Identification of putative vaccine candidates against Helicobacter pylori exploiting exoproteome and secretome: A reverse vaccinology based approach

Infection, Genetics and Evolution

Volumn 32, Issue , 2015, Pages 280-291

  Naz, Anam ^a   Awan, Faryal Mehwish ^a   Obaid, Ayesha ^a   Muhammad, Syed Aun ^b   Paracha, Rehan Zafar ^a   Ahmad, Jamil ^a   Ali, Amjad ^a  

^a NATIONAL UNIVERSITY OF SCIENCES AND TECHNOLOGY   (Pakistan)

^b BAHAUDDIN ZAKARIYA UNIVERSITY   (Pakistan)

Author keywords

Antigenic epitopes; H. pylori; Reverse vaccinology; Vaccine candidates; Vaccine development

Indexed keywords

BABA PROTEIN; BACTERIAL PROTEIN; EPITOPE; EXOPROTEOME; FECA PROTEIN; PEPTIDES AND PROTEINS; PROTEIN OMP16; PROTEOME; SABA PROTEIN; SECRETOME; UNCLASSIFIED DRUG; VACUOLATING TOXIN; ADHESIN; BABA PROTEIN, HELICOBACTER PYLORI; BACTERIAL VACCINE; SABA PROTEIN, HELICOBACTER PYLORI; VACA PROTEIN, HELICOBACTER PYLORI;

ARTICLE; BACTERIAL GENOME; BACTERIAL VIRULENCE; CELLULAR DISTRIBUTION; CONTROLLED STUDY; DRUG TARGETING; EPITOPE MAPPING; GENETIC VARIABILITY; HELICOBACTER PYLORI; HOST PATHOGEN INTERACTION; IMMUNOGENICITY; PRIORITY JOURNAL; PROTEIN ANALYSIS; SIGNAL TRANSDUCTION; AMINO ACID SEQUENCE; B LYMPHOCYTE; CHROMOSOMAL MAPPING; GENETIC VARIATION; GENETICS; HELICOBACTER INFECTIONS; HUMAN; HUMAN GENOME; IMMUNOLOGY; MOLECULAR GENETICS; MOLECULAR WEIGHT; MULTIGENE FAMILY; PROTEIN PROTEIN INTERACTION; PROTEIN TERTIARY STRUCTURE; PROTEOMICS; REPRODUCIBILITY; T LYMPHOCYTE;

HELICOBACTER PYLORI;

ADHESINS, BACTERIAL; AMINO ACID SEQUENCE; B-LYMPHOCYTES; BACTERIAL PROTEINS; BACTERIAL VACCINES; CHROMOSOME MAPPING; EPITOPE MAPPING; EPITOPES; GENETIC VARIATION; GENOME, BACTERIAL; GENOME, HUMAN; HELICOBACTER INFECTIONS; HELICOBACTER PYLORI; HOST-PATHOGEN INTERACTIONS; HUMANS; MOLECULAR SEQUENCE DATA; MOLECULAR WEIGHT; MULTIGENE FAMILY; PROTEIN INTERACTION MAPS; PROTEIN STRUCTURE, TERTIARY; PROTEOMICS; REPRODUCIBILITY OF RESULTS; T-LYMPHOCYTES;

EID: 84926154115     PISSN: 15671348     EISSN: 15677257     Source Type: Journal    
DOI: 10.1016/j.meegid.2015.03.027     Document Type: Article

References (58)

