Distinguishing features of δ-proteobacterial genomes

doi:10.1073/pnas.0604311103

Distinguishing features of δ-proteobacterial genomes

Departments of *Mathematics and
^§Biochemistry, Stanford University, Stanford, CA 94305; and
^‡Department of Microbiology, University of Georgia, Athens, GA 30602

Contributed by Samuel Karlin, June 5, 2006

Abstract

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-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 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 of Myxococcus 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.

Footnotes

^†To whom correspondence should be addressed. E-mail: karlin{at}math.stanford.edu
Author contributions: S.K., L.B., J.M., and D.K. designed research; S.K., L.B., J.M., and D.K. performed research; S.K., L.B., J.M., and D.K. contributed new reagents/analytic tools; S.K., L.B., J.M., and D.K. analyzed data; and S.K. wrote the paper.
Conflict of interest statement: No conflicts declared.
Data deposition: The two new complete genomes referred to in Note have been deposited in the GenBank database [accession nos. NC-007519 (Desulfovibrio desulfuricans) and NC-007517 (Geobacter metallireduceans)].
Abbreviations:

Abbreviations:

PHX,

predicted highly expressed;

RP,

ribosomal protein;

AARS,

asparaginyl and glutaminyl tRNA synthetase;

RR,

response regulator;

HK,

histidine kinase;

TCA,

tricarboxylic acid.