Evolution of Functional Diversity in Nitrogenase Homologs

Abstract

We have investigated the origin and distribution of nitrogen fixation using phylogenetic tools, making use of all publicly available complete bacterial and archaeal genome sequences to understand how the core components of nitrogenase, namely the NifH, NifD and NifK proteins, originated and have evolved. These genes are universal in nitrogen-fixing organisms and have remarkably congruent phylogenetic histories. Additional clues to the early origins of this system are available from two distinct clades of nitrogenase paralogs: (i) a group of Nif-like proteins coded for by genes involved in photosynthetic pigment biosynthesis (bchLNB, bchXYZ); and (ii) a group of previously uncharacterized nif-like genes present in methanogens and in some photosynthetic bacteria (nflH, nflD). We explore the complex genetic history of the nitrogenase family, which is replete with gene duplication, recruitment, fusion, and horizontal gene transfer and discuss these events with respect to where nitrogen fixation may have originated and how it came to have its current complex phylogenetic distribution.