Genome wide search for identifi cation of potential drug targets in Bacillus anthracis

International Journal of Computational Biology and Drug Design

Volumn 5, Issue 2, 2012, Pages 164-179

  Gutlapalli, Ravi V ^a   Ambaru, Jyothsna L ^a   Darla, Pavani ^b   Rao, K R S Sambasiva ^a  

^a ACHARYA NAGARJUNA UNIVERSITY   (India)

^b OSMANIA UNIVERSITY   (India)

Author keywords

Bacillus anthracis; DEG; Modeller9v8; PSORTb 3.0; SVM

Indexed keywords

CELL ADHESION MOLECULE; PEPTIDASE;

ARTICLE; BACILLUS ANTHRACIS; BACTERIAL GENE; BACTERIAL METABOLISM; BACTERIAL VIRULENCE; CELL WALL; DRUG TARGETING; GENE IDENTIFICATION; GENETIC ASSOCIATION; PTSG GENE;

EID: 84864668398     PISSN: 17560756     EISSN: 17560764     Source Type: Journal    
DOI: 10.1504/IJCBDD.2012.048311     Document Type: Article

References (48)

1. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) 'Gapped BLAST and PSI BLAST: A new generation of protein database search programs', Nucleic Acids Res., Vol. 25, No. 17, pp.3389-3402. (Pubitemid 27359211)
2. Allsop, A.E. (1998) 'New antibiotic discovery, novel screens, novel targets and impact of microbial genomics', Curr. Opin. Microbiol., Vol. 1, pp.530-534. (Pubitemid 128433640)
3. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N. and Weissig, H. (2000) 'The protein data bank', Nucl. Acids Res., Vol. 28, pp.235-242. (Pubitemid 30047768)
4. Bhasin, M., Garg, A. and Raghava, G.P. (2005) 'PSLpred: Prediction of subcellular localization of bacterial proteins', Bioinformatics, Vol. 21, No. 10, pp.2522-2524. (Pubitemid 40731613)
5. Brook, I., Elliott, T.B., Pryor, H.I. 2nd, Sautter, T.E., Gnade, B.T., Thakar, J.H. and Knudson, G.B. (2001) 'In vitro resistance of Bacillus anthracis Sterne to doxycycline, macrolides and quinolones', Int. J. Antimicrob. Agents, Vol. 18, pp.559-562. (Pubitemid 33152750)
6. Buhr, A. and Erni, B. (1993) 'Membrane topology of the glucose transporter of Escherichia coli', J. Biol. Chem., Vol. 268, pp.11599-11603. (Pubitemid 23168106)
7. Bongiorni, C., Fukushima, T., Wilson, A.C., Chiang, C., Mansilla, M.C., Hoch, J.A. and Perego, M. (2008) 'Dual promoters control expression of the Bacillus anthracis virulence factor AtxA', J. Bacteriol., Vol. 19, pp.6483-6492.
8. Bourgogne, A., Drysdale, M., Hilsenbeck, S.G., Peterson, S.N. and Koehler, T.M. (2003) 'Global effects of virulence gene regulators in a Bacillus anthracis strain with both virulence plasmids', Infect. Immun., Vol. 5, pp.2736-2743. (Pubitemid 36519888)
9. Bowie, J.U., Luthy, R. and Eisenberg, D. (1991) 'A method to identify protein sequences that fold into a known three-dimensional structure', Science, Vol. 253, pp.164-170. (Pubitemid 21917131)
10. Cazzulo, J.J., Stok, V. and Turk, V. (2001) 'The major cysteine proteinase of trypanosoma cruzi: A valid target for chemotherapy of Chagas disease', Curr. Pharm. Des., Vol. 7, pp.1143-1156. (Pubitemid 32640574)
11. Centers for Disease Control and Prevention (2001) 'Update: Interim recommendations for antimicrobial prophylaxis for children and breastfeeding mothers and treatment of children with anthrax', MMWR Morbidity and Mortal Wkly Rept, Vol. 50, pp.1014-1016.
12. Coutte, L., Alonso, S., Reveneau, N., Willery, E., Quatannens, B., Locht, C. and Jacob-Dubuisson, F. (2003) 'Role of adhesin release for mucosal colonization by a bacterial pathogen', J. Exp. Med., Vol. 197, pp.735-742. (Pubitemid 36350868)
13. Deutscher, J., Francke, C. and Postma, P.W. (2006) 'How phosphotransferase System-related protein phosphorylation regulates carbohydrate metabolism in bacteria', Microbiol. Mol. Biol. Rev., Vol. 70, pp.939-1031. (Pubitemid 44958262)
14. Dodd, D., Reese, J.G., Louer, C.R., Ballard, J.D., Spies, M.A. and Blanke, S.R. (2007) 'Functional comparison of the two Bacillus anthracis glutamate racemases', J. Bacteriol., Vol. 189, pp.5265-5275. (Pubitemid 47076072)
