title: Quantitative exploration of the occurrence of lateral gene transfer by using nitrogen fixation genes as a case study.
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.
authors.affiliation: Department of Biochemistry and Biophysics, University of California-San Francisco, 600 16th Street, San Francisco, CA 94143, USA. katerina.kechris@uchsc.edu
authors.forename: Katherina J
authors.initials: KJ
authors.lastname: Kechris
authors.forename: Jason C
authors.initials: JC
authors.lastname: Lin
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Bickel
authors.forename: Alexander N
authors.initials: AN
authors.lastname: Glazer
mesh_terms: D003062:Codon / Q000235:genetics; D019295:Computational Biology; D022761:Gene Transfer, Horizontal / Q000235:genetics*; D009586:Nitrogen Fixation / Q000235:genetics*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D003062:Codon; D012336:RNA, Ribosomal, 16S