession (PMID): 11675493 | | Abstract: Miniature inverted-repeat transposable elements ( MITEs ) are widespread and abundant in both plant and animal genomes .
Despite the discovery and characterization of many MITE families , their origin and transposition mechanism are still poorly understood , largely because MITEs are nonautonomous elements with no coding capacity .
The starting point for this study was P instability factor ( PIF ) , an active DNA transposable element family from maize that was first identified following multiple mutagenic insertions into exactly the same site in intron 2 of the maize anthocyanin regulatory gene R In this study we report the isolation of a maize Tourist-like MITE family called miniature PIF ( mPIF ) that shares several features with PIF elements , including identical terminal inverted repeats , similar subterminal sequences , and an unusual but striking preference for an extended 9-bp target site .
These shared features indicate that mPIF and PIF elements were amplified by the same or a closely related transposase .
This transposase was identified through the isolation of several PIF elements and the identification of one element ( called PIFa ) that cosegregated with PIF activity .
PIFa encodes a putative protein with homologs in Arabidopsis , rice , sorghum , nematodes , and a fungus .
Our data suggest that PIFa and these PIF-like elements belong to a new eukaryotic DNA transposon superfamily that is distantly related to the bacterial IS5 group and are responsible for the origin and spread of Tourist-like MITEs .
| Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: The starting point for this study was P instability factor ( PIF ) , an active DNA transposable element family from maize that was first identified following multiple mutagenic insertions into exactly the same site in intron 2 of the maize anthocyanin regulatory gene R In this study we report the isolation of a maize Tourist-like MITE family called miniature PIF ( mPIF ) that shares several features with PIF elements , including identical terminal inverted repeats , similar subterminal sequences , and an unusual but striking preference for an extended 9-bp target site .
[ Sen. 4, subscore: 1.00 ]: These shared features indicate that mPIF and PIF elements were amplified by the same or a closely related transposase .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 2.00 |
|---|
| Title: Mobilization of the active MITE transposons mPing and Pong in rice by introgression from wild rice ( Zizania latifolia Griseb . ) .
| | Author: Shan X Liu Z Dong Z Wang Y Chen Y Lin X Long L Han F Dong Y Liu B | | Journal: Mol . Biol . Evol Citation: V : 22 ( 4 ) P : 976-90 Year: 2005 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub15647520 Accession (PMID): 15647520 | | Abstract: Hybridization between different species plays an important role in plant genome evolution , as well as is a widely used approach for crop improvement .
McClintock has predicted that plant wide hybridization constitutes a "genomic shock" whereby cryptic transposable elements may be activated .
However , direct experimental evidence showing a causal relationship between plant wide hybridization and transposon mobilization has not yet been reported .
The miniature-Ping ( mPing ) is a recently isolated active miniature inverted-repeat transposable element transposon from rice , which is mobilized by it issue culture and gamma-ray irradiation .
We show herein that mPing , together with its putative transposase-encoding partner , Pong , is mobilized in three homologous recombinant inbred lines ( RILs ) , derived from hybridization between rice ( cultivar Matsumae ) and wild rice ( Zizania latifolia Griseb . ) , harboring introgressed genomic DNA from wild rice .
In contrast , both elements remain immobile in two lines sharing the same parentage to the RILs but possessing no introgressed DNA .
Thus , we have presented direct evidence that is consistent with McClintocks insight by demonstrating a causal link between wide hybridization and transposon mobilization in rice .
In addition , we report an atypical behavior of mPing/Pong mobilization in these lines , ie , the exclusive absence of footprints after excision . | Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: The miniature-Ping ( mPing ) is a recently isolated active miniature inverted-repeat transposable element transposon from rice , which is mobilized by it issue culture and gamma-ray irradiation .
[ Sen. 5, subscore: 1.00 ]: We show herein that mPing , together with its putative transposase-encoding partner , Pong , is mobilized in three homologous recombinant inbred lines ( RILs ) , derived from hybridization between rice ( cultivar Matsumae ) and wild rice ( Zizania latifolia Griseb . ) , harboring introgressed genomic DNA from wild rice .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 2.00 |
|---|
| Title: Pathogen-induced production of the antifungal AFP protein from Aspergillus giganteus confers resistance to the blast fungus Magnaporthe grisea in transgenic rice .
| | Author: Moreno AB Peas G Rufat M Bravo JM Estop M Messeguer J San Segundo B | | Journal: Mol .
Plant Microbe Interact .
Citation: V : 18 ( 9 ) P : 960-72 Year: 2005 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub16167766 Accession (PMID): 16167766 | | Abstract: Rice blast , caused by Magnaporthe grisea , is the most important fungal disease of cultivated rice worldwide .
We have developed a strategy for creating disease resistance to M grisea whereby pathogen-induced expression of the afp ( antifungal protein ) gene from Aspergillus giganteus occurs in transgenic rice plants .
Here , we evaluated the activity of the promoters from three maize pathogenesis-related ( PR ) genes , ZmPR4 , mpi , and PRms , in transgenic rice .
Chimeric gene fusions were prepared between the maize promoters and the beta-glucuronidase reporter gene ( gus A ) .
Histochemical assays of GUS activity in transgenic rice revealed that the ZmPR4 promoter is strongly induced in response to fungal infection , treatment with fungal elicitors , and mechanical wounding .
The ZmPR4 promoter is not active in the seed endosperm .
The mpi promoter also proved responsiveness to fungal infection and wounding but not to treatment with elicitors .
In contrast , no activity of the PRms promoter in leaves of transgenic rice was observed .
Transgenic plants expressing the afp gene under the control of the ZmPR4 promoter were generated .
Transformants showed resistance to M grisea at various levels .
Our results suggest that pathogen-inducible expression of the afp gene in rice plants may be a practical way for protection against the blast fungus .
Most agricultural crop species suffer from a vast array of fungal diseases that cause severe yield losses all over the world .
Rice blast , caused by the fungus Magnaporthe grisea ( Herbert ) Barr ( anamorph Pyricularia grisea ) , is the most devastating disease of cultivated rice ( Oryza sativa L ) , due to its | Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: Here , we evaluated the activity of the promoters from three maize pathogenesis-related ( PR ) genes , ZmPR4 , mpi , and PRms , in transgenic rice .
[ Sen. 7, subscore: 1.00 ]: The mpi promoter also proved responsiveness to fungal infection and wounding but not to treatment with elicitors .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 2.00 |
|---|
| Title: Bt rice harbouring cry genes controlled by a constitutive or wound-inducible promoter : protection and transgene expression under Mediterranean field conditions .
| | Author: Breitler JC Vassal JM Del Mar Catala M Meynard D MarfEV MelEE Royer M Murillo I San Segundo B Guiderdoni E Messeguer J | | Journal: Plant Biotechnol .
J Citation: V : 2 ( 5 ) P : 417-30 Year: 2004 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub17168888 Accession (PMID): 17168888 | | Abstract: Seven homozygous transgenic lines of two European commercial cultivars of rice ( Ariete ( A ) and Senia ( S ) ) , harbouring the cry1B or cry1Aa Bacillus thuringiensis ( Bt ) delta-endotoxin genes , were field evaluated for protection from striped stem borer ( SSB ) ( Chilo suppressalis ) damage during the 2001 and 2002 summer crop seasons in the Delta de lEbre region , Spain .
The plant codon-optimized toxin gene was placed under the control of the promoter of either the constitutive ubi1 gene or the wound-inducible mpi gene from maize .
Stable , high-level , insecticidal protein accumulation was observed throughout root , leaf and seed it issues of field-grown plants harbouring the cry1B ( lines A64 . 1 , A33 . 1 , A3 . 4 and S98 . 9 ) or cry1Aa ( lines S05 . 1 and A19 . 14 ) genes under the control of the ubi1 promoter .
Conversely , no toxin was detected in unwounded vegetative it issues of the A9 . 1 line harbouring the cry1B gene controlled by the mpi promoter , indicating that natural environmental stresses did not trigger the activity of the wound-inducible promoter .
However , the toxin accumulated at 0 . 2% total soluble proteins in A9 . 1 sheath it issue exhibiting brown lesions resulting from SSB damage .
The agronomical traits and performance of the transgenic lines were generally comparable with parental controls , except in the two lines accumulating Cry1Aa , which exhibited a high frequency of plants non-true to type .
