|
Score: 2.00 |
|---|
| Title: The evolutionarily conserved OsPRR quintet : rice pseudo-response regulators implicated in circadian rhythm .
| | Author: Murakami M Ashikari M Miura K Yamashino T Mizuno T | | Journal: Plant Cell Physiol .
Citation: V : 44 ( 11 ) P : 1229-36 Year: 2003 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub14634161 Accession (PMID): 14634161 | | Abstract: In Arabidopsis thaliana , a number of circadian-associated factors have been identified , including TOC1 ( TIMING OF CAB EXPRESSION 1 ) that is believed to be a component of the central oscillator .
TOC1 is a member of a small family of proteins , designated as ARABIDOPSIS PSEUDO-RESPONSE REGULATORS ( APRR1/TOC1 , APRR3 , APRR5 , APRR7 , and APRR9 ) .
As demonstrated previously , these APRR1/TOC1 quintet members are crucial for a better understanding of the molecular links between circadian rhythms , control of flowering time through photoperiodic pathways , and also photosensory signal transduction in this dicotyledonous plant .
In this respect , both the dicotyledonous ( eg A thaliana ) and monocotyledonous ( eg Oryza sativa ) plants might share the evolutionarily conserved molecular mechanism underlying the circadian rhythm .
Based on such an assumption , and as the main objective of this study , we asked the question of whether rice also has a set of pseudo-response regulators , and if so , whether or not they are associated with the circadian rhythm .
Here we showed that rice has five members of the OsPRR family ( Oryza sativa Pseudo-Response Regulator ) , and also that the expressions of these OsPRR genes are under the control of circadian rhythm .
They are expressed in a diurnal and sequential manner in the order of OsPRR73 ( OsPRR37 ) -->OsPRR95 ( OsPRR59 ) -->OsPRR1 , which is reminiscent of the circadian waves of the APRR1/TOC1 quintet in A thaliana .
These and other results of this study suggested that the OsPRR quintet , including the ortholog of APRR1/TOC1 , might play important roles within , or close to , the circadian clock of rice . | Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: In Arabidopsis thaliana , a number of circadian-associated factors have been identified , including TOC1 ( TIMING OF CAB EXPRESSION 1 ) that is believed to be a component of the central oscillator .
[ Sen. 2, subscore: 1.00 ]: TOC1 is a member of a small family of proteins , designated as ARABIDOPSIS PSEUDO-RESPONSE REGULATORS ( APRR1/TOC1 , APRR3 , APRR5 , APRR7 , and APRR9 ) .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: The evolution of CONSTANS-like gene families in barley , rice , and Arabidopsis .
| | Author: Griffiths S Dunford RP Coupland G Laurie DA .
| | Journal: Plant Physiol .
Citation: V : 131 ( 4 ) P : 1855-67 Year: 2003 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub12692345 Accession (PMID): 12692345 | | Abstract: The CO ( CONSTANS ) gene of Arabidopsis has an important role in the regulation of flowering by photoperiod .
CO is part of a gene family with 17 members that are subdivided into three classes , termed Group I to III here .
All members of the family have a CCT ( CO , CO-like , TOC1 ) domain near the carboxy terminus .
Group I genes , which include CO , have two zinc finger B-boxes near the amino terminus .
Group II genes have one B-box , and Group III genes have one B-box and a second diverged zinc finger .
Analysis of rice ( Oryza sativa ) genomic sequence identified 16 genes ( OsA-OsP ) that were also divided into these three groups , showing that their evolution predates monocot/dicot divergence .
Eight Group I genes ( HvCO1-HvCO8 ) were isolated from barley ( Hordeum vulgare ) , of which two ( HvCO1 and HvCO2 ) were highly CO like .
HvCO3 and its rice counterpart ( OsB ) had one B-box that was distantly related to Group II genes and was probably derived by internal deletion of a two B-box Group I gene .
Sequence homology and comparative mapping showed that HvCO1 was the counterpart of OsA ( Hd1 ) , a major determinant of photoperiod sensitivity in rice .
Major genes determining photoperiod response have been mapped in barley and wheat ( Triticum aestivum ) , but none corresponded to CO-like genes .
Thus , selection for variation in photoperiod response has affected different genes in rice and temperate cereals .
