Identifying co-targets to fight drug resistance based on a random walk model

BMC Systems Biology

Volumn 6, Issue , 2012, Pages

  Chen, Liang Chun ^a   Yeh, Hsiang Yuan ^a   Yeh, Cheng Yu ^a   Arias, Carlos R ^a   Soo, Von Wun ^a  

^a NATIONAL TSING HUA UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); MYCOBACTERIUM TUBERCULOSIS;

ANTIINFECTIVE AGENT; ETHIONAMIDE; FATTY ACID; ISONIAZID; NICOTINAMIDE ADENINE DINUCLEOTIDE;

ALGORITHM; ARTICLE; BIOLOGY; DNA REPAIR; DRUG EFFECT; DRUG RESISTANCE; GENE EXPRESSION REGULATION; GENETICS; HUMAN; METABOLISM; METHODOLOGY; MICROARRAY ANALYSIS; MYCOBACTERIUM TUBERCULOSIS; PHYSIOLOGY; PROTEIN PROTEIN INTERACTION; SEARCH ENGINE; STATISTICS; THEORETICAL MODEL;

ALGORITHMS; ANTI-BACTERIAL AGENTS; COMPUTATIONAL BIOLOGY; DRUG RESISTANCE; ETHIONAMIDE; FATTY ACIDS; GENE EXPRESSION REGULATION, BACTERIAL; HUMANS; ISONIAZID; MICROARRAY ANALYSIS; MODELS, THEORETICAL; MYCOBACTERIUM TUBERCULOSIS; NAD; PROTEIN INTERACTION MAPS; SEARCH ENGINE; SOS RESPONSE (GENETICS); STOCHASTIC PROCESSES;

EID: 84862798394     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-6-5     Document Type: Article

References (71)