Natural infestation was assisted with manual infestations of L2/L3 SSB larvae in border control plants surrounding the experimental plots , which served as a reservoir for the second-cycle SSB population .
The observation of damage ( brown lesions and dead hearts ) during the crop season and dissection of plants at harvest stage revealed a range of protection amongst the transgenic lines , which was highly consistent with the level of toxin accumulation and with previous experience in greenhouse assays .
Lines A3 . 4 and S05 . 1 were found to exhibit stable and full protection against SSB attacks , mediated by the accumulation of Cry1B and Cry1Aa toxin , respectively , which was comparable with that afforded by the spraying of chemical insecticides on control plants .
The wound-induced A9 . 1 line exhibited a satisfactory level of protection , with a notably low level of penetration of SSB larvae in the stems , but higher external symptoms than constitutive lines , probably due to the time lag to benefit from the protective effect of Cry1B .
| Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: The plant codon-optimized toxin gene was placed under the control of the promoter of either the constitutive ubi1 gene or the wound-inducible mpi gene from maize .
[ Sen. 4, subscore: 1.00 ]: Conversely , no toxin was detected in unwounded vegetative it issues of the A9 . 1 line harbouring the cry1B gene controlled by the mpi promoter , indicating that natural environmental stresses did not trigger the activity of the wound-inducible promoter .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 2.00 |
|---|
| Title: Somaclonal variation at the nucleotide sequence level in rice ( Oryza sativa L ) as revealed by RAPD and ISSR markers , and by pairwise sequence analysis .
| | Author: Ngezahayo F Dong Y Liu B | | Journal: J Appl Genet Citation: V : 48 P : 329-36 Year: 2007 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub17998589 Accession (PMID): 17998589 | | Abstract: The nature of somaclonal variation at the nucleotide sequence level was studied in rice cv .
Nipponbare .
First , we investigated genomic variations by using 2 molecular marker systems : RAPD ( random amplified polymorphic DNA ) and ISSR ( inter-simple sequence repeat ) .
This was followed by sequencing of selected bands that represented genomic variations , and pairwise sequence analysis taking advantage of the whole genome sequence of rice .
In addition , transpositional activity of the active MITE , mPing , was analysed by locus-specific PCR amplifications .
The 2-year-old calli and their regenerated plants , analysed with 24 RAPD and 20 ISSR primers , showed moderate levels of genomic variation ( 20 . 83% and 17 . 04% , respectively ) .
To test whether DNA methylation plays a role in somaclonal variation , the calli were treated with 5-azacytidine , a chemical agent that reduces cytosine methylation by blocking the activity of DNA methyltransferase .
Though dwarfism occurred in regenerants from treated calli ( a hallmark of the drug treatment ) , there was only a slight increase in the frequency of somaclonal variation detected in the treated calli and their regenerated plants relative to untreated controls .
The transposon mPing also remained immobile in both treated and untreated calli .
Nevertheless , dendrograms constructed according to the Jaccard coefficient calculated by UPGMA of the ISSR bands revealed that the 5-azacytidine-treated and untreated somaclones were grouped into 2 distinct clusters , suggesting a possible indirect effect of the treatment on the genomic changes , depending on the marker used .
Sequence analysis indicated a low level of variation ( 0 . 31% ) , with single-base-pair substitutions predominating .
| Matching Sentences:
[ Sen. 5, subscore: 1.00 ]: In addition , transpositional activity of the active MITE , mPing , was analysed by locus-specific PCR amplifications .
[ Sen. 9, subscore: 1.00 ]: The transposon mPing also remained immobile in both treated and untreated calli .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 2.00 |
|---|
| Title: The RegEx trial : a randomized , double-blind , placebo and active-controlled pilot study combining regadenoson , a selective A ( 2A ) adenosine agonist , with low-level exercise , in patients undergoing myocardial perfusion imaging .
| | Author: Thomas GS Thompson RC Miyamoto MI Ip TK Rice DL Milikien D Lieu HD Mathur VS | | Journal: J Nucl Cardiol Citation: V : 16 P : 63-72 Year: 2009 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub19152130 Accession (PMID): 19152130 | | Abstract: BACKGROUND : Although vasodilator stress myocardial perfusion imaging ( MPI ) is increasingly performed with exercise , adenosine A ( 2A ) receptor agonists have not been studied with exercise .
OBJECTIVES : To determine the safety of administering regadenoson during exercise and , secondarily , to evaluate image quality , patient acceptance , and detection of perfusion defects .
METHODS : Patients requiring pharmacologic MPI received a standard adenosine-supine protocol ( AdenoSup , n = 60 ) and were then randomized ( 2 : 1 ) in a double-blind manner to low-level exercise with bolus intravenous injection of regadenoson ( RegEx , n = 39 ) or placebo ( PlcEx , n = 21 ) .
RESULTS : Adverse events occurred in 95% , 77% , and 33% of patients receiving AdenoSup , RegEx , and PlcEx , respectively .
Peak heart rate was 13 beats per minute ( bpm ) and 21 bpm greater following RegEx compared to that following PlcEx and AdenoSup , respectively ( P = . 006 and < . 001 ) .
Change from baseline in mean systolic blood pressure ( SBP ) , change from baseline to nadir SBP , and percentage of patients with a decline in SBP by > or = 20 mm Hg showed no important differences between RegEx and PlcEx No occurrences of 2nd degree or higher AV block were observed following RegEx or PlcEx ; one patient developed 2nd degree AV block following AdenoSup .
The mean heart-to-liver and heart-to-gut ratios were improved on RegEx vs AdenoSup : 0 . 85 ( 0 . 34 ) vs 0 . 65 ( 0 . 26 ) , P < . 001 and 1 . 1 ( 0 . 36 ) vs 0 . 97 ( 0 . 34 ) , P < . 001 , respectively .
Compared to AdenoSup , 70% of patients felt RegEx was much or somewhat better .
CONCLUSIONS : Combining regadenoson with low-level exercise is feasible , well tolerated , and associated with fewer side effects compared to AdenoSup .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: BACKGROUND : Although vasodilator stress myocardial perfusion imaging ( MPI ) is increasingly performed with exercise , adenosine A ( 2A ) receptor agonists have not been studied with exercise .
[ Sen. 3, subscore: 1.00 ]: METHODS : Patients requiring pharmacologic MPI received a standard adenosine-supine protocol ( AdenoSup , n = 60 ) and were then randomized ( 2 : 1 ) in a double-blind manner to low-level exercise with bolus intravenous injection of regadenoson ( RegEx , n = 39 ) or placebo ( PlcEx , n = 21 ) .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 2.00 |
|---|
| Title: Molecular characterization of a rice mutator-phenotype derived from an incompatible cross-pollination reveals transgenerational mobilization of multiple transposable elements and extensive epigenetic instability .
| | Author: Wang H Chai Y Chu X Zhao Y Wu Y Zhao J Ngezahayo F Xu C Liu B | | Journal: BMC Plant Biol Citation: V : 9 P : 63 Year: 2009 Type: Publisher | | Literature: oryza Field: abstract Doc ID: pub19476655 Accession (PMID): 19476655 | | Abstract: ABSTRACT : BACKGROUND : Inter-specific hybridization occurs frequently in plants , which may induce genetic and epigenetic instabilities in the resultant hybrids , allopolyploids and introgressants .
It remains unclear however whether pollination by alien pollens of an incompatible species may impose a "biological stress" even in the absence of genome-merger or genetic introgression , whereby genetic and/or epigenetic instability of the maternal recipient genome might be provoked .
RESULTS : We report here the identification of a rice mutator-phenotype from a set of rice plants derived from a crossing experiment involving two remote and apparently incompatible species , Oryza sativa L and Oenothera biennis L .
The mutator-phenotype ( named Tong211-LP ) showed distinct alteration in several traits , with the most striking being substantially enlarged panicles .
Expectably , gel-blotting by total genomic DNA of the pollen-donor showed no evidence for introgression .
Characterization of Tong211-LP ( S0 ) and its selfed progenies ( S1 ) ruled out contamination ( via seed or pollen ) or polyploidy as a cause for its dramatic phenotypic changes , but revealed transgenerational mobilization of several previously characterized transposable elements ( TEs ) , including a MITE ( mPing ) , and three LTR retrotransposons ( Osr7 , Osr23 and Tos17 ) .
