The repeat structure of two paralogous genes, Yersinia ruckeri invasin (yrInv) and a “Y. ruckeri invasin-like molecule”, (yrIlm) sheds light on the evolution of adhesive capacities of a fish pathogen
Tài liệu tham khảo
Aziz, 2008, The RAST Server: rapid annotations using subsystems technology, BMC Genomics, 9, 75, 10.1186/1471-2164-9-75
Bastardo, 2012, Multilocus sequence typing reveals high genetic diversity and epidemic population structure for the fish pathogen Yersinia ruckeri, Environ Microbiol., 14, 1888, 10.1111/j.1462-2920.2012.02735.x
Benson, 1999, Tandem repeats finder: A program to analyze DNA sequences, Nucl. Acids Res., 27, 573, 10.1093/nar/27.2.573
Bernstein, 2014, NIH Public Access, 4, 1
Bertani, 1951, Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli, J. Bacteriol., 62, 293, 10.1128/jb.62.3.293-300.1951
Berven, 2004, BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria, Nucleic Acids Res., 32, W394, 10.1093/nar/gkh351
Blair, 2013, Choice of bacterial growth medium alters the transcriptome and phenotype of Salmonella enterica serovar typhimurium, PLoS One, 8, 10.1371/journal.pone.0063912
Brudal, 2013, Evaluation of reference genes for reverse transcription quantitative PCR analyses of fish-pathogenic Francisella strains exposed to different growth conditions, BMC Res. Notes, 6, 76, 10.1186/1756-0500-6-76
Brzostek, 1999, Osmoregulation-dependent expression of Yersinia enterocolitica virulence factors, Acta Microbiol Pol, 48, 31
Bullock, 1984
Busch, 1978, Enteric red mouth disease, Mar. Fish. Rev., 40, 42
Chauhan, 2016, Yersinia adhesins: an arsenal for infection, Appl. Proteomics Clin., 10.1002/prca.201600012
Darling, 2010, Progressivemauve: Multiple genome alignment with gene gain, loss and rearrangement, PLoS One, 5, 10.1371/journal.pone.0011147
de Keukeleire, 2014, Yersinia ruckeri, an unusual microorganism isolated from a human wound infection, New Microbes New Infect., 2, 134, 10.1002/nmi2.56
Fairman, 2012, Crystal structures of the outer membrane domain of intimin and invasin from enterohemorrhagic E. coli and enteropathogenic Y. pseudotuberculosis, Structure, 20, 1233, 10.1016/j.str.2012.04.011
Fernandez, 2003, In vitro and in vivo studies of the Yrp1 protease from Yersinia ruckeri and its role in protective immunity against enteric red mouth disease of salmonids, Society, 69, 7328
Fernández, 2007, The iron- and temperature-regulated haemolysin YhlA is a virulence factor of Yersinia ruckeri, Microbiology, 153, 483, 10.1099/mic.0.29284-0
Furones, 1993, Yersinia ruckeri, the causal agent of enteric redmouth disease (ERM) in fish, Annu. Rev. Fish Dis., 3, 105, 10.1016/0959-8030(93)90031-6
Gal-Mor, 2008, A novel secretion pathway of Salmonella enterica acts as an antivirulence modulator during salmonellosis, PLoS Pathog., 4, 10.1371/journal.ppat.1000036
Galant, 1990, Expression of Salmonella typhimurium Genes Required for Invasion Is Regulated by Changes in DNA Supercoiling, Infect Immun., 58, 1879, 10.1128/iai.58.6.1879-1885.1990
Garcia, 1998, Ribotyping and plasmid profiling of Yersinia ruckeri, J. Appl. mMcrobiology, 85, 949, 10.1111/j.1365-2672.1998.tb05258.x
Guilvout, 1988, BamHI restriction endonuclease analysis of Yersinia ruckeri plasmids and their relatedness to the genus Yersinia 42- to 47-megadalton plasmid, Appl. Environ. Microbiol., 54, 2594, 10.1128/aem.54.10.2594-2597.1988
Hamburger, 1999, Integrin-Binding Protein Crystal Structure of Invasin: A Bacterial Crystal Structure of Invasin: A Bacterial Integrin-Binding Protein, Science, 80
Heinz, 2016, Conserved features in the structure, mechanism and biogenesis of the inverse autotransporter protein family, Genome Biol. Evol., 8, evw112, 10.1093/gbe/evw112
Henderson, 2000, Autotransporter proteins, evolution and redefining protein secretion: Response, Trends Microbiol., 8, 534, 10.1016/S0966-842X(00)01884-9
http://www.repeatmasker.org [WWW Document], n.d. URL http://www.repeatmasker.org.
