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Applied and Environmental Microbiology, November 2005, p. 7083-7091, Vol. 71, No. 11
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.11.7083-7091.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

New Findings on Evolution of Metal Homeostasis Genes: Evidence from Comparative Genome Analysis of Bacteria and Archaea

J. M. Coombs^* and T. Barkay

Department of Biochemistry and Microbiology, Cook College, Rutgers University, New Brunswick, New Jersey 08901

Received 30 December 2004/ Accepted 22 June 2005

In order to examine the natural history of metal homeostasis genes in prokaryotes, open reading frames with homology to characterized P_IB-type ATPases from the genomes of 188 bacteria and 22 archaea were investigated. Major findings were as follows. First, a high diversity in N-terminal metal binding motifs was observed. These motifs were distributed throughout bacterial and archaeal lineages, suggesting multiple loss and acquisition events. Second, the CopA locus separated into two distinct phylogenetic clusters, CopA1, which contained ATPases with documented Cu(I) influx activity, and CopA2, which contained both efflux and influx transporters and spanned the entire diversity of the bacterial domain, suggesting that CopA2 is the ancestral locus. Finally, phylogentic incongruences between 16S rRNA and P_IB-type ATPase gene trees identified at least 14 instances of lateral gene transfer (LGT) that had occurred among diverse microbes. Results from bootstrapped supported nodes indicated that (i) a majority of the transfers occurred among proteobacteria, most likely due to the phylogenetic relatedness of these organisms, and (ii) gram-positive bacteria with low moles percent G+C were often involved in instances of LGT. These results, together with our earlier work on the occurrence of LGT in subsurface bacteria (J. M. Coombs and T. Barkay, Appl. Environ. Microbiol. 70:1698-1707, 2004), indicate that LGT has had a minor role in the evolution of P_IB-type ATPases, unlike other genes that specify survival in metal-stressed environments. This study demonstrates how examination of a specific locus across microbial genomes can contribute to the understanding of phenotypes that are critical to the interactions of microbes with their environment.

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* Corresponding author. Present address: Department of Biology, Adelphi University, 110 Science Building, 1 South Ave., Garden City, NY 11530. Phone: (516) 877-4196. Fax: (516) 877-4209. E-mail: coombs{at}adelphi.edu.

Supplemental material for this article may be found at http://aem.asm.org/.

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Applied and Environmental Microbiology, November 2005, p. 7083-7091, Vol. 71, No. 11
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.11.7083-7091.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

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