AFLP and MSAP fingerprinting revealed extensive , transgenerational alterations in cytosine methylation and to a less extent also genetic variation in Tong211-LP and its immediate progenies . mPing mobility was found to correlate with cytosine methylation alteration detected by MSAP but not with genetic variation detected by AFLP .
Assay by q-RT-PCR of the steady-state transcript abundance of a set of genes encoding for the various putative DNA methyltransferases , 5-methylcytosine DNA glycosylases , and small interference RNA ( siRNA ) pathway-related proteins showed that , relative to the rice parental line , heritable perturbation in expression of 12 out of the 13 genes occurred in the mutator-phenotype and its sefled progenies .
CONCLUSIONS : Transgenerational epigenetic instability in the form of altered cytosine methylation and its associated TE activity occurred in a rice mutator-phenotype produced by pollinating the rice stigma with pollens of O biennis .
Heritably perturbed homeostatic expression-state of genes involved in maintenance of chromatin structure is likely an underlying cause for the alien pollination-induced transgenerational epigenetic/genetic instability , and which occurred apparently without entailing genome merger or genetic introgression .
| Matching Sentences:
[ Sen. 6, subscore: 1.00 ]: Characterization of Tong211-LP ( S0 ) and its selfed progenies ( S1 ) ruled out contamination ( via seed or pollen ) or polyploidy as a cause for its dramatic phenotypic changes , but revealed transgenerational mobilization of several previously characterized transposable elements ( TEs ) , including a MITE ( mPing ) , and three LTR retrotransposons ( Osr7 , Osr23 and Tos17 ) .
[ Sen. 7, subscore: 1.00 ]: AFLP and MSAP fingerprinting revealed extensive , transgenerational alterations in cytosine methylation and to a less extent also genetic variation in Tong211-LP and its immediate progenies . mPing mobility was found to correlate with cytosine methylation alteration detected by MSAP but not with genetic variation detected by AFLP .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 2.00 |
|---|
| Title: Long-culm mutations with dominant genes are induced by mPing transposon in rice .
| | Author: Tomita M Tanisaka T | | Journal: Hereditas Citation: V : 147 P : 256-63 Year: 2010 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub21166795 Accession (PMID): 21166795 | | Abstract: Development of semidwarf rice cultivars contributed to the epoch of high yielding crops called the Green Revolution .
However , over-reliance on semidwarf rice also has intrinsic limitations to supply food for an ever expanding world population .
As a solution to the food supply problem , we propose the development of tall dwarf rice cultivars that are characterized by increased biomass with long culms or large grains .
However , genetic studies on the elongation of rice culms have remained scarce .
This study seeks to analyze mutant genes involved in culm elongation in long-culm mutants induced by the MITE transposon mPing , which has been shown to be active in the japonica cultivar Gimbozu .
Through analysis of the experimental results , we have confirmed that the three mutant long-culm genes exhibit genetic dominance .
These represent rare cases of artificially induced dominant mutations .
It is very likely that the mPing transposons played an important role in inducing the dominant mutations and also play an evolutionary interesting role .
| Matching Sentences:
[ Sen. 5, subscore: 1.00 ]: This study seeks to analyze mutant genes involved in culm elongation in long-culm mutants induced by the MITE transposon mPing , which has been shown to be active in the japonica cultivar Gimbozu .
[ Sen. 8, subscore: 1.00 ]: It is very likely that the mPing transposons played an important role in inducing the dominant mutations and also play an evolutionary interesting role .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: Species-specific analysis of protein sequence motifs using mutual information .
| | Author: Hummel J Keshvari N Weckwerth W Selbig J | | Journal: BMC Bioinformatics Citation: V : 6 ( ) P : 164 Year: Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub15987530 Accession (PMID): 15987530 | | Abstract: BACKGROUND : Protein sequence motifs are by definition short fragments of conserved amino acids , often associated with a specific function .
Accordingly protein sequence profiles derived from multiple sequence alignments provide an alternative description of functional motifs characterizing families of related sequences .
Such profiles conveniently reflect functional necessities by pointing out proximity at conserved sequence positions as well as depicting distances at variable positions .
Discovering significant conservation characteristics within the variable positions of profiles mirrors group-specific and , in particular , evolutionary features of the underlying sequences .
RESULTS : We describe the tool PROfile analysis based on Mutual Information ( PROMI ) that enables comparative analysis of user-classified protein sequences .
PROMI is implemented as a web service using Perl and R as well as other publicly available packages and tools on the server-side .
On the client-side platform-independence is achieved by generally applied internet delivery standards .
As one possible application analysis of the zinc finger C2H2-type protein domain is introduced to illustrate the functionality of the tool .
CONCLUSION : The web service PROMI should assist researchers to detect evolutionary correlations in protein profiles of defined biological sequences .
It is available at http : //promi . mpimp-golm . mpg . de where additional documentation can be found . | Matching Sentences:
[ Sen. 10, subscore: 1.00 ]: It is available at http : //promi . mpimp-golm . mpg . de where additional documentation can be found .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: Alterations in DNA methylation and genome structure in two rice mutant lines induced by high pressure .
| | Author: Shen S Wang Z Shan X Wang H Li L Lin X Long L Weng K Liu B Zou G | | Journal: Sci .
China , C , Life Sci .
Citation: V : 49 ( 2 ) P : 97-104 Year: 2006 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub16704112 Accession (PMID): 16704112 | | Abstract: By using high-pressure treatment , two mutant lines were obtained from a genetically stable japonica rice cultivar Bijing38 .
Genomic DNA of the mutant lines , together with the original line ( Bijing38 ) , was either undigested or digested by Hpa IIMsp I , and then subjected to molecular analysis using two markers , ISSR and RAPD .
Results indicated that changes in the PCR amplification profiles of both markers are apparent in the two mutant lines compared with the original rice cultivar , suggesting that there had been both sequence changes and DNA methylation modifications in the mutant lines .
Southern blot analysis using diverse sequences , including two cellular genes ( S2 and S3 ) , a set of retrotransposons ( Osr7 , Osr36 , Tos19 and more ) , and a MITE transposon family ( mPing and Pong ) , confirmed the results , and indicated that changes in DNA methylation pattern , genomic structure , and possible activation of some transposons indeed occurred in the mutant lines .
Moreover , these changes are stably maintained through selfed generations and in different organs .
Thus , our results indicate that it is possible to obtain stable mutants in rice by high pressure treatments , and the molecular basis of the mutants may include both genetic and epigenetic changes .
Therefore , high hydrostatic pressure seems a promising approach for plant mutagenesis . | Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: Southern blot analysis using diverse sequences , including two cellular genes ( S2 and S3 ) , a set of retrotransposons ( Osr7 , Osr36 , Tos19 and more ) , and a MITE transposon family ( mPing and Pong ) , confirmed the results , and indicated that changes in DNA methylation pattern , genomic structure , and possible activation of some transposons indeed occurred in the mutant lines .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: The proteins encoded by the pogo-like Lemi1 element bind the TIRs and subterminal repeated motifs of the Arabidopsis Emigrant MITE : consequences for the transposition mechanism of MITEs .
| | Author: Loot C Santiago N Sanz A Casacuberta JM .
| | Journal: Nucleic Acids Res .
Citation: V : 34 ( 18 ) P : 5238-46 Year: Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub17003053 Accession (PMID): 17003053 | | Abstract: MITEs ( miniature inverted-repeated transposable elements ) are a particular class of defective DNA transposons usually present within genomes as high copy number populations of highly homogeneous elements .
Although an active MITE , the mPing element , has recently been characterized in rice , the transposition mechanism of MITEs remains unknown .
It has been proposed that transposases of related transposons could mobilize MITEs in trans .
Moreover , it has also been proposed that the presence of conserved terminal inverted-repeated ( TIR ) sequences could be the only requirement of MITEs for mobilization , allowing divergent or unrelated elements to be mobilized by a particular transposase .
We present here evidence for a recent mobility of the Arabidopsis Emigrant MITE and we report on the capacity of the proteins encoded by the related Lemi1 transposon , a pogo-related element , to specifically bind Emigrant elements .