1. Adu-Bobie J., et al. Two years into reverse vaccinology. Vaccine 2003, 21(7):605-610.
2. Alfizah H., et al. Helicobacter pylori: molecular detection of vacA gene and vacuolating activity in human gastric adenocarcinoma cells. ClinTer 2013, 164(4):301-305.
3. Ali A., et al. Pan-genome analysis of human gastric pathogen H. pylori: comparative genomics and pathogenomics approaches to identify regions associated with pathogenicity and prediction of potential core therapeutic targets. population 2014, 5:6.
4. Atherton J.C., et al. Mosaicism in vacuolating cytotoxin alleles of Helicobacter pylori association of specific vacA types with cytotoxin production and peptic ulceration. J. Biol. Chem. 1995, 270(30):17771-17777.
5. Bambini S., Rappuoli R. The use of genomics in microbial vaccine development. Drug Discov. Today 2009, 14(5):252-260.
6. Barh D., et al. A novel strategy of epitope design in Neisseria gonorrhoeae. Bioinformation 2010, 5(2):77.
7. Barh D., et al. In silico subtractive genomics for target identification in human bacterial pathogens. Drug Dev. Res. 2011, 72(2):162-177.
8. Barh D., et al. Exoproteome and secretome derived broad spectrum novel drug and vaccine candidates in Vibrio cholerae targeted by Piper betel derived compounds. PLoS One 2013, 8(1):e52773.
9. Benson D.A., et al. GenBank. Nucleic Acids Res. 2012, gks1195.
10. Bernstein F.C., et al. The protein data bank. Eur. J. Biochem. 1977, 80(2):319-324.
11. Cavaleiro-Pinto M., et al. Helicobacter pylori infection and gastric cardia cancer: systematic review and meta-analysis. Cancer Causes Control 2011, 22(3):375-387.
12. Chen L., et al. VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res. 2011, gkr989.
13. Doytchinova I.A., Flower D.R. VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinform. 2007, 8(1):4.
14. El-Manzalawy, Y., Dobbs, D., Honovar, V., BCPREDS: B-cell epitope prediction server. Artificial Intelligence Research Laboratory, Department of Computer Science, Iowa State University of Science and Technology. Available (accessed August, 2012). http://ailab.%20cs.%20iastate.%20edu/bcpreds/.
15. Gardy J.L., et al. PSORTb v. 2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics 2005, 21(5):617-623.
16. Garg A., Gupta D. VirulentPred: a SVM based prediction method for virulent proteins in bacterial pathogens. BMC Bioinform. 2008, 9(1):62.
17. Gasteiger, E., et al., 2005. Protein identification and analysis tools on the ExPASy server, in: The Proteomics Protocols Handbook. Springer, pp. 571-607.
18. Geels M.J., et al. European Vaccine Initiative: lessons from developing malaria vaccines. Expert Rev. Vaccines 2011.
19. Genç R., et al. The role of H. pylori in the development of laryngeal squamous cell carcinoma. Dis. Marker. 2013, 35(5):447-449.
20. Giuliani M.M., et al. A universal vaccine for serogroup B meningococcus. Proc. Natl. Acad. Sci. 2006, 103(29):10834-10839.
21. Guan P., et al. MHCPred: a server for quantitative prediction of peptide-MHC binding. Nucleic Acids Res. 2003, 31(13):3621-3624.
22. Kanehisa M., Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000, 28(1):27-30.
23. Kelley L.A., Sternberg M.J. Protein structure prediction on the Web: a case study using the Phyre server. Nat. Protoc. 2009, 4(3):363-371.
24. Krogh A., et al. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 2001, 305(3):567-580.
25. Leuzzi R., et al. Genome Mining and Reverse Vaccinology. Handbook of Meningococcal Disease: Infection Biology, Vaccination, Clinical Management 2006, 391-402. WILEY-VCH, Weinheim, Germany.
26. Luo H., et al. DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements. Nucleic Acids Res. 2014, 42(D1):D574-D580.
27. Mayrose I., et al. Pepitope: epitope mapping from affinity-selected peptides. Bioinformatics 2007, 23(23):3244-3246.
28. McClain M.S., et al. Genome sequence analysis of Helicobacter pylori strains associated with gastric ulceration and gastric cancer. BMC Genom. 2009, 10(1):3.
