Transition to quorum sensing in an Agrobacterium population: A stochastic model

PLoS Computational Biology

Volumn 1, Issue 4, 2005, Pages 0265-0275

  Goryachev, Andrew B ^a   Toh, Da Jun ^a   Wee, Keng Boon ^a   Lee, Travis ^a   Zhang, Hai Bao ^b   Zhang, Lian Hui ^b  

^a BIOINFORMATICS INSTITUTE   (Singapore)

^b INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; CELL PROLIFERATION; COMPLEX NETWORKS; DNA; GENE EXPRESSION; MACHINERY; POPULATION DYNAMICS; POPULATION STATISTICS; STOCHASTIC MODELS; STOCHASTIC SYSTEMS;

AGROBACTERIA; AUTOINDUCERS; COLLECTIVE BEHAVIOUR; GENE NETWORKS; GENETIC PROGRAMS; LIQUID MEDIA; MODERN BIOLOGY; MOLECULAR MACHINERY; QUORUM-SENSING; STOCHASTIC-MODELING;

BIOFILMS;

BACTERIAL PROTEIN; TRAM PROTEIN, BACTERIAL;

ARTICLE; BIOFILM; BIOLOGICAL MODEL; CELL PROLIFERATION; CULTURE MEDIUM; CYTOLOGY; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PLASMID; QUORUM SENSING; RHIZOBIUM RADIOBACTER; SENSITIVITY AND SPECIFICITY; STATISTICS;

AGROBACTERIUM TUMEFACIENS; BACTERIAL PROTEINS; BIOFILMS; CELL PROLIFERATION; CULTURE MEDIA; GENE EXPRESSION REGULATION, BACTERIAL; MODELS, BIOLOGICAL; PLASMIDS; QUORUM SENSING; SENSITIVITY AND SPECIFICITY; STOCHASTIC PROCESSES;

EID: 55449131983     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0010037     Document Type: Article

References (56)