This suggests that Lemi1 could mobilize Emigrant elements and makes the Lemi1/Emigrant couple an ideal system to study the transposition mechanism of MITEs .
Our results show that Lemi1 proteins bind Emigrant TIRs but also bind cooperatively to subterminal repeated motifs .
The requirement of internal sequences for the formation of proper DNA/protein structure could affect the capacity of divergent MITEs to be mobilized by distantly related transposases .
| Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: Although an active MITE , the mPing element , has recently been characterized in rice , the transposition mechanism of MITEs remains unknown .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: A sequence related to rice Pong transposable element displays transcriptional activation by in vitro culture and reveals somaclonal variations in maize .
| | Author: Barret P Brinkman M Beckert M | | Journal: Genome Citation: V : 49 ( 11 ) P : 1399-407 Year: 2006 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub17426755 Accession (PMID): 17426755 | | Abstract: Miniature inverted-repeat transposable elements ( MITEs ) are nonautonomous elements that are abundant in plant genomes .
The rice MITE mPing was shown to be mobilized by anther culture , and the associated transposon Pong was shown to transpose actively in an Oryza sativa indica rice cell-culture line .
We have identified 3 sequences in maize named ZmTPAPong-like 1 , 2 , and 3 that displayed homology with the transposase of Pong .
Here , we show that these sequences are differentially expressed during the in vitro androgenetic process in maize .
We also demonstrate that the ZmTPAPong-like 1 and 3 sequences reveal somaclonal variations among plants regenerated from the calli of a doubled haploid line .
These data suggest that the ZmTPAPong-like sequences could form part of a Zea mays element related to the rice Pong element .
The possible activation of this newly discovered element under stress conditions is discussed .
| Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: The rice MITE mPing was shown to be mobilized by anther culture , and the associated transposon Pong was shown to transpose actively in an Oryza sativa indica rice cell-culture line .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: A transposon , ping , is integrated into intron 4 of the DROOPING LEAF gene of rice , weakly reducing its expression and causing a mild drooping leaf phenotype .
| | Author: Ohmori Y Abiko M Horibata A Hirano HY | | Journal: Plant Cell Physiol Citation: V : 49 P : 1176-84 Year: 2008 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub18593744 Accession (PMID): 18593744 | | Abstract: The YABBY gene DROOPING LEAF ( DL ) regulates midrib formation in the leaves and carpel specification in the flowers of rice ( Oryza sativa L ) .
We found a new dl allele ( dl-5 ) that caused a mild phenotype in the descendants of a mutable line , IM294 .
In plants homozygous for this allele , midrib structures were formed but their sizes were reduced .
Molecular analysis revealed that a transposon , Ping , was inserted in the fourth intron of DL .
Together with mPing and Pong , Ping is a member of a transposon family that was first identified as a group of active transposable elements in rice .
Our finding of the Ping insertion in the DL gene is a first indication that Ping is active in planta , and that it can be transposed and integrated in a new locus .
Ping seems to be still active because it was excised from intron 4 of DL at a relatively high frequency in rice calli .
Real-time PCR analysis and in situ hybridization indicated that DL transcript levels were reduced in dl-5 without alterations in the spatial expression pattern of the DL gene .
The reduction of DL expression may be due to inefficient splicing of the large intron caused by Ping insertion .
By comparing the expression levels of DL and leaf phenotypes in the dl mutants with different severities , we confirmed our previous hypothesis that DL promotes cell proliferation in the central region of leaf primordia , and that this cell proliferation is critical for midrib formation in the mature leaves .
| Matching Sentences:
[ Sen. 5, subscore: 1.00 ]: Together with mPing and Pong , Ping is a member of a transposon family that was first identified as a group of active transposable elements in rice .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: Multiple alleles at Early flowering 1 locus making variation in the basic vegetative growth period in rice ( Oryza sativa L ) .
| | Author: Saito H Yuan Q Okumoto Y Doi K Yoshimura A Inoue H Teraishi M Tsukiyama T Tanisaka T | | Journal: Theor Appl Genet Citation: V : P : Year: 2009 Type: Publisher | | Literature: oryza Field: abstract Doc ID: pub19407983 Accession (PMID): 19407983 | | Abstract: A recently established rice breeding program in low latitudes aims to develop varieties with extremely long basic vegetative growth ( BVG ) periods and weak photoperiod sensitivities .
The Taiwanese japonica variety Taichung 65 ( T65 ) harbors a recessive allele ef1 at the Ef1 ( Early flowering 1 ) locus , thereby exhibiting an extremely long BVG period .
The previous reported functional allele Ehd1 ( Early heading date 1 ) , located on chromosome 10 , encodes a B-type response regulator , thereby shortening the BVG period , whereas its nonfunctional allele ehd1 greatly prolongs the BVG period .
A conventional analysis using F ( 2 ) and F ( 3 ) populations and a subsequent CAPS analysis based on the amino acid sequences of Ehd1 and ehd1 showed that Ef1 and Ehd1 were at the same locus .
The CAPS analysis also indicated that the Taiwanese japonica varieties with extremely long BVG periods all harbor ef1 , but that ef1 does not exist among indica and japonica varieties in the low latitudes .
Since ef1 has not been found in any japonica varieties outside Taiwan , this allele might have originated in Taiwan .
Sequence analysis revealed that the mutant allele ef1-h , which prolongs the BVG period even more than ef1 does , harbors an mPing insertion in exon 2 , which causes the complete loss of gene function .
Our results indicate that both ef1 or ef1-h alleles can be used as new gene sources in developing rice varieties with extremely long BVG periods for low latitudes .
| Matching Sentences:
[ Sen. 7, subscore: 1.00 ]: Sequence analysis revealed that the mutant allele ef1-h , which prolongs the BVG period even more than ef1 does , harbors an mPing insertion in exon 2 , which causes the complete loss of gene function .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: Epidemiological studies on Japanese encephalitis in Kyoto City area , Japan .
I Evidence for decrease of vector mosquitoes .
| | Author: Maeda O Takenokuma K Karoji Y Matsuyama Y | | Journal: Jpn .
J Med . Sci . Biol . Citation: V : 31 ( 1 ) P : 27-37 Year: 1978 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub207913 Accession (PMID): 207913 | | Abstract: Mosquito collections by using light traps have been carried out at 10 to 11 stations in Kyoto City area at intervals of about 10 days every year .
Mean percent indexes ( MPI ) , being calculated from the data of mosquito collections , were used for comparison of the annual abundance of mosquitoes .
It is no doubt that Culex tritaeniorhynchus summorosus has decreased recently and this decrease is correlated with the reduction of human patients of Japanese encephalitis .
Wide use of two herbicides , CNP and nitrofen , for rice plant cultivation , may probably be one of the reasons for the decrease of the mosquitoes .
| Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: Mean percent indexes ( MPI ) , being calculated from the data of mosquito collections , were used for comparison of the annual abundance of mosquitoes .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: Transpositional reactivation of the Dart transposon family in rice lines derived from introgressive hybridization with Zizania latifolia .
| | Author: Wang N Wang H Wang H Zhang D Wu Y Ou X Liu S Dong Z Liu B | | Journal: BMC Plant Biol Citation: V : 10 P : 190 Year: 2010 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub20796287 Accession (PMID): 20796287 | | Abstract: BACKGROUND : It is widely recognized that interspecific hybridization may induce "genome shock" , and lead to genetic and epigenetic instabilities in the resultant hybrids and/or backcrossed introgressants .
A prominent component involved in the genome shock is reactivation of cryptic transposable elements ( TEs ) in the hybrid genome , which is often associated with alteration in the elements epigenetic modifications like cytosine DNA methylation .
We have previously reported that introgressants derived from hybridization between Oryza sativa ( rice ) and Zizania latifolia manifested substantial methylation re-patterning and rampant mobilization of two TEs , a copia retrotransposon Tos17 and a MITE mPing .
It was not known however whether other types of TEs had also been transpositionally reactivated in these introgressants , their relevance to alteration in cytosine methylation , and their impact on expression of adjacent cellular genes .
RESULTS : We document in this study that the Dart TE family was transpositionally reactivated followed by stabilization in all three studied introgressants ( RZ1 , RZ2 and RZ35 ) derived from introgressive hybridization between rice ( cv .