15. Doublet, P., Heijenoort, J.V., Bohin, J.P. and Mengin-Lecreulx, D. (1993) 'The murI gene of Escherichia coli is an essential gene that encodes a glutamate racemaseactivity', J. Bacteriol, Vol. 175, pp.2970-2979. (Pubitemid 23148730)
16. Hoch, J.A. (2000) 'Two-component and phosphorelay signal transduction', Curr. Opin. Microbiol., Vol. 3, pp.165-170. (Pubitemid 30180068)
17. Inglesby, T.V., O'Toole, T., Henderson, D.A., Bartlett, J.G., Ascher, M.S., Eitzen, E., Friedlander, A.M., Gerberding, J., Hauer, J., Hughes, J., McDade, J., Osterholm, M.T., Parker, G., Perl, T.M., Russell, P.K. and Tonat, K. (2002) 'Anthrax as a biological weapon, 2002: Updated recommendations for management', J. Am. Med. Assoc., Vol. 287, pp.2236-2252. (Pubitemid 34441940)
18. Käll, L., Krog, A. and Sonnhammer, E.L. (2007) 'Advantages of combined transmembrane topology and signal peptide prediction-The phobius web server', Nucleic Acids Res., Vol. 35, pp.429-432.
19. Kanehisa, M., Goto, S., Kawashima, S. and Nakaya A. (2002) 'The KEGG databases at genome net', Nucleic Acids Res, Vol. 30, pp.42-46.
20. Kempf, D.J., Sham, H.L., Marsh, K.C., Flentge, C.A., Betebenner, D., Green, B.E., McDonald, E., Vasavanonda, S., Saldivar, A., Wideburg, N.E., Kati, W.M., Ruiz, L., Zhao, C., Fino, L., Patterson, J., Molla, A., Plattner, J.J. and Norbeck, D.W. (1998) 'Discovery of ritonavir, a potent inhibitor of HIV protease with high oral bioavailability and clinical effi cacy', J Med. Chem., Vol. 41, pp.602-617. (Pubitemid 28093094)
21. Klemm, P. and Schembri, M.A. (2004) 'Bacterial adhesins: Function and structure', Int. J. Med Microbiol., Vol. 290, pp.27-35. (Pubitemid 30217988)
22. Kok, M., Bron, G., Erni, B. and Mukhija, S. (2003) 'Effect of enzyme I of the bacterial phosphoenolpyruvate: Sugar phosphotransferase system (PTS) on virulence in a murine model', Microbiology, Vol. 149, pp.2645-2652. (Pubitemid 37160738)
23. Lammertyn, E., Mellaert, L.V., Meyen, E., Lebeau, I., Buck, E.D., Anné, J. and Geukens, N. (2004) 'Molecular and functional characterization of type I signal peptidase from Legionella pneumophila', Microbiology, Vol. 150, pp.1475-1483. (Pubitemid 38744749)
24. Luthy, R., Bowie, J.U. and Eisenberg, D. (1992) 'Assessment of protein models with three-dimensional profi les', Nature, Vol. 356, pp.83-85.
25. Meins, M., Jenö, P., Müller, D., Richter, W.J., Rosenbusch, J.P., Erni, B., (1993) 'Cysteine phosphorylation of the glucose transporter of E. Coli', J. Biol. Chem., Vol. 268, pp.11604-11609. (Pubitemid 23168107)
26. Paetzel, M., Goodall, J.J., Kania, M., Dalbey, R.E. and Page, M.G. (2004) 'Crystallographic and biophysical analysis of a bacterial signal peptidase in complex with a lipopeptide-based inhibitor', J. Biol. Chem., Vol. 279, pp.30781-30790. (Pubitemid 38938011)
27. Poirot, O., Suhre, K., Abergel, C., O'Toole, E. and Notredame, C. (2004) '3DCoffee@igs: A web server for combining sequences and structures into a multiple sequence alignment', Nucleic Acids Res., Vol. 1, No. 32, (Web Server issue), pp.W37-W40. (Pubitemid 38997295)
28. Pomerantsev, A.P., Shishkova, N.A. and Marinin, L.I. (1992) 'Comparison of therapeutic effects of antibiotics of the tetracycline group in the treatment of anthrax caused by a strain inheriting tet-gene of plasmid pBC16', Antibiot Khimioter, Vol. 37, pp.31-34.
29. Price, L.B., Vogler, A., Pearson, T., Busch, J.D., Schupp, J.M. and Keim, P. (2003) 'In vitro selection and characterization of Bacillus anthracis mutants with high-level resistance to ciprofl oxacin', Antimicrob. Agents Chemother., Vol. 47, pp.2362-2365. (Pubitemid 36753604)
30. Rawlings, N.D., Morton, F.R., Kok, C.Y., Kong, J. and Barrett, A.J. (2004) 'MEROPS: The peptidase database', Nucleic Acids Res., Vol. 1, No. 32, (Database issue), pp.D160-D164. (Pubitemid 38081629)
31. Sachdeva, G., Kumar, K., Jain, P. and Ramachandran, S. (2005) 'SPAAN: A software program for prediction of adhesins and adhesin-like proteins using neural networks', Bioinformatics, Vol. 21, pp.483-491. (Pubitemid 40310235)
