Evidence for Horizontal Gene Transfer of Anaerobic Carbon Monoxide Dehydrogenases

Techtmann, Stephen M.; Lebedinsky, Alexander V.; Colman, Albert S.; Sokolova, Tatyana G.; Woyke, Tanja; Goodwin, Lynne; Robb, Frank T.

doi:10.3389/fmicb.2012.00132

Evidence for Horizontal Gene Transfer of Anaerobic Carbon Monoxide Dehydrogenases

Journal Article · Sat Dec 31 23:00:00 EST 2011 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2012.00132· OSTI ID:1628055

Techtmann, Stephen M. ^[1]; Lebedinsky, Alexander V. ^[2]; Colman, Albert S. ^[3]; Sokolova, Tatyana G. ^[2]; Woyke, Tanja ^[4]; Goodwin, Lynne ^[4]; Robb, Frank T. ^[5]

Univ. of Maryland Baltimore County (UMBC), Baltimore, MD (United States). Inst. of Marine and Environmental Technology; Univ. of Maryland Baltimore County (UMBC), Baltimore, MD (United States). Dept. of Microbiology and Immunology; DOE/OSTI
Russian Academy of Sciences (RAS), Moscow (Russian Federation). Winogradsky Inst. of Microbiology
Univ. of Chicago, IL (United States). Dept. of Geophysical Sciences
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Univ. of Maryland Baltimore County (UMBC), Baltimore, MD (United States). Inst. of Marine and Environmental Technology; Univ. of Maryland Baltimore County (UMBC), Baltimore, MD (United States). Dept. of Microbiology and Immunology

Carbon monoxide (CO) is commonly known as a toxic gas, yet both cultivation studies and emerging genome sequences of bacteria and archaea establish that CO is a widely utilized microbial growth substrate. In this study, we determined the prevalence of anaerobic carbon monoxide dehydrogenases ([Ni,Fe]-CODHs) in currently available genomic sequence databases. Currently, 185 out of 2887, or 6% of sequenced bacterial and archaeal genomes possess at least one gene encoding [Ni,Fe]-CODH, the key enzyme for anaerobic CO utilization. Many genomes encode multiple copies of [Ni,Fe]-CODH genes whose functions and regulation are correlated with their associated gene clusters. The phylogenetic analysis of this extended protein family revealed six distinct clades; many clades consisted of [Ni,Fe]- CODHs that were encoded by microbes from disparate phylogenetic lineages, based on 16S rRNA sequences, and widely ranging physiology.To more clearly define if the branching patterns observed in the [Ni,Fe]-CODH trees are due to functional conservation vs. evolutionary lineage, the genomic context of the [Ni,Fe]-CODH gene clusters was examined, and superimposed on the phylogenetic trees. On the whole, there was a correlation between genomic contexts and the tree topology, but several functionally similar [Ni,Fe]-CODHs were found in different clades. In addition, some distantly related organisms have similar [Ni,Fe]-CODH genes. Thermosinus carboxydivorans was used to observe horizontal gene transfer (HGT) of [Ni,Fe]-CODH gene clusters by applying Kullback–Leibler divergence analysis methods. Divergent tetranucleotide frequency and codon usage showed that the gene cluster of T. carboxydivorans that encodes a [Ni,Fe]-CODH and an energyconverting hydrogenase is dissimilar to its whole genome but is similar to the genome of the phylogenetically distant Firmicute, Carboxydothermus hydrogenoformans. These results imply that T carboxydivorans acquired this gene cluster via HGT from a relative of C. hydrogenoformans.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1628055

Journal Information:: Frontiers in Microbiology, Journal Name: Frontiers in Microbiology Vol. 3; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
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