Matsumae ) and Z latifolia , while the TEs remained quiescent in the recipient rice genome .
Transposon-display ( TD ) and sequencing verified the elements mobility and mapped the excisions and re-insertions to the rice chromosomes .
Methylation-sensitive Southern blotting showed that the Dart TEs were heavily methylated along their entire length , and moderate alteration in cytosine methylation patterns occurred in the introgressants relative to their rice parental line .
Real-time qRT-PCR quantification on the relative transcript abundance of six single-copy genes flanking the newly excised or inserted Dart-related TE copies indicated that whereas marked difference in the expression of all four genes in both it issues ( leaf and root ) were detected between the introgressants and their rice parental line under both normal and various stress conditions , the difference showed little association with the presence or absence of the newly mobilized Dart-related TEs .
CONCLUSION : Introgressive hybridization has induced transpositional reactivation of the otherwise immobile Dart-related TEs in the parental rice line ( cv .
Matsumae ) , which was accompanied with a moderate alteration in the elements cytosine methylation .
Significant difference in expression of the Dart-adjacent genes occurred between the introgressants and their rice parental line under both normal and various abiotic stress conditions , but the alteration in gene expression was not coupled with the TEs .
| Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: We have previously reported that introgressants derived from hybridization between Oryza sativa ( rice ) and Zizania latifolia manifested substantial methylation re-patterning and rampant mobilization of two TEs , a copia retrotransposon Tos17 and a MITE mPing .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: Transpositional reactivation of two LTR retrotransposons in rice-Zizania recombinant inbred lines ( RILs ) .
| | Author: Wang HY Tian Q Ma YQ Wu Y Miao GJ Ma Y Cao DH Wang XL Lin C Pang J Liu B | | Journal: Hereditas Citation: V : 147 P : 264-77 Year: 2010 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub21166796 Accession (PMID): 21166796 | | Abstract: Hybridization is prevalent in plants , which plays important roles in genome evolution .
Apart from direct transfer and recombinatory generation of genetic variations by hybridization , de novo genetic instabilities can be induced by the process per se .
One mechanism by which such de novo genetic variability can be generated by interspecific hybridization is transpositional reactivation of quiescent parental transposable elements ( TEs ) in the nascent hybrids .
We have reported previously that introgressive hybridization between rice ( Oryza sativa L ) and Zizania latifolia Griseb had induced rampant mobilization of three TEs , a copia-like LTR retrotransposon Tos17 , a MITE mPing and a class II TE belonging to the hAT superfamily , Dart/nDart .
In this study , we further found that two additional LTR retrotransposons , a gypsy-like ( named RIRE2 ) and a copia-like ( named Copia076 ) , were also transpositionally reactivated in three recombinant inbred lines ( RILs ) derived from introgressive hybridization between rice and Z latifolia .
Novel bands of these two retroelements appeared in the RILs relative to their rice parental line ( cv .
Matsumae ) in Southern blot , suggestive of retrotransposition , which was substantiated by transposon display ( TD ) and locus-specific PCR amplification for insertion sites .
Both elements were found to be transcribed but at variable levels in the leaf it issue of the parental line and the RILs , suggesting that transcriptional control was probably not a mechanism for their transpositional activity in the RILs .
Expression analysis of four genes adjacent to de novo insertions by Copia076 revealed marked difference in the transcript abundance for each of the genes between the RILs and their rice parental line , but the alterations in expression appeared unrelated with the retroelement insertions .
| Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: We have reported previously that introgressive hybridization between rice ( Oryza sativa L ) and Zizania latifolia Griseb had induced rampant mobilization of three TEs , a copia-like LTR retrotransposon Tos17 , a MITE mPing and a class II TE belonging to the hAT superfamily , Dart/nDart .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: Changes in DNA methylation and transgenerational mobilization of a transposable element ( mPing ) by the topoisomerase II inhibitor , etoposide , in rice .
| | Author: Yang X Yu Y Jiang L Lin X Zhang C Ou X Osabe K Liu B | | Journal: BMC Plant Biol Citation: V : 12 P : 48 Year: 2012 Type: Publisher | | Literature: oryza Field: abstract Doc ID: pub22482475 Accession (PMID): 22482475 | | Abstract: ABSTRACT : BACKGROUND : Etoposide ( epipodophyllotoxin ) is a chemical commonly used as an anti-cancer drug which inhibits DNA synthesis by blocking topoisomerase II activity .
Previous studies in animal cells have demonstrated that etoposide constitutes a genotoxic stress which may induce genomic instability including mobilization of normally quiescent transposable elements ( TEs ) .
However , it remained unknown whether similar genetically mutagenic effects could be imposed by etoposide in plant cells .
Also , no information is available with regard to whether the drug may cause a perturbation of epigenetic stability in any organism .
RESULTS : To investigate whether etoposide could generate genetic and/or epigenetic instability in plant cells , we applied etoposide to germinating seeds of six cultivated rice ( Oryza sativa L ) genotypes including both subspecies , japonica and indica .
Based on the methylation-sensitive gel-blotting results , epigenetic changes in DNA methylation of three TEs ( Tos17 , Osr23 and Osr36 ) and two protein-encoding genes ( Homeobox and CDPK-related genes ) were detected in the etoposide-treated plants ( S0 generation ) in four of the six studied japonica cultivars , Nipponbare , RZ1 , RZ2 , and RZ35 , but not in the rest japonica cultivar ( Matsumae ) and the indica cultivar ( 93-11 ) .
DNA methylation changes in the etoposide-treated S0 rice plants were validated by bisulfite sequencing at both of two analyzed loci ( Tos17 and Osr36 ) .
Transpositional activity was tested for eight TEs endogenous to the rice genome in both the S0 plants and their selfed progenies ( S1 and S2 ) of one of the cultivars , RZ1 , which manifested heritable phenotypic variations .
Results indicated that no transposition occurred in the etoposide-treated S0 plants for any of the TEs .
Nonetheless , a MITE transposon , mPing , showed rampant mobilization in the S1 and S2 progenies descended from the drug-treated S0 plants .
CONCLUSIONS : Our results demonstrate that etoposide imposes a similar genotoxic stress on plant cells as it does on animal and human cells , which may induce transgenerational genomic instability by instigating transpositional activation of otherwise dormant TEs .
In addition , we show for the first time that etoposide may induce epigenetic instability in the form of altered DNA methylation patterns in eukaryotes .
However , penetration of the genotoxic effects of etoposide on plant cells , as being reflected as genetic and epigenetic instability , appears to be in a strictly genotype and/or generation-dependent manner .
| Matching Sentences:
[ Sen. 10, subscore: 1.00 ]: Nonetheless , a MITE transposon , mPing , showed rampant mobilization in the S1 and S2 progenies descended from the drug-treated S0 plants .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: A Gaijin-like miniature inverted repeat transposable element is mobilized in rice during cell differentiation .
| | Author: Dong HT Zhang L Zheng KL Yao HG Chen J Yu FC Yu XX Mao BZ Zhao D Yao J Li DB | | Journal: BMC Genomics Citation: V : 13 P : 135 Year: 2012 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub22500940 Accession (PMID): 22500940 | | Abstract: BACKGROUND : Miniature inverted repeat transposable element ( MITE ) is one type of transposable element ( TE ) , which is largely found in eukaryotic genomes and involved in a wide variety of biological events .
However , only few MITEs were proved to be currently active and their physiological function remains largely unknown .
RESULTS : We found that the amplicon discrepancy of a gene locus LOC_Os01g0420 in different rice cultivar genomes was resulted from the existence of a member of Gaijin-like MITEs ( mGing ) .
This result indicated that mGing transposition was occurred at this gene locus .
By using a modified transposon display ( TD ) analysis , the active transpositions of mGing were detected in rice Jiahua No 1 genome under three conditions : in seedlings germinated from the seeds received a high dose gamma-ray irradiation , in plantlets regenerated from anther-derived calli and from scutellum-derived calli , and were confirmed by PCR validation and sequencing .
Sequence analysis revealed that single nucleotide polymorphisms ( SNPs ) or short additional DNA sequences at transposition sites post mGing transposition .
It suggested that sequence modification was possibly taken place during mGing transposition .
