Generate QR code
Open Access
Subscription Access
OMICS TECHNOLOGIES IN THE STUDY OF BACILLUS ANTHRACIS
https://doi.org/10.17021/2020.15.2.13.23
Abstract
This review presents the results of a current study of the anthrax pathogen obtained using omics technologies. The main achievements in the field of genomics, proteomics, transcriptomics, interaсtomics, and metabolomics of Bacillus anthracis as a result of the use of omics technologies are described. The connection of the development of omics technologies and bioinformatics are discussed; further prospects and problems in this area are reflected.
About the Authors
G. A. Pechkovskiy
Stavropol Research Anti-Plague Institute
Russian Federation
Russian Federation
L. D. Timchenko
North-Caucasus Federal University
Russian Federation
Russian Federation
E. I. Eremenko
Stavropol Research Anti-Plague Institute
Russian Federation
Russian Federation
D. A. Kovalev
Stavropol Research Anti-Plague Institute
Russian Federation
Russian Federation
A. N. Kulichenko
Stavropol Research Anti-Plague Institute
Russian Federation
Russian Federation
References
1. Baggerman, G. Gel-based versus gel-free proteomics: a review / G. Baggerman, E. Vierstraete, A. De Loof, L. Schoofs // Combinatorial chemistry & high throughput screening. - 2005. - Vol. 8, № 8. - P. 669-677.
2. Bergman, N. H. Murine macrophage transcriptional responses to Bacillus anthracis infection and intoxication / N. H. Bergman, K. D. Passalacqua, R. Gaspard, L. M. Shetron-Rama, J. Quackenbush, P. C. Hanna // Infection and immunity. - 2005. - Vol. 73, № 2. - P. 1069-1080.
3. Bergman, N. H. Transcriptional profiling of Bacillus anthracis during infection of host macrophages / N. H. Bergman, E. C. Anderson, E. E. Swenson, B. K. Janes, N. Fisher, M. M. Niemeyer, A. D. Miyoshi, P. C. Hanna // Infection and immunity. - 2007. - Vol. 75, № 7. - P. 3434-3444.
4. Bergman, N. H. Transcriptional profiling of the Bacillus anthracis life cycle in vitro and an implied model for regulation of spore formation / N. H. Bergman, E. C. Anderson, E. E. Swenson, M. M. Niemeyer, A. D. Miyoshi, P. C. Hanna // Journal of bacteriology. - 2006. - Vol. 188, № 17. - P. 6092-6100.
5. Booth, J. L. Gene expression profiling of primary human type I alveolar epithelial cells exposed to Bacillus anthracis spores reveals induction of neutrophil and monocyte chemokines / J. L. Booth, E. S. Duggan, V. I. Patel, W. Wu, D. M. Burian, D. C. Hutchings, V. L. White, K. M. Coggeshall, M. G. Dozmorov, J. P. Metcalf // Microbial pathogenesis. - 2018. - Vol. 121. - P. 9-21.
6. Brown, P. O. Exploring the new world of the genome with DNA microarrays / P. O. Brown, D. Botstein // Nature genetics. - 1999. - Vol. 21, № 1. - P. 33-37.
7. Carlson, P. E. Jr. Global gene expression by Bacillus anthracis during growth in mammalian blood / P. E. Jr. Carlson, A. E. T. Bourgis, A. K. Hagan, P. C. Hanna // Pathogens and disease. - 2015. - Vol. 73, № 8. doi: 10.1093/femspd/ftv061.
8. Carlson, P. E. Jr. Transcriptional profiling of Bacillus anthracis Sterne (34F2) during iron starvation / P. E. Jr. Carlson, K. A. Carr, B. K. Janes, E. C. Anderson, P. C. Hanna // PLoS One. - 2009. - Vol. 4, № 9. - P. e 6988.
9. Chenau, J. Identification and validation of specific markers of Bacillus anthracis spores by proteomics and genomics approaches / J. Chenau, F. Fenaille, V. Caro, M. Haustant, L. Diancourt, S. R. Klee, C. Junot, E. Ezan, P. L. Goossens, F. Becher // Molecular & Cellular Proteomics. - 2014. - Vol. 13, № 3. - P. 716-732.
