title: Evolution of rhodopsin ion pumps in haloarchaea.
abstract: BACKGROUND
  The type 1 (microbial) rhodopsins are a diverse group of photochemically reactive proteins that display a broad yet patchy distribution among the three domains of life. Recent work indicates that this pattern is likely the result of lateral gene transfer (LGT) of rhodopsin genes between major lineages, and even across domain boundaries. Within the lineage in which the microbial rhodopsins were initially discovered, the haloarchaea, a similar patchy distribution is observed. In this initial study, we assess the roles of LGT and gene loss in the evolution of haloarchaeal rhodopsin ion pump genes, using phylogenetics and comparative genomics approaches.
  
  
  RESULTS
  Mapping presence/absence of rhodopsins onto the phylogeny of the RNA polymerase B' subunit (RpoB') of the haloarchaea supports previous notions that rhodopsins are patchily distributed. The phylogeny for the bacteriorhodopsin (BR) protein revealed two discrepancies in comparison to the RpoB' marker, while the halorhodopsin (HR) tree showed incongruence to both markers. Comparative analyses of bacteriorhodopsin-linked regions of five haloarchaeal genomes supported relationships observed in the BR tree, and also identified two open reading frames (ORFs) that were more frequently linked to the bacteriorhodopsin gene than those genes previously shown to be important to the function and expression of BR.
  
  
  CONCLUSIONS
  The evidence presented here reveals a complex evolutionary history for the haloarchaeal rhodopsins, with both LGT and gene loss contributing to the patchy distribution of rhodopsins within this group. Similarities between the BR and RpoB' phylogenies provide supportive evidence for the presence of bacteriorhodopsin in the last common ancestor of haloarchaea. Furthermore, two loci that we have designated bacterio-opsin associated chaperone (bac) and bacterio-opsin associated protein (bap) are inferred to have important roles in BR biogenesis based on frequent linkage and co-transfer with bacteriorhodopsin genes.
authors.affiliation: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada. aksharma@dal.ca
authors.forename: Adrian K
authors.initials: AK
authors.lastname: Sharma
authors.forename: David A
authors.initials: DA
authors.lastname: Walsh
authors.forename: Eric
authors.initials: E
authors.lastname: Bapteste
authors.forename: Francisco
authors.initials: F
authors.lastname: Rodriguez-Valera
authors.forename: W
authors.initials: W
authors.lastname: Ford Doolittle
authors.forename: R Thane
authors.initials: RT
authors.lastname: Papke
mesh_terms: D000251:Adenosine Triphosphatases / Q000235:genetics / Q000378:metabolism; D000595:Amino Acid Sequence; D001436:Bacteriorhodopsins / Q000235:genetics / Q000378:metabolism; D018797:Cell Cycle Proteins / Q000235:genetics / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D019766:Genes, Archaeal; D020745:Genome, Archaeal; D006216:Halobacteriaceae / Q000235:genetics* / Q000378:metabolism; D025602:Halorhodopsins / Q000235:genetics / Q000378:metabolism; D016623:Ion Pumps / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D025604:Rhodopsins, Microbial / Q000235:genetics* / Q000378:metabolism; D000074405:Valosin Containing Protein
chemical_list: D018797:Cell Cycle Proteins; D025602:Halorhodopsins; D016623:Ion Pumps; D025604:Rhodopsins, Microbial; D001436:Bacteriorhodopsins; D012321:DNA-Directed RNA Polymerases; C105078:RNA polymerase beta subunit; D000251:Adenosine Triphosphatases; D000074405:Valosin Containing Protein