The peptides of HvCO1 , HvCO2 ( barley ) , and Hd1 ( rice ) show significant structural differences from CO , particularly amino acid changes that are predicted to abolish B-box2 function , suggesting an evolutionary trend toward a one-B-box structure in the most CO-like cereal genes . | Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: All members of the family have a CCT ( CO , CO-like , TOC1 ) domain near the carboxy terminus .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: The GATA family of transcription factors in Arabidopsis and rice .
| | Author: Reyes JC Muro-Pastor MI Florencio FJ .
| | Journal: Plant Physiol .
Citation: V : 134 ( 4 ) P : 1718-32 Year: 2004 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub15084732 Accession (PMID): 15084732 | | Abstract: GATA transcription factors are a group of DNA binding proteins broadly distributed in eukaryotes .
The GATA factors DNA binding domain is a class IV zinc finger motif in the form CX ( 2 ) CX ( 17-20 ) CX ( 2 ) C followed by a basic region .
In plants , GATA DNA motifs have been implicated in light-dependent and nitrate-dependent control of transcription .
Herein , we show that the Arabidopsis and the rice ( Oryza sativa ) genomes present 29 and 28 loci , respectively , that encode for putative GATA factors .
A phylogenetic analysis of the 57 GATA factors encoding genes , as well as the study of their intron-exon structure , indicates the existence of seven subfamilies of GATA genes .
Some of these subfamilies are represented in both species but others are exclusive for one of them .
In addition to the GATA zinc finger motif , polypeptides of the different subfamilies are characterized by the presence of additional domains such as an acidic domain , a CCT ( CONSTANS , CO-like , and TOC1 ) domain , or a transposase-like domain also found in FAR1 and FHY3 .
Subfamily VI comprises genes that encode putative bi-zinc finger polypeptides , also found in metazoan and fungi , and a tri-zinc finger protein which has not been previously reported in eukaryotes .
The phylogeny of the GATA zinc finger motif , excluding flanking regions , evidenced the existence of four classes of GATA zinc fingers , three of them containing 18 residues in the zinc finger loop and one containing a 20-residue loop .
Our results support multiple models of evolution of the GATA gene family in plants including gene duplication and exon shuffling . | Matching Sentences:
[ Sen. 7, subscore: 1.00 ]: In addition to the GATA zinc finger motif , polypeptides of the different subfamilies are characterized by the presence of additional domains such as an acidic domain , a CCT ( CONSTANS , CO-like , and TOC1 ) domain , or a transposase-like domain also found in FAR1 and FHY3 .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: Comparative Overviews of Clock-Associated Genes of Arabidopsis thaliana and Oryza sativa .
| | Author: Murakami M Tago Y Yamashino T Mizuno T | | Journal: Plant Cell Physiol .
Citation: V : 48 ( 1 ) P : 110-21 Year: 2007 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub17132630 Accession (PMID): 17132630 | | Abstract: In higher plants , circadian rhythms are highly relevant to a wide range of biological processes .
To such circadian rhythms , the clock ( oscillator ) is central , and recent intensive studies on the model higher plant Arabidopsis thaliana have begun to shed light on the molecular mechanisms underlying the functions of the central clock .
Such representative clock-associated genes of A thaliana are the homologous CCA1 and LHY genes , and five PRR genes that belong to a small family of pseudo-response regulators including TOC1 .
Others are GI , ZTL , ELF3 , ELF4 , LUX/PCL1 , etc In this context , a simple question arose as to whether or not the molecular picture of the model Arabidopsis clock is conserved in other higher plants .
Here we made an effort to answer the question with special reference to Oryza sativa , providing experimental evidence that this model monocot also has a set of highly conserved clock-associated genes , such as those designated as OsCCA1 , OsPRR-series including OsTOC1/OsPRR1 , OsZTLs , OsPCL1 as well as OsGI .
These results will provide us with insight into the general roles of plant circadian clocks , such as those for the photoperiodic control of flowering time that has a strong impact on the reproduction and yield in many higher plants . | Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: Such representative clock-associated genes of A thaliana are the homologous CCA1 and LHY genes , and five PRR genes that belong to a small family of pseudo-response regulators including TOC1 .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: Characterization of the Rice Circadian Clock-Associated Pseudo-Response Regulators in Arabidopsis thaliana .
| | Author: Murakami M Tago Y Yamashino T Mizuno T | | Journal: Citation: V : ( ) P : Year: 2007 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub17420570 Accession (PMID): 17420570 | | Abstract: Members of the small family of Arabidopsis PSEUDO-RESPONSE REGULATORS ( PRR1/TOC1 , PRR3 , PRR5 , PRR7 , and PRR9 ) play roles close to the circadian clock in Arabidopsis thaliana .
