title: A comparison of the protein-coding genomes of two green sulphur bacteria, Chlorobium tepidum TLS and Pelodictyon phaeoclathratiforme BU-1.
abstract: BACKGROUND
  Chlorobium tepidum and Pelodictyon phaeoclathratiforme are organisms within the green sulphur bacteria family, Chlorobiaceae, occupying very different habitats. It has recently been proposed that the genera Chlorobium and Pelodictyon are synonymous.
  
  
  RESULTS
  To investigate generic boundaries for the two species, protein families were predicted computationally based on sequence similarity across the genome-wide protein sets of Chlorobium tepidum TLS and Pelodictyon phaeoclathratiforme BU-1. The distribution of the resulting protein families across the two species was summarized. The largest number of families exhibited 1:1 putative orthology between the two species (1468 families). Of families unique to one of the species, the largest number was unique to P. phaeoclathratiforme (113 families), of which the largest family contained pentapeptide repeat proteins (16 proteins). Families unique to P. phaeoclathratiforme also included a family of gas vesicle synthesis proteins (four proteins). Although only seven families were identified as containing paralogous proteins in both species (with two or more proteins in each species), this group included families of major biochemical importance. One such family, with three members in each species, contained magnesium chelatase, an enzyme involved in the chlorophyll biosynthetic pathway.
  
  
  CONCLUSIONS
  The unique protein family groups in both C. tepidum and P. phaeoclathratiforme mirror the occupancy of different environments, while key shared family groups provide evidence for a common origin for the species, as previously suggested in the literature. The current study only uses sequence similarity-based protein families for the two species. This, alone, does not permit a firm conclusion to be drawn on the taxonomic question, of whether the two species belong in one genus or two.
authors.affiliation: School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK. kristinwreggelsworth@yahoo.com.
authors.forename: Kristin M
authors.initials: KM
authors.lastname: Wreggelsworth
authors.affiliation: School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK. db60@st-andrews.ac.uk.
authors.forename: Daniel
authors.initials: D
authors.lastname: Barker
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D019414:Chlorobi / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D041883:Chlorobium / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology; D017753:Ecosystem; D015870:Gene Expression; D016680:Genome, Bacterial; D008190:Lyases / Q000235:genetics* / Q000378:metabolism; D053858:Metabolic Networks and Pathways / Q000235:genetics; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid
chemical_list: D001426:Bacterial Proteins; D008190:Lyases; C086788:magnesium chelatase