Stochastic sequence-level model of coupled transcription and translation in prokaryotes

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Mäkelä, Jarno ^a   Lloyd Price, Jason ^a   Yli Harja, Olli ^a,b   Ribeiro, Andre S ^a  

^a TAMPERE UNIVERSITY OF TECHNOLOGY   (Finland)

^b INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEX FORMATIONS; DEGREE OF COUPLING; PREMATURE TERMINATION; RIBOSOME BINDING SITES; SEQUENCE-DEPENDENT; TIGHTLY-COUPLED; TRANSLATION ELONGATION; TRANSLATION RATES;

ELONGATION; ESCHERICHIA COLI; MACROMOLECULES; MICROORGANISMS; PROTEINS; RNA;

TRANSCRIPTION;

ESCHERICHIA COLI; PROKARYOTA;

DNA DIRECTED RNA POLYMERASE;

ARTICLE; BIOLOGICAL MODEL; CODON; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; PROTEIN SYNTHESIS; REGULATORY SEQUENCE; RIBOSOME; STATISTICS;

CODON; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; MODELS, GENETIC; PROTEIN BIOSYNTHESIS; REGULATORY SEQUENCES, NUCLEIC ACID; RIBOSOMES; STOCHASTIC PROCESSES; TRANSCRIPTION, GENETIC;

EID: 79955117238     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-121     Document Type: Article

References (54)

