Phylogenetic Analysis of Zebrafish Basic Helix-Loop-Helix Transcription Factors

The basic helix-loop-helix (bHLH) proteins play important regulatory roles in eukaryotic developmental processes including neurogenesis, myogenesis, hematopoiesis, sex determination, and gut development. Zebrafish is a good model organism for developmental biology. In this study, we identified 139 bHLH genes encoded in the zebrafish genome. Phylogenetic analyses revealed that zebrafish has 58, 29, 21, 5, 19, and 5 bHLH members in groups A, B, C, D, E, and F, respectively, while 2 members were classified as “orphan.” A comparison between zebrafish and human bHLH repertoires suggested that both organisms have a certain number of specific bHLH members. Eight zebrafish bHLH genes were found to have multiple coding regions in the genome. Two of these, Bmal1 and MITF, are good anchor genes for identification of fish-specific whole-genome duplication events in comparison with mouse and chicken genomes. The present study provides useful information for future studies on gene family evolution and vertebrate development. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

绿豆bHLH转录因子家族的鉴定与生物信息学分析

bHLH是真核生物中重要的一类转录因子,其主要由碱性氨基酸区和螺旋-环-螺旋区组成。本研究利用生物信息学的方法鉴定到122个绿豆bHLH转录因子,并对其理化性质、保守结构域、基因结构、在染色体上的分布、系统进化以及部分典型基因的组织表达差异等进行分析。结果表明,bHLH转录因子理化性质差异较大;含有2个保守结构域,分别位于N端的碱性氨基酸区和C端的螺旋-环-螺旋区,碱性氨基酸区含有His5-Glu9-Arg13保守序列,与靶基因结合有关,HLH区含有Arg23和Arg55,与形成二聚体有关,同时含有5种保守元件;bHLH基因在11条染色体上分布不均匀,5号、7号和8号染色体上分布较多,1号、4号和10号染色体上分布较少,大部分基因含有1~9个不等的内含子,在染色体上成簇状分布;122个bHLH转录因子可分为11个亚家族。多数bHLH基因在绿豆根、茎、叶、花和种子等组织中均有表达,但具有组织表达特异性,且不同基因表达量差异较大。本研究为进一步研究绿豆bHLH转录因子家族的生物学功能奠定基础。     

BAC library development for allotetraploid Leymus (Triticeae) wildryes enable comparative genetic analysis of lax-barrenstalk1 orthogene sequences and growth habit QTLs

Tall-caespitose basin wildrye (Leymus cinereus) and rhizomatous creeping wildrye (Leymus triticoides) are perennial Triticeae relatives of wheat and barley. Quantitative trait loci (QTLs) controlling rhizome proliferation were previously detected on homoeologous regions of LG3a and LG3b in two full-sib families derived from allotetraploid hybrids. Triticeae homoeologous group 3 aligns to rice chromosome 1, which contains the rice lax panicle and maize barrenstalk1 orthogene responsible for induction of axillary branch meristems, but this gene has not been mapped or sequenced in Triticeae. We developed bacterial artificial chromosome (BAC) libraries representing 6.1 haploid equivalents of the tetraploid Leymus genome (10.7 Mb). Overgo probes designed from the lax-barrenstalk1 orthogene hybridized to 12 Leymus BAC clones. Deduced amino-acid sequences from seven BAC clones were highly conserved with the rice, maize, and sorghum lax-barrenstalk1orthogenes. Gene specific primers designed from two of the most divergent BAC clones map to homoeologous regions of Leymus LG3a and LG3b and align with the lax-barrenstalk1 orthogene on rice 1L. Comparisons of genomic DNA sequences revealed two other conserved regions surrounding the Leymus LG3a, rice, and sorghum lax-barrenstalk1 ortholoci, and one of these regions was also present in maize and Leymus LG3b sequences. Comparisons of Leymus LG3a and LG3b lax-barrenstalk1 coding sequences and flanking genomic regions elucidate molecular differences between subgenomes.     

Identification and evolution of molecular domains involved in differentiating the cement gland-promoting activity of Otx proteins in Xenopus laevis

Otx genes are a class of vertebrate homeobox genes, homologous to the orthodenticle gene of Drosophila melanogaster, that play a crucial role in anterior embryo patterning and sensory organ formation. In the frog, Xenopus laevis, at least three members of this class have been isolated: otx1, otx2 and otx5 (crx); they are involved in regulating both shared and differential processes during frog development. In particular, while otx2 and otx5 are both capable to promote cement gland (CG) formation, otx1 is not. We performed a molecular dissection of Otx5 and Otx1 proteins to characterize the functional parts of the proteins that make them differently able to promote CG formation. We show that a CG promoting domain (CGPD) is localized at the Otx5 C-terminus, and is bipartite: CGPD1 (aa 210–255) is the most effective domain, while CGPD2 (aa 177–209) has a lower activity. A histidine stretch disrupts CGPD1 continuity in Otx1 determining its loss of CG promoting activity; this histidine-rich region acts as an actively CG repressing domain. Another Otx1 specific domain, a serine-rich stretch, may also be involved in repressing Otx1 potential to trigger CG formation, though at a much lower level. This is the first evidence that these domains, specific of the Otx1 orthology group, play a role during development in differentiating Otx1 action compared to other Otx family members. We discuss the potential implications of their appearance in light of the evolution of Otx functional activities.     

组蛋白与hAMFR基因启动子的结合对体外转录活性的影响

采用从鸡血红细胞中分离纯化的组蛋白,从ＨｅＬａ细胞核中萃取的含有ＲＮＡ聚合酶Ⅱ和多种Ⅱ类基因转录因子的可溶性抽提物,以及从非洲爪蟾卵细胞核中撮以的萃取物热处理物上清用于核小体构建,以含有人自泌移动因子受体基因启动子序列的ＤＮＡ片段为模板进行体外转录实验,结果表明,组蛋白和转录因子在ｈＡＭＦＲ基因启动子序列上的竞争性结合对转录活性具有重要的影响作用,在启动子区域预先构建的核小体能够抑制转录活性;     

Molecular control of myogenesis: antagonism between growth and differentiation

Insight into the molecular mechanisms that control establishment of the skeletal muscle phenotype has recently been obtained through cloning of a family of muscle-specific regulatory factors that can activate myogenesis when transfected into non-muscle cells. This family of factors, which includes MyoD, myogenin, myf-5, and MRF4, can bind DNA and transactivate muscle-specific genes in collaboration with ubiquitous cellular factors. Growth factors play an antagonistic role in myogenesis by suppressing the actions of the myogenic regulatory factor family. This review will focus on the regulation and mechanism of action of this family of myogenic regulatory factors and on the central role of peptide growth factors in modulating their expression and biological activities.