1. Hartwell LH, Hopfield JJ, Leibler S, Murray AW (1999) From molecular to modular cell biology. Nature 402: C47-C52.
2. Parsek MR, Greenberg EP (2005) Sociomicrobiology: The connections between quorum sensing and biofilms. Trends Microbiol 13: 27-33.
3. von Bodman SB, Bauer WD, Coplin DL (2003) Quorum sensing in plant-pathogenic bacteria. Annu Rev Phytopathol 41: 455-482.
4. Henke JM, Bassler BL (2004) Bacterial social engagements. Trends Cell Biol 14: 648-656.
5. Fuqua C, Greenberg EP (2002) Listening in on bacteria: Acyl-homoserine lactone signalling. Nat Rev Mol Cell Biol 3: 685-695.
6. Fuqua C, Parsek MR, Greenberg EP (2001) Regulation of gene expression by cell-to-cell communication: Acyl-homoserine lactone quorum sensing. Annu Rev Genet 35: 439-468.
7. Zhu J, Oger PM, Schrammeijer B, Hooykaas PJ, Farrand SK, Winans SC (2000) The bases of crown gall tumorigenesis. J Bacteriol 182: 3885-3895.
8. Zhang L, Murphy PJ, Kerr A, Tate ME (1993) Agrobacterium conjugation and gene regulation by N-acyl-L-homoserine lactones. Nature 362: 446-448.
9. Redfield RJ (2002) Is quorum sensing a side effect of diffusion sensing? Trends Microbiol 10: 365-370.
10. Dockery JD, Keener JP (2001) A mathematical model for quorum sensing in Pseudomonas aeruginosa. Bull Math Biol 63: 95-116.
11. James S, Nilsson P, James G, Kjelleberg S, Fagerstrom T (2000) Luminescence control in the marine bacterium Vibrio fischeri: An analysis of the dynamics of lux regulation. J Mol Biol 296: 1127-1137.
12. Viretta AU, Fussenegger M (2004) Modeling the quorum sensing regulatory network of human-pathogenic Pseudomonas aeruginosa. Biotechnol Prog 20: 670-678.
13. Cox CD, Peterson GD, Allen MS, Lancaster JM, McCollum JM, et al. (2003) Analysis of noise in quorum sensing. OMICS 7: 317-334.
14. Ward JP, King JR, Koerber AJ, Williams P, Croft JM, et al. (2001) Mathematical modelling of quorum sensing in bacteria. IMAJ Math Appl Med Biol 18: 263-292.
15. Chopp DL, Kirisits MJ, Moran B, Parsek MR (2002) A mathematical model of quorum sensing in a growing bacterial biofilm. J Ind Microbiol Biotechnol 29: 339-346.
16. Nilsson P, Olofsson A, Fagerlind M, Fagerstrom T, Rice S, et al. (2001) Kinetics of the AHL regulatory system in a model biofilm system: How many bacteria constitute a "quorum"? J Mol Biol 309: 631-640.
17. Wang L, Helmann JD, Winans SC (1992) The A. tumefaciens transcriptional activator OccR causes a bend at a target promoter, which is partially relaxed by a plant tumor metabolite. Cell 69: 659-667.
18. Zhu J, Winans SC (1999) Autoinducer binding by the quorum-sensing regulator TraR increases affinity for target promoters in vitro and decreases TraR turnover rates in whole cells. Proc Natl Acad Sci U S A 96: 4832-4837.
19. Zhang RG, Pappas T, Brace JL, Miller PC, Oulmassov T, et al. (2002) Structure of a bacterial quo rum-sensing transcription factor complexed with pheromone and DNA. Nature 417: 971-974.
20. Zhu J, Winans SC (2001) The quorum-sensing transcriptional regulator TraR requires its cognate signaling ligand for protein folding, protease resistance, and dimerization. Proc Natl Acad Sci U S A 98: 1507-1512.
21. Hwang I, Li PL, Zhang L, Piper KR, Cook DM, et al. (1994) Tral, a Luxl homologue, is responsible for production of conjugation factor, the Ti plasmid N-acylhomoserine lactone autoinducer. Proc Natl Acad Sci U S A 91: 4639-4643.
22. Hwang I, Cook DM, Farrand SK (1995) A new regulatory element modulates homoserine lactone-mediated autoinduction of Ti plasmid conjugal transfer. J Bacteriol 177: 449-458.
23. Hwang I, Smyth AJ, Luo ZQ, Farrand SK (1999) Modulating quorum sensing by antiactivation: TraM interacts with TraR to inhibit activation of Ti plasmid conjugal transfer genes. Mol Microbiol 34: 282-294.
24. Swiderska A, Berndtson AK, Cha MR, Li L, Beaudoin GM 3rd, et al. (2001) Inhibition of the Agrobacterium tumefaciens TraR quo rum-sensing regulator. Interactions with the TraM anti-activator. J Biol Chem 276: 49449-49458.
25. Vannini A, Volpari C, Di Marco S (2004) Crystal structure of the quorum-sensing protein TraM and its interaction with the transcriptional regulator TraR. J Biol Chem 279: 24291-24296.
26. Chen G, Malenkos JW, Cha MR, Fuqua C, Chen L (2004) Quorum-sensing antiactivator TraM forms a dimer that dissociates to inhibit TraR. Mol Microbiol 52: 1641-1651.
27. Qin Y, Smyth AJ, Su S, Farrand SK (2004) Dimerization properties of TraM, the antiactivator that modulates TraR-mediated quorum-dependent expression of the Ti plasmid tra genes. Mol Microbiol 53: 1471-1485.
28. Welch M, Todd DE, Whitehead NA, McGowan SJ, Bycroft BW, et al. (2000) N-acyl homoserine lactone binding to the CarR receptor determines quorum-sensing specificity in Erwinia. EMBO J 19: 631-641.