32. Sali, A. and Blundell, T.L. (1993) 'Comparative protein modelling by satisfaction of spatial restraints', J. Mol. Biol., Vol. 234, pp.779-815. (Pubitemid 24007801)
33. Sakharkar, K.R., Sakharkar, M.K. and Chow, V.T. (2004) 'A novel genomics approach for the identifi cation of drug targets in pathogens, with special reference to Pseudomonas aeruginosa', in Silico Biol., Vol. 4, pp.355-360. (Pubitemid 39600481)
34. Salminen, A., Loimaranta, V., Joosten, J.A.F., Khan, A.S., Hacker, J., Pieters, R.J. and Finne, J.S. (2007) 'Inhibition of P-fi mbriated Escherichia coli adhesion by multivalent galabiose derivatives studied by a live-bacteria application of surface plasmon resonance', J. Antimicrob. Chemother, Vol. 60, pp.495-501. (Pubitemid 47299862)
35. Santos, C.C., Sant'anna, C., Terres, A., Cunha-e-Silva, N.L., Scharfstein, J. and de A Lima, A.P. (2005) 'Chagasin, the endogenous cysteine-protease inhibitor of trypanosoma cruzi, modulates parasite differentiation and invasion of mammalian cells', J. Cell Sci., Vol. 118, pp.901-915. (Pubitemid 40484882)
36. Schmid, M.B. (1998) 'Novel approaches to the discovery of antimicrobial agents', Curr. Opin. Chem Biol., Vol. 2, pp.529-534. (Pubitemid 128645707)
37. Shatalin, K., Gusarov, I., Avetissova, E., Shatalina, Y., McQuade, L.E., Lippard, S.J. and Nudler, E. (2008) 'Bacillus anthracis-derived nitric oxide is essential for pathogen virulence and survival in macrophages', Proc. Natl. Acad. Sci., USA, Vol. 105, No. 3, pp.1009-1013. (Pubitemid 351282072)
38. Shen, M.Y. and Sali, A. (2006) 'Statistical potential for assessment and prediction of protein structures', Protein Sci., Vol. 15, pp.2507-2524. (Pubitemid 44771688)
39. Southan, C. (2001) 'A genomic perspective on human proteases as drug targets', Drug Discov. Today, Vol. 6, pp.681-688. (Pubitemid 32590794)
40. Supuran, C.T., Scozzafava, A. and Clare, B.W. (2002) 'Bacterial protease inhibitors', Med. Res. Rev., Vol. 22, pp.329-72. (Pubitemid 34620472)
41. Uchida, I., Makino, S., Sekizaki, T. and Terakado, N. (1997) 'Cross-Talk to the genes for Bacillus anthracis capsule synthesis by atxA, the gene encoding the trans-Activator of anthrax toxin synthesis', Mol. Microbiol., Vol. 6, pp.1229-1240. (Pubitemid 27122208)
42. van Heijenoort, J. (2001) 'Recent advances in the formation of the bacterial peptidoglycan monomer unit', Nat. Prod. Rep., Vol. 18, pp.503-519. (Pubitemid 33016991)
43. Walz, A., Mujer, C.V., Connolly, J.P., Alefantis, T., Chafi n, R., Dake, C., Whittington, J., Kumar, S.P., Khan, A.S. and DelVecchio, V.G. (2007) 'Bacillus anthracis secretome time course under host-simulated conditions and identifi cation of immunogenic proteins', Proteome Sci., Vol. 5, p. 11.
44. Westermann, M., Pop, O.I., Gerlach, R., Appel, T.R., Schlörmann, W., Schreiber, S. and Müller, J.P. (2006) 'The TatAd component of the Bacillus subtilis twin-Arginine protein transport system forms homo-multimeric complexes in its cytosolic and membrane embedded localisation', Biochim. Biophys. Acta., Vo. 1758, pp.443-451. (Pubitemid 43767733)
45. Wiederstein, M. and Sippl, M.J. (2007) 'ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins', Nucleic Acids Res., Vol. 35, pp.W407-W410.
46. Wilson, A.C., Soyer, M., Hoch, J.A. and Perego, M. (2008) 'The bicarbonate transporter is essential for Bacillus anthracis lethality', PLoS Pathog, Vol. 4, No. 11, p.e1000210.
47. Yu, N.Y., Wagner, J.R., Laird, M.R., Melli, G., Rey, S., Lo, R., Dao, P., Sahinalp, S.C., Ester, M., Foster, L.J. and Brinkman, F.S. (2010) 'PSORTb 3.0: Improved protein subcellular localization prediction with refi ned localization subcategories and predictive capabilities for all prokaryotes', Bioinformatics, Vol. 26, pp.1608-1615.
48. Zhang, R. and Lin, Y. (2009) 'DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes', Nucleic Acids Res., Vol. 37, pp.455-458.