Time-Resolved Transcriptome Analysis of Bacillus subtilis Responding to Valine, Glutamate, and Glutamine

Bang-Ce Ye,Wen-Bang Yu,Yuan-Yuan Li,Bao-Hong Liu,Chun-Yun Yin,Si-Liang Zhang,Bin-Cheng Yin,Hui Yu,Yan Zhang,Ju Chu

doi:10.1371/journal.pone.0007073

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.

Highlights

Microorganisms constantly respond to the variations of external and internal conditions, and try to adapt to the environment for survival
We found that the addition of different amino acids resulted in a distinctive massive restructuring of the transcriptional output
A total of 673, 835, and 1135 genes were identified as significantly expressed at one or more time points in response to pulses of valine, glutamate, and glutamine, respectively, including genes, involved in cell wall, cellular import, metabolism of aminoacids, fatty acid, and nucleotides, transcriptional regulation, flagellar motility, chemotaxis, phage proteins, sporulation, and many genes of unknown function (40–62%). 213 genes were induced by both Glu and Gln, and 93 genes were upregulated by both Val and Gln

Summary

Introduction

Microorganisms constantly respond to the variations of external and internal conditions, and try to adapt to the environment for survival. Such work will help develop tools and concepts to handle and to analyze the inherent complexity of biological functions [9] Both transcripts and metabolites change in response to external perturbation have demonstrated that the distinct alterations in transcript levels may lead to multiple changes at the level of the metabolite and vice versa, treatments with external metabolites lead to multiple changes in the abundance of transcripts, implying the bidirectional information exchange between genes and metabolites. Zaman et al found that the five regulatory systems Ras/PKA, Gpr1/Gpa, Sch, Snf and Rgt2/Snf play different roles in responding to changes in glucose concentration and initiate cellular growth and division by using microarray gene expression profiles in conjunction with conditional mutations [10,11,12]

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Results

Conclusion