Transcriptome Analysis Of Bacillus Subtilis Responding To Valine, Glutamate And Glutamine

Microorganisms can restructure their transcriptional output to adapt to environmental conditions. In this paper, an Agilent customized microarray representing 4106 genes was used to study temporal transcript profiles of Bacillus subtilis in response to valine, glutamate and glutamine. The steady-state chemostat culture in a 5-L fermentor was perturbed by the addition of amino acid. The samples were harvested prior to the amino acid pulse (t= 0, as reference samples) and at different time points (5 min,30 min,2 h,8 h/24 h) after the perturbation. 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, sporulation, and many genes of unknown function. A large number of genes involved in transport of various molecules were found to be overrepresented within the first 5 min. In addition to examine the identity of genes regulated by different amino-acid pulses, we also compared the temporal expression log ratios between each pair of amino-acid pulses, yielding 922 between experiment differentially expressed genes that had different temporal expression patterns between some two amino-acid pulses. 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.