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

Proc Natl Acad Sci U S A. 2006 Jun 20;103(25):9584-9. doi: 10.1073/pnas.0603534103. Epub 2006 Jun 12.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Codon / genetics
  • Computational Biology
  • Gene Transfer, Horizontal / genetics*
  • Nitrogen Fixation / genetics*
  • Phylogeny
  • RNA, Ribosomal, 16S / genetics


  • Codon
  • RNA, Ribosomal, 16S