Chapter Two Molecular Markers for Photosynthetic Bacteria and Insights into the Origin and Spread of Photosynthesis

Microbial genomes provide a rich resource for identifying molecular markers that can reliably distinguish different groups of photosynthetic organisms and provide insights into the origin and spread of photosynthesis. This review summarises work on molecular markers consisting of conserved signature indels (CSIs) and signature proteins that are specific for different phyla of photosynthetic bacteria and their major subclades. Based upon these markers and phylogenetic analyses, photosynthetic Chloroflexi are divided into two suborders viz. Chloroflexineae and Roseiflexineae consistent with their biochemical, morphological and molecular characteristics. Within Cyanobacteria three major clades (referred to as Clade A, B and C) are distinguished at the highest phylogenetic/taxonomic levels. Phylogenetic analyses and several CSIs in key bacteriochlorophyll (BChl) biosynthesis proteins, BchL, BchN and BchB, provide evidence that their homologues in Proteobacteria have been acquired from Clade C Cyanobacteria, whereas those in the Chlorobi are derived from Chloroflexi by lateral gene transfers. Phylogenetic analyses and other CSIs in the sequentially duplicated proteins BchL, BchX and NifH provide evidence that the BchX homologues required for anoxygenic photosynthesis originated before the BchL homologues needed for oxygenic photosynthesis. Another CSI in the duplicated BchX–BchL proteins provides evidence that the BchL homologues of Heliobacteriaceae (Firmicutes phylum) are primitive in comparison to other photosynthetic bacteria.