title: Sca1, a previously undescribed paralog from autotransporter protein-encoding genes in Rickettsia species.
abstract: BACKGROUND
  Among the 17 genes encoding autotransporter proteins of the "surface cell antigen" (sca) family in the currently sequenced Rickettsia genomes, ompA, sca5 (ompB) and sca4 (gene D), have been extensively used for identification and phylogenetic purposes for Rickettsia species. However, none of these genes is present in all 20 currently validated Rickettsia species. Of the remaining 14 sca genes, sca1 is the only gene to be present in all nine sequenced Rickettsia genomes. To estimate whether the sca1 gene is present in all Rickettsia species and its usefulness as an identification and phylogenetic tool, we searched for sca1genes in the four published Rickettsia genomes and amplified and sequenced this gene in the remaining 16 validated Rickettsia species.
  
  
  RESULTS
  Sca1 is the only one of the 17 rickettsial sca genes present in all 20 Rickettsia species. R. prowazekii and R. canadensis exhibit a split sca1 gene whereas the remaining species have a complete gene. Within the sca1 gene, we identified a 488-bp variable sequence fragment that can be amplified using a pair of conserved primers. Sequences of this fragment are specific for each Rickettsia species. The phylogenetic organization of Rickettsia species inferred from the comparison of sca1 sequences strengthens the classification based on the housekeeping gene gltA and is similar to those obtained from the analyses of ompA, sca5 and sca4, thus suggesting similar evolutionary constraints. We also observed that Sca1 protein sequences have evolved under a dual selection pressure: with the exception of typhus group rickettsiae, the amino-terminal part of the protein that encompasses the predicted passenger domain, has evolved under positive selection in rickettsiae. This suggests that the Sca1 protein interacts with the host. In contrast, the C-terminal portion containing the autotransporter domain has evolved under purifying selection. In addition, sca1 is transcribed in R. conorii, and might therefore be functional in this species.
  
  
  CONCLUSIONS
  The sca1 gene, encoding an autotransporter protein that evolves under dual evolution pressure, is the only sca-family gene to be conserved by all Rickettsia species. As such, it is a valuable identification target for these bacteria, especially because rickettsial isolates can be identified by amplification and sequencing of a discriminatory gene fragment using a single primer pair. It may also be used as a phylogenetic tool. However, its current functional status remains to be determined although it was found expressed in R. conorii.
authors.affiliation: Unité des Rickettsies, IFR 48, CNRS UMR 6020, Faculté de médecine, Université de la Méditerranée, 13385 Marseille cedex 05, France. maxime.ngwamidiba@medecine.univ-mrs.fr
authors.forename: Maxime
authors.initials: M
authors.lastname: Ngwamidiba
authors.forename: Guillaume
authors.initials: G
authors.lastname: Blanc
authors.forename: Didier
authors.initials: D
authors.lastname: Raoult
authors.forename: Pierre-Edouard
authors.initials: PE
authors.lastname: Fournier
mesh_terms: D000954:Antigens, Surface / Q000378:metabolism*; D001425:Bacterial Outer Membrane Proteins / Q000378:metabolism; D001426:Bacterial Proteins / Q000378:metabolism; D019143:Evolution, Molecular; D015964:Gene Expression Regulation, Bacterial; D009097:Multienzyme Complexes / Q000378:metabolism; D010802:Phylogeny; D012281:Rickettsia / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D000954:Antigens, Surface; D001425:Bacterial Outer Membrane Proteins; D001426:Bacterial Proteins; D009097:Multienzyme Complexes