Furthermore , cell re-differentiation experiment showed that active transpositions of both mGing and mPing ( another well studied MITE ) were identified only in regenerated plantlets .
CONCLUSIONS : It is for the first time that mGing active transposition was demonstrated under gamma-ray irradiation or in cell re-differentiation process in rice .
This newly identified active MITE will provide a foundation for further analysis of the roles of MITEs in biological process .
| Matching Sentences:
[ Sen. 8, subscore: 1.00 ]: Furthermore , cell re-differentiation experiment showed that active transpositions of both mGing and mPing ( another well studied MITE ) were identified only in regenerated plantlets .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: The plant MITE mPing is mobilized in anther culture .
| | Author: Kikuchi K Terauchi K Wada M Hirano HY .
| | Journal: Nature Citation: V : 421 ( 6919 ) P : 167-70 Year: 2003 Type: ARTICLE | | Literature: oryza Field: title Doc ID: pub12520303 Accession (PMID): 12520303 | | Abstract: Transposable elements constitute a large portion of eukaryotic genomes and contribute to their evolution and diversification .
Miniature inverted-repeat transposable elements ( MITEs ) constitute one of the main groups of transposable elements and are distributed ubiquitously in the genomes of plants and animals such as maize , rice , Arabidopsis , human , insect and nematode .
Because active MITEs have not been identified , the transposition mechanism of MITEs and their accumulation in eukaryotic genomes remain poorly understood .
Here we describe a new class of MITE , called miniature Ping ( mPing ) , in the genome of Oryza sativa ( rice ) . mPing elements are activated in cells derived from anther culture , where they are excised efficiently from original sites and reinserted into new loci .
An mPing-associated Ping element , which has a putative PIF family transposase , is implicated in the recent proliferation of this MITE family in a subspecies of rice . | Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: The plant MITE mPing is mobilized in anther culture .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: Mobilization of the active MITE transposons mPing and Pong in rice by introgression from wild rice ( Zizania latifolia Griseb . ) .
| | Author: Shan X Liu Z Dong Z Wang Y Chen Y Lin X Long L Han F Dong Y Liu B | | Journal: Mol . Biol . Evol Citation: V : 22 ( 4 ) P : 976-90 Year: 2005 Type: ARTICLE | | Literature: oryza Field: title Doc ID: pub15647520 Accession (PMID): 15647520 | | Abstract: Hybridization between different species plays an important role in plant genome evolution , as well as is a widely used approach for crop improvement .
McClintock has predicted that plant wide hybridization constitutes a "genomic shock" whereby cryptic transposable elements may be activated .
However , direct experimental evidence showing a causal relationship between plant wide hybridization and transposon mobilization has not yet been reported .
The miniature-Ping ( mPing ) is a recently isolated active miniature inverted-repeat transposable element transposon from rice , which is mobilized by it issue culture and gamma-ray irradiation .
We show herein that mPing , together with its putative transposase-encoding partner , Pong , is mobilized in three homologous recombinant inbred lines ( RILs ) , derived from hybridization between rice ( cultivar Matsumae ) and wild rice ( Zizania latifolia Griseb . ) , harboring introgressed genomic DNA from wild rice .
In contrast , both elements remain immobile in two lines sharing the same parentage to the RILs but possessing no introgressed DNA .
Thus , we have presented direct evidence that is consistent with McClintocks insight by demonstrating a causal link between wide hybridization and transposon mobilization in rice .
In addition , we report an atypical behavior of mPing/Pong mobilization in these lines , ie , the exclusive absence of footprints after excision . | Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Mobilization of the active MITE transposons mPing and Pong in rice by introgression from wild rice ( Zizania latifolia Griseb . ) .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: In planta mobilization of mPing and its putative autonomous element Pong in rice by hydrostatic pressurization .
| | Author: Lin X Long L Shan X Zhang S Shen S Liu B | | Journal: J Exp . Bot . Citation: V : 57 ( 10 ) P : 2313-23 Year: Type: ARTICLE | | Literature: oryza Field: title Doc ID: pub16818484 Accession (PMID): 16818484 | | Abstract: The miniature Ping ( mPing ) is a recently discovered endogenous miniature inverted repeat transposable element ( MITE ) in rice , which can be mobilized by it issue culture or irradiation .
It is reported here that mPing , together with one of its putative transposase-encoding partners , Pong , was efficiently mobilized in somatic cells of intact rice plants of two distinct cultivars derived from germinating seeds subjected to high hydrostatic pressure , whereas the other autonomous element of mPing , Ping , remained static in the plants studied . mPing excision was detected in several plants of both cultivars in the treated generation ( P0 ) , which were selected based on their novel phenotypes .
Southern blot analysis and transposon-display assay on selfed progenies ( P1 generation ) of two selected P0 plants , one from each of the cultivars , revealed polymorphic banding patterns consistent with mobilization of mPing and Pong .
Various mPing excisions and de novo insertions , as detected by element-bracketing , locus-specific PCR assays , occurred in the different P1 plants of both cultivars .
Pong excision at one locus for each cultivar was also detected by using a Pong internal primer together with locus-specific flanking primers in the P1 plants .
In contrast to the pressurized plants , immobility of both mPing and Pong in control plants , and the absence of within-cultivar heterozygosity at the analysed loci were verified by Southern blotting and/or locus-assay .
Sequencing at 18 mPing empty donor sites isolated from the pressurized plants indicated properties characteristic of the element excision .
Sequence-based mapping of 10 identified mPing de novo insertions from P1 progenies of pressurized plants indicated that all were in unique or low-copy regions , conforming with the targeting propensity of mPing .
No evidence for further mPing activity was detected in the P2 plants tested .
In spite of the high activity of mPing and Pong in the pressurized plants , amplified fragment length polymorphism ( AFLP ) analysis denoted their general genomic stability , and several potentially active retrotransposons also remained largely immobile .
Further investigation showed that the same hydrostatic pressure treatments also caused mobilization of mPing in the standard laboratory cultivar for japonica rice , Nipponbare .
Thus , a simple and robust approach for in planta MITE-mobilization in rice has been established by using high hydrostatic pressure treatment , which may be useful as an alternative for gene-tagging in this important crop plant . | Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: In planta mobilization of mPing and its putative autonomous element Pong in rice by hydrostatic pressurization .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: Expression of the maize proteinase inhibitor ( mpi ) gene in rice plants enhances resistance against the striped stem borer ( Chilo suppressalis ) : effects on larval growth and insect gut proteinases .
| | Author: Vila L Quilis J Meynard D Breitler JC MarfEV Murillo I Vassal JM Messeguer J Guiderdoni E San Segundo B | | Journal: Plant Biotechnol .
J Citation: V : 3 ( 2 ) P : 187-202 Year: 2005 Type: ARTICLE | | Literature: oryza Field: title Doc ID: pub17173619 Accession (PMID): 17173619 | | Abstract: The maize proteinase inhibitor ( mpi ) gene was introduced into two elite japonica rice varieties .
Both constitutive expression of the mpi gene driven by the maize ubiquitin 1 promoter and wound-inducible expression of the mpi gene driven by its own promoter resulted in the accumulation of MPI protein in the transgenic plants .
No effect on plant phenotype was observed in mpi-expressing lines .
The stability of transgene expression through successive generations of mpi rice lines ( up to the T ( 4 ) generation ) and the production of functional MPI protein were confirmed .
Expression of the mpi gene in rice enhanced resistance to the striped stem borer ( Chilo suppressalis ) , one of the most important pests of rice .
In addition , transgenic mpi plants were evaluated in terms of their effects on the growth of C suppressalis larvae and the insect digestive proteolytic system .
An important dose-dependent reduction of larval weight of C suppressalis larvae fed on mpi rice , compared with larvae fed on untransformed rice plants , was observed .
Analysis of the digestive proteolytic activity from the gut of C suppressalis demonstrated that larvae adapted to mpi transgene expression by increasing the complement of digestive proteolytic activity : the serine and cysteine endoproteinases as well as the exopeptidases leucine aminopeptidase and carboxypeptidases A and B However , the induction of such proteolytic activity did not prevent the deleterious effects of MPI on larval growth .
