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Evidence of the Red-Queen hypothesis from accelerated rates of evolution of genes involved in biotic interactions in Pneumocystis

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Evidence of the Red-Queen hypothesis from accelerated rates of evolution of genes involved in biotic interactions in Pneumocystis

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Delaye, L.; Ruiz Ruiz, S.; Calderon, E.; Tarazona Campos, S.; Conesa, A.; Moya, A. (2018). Evidence of the Red-Queen hypothesis from accelerated rates of evolution of genes involved in biotic interactions in Pneumocystis. Genome Biology and Evolution. 10(6):1596-1606. https://doi.org/10.1093/gbe/evy116

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Title: Evidence of the Red-Queen hypothesis from accelerated rates of evolution of genes involved in biotic interactions in Pneumocystis
Author: Delaye, Luis Ruiz Ruiz, Susana Calderon, Enrique Tarazona Campos, Sonia Conesa, A. Moya, Andrés
UPV Unit: Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia
Universitat Politècnica de València. Departamento de Estadística e Investigación Operativa Aplicadas y Calidad - Departament d'Estadística i Investigació Operativa Aplicades i Qualitat
Issued date:
Abstract:
[EN] Pneumocystis species are ascomycete fungi adapted to live inside the lungs of mammals. These ascomycetes show extensive stenoxenism, meaning that each species of Pneumocystis infects a single species of host. Here, ...[+]
Subjects: Stenoxenism , Majors surface glycoproteins , Glycosylphosphatidylinositol , Natural selection
Copyrigths: Reconocimiento - No comercial (by-nc)
Source:
Genome Biology and Evolution. (issn: 1759-6653 )
DOI: 10.1093/gbe/evy116
Publisher:
Oxford University Press
Publisher version: https://doi.org/10.1093/gbe/evy116
Project ID:
info:eu-repo/grantAgreement/EC/FP7/612583/EU/Developing an European American NGS Network/
...[+]
info:eu-repo/grantAgreement/EC/FP7/612583/EU/Developing an European American NGS Network/
info:eu-repo/grantAgreement/MINECO//SAF2012-31187/ES/INTERACCION DEL MICROBIOMA Y EL VIROMA DEL INTESTINO HUMANO EN CONDICIONES DE SALUD, ENFERMEDAD Y ESTRES ANTIBIOTICO/
info:eu-repo/grantAgreement/CONACyT//454938/
info:eu-repo/grantAgreement/MINECO//PIE14%2F00045/ES/Identification of novel modulators of chronic inflammation in prevalent diseases: unveiling divergent mechanisms of disease/
info:eu-repo/grantAgreement/ISCIII//AC 15%2F00022/
info:eu-repo/grantAgreement/MINECO//AC15%2F00042/ES/Recognition of the primary infection by Pneumocystis in infants: a silent threat to public health/
info:eu-repo/grantAgreement/GVA//PROMETEOII%2F2014%2F065/
info:eu-repo/grantAgreement/MINECO//SAF2013-49788-EXP/ES/INNOVACION EN MODELOS COMPUTACIONALES PREDICTIVOS EN EPIDEMIOLOGIA EXPERIMENTAL DE LA RESISTENCIA A LOS ANTIBIOTICOS/
info:eu-repo/grantAgreement/MINECO//SAF2015-65878-R/ES/ESTABILIDAD, RESILIENCIA Y REDUNDANCIA FUNCIONAL DE LA MICROBIOTA INTESTINAL HUMANA DURANTE EL DESARROLLO Y EN RESPUESTA AL ESTRES ANTIBIOTICO Y A CLOSTRIDIUM DIFFICILE/
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Thanks:
L.D. wishes to thank Eugenia Flores and Ana Fayos for support provided. This project has received funding from the Marie Curie International Research Staff Exchange Scheme within the 7th European Community Framework Program ...[+]
Type: Artículo

References

Aliouat-Denis, C.-M., Chabé, M., Demanche, C., Aliouat, E. M., Viscogliosi, E., Guillot, J., … Dei-Cas, E. (2008). Pneumocystis species, co-evolution and pathogenic power. Infection, Genetics and Evolution, 8(5), 708-726. doi:10.1016/j.meegid.2008.05.001

Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., … Sherlock, G. (2000). Gene Ontology: tool for the unification of biology. Nature Genetics, 25(1), 25-29. doi:10.1038/75556

