Architecture and inherent robustness of a bacterial cell-cycle control system

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 32, 2008, Pages 11340-11345

  Shen, Xiling ^a   Collier, Justine ^b   Dill, David ^a   Shapiro, Lucy ^b   Horowitz, Mark ^a   McAdams, Harley H ^b  

^a Stanford University   (United States)

^b STANFORD UNIVERSITY   (United States)

Author keywords

Caulobacter; Hybrid system; Model; Regulatory circuit; Symbolic model checking

Indexed keywords

BACTERIAL DNA; MESSENGER RNA; MUTANT PROTEIN;

ANIMAL CELL; ARTICLE; BACTERIAL CELL; CAULOBACTER CRESCENTUS; CELL CYCLE REGULATION; CELL DIVISION; CELL STIMULATION; CELL STRUCTURE; CONTROLLED STUDY; DNA REPLICATION; NONHUMAN; NUTRIENT CYCLE; PHENOTYPE; PRIORITY JOURNAL; PROMOTER REGION; STARVATION; STOCHASTIC MODEL;

CAULOBACTER CRESCENTUS; CELL CYCLE; CHROMOSOMES, BACTERIAL; DNA METHYLATION; DNA REPLICATION; DNA, BACTERIAL; MODELS, BIOLOGICAL; PROMOTER REGIONS (GENETICS); RNA, BACTERIAL; RNA, MESSENGER;

BACTERIA (MICROORGANISMS); CAULOBACTER; CAULOBACTER VIBRIOIDES;

EID: 49649109935     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0805258105     Document Type: Article

References (27)

1. Laub MT, Shapiro L, McAdams HH (2007) Systems biology of Caulobacter. Annu Rev Genet 41:429-441.
2. Chen JC, Stephens C (2007) Bacterial cell cycle: Completing the circuit. Curr Biol 17:R203-R206.
3. McAdams HH, Shapiro L (2003) A bacterial cell-cycle regulatory network operating in time and space. Science 301:1874-1877.
4. McGrath PT, Viollier P, McAdams HH (2004) Setting the pace: Mechanisms tying Caulobacter cell-cycle progression to macroscopic cellular events. Curr Opin Microbiol 7:192-197.
5. Biondi EG, et al. (3006) Regulation of the bacterial cell cycle by an integrated genetic circuit. Nature 444:899-904.
6. Judd EM, et al. (2005) Distinct constrictive processes, separated in time and space, divide Caulobacter inner and outer membranes. J Bacteriol 187:6874-6882.
7. Matroule JY, Lam H, Burnette DT, Jacobs-Wagner C (2004) Cytokinesis monitoring during development; rapid pole-to-pole shuttling of a signaling protein by localized kinase and phosphatase in Caulobacter. Cell 118:579-590.
8. Collier J, McAdams HH, Shapiro L (2007) A DNA methylation ratchet governs progression through a bacterial cell cycle. Proc Natl Acad Sci USA 104:17111-17116.
9. Alur R, et al. (2002) Modeling and analyzing biomolecular networks. Comput Sci Eng 4:20-31.
10. Ghosh R, Tomlin C (2004) Symbolic reachable set computation of piecewise affine hybrid automata and its application to biological modelling: Delta-Notch protein signalling. Syst Biol 1:170-183.
11. Ye P, et al. (2006) Hybrid automata as a unifying framework for modeling excitable cells. Conf Proc IEEE Eng Med Biol Soc 1:4151-4154.
12. Batt G, et al. (2005) Validation of qualitative models of genetic regulatory networks by model checking: Analysis of the nutritional stress response in Escherichia coli. Bioinformatics 21 Suppl 1:i19 -28.
13. Yi TM, Huang Y, Simon MI, Doyle J (2000) Robust perfect adaptation in bacterial chemotaxis through integral feedback control. Proc Natl Acad Sci USA 97:4649-4653.
14. Iniesta AA, McGrath PT, Reisenauer A, McAdams HH, Shapiro L (2006) A phospho-signaling pathway controls the localization and activity of a protease complex critical for bacterial cell cycle progression Proc Natl Acad Sci USA 103:10935-10940.
15. Li S, Brazhnik P, Sobral B, Tyson JJ (2008) A quantitative study of the division cycle of Caulobacter crescentus stalked cells. PLoS Comput Biol 4:e9.
16. Hottes AK, Shapiro L, McAdams HH (2005) DnaA coordinates replication initiation and cell cycle transcription in Caulobacter crescentus. Mol Microbiol 58:1340-1353.
17. Reisenauer A, Shapiro L (2002) DNA methylation affects the cell cycle transcription of the CtrA global regulator in Caulobacter. EMBO J 21:4969-4977.
18. McAdams HH, Arkin A(1997) Stochastic mechanisms in gene expression. Proc Natl Acad Sci USA 94:814-819.
19. Keiler KC, Shapiro L (2003) TmRNA is required for correct timing of DNA replication in Caulobacter crescentus. J Bacteriol 185:573-580.
20. McGrath PT, et al. (2007) High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons. Nat Biotechnol 25:584-592.
21. de Visser JA, et al. (2003) Perspective: Evolution and detection of genetic robustness. Evol Int J Org Evol 57:1959-1972.
22. Clarke EM, Emerson EA, Sistla AP (1986) Automatic verification of finite-state concurrent systems using temporal logic specifications. ACM Trans Program Lang Syst 8:244-263.
23. Cimatti A, et al. (2002) in International Conference on Computer-Aided Verification (CAV 2002) (Copenhagen, Denmark), pp. 359-364.
24. Emerson EA, Halpern JY (1985) Decision procedures and expressiveness in the temporal logic of branching time. J Comput Syst Sci 30:1-24.
25. Gorbatyuk B, Marczynski GT (2001) Physiological consequences of blocked Caulobacter crescentus dnaA expression, nessential DNA replication gene. Mol Microbiol 40:485-497.
26. Collier J, Murray SR, Shapiro L (2006) DnaA couples DNA replication and the expression of two cell cycle master regulators. EMBO J 25:346-356.
27. Gorbatyuk B, Marczynski GT (2005) Regulated degradation of chromosome replication proteins DnaA and CtrA in Caulobacter crescentus. Mol Microbiol 55:1233-1245.