In silico prediction of Gallibacterium anatis pan-immunogens
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- 作者：Ragnhild J Bager (1)
Egle Kudirkiene (1)
Isabelle da Piedade (1)
Torsten Seemann (2)
Tine K Nielsen (3)
Susanne E Pors (1)
Andreas H Mattsson (4) (5)
John D Boyce (6)
Ben Adler (7)
Anders M Bojesen (1)
1. Department of Veterinary Disease Biology ; Faculty of Health and Medical Sciences ; University of Copenhagen ; 1870 ; Frederiksberg C ; Denmark
2. Victorian Bioinformatics Consortium ; Monash University ; 3800 ; Clayton ; Melbourne ; Australia
3. The Novo Nordisk Foundation Center for Protein Research ; Faculty of Health and Medical Sciences ; University of Copenhagen ; 2200 ; Copenhagen N ; Denmark
4. Center for Biological Sequence Analysis ; Technical University of Denmark ; 2800 ; Lyngby ; Denmark
5. Evaxion Biotech North America LLC ; Wilmington ; USA
6. Department of Microbiology ; Monash University ; 3800 ; Clayton ; Melbourne ; Australia
7. Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics ; Department of Microbiology ; Monash University ; 3800 ; Clayton ; Melbourne ; Australia - 刊名：Veterinary Research
- 出版年：2014
- 出版时间：December 2014
- 年：2014
- 卷：45
- 期：1
- 全文大小：822 KB
- 参考文献：Annual report 2011. Assoc Poult Processors Poult Trade EU Ctries 41: pp. 1-52
1. Marangon, S, Busani, L (2007) The use of vaccination in poultry production. Rev Sci Tech 26: pp. 265-274
2. Christensen H, Bisgaard M, Bojesen AM, Mutters R, Olsen JE: Genetic relationships among avian isolates classified as Pasteurella haemolytica , 鈥?/strong> Actinobacillus salpingitidis 鈥?or Pasteurella anatis with proposal of Gallibacterium anatis gen. nov., comb. nov. and description of additional genomospecies within Gallibacterium gen. nov. / Int J Syst Evol Microbiol 2003, 53:275鈥?87.
3. Bisgaard M, Korczak BM, Busse H-J, Kuhnert P, Bojesen AM, Christensen H: Classification of the taxon 2 and taxon 3 complex of Bisgaard within Gallibacterium and description of Gallibacterium melopsittaci sp. nov., Gallibacterium trehalosifermentans sp. nov. and Gallibacterium salpingitidis sp. nov. / Int J Syst Evol Microbiol 2009, 59:735鈥?44.
4. Bisgaard M: Incidence of Pasteurella haemolytica in the respiratory tract of apparently healthy chickens and chickens with infectious bronchitis: characterisation of 213 strains. / Avian Pathol 1977, 6:285鈥?92.
5. Bojesen AM, Nielsen SS, Bisgaard M: Prevalence and transmission of haemolytic Gallibacterium species in chicken production systems with different biosecurity levels. / Avian Pathol 2003, 5:503鈥?10.
6. Mirle C, Sch枚ngarth M, Meinhart H, Olm U: Untersuchungen zu auftreten and bedeutung von Pasteurella haemolytica infektionen bei hennen unter besonderer ber眉cksichtigung von erkrankungen des legeapparates. / Mh Vet Med 1991, 46:545鈥?49 (in German).
7. Jordan, FTW, Williams, NJ, Wattret, A, Jones, T (2005) Observations on salpingitis, peritonitis and salpingoperitonitis in a layer breeder flock. Vet Rec 157: pp. 573-577
8. Neubauer C, De Souza-Pilz M, Bojesen AM, Bisgaard M, Hess M: Tissue distribution of haemolytic Gallibacterium anatis isolates in laying birds with reproductive disorders. / Avian Pathol 2009, 38:1鈥?.
9. Bojesen, AM, Christensen, JP, Bisgaard, M Gallibacterium infections and other avian Pasteurellaceae. In: Pattison, M, Mcmullin, PF, Bradbury, JM, Alexander, DJ eds. (2008) Poultry diseases. Saunders Elsevier, Edinburg, pp. 160-163 CrossRef
10. Bojesen AM, Vazquez ME, Bager RJ, Ifrah D, Gonzalez C, Aarestrup FM: Antimicrobial susceptibility and tetracycline resistance determinant genotyping of Gallibacterium anatis . / Vet Microbiol 2011, 148:105鈥?10.
