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The basic helix-loop-helix transcription factor family in Bombyx mori

DEVELOPMENT GENES AND EVOLUTION 2007年第10期217卷 715-723页

作者： Wang, Yong Chen, Keping Yao, Qin Wang, Wenbing Zhu, Zhi Jiangsu Univ Inst Life Sci Zhenjiang 212013 Peoples R China Jiangsu Univ Dept Biotechnol Fac Food & Biol Engn Zhenjiang 212013 Peoples R China

The basic helix-loop-helix (bHLH) proteins are a superfamily of transcription factors that play important roles in a wide range of developmental processes in higher organisms. bHLH family members have been identified in a dozen of organisms including fruit fly, mouse and human. We identified 52 bHLH members in silico in the silkworm genome. Phylogenetic analyses revealed that they belong to 39 bHLH families with 21, 10, 12, 1, 7 and 1 members in groups A, B, C, D, E and F, respectively. Genes that encode ASCb, NeuroD, Oligo, MyoRb, Fig alpha and Mad were not found in the silkworm genome. The present study provides important background information for future studies using the silkworm as a model system for insect development. Besides, the in-group phylogenetic analysis was demonstrated to be effective in classifying identified bHLH sequences into corresponding families, which can be helpful in the classification of bHLH members of other organisms.

关键词： basic helix-loop-helix transcription factor Bombyx mori phylogeny genome searching BLAST search

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Relaxed constraint and evolutionary rate variation between basic helix-loop-helix floral anthocyanin regulators in Ipomoea

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MOLECULAR BIOLOGY AND EVOLUTION 2007年第12期24卷 2816-2826页

作者： Streisfeld, Matthew A. Rausher, Mark D. Duke Univ Dept Biol Durham NC 27706 USA

Regulatory genes are believed to play a large role in morphological diversification and are often characterized by elevated rates of evolution. Whether this rapid evolution is primarily due to adaptive differentiation or relaxed selective constraint remains an open question. We attempted to distinguish between these alternative outcomes in 2 transcription factors known to regulate the expression of anthocyanin pigmentation genes in flowers. We cloned the full-length coding region from 2 basic helix-loop-helix transcription factors from several species of Ipomoea with diverse flower colors and determined the selective forces operating on them. In both genes, rapidly evolving sites and indel mutations are clustered in nonbinding domains, but the extent of rate acceleration in these domains is reduced relative to most previously characterized plant transcription factors. Moreover, codon models of substitution rates and models evaluating the magnitude of change to physical amino acid properties demonstrate little evidence for adaptive evolution and suggest that elevated nonsynonymous substitution rates in these domains represent relaxed selective constraint. Although both genes show qualitatively similar patterns, their rates of evolution differ significantly due to an increased rate of nonsynonymous substitutions in the nonbinding domains in one copy, suggesting substantial differences in functional constraint on each gene. In general, these results provide additional evidence demonstrating that decreased constraint as opposed to positive selection is largely responsible for the frequently observed pattern of rapid evolution in particular domains of plant transcription factors. More specifically, they suggest that most of the amino acid substitutions are neutral and do not implicate a role for natural selection on these regulatory genes in the diversification of flower color in Ipomoea.

关键词： Ipomoea positive selection rate variation anthocyanin basic helix-loop-helix transcription factor

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Isolation and Characterization of the Iron-Regulated MxbHLH01 Gene in Malus xiaojinensis

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PLANT MOLECULAR BIOLOGY REPORTER 2011年第4期29卷 936-942页

作者： Xu, Hong-Mei Wang, Yi Chen, Feng Zhang, Xin-Zhong Han, Zhen-Hai China Agr Univ Inst Hort Plants Beijing 100193 Peoples R China

Some of the genes involved in iron signaling in Malus xiaojinensis have been isolated and characterized;however, their regulatory control is yet to be elucidated. In this study, rapid amplification of complementary DNA ends was used to obtain a full-length cDNA fragment of the MxbHLH01 gene encoding a basic helix-loop-helix (bHLH) protein. This protein shared 35.31% amino acid sequence identity with AtFRU and 31.88% amino acid sequence identify with LeFER. Real-time quantitative PCR revealed that MxbHLH01 was upregulated in roots grown under iron-deficient conditions. In addition, the MxbHLH01 protein was localized within the nuclei of plant cells and incapable of activating transcription in yeast. This indicated that MxbHLH01 might act as an iron regulator, but requiring other proteins to form heterodimer(s) to regulate gene expression response to iron deficiency.

