title: Regulation of biosynthesis and transport of aromatic amino acids in low-GC Gram-positive bacteria.
abstract: Computational comparative techniques were applied to analysis of the aromatic amino acid regulon in Gram-positive bacteria. A new candidate transcription regulation signal of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase and shikimate kinase genes was identified in Streptococcus and Lactococcus species. New T-boxes were found upstream of aromatic amino acid biosynthesis and transport genes in the Bacillus/Clostridium group. The substrate specificity of proteins from the PabA/TrpG family was assigned based on metabolic reconstruction and analysis of regulatory signals and phylogenetic patterns. New candidate tryptophan transporters were identified; their specificity was predicted by analysis of T-box regulatory sites. Comparison of all available genomes shows that regulation of genes of the aromatic amino acid biosynthesis pathway is quite labile and involves at least four regulatory systems, two at the DNA level and two more involving competition of alternative RNA secondary structures for transcription and/or translation regulation at the RNA level.
authors.affiliation: Graduate Program in Molecular, Cellular and Integrative Life Sciences, 172 Molecular Science Building, University of California at Los Angeles, Los Angeles, CA 90095-1570, USA.
authors.forename: Ekaterina M
authors.initials: EM
authors.lastname: Panina
authors.forename: Alexey G
authors.initials: AG
authors.lastname: Vitreschak
authors.forename: Andrey A
authors.initials: AA
authors.lastname: Mironov
authors.forename: Mikhail S
authors.initials: MS
authors.lastname: Gelfand
mesh_terms: D010723:3-Deoxy-7-Phosphoheptulonate Synthase / Q000235:genetics; D024322:Amino Acids, Aromatic / Q000096:biosynthesis* / Q000378:metabolism*; D000878:Anthranilate Synthase; D001421:Bacteria, Anaerobic / Q000235:genetics / Q000378:metabolism; D002352:Carrier Proteins / Q000235:genetics / Q000378:metabolism; D004269:DNA, Bacterial / Q000235:genetics; D016983:Enterococcus / Q000235:genetics / Q000378:metabolism; D019143:Evolution, Molecular; D015964:Gene Expression Regulation, Bacterial; D015971:Gene Expression Regulation, Enzymologic; D006094:Gram-Positive Bacteria / Q000235:genetics* / Q000378:metabolism*; D017045:Lactococcus / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D019884:Nitrogenous Group Transferases / Q000235:genetics; D009876:Operon; D017853:Phosphotransferases (Alcohol Group Acceptor) / Q000235:genetics; D010802:Phylogeny; D012329:RNA, Bacterial / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D013291:Streptococcus / Q000235:genetics / Q000378:metabolism; D000637:Transaminases / Q000235:genetics; D015533:Transcriptional Activation
chemical_list: D024322:Amino Acids, Aromatic; D002352:Carrier Proteins; D004269:DNA, Bacterial; D012329:RNA, Bacterial; D010723:3-Deoxy-7-Phosphoheptulonate Synthase; D019884:Nitrogenous Group Transferases; C022309:PABA synthase; D000637:Transaminases; D017853:Phosphotransferases (Alcohol Group Acceptor); C022642:shikimate kinase; D000878:Anthranilate Synthase; C020655:anthranilate synthase, glutamine amidotransferase subunit