1. Tan YT, Tillett DJ, McKay IA. Molecular strategies for overcoming antibiotic resistance in bacteria. Molecular medicine today 2000, 6(8):309-314. 10.1016/S1357-4310(00)01739-1, 10904248.
2. Raman K, Chandra N. Mycobacterium tuberculosis interactome analysis unravels potential pathways to drug resistance. BMC Microbiology 2008, 8(234):1471-2180.
3. Simon JW, Richard AS, Ken L, Laurent K, Robert CR, Gurdyal SB. The use of microarray analysis to determine the gene expression profiles of mycobacterium tuberculosis in response to anti-bacterial compounds. Tuberculosis (Edinburgh, Scotland) 2004, 84(3):263-274.
4. Nacu S, Rebecca CT, Lee P, Holmes S. Gene expression network analysis and applications to immunology. Bioinformatics 2007, 23(7):850-858. 10.1093/bioinformatics/btm019, 17267429.
5. Qiu YQ, Zhang S, Zhang XS. Uncovering differentially expressed pathways with protein interaction and gene expression data. The Second International Symposium on Optimization and Systems Biology 2008, 74-82.
6. Scott J, Ideker T, Karp RM, Sharan R. Efficient algorithms for detecting signaling pathways in protein interaction networks. Ninth Annual International Conference on Research in Computational Molecular Biology 2005, 3500:1-13.
7. Sohler F, Hanisch D, Zimmer R. New methods for joint analysis of biological networks and expression data. Bioinformatics 2004, 20(10):1517-1521. 10.1093/bioinformatics/bth112, 15231545.
8. Zhao X, Wang R, Chen L, Aihara K. Automatic modeling of signal pathways from protein-protein interaction networks. J Bioinform Comput Biol 2009, 7(2):309-322. 10.1142/S0219720009004138, 19340917.
9. ldeker T, Ozier O, Schwikowski B, Siegel AF. Discovering regulatory and signaling circuits in molecular interaction networks. Bioinformatics 2002, 18:S233-S240. 10.1093/bioinformatics/18.suppl_1.S233, 12169552.
10. Dittrich MT, Klau GW, Rosenwald A, Dandekar T, Müller T. Identifying functional modules in protein-protein interaction networks. Bioinformatics 2008, 24(13):i223-i231. 10.1093/bioinformatics/btn161, 2718639, 18586718.
11. Breitling R, Amtmann A, Herzyk P. Graph-based iterative Group Analysis enhances microarray interpretation. BMC Bioinformatics 2004, 5:100. 10.1186/1471-2105-5-100, 509016, 15272936.
12. Guo Z, Li Y, Gong X, Yao C, Ma W, Wang D, Li Y, Zhu J, Zhang M, Yang D, Wang J. Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network. Bioinformatics 2007, 23(16):2121-2128. 10.1093/bioinformatics/btm294, 17545181.
13. Han J, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, Dupuy D, Walhout AJM, Cusick ME, Roth FP, Vidal M. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 2004, 430:88-93. 10.1038/nature02555, 15190252.
14. Zhao XM, Wang RS, Chen L, Aihara K. Uncovering signal transduction networks from high-throughput data by integer linear programming. Nucl Acids Res 2008, 36(9):e48. 10.1093/nar/gkn145, 2396433, 18411207.
15. Wu Z, Zhao XM, Chen L. A systems biology approach to identify effective cocktail drugs. BMC Systems Biology 2010, 4(Suppl 2):S7. 10.1186/1752-0509-4-S2-S7, 2982694, 20840734.
16. Maslov S, Sneppen K. Specificity and Stability in Topology of Protein Networks. Science 2002, 296(5569):910-913. 10.1126/science.1065103, 11988575.
17. Yook S, Oltvai Z, Barabasi A. Functional and topological characterization of protein interaction networks. Proteomics 2004, 4:928-942. 10.1002/pmic.200300636, 15048975.
18. Ayati M, Taheri G, Arab S, Wong L, Eslahchi C. Overcoming Drug Resistance by Co-Targeting. IEEE International Conference on Bioinformatics & Biomedicine 2010, 198-202.
19. Smith PA, Romesberg FE. Combating bacteria and drug resistance by inhibiting mechanisms of persistence and adaptation. Nature chemical biology 2007, 3(9):549-556. 10.1038/nchembio.2007.27, 17710101.