10. Chitlaru, T. Differential proteomic analysis of the Bacillus anthracis secretome: distinct plasmid and chromosome CO2-dependent cross talk mechanisms modulate extracellular proteolytic activities / T. Chitlaru, O. Gat, Y. Gozlan, N. Ariel, A. Shafferman // Journal of bacteriology. - 2006. - Vol. 188, № 10. - P. 3551-3571.
11. Chitlaru, T. Identification of in vivo-expressed immunogenic proteins by serological proteome analysis of the Bacillus anthracis secretome / T. Chitlaru, O. Gat, H. Grosfeld, I. Inbar, Y. Gozlan, A. Shafferman // Infection and immunity. - 2007. - Vol. 75, № 6. - P. 2841-2852.
12. Daligault, H. E. Twenty Whole-Genome Bacillus sp. Assemblies / H. E. Daligault, K. W. Davenport, T. D. Minogue, K. A. Bishop-Lilly, S. M. Broomall, D. C Bruce, P. S. Chain, S. R. Coyne, K. G. Frey, H. S. Gibbons, J. Jaissle, G. I. Koroleva, J. T. Ladner, C. C. Lo, C. Munk, G. F. Palacios, C. L. Redden, C. N. Rosenzweig, M. B. Scholz, S. L. Johnson // Genome Announc. - 2014. - Vol. 2, № 5. - P. e00958-14. doi: 10.1128/genomeA.00958-14.
13. Dozmorov, M. Gene expression profiling of human alveolar macrophages infected by B. anthracis spores demonstrates TNF-alpha and NF-kappab are key components of the innate immune response to the pathogen / M. Dozmorov, W. Wu, K. Chakrabarty, J. L. Booth, R. E. Hurst, K. M. Coggeshall, J. P. Metcalf // BMC infectious diseases. - 2009. - Vol. 9, № 1. - P. 152.
14. Dyer, M. D. The human-bacterial pathogen protein interaction networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis / M. D. Dyer, C Neff, M. Dufford, C. G. Rivera, D. Shattuck, J. Bassaganya-Riera, T. M. Murali, B. W. Sobral // PloS one. - 2010. - Vol. 5, № 8. - P. e 12089.doi: 10.1371/journal.pone.0012089.
15. Gohar, M. A comparative study of Bacillus cereus, Bacillus thuringiensis and Bacillus anthracis extracellular proteomes / M. Gohar, N. Gilois, R. Graveline, C. Garreau, V. Sanchis, D. Lereclus // Proteomics. - 2005. - Vol. 5, № 14. - P. 3696-3711.
16. Guidi-Rontani, C. The alveolar macrophage: The Trojan horse of Bacillus anthracis / C. Guidi-Rontani // Trends in microbiology. - 2002. - Vol. 10, № 9. - P. 405-409.
17. Helgason, E. Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis-one species on the basis of genetic evidence / E. Helgason, O. A. Okstad, D. A. Caugant, H. A. Johansen, A. Fouet, M. Mock, I. Hegna, A. B. Kolstø // Appl. Environ. Microbiol. - 2000. - Vol. 66, № 6. - P. 2627-2630.
18. Hoheisel, J. D. Microarray technology: beyond transcript profiling and genotype analysis / J. D. Hoheisel // Nature reviews genetics. - 2006. - Vol. 7, № 3. - P. 200-210.
19. Humphrey, S. J. Protein Phosphorylation: A Major Switch Mechanism for Metabolic Regulation / S. J. Humphrey, D. E. James, M. Mann // Trends in Endocrinology & Metabolism. - 2015. - Vol. 26, № 12. - P. 676-687.
