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.

Genome‐wide mapping of TnrA‐binding sites provides new insights into the TnrA regulon in Bacillus subtilis

“…This was in agreement with a previous report, which showed by transcriptomic analysis that hom expression was downregulated by glutamine (Ye et al. 2009 ).…”

“… 2002 ; Ye et al. 2009 ). Seventeen TnrA targets were detected by a combination of DNA microarray hybridization, a genome-wide search for TnrA boxes, and gel retardation assays (Yoshida et al.…”

A novel amidotransferase required for lipoic acid cofactor assembly in Bacillus subtilis

“…Cronan, unpublished) or Salmonella enterica (Smith et al ., 1991). However, B. subtilis lplJ has been shown to be induced during spore outgrowth (Keijser et al ., 2007) and lipM and lplJ are induced in response to valine (Ye et al ., 2009). Constitutive expression of GcvH would allow it to be always available to act as a lipoate transfer protein regardless of glycine supplementation.…”

The Synergistic Effect of Exogenous Glutamine and Rifampicin Against Mycobacterium Persisters

“…The synergistic effect of glutamine on rifampicin against Mycobacteria might be indirectly mediated by the central metabolism ( Lewis, 2010 ), like other amino acids ( Shan et al, 2015 ; Vilcheze et al, 2017 ). The glutamine starvation represents a good window to understand the changed central metabolism, respiration and the expression of stress-responsive genes ( Ye et al, 2009 ; Jessberger et al, 2013 ). The data are consistent with the previous reports ( Ye et al, 2009 ; Keren et al, 2011 ) that the addition of glutamine accelerated both the central metabolism and TCA cycle ( Table 1 ), fueled by the influx of degraded amino acids.…”

“…Glutamine is essential for bacterial metabolism ( di Mauro et al, 1969 ; Campbell et al, 2001 ; Keren et al, 2004 , 2011 ; Gouzy et al, 2014b ). Glutamine starvation can up-regulate the expression of stress responsive genes ( Betts et al, 2002 ; Ye et al, 2009 ; Jessberger et al, 2013 ). Some amino acids, alone or with antibiotics, can inhibit the bacterial growth ( Rowley, 1953 ; Amos and Cohen, 1954 ).…”