1. Rajala T, Häkkinen A, Healy S, Yli-Harja O, Ribeiro AS. Effects of transcriptional pausing on gene expression dynamics. PLOS Comput Biol 2010, 6(3):e1000704. 10.1371/journal.pcbi.1000704, 2837387, 20300642.
2. Greive SJ, von Hippel PH. Thinking quantitatively about transcriptional regulation. Nat Rev Mol Cell Biol 2005, 6:221-232.
3. Wen JD, Lancaster L, Hodges C, Zeri AC, Yoshimura SH, Noller HF, Bustamante C, Tinoco I. Following translation by single ribosomes one codon at a time. Nature 2008, 452:598-603. 10.1038/nature06716, 2556548, 18327250.
4. Landick R. The regulatory roles and mechanism of transcriptional pausing. Biochem Soc Trans 2006, 34(6):1062-1066.
5. Ribeiro AS, Rajala T, Smolander OP, Häkkinen A, Yli-Harja O. Delayed Stochastic Model of Transcription at the Single Nucleotide Level. J Comput Biol 2009, 16:539-553. 10.1089/cmb.2008.0153, 19361326.
6. Ribeiro AS, Häkkinen A, Mannerstrom H, Lloyd-Price J, Yli-Harja O. Effects of the promoter open complex formation on gene expression dynamics. Phys Rev E 2010, 81(1):011912.
7. Kaern M, Elston TC, Blake WJ, Collins JJ. Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet 2005, 6:451-464. 10.1038/nrg1615, 15883588.
8. Pedraza J, Paulsson J. Effects of Molecular Memory and Bursting on Fluctuations in Gene Expression. Science 2008, 319:339-334. 10.1126/science.1144331, 18202292.
9. Murphy KF, Balazsi G, Collins JJ. Combinatorial promoter design for engineering noisy gene expression. Proc Natl Acad Sci USA 2007, 104:12726-12731. 10.1073/pnas.0608451104, 1931564, 17652177.
10. Mayr E. What evolution is 2001, Basic Books, NY, USA.
11. Lee HH, Molla MN, Cantor CR, Collins JJ. Bacterial charity work leads to population-wide resistance. Nature 2010, 467:82-86. 10.1038/nature09354, 2936489, 20811456.
12. Acar M, Mettetal J, van Oudenaarden A. Stochastic switching as a survival strategy in fluctuating environments. Nature Genetics 2008, 40:471-475. 10.1038/ng.110, 18362885.
13. Yu J, Xiao J, Ren X, Lao K, Xie XS. Probing gene expression in live cells, one protein molecule at a time. Science 2006, 311:1600-1603. 10.1126/science.1119623, 16543458.
14. Golding I, Paulsson J, Zawilski SM, Cox EC. Real-time kinetics of gene activity in individual bacteria. Cell 2005, 123:1025-1036. 10.1016/j.cell.2005.09.031, 16360033.
15. Ribeiro AS. Stochastic and delayed stochastic models of gene expression and regulation. Mathematical Biosciences 2010, 223(1):1-11. 10.1016/j.mbs.2009.10.007, 19883665.
16. Herbert KM, La Porta A, Wong BJ, Mooney RA, Neuman KC, Landick R, Block SM. Sequence-resolved detection of pausing by single RNA polymerase molecules. Cell 2006, 125:1083-1094. 10.1016/j.cell.2006.04.032, 1483142, 16777599.
17. Sorensen MA, Pedersen S. Absolute in vivo translation rates of individual codons in Escherichia coli. J Mol Biol 1991, 222:265-280. 10.1016/0022-2836(91)90211-N, 1960727.
18. Bernstein J, Khodursky A, Lin P, Lin-Chao S, Cohen S. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc Natl Acad Sci USA 2002, 99:9697-9702. 10.1073/pnas.112318199, 124983, 12119387.
19. Roussel MR, Zhu R. Validation of an algorithm for delay stochastic simulation of transcription and translation in prokaryotic gene expression. Phys Biol 2006, 3:274-284. 10.1088/1478-3975/3/4/005, 17200603.
20. Mitarai N, Sneppen K, Pedersen S. Ribosome collisions and translation efficiency: optimization by codon usage and mRNA destabilization. J Mol Biol 2008, 382(1):236-245. 10.1016/j.jmb.2008.06.068, 18619977.
21. Zhu R, Ribeiro AS, Salahub D, Kauffman SA. Studying genetic regulatory networks at the molecular level: delayed reaction stochastic models. J Theor Biol 2007, 246:725-745. 10.1016/j.jtbi.2007.01.021, 17350653.
22. Voliotis M, Cohen N, Molina-Paris C, Liverpool TB. Fluctuations, pauses and backtracking in DNA transcription. Biophys J 2008, 94:334-348. 2157217, 17720732.
23. Ribeiro AS, Zhu R, Kauffman SA. A general modeling strategy for gene regulatory networks with stochastic dynamics. J Comput Biol 2006, 13:1630-1639. 10.1089/cmb.2006.13.1630, 17147485.
24. Ribeiro AS, Lloyd-Price J. SGN Sim, a Stochastic Genetic Networks Simulator. Bioinformatics 2007, 23(6):777-779. 10.1093/bioinformatics/btm004, 17267430.
25. Lutz R, Lozinski T, Ellinger T, Bujard H. Dissecting the functional program of Escherichia coli promoters: the combined mode of action of Lac repressor and AraC activator. Nuc Ac Res 2001, 29:3873-3881.
26. Gillespie DT. Exact stochastic simulation of coupled chemical reactions. J Phys Chem 1977, 81:2340-2361.
27. Arkin A, Ross J, McAdams H. Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected E. coli cells. Genetics 1998, 149:1633-1648. 1460268, 9691025.