11. Schumacher, T, Vazquez, ME, Leon-Kempis, MR (2008) Analysis of strains of Gallibacterium anatis by agar gel precipitation and determination of cross reactivity [Poster]. International Pasteurellaceae Society Meeting, Sorrento, Italy
12. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM: Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. / Science 1995, 269:496鈥?12.
13. Rinaudo, CD, Telford, JL, Rappuoli, R, Seib, KL (2009) Vaccinology in the genome era. J Clin Invest 119: pp. 2515-2525 CrossRef
14. Rappuoli, R (2001) Reverse vaccinology, a genome-based approach to vaccine development. Vaccine 19: pp. 2688-2691 CrossRef
15. Pizza, M, Scarlato, V, Masignani, V, Giuliani, MM, Aric貌, B, Comanducci, M, Jennings, GT, Baldi, L, Bartolini, E, Capecchi, B, Galeotti, CL, Luzzi, E, Manetti, R, Marchetti, E, Mora, M, Nuti, S, Ratti, G, Santini, L, Savino, S, Scarselli, M, Storni, E, Zuo, P, Broeker, M, Hundt, E, Knapp, B, Blair, E, Mason, T, Tettelin, H, Hood, DW, Jeffries, AC (2000) Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. Science 287: pp. 1816-1820 CrossRef
16. Tettelin H, Saunders NJ, Heidelberg J, Jeffries AC, Nelson KE, Eisen JA, Ketchum KA, Hood DW, Peden JF, Dodson RJ, Nelson WC, Gwinn ML, DeBoy R, Peterson JD, Hickey EK, Haft DH, Salzberg SL, White O, Fleischmann RD, Dougherty BA, Mason T, Ciecko A, Parksey DS, Blair E, Cittone H, Clark EB, Cotton MD, Utterback TR, Khouri H, Qin H, / et al: Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. / Science 2000, 287:1809鈥?815.
17. Giuliani, MM, Adu-Bobie, J, Comanducci, M, Aric貌, B, Savino, S, Santini, L, Brunelli, B, Bambini, S, Biolchi, A, Capecchi, B, Cartocci, E, Ciucchi, L, Marcello, F, Ferlicca, F, Galli, B, Luzzi, E, Masignani, V, Serruto, D, Veggi, D, Contorni, M, Morandi, M, Bartalesi, A, Cinotti, V, Mannucci, D, Titta, F, Ovidi, E, Welsch, JA, Granoff, D, Rappuoli, R, Pizza, M (2006) A universal vaccine for serogroup B meningococcus. Proc Natl Acad Sci U S A 103: pp. 10834-10839 CrossRef
18. Carter, N (2013) Multicomponent meningococcal serogroup B vaccine (4CMenB; Bexsero庐): a review of its use in primary and booster vaccination. BioDrugs 3: pp. 263-274 CrossRef
19. Donati, C, Rappuoli, R (2013) Reverse vaccinology in the 21st century: improvements over the original design. Ann N Y Acad Sci 1285: pp. 115-132 CrossRef
20. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, Deboy RT, Davidsen TM, Mora M, Scarselli M, Margarit y Ros I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Selengut J, Gwinn ML, Zhou L, Zafar N, / et al: Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae : implications for the microbial 鈥減an-genome鈥? / Proc Natl Acad Sci U S A 2005, 102:13950鈥?3955.
21. Maione D, Margarit I, Rinaudo CD, Masignani V, Mora M, Scarselli M, Tettelin H, Brettoni C, Iacobini ET, Rosini R, D鈥橝gostino N, Miorin L, Buccato S, Mariani M, Galli G, Nogarotto R, Nardi-Dei V, Vegni F, Fraser C, Mancuso G, Teti G, Madoff LC, Paoletti LC, Rappuoli R, Kasper DL, Telford JL, Grandi G: Identification of a universal Group B streptococcus vaccine by multiple genome screen. / Science 2005, 309:148鈥?50.
22. Medini, D, Donati, C, Tettelin, H, Masignani, V, Rappuoli, R (2005) The microbial pan-genome. Curr Opin Genet Dev 15: pp. 589-594 CrossRef
23. Bager RJ, Nesta B, Pors SE, Soriani M, Serino L, Boyce JD, Adler B, Bojesen AM: The fimbrial protein FlfA from Gallibacterium anatis is a virulence factor and vaccine candidate. / Infect Immun 2013, 81:1964鈥?973.
