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Comparative and Functional Genomics
Volume 2012 (2012), Article ID 362104, 13 pages
Evolution and Conservation of Predicted Inclusion Membrane Proteins in Chlamydiae
1Host-Parasite Interactions Section, Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
2Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
Received 21 September 2011; Accepted 30 November 2011
Academic Editor: Shen Liang Chen
Copyright © 2012 Erika I. Lutter et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- J. Schachter, “Infection and disease epidemiology,” in Chlamydia: Intracellular Biology, Pathogenesis, and Immunity, R. S. Stephens, Ed., pp. 139–169, ASM Press, Washington, DC, USA, 1999.
- J. T. Grayston, M. B. Aldous, A. Easton et al., “Evidence that Chlamydia pneumoniae causes pneumonia and bronchitis,” Journal of Infectious Diseases, vol. 168, no. 5, pp. 1231–1235, 1993.
- P. Saikku, K. Mattila, M. S. Nieminen et al., “Serological evidence of an association of a novel chlamydia, TWAR, with chronic coronary heart disease and acute myocardial infarction,” The Lancet, vol. 2, no. 8618, pp. 983–986, 1988.
- J. E. Sykes, “Feline chlamydiosis,” Clinical Techniques in Small Animal Practice, vol. 20, no. 2, pp. 129–134, 2005.
- C. Nigg and M. D. Eaton, “Isolation from normal mice of a pneumotropic virus which forms elementary bodies,” Journal of Experimental Medicine, vol. 79, pp. 497–510, 1944.
- R. A. Carabeo, D. J. Mead, and T. Hackstadt, “Golgi-dependent transport of cholesterol to the Chlamydia trachomatis inclusion,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 11, pp. 6771–6776, 2003.
- T. Hackstadt, D. D. Rockey, R. A. Heinzen, and M. A. Scidmore, “Chlamydia trachomatis interrupts an exocytic pathway to acquire endogenously synthesized sphingomyelin in transit from the Golgi apparatus to the plasma membrane,” EMBO Journal, vol. 15, no. 5, pp. 964–977, 1996.
- T. Hackstadt, M. A. Scidmore, and D. D. Rockey, “Lipid metabolism in Chlamydia trachomatis-infected cells: directed trafficking of Golgi-derived sphingolipids to the chlamydial inclusion,” Proceedings of the National Academy of Sciences of the United States of America, vol. 92, no. 11, pp. 4877–4881, 1995.
- W. L. Beatty, “Late endocytic multivesicular bodies intersect the chlamydial inclusion in the absence of CD63,” Infection and Immunity, vol. 76, no. 7, pp. 2872–2881, 2008.
- Y. Kumar, J. Cocchiaro, and R. H. Valdivia, “The obligate intracellular pathogen chlamydia trachomatis targets host lipid droplets,” Current Biology, vol. 16, no. 16, pp. 1646–1651, 2006.
- J. Mital, N. J. Miller, E. R. Fischer, and T. Hackstadt, “Specific chlamydial inclusion membrane proteins associate with active Src family kinases in microdomains that interact with the host microtubule network,” Cellular Microbiology, vol. 12, no. 9, pp. 1235–1249, 2010.
- E. R. Moore, E. R. Fischer, D. J. Mead, and T. Hackstadt, “The chlamydial inclusion preferentially intercepts basolaterally directed sphingomyelin-containing exocytic vacuoles,” Traffic, vol. 9, no. 12, pp. 2130–2140, 2008.
- M. A. Scidmore and T. Hackstadt, “Mammalian 14-3-3β associates with the Chlamydia trachomatis inclusion membrane via its interaction with IncG,” Molecular Microbiology, vol. 39, no. 6, pp. 1638–1650, 2001.
- T. Hackstadt, M. A. Scidmore-Carlson, E. I. Shaw, and E. R. Fischer, “The Chlamydia trachomatis IncA protein is required for homotypic vesicle fusion,” Cellular Microbiology, vol. 1, no. 2, pp. 119–130, 1999.
