Extensive inter-domain lateral gene transfer in the evolution of the human commensal Methanosphaera stadtmanae

Mor Nadia Lurie-Weinberger

doi:10.3389/fgene.2012.00182

Abstract

Methanosphaera stadtmanae is a commensal methanogenic archaeon found in the human gut. As most of its niche-neighbors are bacteria, it is expected that lateral gene transfer (LGT) from bacteria might have contributed to the evolutionary history of this organism. We performed a phylogenomic survey of putative LGT events in M. stadtmanae, using a phylogenetic pipeline. Our analysis indicates that a substantial fraction of the proteins of M. stadtmanae are inferred to have been involved in inter-domain LGT. Laterally acquired genes have had a large contribution to surface functions, by providing novel glycosyltransferase functions. In addition, several ABC transporters seem to be of bacterial origin, including the molybdate transporter. Thus, bacterial genes contributed to the adaptation of M. stadtmanae to a host-dependent lifestyle by allowing a larger variation in surface structures and increasing transport efficiency in the gut niche which is diverse and competitive.

Highlights

Lateral gene transfer (LGT) is an important force in microbial evolution and a major source of genetic variation and innovation (Doolittle et al, 2003)
IDENTIFICATION OF LATERAL GENE TRANSFER CANDIDATES To test the hypothesis that M. stadtmanae has had major contributions to its gene repertoire through inter-domain LGT from bacterial species, an automatic pipeline was used to generate phylogenetic trees for the entire proteome of that archaeon
137 trees had bacteria as the closest phylogenetic neighbor of Methanosphaera, representing possible inter-domain LGTs, while in 72 additional trees Methanobrevibacter was sister to Methanosphaera, but with the two methanogens nested within bacterial clades

Summary

Introduction

Lateral gene transfer (LGT) is an important force in microbial evolution and a major source of genetic variation and innovation (Doolittle et al, 2003). It is interesting to note that of the trees in which no direction could be inferred, in 12 cases Methanosphaera and Methanobrevibacter were the only archaea present in the phylogeny, implying a likely bacterial origin of these genes, the number of genes that warrant further inspection should be 121, all of which cases which represent possible transfers of bacterial origin (see Table S1 in Supplementary Material, marked “Direction unknown∗”).

Results

Conclusion