生菜bHLH转录因子家族的鉴定与生物信息学分析

Identification and Bioinformatics Analysis of bHLH Transcription Factor Family in Lactuca sativa L.

本研究旨在对生菜(Lactuca sativa L.)bHLH转录因子进行全基因组鉴定与系统分析,以期为生菜bHLH家族基因的生物学功能的研究提供理论基础。通过Pfam下载bHLH结构域的隐马氏模型,利用HMMER3.0和SMART鉴定生菜bHLH基因。使用ExPASy ProtParam tool、DNAMAN 5.0、ClustalX和MEGA 7.0等软件对bHLH的蛋白序列进行生物信息学分析。在生菜全基因组中共鉴定出135个bHLH转录因子,其编码蛋白的相对分子量为17843.82~75409.15 Da,理论等电点为0.63~9.51,其中有92个酸性蛋白,43个碱性蛋白。123个bHLH蛋白为不稳定蛋白,135个bHLH蛋白均为亲水性蛋白。各家族成员均含有N端碱性结构域和C端HLH结构域,其中N端可结合特定的DNA顺式元件,C端可维持bHLH蛋白二级结构的稳定。系统进化分析将生菜中135个bHLH蛋白分为10个亚家族。通过全基因组分析,共鉴定出135个生菜bHLH转录因子,为生菜bHLH家族基因的功能研究提供借鉴。

The aim of this study is to conduct genome-wide identification and systematic analysis of lettuce(Lactuca sativa L.)bHLH transcription factors in order to provide a theoretical basis for studying the biological function of lettuce bHLH gene family.The Hidden Markov Model profiles of the bHLH domains downloaded from Pfam were used to search the database using HMMER ver.3.0.and SMART.The obtained amino acid sequences were analyzed by bioinformatics using software such as ExPASy ProtParam tool,DNAMAN 5.0,ClustalX and MEGA 7.0.In this study,135 bHLH transcription factors were identified from lettuce and the relative molecular weight of the encoding proteins ranged from 17843.82 Da to 75409.15 Da with theoretical isoelectric points of 0.63-9.51,among which there were 92 acidic proteins and 43 basic proteins.In addition,123 bHLH proteins were unstable proteins and all 135 bHLH proteins were hydrophilic proteins.Each family member contained an N-terminal basic structural domain and a C-terminal HLH structural domain,where the N-terminal could bind specific DNA cis-elements and the C-terminal could maintain the stability of the bHLH protein secondary structure.The 135 bHLH proteins could be divided into 10 sub-families by phylogenetic analysis.In conclusion,135 bHLH transcription factors in lettuce are identified by genome-wide screening,and the study can provide reference for exploring the biological function of lettuce bHLH gene family.