20. Johnson, S. L. Complete genome sequences for 35 biothreat assay-relevant bacillus species / S. L. Johnson, H. E. Daligault, K. W. Davenport, J. Jaissle, K. G. Frey, J. T. Ladner, S. M. Broomall, K. A. Bishop-Lilly, D. C. Bruce, H. S. Gibbons, S. R. Coyne, C. C. Lo, L. Meincke, A. C. Munk, G. I. Koroleva, C. N. Rosenzweig, G. F. Palacios, C. L. Redden, T. D. Minogue, P. S. Chain // Genome Announc. - 2015. - Vol. 3, № 2. - P. e00151-15.doi: 10.1128/genomeA.00151-15.
21. Keim, P. Anthrax molecular epidemiology and forensics: using the appropriate marker for different evolutionary scales / P. Keim, M. N. Van Ert, T. Pearson, A. J. Vogler, L. Y. Huynh, D. M. Wagner // Infection, Genetics and Evolution. - 2004. - Vol. 4, № 3. - P. 205-213.
22. Keim, P. Molecular evolution and diversity in Bacillus anthracis as detected by amplified fragment length polymorphism markers / P. Keim, A. Kalif, J. Schupp, K. Hill, S. E. Travis, K. Richmond, D. M. Adair, M. Hugh-Jones, C. R. Kuske, P. Jackson // Journal of bacteriology. - 1997. - Vol. 179, № 3. - P. 818-824.
23. Keim, P. Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis / P. Keim, L. B. Price, A. M. Klevytska, K. L. Smith, J. M. Schupp, R. Okinaka, P. J. Jackson, M. E. Hugh-Jones // Journal of bacteriology. - 2000. - Vol. 182, № 10. - P. 2928-2936.
24. Lamonica, J. M. Comparative secretome analyses of three Bacillus anthracis strains with variant plasmid contents / J. M. Lamonica, M. Wagner, M. Eschenbrenner, L. E. Williams, T. L. Miller, G. Patra, V. G. DelVecchio // Infection and immunity. - 2005. - Vol. 73, № 6. - P. 3646-3658.
25. Langel, F. D. Alveolar macrophages infected with Ames or Sterne strain of Bacillus anthracis elicit differential molecular expression patterns / F. D. Langel, C. Y. Chiang, D. Lane, T. Kenny, J. F. Ojeda, Y. Zhong, J. Che, Y. Zhou, W. Ribot, K. P. Kota, S. Bavari, R. G. Panchal // PloS one. - 2014. - Vol. 9, № 2. - P. e 87201. doi: 10.1371/journal.pone.0087201.
26. Liu, H. Formation and composition of the Bacillus anthracis endospore / H. Liu, N. H. Bergman, B. Thomason, S. Shallom, A. Hazen, J. Crossno, D. A. Rasko, J. Ravel, T. D. Read, S. N. Peterson, J. 3rd Yates, P. C. Hanna // Journal of bacteriology. - 2004. - Vol. 186, № 1. - P. 164-178.
27. Manes, N. P. Discovery of mouse spleen signaling responses to anthrax using label-free quantitative phosphoproteomics via mass spectrometry / N. P. Manes, L Dong, W Zhou, X Du, N Reghu, A. C. Kool, D. Choi, C. L. Bailey, E. F. 3rd Petricoin, L. A. Liotta, S. G. Popov // Molecular & Cellular Proteomics. - 2011. - Vol. 10, № 3.doi: 10.1074/mcp.M110.000927.
28. Martin, J. Bacillus anthracis genome organization in light of whole transcriptome sequencing / J. Martin, W. Zhu, K. D. Passalacqua, N. Bergman, M. Borodovsky // BMC bioinformatics. - BioMed Central, 2010. - Vol. 11, № S3. - P. S10.doi: 10.1186/1471-2105-11-S3-S10.
29. Nguyen, C. T. Global metabolomic analysis of a mammalian host infected with Bacillus anthracis / C. T. Nguyen, V. Shetty, A. W. Maresso // Infection and immunity. - 2015. - Vol. 83, № 12. - P. 4811-4825.
