Modeling classic attenuation regulation of gene expression in bacteria

Journal of Bioinformatics and Computational Biology

Volumn 5, Issue 1, 2007, Pages 155-180

  Lyubetsky, Vassily A ^a   Pirogov, Sergey A ^a   Rubanov, Levi I ^a   Seliverstov, Alexander V ^a  

^a INSTITUTE FOR INFORMATION TRANSMISSION PROBLEMS   (Russian Federation)

Author keywords

Attenuation; Mathematic modeling; Transcription regulation model

Indexed keywords

BACTERIAL RNA; DNA; RNA POLYMERASE; TRANSFER RNA;

ARTICLE; BACTERIAL GENETICS; BATCH PROCESS; COMPUTER INTERFACE; COMPUTER PROGRAM; COMPUTER SYSTEM; CONTROLLED STUDY; CORRELATION ANALYSIS; DNA STRAND; ENZYME ACTIVITY; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE MUTATION; GENETIC MODEL; GENETIC PARAMETERS; MATHEMATICAL MODEL; MONTE CARLO METHOD; NONHUMAN; PROBABILITY; PROCESS DEVELOPMENT; PROCESS MODEL; PUBLISHING; REGULATOR GENE; RIBOSOME; RNA STRUCTURE; RNA TRANSCRIPTION; TRANSLATION INITIATION;

BACTERIAL PHYSIOLOGY; BACTERIAL PROTEINS; COMPUTER SIMULATION; GENE EXPRESSION REGULATION, BACTERIAL; MODELS, GENETIC; PROTEIN BIOSYNTHESIS; RNA, MESSENGER; TRANS-ACTIVATION (GENETICS);

BACTERIA (MICROORGANISMS);

EID: 34248154743     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720007002576     Document Type: Article

References (55)

