RERJ1, a jasmonic acid-responsive gene from rice, encodes a basic helix–loop–helix protein

Kiribuchi, Kyoko; Sugimori, Miho; Takeda, Masatami; Otani, Takashi; Okada, Kazunori; Onodera, Hidehiro; Ugaki, Masashi; Tanaka, Yuji; Tomiyama-Akimoto, Chiharu; Yamaguchi, Takeshi; Minami, Eiichi; Shibuya, Naoto; Omori, Toshio; Nishiyama, Makoto; Nojiri, Hideaki; Yamane, Hisakazu

doi:10.1016/j.bbrc.2004.10.126

Cited by 61 publications

(41 citation statements)

References 30 publications

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“…Several genes are important for stress responses, including OsbHLH1 (i.e. OsbHLH062 in this study) in cold response , OsPTF1(OsbHLH096) in tolerance to phosphate starvation (Yi et al, 2005), and RERJ1 (OsbHLH006) in wound and drought responses (Kiribuchi et al, 2004(Kiribuchi et al, , 2005. Also, OsBP-5 (OsbHLH102) is involved in transcriptional regulation of the rice Wx gene (Zhu et al, 2003), and Ra (OsbHLH013) and Rb (OsbHLH165; Hu et al, 1996) are homologs of the maize (Zea maize) Lc gene; OsMYC (OsbHLH009; Zhu et al, 2005) is a homolog of AtMYC2.…”

Section: The Expression Pattern Of Osbhlh and Atbhlh Genesmentioning

confidence: 84%

Genome-Wide Analysis of Basic/Helix-Loop-Helix Transcription Factor Family in Rice and Arabidopsis

et al. 2006

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The basic/helix-loop-helix (bHLH) transcription factors and their homologs form a large family in plant and animal genomes. They are known to play important roles in the specification of tissue types in animals. On the other hand, few plant bHLH proteins have been studied functionally. Recent completion of whole genome sequences of model plants Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) allows genome-wide analysis and comparison of the bHLH family in flowering plants. We have identified 167 bHLH genes in the rice genome, and their phylogenetic analysis indicates that they form well-supported clades, which are defined as subfamilies. In addition, sequence analysis of potential DNA-binding activity, the sequence motifs outside the bHLH domain, and the conservation of intron/exon structural patterns further support the evolutionary relationships among these proteins. The genome distribution of rice bHLH genes strongly supports the hypothesis that genome-wide and tandem duplication contributed to the expansion of the bHLH gene family, consistent with the birth-and-death theory of gene family evolution. Bioinformatics analysis suggests that rice bHLH proteins can potentially participate in a variety of combinatorial interactions, endowing them with the capacity to regulate a multitude of transcriptional programs. In addition, similar expression patterns suggest functional conservation between some rice bHLH genes and their close Arabidopsis homologs.

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Section: The Expression Pattern Of Osbhlh and Atbhlh Genesmentioning

confidence: 84%

Genome-Wide Analysis of Basic/Helix-Loop-Helix Transcription Factor Family in Rice and Arabidopsis

et al. 2006

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“…The corresponding rice orthologs of subfamily 10 also provide an interesting example of functional conservation (Liu et al, 2009). An outstanding example of functional diversification is encountered in subfamily 1, which clusters nine plant bHLH genes involved in very diverse biological roles (Table III; Chinnusamy et al, 2003;Sorensen et al, 2003;Jakoby et al, 2004;Kiribuchi et al, 2004;Li et al, 2006a;Zhang et al, 2006;Kanaoka et al, 2008).…”

Section: Discussionmentioning

confidence: 99%

“…They have been reported to function in light signaling (Ni et al, 1998;Halliday et al, 1999;Fairchild et al, 2000;Huq and Quail, 2002;Khanna et al, 2004;Oh et al, 2004;Hyun and Lee, 2006;Roig-Villanova et al, 2007;Leivar et al, 2008), hormone signaling (Abe et al, 1997;Friedrichsen et al, 2002;Yin et al, 2005;Lee et al, 2006), wound and drought stress responses (de Pater et al, 1997;Smolen et al, 2002;Chinnusamy et al, 2003;Kiribuchi et al, 2004), symbiotic ammonium transport (Kaiser et al, 1998), shoot branching (Komatsu et al, 2001), fruit and flower development (Rajani and Sundaresan, 2001;Liljegren et al, 2004;Szecsi et al, 2006;Zhang et al, 2006;Gremski et al, 2007), and microspore (Sorensen et al, 2003), trichome (Payne et al, 2000;Morohashi et al, 2007), stomata (Pillitteri et al, 2007;Kanaoka et al, 2008), and root (Menand et al, 2007;Ohashi-Ito and Bergmann, 2007) development.…”