24. Bojesen AM, Torpdahl M, Christensen H, Olsen JE, Bisgaard M: Genetic diversity of Gallibacterium anatis isolates from different chicken flocks. / J Clin Microbiol 2003, 41:2737鈥?740.
25. Kristensen BM, Frees D, Bojesen AM: Expression and secretion of the RTX-toxin GtxA among members of the genus Gallibacterium . / Vet Microbiol 2011, 153:116鈥?23.
26. Johnson TJ, Danzeisen JL, Trampel D, Nolan LK, Seemann T, Bager RJ, Bojesen AM: Genome analysis and phylogenetic relatedness of Gallibacterium anatis strains from poultry. / PLoS One 2013, 1:e54844.
27. 釁? The VelvetOptimiser 2.0 de novo sequence assembler. In / 釁? ; 釁?[formatics.com/software.velvetoptimiser.shtml" class="a-plus-plus">http://www.vicbioinformatics.com/software.velvetoptimiser.shtml]
28. Seemann, T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30: pp. 2068-2069 formatics/btu153" target="_blank" title="It opens in new window">CrossRef
29. Yu, NY, Wagner, JR, Laird, MR, Melli, G, Rey, S, Lo, R, Dao, P, Sahinalp, SC, Ester, M, Foster, LJ, Brinkman, FS (2010) PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics 13: pp. 1608-1615 formatics/btq249" target="_blank" title="It opens in new window">CrossRef
30. Bendtsen, JD, Nielsen, H, Heijne, G, Brunak, S (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 4: pp. 783-795 CrossRef
31. Krogh, A, Larsson, B, Heijne, G, Sonnhammer, EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 3: pp. 567-580 CrossRef
32. Altschul, SF, Gish, W, Miller, W, Myers, EW, Lipman, DJ (1990) Basic local alignment search tool. J Mol Biol 215: pp. 403-410 CrossRef
33. Rice, P, Longden, I, Bleasby, A (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16: pp. 276-277 CrossRef
34. Kristensen BM, Frees D, Bojesen AM: GtxA from Gallibacterium anatis , a cytolytic RTX-toxin with a novel domain organisation. / Vet Res 2010, 41:25.
35. Bager RJ, Persson G, Nesta B, Soriani M, Serino L, Jeppsson M, Nielsen TK, Bojesen AM: Outer membrane vesicles reflect environmental cues in Gallibacterium anatis . / Vet Microbiol 2013, 167:565鈥?72.
36. Al-Hasani K, Boyce J, McCarl VP, Bottomley S, Wilkie I, Adler B: Identification of novel immunogens in Pasteurella multocida . / Microb Cell Fact 2007, 6:3.
37. Gr盲slund, S, Sagemark, J, Berglund, H, Dahlgren, L-G, Flores, A, Hammarstr枚m, M, Johansson, I, Kotenyova, T, Nilsson, M, Nordlund, P, Weigelt, J (2008) The use of systematic N- and C-terminal deletions to promote production and structural studies of recombinant proteins. Protein Expr Purif 2: pp. 210-221 CrossRef
38. Bojesen AM, Nielsen OL, Christensen JP, Bisgaard M: In vivo studies of Gallibacterium anatis infection in chickens. / Avian Pathol 2004, 33:145鈥?52.
39. Raida MK, Nyl茅n J, Holten-Andersen L, Buchmann K: Association between plasma antibody response and protection in rainbow trout Oncorhynchus mykiss immersion vaccinated against Yersinia ruckeri . / PLoS One 2011, 6:e18832.
40. Villumsen KR, Dalsgaard I, Holten-Andersen L, Raida MK: Potential role of specific antibodies as important vaccine induced protective mechanism against Aeromonas salmonicida in rainbow trout. / PLoS One 2012, 7:e46733.