关键词： Malus xiaojinensis RACE basic helix-loop-helix Iron

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Hand Factors as Regulators of Cardiac Morphogenesis and Implications for Congenital Heart Defects

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BIRTH DEFECTS RESEARCH PART A-CLINICAL AND MOLECULAR TERATOLOGY 2011年第6期91卷 485-494页

作者： Vincentz, Joshua W. Barnes, Ralston M. Firulli, Anthony B. Indiana Med Sch Riley Heart Res Ctr Wells Ctr Pediat Res Div Pediat CardiolDept Anat Indianapolis IN USA Indiana Med Sch Riley Heart Res Ctr Wells Ctr Pediat Res Div Pediat CardiolDept Biochem Indianapolis IN USA Indiana Med Sch Riley Heart Res Ctr Wells Ctr Pediat Res Div Pediat CardiolDept Med & Mol Genet Indianapolis IN USA

Almost 15 years of careful study have established the related basic helix-loop-helix (bHLH) transcription factors Hand1 and Hand2 as critical for heart development across evolution. Hand factors make broad contributions, revealed through animal models, to the development of multiple cellular lineages that ultimately contribute to the heart. They perform critical roles in ventricular cardiomyocyte growth, differentiation, morphogenesis, and conduction. They are also important for the proper development of the cardiac outflow tract, epicardium, and endocardium. Molecularly, they function both through DNA binding and through protein-protein interactions, which are regulated transcriptionally, posttranscriptionally by microRNAs, and posttranslationally through phosphoregulation. Although direct Hand factor transcriptional targets are progressively being identified, confirmed direct targets of Hand factor transcriptional activity in the heart are limited. Identification of these targets will be critical to model the mechanisms by which Hand factor bHLH interactions affect developmental pathways. Improved understanding of Hand factor-mediated transcriptional cascades will be necessary to determine how Hand factor dysregulation translates to human disease phenotypes. This review summarizes the insight that animal models have provided into the regulation and function of these factors during heart development, in addition to the recent findings that suggest roles for HAND1 and HAND2 in human congenital heart disease. Birth Defects Research (Part A) 91:485-494, 2011. (C) 2011Wiley-Liss, Inc.

关键词： basic helix-loop-helix HAND1 HAND2 dimerization Transcription DNA-binding cardiogenesis heart development congenital heart defect

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Isoquinoline Alkaloid Biosynthesis is Regulated by a Unique bHLH-Type Transcription Factor in Coptis japonica

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PLANT AND CELL PHYSIOLOGY 2011年第7期52卷 1131-1141页

作者： Yamada, Yasuyuki Kokabu, Yasuhisa Chaki, Kaori Yoshimoto, Tadashi Ohgaki, Mai Yoshida, Sayumi Kato, Nobuhiko Koyama, Tomotsugu Sato, Fumihiko Kyoto Univ Grad Sch Biostudies Div Integrated Life Sci Kyoto 6068502 Japan

Specific plant species produce unique isoquinoline alkaloids (IQAs);however, the mechanism of their evolution and the regulation of their biosynthesis are largely unknown. We report here the isolation of a novel basic helix-loop-helix protein, CjbHLH1, from IQA-producing Coptis japonica. A BLAST search indicated that CjbHLH1 homologs were only found in plant species that produce IQAs. Transient RNA interference (RNAi) and overexpression of CjbHLH1 in C. japonica protoplasts revealed the activity of CjbHLH1 in transcription of IQA biosynthetic genes, and little activity in the transcription of genes involved in primary metabolism or the stress response. A chromatin immunoprecipitation experiment using CjbHLH1-specific antibodies revealed the direct interaction of CjbHLH1 with promoter sequences of IQA biosynthetic genes in vivo. We discuss the unique role of CjbHLH1 in IQA biosynthesis.

关键词： basic helix-loop-helix Coptis japonica Isoquinoline alkaloid biosynthesis Transcriptional regulation

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hnulp1, a basic helix-loop-helix protein with a novel transcriptional repressive domain, inhibits transcriptional activity of serum response factor

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BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 2006年第3期343卷 973-981页

作者： Cai, ZY Wang, YQ Yu, WS Xiao, J Li, YQ Liu, L Zhu, CB Tan, KR Deng, Y Yuan, WZ Liu, MY Wu, XS Hunan Normal Univ Coll Life Sci Ctr Heart Dev Changsha 410081 Hunan Peoples R China