The introduction of the mpi gene into rice plants can thus be considered as a promising strategy to protect rice plants against striped stem borer .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Expression of the maize proteinase inhibitor ( mpi ) gene in rice plants enhances resistance against the striped stem borer ( Chilo suppressalis ) : effects on larval growth and insect gut proteinases .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: Transposition of the rice miniature inverted repeat transposable element mPing in Arabidopsis thaliana .
| | Author: Yang G Zhang F Hancock CN Wessler SR | | Journal: Proc Natl Acad Sci U S A Citation: V : 104 P : 10962-7 Year: 2007 Type: MEDLINE | | Literature: oryza Field: title Doc ID: pub17578919 Accession (PMID): 17578919 | | Abstract: An active miniature inverted repeat transposable element ( MITE ) , mPing , was discovered by computer-assisted analysis of rice genome sequence .
The mPing element is mobile in rice cell culture and in a few rice strains where it has been amplified to >1 , 000 copies during recent domestication .
However , determination of the transposase source and characterization of the mechanism of transposition have been hampered by the high copy number of mPing and the presence of several candidate autonomous elements in the rice genome .
Here , we report that mPing is active in Arabidopsis thaliana , where its transposition is catalyzed by three sources of transposase from rice : the autonomous Ping and Pong elements and by a cDNA derived from a Ping transcript .
In addition to transposase , the product of a second element-encoded ORF of unknown function is also required for mPing transposition .
Excision of mPing in A thaliana is usually precise , and transposed copies usually insert into unlinked sites in the genome that are preferentially in or near genes .
As such , this will be a valuable assay system for the dissection of MITE transposition and a potentially powerful tagging system for gene discovery in eukaryotes .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Transposition of the rice miniature inverted repeat transposable element mPing in Arabidopsis thaliana .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: High potential of a transposon mPing as a marker system in japonica x japonica cross in rice .
| | Author: Monden Y Naito K Okumoto Y Saito H Oki N Tsukiyama T Ideta O Nakazaki T Wessler SR Tanisaka T | | Journal: DNA Res Citation: V : 16 P : 131-40 Year: 2009 Type: In-Process | | Literature: oryza Field: title Doc ID: pub19270311 Accession (PMID): 19270311 | | Abstract: Although quantitative traits loci ( QTL ) analysis has been widely performed to isolate agronomically important genes , it has been difficult to obtain molecular markers between individuals with similar phenotypes ( assortative mating ) .
Recently , the miniature inverted-repeat transposable element mPing was shown to be active in the japonica strain Gimbozu EG4 where it had accumulated more than 1000 copies .
In contrast , most other japonicas , including Nipponbare , have 50 or fewer mPing insertions in their genome .
In this study we have exploited the polymorphism of mPing insertion sites to generate 150 PCR markers in a cross between the closely related japonicas , Nipponbare x Gimbozu ( EG4 ) .
These new markers were distributed in genic regions of the whole genome and showed significantly higher polymorphism ( 150 of 183 ) than all other molecular markers tested including short sequence repeat markers ( 46 of 661 ) .
In addition , we performed QTL analysis with these markers using recombinant inbred lines derived from Nipponbare x Gimbozu EG4 , and successfully mapped a locus involved in heading date on the short arm of chromosome 6 .
Moreover , we could easily map two novel loci involved in the culm length on the short arms of chromosomes 3 and 10 .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: High potential of a transposon mPing as a marker system in japonica x japonica cross in rice .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: Tissue culture-induced transpositional activity of mPing is correlated with cytosine methylation in rice .
| | Author: Ngezahayo F Xu C Wang H Jiang L Pang J Liu B | | Journal: BMC Plant Biol Citation: V : 9 P : 91 Year: 2009 Type: MEDLINE | | Literature: oryza Field: title Doc ID: pub19604382 Accession (PMID): 19604382 | | Abstract: BACKGROUND : mPing is an endogenous MITE in the rice genome , which is quiescent under normal conditions but can be induced towards mobilization under various stresses .
The cellular mechanism responsible for modulating the activity of mPing remains unknown .
Cytosine methylation is a major epigenetic modification in most eukaryotes , and the primary function of which is to serve as a genome defense system including taming activity of transposable elements ( TEs ) .
Given that it issue-culture is capable of inducing both methylation alteration and mPing transposition in certain rice genotypes , it provides a tractable system to investigate the possible relationship between the two phenomena .
RESULTS : mPing transposition and cytosine methylation alteration were measured in callus and regenerated plants in three rice ( ssp . indica ) genotypes , V14 , V27 and R09 .
All three genotypes showed transposition of mPing , though at various frequencies .
Cytosine methylation alteration occurred both at the mPing-flanks and at random loci sampled globally in callus and regenerated plants of all three genotypes .
However , a sharp difference in the changing patterns was noted between the mPing-flanks and random genomic loci , with a particular type of methylation modification , ie , CNG hypermethylation , occurred predominantly at the mPing-flanks .
Pearsons test on pairwise correlations indicated that mPing activity is positively correlated with specific patterns of methylation alteration at random genomic loci , while the elements immobility is positively correlated with methylation levels of the mPings 5-flanks .
Bisulfite sequencing of two mPing-containing loci showed that whereas for the immobile locus loss of CG methylation in the 5-flank was accompanied by an increase in CHG methylation , together with an overall increase in methylation of all three types ( CG , CHG and CHH ) in the mPing-body region , for the active locus erasure of CG methylation in the 5-flank was not followed by such a change .
CONCLUSION : Our results documented that it issue culture-induced mPing activity in rice ssp . indica is correlated with alteration in cytosine methylation patterns at both random genomic loci and the elements flanks , while the stability of mPing positively correlates with enhanced methylation levels of both the flanks and probably the elements per se .
Thus , our results implicate a possible role of cytosine methylation in maintaining mPing stability under normal conditions , and in releasing the elements activity as a consequence of epigenetic perturbation in a locus-specific manner under certain stress conditions .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Tissue culture-induced transpositional activity of mPing is correlated with cytosine methylation in rice .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: Transpositional activation of mPing in an asymmetric nuclear somatic cell hybrid of rice and Zizania latifolia was accompanied by massive element loss .
| | Author: Shan XH Ou XF Liu ZL Dong YZ Lin XY Li XW Liu B | | Journal: Theor Appl Genet Citation: V : 119 P : 1325-33 Year: 2009 Type: MEDLINE | | Literature: oryza Field: title Doc ID: pub19711051 Accession (PMID): 19711051 | | Abstract: We have reported previously that the most active miniature inverted terminal repeat transposable element ( MITE ) of rice , mPing , was transpositionally mobilized in several rice recombinant inbred lines ( RILs ) derived from an introgressive hybridization between rice and wild rice ( Zizania latifolia Griseb . ) .
To further study the phenomenon of hybridization-induced mPing activity , we undertook the present study to investigate the elements behavior in a highly asymmetric somatic nuclear hybrid ( SH6 ) of rice and Z latifolia , which is similar in genomic composition to that of the RILs , though probably contains more introgressed alien chromatins from the donor species than the RILs .
We found that mPing , together with its transposase-donor , Pong , underwent rampant transpositional activation in the somatic hybrid ( SH6 ) .
Because possible effects of protoplast isolation and cell culture can be ruled out , we attribute the transpositional activation of mPing and Pong in SH6 to the process of asymmetric somatic hybridization , namely , one-step introgression of multiple chromatin segments of the donor species Z latifolia into the recipient rice genome .
A salient feature of mPing transposition in the somatic hybrid is that the elements activation was accompanied by massive loss of its original copies , ie , abortive transpositions , which was not observed in previously reported cases of mPing activity .
These data not only corroborated our earlier finding that wide hybridization and introgression may trigger transpositional activation of otherwise quiescent transposable elements , but also suggest that transpositional mobilization of a MITE like mPing can be accompanied by dramatic reduction of its original copy numbers under certain conditions , thus provide novel insights into the dynamics of MITEs in the course of genome evolution .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Transpositional activation of mPing in an asymmetric nuclear somatic cell hybrid of rice and Zizania latifolia was accompanied by massive element loss .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: Transposition of the Tourist-MITE mPing in yeast : an assay that retains key features of catalysis by the class 2 PIF/Harbinger superfamily .
| | Author: Hancock CN Zhang F Wessler SR | | Journal: Mob DNA Citation: V : 1 P : 5 Year: 2010 Type: PubMed-not-MEDLINE | | Literature: oryza Field: title Doc ID: pub20226077 Accession (PMID): 20226077 | | Abstract: BACKGROUND : PIF/Harbinger is the most recently discovered DNA transposon superfamily and is now known to populate genomes from fungi to plants to animals .
