Precise detection of L. monocytogenes hitting its highly conserved region possessing several specific antibody binding sites

Journal of Theoretical Biology

Volumn 305, Issue , 2012, Pages 15-23

  Jahangiri, Abolfazl ^a   Rasooli, Iraj ^a   Reza Rahbar, Mohammad ^b   Khalili, Saeed ^c   Amani, Jafar ^d   Ahmadi Zanoos, Kobra ^a  

^a SHAHED UNIVERSITY   (Iran)

^b Molecular Biology Department   (Iran)

^c TARBIAT MODARES UNIVERSITY   (Iran)

^d BAQIYATALLAH UNIVERSITY OF MEDICAL SCIENCES   (Iran)

Author keywords

ActA; B cell epitope; Bioinformatics; Diagnostic test; In silico

Indexed keywords

MEMBRANE PROTEIN; PROTEIN ACTA; UNCLASSIFIED DRUG;

ANTIBODY; ANTIGEN; BIOINFORMATICS; DETECTION METHOD; IMMUNOASSAY; MEMBRANE; PATHOGEN; PROTEIN; TESTING METHOD; VIRULENCE;

ACCURACY; ANTIBODY COMBINING SITE; ANTIBODY SPECIFICITY; ANTIGEN ANTIBODY COMPLEX; ANTIGEN SPECIFICITY; ARTICLE; BACTERIUM DETECTION; BIOINFORMATICS; COMPUTER PROGRAM; CONTROLLED STUDY; DATA BASE; DIAGNOSTIC TEST; DIAGNOSTIC TEST ACCURACY STUDY; LISTERIA MONOCYTOGENES; ONLINE SYSTEM; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BACTERIAL TYPING TECHNIQUES; BINDING SITES, ANTIBODY; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; EPITOPES, B-LYMPHOCYTE; HUMANS; LISTERIA MONOCYTOGENES; LISTERIOSIS; MEMBRANE PROTEINS; MOLECULAR SEQUENCE DATA; SEQUENCE ALIGNMENT;

LISTERIA; LISTERIA MONOCYTOGENES; POSIBACTERIA;

EID: 84859931126     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2012.04.010     Document Type: Article

References (71)

