热带爪蟾bHLH转录因子鉴定与进化分析

Identification and evolutionary analysis of the Xenopus tropicalis bHLH transcription factors

爪蟾是重要的生物医学模式动物。文章根据NCBI公布的热带爪蟾(Xenopus tropicalis)基因组数据,利用生物信息学方法提取和鉴定了爪蟾全基因组范围的碱性螺旋-环-螺旋(bHLH)基因信息,应用系统发生方法进行分类并做基因本体论(Gene Ontology,GO)功能富集分布分析,以期从整体上探讨爪蟾bHLH转录因子基因家族的分类及功能。结果表明,在热带爪蟾基因组数据库中发现了70个bHLH转录因子,其中69个可以分别归到6大组(A^F)的34个亚家族中,另一个为"孤儿因子"(Orphan)基因。GO富集分布统计发现有51个显著富集分布的GO注释语句,其中转录调控活性、转录调控、DNA结合、RNA代谢过程调控、DNA依赖的转录调控、转录和转录因子活性等出现频率很高,表明这些GO术语是爪蟾bHLH基因最常见的功能;许多bHLH转录因子在一些重要的发育或生理过程中发挥调控作用,如肌肉组织和器官(横纹肌、骨骼肌、眼部和咽部肌肉)的分化和发育、消化系统发育、咽部和感觉器官的发育、碱基和核苷及核酸的代谢调控、生物合成过程调控、DNA结合和蛋白质异聚化活性等。另外,还有一些重要信号通路(Signaling pathway)的GO术语显著地富集。文章还对Hes转录因子家族做了进化分析。这些结果为热带爪蟾bHLH基因的进一步研究打下了很好的基础。

Xenopus is an important model animal for biomedicine researches. In order to probe into the classification and function of the basic helix-loop-helix （bHLH） transcription factor family, we conducted a genome-wide survey and identified 70 bHLH transcription factors using the Xenopus tropicalis genome project data in the study. Among these tran- scription factors, 69 bHLH transcription factors were classified into 6 large groups composed of 34 sub-families and the remaining one was classified as ＇orphan＇. Results of Gene Ontology （GO） enrichment statistics showed 51 frequent GO annotation categories. Statistical analysis of the GO annotations showed that these 70 bHLH proteins tended to be fre-quently related to transcription regulator activity, regulation of transcription, DNA binding, regulation of RNA metabolic process, DNA-dependent regulation of transcription, transcription, and transcription factor activity, indicating that they were expected to be the most common GO categories of transcriptional factors. Moreover, a number of bHLH genes were revealed to play important regulation roles in special development and physiological processes, such as muscle tissue and organ （striated muscle, skeletal muscle, eye muscle, and pharyngeal muscle） differentiation and development, e.g., digestive system development, pharynx development and sensory organ development, regulation of nucleobase, nucleoside and nu- cleotide and nucleic acid metabolic process, regulation of biosynthetic process, DNA binding, and protein heterodimeriza- tion activity, etc. There were also some important signaling pathways in the significant GO categories. We made the evolu- tionary analysis of Hes transcription factor family as well. This preliminary result lays a solid foundation for further re- searches on X. tropicalis.