Many bHLH proteins are involved in cardiac development and cardiovascular diseases. Herein, we identified and characterized the human homologue (hnulp1) of mouse gene nulp1. The predicted protein contains a bHLH domain and a DUF654 domain in N-terminal and C-terminal, respectively. Northern blot analysis shows that a 2.3-kb transcript expressed broadly in early human embryonic and adult tissues, especially with a higher level in adult heart. hnulp1 is a transcription repressor when fused to GAL4 DNA-binding domain and co-transfected with VP-16, in which DUF654 motif represents the basal transcriptional repressive activity. Treatment of cells with trichostatin A can relieve this repression, suggesting that the DUF654 motif acts through increasing deacetylase activity at the GAL4-driven promoter. Overexpression of hnulp1 protein in COS-7 cells inhibits the transcriptional activity of serum response factor (SRF), suggesting that hnulp1 may act as a novel bHLH transcriptional repressor in SRF signaling pathway to mediate cellular functions. (c) 2006 Elsevier Inc. All rights reserved.

关键词： transcription factor basic helix-loop-helix DUF654 serum response factor heart development

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Multiple mechanisms induce ectopic expression of LYL1 in subsets of T-ALL cell lines

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LEUKEMIA RESEARCH 2010年第4期34卷 521-528页

作者： Nagel, Stefan Venturini, Letizia Meyer, Corinna Kaufmann, Maren Scherr, Michaela Drexler, Hans G. MacLeod, Roderick A. F. German Collect Microorganisms & Cell Cultures DSMZ Dept Human & Anim Cell Lines D-38124 Braunschweig Germany Hannover Med Sch Dept Hematol Hemostasis Oncol & Stem Cell Transpl D-30125 Hannover Germany

basic helix-loop-helix ( bHLH) transcription factors are essential for lymphocytic differentiation. Here, we have analyzed the complete bHLH family in T-cell acute lymphoblastic leukemia cell lines by expression profiling. Differential expression was detected for BHLHB2, HES1, HES4, HEY1, ID1, ID2, ID3, LYL1 and TAL1, highlighting dysregulation of family members with inhibitory activity. Subsequently we focused on the mechanisms responsible for aberrant expression of LYL1 in comparison to TAL1. Quantitative genomic PCR indicated microdeletions upstream of both, TAL1 and LYL1, targeting STIL/SIL and TRMT1, respectively. Additionally, one LYL1-expressing cell line exhibited amplification of TRMT1. While deletion of STIL correlated with expression of the STIL-TAL1 fusion transcript, no TRMT-LYL1 fusion transcripts were detected in parallel with genomic rearrangements thereof. Sequence analysis of the LYL1 promoter region revealed potential binding sites for transcription factors HOXA10, LMO2 and NKX2-5. Overexpression analysis, reporter gene assays and chromatin immuno-precipitation confirmed their activating impact on LYL1 expression. In conclusion, we identified multiple mechanisms which activate LYL1 in leukemic cells, including structural genomic alterations, namely microdeletion or amplification, together with the involvement of prominent oncogenic transcription factors. (C) 2009 Elsevier Ltd. All rights reserved.

关键词： basic helix-loop-helix Homeobox LIM domain Microdeletion

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The intrinsic electrophysiological properties of neurons derived from mouse embryonic stem cells overexpressing neurogenin-1

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AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY 2010年第6期299卷 C1335-C1344页

作者： Tong, Mingjie Hernandez, Jeannie L. Purcell, Erin K. Altschuler, Richard A. Duncan, R. Keith Univ Michigan Kresge Hearing Res Inst Dept Otolaryngol Ann Arbor MI 48109 USA Harvard Univ Massachusetts Eye & Ear Infirm Sch Med Boston MA USA

Tong M, Hernandez JL, Purcell EK, Altschuler RA, Duncan RK. The intrinsic electrophysiological properties of neurons derived from mouse embryonic stem cells overexpressing neurogenin-1. Am J Physiol Cell Physiol 299: C1335-C1344, 2010. First published September 22, 2010;doi:10.1152/ajpcell.00207.2010.-A mouse embryonic stem (ES) cell line containing an inducible transgene for the proneural gene Neurog1 has been used to generate glutamatergic neurons at a high efficiency. The present study used in vitro electrophysiology to establish the timeline for acquiring a functional neuronal phenotype in Neurog1-induced cells exhibiting a neuronal morphology. TTX-sensitive action potentials could be evoked from over 80% of the cells after only 4.5 days in vitro (DIV). These cells uniformly showed rapidly adapting responses to current injection, firing one to three action potentials at the onset of the stimulus. In the absence of Neurog1, a limited number of ES cells adopted a neuronal morphology, but these cells displayed slow calcium depolarizations rather than sodium-based spikes. Voltage-gated Na+, K+, and Ca2+ currents were present in nearly all induced cells as early as 4.5 DIV. The voltage-dependent properties of these currents changed little from 4 to 12 DIV with half-activation voltage varying by < 10 mV for any current type throughout the culture period. This study demonstrates that forced expression of proneural genes can induce ES cells to quickly acquire a functional neuronal phenotype with mature electrophysiological properties. Transient overexpression of Neurog1 may be used in neural repair strategies that require the rapid induction of functional neurons from pluripotent stem cells.

