ISSN 2410-7751 (Print)
ISSN 2410-776X (Online)
"Biotechnologia Acta" v. 7, no 6, 2014
Р. 9-16, Bibliography 32, Ukrainian
Universal Decimal classification: 571.27:004.9
https://doi.org/10.15407/biotech7.06.009
In silico DETERMINATION OF T-EPITOPES OF Mycobacterium tuberculosis PROTEINS
O. I. Krynina, D. V. Kolibo, S. V. Komisarenko
Palladian Institute of Biochemistry of the National Academy of Sciences of Ukraine, Kyiv
The comparative analysis of 8 antigens of Mycobacterium tuberculosis (MPT83, MPT63, ESAT-6, CFP10, SodA, leuD, panD and HBHA) in silico to determine T-epitopes that can bind MHC class II molecules coding the most common in Eastern Europe HLA-DRB1 alleles was the goal of the work.
The results show that the most immunogenic proteins are SodA, MPT83, leuD and MPT63, which has the largest number of T-epitopes for the alleles of interest. Accordingly, these antigens or their combinations could be promising candidates for development of new vaccines and diagnostics to form anti-TB immunity in Eastern European region and to determine the state of protection of the population.
Key words: Mycobacterium tuberculosis, T-epitope.
© Palladin Institute of Biochemistry of the National Academy of Sciences of Ukraine, 2014
References
1. World Health Organization. Global tuberculosis report 2013. Available at: http://www.who.int/tb/publications/global_report/en/.
2. Yang X., Yu X. An introduction to epitope prediction methods and software. Rev. Med. Virol. 2009, 19 (2), 77–96.
http://dx.doi.org/10.1002/rmv.602
3. Orme I. M., Cooper A. M. Cytokine/chemokine cascades in immunity to tuberculosis. Immunol. Today. 1999, 20 (7), 307–312.
http://dx.doi.org/10.1016/S0167-5699(98)01438-8
4. Lin H. H., Zhang G. L., Tongchusak S., Reinherz E. L., Brusic V. Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research. BMC Bioinformatics. 2008, 9 (12). doi: 10.1186/ 1471-2105-9-S12-S22.
5. Wang P., Sidney J., Dow C., Moth? B., Sette A., Peters B. A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach. PLoS Comput. Biol. 2008, 4 (4).
http://dx.doi.org/10.1371/journal.pcbi.1000048
6. Xiang Z., Todd T., Ku K. P. Kovacic B. L., Larson C. B., Chen F., Hodges A. P., Tian Y., Olenzek E. A., Zhao B., Colby L. A., Rush H. G., Gilsdorf J. R., Jourdian G. W., He Y. VIOLIN: vaccine investigation and online information network. Nucleic Acids Res. 2008, 36 (Database issue), 923–928.
7. Vaccine Investigation and Online Information Network (VIOLIN) Statistics. Available at: http://www.violinet.org/stat.php.
8. Gonzalez-Galarza F. F., Christmas S., Middleton D., Jones A. R. Allele frequency net: database and online repository for immune gene frequencies in worldwide populations. Nucleic Acid Research. 2011, 39 (Database issue), 913–919.
http://dx.doi.org/10.1093/nar/gkq1128
9. Singh H., Raghava G. P. S. ProPred: Prediction of HLA-DR binding sites. Bioinformatics. 2001, 17 (12), 1236–1237.
http://dx.doi.org/10.1093/bioinformatics/17.12.1236
10. Reche P. A. Glutting J. P., Reinherz E. L. Prediction of MHC class I binding peptides using profile motifs. Human Immunolog. 200, 63 (9), 701–709.
11. Nielsen M., Justesen S., Lund O., Lundegaard C., Buus S. NetMHCIIpan-2.0 — Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure. Immun. Res. 2010, 6 (9), 1–10.
http://dx.doi.org/10.1186/1745-7580-6-9
12. Kim Y., Ponomarenko J., Zhu Z. Tamang D., Wang P., Greenbaum J., Lundegaard C., Sette A., Lund O., Bourne P. E., Nielsen M., Peters B. Immune epitope database analysis resource. Nucl. Acids Res. 2012, 40 (Database issue), 525–530.
http://dx.doi.org/10.1093/nar/gks438
13. Juarez M. D., Torres A., Espitia C. Characterization of the Mycobacterium tuberculosis region containing the mpt83 and mpt70 genes. FEMS Microbiol Lett. 2001, 203 (1), 95–102.
http://dx.doi.org/10.1111/j.1574-6968.2001.tb10826.x
14. Menozzi F. D., Bischoff R., Fort E., Brennan M. J., Locht C. Molecular characterization of the mycobacterial heparin-binding hemagglutinin, a mycobacterial adhesion. Proc. Natl. Acad. Sci. 1998, 95 (21), 12625–12630.
http://dx.doi.org/10.1073/pnas.95.21.12625
15. Manca C., Lyashchenko K., Wiker H. G., Usai D., Colangeli R., Gennaro M. L. Molecular cloning, purification, and serological characterization of MPT63, a novel antigen secreted by Mycobacterium tuberculosis. Infect. Immun. 1997, 65 (1), 16–23.