41. 釁? The MyAssays庐 Antibody Titer Calculation Software.In / 釁? ; 釁? [http://www.myassays.com/antibody-titers.assay]
42. Case, JT, Ardans, AA, Bolton, DC, Reynolds, BJ (1983) Optimization of parameters for detecting antibodies against infectious bronchitis virus using an enzyme-linked immunosorbent assay: temporal response to vaccination and challenge with live virus. Avian Dis 27: pp. 196-210 CrossRef
43. Doytchinova, IA, Flower, DR (2007) VaxiJen: a server for prediction of protective antigens, tumor antigens and subunit vaccines. BMC Bioinformatics 8: pp. 4 CrossRef
44. Katoh, K, Standley, DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30: pp. 772-780 CrossRef
45. Waterhouse, AM, Procter, JB, Martin, DMA, Clamp, M, Barton, GJ (2009) Jalview Version 2 - a multiple sequence alignment editor and analysis workbench. Bioinformatics 25: pp. 1189-1191 formatics/btp033" target="_blank" title="It opens in new window">CrossRef
46. Kudirkiene E, Christensen H, Bojesen AM: Draft genome sequence of Gallibacterium anatis biovar haemolytica 12656鈥?2 Liver, an isolate obtained from the liver of a septicaemic chicken. / Genome Announc 2013, 1:e00810-13.
47. 釁? The NCBI Sequence Read Archive (SRA). In / 釁? ; 釁?[https://www.ncbi.nlm.nih.gov/sra]
48. Korepanova A, Gao FP, Hua Y, Qin H, Nakamoto RK, Cross TA: Cloning and expression of multiple integral membrane proteins from Mycobacterium tuberculosis in Escherichia coli . / Protein Sci 2005, 14:148鈥?58.
49. Babu, MM, Sankaran, K (2002) DOLOP鈥揹atabase of bacterial lipoproteins. Bioinformatics 18: pp. 641-643 formatics/18.4.641" target="_blank" title="It opens in new window">CrossRef
50. Tidhar A, Flashner Y, Cohen S, Levi Y, Zauberman A, Gur D, Aftalion M, Elhanany E, Zvi A, Shafferman A, Mamroud E: The NlpD lipoprotein is a novel Yersinia pestis virulence factor essential for the development of plague. / PLoS One 2009, 4:e7023.
51. Marchler-Bauer, A, Lu, S, Anderson, JB, Chitsaz, F, Derbyshire, MK, DeWeese-Scott, C, Fong, JH, Geer, LY, Geer, RC, Gonzales, NR, Gwadz, M, Hurwitz, DI, Jackson, JD, Ke, Z, Lanczycki, CJ, Lu, F, Marchler, GH, Mullokandov, M, Omelchenko, MV, Robertson, CL, Song, JS, Thanki, N, Yamashita, RA, Zhang, D, Zhang, N, Zheng, C, Bryant, SH (2011) CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 39: pp. D225-D229 CrossRef
52. Bateman A, Bycroft M: The structure of a LysM domain from E. coli membrane-bound lytic murein transglycosylase D (MltD). / J Mol Biol 2000, 299:1113鈥?139.
53. Buist, G, Steen, A, Kok, J, Kuipers, OP (2008) LysM, a widely distributed protein motif for binding to (peptido)glycans. Mol Microbiol 68: pp. 838-847 CrossRef
54. Bernhardt TG, de Boer PA: Screening for synthetic lethal mutants in Escherichia coli and identification of EnvC (YibP) as a periplasmic septal ring factor with murein hydrolase activity. / Mol Microbiol 2004, 52:1255鈥?269.
55. Mintz KP: Identification of an extracellular matrix protein adhesin, EmaA, which mediates the adhesion of Actinobacillus actinomycetemcomitans to collagen. / Microbiology 2004, 150:2677鈥?688.
56. Linke, D, Riess, T, Autenrieth, IB, Lupas, A, Kempf, VAJ (2006) Trimeric autotransporter adhesins: variable structure, common function. Trends Microbiol 14: pp. 264-270 CrossRef
57. 艁yskowski, A, Leo, JC, Goldman, A (2011) Structure and biology of trimeric autotransporter adhesins. Adv Exp Med Biol 715: pp. 143-158 CrossRef
58. Serruto, D, Bottomley, MJ, Ram, S, Giuliani, MM, Rappuoli, R (2012) The new multicomponent vaccine against meningococcal serogroup B, 4CMenB: immunological, functional and structural characterization of the antigens. Vaccines 30: pp. B87-B97 CrossRef
59. Szczesny, P, Lupas, A (2008) Domain annotation of trimeric autotransporter adhesins鈥揹aTAA. Bioinformatics 24: pp. 1251-1256 formatics/btn118" target="_blank" title="It opens in new window">CrossRef
60. Ooka H, Terkawi MA, Goo Y-K, Luo Y, Li Y: Babesia microti : molecular and antigenic characterizations of a novel 94-kDa protein (BmP94). / Exp Parasitol 2011, 127:287鈥?93.
