| 133 matches found in 48 documents. Search time: 0.004 seconds. |
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| 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 .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 4.00 |
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| 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 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 3.00 |
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| 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 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 6.00 |
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| 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 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 15.00 |
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| 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 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 2.00 |
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| 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 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| 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 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 2.00 |
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| 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 | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| 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 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 13.00 |
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| 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 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
