Kechris Katherina J, Lin Jason C, Bickel Peter J, Glazer Alexander N
Department of Biochemistry and Biophysics, University of California-San Francisco, 600 16th Street, San Francisco, CA 94143, USA.
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.
横向基因转移（LGT）如今已被公认为原核生物进化中的一个重要因素。确定LGT的发生通常会尝试多种方法，包括比较重建的系统发育树、在基因组内寻找异常的GC组成或密码子使用情况，以及通过最佳比对命中确定的远缘物种之间的相似性鉴定。我们探索这些策略的定量评估，以研究固氮这一原核生物特性，即酶催化将N₂还原为氨的过程。基于固氮基因构建的系统发育与基于16S rRNA的生命树不一致，但并未明确区分基因丢失和LGT假说。通过对一组完整基因组进行一系列分析，我们的结果区分出两类结构不同的钼铁固氮酶，其分布跨越垂直遗传谱系，这使我们相信已经有确凿证据证明了LGT的存在。
