Multi-genome identification and characterization of chlamydiae-specific type III secretion substrates: the Inc proteins

Pierre Dehoux, Rhonda Flores, Catherine Dauga, Guangming Zhong, Agathe Subtil
<span title="2011-02-16">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
Chlamydiae are obligate intracellular bacteria that multiply in a vacuolar compartment, the inclusion. Several chlamydial proteins containing a bilobal hydrophobic domain are translocated by a type III secretion (TTS) mechanism into the inclusion membrane. They form the family of Inc proteins, which is specific to this phylum. Based on their localization, Inc proteins likely play important roles in the interactions between the microbe and the host. In this paper we sought to identify and
more &raquo; ... , using bioinformatics tools, all putative Inc proteins in published chlamydial genomes, including an environmental species. Results Inc proteins contain at least one bilobal hydrophobic domain made of two transmembrane helices separated by a loop of less than 30 amino acids. Using bioinformatics tools we identified 537 putative Inc proteins across seven chlamydial proteomes. The aminoterminal segment of the putative Inc proteins was recognized as a functional TTS signal in 90% of the C. trachomatis and C. pneumoniae sequences tested, validating the data obtained in silico. We identified a macro domain in several putative Inc proteins, and observed that Inc proteins are enriched in segments predicted to form coiled coils. A surprisingly large proportion of the putative Inc proteins are not constitutively translocated to the inclusion membrane in culture conditions. Conclusions The Inc proteins represent 7 to 10 % of each proteome and show a great degree of sequence diversity between species. The abundance of segments with a high probability for coiled coil conformation in Inc proteins support the hypothesis that they interact with host proteins. While the large majority of Inc proteins possess a functional TTS signal, less than half may be constitutively translocated to the inclusion surface in some species. This suggests the novel finding that translocation of Inc proteins may be regulated by as-yet undetermined mechanisms. 12(9):1235. 36. Subtil A, Delevoye C, Balañá ME, Tastevin L, Perrinet S, Dautry-Varsat A: A directed screen for chlamydial proteins secreted by a type III mechanism identifies a translocated protein and numerous other new candidates. Mol Microbiol 2005, 56(6):1636-1647. 37. : Characterization of hypothetical proteins Cpn0146, 0147, 0284 & 0285 that are predicted to be in the Chlamydia pneumoniae inclusion membrane. BMC Microbiol 2007, 7:38. 38. Dani N, Stilla A, Marchegiani A, Tamburro A, Till S, Ladurner AG, Corda D, Di Girolamo M: Combining affinity purification by ADP-ribose-binding macro domains with mass spectrometry to define the mammalian ADP-ribosyl proteome. Proc Natl Acad Sci U S A 2009, 106(11):4243-4248. 39. Karras GI, Kustatscher G, Buhecha HR, Allen MD, Pugieux C, Sait F, Bycroft M, Ladurner AG: The macro domain is an ADP-ribose binding module. The EMBO Journal 2005, 24(11):1911-1920. 40. Neuvonen M, Ahola T: Differential activities of cellular and viral macro domain proteins in binding of ADP-ribose metabolites. J Mol Biol 2009, 385(1):212-225. 41. Delahay RM, Frankel G: Coiled-coil proteins associated with type III secretion systems: a versatile domain revisited. Mol Microbiol 2002, 45(4):905-916. 42. Gazi AD, Charova SN, Panopoulos NJ, Kokkinidis M: Coiled-coils in type III secretion systems: structural flexibility, disorder and biological implications. Cell Microbiol 2009, 11(5):719-729. 43. D'Andrea LD, Regan L: TPR proteins: the versatile helix. Trends Biochem Sci 2003, 28(12):655-662. 44. Liu J, Rost B: Comparing function and structure between entire proteomes. Protein Sci 2001, 10(10):1970-1979. 45. Odgren P, Harvie LJ, Fey E: Phylogenetic occurrence of coiled coil proteins: implications for tissue structure in metazoa via a coiled coil tissue matrix. Proteins 1996, 24:467-484. 46. Rose A, Schraegle SJ, Stahlberg EA, Meier I: Coiled-coil protein composition of 22 proteomes--differences and common themes in subcellular infrastructure and traffic control. BMC Evol Biol 2005, 5:66. 47. Arnold R, Brandmaier S, Kleine F, Tischler P, Heinz E, Behrens S, Niinikoski A, Mewes HW, Horn M, Rattei T: Sequence-based prediction of type III secreted proteins. PLoS Pathog 2009, 5(4):e1000376. 48. Samudrala R, Heffron F, McDermott JE: Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems. PLoS Pathog 2009, 5(4):e1000375. 49. Parsot C, Hamiaux C, Page AL: The various and varying roles of specific chaperones in type III secretion systems. Curr Opin Microbiol 2003, 6(1):7-14. 50. Remm M, Storm CE, Sonnhammer EL: Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 2001, 314(5):1041-1052. 51. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 52.
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