Isberg, 1990, Multiple β1 chain integrins are receptors for invasin, a protein that promotes bacterial penetration into mammalian cells, Cell, 60, 861, 10.1016/0092-8674(90)90099-Z
Isberg, 1988, Analysis of expression and thermoregulation of the Yersinia pseudotuberculosis inv gene with hybrid proteins, Infect. Immun., 56, 2133, 10.1128/iai.56.8.2133-2138.1988
Käll, 2004, A combined transmembrane topology and signal peptide prediction method, J. Mol. Biol., 338, 1027, 10.1016/j.jmb.2004.03.016
Kawula, 1996, Using a new inbred fish model and cultured fish tissue cells to study Aeromonas hydrophila and Yersinia ruckeri pathogenesis, Microb. Pathog., 20, 119, 10.1006/mpat.1996.0011
Kearse, 2012, Geneious, Bioinformatics
LeJeune, 2000, Polymerase chain reaction for definitive identification of Yersinia ruckeri, J. Vet. Diagn. Invest., 12, 558, 10.1177/104063870001200611
Leo, 2012, Type V secretion: mechanism(s) of autotransport through the bacterial outer membrane, Philos. Trans. R. Soc. Lond. B. Biol. Sci., 367, 1088, 10.1098/rstb.2011.0208
Leo, 2015, The Intimin periplasmic domain mediates dimerisation and binding to peptidoglycan, Mol. Microbiol., 95, 80, 10.1111/mmi.12840
Leo, 2015, The inverse autotransporter family: Intimin, invasin and related proteins, J. Med. Microbiol Int., 10.1016/j.ijmm.2014.12.011
Litwin, 1993, Role of iron in regulation of virulence genes, Clin. Microbiol. Rev., 6, 137, 10.1128/CMR.6.2.137
Mammeri, 2006, Cloning and functional characterization of the ambler class C beta-lactamase of Yersinia ruckeri, FEMS Microbiol. Lett., 257, 57, 10.1111/j.1574-6968.2006.00148.x
Marteyn, 2010, Modulation of Shigella virulence in response to available oxygen in vivo, Nature, 465, 355, 10.1038/nature08970
Messenger, 1983, Bacteria, iron and pathogenicity, Biochem. Educ., 11, 54, 10.1016/0307-4412(83)90043-2
Miller, 1988, A novel suicide vector and its use in construction of insertion mutations: Osmoregulation of outer membrane proteins and virulence determinants in Vibrio cholerae requires toxR, J. Bacteriol., 170, 2575, 10.1128/jb.170.6.2575-2583.1988
Mittal, 2009, Effect of Osmolarity on Virulence of Uropathogenic Pseudomonas Aeruginosa, Am. J. Biomed. Sci., 1, 12, 10.5099/aj090100012
Mota, 2005, Bacterial injectisomes: needle length does matter, Science, 307, 1278, 10.1126/science.1107679
Mouriño, 1996, The Hha protein as a modulator of expression of virulence factors in Escherichia coli, Infect. Immun., 64, 2881, 10.1128/iai.64.7.2881-2884.1996
Nelson, 2015, Complete genome sequence of Yersinia ruckeri strain CSF007-82, etiologic agent of red mouth disease in salmonid fish, Genome Announc., 3, 4, 10.1128/genomeA.01491-14
Oberhettinger, 2015, The inverse autotransporter intimin exports its passenger domain via a hairpin intermediate, J. Biol. Chem., 290, 1837, 10.1074/jbc.M114.604769
Oberhettinger, 2012, Intimin and invasin export their c-terminus to the bacterial cell surface using an inverse mechanism compared to classical autotransport, PLoS One, 7, 10.1371/annotation/cb7e47be-dd4b-46cd-b4e5-18b7077f64df
Ohtani, 2014, 3D visualization of the initial Yersinia ruckeri infection route in rainbow trout (Oncorhynchus mykiss) by optical projection tomography, PLoS One, 9, 10.1371/journal.pone.0089672
Pepe, 1994, Growth phase and low pH affect the thermal regulation of the Yersinia enterocolitica inv gene, Mol. Microbiol., 11, 123, 10.1111/j.1365-2958.1994.tb00295.x
Pisano, 2012, In vivo-induced inva-like autotransporters Ifp and invc of Yersinia pseudotuberculosis promote interactions with intestinal epithelial cells and contribute to virulence, Infect. Immun., 80, 1050, 10.1128/IAI.05715-11
Porter, 1994, A role for H-NS in the thermo-osmotic regulation of virulence gene expression in Shigella flexneri, J. Bacteriol., 10.1128/jb.176.13.4187-4191.1994
Price, 2005, De novo identification of repeat families in large genomes, Bioinformatics, 21, 10.1093/bioinformatics/bti1018