30. Ogawa, H. A novel multiplex PCR discriminates Bacillus anthracis and its genetically related strains from other Bacillus cereus group species / H. Ogawa, D. Fujikura, M. Ohnuma, N. Ohnishi, B. M. Hang'ombe, H. Mimuro, T. Ezaki, A. S. Mweene, H. Higashi // PLoS One. - 2015. - Vol. 10, № 3. - P. e 0122004.doi: 10.1371/journal.pone.0122004.
31. Passalacqua, K. D. Comparative transcriptional profiling of Bacillus cereus sensu lato strains during growth in CO2-bicarbonate and aerobic atmospheres / K. D. Passalacqua, A. Varadarajan, B. Byrd, N. H. Bergman // PloS one. - 2009. - Vol. 4, № 3. - P. e 4904.doi: 10.1371/journal.pone.0004904.
32. Passalacqua, K. D. Strand-specific RNA-seq reveals ordered patterns of sense and antisense transcription in Bacillus anthracis / K. D. Passalacqua, A. Varadarajan, C. Weist, B. D. Ondov, B. Byrd, T. D. Read, N. H. Bergman // PLoS One. - 2012. - Vol. 7, № 8. - P. e 43350.doi: 10.1371/journal.pone.0043350.
33. Passalacqua, K. D. Structure and complexity of a bacterial transcriptome / K. D. Passalacqua, A. Varadarajan, B. D. Ondov, D. T. Okou, M. E. Zwick, N. H. Bergman// Journal of bacteriology. - 2009. - Vol. 191, № 10. - P. 3203-3211.
34. Passalacqua, K. D. The global transcriptional responses of Bacillus anthracis Sterne (34F2) and a ΔsodA1 mutant to paraquat reveal metal ion homeostasis imbalances during endogenous superoxide stress / K. D. Passalacqua, N. H. Bergman, J. Y. Lee, D. H. Sherman, P. C. Hanna // Journal of bacteriology. - 2007. - Vol. 189, № 11. - P. 3996-4013.
35. Pearson, T. Phylogenetic discovery bias in Bacillus anthracis using single-nucleotide polymorphisms from whole-genome sequencing / T. Pearson, J. D. Busch, J. Ravel, T. D. Read, S. D. Rhoton, J. M. U'Ren, T. S. Simonson, S. M. Kachur, R. R. Leadem, M. L. Cardon, M. N. Van Ert, L. Y. Huynh, C. M. Fraser, P. Keim // Proceedings of the National Academy of Sciences. - 2004. - Vol. 101, № 37. - P. 13536-13541.
36. Ravel, J. The complete genome sequence of Bacillus anthracis Ames “Ancestor” / J. Ravel, L. Jiang, S. T. Stanley, M. R. Wilson, R. S. Decker, T. D. Read, P. Worsham, P. S. Keim, S. L. Salzberg, C. M. Fraser-Liggett, D. A. Rasko // Journal of bacteriology. - 2009. - Vol. 191, № 1. - P. 445-446.
37. Read, T. D. Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis / T. D. Read, S. L. Salzberg, M. Pop, M. Shumway, L. Umayam, L. Jiang, E. Holtzapple, J. D. Busch, K. L. Smith, J. M. Schupp, D. Solomon, P. Keim, C. M. Fraser // Science. - 2002. - Vol. 296, № 5575. - P. 2028-2033.
38. Read, T. D. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria / T. D. Read, S. N. Peterson, N. Tourasse, L. W. Baillie, I. T. Paulsen, K. E. Nelson, H. Tettelin, D. E. Fouts, J. A. Eisen, S. R. Gill, E. K. Holtzapple, O. A. Okstad, E. Helgason, J. Rilstone, M. Wu, J. F. Kolonay, M. J. Beanan, R. J. Dodson, L. M. Brinkac, M. Gwinn, R. T. DeBoy, R. Madpu, S. C. Daugherty, A. S. Durkin, D. H. Haft, W. C. Nelson, J. D. Peterson, M. Pop, H. M. Khouri, D. Radune, J. L. Benton, Y. Mahamoud, L. Jiang, I. R. Hance, J. F. Weidman, K. J. Berry, R. D. Plaut, A. M. Wolf, K. L. Watkins, W. C. Nierman, A. Hazen, R. Cline, C. Redmond, J. E. Thwaite, O. White, S. L. Salzberg, B. Thomason, A. M. Friedlander, T. M. Koehler, P. C. Hanna, A. B. Kolstø, C. M. Fraser // Nature. - 2003. - Vol. 423, № 6935. - P. 81-86.
