title: Analyses of six homologous proteins of Protochlamydia amoebophila UWE25 encoded by large GC-rich genes (lgr): a model of evolution and concatenation of leucine-rich repeats.
abstract: BACKGROUND
  Along the chromosome of the obligate intracellular bacteria Protochlamydia amoebophila UWE25, we recently described a genomic island Pam100G. It contains a tra unit likely involved in conjugative DNA transfer and lgrE, a 5.6-kb gene similar to five others of P. amoebophila: lgrA to lgrD, lgrF. We describe here the structure, regulation and evolution of these proteins termed LGRs since encoded by "Large G+C-Rich" genes.
  
  
  RESULTS
  No homologs to the whole protein sequence of LGRs were found in other organisms. Phylogenetic analyses suggest that serial duplications producing the six LGRs occurred relatively recently and nucleotide usage analyses show that lgrB, lgrE and lgrF were relocated on the chromosome. The C-terminal part of LGRs is homologous to Leucine-Rich Repeats domains (LRRs). Defined by a cumulative alignment score, the 5 to 18 concatenated octacosapeptidic (28-meric) LRRs of LGRs present all a predicted alpha-helix conformation. Their closest homologs are the 28-residue RI-like LRRs of mammalian NODs and the 24-meres of some Ralstonia and Legionella proteins. Interestingly, lgrE, which is present on Pam100G like the tra operon, exhibits Pfam domains related to DNA metabolism.
  
  
  CONCLUSIONS
  Comparison of the LRRs, enable us to propose a parsimonious evolutionary scenario of these domains driven by adjacent concatenations of LRRs. Our model established on bacterial LRRs can be challenged in eucaryotic proteins carrying less conserved LRRs, such as NOD proteins and Toll-like receptors.
authors.affiliation: Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland. myriam.eugster@gmail.com
authors.forename: Myriam
authors.initials: M
authors.lastname: Eugster
authors.forename: Claude-Alain H
authors.initials: CA
authors.lastname: Roten
authors.forename: Gilbert
authors.initials: G
authors.lastname: Greub
mesh_terms: D020816:Amino Acid Motifs; D001426:Bacterial Proteins / Q000235:genetics; D002695:Chlamydiales / Q000235:genetics*; D019143:Evolution, Molecular; D020862:GC Rich Sequence; D005798:Genes, Bacterial; D044404:Genomic Islands; D007930:Leucine / Q000235:genetics*; D000090263:Leucine-Rich Repeat Proteins; D011506:Proteins / Q000235:genetics*; D020449:Repetitive Sequences, Amino Acid; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid
chemical_list: D001426:Bacterial Proteins; D000090263:Leucine-Rich Repeat Proteins; D011506:Proteins; D007930:Leucine