Brockhurst, M. A., Chapman, T., King, K. C., Mank, J. E., Paterson, S., & Hurst, G. D. D. (2014). Running with the Red Queen: the role of biotic conflicts in evolution. Proceedings of the Royal Society B: Biological Sciences, 281(1797), 20141382. doi:10.1098/rspb.2014.1382 [+]
Aliouat-Denis, C.-M., Chabé, M., Demanche, C., Aliouat, E. M., Viscogliosi, E., Guillot, J., … Dei-Cas, E. (2008). Pneumocystis species, co-evolution and pathogenic power. Infection, Genetics and Evolution, 8(5), 708-726. doi:10.1016/j.meegid.2008.05.001

Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., … Sherlock, G. (2000). Gene Ontology: tool for the unification of biology. Nature Genetics, 25(1), 25-29. doi:10.1038/75556

Brockhurst, M. A., Chapman, T., King, K. C., Mank, J. E., Paterson, S., & Hurst, G. D. D. (2014). Running with the Red Queen: the role of biotic conflicts in evolution. Proceedings of the Royal Society B: Biological Sciences, 281(1797), 20141382. doi:10.1098/rspb.2014.1382

Brown, G. D., Denning, D. W., Gow, N. A. R., Levitz, S. M., Netea, M. G., & White, T. C. (2012). Hidden Killers: Human Fungal Infections. Science Translational Medicine, 4(165), 165rv13-165rv13. doi:10.1126/scitranslmed.3004404

Cagan, A., Theunert, C., Laayouni, H., Santpere, G., Pybus, M., Casals, F., … Andrés, A. M. (2016). Natural Selection in the Great Apes. Molecular Biology and Evolution, 33(12), 3268-3283. doi:10.1093/molbev/msw215

Catherinot, E., Lanternier, F., Bougnoux, M.-E., Lecuit, M., Couderc, L.-J., & Lortholary, O. (2010). Pneumocystis jirovecii Pneumonia. Infectious Disease Clinics of North America, 24(1), 107-138. doi:10.1016/j.idc.2009.10.010

Chagas, C. (1909). Nova tripanozomiaze humana: estudos sobre a morfolojia e o ciclo evolutivo do Schizotrypanum cruzi n. gen., n. sp., ajente etiolojico de nova entidade morbida do homem. Memórias do Instituto Oswaldo Cruz, 1(2), 159-218. doi:10.1590/s0074-02761909000200008

Cissé, O. H., Pagni, M., & Hauser, P. M. (2014). Comparative Genomics Suggests That the Human Pathogenic Fungus Pneumocystis jirovecii Acquired Obligate Biotrophy through Gene Loss. Genome Biology and Evolution, 6(8), 1938-1948. doi:10.1093/gbe/evu155

Cushion, M. T., Smulian, A. G., Slaven, B. E., Sesterhenn, T., Arnold, J., Staben, C., … Meller, J. (2007). Transcriptome of Pneumocystis carinii during Fulminate Infection: Carbohydrate Metabolism and the Concept of a Compatible Parasite. PLoS ONE, 2(5), e423. doi:10.1371/journal.pone.0000423

Daub, J. T., Moretti, S., Davydov, I. I., Excoffier, L., & Robinson-Rechavi, M. (2017). Detection of Pathways Affected by Positive Selection in Primate Lineages Ancestral to Humans. Molecular Biology and Evolution, 34(6), 1391-1402. doi:10.1093/molbev/msx083

Deitsch, K. W., Lukehart, S. A., & Stringer, J. R. (2009). Common strategies for antigenic variation by bacterial, fungal and protozoan pathogens. Nature Reviews Microbiology, 7(7), 493-503. doi:10.1038/nrmicro2145

Demanche, C., Berthelemy, M., Petit, T., Polack, B., Wakefield, A. E., Dei-Cas, E., & Guillot, J. (2001). Phylogeny of Pneumocystis carinii from 18 Primate Species Confirms Host Specificity and Suggests Coevolution. Journal of Clinical Microbiology, 39(6), 2126-2133. doi:10.1128/jcm.39.6.2126-2133.2001

Derouiche, S., Deville, M., Taylor, M., Akbar, H., Guillot, J., Carreto-Binaghi, L., … Demanche, C. (2009). Pneumocystis diversity as a phylogeographic tool. Memórias do Instituto Oswaldo Cruz, 104(1), 112-117. doi:10.1590/s0074-02762009000100017

Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32(5), 1792-1797. doi:10.1093/nar/gkh340

Edman, J. C., Kovacs, J. A., Masur, H., Santi, D. V., Elwood, H. J., & Sogin, M. L. (1988). Ribosomal RNA sequence shows Pneumocystis carinii to be a member of the Fungi. Nature, 334(6182), 519-522. doi:10.1038/334519a0

Finn, R. D., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Mistry, J., Mitchell, A. L., … Bateman, A. (2015). The Pfam protein families database: towards a more sustainable future. Nucleic Acids Research, 44(D1), D279-D285. doi:10.1093/nar/gkv1344

