毛竹bHLH转录因子的鉴定及其在干旱和盐胁迫条件下的表达分析

以毛竹（Phyllostachys edulis（Carr.）Lehaie）为材料,利用生物信息学方法,在基因组水平上对其bHLH基因家族成员进行鉴定和分析,并对不同组织中该基因的表达模式以及部分基因在干旱和高盐胁迫条件下的表达情况进行研究。结果显示：在毛竹中共鉴定出153个具有完整保守结构域的bHLH基因家族成员（PebHLH001~PebHLH153）,这些基因内含子数量为0~14,其中137个基因的启动子均含有与干旱、盐胁迫相关的顺式作用元件;PebHLHs编码的蛋白长度为134~1401 aa;bHLH家族成员的系统进化分析结果表明,153个PebHLHs可被分为17个亚类,其中C亚类的成员数量最多,为42个;基于转录组数据的表达谱分析结果发现,有151个PebHLHs在毛竹不同组织和不同生长发育时期有不同程度的表达量;实时荧光定量PCR实验结果显示,在干旱和盐胁迫处理后,分别有14和13个PebHLHs基因的表达量上调,分别有2和3个表达量下调,但表达模式存在一定差异,说明他们在应答干旱和盐胁迫过程中可能发挥不同的作用。     

bHLH转录因子家族研究进展

bHLH转录因子在真核生物生长发育调控中具有重要作用, 它们组成了转录因子的一个大家族。已经有20种生物基因组中bHLH家族的成员得到鉴定, 其中动物17种、植物2种、酵母1种。动物bHLH因其调控基因表达的功能不同而被分成45个家族; 此外, 根据它们所作用DNA元件和自身结构特点又被分成6个组。A组包含22个家族, 主要调控神经细胞生成、肌细胞生成和中胚层形成; B组包含12个家族, 主要调控细胞增殖与分化、固醇代谢与脂肪细胞形成以及葡萄糖响应基因的表达; C组包含7个家族, 主要负责调控中线与气管发育和昼夜节律、激活环境毒素响应基因的转录; D组只有1个家族, 它与A组bHLH蛋白形成无活性的异源二聚体; E组有2个家族, 调控胚胎分节、体节形成与器官发生等; F组也只有1个家族, 调控头部发育、嗅觉神经元生成等。文章综述了bHLH转录因子家族分类、起源、功能方面的研究进展情况。     

Computational identification of novel chitinase-like proteins in the Drosophila melanogaster genome

MOTIVATION: Multiple chitinases as well as lectins closely related to them have been characterized previously from many insect species and the corresponding genes/cDNAs have been cloned. However, the identification of the entire assortment of genes for chitinase family proteins and their differences in biochemical properties have not been carried out in any individual insect species. The completion of the entire DNA sequence of Drosophila melanogaster (fruit fly) genome and identification of open reading frames presents an opportunity to study the structures and functions of chitinase-like proteins, and also to identify new members of this family in DROSOPHILA: We are, therefore, interested in studying the functional genomics of chitinase-like gene families in insects. METHODS: We searched the Drosophila protein sequences database using fully characterized insect chitinase sequences and BLASTP software, identified all the putative chitinase-like proteins encoded in Drosophila genome, and predicted their structures using domain analysis tools. A phylogenetic analysis of the chitinase-like proteins from Drosophila and several other insect species was carried out. The structures of these chitinases were modeled using homology modeling software. RESULTS: Our analysis revealed the presence of 18 chitinase-like proteins in the Drosophila protein database. Among these are seven novel chitinase-like proteins that contain four signature amino acid sequences of chitinases belonging to family 18 glycosylhydrolases, including both acidic and hydrophobic amino acid residues critical for enzyme activity. All the proteins contain at least one catalytic domain with one having four catalytic domains. Phylogenetic analysis of chitinase-like proteins from Drosophila and other insects revealed an evolutionary relationship among all these proteins, which indicated gene duplication and domain shuffling to generate the observed diversity in the encoded proteins. Homology modeling showed that all the Drosophila chitinase-like proteins contain one or more catalytic domains with a (alpha/beta)8 barrel-like structure. Our results suggest that insects utilize multiple family 18 chitinolytic enzymes and also non-enzymatic chitinase-like proteins for degrading/remodeling/binding to chitin in different insect anatomical extracellular structures, such as the cuticle, peritrophic membrane, trachea and mouth parts during insect development, and possibly for other roles including chitin synthesis. AVAILABILITY: Perl program and supplementary material are available at http://www.ksu.edu/bioinformatics/supplementary.htm     

A short interspersed repetitive element found near some mouse structural genes.