20. Von-mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B. STRING: a database of predicted functional associations between proteins. Nucleic Acids Research 2003, 31(1):258-261. 10.1093/nar/gkg034, 165481, 12519996.
21. Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, Tzur D, Gautam B, Hassanali M. DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Research 2008, 36:D901-D906. 2238889, 18048412.
22. Nguyen L, Thompson CJ. Foundations of antibiotic resistance in bacterial physiology: the mycobacterial paradigm. TRENDS in Microbiology 2006, 14(7):304-312. 10.1016/j.tim.2006.05.005, 16759863.
23. Mdluli K, Slayden RA, Zhu Y, Ramaswamy S, Pan X, Mead D, Crane DD, Musser JM, Barry CE. Inhibition of a Mycobacterium tuberculosis β-ketoacyl ACP Synthase by Isoniazid. Science 1998, 280:1607-1610. 10.1126/science.280.5369.1607, 9616124.
24. Dijkstra EW. A Note on Two Problems in Connexion with Graphs. Numerische Mathematik 1959, 1:269-271.
25. Yeh CY, Yeh HY, Arias CR, Soo VW. Pathway detection from protein interaction networks and gene expression data using color-coding methods and A* search algorithms. The Scientific World Journal 2011,
26. Köhler S, Bauer S, Horn D, Robinson PN. Walking the Interactome for Prioritization of Candidate Disease Genes. The American Journal of Human Genetics 2008, 82(4):949-958.
27. Bhalla US, Iyengar R. Emergent properties of networks of biological signaling pathways. Science 1999, 283(5400):381-387. 10.1126/science.283.5400.381, 9888852.
28. Scardon G, Laudanna C. Network centralities Interference and Robustness. Int J Complex Systems in Science 2011, 1(2):164-168.
29. Boshoff HIM, Myers TG, Copp BR, McNeil MR, Wilson MA, Barry CE. The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: novel insights into drug mechanisms of action. The Journal of Biological Chemistry 2004, 279(38):40174-40184. 10.1074/jbc.M406796200, 15247240.
30. Raman K, Rajagopalan P, Chandra N. Flux Balance Analysis of Mycolic Acid Pathway: Targets for Anti-Tubercular Drugs. PLoS Comput Biol 2005, 1(5):e46. 10.1371/journal.pcbi.0010046, 1246807, 16261191.
31. Nguyen L, Thompson CJ. Foundations of antibiotic resistance in bacterial physiology: the mycobacterial paradigm. Trends Microbiol 2006, 14(7):304-312. 10.1016/j.tim.2006.05.005, 16759863.
32. Wright GD. The antibiotic resistome: the nexus of chemical and genetic diversity. Nat Rev Microbiol 2007, 5(3):175-186. 10.1038/nrmicro1614, 17277795.
33. Gupta AK, Katoch VM, Chauhan DS, Sharma R, Singh M, Venkatesan K, Sharma VD. Microarray analysis of efflux pump genes in multidrug-resistant mycobacterium tuberculosis during stress induced by common anti-tuberculous drugs. Microb Drug Resist 2009, 16(1):21-28.
34. McKeegan KS, Borges-Walmsley MI, Walmsley AR. Microbial and viral drug resistance mechanisms. Trends Microbiol 2002, 10(10 Suppl):S8-S14.
35. O'Sullivan DM, Hinds J, Butcher PD, Gillespie SH, McHugh TD. Mycobacterium tuberculosis DNA repair in response to subinhibitory concentrations of ciprofloxacin. J Antimicrob Chemother 2008, 62(6):1199-1202. 10.1093/jac/dkn387, 2583065, 18799471.
36. Kurland CG, Canback B, Berg OG. Horizontal gene transfer: a critical view. Proc Natl Acad Sci USA 2003, 100(17):9658-9662. 10.1073/pnas.1632870100, 187805, 12902542.
37. Coros A, DeConno E, Derbyshire KM. Is6110, a mycobacterium tuberculosis complex-specific insertion sequence, is also present in the genome of mycobacterium smegmatis, suggestive of lateral gene transfer among mycobacterial species. J Bacteriol 2008, 190(9):3408-3410. 10.1128/JB.00009-08, 2347380, 18326566.
38. Alekshun MN, Levy SB. Molecular mechanisms of antibacterial multidrug resistance. Cell 2007, 128(6):1037-1050. 10.1016/j.cell.2007.03.004, 17382878.
39. Huang D, Sherman B, Lempicki R. Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nat Protoc 2009, 4(1):44-57.
40. Bhat AG, Vashisht R, Chandra N. Modeling metabolic adjustment in Mycobacterium tuberculosis upon treatment with isoniazid. Systems and Synthetic Biology 2011, 4(4):299-309.