We have reported that the rice ( Oryza sativa ) genome also encodes a set of PRR counterparts ( designated OsPRR1 , OsPRR37 , OsPRR59 , OsPRR73 , and OsPRR95 respectively ) .
To gain new insight into the molecular functions of OsPRRs , we carried out genetic complementation analyses by introducing two representative rice genes , OsPRR1 and OsPRR37 , into the corresponding Arabidopsis loss-of-function mutants ( toc1 and prr7 respectively ) .
The results showed that these OsPRR and AtPRR genes are genetically interchangeable at least in part , suggesting the conserved clock-associated function of these OsPRRs .
| Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: To gain new insight into the molecular functions of OsPRRs , we carried out genetic complementation analyses by introducing two representative rice genes , OsPRR1 and OsPRR37 , into the corresponding Arabidopsis loss-of-function mutants ( toc1 and prr7 respectively ) .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: Tandem duplications of a degenerated GTP-binding domain at the origin of GTPase receptors Toc159 and thylakoidal SRP .
| | Author: Hernandez Torres J Maldonado MA Chomilier J | | Journal: Biochem Biophys Res Commun Citation: V : 364 P : 325-31 Year: 2007 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub17950698 Accession (PMID): 17950698 | | Abstract: The evolutionary origin of some nuclear encoded proteins that translocate proteins across the chloroplast envelope remains unknown .
Therefore , sequences of GTPase proteins constituting the Arabidopsis thaliana translocon at the outer membrane of chloroplast ( atToc ) complexes were analyzed by means of HCA .
In particular , atToc159 and related proteins ( atToc132 , atToc120 , and atToc90 ) do not have proven homologues of prokaryotic or eukaryotic ancestry .
We established that the three domains commonly referred to as A , G , and M originate from the GTPase G domain , tandemly repeated , and probably evolving toward an unstructured conformation in the case of the A domain .
It resulted from this study a putative common ancestor for these proteins and a new domain definition , in particular the splitting of A into three domains ( A1 , A2 , and A3 ) , has been proposed .
The family of Toc159 , previously containing A thaliana and Pisum sativum , has been extended to Medicago truncatula and Populus trichocarpa and it has been revised for Oryza sativa .
They have also been compared to GTPase subunits involved in the cpSRP system .
A distant homology has been revealed among Toc and cpSRP GTP-hydrolyzing proteins of A thaliana , and repetitions of a GTPase domain were also found in cpSRP protein receptors , by means of HCA analysis .
| Matching Sentences:
[ Sen. 6, subscore: 1.00 ]: The family of Toc159 , previously containing A thaliana and Pisum sativum , has been extended to Medicago truncatula and Populus trichocarpa and it has been revised for Oryza sativa .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: The plant WNK gene family and regulation of flowering time in Arabidopsis .
| | Author: Wang Y Liu K Liao H Zhuang C Ma H Yan X | | Journal: Plant Biol ( Stuttg ) Citation: V : 10 P : 548-62 Year: 2008 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub18761494 Accession (PMID): 18761494 | | Abstract: The WNK ( with no lysine kinase ) protein kinase gene family may be involved in regulating ion homeostasis and other physiological processes in mammals .
WNK-like genes have also been identified in plants , including nine in Arabidopsis , designated AtWNK1-AtWNK9 .
However , it is not clear if there are further plant WNK genes , and what the evolutionary relationships are among these genes , nor if these genes have functions other than their roles in regulating circadian rhythms and vacuolar H ( + ) -ATPase .
In the present study , we found a tenth Arabidopsis WNK gene , designated AtWNK10 .
Further phylogenetic analysis of Arabidopsis and rice WNK genes suggests that the most recent common ancestor of monocots and eudicots had 4-8 WNK genes , and that the WNK gene family has experienced duplication events and possible gene losses .
Semi-quantitative RT-PCR revealed that all Arabidopsis WNK genes except AtWNK6 are expressed in organs from the seedling to the flowering plant .
