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Analysis of Gene Islands Involved in Methanopterin-Linked C₁ Transfer Reactions Reveals New Functions and Provides Evolutionary Insights

Marina G. Kalyuzhnaya,¹ Natalia Korotkova,^1, Gregory Crowther,¹ Christopher J. Marx,^1, Mary E. Lidstrom,^1,2 and Ludmila Chistoserdova^1*

Department of Chemical Engineering,¹ Department of Microbiology, University of Washington, Seattle, Washington 98195²

Received 24 January 2005/ Accepted 15 March 2005

In this study, the occurrence and chromosomal clustering of genes encoding C₁ transfer reactions linked to tetrahydromethanopterin (H₄MPT) were analyzed in a variety of proteobacteria and in representatives of the Planctomycetes via genomic analysis or via partial sequencing by cosmid walking. Although a tendency for clustering was found common for the genes of interest, significant variations in gene order and the degree of clustering were uncovered both between and within different groups of Proteobacteria and between Proteobacteria and Planctomycetes. Phylogenetic analyses suggested that the evolution of genes encoding H₄MPT-linked reactions in Proteobacteria involved lateral transfers within Proteobacteria and possibly between Proteobacteria and other phyla. Gene cluster comparisons revealed a number of novel genes potentially involved in the C₁ transfer reactions, and these were analyzed by mutation and expression analyses. Four genes, a homolog of pabB, and three genes conserved between methanogenic Archaea and Bacteria possessing H₄MPT-linked functions, orfY, orf1, and afpA were shown to be involved in formaldehyde oxidation/detoxification, as judged by specific mutant phenotypes. In particular, pabB contributes to the biosynthesis of para-aminobenzoic acid, a precursor of both tetrahydrofolate and H₄MPT, and afpA apparently encodes a novel dihydromethanopterin reductase, based on mutant complementation experiments.

Present address: Department of Microbiology, University of Washington, Seattle, WA 98195.

Present address: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138.

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