16. Shams H., Klucar P., Weis S. E., Lalvani A., Moonan P. K., Safi H., Wizel B., Ewer K., Nepom G. T., Lewinsohn D. M., Andersen P., Barnes P. F. Characterzation of Mycobacterium tuberculosis peptide that is recognized by human CD4+ and CD8+ T cells in the context of multiple HLA alleles. J. Immunol. 2004, 173 (3), 1966–1977.
http://dx.doi.org/10.4049/jimmunol.173.3.1966
17. Tully G., Kortsik C., Hohn H., Zehbe I., Hitzler W. E., Neukirch C., Freitag K., Kayser K., Maeurer M. J. Highly focused T cell responses in latent human pulmonary Mycobacterium tuberculosis infection. J. Immunol. 2005, 174 (4), 2174–2184.
http://dx.doi.org/10.4049/jimmunol.174.4.2174
18. Stewart G. R., Wernisch L., Stabler R., Mangan J. A., Hinds J., Laing K. G., Young D. B., Butcher P. D. Dissection of the heat-shock response in Mycobacterium tuberculosis using mutants and microarrays. Microbiology. 2002, 148 (10), 3129–3138.
19. Gopalan G., Chopra S., Ranganathan A., Swaminathan K. Crystal structure of uncleaved L-aspartate-alpha-decarboxylase from Mycobacterium tuberculosis. Proteins. 2006, 65 (4), 796–802.
http://dx.doi.org/10.1002/prot.21126
20. Kumar M. L., Khan F. G., Sharma S., Kumar R., Faujdar J., Sharma R., Chauhan D. S., Singh R., Magotra S. K., Khan I. A. Identification of Mycobacterium tuberculosis genes preferentially expressed during human infection. Microb Pathog. 2011, 50 (1), 31–38.
http://dx.doi.org/10.1016/j.micpath.2010.10.003
21. Hondalus M. K., Bardarov S., Russell R., Chan J., Jacobs W. R. Jr., Bloom B. R. Attenuation of and protection induced by a leucine auxotroph of Mycobacterium tuberculosis. Infect Immun. 2000, 68 (5), 2888–2898.
http://dx.doi.org/10.1128/IAI.68.5.2888-2898.2000
22. Sambandamurthy V. K., Wang X., Chen B., Russell R. G., Derrick S., Collins F. M., Morris S. L., Jacobs W. R. Jr. A pantothenate auxotroph of Mycobacterium tuberculosis is highly attenuated and protects mice against tuberculosis. Nath. Med. 2002, 8 (10), 1171–1174.
http://dx.doi.org/10.1038/nm765
23. Jain R., Dey B., Khera A., Srivastav P., Gupta U. D., Katoch V. M., Ramanathan V. D., Tyagi A. K. Overexpression of superoxide dismutase obliterates the protective effect of BCG against tuberculosis by modulating innate and adaptive immune responses. Vaccine. 2011, 29 (45), 8118–8125.
http://dx.doi.org/10.1016/j.vaccine.2011.08.029
24. Liao D., Fan Q., Bao L. The role of superoxide dismutase in the survival of Mycobacterium tuberculosis in macrophages. Jpn. J. Infect. Dis. 2013, 66 (6), 480–488.
http://dx.doi.org/10.7883/yoken.66.480
25. Edwards K. M., Cynamon M. H., Voladri R. K., Hager C. C., DeStefano M. S., Tham K. T., Lakey D. L., Bochan M. R., Kernodle D. S. Iron-cofactored superoxide dismutase inhibits host responses to Mycobacterium tuberculosis. Am. J. Resp. Crit. Care Med. 2001, 164 (12), 2213–2219.
http://dx.doi.org/10.1164/ajrccm.164.12.2106093
26. Nagai S., Wiker H. G., Harboe M., Kinomoto M. Isolation and partial characterization of major protein antigens in the culture fluid of Mycobacterium tuberculosis. Infect. Immun. 1991, 59 (1), 372–382.
27. Mustafa A. S. Th1 cell reactivity and HLA-DR binding prediction for promiscuous recognition of MPT63 (Rv1926c), a major secreted protein of Mycobacterium tuberculosis. Scand. J. Immunol. 2009, 69 (32), 13–22.
28. Berthet F. X., Ramussen P. B., Rosenkrands I., Andersen P., Gicquel B. A Mycobacterium tuberculosis operon encoding ESAT-6 and a novel low-molecular-mass culture filtrate protein (CFP-10). Microbiology. 1998, V. 144, P. 3195–3203.
http://dx.doi.org/10.1099/00221287-144-11-3195
29. Wang X., Barnes P. F., Dobos-Elder R. M., Townsend J. C., Chung Y. T., Shams H., Weis S. E., Samten B. ESAT-6 inhibits production of IFN?? by Mycobacterium tuberculosis-responsive human T cells. J. Immunol. 2009, 182 (6), 3668–3677.
http://dx.doi.org/10.4049/jimmunol.0803579
30. Mustafa A. S. Comparative evaluation of MPT83 (Rv2873) for T helper-1 cell reactivity and identification of HLA-promiscuous peptides in Mycobacterium bovis BCG-vaccinated healthy subjects. Clin. Vaccine Immunol. 2011, 1752–1759.
http://dx.doi.org/10.1128/CVI.05260-11
31. Menozzi F. D., Rouse J. H., Alavi M., Laude-Sharp M., Muller J., Bischoff R., Brennan M. J., Locht C. Identification of a heparin-binding hemagglutinin present in mycobacteria. J. Exp. Med. 1996, 184 (3), 993–1001.
http://dx.doi.org/10.1084/jem.184.3.993
32. Krishnan N., Robertson B. D., Thwaites G. The mechanisms and consequences of the extra-pulmonary dissemination of Mycobacterium tuberculosis. Tuberculosis (Edinb). 2010, 90 (6), 361–366.
http://dx.doi.org/10.1016/j.tube.2010.08.005