Proteorhodopsin photosystem gene clusters exhibit co-evolutionary trends and shared ancestry among diverse marine microbial phyla

Since the recent discovery of retinylidene proteins in marine bacteria (proteorhodopsins), the estimated abundance and diversity of this gene family has expanded rapidly. To explore proteorhodopsin photosystem evolutionary and distributional trends, we identified and compared 16 different proteorhodopsin-containing genome fragments recovered from naturally occurring bacterioplankton populations. In addition to finding several deep-branching proteorhodopsin sequences, proteorhodopsins were found in novel taxonomic contexts, including a betaproteobacterium and a planctomycete. Approximately one-third of the proteorhodopsin-containing genome fragments analysed, as well as a number of recently reported marine bacterial whole genome sequences, contained a linked set of genes required for biosynthesis of the rhodopsin chromophore, retinal. Phylogenetic analyses of the retinal biosynthetic genes suggested their co-evolution and probable coordinated lateral gene transfer into disparate lineages, including Euryarchaeota, Planctomycetales, and three different proteobacterial lineages. The lateral transfer and retention of genes required to assemble a functional proteorhodopsin photosystem appears to be a coordinated and relatively frequent evolutionary event. Strong selection pressure apparently acts to preserve these light-dependent photosystems in diverse marine microbial lineages.