Abstract
Leucine-responsive regulatory protein (Lrp) is a transcriptional regulator for the genes involved in transport, biosynthesis and catabolism of amino acids 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 acid metabolism to a set of novel target genes for utilization of amino acids for protein synthesis, including tRNAs, aminoacyl-tRNA synthases and rRNAs. Northern blot analysis indicated alteration of mRNA levels for at least some novel targets, including the aminoacyl-tRNA synthetase genes. Phenotype MicroArray of the lrp mutant indicated significant alteration in utilization of amino acids and peptides, whilst metabolome analysis showed variations in the concentration of amino acids in the lrp mutant. From these two datasets we realized a reverse correlation between amino acid levels and cell growth rate: fast-growing cells contain low-level amino acids, whilst a high level of amino acids 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 acid transport and metabolism, but also amino acid utilization.
Highlights
CitAB TCS sensor kinase palmitoyl transferase for Lipid A predicted protein 2-dehydro-3-deoxyphosphoheptonate aldolase molybdopterin biosynthesis protein A predicted IM protein L-asparaginase nucleoside triphosphate hydrolase transcription factor predicted diguanylate cyclase e14 prophage cell death peptidase D-amino acid dehydrogenase predicted cation regulator predicted IM protein DNA topoisomerase I predicted Zn(II) transporter osmotically inducible membrane predicted protein predicted IM protein predicted lipoprotein Val tRNA PEP synthetase regulatory protein exonuclease III universal stress protein predicted ferritin-like protein tyrosine transporter conserved protein CP4-44 hemin or colicin receptor phosphatidylglycerol kinase D-lactate dehydrogenase
Predicted transposase predicted transposase predicted hydratase conserved protein putrescine transporter predicted lipoprotein chaperone for lipoproteins seryl-tRNA synthetase predicted transporter phosphohydroxythreonine aminotransferase OM porin 1a asparaginyl tRNA synthetase predicted methyltransferase nucleoside triphosphate hydrolase DNA damage-inducible protein I glutaredoxin 2 e14 prophage IM protein predicted protein FAD-binding phosphodiesterase predicted protein predicted GTP-binding protein D-manno-octulosonate 8-phosphate synthase nitrate reductase 1 oligopeptide transporter 23S rRNA pseudouridylate synthase transcription factor hypothetical protein RNase II modlator ribonuclease II transcription factor Rac transcription factor predicted lipoprotein predicted protein methyl viologen efflux pump predicted liprotein predicted peptidase transcription factor autoinducer-2 (AI-2) kinase conserved protein conserved protein Qin site-specific recombinase arginine/ornithine antiporter transporter predicted transporter predicted lipoprotein predicted diguanylate cyclase transcription factor L-serine deaminase I Hsp31 molecular chaperone conserved protein IS5 transposase and trans-activator predicted amino-acid transporter ncRNA D-tagatose 1,6-bisphosphate aldolase predicted transporter subunit YehUT TCS response regulator Dihydropyrimidine dehydrogenase predicted kinase predicted peptidase serine protease inhibitor ecptin RcsBC TCS phospho transfer predicted protein transcription factor predicted IM protein stationary phase inducible protein protein disaggregation chaperone pheA gene leader peptide
Summary
Predicted oxidoreductase citrate lyase synthetase anaerobic C4-dicarboxylate transport conserved protein ddlA ompT ydbH-ynbE- CitAB TCS sensor kinase palmitoyl transferase for Lipid A predicted protein 2-dehydro-3-deoxyphosphoheptonate aldolase molybdopterin biosynthesis protein A predicted IM protein L-asparaginase nucleoside triphosphate hydrolase transcription factor predicted diguanylate cyclase e14 prophage cell death peptidase D-amino acid dehydrogenase predicted cation regulator predicted IM protein DNA topoisomerase I predicted Zn(II) transporter osmotically inducible membrane predicted protein predicted IM protein predicted lipoprotein Val tRNA PEP synthetase regulatory protein exonuclease III universal stress protein predicted ferritin-like protein tyrosine transporter conserved protein CP4-44 hemin or colicin receptor phosphatidylglycerol kinase D-lactate dehydrogenase
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