1. Danilova LV, Pervouchine DD, Favorov AV, Mironov AA, RNAKINETICS: A web server that models secondary structure kinetics of an elongating RNA, J Bioinform Comput Biol 4(2):589-596, 2006.
2. Yin H, Artsimovitch I, Landick R, Gelles J, Nonequilibrium mechanism of translation termination from observations of single RNA polymerase molecules, PNAS 96(23):13124-13129, 1999.
3. World Wide Web server at (http://lab6.iitp.ru/rnamodel).
4. Henkin TM, Yanofsky C, Regulation by transcription attenuation in bacteria: How RNA provides instructions for transcription termination/ antitermination decisions, Bioessays 24(8):700-707, 2002.
5. Grundy FJ, Henkin TM, The T box and S box transcription termination control systems, Front Biosci 8:d20-d31, 2003.
6. Grundy FJ, Henkin TM, Regulation of gene expression by effectors that bind to RNA, Curr Opin Microbiol 7(2):126-131, 2004.
7. Mandal M, Breaker RR, Gene regulation by riboswitches, Nat Rev Mol Cell Biol 5(6):451-463, 2004.
8. Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS, Riboswitches: The oldest mechanism for the regulation of gene expression?, Trends Genet 20(1):44-50, 2004.
9. Yanofsky C, The different roles of tryptophan transfer RNA in regulating trp operon expression in E. coli versus B. subtilis, Trends Geneti 20(8):367-374, 2004.
10. Panina EM, Vitreschak AG, Mironov AA, Gelfand MS, Regulation of aromatic amino acid biosynthesis in gamma-proteobacteria, J Mol Microbiol Biotechnol 3(4):529-543, 2001.
11. Vitreschak AG, Lyubetskaya EV, Shirshin MA, Gelfand MS, Lyubetsky VA, Attenuation regulation of amino acid biosynthetic operons in proteobacteria: Comparative genomics analysis, FEMS Microbiol Lett 234:357-370, 2004.
12. Grundy FJ, Henkin TM, Conservation of a transcription antitermination mechanism in amino acyl-tRNA synthetase and amino acid biosynthesis genes in gram-positive bacteria, J Mol Biol 235(2):798-804, 1994.
13. Grundy FJ, Henkin TM, The S box regulon: A new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria, Mol Microbiol 30(4):737-749, 1998.
14. Murphy BA, Grundy FJ, Henkin TM, Prediction of gene function in methylthioadenosine recycling from regulatory signals, J Bacteriol 184(8):2314-2318, 2002.
15. Panina EM, Vitreschak AG, Mironov AA, Gelfand MS, Regulation of biosynthesis and transport of aromatic amino acid in low-GC Gram-positive bacteria, FEMS Microbiol Lett 222:211-220, 2003.
16. Henkin TM, Glass BL, Grundy FJ, Analysis of the Bacillus subtilis tyrS gene: Conservation of a regulatory sequence in multiple tRNA synthetase genes, J Bacteriol 174(4):1299-1306, 1992.
17. Sudarsan N, Barrick JE, Breaker RR, Metabolite-binding RNA domains are present in the genes of eukaryotes, RNA 9(6):644-647, 2003.
18. Rodionov DA, Vitreschak AA, Mironov AA, Gelfand MS, Computational analysis of thiamin regulation in bacteria: Possible mechanisms and new THI-element-regulated genes, J Biol Chem 277(50):48949-48959, 2003.
19. Seliverstov AV, Putzer H, Gelfand MS, Lyubetsky VA, Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria, BMC Microbiol 5(54): 2005.
20. Seliverstov AV, Lyubetsky VA, Translation regulation of intron containing genes in chloroplasts, J Bioinform Comput Biol (in print).
21. Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M, Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR, New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control, Proc Natl Acad Sci USA 101(17):6421-6426, 2004.
22. Abreu-Goodger C, Ontiveros-Palacios N, Ciria R, Merino E, Conserved regulatory motifs in bacteria: Riboswitches and beyond, Trends Genet 20(10):475-479, 2004.
23. Vitreschak AA, Rodionov DA, Mironov AA, Gelfand MS, Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation, Nucl Acids Res 30(14):3141-3151, 2002.
24. Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS, Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element, RNA 9(9):1084-1097, 2003.
25. Das A, Crawford IP, Yanofsky C, Regulation of tryptophan operon expression by attenuation in cell free extracts of E. coli, J Biol Chem 257(15):8795-8798, 1982.
26. Nudler E, Mironov AS, The riboswitch control of bacterial metabolism, Trends Biochem Sci 29:11-17, 2004.
27. Landick R, Turnbough CL, Yanofsky C, Transcription attenuation, in Neidhardt FC, Curtiss R, Linn EC (eds.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed., American Society for Microbiology, Washington, DC, pp. 1263-1286, 1996.
28. Lyubetsky VA, Rubanov LI, Seliverstov AV, Pirogov SA, Model of gene expression regulation in bacteria via formation of RNA secondary structures, Mol Biol 40(3):440-453, 2006.
29. Mironov AA, Kister AE, Theoretical analysis of RNA secondary structure formation kinetics during transcription and translation. Accounting for imperfect helices, Mol Biol (Mosk) 19:1350-1357, 1985 (in Russian).
30. Mironov AA, Kister AE, A theoretical analysis of structural restructuring during formation of secondary RNA structures, Mol Biol (Mosk) 23:61-71, 1989, in Russian.
31. Mironov AA, Lebedev VF, A kinetic model of RNA folding, BioSystems 30:49-56, 1993.
32. Xayaphoummine A, Bucher T, Thalmann F, Isambert H, Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations, Proc Natl Acad Sci USA 100 15310-15315, 2003.
33. Xayaphoummine A, Bucher T, Isambert H, Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots, Nucl Acids Res 33(Web Server issue):W605-W610, 2005.
34. Elf J, Ehrenberg M, What Makes Ribosome-mediated transcriptional attenuation sensitive to amino acid limitation?" PLoS Comput Biol 1(1):e2, 2005.
35. Liu F, Ou-Yang ZC, Monte Carlo simulation for single RNA unfolding by force, Biophys J 88:76-84, 2005.
36. Gultyaev AP, van Batenburg FH, Pleij CW, The computer simulation of RNA folding pathways using a genetic algorithm, J Mol Biol 250 37-51, 1995.
37. Onoa B, Tinoco Jr. I, RNA folding and unfolding, Curr Opin Struct Biol 14:374-379, 2004.
38. Dirks RM, Lin M, Winfree E, Pierce NA, Paradigms for computational nucleic acid design, Nucl Acids Res 32:1392-1403, 2004.
39. Flamm C, Fontana W, Hofacker IL, Schuster P, RNA folding at elementary step resolution, RNA 6:325-338, 2000.
40. Kawasaki K, Diffusion constants near the critical point for timedependent Ising models, Phys Rev 145:224-230, 1966.
41. Zuker M, Mfold web server for nucleic acid folding and hybridization prediction, Nucl Acids Res 31(13):3406-3415, 2003.
42. Berg P, Singer M, Genes and Genomes, University Science Books, Mill Valley, 1991.
43. Mathews DH, Sabina J, Zuker M, Turner DH, Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure, J Mol Biol 288:911-940, 1999.
44. Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH, Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure, PNAS 101(19):7287-7292, 2004.
45. Dima I, Hyeon C, Thirumalai D, Extracting stacking interaction parameters for RNA from the data set of native structures, J Mol Biol 347(1):53-69, 2005.
46. Lawler GF, Coyle LN, Lectures on Contemporary Probability, AMS, 1999.
47. Pirogov SA, Gorbunov KY, Lyubetsky VA, Macro- and microstates in a model of attenuator regulation of gene expression in bacteria, Proc RAS Conf "Issues of control and modeling in complex systems, VII International conference", 27 June-1 July 2005, RAS (Samara), pp. 210-215 (in Russian).
48. Lyubetsky VA, Pirogov SA, A model of attenuator regulation in bacteria, Proc RAS Conf "Issues of control and modeling in complex systems, VII International conference," 27 June-1 July 2005, RAS (Samara), pp. 205-210 (in Russian).
49. Lynn S, Kasper L, Gardner J, Contributions of RNA secondary structure and length of the thymidine tract to transcription termination at the thr operon attenuator, J Biol Chem 263:472-479, 1988.
50. Gotta SL, Miller OL Jr., French SL, rRNA transcription rate in Escherichia coli, J Bacteriol, 173(20):6647-6649, 1991.
51. Ventzel AD, Freydlin MI, Fluctuations in Dynamic Systems Under Minor Random Perturbances, Nauka, Moscow, 1979 (in Russian).
52. Wilson K, von Hippel P, Transcription termination at intrinsic terminators: The role of the RNA hairpin, Proc Natl Acad Sci USA 92:8793-8797, 1995.
53. Lin C, Paradkar AS, Vining LC, Regulation of an anthranilate synthase gene in Streptomyces venezuelae by a trp attenuator, Microbiology, 144:1971-1980, 1998.
54. Lyubetsky VA, Seliverstov AV, Estimating effectiveness of tryptophan biosynthesis regulation in bacteria with a classic attenuation model, Inform Process 6(1):55-57, 2006 (in Russian).
55. Heery DM, Dunican LK, "Cloning of the trp gene cluster from a tryptophanhyperproducing strain of Corynebacterium glutamicum: Identification of a mutation in the trp leader sequence", Appl Environ Microbiol 59:791-799, 1993.