29. McColl K.E. Helicobacter pylori infection. N. Engl. J. Med. 2010, 362(17):1597-1604.
30. Michetti P. Vaccine against Helicobacter pylori: fact or fiction?. Gut 1997, 41(6):728-730.
31. Mora M., et al. Microbial genomes and vaccine design: refinements to the classical reverse vaccinology approach. Curr. Opin. Microbiol. 2006, 9(5):532-536.
32. Muhammad S.A., et al. Prioritizing drug targets in Clostridium botulinum with a computational systems biology approach. Genomics 2014.
33. Naumann M., Crabtree J.E. Helicobacter pylori-induced epithelial cell signalling in gastric carcinogenesis. Trends Microbiol. 2004, 12(1):29-36.
34. Neić D., et al. Helicobacter pylori CagA inhibits PAR1-MARK family kinases by mimicking host substrates. Nat. Struct. Mol. Biol. 2010, 17(1):130-132.
35. Pruitt K.D., Tatusova T., Maglott D.R. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2007, 35(Suppl. 1):D61-D65.
36. Ramaswamy V., et al. Listeria-review of epidemiology and pathogenesis. J. Microbiol. Immunol. Infect. 2007, 40(1):4.
37. Reid G., Howard J., Gan B.S. Can bacterial interference prevent infection?. Trends Microbiol. 2001, 9(9):424-428.
38. Ruggiero P., Censini S. Helicobacter pylori: a brief history of a still lacking vaccine. Diseases 2014, 2(2):187-208.
39. Saadat I., et al. Helicobacter pylori CagA targets PAR1/MARK kinase to disrupt epithelial cell polarity. Nature 2007, 447(7142):330-333.
40. Santos A., et al. The reverse vaccinology - a contextual overview. IIOABJ 2011, 2:8-15.
41. Sarangi A.N., et al. Subtractive genomics approach for in silico identification and characterization of novel drug targets in Neisseria meningitides Serogroup B. J. Comput. Sci. Syst. Biol. 2009, 2(5):255-258.
42. Serruto D., Rappuoli R. Post-genomic vaccine development. FEBS Lett. 2006, 580(12):2985-2992.
43. Shanmugham B., Pan A. Identification and characterization of potential therapeutic candidates in emerging human pathogen Mycobacterium abscessus: a novel hierarchical in silico approach. PLoS One 2013, 8(3):e59126.
44. Singh H., Raghava G. ProPred: prediction of HLA-DR binding sites. Bioinformatics 2001, 17(12):1236-1237.
45. Singh H., Raghava G. ProPred1: prediction of promiscuous MHC Class-I binding sites. Bioinformatics 2003, 19(8):1009-1014.
46. Szklarczyk D., et al. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 2011, 39(Suppl. 1):D561-D568.
47. Tamura K., et al. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 2013, 30(12):2725-2729.
48. Tatusov R.L., et al. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 2001, 29(1):22-28.
49. Tatusov R.L., et al. The COG database: an updated version includes eukaryotes. BMC Bioinform. 2003, 4(1):41.
50. Torres V.J., et al. Functional properties of the p33 and p55 domains of the Helicobacter pylori vacuolating cytotoxin. J. Biol. Chem. 2005, 280(22):21107-21114.
51. Tusnady G.E., Simon I. The HMMTOP transmembrane topology prediction server. Bioinformatics 2001, 17(9):849-850.
52. Vivona S., Bernante F., Filippini F. NERVE: new enhanced reverse vaccinology environment. BMC Biotechnol. 2006, 6(1):35.
53. Wattam A.R., et al. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res. 2013, gkt1099.
54. Workbench, C.G., v3. 6., 2010. Now new version can be available at . http://www.%20clcbio.%20com/products/clcgenomicsworkbench.
55. Yu C.S., Lin C.J., Hwang J.K. Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions. Protein Sci. 2004, 13(5):1402-1406.
56. Yu C.-S., et al. CELLO2GO: a web server for protein subcellular localization prediction with functional gene ontology annotation. PLoS One 2014, 9(6):e99368.
57. Yue W.W., Grizot S., Buchanan S.K. Structural evidence for iron-free citrate and ferric citrate binding to the TonB-dependent outer membrane transporter FecA. J. Mol. Biol. 2003, 332(2):353-368.
58. Zhou C., et al. MvirDB - a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications. Nucleic Acids Res. 2007, 35(Suppl. 1):D391-D394.