29. Pearson JP, van Delden C, Iglewski BH (1999) Active efflux and diffusion are involved in transport of Pseudomonas aeruginosa cell-to-cell signals. J Bacteriol 181: 1203-1210.
30. Fuqua C, Winans SC (1996) Localization of OccR-activated and TraR-activated promoters that express two ABC-type permeases and the traR gene of Ti plasmid pTiR10. Mol Microbiol 20: 1199-1210.
31. Fuqua C, Burbea M, Winans SC (1995) Activity of the Agrobacterium Ti plasmid conjugal transfer regulator TraR is inhibited by the product of the traM gene. J Bacteriol 177: 1367-1373.
32. Ortega F, Ehrenberg M, Acerenza L, Westerhoff HV, Mas F, et al. (2002) Sensitivity analysis of metabolic cascades catalyzed by bifunctional enzymes. Mol Biol Rep 29: 211-215.
33. Ingalls BP, Sauro HM (2003) Sensitivity analysis of stoichiometric networks: An extension of metabolic control analysis to non-steady state trajectories. J Theor Biol 222: 23-36.
34. Kacser H, Burns JA (1973) The control of flux. Symp Soc Exp Biol 27: 65-104.
35. Morohashi M, Winn AE, Borisuk MT, Bolouri H, Doyle J, et al. (2002) Robustness as a measure of plausibility in models of biochemical networks. J Theor Biol 216: 19-30.
36. Eberl L, Winson MK, Sternberg C, Stewart GSAB, Christiansen G, et al. (1996) Involvement of N-acyl-L-homoserine lactone autoinducers in controlling the multicellular behaviour of Serratia liquefaciens. Mol Microbiol 20: 127-136.
37. Zhang HB, Wang C, Zhang LH (2004) The quormone degradation system of Agrobacterium tumefaciens is regulated by starvation signal and stress alarmone (p)ppGpp. Mol Microbiol 52: 1389-1401.
38. Dong YH, Wang LH, Xu JL, Zhang HB, Zhang XF, et al. (2001) Quenching quorum-sensing-dependent bacterial infection by an N-acyl homoserine lactonase. Nature 411: 813-817.
39. Zhang HB, Wang LH, Zhang LH (2002) Genetic control of quorum-sensing signal turnover in Agrobacterium tumefaciens. Proc Natl Acad Sci U S A 99: 4638-4643.
40. Levin RA, Farrand SK, Gordon MP, Nester EW (1976) Conjugation in Agrobacterium tumefaciens in the absence of plant tissue. J Bacteriol 127: 1331-1336.
41. Kaláb M (2004) Agrobacterium tumefaciens. Lund (Sweden): SciMAT. Available: http://anka.livstek.lth.se:2080/microscopy/Agrobact.htm. Accessed 15 August 2005.
42. Rosenfeld N, Young JW, Alon U, Swain PS, Elowitz MB (2005) Gene regulation at the single-cell level. Science 307: 1962-1965.
43. Elowitz MB, Levine AJ, Siggia ED, Swain PS (2002) Stochastic gene expression in a single cell. Science 297: 1183-1186.
44. Ozbudak EM, Thattai M, Kurtser I, Grossman AD, van Oudenaarden A (2002) Regulation of noise in the expression of a single gene. Nat Genet 31: 69-73.
45. Balaban NQ, Merrin J, Chait R, Kowalik L, Leibler S (2004) Bacterial persistence as a phenotypic switch. Science 305: 1622-1625.
46. Kussell E, Kishony R, Balaban NQ, Leibler S (2005) Bacterial persistence: A model of survival in changing environments. Genetics 169: 1807-1814.
47. Piper KR, Farrand SK (1999) Conjugal transfer but not quorum-dependent tra gene induction of pTiC58 requires a solid surface. Appl Environ Microbiol 65: 2798-2801.
48. Ozbudak EM, Thattai M, Lim HN, Shraiman BI, van Oudenaarden A (2004) Multistability in the lactose utilization network of Escherichia coli. Nature 427: 737-740.
49. Kholodenko BN, Kiyatkin A, Bruggeman FJ, Sontag E, Westerhoff HV, et al. (2002) Untangling the wires: A strategy to trace functional interactions in signaling and gene networks. Proc Natl Acad Sci U S A 99: 12841-12846.
50. Bruggeman FJ, Westerhoff HV, Hoek JB, Kholodenko BN (2002) Modular response analysis of cellular regulatory networks. J Theor Biol 218: 507-520.
51. Sauro HM, Hucka M, Finney A, Wellock C, Bolouri H, et al. (2003) Next generation simulation tools: The Systems Biology Workbench and BioSPICE integration. OMICS 7: 355-372.
52. Berg HC (1993) Random walks in biology, expanded ed. Princeton (New Jersey): Princeton University Press. 152 p.
53. Gillespie DT (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81: 2340-2361.
54. Dhar P, Meng TC, Somani S, Ye L, Sakharkar K, et al. (2004) Grid Cellware: The first grid-enabled tool for modeling and simulating cellular processes. Bioinformatics 21: 1284-1287.
55. Dhar P, Meng TC, Somani S, Ye L, Sairam A, et al. (2004) Cellware - A multi-algorithmic software for computational systems biology. Bioinformatics 20: 1319-1321.
56. Toh DJ, Tang F, Lee T, Sarda D, Krishnan A, et al. (2004) Parallel computing platform for the agent-based modeling of multicellular biological systems. In: Liew KM, Shen H, See S, editors. Parallel and distributed computing: Applications and technologies. Heidelberg: Springer, pp. 5-9