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confidence: 99%

Genome-Wide Classification and Evolutionary Analysis of the bHLH Family of Transcription Factors in Arabidopsis, Poplar, Rice, Moss, and Algae

et al. 2010

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Basic helix-loop-helix proteins (bHLHs) are found throughout the three eukaryotic kingdoms and constitute one of the largest families of transcription factors. A growing number of bHLH proteins have been functionally characterized in plants. However, some of these have not been previously classified. We present here an updated and comprehensive classification of the bHLHs encoded by the whole sequenced genomes of Arabidopsis (Arabidopsis thaliana), Populus trichocarpa, Oryza sativa, Physcomitrella patens, and five algae species. We define a plant bHLH consensus motif, which allowed the identification of novel highly diverged atypical bHLHs. Using yeast two-hybrid assays, we confirm that (1) a highly diverged bHLH has retained protein interaction activity and (2) the two most conserved positions in the consensus play an essential role in dimerization. Phylogenetic analysis permitted classification of the 638 bHLH genes identified into 32 subfamilies. Evolutionary and functional relationships within subfamilies are supported by intron patterns, predicted DNA-binding motifs, and the architecture of conserved protein motifs. Our analyses reveal the origin and evolutionary diversification of plant bHLHs through differential expansions, domain shuffling, and extensive sequence divergence. At the functional level, this would translate into different subfamilies evolving specific DNA-binding and protein interaction activities as well as differential transcriptional regulatory roles. Our results suggest a role for bHLH proteins in generating plant phenotypic diversity and provide a solid framework for further investigations into the role carried out in the transcriptional regulation of key growth and developmental processes.

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“…1) To obtain basic information on the biological functions and signal transduction pathways of JA, we have isolated and characterized cDNAs for JA-responsive genes such as RRJ1, RRJ2, and OsOPR1 from suspension-cultured rice cells treated with JA for 2 h. 2,3) In addition to these JA-responsive genes, we isolated a cDNA for a JA-responsive gene named RERJ1 that encodes a novel transcription factor with a basic helixloop-helix (bHLH) motif from suspension-cultured rice cells treated with JA for 1/2 h. 4) Plant bHLH proteins are a multigene family of transcription factors. More than 100 bHLH genes have been identified in the rice and Arabidopsis thaliana genomes respectively.…”

mentioning

confidence: 99%

“…5) In a phylogenetic tree of plant bHLH proteins that we constructed, RERJ1 was classified into a clade consisting of functionally unknown bHLH proteins, suggesting that RERJ1 plays novel biological functions in rice. 4) Analysis of the phenotypes of rice plants expressing sense-and antisense-RERJ1 mRNA indicated that RERJ1 is involved in the inhibition of shoot growth caused by exogenously applied JA, 4) but the other biological functions of RERJ1 in rice remain unknown. Since JA is involved in various stress responses in higher plants and RERJ1 is a JAresponsive gene, as already described, RERJ1 is likely to be involved in stress responses in rice.…”

mentioning

confidence: 99%

Involvement of the Basic Helix-Loop-Helix Transcription Factor RERJ1 in Wounding and Drought Stress Responses in Rice Plants

Kiribuchi¹,

Jikumaru²,

Kaku³

et al. 2005

Bioscience, Biotechnology, and Biochemistry

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RERJ1, a jasmonic acid-responsive gene from rice, encodes a basic helix–loop–helix protein

Cited by 61 publications

References 30 publications

Genome-Wide Analysis of Basic/Helix-Loop-Helix Transcription Factor Family in Rice and Arabidopsis

Genome-Wide Analysis of Basic/Helix-Loop-Helix Transcription Factor Family in Rice and Arabidopsis

Genome-Wide Classification and Evolutionary Analysis of the bHLH Family of Transcription Factors in Arabidopsis, Poplar, Rice, Moss, and Algae

Involvement of the Basic Helix-Loop-Helix Transcription Factor RERJ1 in Wounding and Drought Stress Responses in Rice Plants

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