Complete genome and proteome of Acholeplasma laidlawii.

We present the complete genome sequence and proteogenomic map for Acholeplasma laidlawii PG-8A (class Mollicutes, order Acholeplasmatales, family Acholeplasmataceae). The genome of A. laidlawii is represented by a single 1,496,992-bp circular chromosome with an average G+C content of 31 mol%. This is the longest genome among the Mollicutes with a known nucleotide sequence. It contains genes of polymerase type I, SOS response, and signal transduction systems, as well as RNA regulatory elements, riboswitches, and T boxes. This demonstrates a significant capability for the regulation of gene expression and mutagenic response to stress. Acholeplasma laidlawii and phytoplasmas are the only Mollicutes known to use the universal genetic code, in which UGA is a stop codon. Within the Mollicutes group, only the sterol-nonrequiring Acholeplasma has the capacity to synthesize saturated fatty acids de novo. Proteomic data were used in the primary annotation of the genome, validating expression of many predicted proteins. We also detected posttranslational modifications of A. laidlawii proteins: phosphorylation and acylation. Seventy-four candidate phosphorylated proteins were found: 16 candidates are proteins unique to A. laidlawii, and 11 of them are surface-anchored or integral membrane proteins, which implies the presence of active signaling pathways. Among 20 acylated proteins, 14 contained palmitic chains, and six contained stearic chains. No residue of linoleic or oleic acid was observed. Acylated proteins were components of mainly sugar and inorganic ion transport systems and were surface-anchored proteins with unknown functions.

Regulation of aromatic amino acid biosynthesis in gamma-proteobacteria.

Computational comparative techniques were applied to analysis of the aromatic amino acid regulons in gamma-proteobacteria. This resulted in characterization of the TrpR and TyrR regulons in the genomes of Yersinia pestis, Haemophilus influenzae, Vibrio cholerae and other bacteria and identification of new members of the PhhR regulon in the genome of Pseudomonas aeruginosa. Candidate attenuators were constructed for all studied genomes, including the trpBA operon of the very distantly related bacterium Chlamidia trachomatis. The pheA attenuator of Y. pestis is an integration site for the insertion element IS-200. It was shown that the triplication of the DAHP-synthase genes occurred prior to the divergence of families Enterobacteriaceae, Vibrionaceae and Alteromonadaceae. The candidate allosteric control site of the DAHP-syntheases was identified. This site is deteriorated in AroH of Buchnera sp. APS. The known DAHP-synthase of Bordetella pertussis is likely to be feedback-inhibited by phenylalanine, and the DAHP-synthase of Corynebacterium glutamicum could be inhibited by tyrosine. Overall, the most extensive regulation was observed in Escherichia coli, whereas the regulation in other genomes seems to be less developed. At the extreme, the tryptophan production in the aphid endosymbiont Buchnera sp. APS is free from transcriptional, attenuation, and allosteric control.