Phylogenetic reconstruction of ancient photosynthetic lineages using chlorophyll and bacteriochlorophyll biosynthetic genes

Abstract

Phylogenetic reconstruction has been carried out using two sets of three genes involved in the synthesis of bacteriochlorophyll and chlorophyll (BChl & Chl) and one set of three genes involved in nitrogen fixation (Nif). Functionally, the X, Y, and Z genes encode peptides involved in the reduction of the chlorin B ring, the L, N, and B genes encode peptides involved in the reduction of the porphyrin D ring, and the H, D, and K genes encode peptides involved in the fixation of nitrogen. Sequences were obtained from Chlorobium tepidum, Chloroflexus aurantiacus, Heliobacillus mobilus and Rhodobacter capsulatus (all photosynthetic bacteria); from Synechocystis PCC6803 (a cyanobacterium); and fromChlorella vulgaris (Chlorophyta) and Porphyra purpurea (Rhodophyta) (photosynthetic eukaryotes). The inferred phylogeny was rooted using Klebsiella pneumoniae and Azotobacter vinelandii (non-photosynthetic nitrogen fixing eubacteria). Aligned amino acid data were analysed using ProtML for all sites and for all sites without gaps. Inclusion or exclusion of the X, Y, and Z peptides as well as of the constant sites did not alter the phylogenetic result. For the data set including the X, Y, and Z peptides but excluding all sites with gaps, we obtained a small number of Good Trees for each of the three alignments (LXH, NYD, and BZK) After individual comparison, we concatenated the three alignments before reanalysing the phylogenetic data. Phylogenetic reconstruction favoured grouping species with the H, D, and K peptides, with the X, Y, and Z peptides, and with the L, N, and B peptides. The simplest interpretation of these data is that the X, Y, and Z genes diverged from a lineage carrying the L, N, and B genes before the emergence of oxygenic photosynthesis.