61. Chao C-C, Huber ES, Porter TB, Zhang Z, Ching W-M: Analysis of the cross-reactivity of various 56聽kDa recombinant protein antigens with serum samples collected after Orientia tsutsugamushi infection by ELISA. / Am J Trop Med Hyg 2011, 84:967鈥?72.
62. Seah JN, Frey J, Kwang J: The N-terminal domain of RTX toxin ApxI of Actinobacillus pleuropneumoniae elicits protective immunity in mice. / Infect Immun 2002, 70:6464鈥?467.
63. Ariel N, Zvi A, Grosfeld H, Gat O, Inbar Y, Velan B, Cohen S, Shafferman A: Search for potential vaccine candidate open reading frames in the Bacillus anthracis virulence plasmid pXO1: in silico and in vitro screening. / Infect Immun 2002, 70:6817鈥?827.
64. St氓lhammar-Carlemalm, M, Waldemarsson, J, Johnsson, E, Areschoug, T, Lindahl, G (2007) Nonimmunodominant regions are effective as building blocks in a streptococcal fusion protein vaccine. Cell Host Microbe 2: pp. 427-434 CrossRef
65. Ito, H, Nakashima, T, So, T, Hirata, M, Inoue, M (2003) Immunodominance of conformation-dependent B-cell epitopes of protein antigens. Biochem Biophys Res Commun 308: pp. 770-776 CrossRef
66. Keyburn, AL, Boyce, JD, Vaz, P, Bannam, TL, Ford, ME, Parker, D, Rubbo, A, Rood, JI, Moore, RJ (2008) NetB, a new toxin that is associated with avian necrotic enteritis caused by Clostridium perfringens. PLoS Pathog 2: pp. e26 CrossRef
67. Gileadi, O, Burgess-Brown, NA, Colebrook, SM, Berridge, G, Savitsky, P, Smee, CE, Loppnau, P, Johansson, C, Salah, E, Pantic, NH (2008) High throughput production of recombinant human proteins for crystallography. Methods Mol Biol 426: pp. 221-246 CrossRef
68. Vernet E, Kotzsch A, Voldborg B, Sundstr枚m M: Screening of genetic parameters for soluble protein expression in Escherichia coli . / Protein Expr Purif 2011, 77:104鈥?11.
69. Gasteiger, E, Hoogland, C, Gattiker, A, Duvaud, S, Wilkins, MR, Appel, RD, Bairoch, A Protein identification and analysis tools in the ExPASy server. In: Walker, JM eds. (2005) The Proteomics Protocols Handbook. Humana Press, Totowa, NJ, pp. 571-607 CrossRef - 刊物主题：Veterinary Medicine;
- 出版者：BioMed Central
- ISSN：1297-9716
文摘
The Gram-negative bacterium Gallibacterium anatis is a major cause of salpingitis and peritonitis in commercial egg-layers, leading to reduced egg production and increased mortality. Unfortunately, widespread multidrug resistance and antigenic diversity makes it difficult to control infections and novel prevention strategies are urgently needed. In this study, a pan-genomic reverse vaccinology (RV) approach was used to identify potential vaccine candidates. Firstly, the genomes of 10 selected Gallibacterium strains were analyzed and proteins selected on the following criteria; predicted surface-exposure or secretion, none or one transmembrane helix (TMH), and presence in six or more of the 10 genomes. In total, 42 proteins were selected. The genes encoding 27 of these proteins were successfully cloned in Escherichia coli and the proteins expressed and purified. To reduce the number of vaccine candidates for in vivo testing, each of the purified recombinant proteins was screened by ELISA for their ability to elicit a significant serological response with serum from chickens that had been infected with G. anatis. Additionally, an in silico prediction of the protective potential was carried out based on a protein property prediction method. Of the 27 proteins, two novel putative immunogens were identified; Gab_1309 and Gab_2312. Moreover, three previously characterized virulence factors; GtxA, FlfA and Gab_2156, were identified. Thus, by combining the pan-genomic RV approach with subsequent in vitro and in silico screening, we have narrowed down the pan-proteome of G. anatis to five vaccine candidates. Importantly, preliminary immunization trials indicated an in vivo protective potential of GtxA-N, FlfA and Gab_1309.