On the selection and evolution of regulatory DNA motifs

Journal of Molecular Evolution

Volumn 55, Issue 4, 2002, Pages 386-400

  Gerland, Ulrich ^a,b   Hwa, Terence ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Error threshold; Mutation selection model; Regulatory sequences; Transcription regulation

Indexed keywords

REGULATOR PROTEIN;

ANALYTICAL ERROR; ARTICLE; BINDING SITE; DNA SEQUENCE; GENE MUTATION; GENETIC SELECTION; GENETIC TRANSCRIPTION; MOLECULAR EVOLUTION; MOLECULAR MODEL; NONHUMAN; PROTEIN BINDING; REGULATORY SEQUENCE; TRANSCRIPTION REGULATION;

BINDING SITES; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, BACTERIAL; GENE EXPRESSION REGULATION, VIRAL; GENES, REGULATOR; MODELS, GENETIC; MUTATION; SELECTION (GENETICS);

EID: 0036787402     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-002-2335-z     Document Type: Article

References (37)

1. Atkins PW (1998) Physical chemistry. Freeman, New York
2. Baake E, Baake M, Wagner H (1997) Ising quantum chain is equivalent to a model of biological evolution. Phys Rev Lett 78:559-562
3. Berg OG, Winter RB, von Hippel PH (1981) Diffusion-driven mechanisms of protein translocation on nucleic acids. I. Models and theory. Biochemistry 20:6929-6948
4. Berg OG, von Hippel PH (1987) Selection of DNA binding sites by regulatory proteins. 1. Statistical-mechanical theory and application to operators and promoters. J Mol Biol 193:723-750
5. Busby S, Ebright R (1999) Transcription activation by catabolite activator protein (CAP). J Mol Biol 293:199-213
6. Eigen M (1971) Self-organization of matter and the evolution of biological macromolecules. Naturwissenschaften 58:465-523
7. Eigen M, McCaskill JS, Schuster P (1989) The molecular quasispecies. Adv Chem Phys 75:149-263
8. Fields DS, He Y, Al-Uzri AY, Stormo GD (1997) Quantitative specificity of the mnt represson. J Mol Biol 271:178-194
9. Gerhart J, Kirschner M (1997) Cells, embryos and evolution. Blackwell Scientific, Oxford
10. Goldstein RA (2001) Evolutionary perspectives on protein structure, stability, and functionality. In: Broglia RA, Shaknovich EJ (eds) Proceedings of the International School of Physics "E. Fermi," Course CXLV
11. Gralla JD, Collado-Vides J (1996) Organization and function of transcription regulatory elements. In: Neidhardt FC et al. (eds) Cellular and molecular biology: Escherichia coli and Salmonella, 2nd ed. American Society for Microbiology, Washington, DC, pp 1232-1245
12. Hatano N, Nelson DR (1997) Vortex pinning and non-Hermitian quantum mechanics. Phys Rev B 56:8651-8673
13. Hermisson J, Wagner H, Baake M (2001) Four-state quantum chain as a model of sequence evolution. J Stat Phys 102:315-343
14. Higgs P (1994) Error thresholds and stationary mutant distributions in multilocus diploid genetics models. Genet Res 63:63-78
15. Kondrashov AS (1988) Deleterious mutations and the evolution of sexual reproduction. Nature 336:435-440
16. Langdon RC, Hochschild A (1999) A genetic method for dissecting the mechanism of transcriptional activator synergy by identical activators. Proc Natl Acad Sci USA 96:12673-12678
17. Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC (1993) Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment. Science 262:208-214
18. Lubensky DK, Nelson DR (2000) Pulling pinned polymers and unzipping DNA. Phys Rev Lett 85:1572-1575
19. Nowak M, Schuster P (1989) Error thresholds of replication in finite populations: Mutation frequencies and the onset of Muller's ratchet. J Theor Biol 137:375-395
20. Oda M, Furukawa K, Ogata K, Sarai A, Nakamura H (1998) Thermodynamics of specific and non-specific DNA binding by the c-Myb DNA-binding domain. J Mol Biol 276:571-590
21. Ohta T (1992) The nearly neutral theory of molecular evolution. Annu Rev Ecol Syst 23:263-286
22. Peliti L (2002) Quasispecies evolution in general mean-field landscapes. Europhys Lett 57:745-751
23. Ptashne M (1992) A genetic switch: Phage [lambda] and higher organisms. Cell Press/Blackwell Scientific, Cambridge, MA
24. Saier MH, Ramseier TM, Reizer J (1996) Regulation of carbon utilization. In: Neidhardt FC, et al. (eds) Escherichia coli and Salmonella: Cellular and molecular biology. ASM, Washington, DC, pp 1325-1343
25. Salgado H, Santos-Zavaleta A, Gama-Castro S, Millan-Zarate D, Blattner FR, Collado-Vides J (2000) RegulonDB (version 3.0): transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Res 28:65-67
26. Sarai A, Takeda Y (1989) Lambda repressor recognizes the approximately 2-fold symmetric half-operator sequences asymmetrically. Proc Natl Acad Sci USA 86:6513-6517
27. Schuster P, Swetina J (1988) Stationary mutant distributions and evolutionary optimization. Bull Math Biol 50:635-660
28. Sengupta AM, Djordjevic M, Shraiman BI (2002) Specificity and robustness in transcription control networks. Proc Natl Acad Sci USA 99:2072-2077
29. Stormo GD, Fields DS (1998) Specificity, free energy and information content in protein-DNA interactions. TIBS 23:109-113
30. Stormo GD, Hartzell GW (1989) Identifying protein-binding sites from unaligned DNA fragments. Proc Natl Acad Sci USA 86:1183-1187
31. Takeda Y, Sarai A, Rivera VM (1989) Analysis of the sequence-specific interactions between Cro repressor and operator DNA by systematic base substitution experiments. Proc Natl Acad Sci USA 86:439-443
32. Tsimring LS, Levine H, Kessler DA (1996) RNA virus evolution via a fitness-space model. Phys Rev Lett 76:4440-4443
33. von Hippel PH (1979) In: Goldberger RF (eds) Biological regulation and development. Plenum, New York, pp 279-347
34. von Hippel PH, Berg OG (1986) On the specificity of DNA-protein interactions. Proc Natl Acad Sci USA 83:1608-1612
35. Wagner A (2000) The role of population size, pleiotropy and fitness effects of mutations in the evolution of overlapping gene functions. Genetics 154:1389-1401
36. Winter RB, von Hippel PH (1981) Diffusion-driven mechanisms of protein translocation on nucleic acids. 2. The Escherichia coli repressor-operator interaction: Equilibrium measurements. Biochemistry 20:6948-6960
37. Winter RB, Berg OG, von Hippel PH (1981) Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli repressor-operator interaction: kinetic measurements and conclusions. Biochemistry 20:6961-6977