1. Aagaard C., Govaerts M., Meng Okkels L., Andersen P., Pollock J.M. Genomic approach to identification of Mycobacterium bovis diagnostic antigens in cattle. J. Clin. Microbiol. 2003, 41:3719.
2. Alvarez-Dominguez C., Vazquez-Boland J., Carrasco-Marin E., Lopez-Mato P., Leyva-Cobian F. Host cell heparan sulfate proteoglycans mediate attachment and entry of Listeria monocytogenes, and the listerial surface protein ActA is involved in heparan sulfate receptor recognition. Infect. Immun. 1997, 65:78.
3. Amani J., Mousavi S.L., Rafati S., Salmanian A.H. Theoretical Biology and Medical Modelling. Theor. Biol. Med.Model. 2009, 6:28.
4. Bannantine J.P., Baechler E., Zhang Q., Li L.L., Kapur V. Genome scale comparison of Mycobacterium avium subsp. paratuberculosis with Mycobacterium avium subsp. avium reveals potential diagnostic sequences. J. Clin. Microbiol. 2002, 40:1303.
5. Bernsel A., Viklund H., Hennerdal A., Elofsson A. TOPCONS: consensus prediction of membrane protein topology. Nucleic Acids Res. 2009, 37:W465-W468.
6. Brundage R., Smith G., Camilli A., Theriot J., Portnoy D. Expression and phosphorylation of the Listeria monocytogenes ActA protein in mammalian cells. Proc. Nat. Acad. Sci. USA 1993, 90:11890.
7. Cai H., Tian S., Dong H. Large Scale In Silico Identification of MYB Family Genes from Wheat Expressed Sequence Tags. Mol. Biotechnol. 2011, 1-9.
8. Chong R., Swiss R., Briones G., Stone K., Gulcicek E., Agaisse H. Regulatory mimicry in Listeria monocytogenes actin-based motility. Cell Host Microbe 2009, 6:268-278.
9. Chou P., Fasman G. Prediction of the secondary structure of proteins from their amino acid sequence. Adv Enzymol. Relat. Areas Mol. Biol. 1978, 47:45.
10. Clermont G., Bartels J., Kumar R., Constantine G., Vodovotz Y., Chow C. In silico design of clinical trials: a method coming of age. Crit. Care Med. 2004, 32:2061.
11. Cossart P., Lecuit M. Interactions of Listeria monocytogenes with mammalian cells during entry and actin-based movement: bacterial factors, cellular ligands and signaling. EMBO J. 1998, 17:3797-3806.
12. Cossart P., Portnoy D. The cell biology of invasion and intracellular growth by Listeria monocytogenes. Gram-Positive Pathogens 2000, 507-513.
13. Czuprynski C. Listeria monocytogenes: silage, sandwiches and science. Anim. Health Res. Rev. 2005, 6:211-217.
14. Darji A., Bruder D., zur Lage S., Gerstel B., Chakraborty T., Wehland J., Weiss S. The role of the bacterial membrane protein ActA in immunity and protection against Listeria monocytogenes. J. Immunol. 1998, 161:2414.
15. Davies M.N., Flower D.R. Harnessing bioinformatics to discover new vaccines. Drug Discov Today 2007, 12:389-395.
16. Davis G.D., Elisee C., Newham D.M., Harrison R.G. New fusion protein systems designed to give soluble expression in Escherichia coli. Biotechnol. Bioeng. 1999, 65:382-388.
17. De Groot A.S., Bosma A., Chinai N., Frost J., Jesdale B.M., Gonzalez M.A., Martin W., Saint-Aubin C. From genome to vaccine: in silico predictions, ex vivo verification. Vaccine 2001, 19:4385-4395.
18. Doytchinova I., Flower D. VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC bioinformatics 2007, 8:4.
19. Emini E., Hughes J., Perlow D., Boger J. Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide. J. Virol. 1985, 55:836.
20. Fattahian Y., Rasooli I., Mousavi Gargari S.L., Rahbar M.R., Darvish Alipour Astaneh S., Amani J. Protection against Acinetobacter baumannii infection via its functional deprivation of biofilm associated protein (Bap). Microb. Pathog. 2011.
21. Garnier J., Gibrat J.F., Robson B. GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol 1996, 266:540-553.
22. Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., Appel R.D., Bairoch A. Protein identification and analysis tools on the ExPASy server. The Proteomics Protocols Handbook 2005, pp. 571-607.
23. Granseth E., Viklund H., Elofsson A. ZPRED: Predicting the distance to the membrane center for residues in α-helical membrane proteins. Bioinformatics 2006, 22:e191-e196.
