J. Mol. Microbiol. Biotechnol. (2001) 3(4): 529-543. AromaticJMMB Amino ResearchAcid Biosynthesis Article 529 Regulation of Aromatic Amino Acid Biosynthesis in Gamma-Proteobacteria E.M. Panina1, A.G. Vitreschak2, A.A. Mironov3, absence of reliable algorithms for recognition of functional and M.S. Gelfand3* sites in DNA sequences (Fickett and Hatzigeorgiou, 1997; Frech et al., 1997). 1Department of Mathematics, Moscow State University, Availability of genomes of related bacteria allows one Moscow, 119899, Russia to apply the comparative approach to analysis of not only 2Institute for Problems of Information Transmission, protein sequences, but regulatory patterns as well. At that, RAS, Moscow, 101447, Russia the search space is restricted to genes from a specific 3State Scientific Center GosNIIGenetika, Moscow, pathway, thus reducing the combinatorial space for false 113545, Russia positives. Another important advantage of simultaneous analysis of several genomes is the possibility to distinguish true sites, occurring upstream of orthologous genes, from Abstract false positives scattered at random across the genome. The latter technique allowed us to analyze several regulons Computational comparative techniques were applied and obtain a number of promising predictions (Mironov et to analysis of the aromatic amino acid regulons in al., 1999; Gelfand et al., 1999; Gelfand et al., 2000; gamma-proteobacteria. This resulted in Rodionov et al., 2000), some of which were subsequently characterization of the TrpR and TyrR regulons in the confirmed in experiments (Kreneva et al., 2000). Similar, genomes of Yersinia pestis, Haemophilus influenzae, although not exactly identical, techniques were developed Vibrio cholerae and other bacteria and identification in (Stojanovich et al., 1999; McGuire et al., 2000; Ramirez- of new members of the PhhR regulon in the genome Santos, 2001). For a review of these and related studies of Pseudomonas aeruginosa. Candidate attenuators see (Gelfand, 1999). were constructed for all studied genomes, including Here we study the evolution of regulation of the the trpBA operon of the very distantly related bacterium aromatic amino acid biosynthesis in the gamma subdivision Chlamidia trachomatis. The pheA attenuator of Y. of proteobacteria. This system is especially interesting, pestis is an integration site for the insertion element since it involves at least two transcriptional regulators, TrpR IS-200. It was shown that the triplication of the DAHP- and TyrR, attenuation, and allosteric control by feedback synthase genes occurred prior to the divergence of inhibition. All these systems were well studied in E. coli, families Enterobacteriaceae, Vibrionaceae and whereas the data for other bacteria are sporadic and Alteromonadaceae. The candidate allosteric control incomplete. In this paper we consider the regulatory site of the DAHP-syntheases was identified. This site patterns in the bacteria whose genomes are complete or is deteriorated in AroH of Buchnera sp. APS. The almost complete (Salmonella typhimurium, Yersinia pestis, known DAHP-synthase of Bordetella pertussis is likely Haemophilus influenzae, Vibrio cholerae, Buchnera sp. to be feedback-inhibited by phenylalanine, and the APS, and Pseudomonas aeruginosa). We also mention DAHP-synthase of Corynebacterium glutamicum could the regulatory signals in the available fragments of other be inhibited by tyrosine. Overall, the most extensive genomes, if these signals provide additional insight into regulation was observed in Escherichia coli, whereas the evolution of regulatory interactions. We describe the the regulation in other genomes seems to be less possible site of allosteric control of DAHP-synthases and developed. At the extreme, the tryptophan production use it to predict modes of feedback inhibition of this enzyme in the aphid endosymbiont Buchnera sp. APS is free in several bacterial species. Finally, we discuss the general from transcriptional, attenuation, and allosteric control. trends in regulation of aromatic amino acid biosynthesis in this group of bacteria. Introduction Biosynthesis of all three aromatic amino acids starts with the common pathway leading from Traditional analysis of complete bacterial genomes involves phosphoenolpyruvate and erythrose 4-phosphate through functional gene annotation and metabolic reconstruction. 3-deoxy-D-arabino-heptulosonate-7-phosphate and Recently, large-scale genomic analyses were performed shikimate to chorismate. Then the pathway divides into in order to study the evolution of metabolic pathways the terminal pathways, specific for each aromatic amino (Galperin and Koonin, 1999; Forst and Schulten, 1999; acid. Key enzymes of the latter pathways were extensively Dandekar et al., 1999). However, the evolution of regulation studied and all of them had been identified by early 1970s. is still largely unexplored. One of the reasons for this is the There are three regulated transporter systems for aromatic amino acids, namely the general permease AroP, the tryptophan permease Mtr, and the tyrosine permease TyrP (Figure 1; for a review see Pittard, 1996). The transcription of the genes for aromatic amino acid *For correspondence. Email [email protected]; Fax. +7-(095)-315-05-01. metabolism is regulated by two repressors, TrpR and TyrR © 2001 Horizon Scientific Press Further Reading Caister Academic Press is a leading academic publisher of advanced texts in microbiology, molecular biology and medical research. 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Genes encoding the enzymes of the aromatic amino acids biosynthesis pathway, their regulators and the transporters of tryptophan, tyrosin and phenylalanine. Regulation is shown by dotted lines. Underlined: genes regulated on the level of transcription (filled arrows: by TrpR; empty arrows: by TyrR); boldface: genes regulated by attenuation; shaded: enzymes inhibited by the end products (blunt arrows). (Otwinowski et al., 1988; Pittard and Davidson, 1991). In operon trpBA, and the remaining genes are scattered E. coli and S. typhimurium the operons mtr and aroL are across the genome.