Mobilization of superfamily members requires two separate element-encoded proteins ( ORF1 and TPase ) .
Members of this superfamily also mobilize Tourist-like miniature inverted repeat transposable elements ( MITEs ) , which are the most abundant transposable elements associated with the genes of plants , especially the cereal grasses .
The phylogenetic analysis of many plant genomes indicates that MITEs can amplify rapidly from one or a few elements to hundreds or thousands . The most active DNA transposon identified to date in plants or animals is mPing , a rice Tourist-like MITE that is a deletion derivative of the autonomous Ping element .
Ping and the closely related Pong are the only known naturally active PIF/Harbinger elements .
Some rice strains accumulate 40 new mPing insertions per plant per generation .
In this study we report the development of a yeast transposition assay as a first step in deciphering the mechanism underlying the amplification of Tourist-MITEs .
RESULTS : The ORF1 and TPase proteins encoded by Ping and Pong have been shown to mobilize mPing in rice and in transgenic Arabidopsis .
Initial tests of the native proteins in a yeast assay resulted in very low transposition .
Significantly higher activities were obtained by mutation of a putative nuclear export signal ( NES ) in the TPase that increased the amount of TPase in the nucleus .
When introduced into Arabidopsis , the NES mutant protein also catalyzed higher frequencies of mPing excision from the gfp reporter gene .
Our yeast assay retains key features of excision and insertion of mPing including precise excision , extended insertion sequence preference , and a requirement for two proteins that can come from either Ping or Pong or both elements .
CONCLUSIONS : The yeast transposition assay provides a robust platform for analysis of the mechanism underlying transposition catalyzed by the two proteins of PIF/Harbinger elements .
It recapitulates all of the features of excision and reinsertion of mPing as seen in plant systems .
Furthermore , a mutation of a putative NES in the TPase increased transposition both in yeast and plants .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Transposition of the Tourist-MITE mPing in yeast : an assay that retains key features of catalysis by the class 2 PIF/Harbinger superfamily .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: Long-culm mutations with dominant genes are induced by mPing transposon in rice .
| | Author: Tomita M Tanisaka T | | Journal: Hereditas Citation: V : 147 P : 256-63 Year: 2010 Type: MEDLINE | | Literature: oryza Field: title Doc ID: pub21166795 Accession (PMID): 21166795 | | Abstract: Development of semidwarf rice cultivars contributed to the epoch of high yielding crops called the Green Revolution .
However , over-reliance on semidwarf rice also has intrinsic limitations to supply food for an ever expanding world population .
As a solution to the food supply problem , we propose the development of tall dwarf rice cultivars that are characterized by increased biomass with long culms or large grains .
However , genetic studies on the elongation of rice culms have remained scarce .
This study seeks to analyze mutant genes involved in culm elongation in long-culm mutants induced by the MITE transposon mPing , which has been shown to be active in the japonica cultivar Gimbozu .
Through analysis of the experimental results , we have confirmed that the three mutant long-culm genes exhibit genetic dominance .
These represent rare cases of artificially induced dominant mutations .
It is very likely that the mPing transposons played an important role in inducing the dominant mutations and also play an evolutionary interesting role .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Long-culm mutations with dominant genes are induced by mPing transposon in rice .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: The rice miniature inverted repeat transposable element mPing is an effective insertional mutagen in soybean .
| | Author: Hancock CN Zhang F Floyd K Richardson AO Lafayette P Tucker D Wessler SR Parrott WA | | Journal: Plant Physiol Citation: V : 157 P : 552-62 Year: 2011 Type: In-Process | | Literature: oryza Field: title Doc ID: pub21844309 Accession (PMID): 21844309 | | Abstract: Insertional mutagenesis of legume genomes such as soybean ( Glycine max ) should aid in identifying genes responsible for key traits such as nitrogen fixation and seed quality .
The relatively low throughput of soybean transformation necessitates the use of a transposon-tagging strategy where a single transformation event will produce many mutations over a number of generations .
However , existing transposon-tagging tools being used in legumes are of limited utility because of restricted transposition ( Ac/Ds : soybean ) or the requirement for it issue culture activation ( Tnt1 : Medicago truncatula ) .
A recently discovered transposable element from rice ( Oryza sativa ) , mPing , and the genes required for its mobilization , were transferred to soybean to determine if it will be an improvement over the other available transposon-tagging tools .
Stable transformation events in soybean were tested for mPing transposition .
Analysis of mPing excision at early and late embryo developmental stages revealed increased excision during late development in most transgenic lines , suggesting that transposition is developmentally regulated .
Transgenic lines that produced heritable mPing insertions were identified , with the plants from the highest activity line producing at least one new insertion per generation .
Analysis of the mPing insertion sites in the soybean genome revealed that features displayed in rice were retained including transposition to unlinked sites and a preference for insertion within 2 . 5 kb of a gene .
Taken together these findings indicate that mPing has the characteristics necessary for an effective transposon-tagging resource .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: The rice miniature inverted repeat transposable element mPing is an effective insertional mutagen in soybean .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: Changes in DNA methylation and transgenerational mobilization of a transposable element ( mPing ) by the topoisomerase II inhibitor , etoposide , in rice .
| | Author: Yang X Yu Y Jiang L Lin X Zhang C Ou X Osabe K Liu B | | Journal: BMC Plant Biol Citation: V : 12 P : 48 Year: 2012 Type: Publisher | | Literature: oryza Field: title Doc ID: pub22482475 Accession (PMID): 22482475 | | Abstract: ABSTRACT : BACKGROUND : Etoposide ( epipodophyllotoxin ) is a chemical commonly used as an anti-cancer drug which inhibits DNA synthesis by blocking topoisomerase II activity .
Previous studies in animal cells have demonstrated that etoposide constitutes a genotoxic stress which may induce genomic instability including mobilization of normally quiescent transposable elements ( TEs ) .
However , it remained unknown whether similar genetically mutagenic effects could be imposed by etoposide in plant cells .
Also , no information is available with regard to whether the drug may cause a perturbation of epigenetic stability in any organism .
RESULTS : To investigate whether etoposide could generate genetic and/or epigenetic instability in plant cells , we applied etoposide to germinating seeds of six cultivated rice ( Oryza sativa L ) genotypes including both subspecies , japonica and indica .
Based on the methylation-sensitive gel-blotting results , epigenetic changes in DNA methylation of three TEs ( Tos17 , Osr23 and Osr36 ) and two protein-encoding genes ( Homeobox and CDPK-related genes ) were detected in the etoposide-treated plants ( S0 generation ) in four of the six studied japonica cultivars , Nipponbare , RZ1 , RZ2 , and RZ35 , but not in the rest japonica cultivar ( Matsumae ) and the indica cultivar ( 93-11 ) .
DNA methylation changes in the etoposide-treated S0 rice plants were validated by bisulfite sequencing at both of two analyzed loci ( Tos17 and Osr36 ) .
Transpositional activity was tested for eight TEs endogenous to the rice genome in both the S0 plants and their selfed progenies ( S1 and S2 ) of one of the cultivars , RZ1 , which manifested heritable phenotypic variations .
Results indicated that no transposition occurred in the etoposide-treated S0 plants for any of the TEs .
Nonetheless , a MITE transposon , mPing , showed rampant mobilization in the S1 and S2 progenies descended from the drug-treated S0 plants .
CONCLUSIONS : Our results demonstrate that etoposide imposes a similar genotoxic stress on plant cells as it does on animal and human cells , which may induce transgenerational genomic instability by instigating transpositional activation of otherwise dormant TEs .
In addition , we show for the first time that etoposide may induce epigenetic instability in the form of altered DNA methylation patterns in eukaryotes .
However , penetration of the genotoxic effects of etoposide on plant cells , as being reflected as genetic and epigenetic instability , appears to be in a strictly genotype and/or generation-dependent manner .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Changes in DNA methylation and transgenerational mobilization of a transposable element ( mPing ) by the topoisomerase II inhibitor , etoposide , in rice .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