- D. D. Rockey, D. Grosenbach, D. E. Hruby, M. G. Peacock, R. A. Heinzen, and T. Hackstadt, “Chlamydia psittaci IncA is phosphorylated by the host cell and is exposed on the cytoplasmic face of the developing inclusion,” Molecular Microbiology, vol. 24, no. 1, pp. 217–228, 1997.
- J. P. Bannantine, R. S. Griffiths, W. Viratyosin, W. J. Brown, and D. D. Rockey, “A secondary structure motif predictive of protein localization to the chlamydial inclusion membrane,” Cellular Microbiology, vol. 2, no. 1, pp. 35–47, 2000.
- D. D. Rockey, M. A. Scidmore, J. P. Bannantine, and W. J. Brown, “Proteins in the chlamydial inclusion membrane,” Microbes and Infection, vol. 4, no. 3, pp. 333–340, 2002.
- H. Toh, K. Miura, M. Shirai, and M. Hattori, “In silico inference of inclusion membrane protein family in obligate intracellular parasites chlamydiae,” DNA Research, vol. 10, no. 1, pp. 9–17, 2003.
- P. Dehoux, R. Flores, C. Dauga, G. Zhong, and A. Subtil, “Multi-genome identification and characterization of chlamydiae-specific type III secretion substrates: the Inc proteins,” BMC Genomics, vol. 12, article 109, 2011.
- Z. Li, C. Chen, D. Chen, Y. Wu, Y. Zhong, and G. Zhong, “Characterization of fifty putative inclusion membrane proteins encoded in the Chlamydia trachomatis genome,” Infection and Immunity, vol. 76, pp. 2746–2757, 2008.
- E. I. Shaw, C. A. Dooley, E. R. Fischer, M. A. Scidmore, K. A. Fields, and T. Hackstadt, “Three temporal classes of gene expression during the Chlamydia trachomatis developmental cycle,” Molecular Microbiology, vol. 37, pp. 913–925, 2000.
- Y. Azuma, H. Hirakawa, A. Yamashita et al., “Genome sequence of the cat pathogen, Chlamydophila felis,” DNA Research, vol. 13, no. 1, pp. 15–23, 2006.
- J. Kyte and R. F. Doolittle, “A simple method for displaying the hydropathic character of a protein,” Journal of Molecular Biology, vol. 157, no. 1, pp. 105–132, 1982.
- A. Krogh, B. Larsson, G. von Heijne, and E. L. L. Sonnhammer, “Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes,” Journal of Molecular Biology, vol. 305, no. 3, pp. 567–580, 2001.
- S. F. Altschul, T. L. Madden, A. A. Schaffer et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,” Nucleic Acids Research, vol. 25, no. 17, pp. 3389–3402, 1997.
- J. D. Thompson, D. G. Higgins, and T. J. Gibson, “CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice,” Nucleic Acids Research, vol. 22, no. 22, pp. 4673–4680, 1994.
- N. Saitou and M. Nei, “The neighbor-joining method: a new method for reconstructing phylogenetic trees,” Molecular Biology and Evolution, vol. 4, no. 4, pp. 406–425, 1987.
- K. Tamura, J. Dudley, M. Nei, and S. Kumar, “MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0,” Molecular Biology and Evolution, vol. 24, no. 8, pp. 1596–1599, 2007.
- J. Felsenstein, “Confidence-limits on phylogenies—an approach using the bootstrap,” Evolution, vol. 39, pp. 783–791, 1985.
- K. Tamura, M. Nei, and S. Kumar, “Prospects for inferring very large phylogenies by using the neighbor-joining method,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 30, pp. 11030–11035, 2004.
- M. Nei and T. Gojobori, “Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions,” Molecular Biology and Evolution, vol. 3, no. 5, pp. 418–426, 1986.
- J. P. Gomes, A. Nunes, W. J. Bruno, M. J. Borrego, C. Florindo, and D. Dean, “Polymorphisms in the nine polymorphic membrane proteins of Chlamydia trachomatis across all serovars: evidence for serovar da recombination and correlation with tissue tropism,” Journal of Bacteriology, vol. 188, no. 1, pp. 275–286, 2006.
