Open AccessDistinguishing features of δ-proteobacterial genomes
Author(s) -
Samuel Karlin,
Luciano Brocchieri,
Jan Mrázek,
Dale Kaiser
Publication year - 2006
Publication title -
proceedings of the national academy of sciences of the united states of america
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.011
H-Index - 771
eISSN - 1091-6490
pISSN - 0027-8424
DOI - 10.1073/pnas.0604311103
Subject(s) - genome , biology , bacterial genome size , gene , horizontal gene transfer , transfer rna , bacteria , myxococcus xanthus , genetics , rna , mutant
We analyzed several features of five currently available δ-proteobacterial genomes, including two aerobic bacteria exhibiting predatory behavior and three anaerobic sulfate-reducing bacteria. The δ genomes are distinguished from other bacteria by several properties: (i ) The δ 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 δ-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 δ genomes possess the rare combination of discriminating asparaginyl and glutaminyl tRNA synthetase (AARS) together with the amido-transferase complex (Gat CAB) genes that modify Asp-tRNAAsn into Asn-tRNAAsn and Glu-tRNAGln into Gln-tRNAGln ; (iv ) the TonB receptors and ferric siderophore receptors that facilitate uptake and removal of complex metals are common among δ genomes; (v ) the anaerobic δ genomes encode multiple copies of the anaerobic detoxification protein rubrerythrin that can neutralize hydrogen peroxide; and (vi ) σ54 activators play a more important role in the δ genomes than in other bacteria. δ genomes have a plethora of enhancer binding proteins that respond to environmental and intracellular cues, often as part of two-component systems; (vii ) δ genomes encode multiple copies of metallo-β-lactamase enzymes; (viii ) a host of secretion proteins emphasizing SecA, SecB, and SecY may be especially useful in the predatory activities ofMyxococcus xanthus ; (ix ) δ proteobacteria drive many multiprotein machines in their periplasms and outer membrane, including chaperone-feeding machines, jets for slime secretion, and type IV pili.Bdellovibrio replicates in the periplasm of prey cells. The sulfate-reducing δ proteobacteria metabolize hydrogen and generate a proton gradient by electron transport. The predicted highly expressed genes from δ genomes reflect their different ecologies, metabolic strategies, and adaptations.