Fujita, M., & Kinoshita, T. (2009). Structural remodeling of GPI anchors during biosynthesis and after attachment to proteins. FEBS Letters, 584(9), 1670-1677. doi:10.1016/j.febslet.2009.10.079

Gerton, J. L., DeRisi, J., Shroff, R., Lichten, M., Brown, P. O., & Petes, T. D. (2000). Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences, 97(21), 11383-11390. doi:10.1073/pnas.97.21.11383

Gotz, S., Garcia-Gomez, J. M., Terol, J., Williams, T. D., Nagaraj, S. H., Nueda, M. J., … Conesa, A. (2008). High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Research, 36(10), 3420-3435. doi:10.1093/nar/gkn176

Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010). New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0. Systematic Biology, 59(3), 307-321. doi:10.1093/sysbio/syq010

Hall, J. P. J., Wang, H., & Barry, J. D. (2013). Mosaic VSGs and the Scale of Trypanosoma brucei Antigenic Variation. PLoS Pathogens, 9(7), e1003502. doi:10.1371/journal.ppat.1003502

Hauser, P. M. (2014). Genomic Insights into the Fungal Pathogens of the Genus Pneumocystis: Obligate Biotrophs of Humans and Other Mammals. PLoS Pathogens, 10(11), e1004425. doi:10.1371/journal.ppat.1004425

Huerta-Cepas, J., Serra, F., & Bork, P. (2016). ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data. Molecular Biology and Evolution, 33(6), 1635-1638. doi:10.1093/molbev/msw046

Hughes, A. L. (2007). Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level. Heredity, 99(4), 364-373. doi:10.1038/sj.hdy.6801031

Jackson, A. P., Otto, T. D., Darby, A., Ramaprasad, A., Xia, D., Echaide, I. E., … Pain, A. (2014). The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction. Nucleic Acids Research, 42(11), 7113-7131. doi:10.1093/nar/gku322

Keely, S. P., Renauld, H., Wakefield, A. E., Cushion, M. T., Smulian, A. G., Fosker, N., … Hall, N. (2005). Gene Arrays atPneumocystis cariniiTelomeres. Genetics, 170(4), 1589-1600. doi:10.1534/genetics.105.040733

Keely, S. P., & Stringer, J. R. (2009). Complexity of the MSG gene family of Pneumocystis carinii. BMC Genomics, 10(1), 367. doi:10.1186/1471-2164-10-367

Kosakovsky Pond, S. L., Posada, D., Gravenor, M. B., Woelk, C. H., & Frost, S. D. W. (2006). GARD: a genetic algorithm for recombination detection. Bioinformatics, 22(24), 3096-3098. doi:10.1093/bioinformatics/btl474

Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Molecular Biology and Evolution, 33(7), 1870-1874. doi:10.1093/molbev/msw054

Kutty, G., England, K. J., & Kovacs, J. A. (2013). Expression of Pneumocystis jirovecii Major Surface Glycoprotein in Saccharomyces cerevisiae. The Journal of Infectious Diseases, 208(1), 170-179. doi:10.1093/infdis/jit131

Kutty, G., Maldarelli, F., Achaz, G., & Kovacs, J. A. (2008). Variation in the Major Surface Glycoprotein Genes inPneumocystis jirovecii. The Journal of Infectious Diseases, 198(5), 741-749. doi:10.1086/590433

Kutty, G., Shroff, R., & Kovacs, J. A. (2013). Characterization of Pneumocystis Major Surface Glycoprotein Gene (msg) Promoter Activity in Saccharomyces cerevisiae. Eukaryotic Cell, 12(10), 1349-1355. doi:10.1128/ec.00122-13

Kyes, S. A., Kraemer, S. M., & Smith, J. D. (2007). Antigenic Variation in Plasmodium falciparum: Gene Organization and Regulation of the var Multigene Family. Eukaryotic Cell, 6(9), 1511-1520. doi:10.1128/ec.00173-07

Li, L. (2003). OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes. Genome Research, 13(9), 2178-2189. doi:10.1101/gr.1224503

Liang, M., Raley, C., Zheng, X., Kutty, G., Gogineni, E., Sherman, B. T., … Huang, D. W. (2016). Distinguishing highly similar gene isoforms with a clustering-based bioinformatics analysis of PacBio single-molecule long reads. BioData Mining, 9(1). doi:10.1186/s13040-016-0090-8

Ma, L., Chen, Z., Huang, D. W., Kutty, G., Ishihara, M., Wang, H., … Kovacs, J. A. (2016). Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts. Nature Communications, 7(1). doi:10.1038/ncomms10740

