Distinguishing features of δ-proteobacterial genomes

Abstract

We analyzed several features of five currently available ␦-proteobacterial genomes, including two aerobic bacteria exhibiting predatory behavior and three anaerobic sulfate-reducing bacteria. The ␦ genomes are distinguished from other bacteria by several properties: (i) The ␦ genomes contain two ''giant'' S1 ribosomal protein genes in contrast to all other bacterial types, which encode a single or no S1; (ii) in most ␦-proteobacterial genomes the major ribosomal protein (RP) gene cluster is near the replication terminus whereas most bacterial genomes place the major RP cluster near the origin of replication; (iii) the ␦ genomes possess the rare combination of discriminating asparaginyl and glutaminyl tRNA synthetase (AARS) together with the amidotransferase complex (Gat CAB) genes that modify Asp-tRNA Asn into Asn-tRNA Asn and Glu-tRNA Gln into Gln-tRNA Gln ; (iv) the TonB receptors and ferric siderophore receptors that facilitate uptake and removal of complex metals are common among ␦ genomes; (v) the anaerobic ␦ genomes encode multiple copies of the anaerobic detoxification protein rubrerythrin that can neutralize hydrogen peroxide; and (vi) 54

Evolution of sensory complexity recorded in a myxobacterial genome

“…In E. coli and mitochondria, the products of these genes are thought to degrade misfolded and damaged proteins, allowing their amino acids to be recycled (68,69), but in M. xanthus they could be used for feeding. Second, an examination of the whole genome for genes with codon-usage frequencies that are similar to the genes encoding ribosomal proteins (the mark of ''highly expressed genes'') indicates that many M. xanthus ATP-dependent proteases and many chaperones were highly expressed (70). They are as highly expressed by M. xanthus as its tricarboxylic acid cycle enzymes and electron transport proteins.…”

“…The E. coli FtsH protein is an integral inner membrane protein that projects its ATPase domain into the periplasm. If the M. xanthus FtsH protein, one of its most highly expressed proteins (70), is similar, it would be in a position to draw denatured prey proteins into its protease cavity (71). ␦-Proteobacteria generally possess large, multiprotein networks in their periplasm involved in generating energy, like the hydrogen oxidase complex of De.…”

Predicting Gene Expression Level from Codon Usage Bias

“…It follows that the strength of codon usage bias in a gene can be used to make predictions about its expression level. Karlin and colleagues have devised a codon usage statistic termed E(g), the ''expression measure'' of a gene, which they have used in attempts to identify predicted highly expressed (PHX) genes in a wide range of prokaryotic genomes Mrazek 2000, 2001;Karlin et al , 2003Karlin et al , 2004Karlin et al , 2005Karlin et al , 2006Mrazek et al 2001Mrazek et al , 2006Ma et al 2002). Here we discuss problems with the E(g) statistic and with its application to diverse species.…”

Proteome-Based Comparative Analyses of Growth Stages Reveal New Cell Cycle-Dependent Functions in the Predatory Bacterium Bdellovibrio bacteriovorus

“…The ratio presented is the highest ratio of the differential spot intensities obtained between life stages. b Predicted as highly expressed genes according to the work of Karlin et al (34). c Data from 2DE gels in the pH 3 to 10 range.…”