Quevillon, 2005, InterProScan: Protein domains identifier, Nucleic Acids Res., 33, 10.1093/nar/gki442
Quinlan, 2010, BEDTools: A flexible suite of utilities for comparing genomic features, Bioinformatics, 26, 841, 10.1093/bioinformatics/btq033
Rasmussen, 2015, Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago, Cell, 163, 571, 10.1016/j.cell.2015.10.009
Ren, 2010, Complete genome sequence of Enterobacter cloacae subsp. cloacae type strain ATCC 13047, J. Bacteriol., 192, 2463, 10.1128/JB.00067-10
Reuter, 2014, Parallel independent evolution of pathogenicity within the genus Yersinia, Proc. Natl. Acad. Sci., 111, 6768, 10.1073/pnas.1317161111
Riess, 2004, Bartonella adhesin a mediates a proangiogenic host cell response, J. Exp. Med., 200, 1267, 10.1084/jem.20040500
Riess, 2007, Analysis of Bartonella adhesin A expression reveals differences between various B. henselae strains, Infect. Immun., 75, 35, 10.1128/IAI.00963-06
Rocha, 2015, Bacterial reference genes for gene expression studies by RT-qPCR: survey and analysis, Antonie Van Leeuwenhoek, 108, 685, 10.1007/s10482-015-0524-1
Romalde, 1993, Antigenic and molecular characterization of Yersinia ruckeri proposal for a new intraspecies classification, Syst. Appl Microbiol., 16, 10.1016/S0723-2020(11)80274-2
Romalde, 1993, Pathological activities of Yersinia ruckeri, the enteric redmouth (ERM) bacterium, FEMS Microbiol. Lett., 112, 291, 10.1111/j.1574-6968.1993.tb06465.x
Ross, 1966, Description of a Bacterium Associated with Redmouth Disease of Rainbow Trout (Salmo gairdneri), Can. J. Microbiol., 12, 763, 10.1139/m66-103
Rucker, 1966, Redmouth disease of rainbow trout (Salmo gairdneri), Bull Off Int Epizoot., 825
Sadana, 2017, Structure of the Y. pseudotuberculosis adhesin InvasinE, Protein Sci., 10.1002/pro.3171
Savin, 2014, The Yersinia pseudotuberculosis complex: Characterization and delineation of a new species, Yersinia wautersii, Int. J. Med. Microbiol., 304, 452, 10.1016/j.ijmm.2014.02.002
Secades, 1999, Purification and Characterization of an Extracellular Protease from the Fish pathogen Yersinia ruckeri and effect of culture condition on production, Appl. Environ. Microbiol., 65, 3969, 10.1128/AEM.65.9.3969-3975.1999
Shaowu, 2013, Isolation of Yersinia ruckeri strain H01 from farm-raised Amur Sturgeon Acipenser schrencki in China, J. Aquat. Anim. Health, 25, 9, 10.1080/08997659.2012.728169
Sievers, 2011, Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega, Mol. Syst. Biol., 7, 539, 10.1038/msb.2011.75
Simonet, 1992
Söding, 2005, The HHpred interactive server for protein homology detection and structure prediction, Nucleic Acids Res., 33, 10.1093/nar/gki408
Stevenson, 1982, Biochemical AND serological characteristics of ontario isolates of Yersinia ruckeri, Can. J. Fish. Aquat. Sci., 39, 870, 10.1139/f82-118
Strong, 2011, Identification and characterisation of a novel adhesin Ifp in Yersinia pseudotuberculosis, BMC Microbiol., 11, 85, 10.1186/1471-2180-11-85
Sun, 2015, Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera, Nat. Commun., 6, 8322, 10.1038/ncomms9322
Szabady, 2005, An unusual signal peptide facilitates late steps in the biogenesis of a bacterial autotransporter, Proc. Natl. Acad. Sci. U. S. A., 102, 221, 10.1073/pnas.0406055102
Thompson, 1994, CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res., 22, 4673, 10.1093/nar/22.22.4673
Trivier, 1996
Tsai, 2010, The bacterial intimins and invasins: A large and novel family of secreted proteins, PLoS One, 5, 10.1371/journal.pone.0014403
Wasteson, 1989, Antibacterial Spectrum and some other Characteristics of an Antimicrobial Factor produced by Yersinia ruckeri, Acta vet. scand., 30, 253, 10.1186/BF03548029
Willumsen, 1989, Birds and wild fish as potential vectors of Yersinia ruckeri, J. Fish Dis., 12, 275, 10.1111/j.1365-2761.1989.tb00313.x