Mancera, E., Bourgon, R., Brozzi, A., Huber, W., & Steinmetz, L. M. (2008). High-resolution mapping of meiotic crossovers and non-crossovers in yeast. Nature, 454(7203), 479-485. doi:10.1038/nature07135

Murrell, B., Wertheim, J. O., Moola, S., Weighill, T., Scheffler, K., & Kosakovsky Pond, S. L. (2012). Detecting Individual Sites Subject to Episodic Diversifying Selection. PLoS Genetics, 8(7), e1002764. doi:10.1371/journal.pgen.1002764

Palmer, G. H., & Brayton, K. A. (2007). Gene conversion is a convergent strategy for pathogen antigenic variation. Trends in Parasitology, 23(9), 408-413. doi:10.1016/j.pt.2007.07.008

Paradis, E., Claude, J., & Strimmer, K. (2004). APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics, 20(2), 289-290. doi:10.1093/bioinformatics/btg412

Paterson, S., Vogwill, T., Buckling, A., Benmayor, R., Spiers, A. J., Thomson, N. R., … Brockhurst, M. A. (2010). Antagonistic coevolution accelerates molecular evolution. Nature, 464(7286), 275-278. doi:10.1038/nature08798

Petersen, B., Petersen, T., Andersen, P., Nielsen, M., & Lundegaard, C. (2009). A generic method for assignment of reliability scores applied to solvent accessibility predictions. BMC Structural Biology, 9(1), 51. doi:10.1186/1472-6807-9-51

Petes, T. D. (2001). Meiotic recombination hot spots and cold spots. Nature Reviews Genetics, 2(5), 360-369. doi:10.1038/35072078

Pittet, M., & Conzelmann, A. (2007). Biosynthesis and function of GPI proteins in the yeast Saccharomyces cerevisiae. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, 1771(3), 405-420. doi:10.1016/j.bbalip.2006.05.015

Pond, S. L. K., Frost, S. D. W., & Muse, S. V. (2004). HyPhy: hypothesis testing using phylogenies. Bioinformatics, 21(5), 676-679. doi:10.1093/bioinformatics/bti079

Schmid-Siegert, E., Richard, S., Luraschi, A., Mühlethaler, K., Pagni, M., & Hauser, P. M. (2017). Mechanisms of Surface Antigenic Variation in the Human Pathogenic Fungus Pneumocystis jirovecii. mBio, 8(6). doi:10.1128/mbio.01470-17

Serra, F., Arbiza, L., Dopazo, J., & Dopazo, H. (2011). Natural Selection on Functional Modules, a Genome-Wide Analysis. PLoS Computational Biology, 7(3), e1001093. doi:10.1371/journal.pcbi.1001093

STRINGER, J. R. (2007). Antigenic Variation in Pneumocystis. The Journal of Eukaryotic Microbiology, 54(1), 8-13. doi:10.1111/j.1550-7408.2006.00225.x

Stringer, S. L., Stringer, J. R., Blase, M. A., Walzer, P. D., & Cushion, M. T. (1989). Pneumocystis carinii: Sequence from ribosomal RNA implies a close relationship with fungi. Experimental Parasitology, 68(4), 450-461. doi:10.1016/0014-4894(89)90130-6

Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., … Mesirov, J. P. (2005). Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences, 102(43), 15545-15550. doi:10.1073/pnas.0506580102

Thomas, C. F., & Limper, A. H. (2007). Current insights into the biology and pathogenesis of Pneumocystis pneumonia. Nature Reviews Microbiology, 5(4), 298-308. doi:10.1038/nrmicro1621

Vink, C., Rudenko, G., & Seifert, H. S. (2012). Microbial antigenic variation mediated by homologous DNA recombination. FEMS Microbiology Reviews, 36(5), 917-948. doi:10.1111/j.1574-6976.2011.00321.x

Vinuesa, P., & Contreras-Moreira, B. (2015). Robust Identification of Orthologues and Paralogues for Microbial Pan-Genomics Using GET_HOMOLOGUES: A Case Study of pIncA/C Plasmids. Bacterial Pangenomics, 203-232. doi:10.1007/978-1-4939-1720-4_14

Weatherly, D. B., Peng, D., & Tarleton, R. L. (2016). Recombination-driven generation of the largest pathogen repository of antigen variants in the protozoan Trypanosoma cruzi. BMC Genomics, 17(1). doi:10.1186/s12864-016-3037-z

Yang, Z. (2007). PAML 4: Phylogenetic Analysis by Maximum Likelihood. Molecular Biology and Evolution, 24(8), 1586-1591. doi:10.1093/molbev/msm088

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