- J. H. Carlson, S. F. Porcella, G. McClarty, and H. D. Caldwell, “Comparative genomic analysis of Chlamydia trachomatis oculotropic and genitotropic strains,” Infection and Immunity, vol. 73, no. 10, pp. 6407–6418, 2005.
- R. S. Stephens, S. Kalman, C. Lammel et al., “Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis,” Science, vol. 282, no. 5389, pp. 754–759, 1998.
- N. R. Thomson, M. T. G. Holden, C. Carder et al., “Chlamydia trachomatis: genome sequence analysis of lymphogranuloma venereum isolates,” Genome Research, vol. 18, no. 1, pp. 161–171, 2008.
- D. R. Stothard, G. A. Toth, and B. E. Batteiger, “Polymorphic membrane protein H has evolved in parallel with the three disease-causing groups of Chlamydia trachomatis,” Infection and Immunity, vol. 71, no. 3, pp. 1200–1208, 2003.
- E. I. Lutter, C. Bonner, M. J. Holland et al., “Phylogenetic analysis of Chlamydia trachomatis tarp and correlation with clinical phenotype,” Infection and Immunity, vol. 78, no. 9, pp. 3678–3688, 2010.
- R. J. Belland, M. A. Scidmore, D. D. Crane et al., “Chlamydia trachomatis cytotoxicity associated with complete and partial cytotoxin genes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 24, pp. 13984–13989, 2001.
- J. H. Carlson, S. Hughes, D. Hogan et al., “Polymorphisms in the Chlamydia trachomatis cytotoxin locus associated with ocular and genital isolates,” Infection and Immunity, vol. 72, no. 12, pp. 7063–7072, 2004.
- H. D. Caldwell, H. Wood, D. Crane et al., “Polymorphisms in Chlamydia trachomatis tryptophan synthase genes differentiate between genital and ocular isolates,” Journal of Clinical Investigation, vol. 111, no. 11, pp. 1757–1769, 2003.
- C. Fehlner-Gardiner, C. Roshick, J. H. Carlson et al., “Molecular basis defining human Chlamydia trachomatis tissue tropism: a possible role for tryptophan synthase,” The Journal of Biological Chemistry, vol. 277, no. 30, pp. 26893–26903, 2002.
- A. C. Shaw, G. Christiansen, P. Roepstorff, and S. Birkelund, “Genetic differences in the Chlamydia trachomatis tryptophan synthase α- subunit can explain variations in serovar pathogenesis,” Microbes and Infection, vol. 2, no. 6, pp. 581–592, 2000.
- T. Hackstadt, T. J. Brickman, C. E. Barry, and J. Sager, “Diversity in the Chlamydia trachomatis histone homologue Hc2,” Gene, vol. 132, no. 1, pp. 137–141, 1993.
- M. Klint, M. Thollesson, E. Bongcam-Rudloff, S. Birkelund, A. Nilsson, and B. Herrmann, “Mosaic structure of intragenic repetitive elements in histone H1-like protein Hc2 varies within serovars of Chlamydia trachomatis,” BMC Microbiology, vol. 10, article 81, 2010.
- B. W. Brunelle, T. L. Nicholson, and R. S. Stephens, “Microarray-based genomic surveying of gene polymorphisms in Chlamydia trachomatis,” Genome Biology, vol. 5, no. 6, article R42, 2004.
- E. C. Yong, E. Y. Chi, and C. C. Kuo, “Differential antimicrobial activity of human mononuclear phagocytes against the human biovars of Chlamydia trachomatis,” Journal of Immunology, vol. 139, no. 4, pp. 1297–1302, 1987.
- D. D. Rockey, R. A. Heinzen, and T. Hackstadt, “Cloning and characterization of a Chlamydia psittaci gene coding for a protein localized in the inclusion membrane of infected cells,” Molecular Microbiology, vol. 15, no. 4, pp. 617–626, 1995.
