Update on the Basic Helix-Loop-Helix Transcription Factor Gene Family in <i>Arabidopsis thaliana</i>

Bailey, Paul; Martin, Cathie; Toledo‐Ortiz, Gabriela; Quail, Peter H.; Huq, Enamul; Heim, Marc A.; Jakoby, Marc; Werber, Martin; Weißhaar, Bernd

doi:10.1105/tpc.151140

Cited by 288 publications

(184 citation statements)

References 20 publications

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“…In Arabidopsis, there are >162 bHLH proteins of which >27 are predicted to be non-DNA binding HLH proteins (Bailey et al, 2003;Toledo-Ortiz et al, 2003). Plants have more bHLH and HLH proteins compared with animals, and these proteins function in many signaling pathways in plants (Leivar and Monte, 2014).…”

Section: Discussionmentioning

confidence: 99%

“…Although the Arabidopsis genome has >160 bHLH transcription factors and >27 are predicted to be HLH factors (Bailey et al, 2003;Toledo-Ortiz et al, 2003), only four (HFR1, PRE6/KIDARI, and PAR1/2) have been shown to interact with PIFs and regulate PIF function (Hyun and Lee, 2006;Roig-Villanova et al, 2006;Hornitschek et al, 2009;Hao et al, 2012;Shi et al, 2013;Zhou et al, 2014). In an effort to identify additional factors interacting with PIF1, we performed a yeast two-hybrid screening (Bu et al, 2011a).…”

Section: Introductionmentioning

confidence: 99%

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A Negative Feedback Loop between PHYTOCHROME INTERACTING FACTORs and HECATE Proteins Fine-Tunes Photomorphogenesis in Arabidopsis

Zhu

Xin

et al. 2016

Plant Cell

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The phytochrome interacting factors (PIFs), a small group of basic helix-loop-helix transcription factors, repress photomorphogenesis both in the dark and light. Light signals perceived by the phytochrome family of photoreceptors induce rapid degradation of PIFs to promote photomorphogenesis. Here, we show that HECATE (HEC) proteins, another small group of HLH proteins, antagonistically regulate PIFs to promote photomorphogenesis. HEC1 and HEC2 heterodimerize with PIF family members. PIF1, HEC1, and HEC2 genes are spatially and temporally coexpressed, and HEC2 is localized in the nucleus. hec1, hec2, and hec3 single mutants and the hec1 hec2 double mutant showed hyposensitivity to light-induced seed germination and accumulation of chlorophyll and carotenoids, hallmark processes oppositely regulated by PIF1. HEC2 inhibits PIF1 target gene expression by directly heterodimerizing with PIF1 and preventing DNA binding and transcriptional activation activity of PIF1. Conversely, PIFs directly activate the expression of HEC1 and HEC2 in the dark, and light reduces the expression of these HECs possibly by degrading PIFs. HEC2 is partially degraded in the dark through the ubiquitin/26S-proteasome pathway and is stabilized by light. HEC2 overexpression also reduces the light-induced degradation of PIF1. Taken together, these data suggest that PIFs and HECs constitute a negative feedback loop to fine-tune photomorphogenesis in Arabidopsis thaliana.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A Negative Feedback Loop between PHYTOCHROME INTERACTING FACTORs and HECATE Proteins Fine-Tunes Photomorphogenesis in Arabidopsis

Zhu

Xin

et al. 2016

Plant Cell

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“…Using TBLASTN against the rice genome database, we obtained all putative bHLH proteins that had more than 11 conserved amino acids among the 19 residues. In addition, because members of group C and group D do not have the typical basic region (Murre et al, 1994;Swanson et al, 1995;Bailey et al, 2003) and can interact with some bHLH proteins (Sun et al, 1991), we identified putative HLH proteins that had nine or 10 amino acids that matched the 14 amino acids in the HLH region. Another family called TCP family also has a bHLH structure (Kosugi and Ohashi, 1997), but the structure and DNA-binding specificity of the TCP motif are different from those of the bHLH motif.…”

Section: Identification Of 167 Osbhlh Genesmentioning

confidence: 99%

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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“…bHLH transcription factors are proteins that bind as dimers to specific DNA targets and have been characterized as important regulators in diverse biological processes (Bailey et al 2003;Li et al 2006b;Toledo-Ortiz et al 2003). The closest homologue of bHLH162 (CS-07) according to the Database of Arabidopsis Transcription Factors (Guo et al 2005) is At1g10585.…”

Section: Cs Transcription Factorsmentioning

confidence: 99%

Disease-Specific Expression of Host Genes During Downy Mildew Infection of Arabidopsis

Huibers¹,

Jong²,

Dekter³

et al. 2009

MPMI

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Here, we report on the identification of Arabidopsis genes that are induced during compatible but not during incompatible interactions with the downy mildew pathogen Hyaloperonospora arabidopsidis. This set of so-called compatible specific (CS) genes contrasts with the large group of defense-associated genes that is differentially expressed during both compatible and incompatible interactions. From the 17 identified CS genes, 6 belong to the ethylene response factor (ERF) family of transcription factor genes, suggesting that these ERF have a role during compatibility. The majority of CS genes are differentially regulated in response to various forms of abiotic stress. In silico analysis of the CS genes revealed an over-representation of dehydration-responsive element/C-repeat binding factor (DREB1A/ CBF3) binding sites and EveningElement motifs in their promoter regions. The CS-ERF are closely related to the CBF transcription factors and could potentially bind the DREB1A/CBF3 promoter elements in the CS genes. Transcript levels of CS genes peak at 2 to 3 days postinoculation, when pathogen growth is highest, and decline at later stages of infection. The induction of several CS genes was found to be isolate specific. This suggests that the identified CS genes could be the direct or indirect targets of downy mildew effector proteins that promote disease susceptibility.

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Update on the Basic Helix-Loop-Helix Transcription Factor Gene Family in Arabidopsis thaliana

Cited by 288 publications

References 20 publications

A Negative Feedback Loop between PHYTOCHROME INTERACTING FACTORs and HECATE Proteins Fine-Tunes Photomorphogenesis in Arabidopsis

A Negative Feedback Loop between PHYTOCHROME INTERACTING FACTORs and HECATE Proteins Fine-Tunes Photomorphogenesis in Arabidopsis

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

Disease-Specific Expression of Host Genes During Downy Mildew Infection of Arabidopsis

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