39. Riojas, M. A. Multiplex PCR for species-level identification of Bacillus anthracis and detection of pXO1, pXO2, and related plasmids / M. A. Riojas, K. Kiss, M. L. McKee, M. H. Hazbón // Health security. - 2015. - Vol. 13, № 2. - P. 122-129.
40. Seo, G. M. Bacillus anthracis spores influence ATP synthase activity in murine macrophages / G. M. Seo, K. H. Jung, S. J. Kim, J. C. Kim, J. W. Yoon, K. K. Oh, J. H. Lee, Y. G. Chai // Journal of microbiology and biotechnology. - 2008. - Vol. 18, № 4. - P. 778-783.
41. Seo G. M. Targeting of Bacillus anthracis interaction factors for human macrophages using two-dimensional gel electrophoresis / G. M. Seo, S. J. Kim, J. C. Kim, D. H. Nam, M. Y. Yoon, B. S. Koo, Y. G. Chai // Biochemical and biophysical research communications. - 2004. - Vol. 322, № 3. - P. 854-859.
42. Spratlin, J. L. Clinical applications of metabolomics in oncology: a review / J. L. Spratlin, N. J. Serkova, S. G. Eckhardt // Clinical cancer research. - 2009. - Vol. 15, № 2. - P. 431-440.
43. Van Ert, M. N. Global genetic population structure of Bacillus anthracis / M. N. Van Ert, W. R. Easterday, L. Y. Huynh, R. T. Okinaka, M. E. Hugh-Jones, J. Ravel, S. R. Zanecki, T. Pearson, T. S. Simonson, J. M. U'Ren, S. M. Kachur, R. R. Leadem-Dougherty, S. D. Rhoton, G. Zinser, J. Farlow, P. R. Coker, K. L. Smith, B. Wang, L. J. Kenefic, C. M. Fraser-Liggett, D. M. Wagner, P. Keim // PloS one. - 2007. - Vol. 2, № 5. - P. e 461.doi: 10.1371/journal.pone.0000461.
44. Vitzthum, F. Proteomics: from basic research to diagnostic application. A review of requirements & needs / F. Vitzthum, F. Behrens, N. L. Anderson, J. H. Shaw // Journal of proteome research. - 2005. - Vol. 4, № 4. - P. 1086-1097.
45. Wang, Z. RNA-Seq: a revolutionary tool for transcriptomics / Z. Wang, M. Gerstein, M. Snyder // Nature reviews genetics. - 2009. - Vol. 10, № 1. - P. 57-63.
46. Wunschel, D. S. Proteomic signatures differentiating Bacillus anthracis Sterne sporulation on soil relative to laboratory media / D. S. Wunschel, J. R. Hutchison, B. L. Deatherage Kaiser, E. D. Merkley, B. M. Hess, A. Lin, M. G. Warner // Analyst. - 2018. - Vol. 143, № 1. - P. 123-132.
47. Zhong, W. Differentiation of Bacillus anthracis, B. cereus, and B. thuringiensis by using pulsed-field gel electrophoresis / W. Zhong, Y. Shou, T. M. Yoshida, B. L. Marrone // Appl. Environ. Microbiol. - 2007. - Vol. 73, № 10. - P. 3446-3449.
Review
For citations:
Pechkovskiy G.A., Timchenko L.D., Eremenko E.I., Kovalev D.A., Kulichenko A.N. OMICS TECHNOLOGIES IN THE STUDY OF BACILLUS ANTHRACIS. Astrakhan medical journal. 2020;15(2):13-23. (In Russ.) https://doi.org/10.17021/2020.15.2.13.23
Views:
211
Email this article 