24. Graves L.M., Hunter S.B., Ong A.R., Schoonmaker-Bopp D., Hise K., Kornstein L., DeWitt W.E., Hayes P.S., Dunne E., Mead P. Microbiological aspects of the investigation that traced the 1998 outbreak of listeriosis in the United States to contaminated hot dogs and establishment of molecular subtyping-based surveillance for Listeria monocytogenes in the PulseNet network. J. Clin. Microbiol. 2005, 43:2350.
25. Harrison R.G. Expression of soluble heterologous Proteins via fusion with NusA protein. Innovation 2000, 11:4-7.
26. Hofmann, K., Baron, M., 1996. Boxshade 3.21. Pretty printing and shading of multiple-alignment files. Kay Hofmann ISREC Bioinformatics Group. Lausanne, Switzerland.
27. Jahangiri A., Rasooli I., Gargari S.L.M., Owlia P., Rahbar M.R., Amani J., Khalili S. An in silico DNA vaccine against Listeria monocytogenes. Vaccine 2011, 6948-6958.
28. Junier T., Pagni M. Dotlet: diagonal plots in a web browser. Bioinformatics 2000, 16:178.
29. Karplus P., Schulz G. Prediction of chain flexibility in proteins. Naturwissenschaften 1985, 72:212-213.
30. Kemp D., Coppel R., Anders R. Repetitive proteins and genes of malaria. Annu. Rev. Microbiol. 1987, 41. 181-181.
31. Korber B., LaBute M., Yusim K. Immunoinformatics comes of age. PloS Comput. Biol. 2006, 2:e71.
32. Larsen J.E.P., Lund O., Nielsen M. Improved method for predicting linear B-cell epitopes. Immunome Res. 2006, 2:2.
33. Le Monnier A., Autret N., Join-Lambert O., Jaubert F., Charbit A., Berche P., Kayal S. ActA is required for crossing of the fetoplacental barrier by Listeria monocytogenes. Infect. Immun. 2007, 75:950.
34. Leerkes M.R., Caballero O.L., Mackay A., Torloni H., O'Hare M.J., Simpson A.J.G., de Souza S.J. In silico comparison of the transcriptome derived from purified normal breast cells and breast tumor cell lines reveals candidate upregulated genes in breast tumor cells. Genomics 2002, 79:257-265.
35. Leong M., Hampl J., Liu W., Mathur S., Bahjat K., Luckett W., Dubensky T., Brockstedt D. Impact of preexisting vector-specific immunity on vaccine potency: characterization of listeria monocytogenes-specific humoral and cellular immunity in humans and modeling studies using recombinant vaccines in mice. Infect Immun. 2009, 77:3958.
36. Levitt M. Conformational preferences of amino acids in globular proteins. Biochemistry 1978, 17:4277-4285.
37. Notredame C., Higgins D.G., Heringa J. T-coffee: a novel method for fast and accurate multiple sequence alignment1. J. Mol. Biol. 2000, 302:205-217.
38. Olfa, F.G., Radhouane, G., Abir, Z., Boutheina, G., Jalel, G., Ahmed, R., Adnene, H.. Evaluation of an in silico predicted specific and immunogenic antigen from the OmcB protein for the serodiagnosis of Chlamydia trachomatis infections. BMC Microbiol. 8.
39. Paillard D., Dubois V., Duran R., Nathier F., Guittet C., Caumette P., Quentin C. Rapid identification of Listeria species by using restriction fragment length polymorphism of PCR-amplified 23S rRNA gene fragments. Appl. Environ. Microbiol. 2003, 69:6386-6392.
40. Parker J., Guo D., Hodges R. New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites. Biochemistry 1986, 25:5425-5432.
41. Petersen T.N., Brunak S., von Heijne G., Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods 2011, 8:785-786.
42. Portnoy D., Auerbuch V., Glomski I. The cell biology of Listeria monocytogenes infection: the intersection of bacterial pathogenesis and cell-mediated immunity. J. Cell Biol. 2002, 158:409.
43. Poussin M., Goldfine H. Evidence for the involvement of ActA in maturation of the Listeria monocytogenes phagosome. Cell Res. 2009, 20:109-112.
44. Rafelski S., Theriot J. Mechanism of polarization of Listeria monocytogenes surface protein ActA. Mol. Microbiol. 2006, 59:1262-1279.
45. Rahbar M.R., Rasooli I., Mousavi Gargari S.L., Amani J., Fattahian Y. In silico analysis of antibody triggering biofilm associated protein in Acinetobacter baumannii. J. Theor. Biol. 2010, 266:275-290.
46. Rahbar, M.R., Rasooli, I., Gargari, S.L.M., Sandstrom, G., Amani, J., Fattahian, Y., Jahangiri, A., and Jalali, M., 2011. A potential in silico antibody-antigen based diagnostic test for precise identification of 〈i〉 Acinetobacter baumannii〈/i〉. J. Theor. Biol.
47. Reeder J., Brown G. Antigenic variation and immune evasion in Plasmodium falciparum malaria. Immunol. Cell Biol. 1996, 74:546-554.
