title: Sequence determinants of prokaryotic gene expression level under heat stress.
abstract: Prokaryotic gene expression is environment-dependent and temperature plays an important role in shaping the gene expression profile. Revealing the regulation mechanisms of gene expression pertaining to temperature has attracted tremendous efforts in recent years particularly owning to the yielding of transcriptome and proteome data by high-throughput techniques. However, most of the previous works concentrated on the characterization of the gene expression profile of individual organism and little effort has been made to disclose the commonality among organisms, especially for the gene sequence features. In this report, we collected the transcriptome and proteome data measured under heat stress condition from recently published literature and studied the sequence determinants for the expression level of heat-responsive genes on multiple layers. Our results showed that there indeed exist commonness and consistent patterns of the sequence features among organisms for the differentially expressed genes under heat stress condition. Some features are attributed to the requirement of thermostability while some are dominated by gene function. The revealed sequence determinants of bacterial gene expression level under heat stress complement the knowledge about the regulation factors of prokaryotic gene expression responding to the change of environmental conditions. Furthermore, comparisons to thermophilic adaption have been performed to reveal the similarity and dissimilarity of the sequence determinants for the response to heat stress and for the adaption to high habitat temperature, which elucidates the complex landscape of gene expression related to the same physical factor of temperature.
authors.affiliation: Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Heng
authors.initials: H
authors.lastname: Xiong
authors.affiliation: Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Xiao-Pan
authors.initials: XP
authors.lastname: Hu
authors.affiliation: Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Yi-Ming
authors.initials: YM
authors.lastname: He
authors.affiliation: Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China. Electronic address: mbg@mail.hzau.edu.cn.
authors.forename: Bin-Guang
authors.initials: BG
authors.lastname: Ma
mesh_terms: D000595:Amino Acid Sequence; D001419:Bacteria / Q000235:genetics* / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics; D003062:Codon; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D018869:Heat-Shock Response / Q000235:genetics*; D009690:Nucleic Acid Conformation; D009876:Operon; D011387:Prokaryotic Cells; D017510:Protein Folding; D017433:Protein Structure, Secondary; D020543:Proteome; D012333:RNA, Messenger / Q000737:chemistry; D059467:Transcriptome
chemical_list: D001426:Bacterial Proteins; D003062:Codon; D020543:Proteome; D012333:RNA, Messenger
keywords: Gene regulation; Proteome; Sequence analysis; Temperature adaptation; Transcriptome