28. Yarchuk O, Jacques N, Guillerez J, Dreyfus M. Interdependence of translation, transcription and mRNA degradation in the lacZ gene. J Mol Biol 1992, 226:581-596. 10.1016/0022-2836(92)90617-S, 1507217.
29. Paulsson J. Models of stochastic gene expression. Phys Life Rev 2005, 2(2):157-175.
30. Shaevitz JW, Abbondanzieri EA, Landick R, Block SM. Backtracking by single RNA polymerase molecules observed at near-base-pair resolution. Nature 2003, 426:684-687. 10.1038/nature02191, 1483218, 14634670.
31. Landick R. Transcriptional pausing without backtracking. Proc Natl Acad Sci USA 2009, 106(22):8797-8798. 10.1073/pnas.0904373106, 2690019, 19470457.
32. Ribeiro AS, Häkkinen A, Healy S, Yli-Harja O. Dynamical effects of transcriptional pause-prone sites. Comput Biol Chem 2010, 34(3):143-148. 10.1016/j.compbiolchem.2010.04.003, 20537588.
33. Choi PJ, Cai L, Frieda K, Xie XS. A Stochastic Single-Molecule Event Triggers Phenotype Switching of a Bacterial Cell. Science 2008, 322(5900):442-446. 10.1126/science.1161427, 2819113, 18927393.
34. Xie XS, Choi PJ, Li GW, Lee NK, Lia G. Single-molecule approach to molecular biology in living bacterial cells. Annu Rev Biophys 2008, 37:417-444. 10.1146/annurev.biophys.37.092607.174640, 18573089.
35. Burmann BM, Schweimer K, Luo X, Wahl MC, Stitt BL, Gottesman ME, Rösch P. A NusE:NusG Complex Links Transcription and Translation. Science 2010, 328(5977):501-504. 10.1126/science.1184953, 20413501.
36. Ota K, Yamada T, Yamanishi Y, Goto S, Kanehisa M. Comprehensive Analysis of Delay in Transcriptional Regulation Using Expression Profiles. Genome Informatics 2003, 14:302-303.
37. Phroskin S, Rachid Rahmouni A, Mironov A, Nudler E. Cooperation between translating ribosomes and RNA polymerase in transcription elongation. Science 2010, 328(5977):504-508. 10.1126/science.1184939, 2930199, 20413502.
38. Epshtein V, Nudler E. Cooperation between RNA polymerase molecules in transcription elongation. Science 2003, 300(5620):801-805. 10.1126/science.1083219, 12730602.
39. Lewin B. Genes IX 2008, 256-299. Jones and Bartlett Publishers, USA.
40. Erie DA, Hajiseyedjavadi O, Young MC, von Hippel PH. Multiple RNA polymerase conformations and GreA: control of the fidelity of transcription. Science 1993, 262:867-873. 10.1126/science.8235608, 8235608.
41. Greive SJ, Weitzel SE, Goodarzi JP, Main LJ, Pasman Z, von Hippel PH. Monitoring RNA transcription in real time by using surface plasmon resonance. Proc Natl Acad Sci USA 2008, 105:3315-3320. 10.1073/pnas.0712074105, 2265150, 18299563.
42. McClure WR. Rate-limiting steps in RNA chain initiation. Proc Natl Acad Sci USA 1980, 77:5634-5638. 10.1073/pnas.77.10.5634, 350123, 6160577.
43. Balesco JG. All things must pass: Contrasts and commonalities in eukaryotic and bacterial mRNA decay. Nat Rev Mol Cell Biol 2010, 11(7):467-478. 10.1038/nrm2917, 20520623.
44. Hsu LM. Promoter clearance and escape in prokaryotes. Biochimica et Biophysica Acta - Gene Structure and Expression 2002, 1577(2):191-207.
45. Jorgensen F, Kurland CG. Processivity errors of gene expression in Escherichia coli. J Mol Biol 1990, 215:511-521. 10.1016/S0022-2836(05)80164-0, 2121997.
46. Moore SD, Sauer RT. Ribosome rescue: tmRNA tagging activity and capacity in Escherichia coli. Mol Microbiol 2005, 58:456-466. 10.1111/j.1365-2958.2005.04832.x, 16194232.
47. Cormack BP, Valdivia RH, Falkow S. FACS-optimized mutants of the green fluorescent protein (GFP). Gene 1996, 173(1):33-38. 10.1016/0378-1119(95)00685-0, 8707053.
48. Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P. Molecular biology of the cell 2002, Garland Science, USA.
49. Sorensen MA, Kurland CG, Pedersen S. Codon usage determines translation rate in Escherichia coli. J Mol Biol 1989, 207:365-377. 10.1016/0022-2836(89)90260-X, 2474074.
50. Menninger JR. Peptidyl transfer RNA dissociates during protein synthesis from ribosomes of Escherichia coli. J Biol Chem 1976, 251:3392-3398.
51. Shoji S, Walker SE, Fredrick K. Ribosomal translocation: One step closer to the molecular mechanism. ACS Chem Biol 2009, 4:93-107. 10.1021/cb8002946, 3010847, 19173642.
52. Qin Y, Polacek N, Vesper O, Staub E, Einfeldt E, Wilson DN, Nierhaus KH. The highly conserved LepA is a ribosomal elongation factor that back-translocates the ribosome. Cell 2006, 127:721-733. 10.1016/j.cell.2006.09.037, 17110332.
53. Keiler KC. Biology of trans-translation. Annu Rev Microbiol 2008, 62:133-151. 10.1146/annurev.micro.62.081307.162948, 18557701.
54. Bracewell R. Pentagram Notation for Cross Correlation. The Fourier Transform and Its Applications 1965, 46-243. New York: McGraw-Hill.