48. Reza Rahbar M., Rasooli I., Mousavi Gargari S., Amani J., Fattahian Y. In silico analysis of antibody triggering biofilm associated protein in Acinetobacter baumannii. J. Theor. Biol. 2010.
49. Romero S., Van Nhieu G. A bacterial virulence factor that dissipates tension. Nat Cell Biol 2009, 11:1174-1175.
50. Roukos D.H. Personalized cancer diagnostics and therapeutics. Expert Rev. Mol. Diagn. 2009, 9:227-229.
51. Saha S., Raghava G. Prediction of continuous B cell epitopes in an antigen using recurrent neural network. Proteins: Struct., Funct., Bioinf. 2006, 65:40-48.
52. Shukla S., Dixit S. In Silico Identification of Drug Targets for Antifertility from Natural Products by Differential Reaction Content Analysis of Metabolic Pathways. Malays. J. Med. Sci.: MJMS 2011, 18:13.
53. Skeiky Y., Benson D., Elwasila M., Badaro R., Burns J., Reed S. Antigens shared by Leishmania species and Trypanosoma cruzi: immunological comparison of the acidic ribosomal P0 proteins. Infect. Immun. 1994, 62:1643.
54. Smith G., Theriot J., Portnoy D. The tandem repeat domain in the Listeria monocytogenes ActA protein controls the rate of actin-based motility, the percentage of moving bacteria, and the localization of vasodilator-stimulated phosphoprotein and profilin. J. Cell Biol. 1996, 135:647.
55. Suárez M., González Zorn B., Vega Y., Chico Calero I., Vázquez Boland J. A role for ActA in epithelial cell invasion by Listeria monocytogenes. Cell Microbiol. 2001, 3:853-864.
56. Sweredoski M.J., Baldi P. COBEpro: a novel system for predicting continuous B-cell epitopes. Protein Eng. Des. Select. 2009, 22:113-120.
57. Szklarczyk D., Franceschini A., Kuhn M., Simonovic M., Roth A., Minguez P., Doerks T., Stark M., Muller J., Bork P. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 2011, 39:D561.
58. Tomás-Roca L., Pérez-Aytés A., Puelles L., Marín F. In silico identification of new candidate genes for hereditary congenital facial paresis. Int. J. Dev. Neurosci. 2011.
59. Vazquez-Boland J., Kuhn M., Berche P., Chakraborty T., Dominguez-Bernal G., Goebel W., Gonzalez-Zorn B., Wehland J., Kreft J. Listeria pathogenesis and molecular virulence determinants. Clin. Microbiol. Rev. 2001, 14:584.
60. Vazquez-Boland J.A., Kuhn M., Berche P., Chakraborty T., Dominguez-Bernal G., Goebel W., Gonzalez-Zorn B., Wehland J., Kreft J. Listeria pathogenesis and molecular virulence determinants. Clin. Microbiol. Rev. 2001, 14:584.
61. Viklund H., Elofsson A. Best α-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. Prot Sci. 2004, 13:1908-1917.
62. Viklund H., Elofsson A. OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar. Bioinformatics 2008, 24:1662-1668.
63. Volokhov D., Rasooly A., Chumakov K., Chizhikov V. Identification of Listeria species by microarray-based assay. J. Clin. Microbiol. 2002, 40:4720.
64. Watson R. Listeriosis remains a cause for concern in Europe. BMJ 2009, 338.
65. Wilkinson D.L., Harrison R.G. Predicting the solubility of recombinant Proteins in Escherichia coli. Bio/technology 1991, 9. Nature Publishing Company, pp. 443-448.
66. Yoshikawa Y., Ogawa M., Hain T., Chakraborty T., Sasakawa C. Listeria monocytogenes ActA is a key player in evading autophagic recognition. Autophagy 2009, 5.
67. Yoshikawa Y., Ogawa M., Hain T., Yoshida M., Fukumatsu M., Kim M., Mimuro H., Nakagawa I., Yanagawa T., Ishii T. Listeria monocytogenes ActA-mediated escape from autophagic recognition. Nat. Cell Biol. 2009, 11:1233-1240.
68. Yu K.Y., Noh Y., Chung M., Park H.J., Lee N., Youn M., Jung B.Y., Youn B.S. Use of monoclonal antibodies that recognize p60 for identification of Listeria monocytogenes. Clin. Vaccine Immunol. 2004, 11:446.
69. Zenewicz L., Shen H. Innate and adaptive immune responses to Listeria monocytogenes: a short overview. Microb. Infect. 2007, 9:1208-1215.
70. Zhang T., Xin R., Zhang Q., Bao Y., Wu J. Characterization of intertype specific epitopes on adenoviruses hexon. Zhonghua shi yan he lin chuang bing du xue za zhi= Zhonghua shiyan he linchuang bingduxue zazhi= Chinese. J. Exp. Clin. Virol. 2002, 16:44.
71. Zhou Y., Landweber L.F. BLASTO: a tool for searching orthologous groups. Nucleic Acids Res. 2007, 35:W678-W682.