Bioinformatic analysis of Ci proteins of Apis mellifera
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摘要: 【目的】掌握意大利蜜蜂转录因子(Ci)的生物信息学并阐述其功能,为揭示Ci蛋白在意大利蜜蜂Hh信号通路中的功能和作用打下基础。【方法】从NCBI获取意大利蜜蜂Ci蛋白氨基酸序列,分别使用ProtParam预测其理化性质、SignalP-5.0预测信号肽、TMHMM-2.0预测跨膜结构,通过NetOGlyc 3.0、NetNGlyc 1.0、NetPhos 3.1、SUMOplot等进行O-糖基化位点、N-糖基化位点、磷酸化位点及苏木化位点预测,采用GOR4、SWISS-MODEL、CD-Search等预测意大利蜜蜂Ci蛋白高级结构,在多重序列比对分析的基础上利用MEGA 11.0构建系统发育进化树,并通过String数据库预测相互作用蛋白。【结果】意大利蜜蜂Ci蛋白存在2个亚型,分别是XP_624136.4和XP_006558245.2。其中,XP_624136.4亚型的开放阅读(ORF)为4338 bp,编码1445个氨基酸残基,编码蛋白分子量为15.50 kD,理论等电点(pI)为8.39;XP_006558245.2亚型的ORF为3873 bp,编码1290个氨基酸残基,编码蛋白分子量13.99 kD,pI为8.48。2个亚型均属于不稳定的两性蛋白,无信号肽,无跨膜结构,主要定位于在细胞核,少数分布在囊细胞质,XP_006558245.2亚型在线粒体中也有少量分布。XP_624136.4亚型存在2个O-糖基化位点、9个N-糖基化位点、174个磷酸化位点及5个苏木素化位点;XP_006558245.2亚型存在26个O-糖基化位点、8个N-糖基化位点、156个磷酸化位点及5个苏木素化位点。意大利蜜蜂Ci蛋白二级结构主要有α-螺旋、延伸链和无规则卷曲,其三级结构中无规则卷曲、延伸链分布较多,α-螺旋分布较少;2个亚型均具有5个典型的C2H2型锌指蛋白结构域,且从昆虫到哺乳动物Ci蛋白序列高度保守。意大利蜜蜂Ci蛋白与Kinesin-B、Ptc、Poz、Su(fu)、Slmb、Smo、Csnk1a1、Cul-3和Fu等驱动蛋白样蛋白形成相互作用网络。【结论】意大利蜜蜂Ci蛋白属于不稳定的两性蛋白,主要定位于细胞核中,少量分布在囊细胞质或线粒体中,具有5个典型的C2H2型锌指蛋白结构域,蛋白序列高度保守,在意大利蜜蜂Hh信号通路中主要承担转录功能,对意大利蜜蜂的生长发育、跨膜运输、突触传递、信号转导及蛋白生成等起重要调控作用。Abstract: 【Objective】To apprehend bioinformatics of transcription factor Apis mellifera(Ci) and elucidate its functions,and to lay a foundation for exploring functions and roles of Ci proteins in Hh signaling pathway of A. mellifera.【Method】Ci protein amino acid sequences of A. mellifera were obtained from NCBI,and their physicochemical properties were predicted using ProtParam,predicting signal peptides by SignalP-5.0,transmembrane structures by TMHMM-2.0,O-glycosylation sites by NetOGlyc 3.0,N-glycosylation sites by NetNGlyc 1.0,phosphorylation sites by NetPhos 3.1,sumoylation sites by SUMOplot and tertiary structure of Ci proteins in A. mellifera by GOR4,SWISS-MODEL,CDSearch. Based on multiple sequence alignment,phylogenetic trees were constructed by MEGA 11.0 and interacting proteins were predicted by String database.【Result】Ci proteins in A. mellifera had two subtypes,XP_624136.4 and XP_006558245.2. XP_624136.4 contained open reading frames(ORF) of 4338 bp,encoding 1445 amino acid residues,encoding protein molecular mass of 15.50 kD and a theoretical isoelectric point(pI) of 8.39;XP_006558245.2 contained ORF of 3873 bp,encoding 1290 amino acid residues,encoding protein molecular mass of 13.99 kD and a pI of 8.48. Both were unstable amphiphilic proteins with no signal peptide or transmembrane structure,and they localized mainly in nucleus and a few of them in the vesicle cytoplasm. A few of XP_006558245.2 localized in mitochondria. XP_624136.4 had 2O-glycosylation sites,9 N-glycosylation sites,174 phosphorylation sites and 5 hematoxylation sites;XP_006558245.2had 26 O-glycosylation sites,8 N-glycosylation sites,156 phosphorylation sites and 5 hematoxylation sites. In secondary structures of Ci proteins A. mellifera were mainly α-helix,folded extended chains and irregular curls;in tertiary structures of the protein were mainly irregular curls and extended chains and a few α-helix;both subtypes had 5 typical C2H2-type zinc finger protein structural domains with highly conserved Ci protein sequences from insects to mammals. Ci proteins in A. mellifera and kinesin-like proteins such as Kinesin-B,Ptc,Poz,Su(fu),Slmb,Smo,Csnk1a1,Cul-3 and Fu proteins formed an interaction network.【Conclusion】Ci proteins in A. mellifera are unstable amphiphilic proteins,mainly localize in the nucleus,and a few distribute in vesicle cytoplasm or mitochondria. The proteins have 5 typical C2H2-type zinc finger protein structural domains and highly conserved protein sequences,which mainly work for transcription in Hh signaling pathway of A. mellifera,probably play an important role in regulation of A. mellifera growth and development,transmembrane transport,synaptic transmission,signal transduction and protein production.
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Keywords:
- Apis mellifera /
- Ci protein /
- Hh signaling pathway /
- structure /
- function /
- bioinformatics
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