Unexpected Coregulator Range for the Global Regulator Lrp of Escherichia coli and Proteus mirabilis

Abstract

The Lrp/AsnC family of transcription factors links gene regulation to metabolism in bacteria and archaea. Members of this family, collectively, respond to a wide range of amino acids as coregulators. In Escherichia coli, Lrp regulates over 200 genes directly and is well known to respond to leucine and, to a somewhat lesser extent, alanine. We focused on Lrp from Proteus mirabilis and E. coli, orthologs with 98% identity overall and identical helix-turn-helix motifs, for which a previous study nevertheless found functional differences. Sequence differences between these orthologs, within and adjacent to the amino acid-responsive RAM domain, led us to test for differential sensitivity to coregulatory amino acids. In the course of this investigation, we found, via in vivo reporter fusion assays and in vitro electrophoretic mobility shift experiments, that E. coli Lrp itself responded to a broader range of amino acids than was previously appreciated. In particular, for both the E. coli and P. mirabilis orthologs, Lrp responsiveness to methionine was similar in magnitude to that to leucine. Both Lrp orthologs are also fairly sensitive to Ile, His, and Thr. These observations suggest that Lrp ties gene expression in the Enterobacteriaceae rather extensively to physiological status, as reflected in amino acid pools. These findings also have substantial implications for attempts to model regulatory architecture from transcriptome measurements or to infer such architecture from genome sequences, and they suggest that even well-studied regulators deserve ongoing exploration.

The TonB3 System in the Human Pathogen Vibrio vulnificus Is under the Control of the Global Regulators Lrp and Cyclic AMP Receptor Protein

“…In addition to L-leucine, other amino acids, such as L-alanine, L-isoleucine, L-valine, and L-methionine, repressed the expression of the TonB3 system when added to the minimal medium (data not shown). This result is consistent with a recent discovery that E. coli Lrp responds to several of these amino acids (25). In line with those observations, when we performed a microarray analysis with total RNA obtained from V. vulnificus cells growing in HS-FAC, we found that the genes that encode enzymes involved in the glyoxylate shunt as well as glycerol metabolism were clearly induced after 4 to 6 h of growth in serum (Alice and Crosa, unpublished data), indicating the utilization of glycerol and/or lipids as carbon sources after the glucose depletion.…”

Distinct transcriptional regulation of the two Escherichia coli transhydrogenases PntAB and UdhA

“…Methionine activated udhA transcription, whereas histidine repressed pntAB transcription. Although methionine and histidine are described to affect Lrp activity (Hart & Blumenthal, 2011), the mechanism is not clear because one would then also expect lower pntAB and higher udhA expression, respectively, which was not observed.…”

Regulation of the ald Gene Encoding Alanine Dehydrogenase by AldR in Mycobacterium smegmatis

“…Some Lrp/AsnC family regulators, like E. coli Lrp and M. tuberculosis LrpA, are known to recognize a broad range of amino acids as effector molecules (26,27). This fact led us to determine the effect of various amino acids on both ald expression and binding of AldR to the ald control region (Fig.…”