The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation

Abstract

Analysis of the response to arginine of the Escherichia coli K-12 transcriptome by microarray hybridization and real-time quantitative PCR provides the first coherent quantitative picture of the ArgR-mediated repression of arginine biosynthesis and uptake genes. Transcriptional repression was shown to be the major control mechanism of the biosynthetic genes, leaving only limited room for additional transcriptional or post-transcriptional regulation. The art genes, encoding the specific arginine uptake system, are subject to ArgR-mediated repression, with strong repression of artJ, encoding the periplasmic binding protein of the system. The hisJQMP genes of the histidine transporter (part of the lysine-arginine-ornithine uptake system) were discovered to be a part of the arginine regulon. Analysis of their control region with reporter gene fusions and electrophoretic mobility shift in the presence of pure ArgR repressor showed the involvement in repression of the ArgR protein and an ARG box 120 bp upstream of hisJ. No repression of the genes of the third uptake system, arginine-ornithine, was observed. Finally, comparison of the time course of arginine repression of gene transcription with the evolution of the specific activities of the cognate enzymes showed that while full genetic repression was achieved 2 min after arginine addition, enzyme concentrations were diluted at the rate of cell division. This emphasizes the importance of feedback inhibition of the first enzymic step in the pathway in controlling the metabolic flow through biosynthesis in the period following the onset of repression.

Role of ArgP (IciA) in Lysine-Mediated Repression in Escherichia coli

“…The respective promoter- (Table 9). Consistent with earlier reports (8,9), the lac fusions with the promoters of hisJ, artJ, and artP exhibited repression by Arg in the wild-type strain and derepressed expression in a ⌬argR mutant (Table 9). EMSA experiments undertaken with the regulatory region of one of the genes, argT, revealed a very low affinity of binding by ArgP that was Lys independent (Fig.…”

σSControls Multiple Pathways Associated with Intracellular Multiplication ofLegionella pneumophila

“…Subsequent steps of arginine biosynthesis can be accomplished (100), and the genes required for the conversion of ornithine to arginine, argFGH, are divergent from argR (lpg0490) in a region that also includes a putative ABC transporter (lpg0491-lpg0496). In E. coli and P. aeruginosa, ArgR regulates the expression of a number of transporters required for the uptake of amino acids and other compounds (13,60), and ArgR has been predicted to regulate arginine uptake from the host cell in some members of the Chlamydiaceae (88). It is intriguing to speculate that ArgR regulates one or more L. pneumophila transporters required for the acquisition of critical nutrients from the host cell.…”

Metabolic engineering of Escherichia coli for the production of putrescine: A four carbon diamine

“…However, deletion of both genes is not desirable because cells would become arginine auxotrophic, requiring the addition of arginine to the minimal medium for the growth, which adds additional cost (also see Discussion Section). The argI gene was selected as a knockout target since it is a major one (Caldara et al, 2006).…”

“…One possible explanation is that the deletion of the argR gene derepressed the argF-H genes (Caldara et al, 2006(Caldara et al, , 2008, which would increase the metabolic flux from ornithine to arginine and decrease the ornithine pool for putrescine production via ornithine decarboxylation (Fig. 1).…”