We have isolated and characterized a family of interspersed repetitive elements which make up about 1% of the mouse genome. The elements represent a group of homologous but non-identical units about 400 bp in length. Individual members of the family show considerable divergence from one another. The spacial relationships between members of the family and a number of other identified mouse sequences including structural genes have been determined; these elements are found on the 5' as well as 3' sides of various genes at distances ranging from less than 1 to 7.5 kilobases (Kb). The sequences are present in the DNA of all species of Mus. Related sequences are present in the rat genome at a repetition frequency similar to that in the mouse genome. A partial sequence of one member of the family is presented.     

曲霉属bHLH转录因子的研究进展

bHLH(Basichelix-loop-helix)转录因子广泛存在于真核生物中,它可以通过同源或异源二聚体的形式与基因启动子上的E-box结合来调控基因的表达。转录因子的bHLH家族由广泛涉及发育过程(包括细胞增殖和分化)的大量蛋白组成,在生物的生长发育调控过程中起着极为重要的作用。本文对包括构巢曲霉、烟曲霉、米曲霉等曲霉属中现已发现bHLH转录因子的调控过程和生物功能进行概述,以期为深入研究曲霉属的生长发育及bHLH转录因子的功能提供理论参考。     

A genome-wide survey on basic helix-loop-helix transcription factors in giant panda

The giant panda (Ailuropoda melanoleuca) is a critically endangered mammalian species. Studies on functions of regulatory proteins involved in developmental processes would facilitate understanding of specific behavior in giant panda. The basic helix-loop-helix (bHLH) proteins play essential roles in a wide range of developmental processes in higher organisms. bHLH family members have been identified in over 20 organisms, including fruit fly, zebrafish, mouse and human. Our present study identified 107 bHLH family members being encoded in giant panda genome. Phylogenetic analyses revealed that they belong to 44 bHLH families with 46, 25, 15, 4, 11 and 3 members in group A, B, C, D, E and F, respectively, while the remaining 3 members were assigned into "orphan". Compared to mouse, the giant panda does not encode seven bHLH proteins namely Beta3a, Mesp2, Sclerax, S-Myc, Hes5 (or Hes6), EBF4 and Orphan 1. These results provide useful background information for future studies on structure and function of bHLH proteins in the regulation of giant panda development.     

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.     

Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature

A phylogenetic analysis of the basic helix-loop-helix (bHLH) gene superfamily was performed using seven different species (human, mouse, rat, worm, fly, yeast, and plant Arabidopsis) and involving over 600 bHLH genes ( Stevens et al., 2008). All bHLH genes were identified in the genomes of the various species, including expressed sequence tags, and the entire coding sequence was used in the analysis. Nearly 15% of the gene family has been updated or added since the original publication. A super-tree involving six clades and all structural relationships was established and is now presented for four of the species. The wealth of functional data available for members of the bHLH gene superfamily provides us with the opportunity to use this exhaustive phylogenetic tree to predict potential functions of uncharacterized members of the family. This phylogenetic and genomic analysis of the bHLH gene family has revealed unique elements of the evolution and functional relationships of the different genes in the bHLH gene family.     

马铃薯bHLH转录因子家族全基因组鉴定与表达分析

对马铃薯bHLH转录因子进行全基因组鉴定与表达模式分析,为其生物学功能研究提供借鉴.基于马铃薯基因组数据库和Pfam数据库,运用HMMER对马铃薯bHLH家族成员进行全基因组鉴定,剔除冗余序列后,利用ExPASy和MEME软件对候选序列进行基本理化性质及保守元件分析,并使用MEGA-X软件进行聚类分析;用MG2C和TB...