title: Time-resolved transcriptome analysis of Bacillus subtilis responding to valine, glutamate, and glutamine.
abstract: Microorganisms can restructure their transcriptional output to adapt to environmental conditions by sensing endogenous metabolite pools. In this paper, an Agilent customized microarray representing 4,106 genes was used to study temporal transcript profiles of Bacillus subtilis in response to valine, glutamate and glutamine pulses over 24 h. A total of 673, 835, and 1135 amino-acid-regulated genes were identified having significantly changed expression at one or more time points in response to valine, glutamate, and glutamine, respectively, including genes involved in cell wall, cellular import, metabolism of amino-acids and nucleotides, transcriptional regulation, flagellar motility, chemotaxis, phage proteins, sporulation, and many genes of unknown function. Different amino acid treatments were compared in terms of both the global temporal profiles and the 5-minute quick regulations, and between-experiment differential genes were identified. The highlighted genes were analyzed based on diverse sources of gene functions using a variety of computational tools, including T-profiler analysis, and hierarchical clustering. The results revealed the common and distinct modes of action of these three amino acids, and should help to elucidate the specific signaling mechanism of each amino acid as an effector.
authors.affiliation: Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, China. bcye@ecust.edu.cn
authors.forename: Bang-Ce
authors.initials: BC
authors.lastname: Ye
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.forename: Hui
authors.initials: H
authors.lastname: Yu
authors.forename: Wen-Bang
authors.initials: WB
authors.lastname: Yu
authors.forename: Bao-Hong
authors.initials: BH
authors.lastname: Liu
authors.forename: Bin-Cheng
authors.initials: BC
authors.lastname: Yin
authors.forename: Chun-Yun
authors.initials: CY
authors.lastname: Yin
authors.forename: Yuan-Yuan
authors.initials: YY
authors.lastname: Li
authors.forename: Ju
authors.initials: J
authors.lastname: Chu
authors.forename: Si-Liang
authors.initials: SL
authors.lastname: Zhang
mesh_terms: D001412:Bacillus subtilis / Q000378:metabolism*; D018407:Bacterial Physiological Phenomena; D001426:Bacterial Proteins / Q000378:metabolism; D001692:Biological Transport; D002244:Carbon / Q000378:metabolism; D005227:Fatty Acids / Q000378:metabolism; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects*; D005798:Genes, Bacterial; D018698:Glutamic Acid / Q000737:chemistry*; D005973:Glutamine / Q000737:chemistry*; D008954:Models, Biological; D009584:Nitrogen / Q000378:metabolism; D014158:Transcription, Genetic; D014633:Valine / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; D005227:Fatty Acids; D005973:Glutamine; D018698:Glutamic Acid; D002244:Carbon; D014633:Valine; D009584:Nitrogen