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Proc Natl Acad Sci U S A. 2006 Jun 20;103(25):9584-9. Epub 2006 Jun 12.

Quantitative exploration of the occurrence of lateral gene transfer by using nitrogen fixation genes as a case study.

Author information

1
Department of Biochemistry and Biophysics, University of California-San Francisco, 600 16th Street, San Francisco, CA 94143, USA. katerina.kechris@uchsc.edu

Abstract

Lateral gene transfer (LGT) is now accepted as an important factor in the evolution of prokaryotes. Establishment of the occurrence of LGT is typically attempted by a variety of methods that includes the comparison of reconstructed phylogenetic trees, the search for unusual GC composition or codon usage within a genome, and identification of similarities between distant species as determined by best blast hits. We explore quantitative assessments of these strategies to study the prokaryotic trait of nitrogen fixation, the enzyme-catalyzed reduction of N(2) to ammonia. Phylogenies constructed on nitrogen fixation genes are not in agreement with the tree-of-life based on 16S rRNA but do not conclusively distinguish between gene loss and LGT hypotheses. Using a series of analyses on a set of complete genomes, our results distinguish two structurally distinct classes of MoFe nitrogenases whose distribution cuts across lines of vertical inheritance and makes us believe that a conclusive case for LGT has been made.

PMID:
16769896
PMCID:
PMC1480450
DOI:
10.1073/pnas.0603534103
[Indexed for MEDLINE]
Free PMC Article

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