title: Attenuation regulation of amino acid biosynthetic operons in proteobacteria: comparative genomics analysis.
abstract: Candidate attenuators were identified that regulate operons responsible for biosynthesis of branched amino acids, histidine, threonine, tryptophan, and phenylalanine in gamma- and alpha-proteobacteria, and in some cases in low-GC Gram-positive bacteria, Thermotogales and Bacteroidetes/Chlorobi. This allowed us not only to describe the evolutionary dynamics of regulation by attenuation of transcription, but also to annotate a number of hypothetical genes. In particular, orthologs of ygeA of Escherichia coli were assigned the branched chain amino acid racemase function. Three new families of histidine transporters were predicted, orthologs of yuiF and yvsH of Bacillus subtilis, and lysQ of Lactococcus lactis. In Pasteurellales, the single bifunctional aspartate kinase/homoserine dehydrogenase gene thrA was predicted to be regulated not only by threonine and isoleucine, as in E. coli, but also by methionine. In alpha-proteobacteria, the single acetolactate synthase operon ilvIH was predicted to be regulated by branched amino acids-dependent attenuators. Histidine biosynthetic operons his were predicted to be regulated by histidine-dependent attenuators in Bacillus cereus and Clostridium difficile, and by histidine T-boxes in L. lactis and Streptococcus mutans.
authors.affiliation: Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetnyi per. 19, Moscow 127994, GSP-4, Russia. vitresch@loria.fr
authors.forename: Alexey G
authors.initials: AG
authors.lastname: Vitreschak
authors.forename: Elena V
authors.initials: EV
authors.lastname: Lyubetskaya
authors.forename: Maxim A
authors.initials: MA
authors.lastname: Shirshin
authors.forename: Mikhail S
authors.initials: MS
authors.lastname: Gelfand
authors.forename: Vassily A
authors.initials: VA
authors.lastname: Lyubetsky
mesh_terms: D020561:Alphaproteobacteria / Q000145:classification / Q000235:genetics*; D000596:Amino Acids / Q000096:biosynthesis* / Q000235:genetics*; D001483:Base Sequence; D020562:Betaproteobacteria / Q000145:classification / Q000235:genetics*; D020563:Gammaproteobacteria / Q000145:classification / Q000235:genetics*; D016680:Genome, Bacterial; D023281:Genomics; D008969:Molecular Sequence Data; D009876:Operon; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D000596:Amino Acids