Expanded roles of leucine-responsive regulatory protein in transcription regulation of the Escherichia coli genome: Genomic SELEX screening of the regulation targets.

Leucine-responsive regulatory protein (Lrp) Is a transcriptional regulator for the genes Involved In transport, biosynthesis and catabolism of amino adds in Escherichia coli. In order to identify the whole set of genes under the direct control of Lrp, we performed Genomic SELEX screening and identified a total of 314 Lrp-binding sites on the E. coli genome. As a result, the regulation target of Lrp was predicted to expand from the hitherto identified genes for amino add metabolism to a set of novel target genes for utilization of amino adds for protein synthesis, Inducing tRNAs, aminoacyl-tRNA synthases and rRNAs. Northern blot analysis indicated alteration of mRNA levels for at least some novel targets, Inducing the aminoacyl-tRNA synthetase genes. Phenotype MicroArray of the lrp mutant indicated significant alteration in utilization of amino adds and peptides, whilst metabolome analysis showed variations In the concentration of amino adds In the lrp mutant. From these two datasets we realized a reverse correlation between amino add levels and cell growth rate: fast-growing cells contain low-level amino adds, whilst a high level of amino adds exists in slow-growing cells. Taken together, we propose that Lrp is a global regulator of transcription of a large number of the genes Involved In not only amino add transport and metabolism, but also amino acid utilization.