The Arabidopsis basic/helix-loop-helix transcription factor family.
TLDR
Observations suggest that the Arabidopsis bHLH proteins have the potential to participate in an extensive set of combinatorial interactions, endowing them with the capacity to be involved in the regulation of a multiplicity of transcriptional programs.Abstract:
The basic/helix-loop-helix (bHLH) proteins are a superfamily of transcription factors that bind as dimers to specific DNA target sites and that have been well characterized in nonplant eukaryotes as important regulatory components in diverse biological processes. Based on evidence that the bHLH protein PIF3 is a direct phytochrome reaction partner in the photoreceptor’s signaling network, we have undertaken a comprehensive computational analysis of the Arabidopsis genome sequence databases to define the scope and features of the bHLH family. Using a set of criteria derived from a previously defined consensus motif, we identified 147 bHLH protein‐encoding genes, making this one of the largest transcription factor families in Arabidopsis. Phylogenetic analysis of the bHLH domain sequences permits classification of these genes into 21 subfamilies. The evolutionary and potential functional relationships implied by this analysis are supported by other criteria, including the chromosomal distribution of these genes relative to duplicated genome segments, the conservation of variant exon/intron structural patterns, and the predicted DNA binding activities within subfamilies. Considerable diversity in DNA binding site specificity among family members is predicted, and marked divergence in protein sequence outside of the conserved bHLH domain is observed. Together with the established propensity of bHLH factors to engage in varying degrees of homodimerization and heterodimerization, these observations suggest that the Arabidopsis bHLH proteins have the potential to participate in an extensive set of combinatorial interactions, endowing them with the capacity to be involved in the regulation of a multiplicity of transcriptional programs. We provide evidence from yeast two-hybrid and in vitro binding assays that two related phytochrome-interacting members in the Arabidopsis family, PIF3 and PIF4, can form both homodimers and heterodimers and that all three dimeric configurations can bind specifically to the G-box DNA sequence motif CACGTG. These data are consistent, in principle, with the operation of this combinatorial mechanism in Arabidopsis.read more
Citations
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Genome-Wide Analysis of the ERF Gene Family in Arabidopsis and Rice
TL;DR: It was concluded that the major functional diversification within the ERF family predated the monocot/dicot divergence and might have been due to chromosomal/segmental duplication and tandem duplication, as well as more ancient transposition and homing.
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Transcriptional control of flavonoid biosynthesis by MYB–bHLH–WDR complexes
TL;DR: Recent advances in the characterization of the underlying regulatory mechanisms of flavonoid biosynthesis are reviewed, with a special focus on the MBW (MYB-bHLH-WDR) protein complexes.
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Coordinated regulation of Arabidopsis thaliana development by light and gibberellins
Suhua Feng,Cristina Martinez,Giuliana Gusmaroli,Yu Wang,Junli Zhou,Feng Wang,Liying Chen,Lu Yu,Juan Manuel Iglesias-Pedraz,Stefan Kircher,Eberhard Schäfer,Xiangdong Fu,Liu-Min Fan,Xing Wang Deng,Xing Wang Deng +14 more
TL;DR: This work characterize a nuclear protein interaction cascade mediating transduction of GA signals to the activity regulation of a light-responsive transcription factor in the presence of GA, and releases PIF3 from the negative effect of DELLA proteins.
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Evolutionary and comparative analysis of MYB and bHLH plant transcription factors
TL;DR: This review compares the MYB and bHLH gene families from structural, evolutionary and functional perspectives and suggests that the next few years are likely to witness an increasing understanding of the extent to which conserved transcription factors participate at similar positions in gene regulatory networks across plant species.
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Light-regulated transcriptional networks in higher plants.
TL;DR: Genomic studies have further revealed that light induces massive reprogramming of the plant transcriptome, and that the early light-responsive genes are enriched in transcription factors, and these combined approaches provide new insights into light-regulated transcriptional networks.
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TL;DR: The results of an international collaboration to produce a high-quality draft sequence of the mouse genome are reported and an initial comparative analysis of the Mouse and human genomes is presented, describing some of the insights that can be gleaned from the two sequences.
Journal ArticleDOI
Multiple sequence alignment with hierarchical clustering
TL;DR: An algorithm is presented for the multiple alignment of sequences, either proteins or nucleic acids, that is both accurate and easy to use on microcomputers, based on the conventional dynamic-programming method of pairwise alignment.
Journal ArticleDOI
Sequence the Human Genome
TL;DR: This book aims to provide a history of Chinese modern art from 17th Century to the present day through the lens of 20th Century critics, practitioners, journalists, and mediaeval and modern-day critics.
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MYB transcription factors in Arabidopsis
TL;DR: The elucidation ofMYB protein function and regulation that is possible in Arabidopsis will provide the foundation for predicting the contributions of MYB proteins to the biology of plants in general.
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