41. Savvi S, Warner DF, Kana BD, McKinney JD, Mizrahi V, Dawes SS. Functional Characterization of a Vitamin B12-Dependent Methylmalonyl Pathway in Mycobacterium tuberculosis: Implications for Propionate Metabolism during Growth on Fatty Acids. Journal of Bacteriology 2008, 190(11):3886-3895. 10.1128/JB.01767-07, 2395058, 18375549.
42. Morita YS, Velasquez R, Taig E, Waller RF, Patterson JH, Tull D, Williams SJ, Billman-Jacobe H, McConville MJ. Compartmentalization of lipid biosynthesis in mycobacteria. J Biol Chem 2005, 280:21645-21652. 10.1074/jbc.M414181200, 15805104.
43. Besra GS, Brennan PJ. The mycobacterial cell wall: biosynthesis of arabinogalactan and lipoarabinomannan. Biochem Soc Trans 1997, 25:845-850.
44. Barry CE, Lee RE, Mdluli K, Sampson AE, Schroeder BG, Slayden RA, Yuan Y. Mycolic acids: structure, biosynthesis and physiological functions. Prog Lipid Res 1998, 37:143-179. 10.1016/S0163-7827(98)00008-3, 9829124.
45. Ehrt S, Schnappinger D. Mycobacterial survival strategies in the phagosome: defence against host stresses. Cell Microbiol 2009, 11:1170-1178. 10.1111/j.1462-5822.2009.01335.x, 3170014, 19438516.
46. Banerjee A, Dubnau E, Quemard A, Balasubramanian V, Urn KS, Wilson T, Collins D, de Lisle G, Jacobs WR. inhA, a gene encoding a target for isoniazid and ethionamide in Mycobacterium tuberculosis. Science 1994, 263(5144):227-230. 10.1126/science.8284673, 8284673.
47. Wilson M, DeRisi J, Kristensen HH, Imboden P, Rane S, Brown PO, Schoolnik GK. Exploring drug-induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridization. PANS 1999, 96(22):12833-12838.
48. Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE, Tekaia F, Badcock K, Basham D, Brown D, Chillingworth T, Connor R, Davies R, Devlin K, Feltwell T, Gentles S, Hamlin N, Holroyd S, Hornsby T, Jagels K, Krogh A, McLean J, Moule S, Murphy L, Oliver K, Osborne J, Quail MA, Rajandream MA, Rogers J, Rutter S, Seeger K, Skelton J, Squares R, Squares S, Sulston JE, Taylor K, Whitehead S, Barrell BG. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 1998, 393(6685):537-544. 10.1038/31159, 9634230.
49. de Steenwinkel JE, de Knegt GJ, ten Kate MT, van Belkum A, Verbrugh HA, Kremer K, van Soolingen D, Bakker-Woudenberg IA. Time-kill kinetics of anti-tuberculosis drugs, and emergence of resistance, in relation to metabolic activity of mycobacterium tuberculosis. J Antimicrob Chemother 2010, 65(12):2582-2589. 10.1093/jac/dkq374, 20947621.
50. Ouellet H, Podust LM, de Montellano PR. Mycobacterium tuberculosis cyp130: crystal structure, biophysical characterization, and interactions with antifungal azole drugs. J Biol Chem 2008, 283(8):5069-5080. 2958778, 18089574.
51. Minnikin DE, Kremer L, Dover LG, Besra GS. The methyl-branched fortifications of. Mycobacterium tuberculosis. Chem Biol 2002, 9:545-553. 10.1016/S1074-5521(02)00142-4, 12031661.
52. Trivedi OA, Arora P, Vats A, Ansari MZ, Tickoo R, Sridharan V, Mohanty D, Gokhale RS. Dissecting the mechanism and assembly of a complex virulence mycobacterial lipid. Mol Cell 2005, 17(5):631-643. 10.1016/j.molcel.2005.02.009, 15749014.
53. Rainwater DL, Kolattukudy PE. Synthesis of mycocerosic acids from methylmalonyl coenzyme A by cell-free extracts of Mycobacterium tuberculosis var. bovis BCG. Biological Chemistry 1983, 258:2979-2985.
54. Gerdes SY, Scholle MD, D'Souza M, Bernal A, Baev MV, Farrell M, Kurnasov OV, Daugherty MD, Mseeh F, Polanuyer BM, Campbell JW, Anantha S, Shatalin KY, Chowdhury SA, Fonstein MY, Osterman AL. From Genetic Footprinting to Antimicrobial Drug Targets: Examples in Cofactor Biosynthetic Pathways. J Bacteriol 2002, 184(16):4555-4572. 10.1128/JB.184.16.4555-4572.2002, 135229, 12142426.
55. Raman K, Yeturu K, Chandra N. targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis. BMC Syst Biol 2008, 2:109. 2651862, 19099550.