- D. Alzhanov, J. Barnes, D. E. Hruby, and D. D. Rockey, “Chlamydial development is blocked in host cells transfected with Chlamydophila caviae incA,” BMC Microbiology, vol. 4, article 24, 2004.
- R. J. Suchland, D. D. Rockey, J. P. Bannantine, and W. E. Stamm, “Isolates of Chlamydia trachomatis that occupy nonfusogenic inclusions lack IncA, a protein localized to the inclusion membrane,” Infection and Immunity, vol. 68, no. 1, pp. 360–367, 2000.
- C. Delevoye, M. Nilges, P. Dehoux et al., “SNARE protein mimicry by an intracellular bacterium,” PLoS Pathogens, vol. 4, no. 3, Article ID e1000022, 2008.
- K. A. Rzomp, L. D. Scholtes, B. J. Briggs, G. R. Whittaker, and M. A. Scidmore, “Rab GTPases are recruited to chlamydial inclusions in both a species-dependent and species-independent manner,” Infection and Immunity, vol. 71, no. 10, pp. 5855–5870, 2003.
- K. A. Rzomp, A. R. Moorhead, and M. A. Scidmore, “The GTPase Rab4 interacts with Chlamydia trachomatis inclusion membrane protein CT229,” Infection and Immunity, vol. 74, no. 9, pp. 5362–5373, 2006.
- C. Cortes, K. A. Rzomp, A. Tvinnereim, M. A. Scidmore, and B. Wizel, “Chlamydia pneumoniae inclusion membrane protein Cpn0585 interacts with multiple Rab GTPases,” Infection and Immunity, vol. 75, no. 12, pp. 5586–5596, 2007.
- S. Kalman, W. Mitchell, R. Marathe et al., “Comparative genomes of Chlamydia pneumoniae and C. trachomatis,” Nature Genetics, vol. 21, no. 4, pp. 385–389, 1999.
- T. D. Read, R. C. Brunham, C. Shen et al., “Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39,” Nucleic Acids Research, vol. 28, no. 6, pp. 1397–1406, 2000.
- T. D. Read, G. S. A. Myers, R. C. Brunham et al., “Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae,” Nucleic Acids Research, vol. 31, no. 8, pp. 2134–2147, 2003.
- W. Viratyosin, L. A. Campbell, C. C. Kuo, and D. D. Rockey, “Intrastrain and interstrain genetic variation within a paralogous gene family in Chlamydia pneumoniae,” BMC Microbiology, vol. 2, no. 1, article 38, 2002.
- M. Horn, A. Collingro, S. Schmitz-Esser et al., “Illuminating the evolutionary history of chlamydiae,” Science, vol. 304, no. 5671, pp. 728–730, 2004.
- E. Heinz, D. D. Rockey, J. Montanaro, K. Aistleitner, M. Wagner, and M. Horn, “Inclusion membrane proteins of Protochlamydia amoebophila UWE25 reveal a conserved mechanism for host cell interaction among the Chlamydiae,” Journal of Bacteriology, vol. 192, no. 19, pp. 5093–5102, 2010.
- J. D. Clausen, G. Christiansen, H. U. Holst, and S. Birkelund, “Chlamydia trachomatis utilizes the host cell microtubule network during early events of infection,” Molecular Microbiology, vol. 25, no. 3, pp. 441–449, 1997.
- S. S. Grieshaber, N. A. Grieshaber, and T. Hackstadt, “Chlamydia trachomatis uses host cell dynein to traffic to the microtubule-organizing center in a p50 dynamitin-independent process,” Journal of Cell Science, vol. 116, no. 18, pp. 3793–3802, 2003.
- M. A. Scidmore, D. D. Rockey, E. R. Fischer, R. A. Heinzen, and T. Hackstadt, “Vesicular interactions of the Chlamydia trachomatis inclusion are determined by chlamydial early protein synthesis rather than route of entry,” Infection and Immunity, vol. 64, no. 12, pp. 5366–5372, 1996.