关键词： neuronal differentiation neurogenesis electrophysiology basic helix-loop-helix voltage-gated ion channel

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Multiple bHLH proteins regulate CIT2 expression in Saccharomyces cerevisiae

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YEAST 2010年第6期27卷 345-359页

作者： Chen, Linan Lopes, John M. Univ Massachusetts Dept Microbiol Amherst MA 01003 USA Univ Massachusetts Mol Cellular Biol Grad Program Amherst MA 01003 USA Wayne State Univ Dept Biol Sci Detroit MI 48202 USA

The basic helix-loop-helix (bHLH) proteins comprise a eukaryotic transcription factor family involved in multiple biological processes. They have the ability to form multiple dimer combinations and most of them also bind a 6 bp site (E-box) with limited specificity. These properties make them ideal for combinatorial regulation of gene expression. The Saccharomyces cerevisiae CIT2 gene, which encodes citrate synthase, was previously known to be induced by the bHLH proteins Rtg1p and Rtg3p in response to mitochondrial damage. Rtg1p-Rtg3p dimers bind two R-boxes (modified E-boxes) in the CIT2 promoter. The current study tested the ability of all nine S. cerevisiae bHLH proteins to regulate the CIT2 gene. The results showed that expression of CIT2-lacZ reporter was induced in a rho(0) strain by the presence of inositol via the Ino2p and Ino4p bHLH proteins, which are known regulators of phospholipid synthesis. Promoter mutations revealed that inositol induction required a distal E-box in the CIT2 promoter. Interestingly, deleting the INO2, INO4 genes or the cognate E-box revealed phosphate induction of CIT2 expression. This layer of expression required the two R-boxes and the Pho4p bHLH protein, which is known to be required for phosphate-specific regulation. Lastly, the data show that the Hms1p and Sgc1p bHLH proteins also play important roles in repression of CIT2-lacZ expression. Collectively, these results support the model that yeast bHLH proteins coordinate different biological pathways. Copyright (C) 2010 John Wiley & Sons, Ltd.

关键词： retrograde response CIT2 transcriptional regulation basic helix-loop-helix INO2 INO4 PHO4

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Hand2 regulates chondrogenesis in vitro and in vivo

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BONE 2010年第5期46卷 1359-1368页

作者： Abe, Makoto Michikami, Ikumi Fukushi, Toshiya Abe, Akiko Maeda, Yoshinobu Ooshima, Takashi Wakisaka, Satoshi Osaka Univ Grad Sch Dent Dept Oral Anat & Dev Biol Suita Osaka 5650871 Japan Osaka Univ Grad Sch Dent Dept Removable Prosthodont Suita Osaka 5650871 Japan Osaka Univ Grad Sch Dent Dept Pediat Dent Suita Osaka 5650871 Japan

Hand2 is a transcription factor of the basic helix-loop-helix family that plays essential roles during development. Hand2 determines the anterior-posterior axis during limb development and there is also substantial evidence that Hand2 regulates limb skeletogenesis. However, little is known about how Hand2 might regulate skeletogenesis. Here we show that, in a limb bud micromass culture system, over-expression of Hand2 represses chondrogenesis and the expression of chondrocytic genes, Sox9, type II collagen and aggrecan. Furthermore, we show that Hand2 is induced by the activation of canonical Wnt signaling, which strongly represses chondrogenesis. Surprisingly, Hand2 repressed chondrogenesis in a DNA binding- and dimer formation-independent manner. To examine the in vivo role of Hand2 in mice, we targeted the expression of Hand2 to the cartilage using regulatory elements from the collagen II gene. The resulting transgenic mice displayed a dwarf phenotype, with axial, appendicular and craniofacial skeletal deformities. Hand2 strongly inhibited chondrogenesis in the axial and cranial base skeleton. In the sternum. Hand2 inhibited endochondral ossification by slowing chondrocyte maturation. These data support a model of Hand2 regulating endochondral ossification via at least two steps: (1) determination of the site of chondrogenesis by outlining the region of the future cartilage template and (2) regulation of the rate of chondrocyte maturation. (C) 2009 Elsevier Inc. All rights reserved.

关键词： Hand2 Chondrogenesis Collagen Transgenic basic helix-loop-helix

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