56. Mann S, Ploux O. 7,8-Diaminoperlargonic acid aminotransferase from Mycobacterium tuberculosis, a potential therapeutic target. Characterization and inhibition studies 2006, 273(20):4778-4789.
57. Ramaswamy SV, Reich R, Dou SJ, Jasperse L, Pan X, Wanger A, Quitugua T, Graviss EA. Single Nucleotide Polymorphisms in Genes Associated with Isoniazid Resistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2003, 47(4):1241-1250. 10.1128/AAC.47.4.1241-1250.2003, 152487, 12654653.
58. Krithika R, Marathe U, Saxena P, Ansari MZ, Mohanty D, Gokhale RS. A genetic locus required for iron acquisition in Mycobacterium tuberculosis. Proc Natl Acad Sci USA 2006, 103:2069-2074. 10.1073/pnas.0507924103, 1413701, 16461464.
59. Amer FA, El-Behedy EM, Mohtady HA. New Targets for Antibacterial Agents. Biotechnology and Molecular Biology Reviews 2008, 3(3):46-57.
60. Lin TW, Melgar MM, Kurth D, Swamidass SJ, Purdon J, Tseng T, Gago G, Baldi P, Gramajo H, Tsai SC. Structure-based inhibitor design of AccD5, an essential acyl-CoA carboxylase carboxyltransferase domain of Mycobacterium tuberculosis. Proc Natl Acad Sci USA 2006, 103:3072-3077. 10.1073/pnas.0510580103, 1413898, 16492739.
61. Xie K, Dalbey RE. Inserting proteins into the bacterial cytoplasmic membrane using the Sec and YidC translocases. Nature Reviews Microbiology 2008, 6:234-244.
62. Feltcher ME, Sullivan JT, Braunstein M. Protein export systems of Mycobacterium tuberculosis: novel targets for drug development?. Future Microbiol 2010, 5(10):1581-1597. 10.2217/fmb.10.112, 3034451, 21073315.
63. Mir MA, Rajeswari HS, Veeraraghavan U, Ajitkumar P. Molecular characterisation of ABC transporter type FtsE and FtsX proteins of Mycobacterium tuberculosis. Arch Microbiol 2006, 185:147-158. 10.1007/s00203-005-0079-z, 16416128.
64. Hughes D. Exploiting genomics, genetics and chemistry to combat antibiotic resistance. Nat Rev Genet 2003, 4(6):432-441.
65. McDonough JA, McCann JR, Tekippe EM, Silverman JS, Rigel NW, Braunstein M. Identification of functional Tat signal sequences in Mycobacterium tuberculosis proteins. Journal of Bacteriology 2008, 190(19):6428-6438. 10.1128/JB.00749-08, 2566002, 18658266.
66. Morita YS, Velasquez R, Taig E, Waller RF, Patterson JH, Tull D, Williams SJ, Billman-Jacobe H, McConville MJ. Compartmentalization of lipid biosynthesis in mycobacteria. J Biol Chem 2005, 280:21645-21652. 10.1074/jbc.M414181200, 15805104.
67. Andries K, Verhasselt P, Guillemont J, Gohlmann HW, Neefs JM, Winkler H, Van Gestel J, Timmerman P, Zhu M, Lee E, Williams P, de Chaffoy D, Huitric E, Hoffner S, Cambau E, Truffot-Pernot C, Lounis N, Jarlier V. A diarylquinoline drug active on the ATP synthase of Mycobacterium tuberculosis. Science 2005, 307(5707):223-227. 10.1126/science.1106753, 15591164.
68. Vergne I, Chua J, Lee HH, Lucas M, Belisle J, Deretic V. Mechanism of phagolysosome biogenesis block by viable Mycobacterium tuberculosis. Proc Natl Acad Sci USA 2005, 102(11):4033-4038. 10.1073/pnas.0409716102, 554822, 15753315.
69. Boshoff HI, Xu X, Tahlan K, Dowd CS, Pethe K, Camacho LR, Park TH, Yun CS, Schnappinger D, Ehrt S, Williams KJ, Barry CE. Biosynthesis and recycling of nicotinamide cofactors in mycobacterium tuberculosis. An essential role for NAD in nonreplicating bacilli. J Biol Chem 2008, 283(28):19329-19341. 10.1074/jbc.M800694200, 2443648, 18490451.
70. Reddy TB, Riley R, Wymore F, Montgomery P, DeCaprio D, Engels R, Gellesch M, Hubble J, Jen D, Jin H, Koehrsen M, Larson L, Mao M, Nitzberg M, Sisk P, Stolte C, Weiner B, White J, Zachariah ZK, Sherlock G, Galagan JE, Ball CA, Schoolnik GK. TB database: an integrated platform for tuberculosis research. Nucleic Acids Res 2009, (37 Database):D499-508.
71. Zhang R, Lin Y. DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Res 2009, (37 Database):D455-D458.