T-DNA knockout mutations in the AtWNK2 , AtWNK5 and AtWNK8 genes in different phylogenetic clades caused early flowering .
In contrast , a T-DNA knockout wnk1 mutant had a much delayed flowering time .
In addition , the transcript levels of several genes in the photoperiod pathway for flowering , such as ELF4 , TOC1 , CO and FT , were altered in atwnk mutants .
Taken together , our results suggest that the Arabidopsis WNK gene family regulates flowering time by modulating the photoperiod pathway .
| Matching Sentences:
[ Sen. 9, subscore: 1.00 ]: In addition , the transcript levels of several genes in the photoperiod pathway for flowering , such as ELF4 , TOC1 , CO and FT , were altered in atwnk mutants .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: Os-GIGANTEA confers robust diurnal rhythms on the global transcriptome of rice in the field .
| | Author: Izawa T Mihara M Suzuki Y Gupta M Itoh H Nagano AJ Motoyama R Sawada Y Yano M Hirai MY Makino A Nagamura Y | | Journal: Plant Cell Citation: V : 23 P : 1741-55 Year: 2011 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub21571948 Accession (PMID): 21571948 | | Abstract: The circadian clock controls physiological traits such as flowering time , photosynthesis , and growth in plants under laboratory conditions .
Under natural field conditions , however , little is known about the significance of the circadian clock in plants .
By time-course transcriptome analyses of rice ( Oryza sativa ) leaves , using a newly isolated rice circadian clock-related mutant carrying a null mutation in Os-GIGANTEA ( Os-GI ) , we show here that Os-GI controlled 75% ( false discovery rate = 0 . 05 ) of genes among 27 , 201 genes tested and was required for strong amplitudes and fine-tuning of the diurnal rhythm phases of global gene expression in the field .
However , transcripts involved in primary metabolism were not greatly affected by osgi .
Time-course metabolome analyses of leaves revealed no trends of change in primary metabolites in osgi plants , and net photosynthetic rates and grain yields were not affected .
By contrast , some transcripts and metabolites in the phenylpropanoid metabolite pathway were consistently affected .
Thus , net primary assimilation of rice was still robust in the face of such osgi mutation-related circadian clock defects in the field , unlike the case with defects caused by Arabidopsis thaliana toc1 and ztl mutations in the laboratory .
| Matching Sentences:
[ Sen. 7, subscore: 1.00 ]: Thus , net primary assimilation of rice was still robust in the face of such osgi mutation-related circadian clock defects in the field , unlike the case with defects caused by Arabidopsis thaliana toc1 and ztl mutations in the laboratory .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
|---|
| Title: Tandem duplications of a degenerated GTP-binding domain at the origin of GTPase receptors Toc159 and thylakoidal SRP .
| | Author: Hernandez Torres J Maldonado MA Chomilier J | | Journal: Biochem Biophys Res Commun Citation: V : 364 P : 325-31 Year: 2007 Type: MEDLINE | | Literature: oryza Field: title Doc ID: pub17950698 Accession (PMID): 17950698 | | Abstract: The evolutionary origin of some nuclear encoded proteins that translocate proteins across the chloroplast envelope remains unknown .
Therefore , sequences of GTPase proteins constituting the Arabidopsis thaliana translocon at the outer membrane of chloroplast ( atToc ) complexes were analyzed by means of HCA .
In particular , atToc159 and related proteins ( atToc132 , atToc120 , and atToc90 ) do not have proven homologues of prokaryotic or eukaryotic ancestry .
We established that the three domains commonly referred to as A , G , and M originate from the GTPase G domain , tandemly repeated , and probably evolving toward an unstructured conformation in the case of the A domain .
It resulted from this study a putative common ancestor for these proteins and a new domain definition , in particular the splitting of A into three domains ( A1 , A2 , and A3 ) , has been proposed .
The family of Toc159 , previously containing A thaliana and Pisum sativum , has been extended to Medicago truncatula and Populus trichocarpa and it has been revised for Oryza sativa .
They have also been compared to GTPase subunits involved in the cpSRP system .
A distant homology has been revealed among Toc and cpSRP GTP-hydrolyzing proteins of A thaliana , and repetitions of a GTPase domain were also found in cpSRP protein receptors , by means of HCA analysis .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Tandem duplications of a degenerated GTP-binding domain at the origin of GTPase receptors Toc159 and thylakoidal SRP .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
