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.

Fig. 1.

Plot of best blast hits E value for rib S2. NIF organisms are indicated by filled circles.

Fig. 2.

Plot of best blast hits E value for CTX-M. E values between the query sequence and the CTX-M enzymes given in ref. are indicated by filled circles.

Fig. 3.

Plot of best blast hits E value for nifD. NIF organisms are indicated by filled circles.

Fig. 4.

Plot of sorted list of top 20 best blast hits E value to Nostoc sp. PCC 7120 nifD. Non-NIF organisms are indicated by filled circles. Labels for the NIF organisms are listed in the key (see Table 1 for full names).

Fig. 5.

Phylogeny of 14 NIF organisms based on 16S rRNA. The two subfamilies are labeled with solid (subfamily 1) and dotted boxes (subfamily 2). Branch lengths are the bootstrap frequencies.