The fitness landscapes of cis-Acting binding sites in different promoter and environmental contexts

PLoS Genetics

Volumn 6, Issue 7, 2010, Pages 1-14

  Shultzaberger, Ryan K ^a   Malashock, Daniel S ^a   Kirsch, Jack F ^a   Eisen, Michael B ^a,b,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; TETRACYCLINE RESISTANCE GENE; UNCLASSIFIED DRUG; DNA DIRECTED RNA POLYMERASE; RNA POLYMERASE SIGMA 70; SIGMA FACTOR; TETRACYCLINE; TRANSCRIPTION FACTOR;

ARTICLE; BINDING AFFINITY; BINDING SITE; CELL GROWTH; CONTROLLED STUDY; DNA SEQUENCE; DNA STRUCTURE; ENVIRONMENTAL FACTOR; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; GENE LIBRARY; NONHUMAN; OPERON; PLASMID; POLYMERASE CHAIN REACTION; PROMOTER REGION; PROTEIN EXPRESSION; QUANTITATIVE ANALYSIS; TRANSCRIPTION INITIATION; BIOLOGICAL MODEL; DRUG RESISTANCE; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE; REGULATORY SEQUENCE; THERMODYNAMICS;

ESCHERICHIA COLI;

BASE SEQUENCE; BINDING SITES; DNA-DIRECTED RNA POLYMERASES; DRUG RESISTANCE; ESCHERICHIA COLI; MODELS, GENETIC; PROMOTER REGIONS, GENETIC; REGULATORY SEQUENCES, NUCLEIC ACID; SIGMA FACTOR; TETRACYCLINE; THERMODYNAMICS; TRANSCRIPTION FACTORS;

EID: 77957357763     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1001042     Document Type: Article

References (34)

1. von Hippel PH, Berg OG (1986) On the specificity of DNA-protein interactions. Proc Natl Acad Sci USA 83: 1608-1612.
2. Schneider TD (1997) Information content of individual genetic sequences. J Theor Biol 189: 427-441.
3. Maerkl SJ, Quake SR (2007) A systems approach to measuring the binding energy landscapes of transcription factors. Science 315: 233-237.
4. Shultzaberger RK, Roberts LR, Lyakhov IG, Sidorov IA, Stephen AG, et al. (2007) Correlation between binding rate constants and individual information of E. coli Fis binding sites. Nucleic Acids Res 35: 5275-5283.
5. Dombroski AJ, Johnson BD, Lonetto M, Gross CA (1996) The sigma subunit of Escherichia coli RNA polymerase senses promoter spacing. Proc Natl Acad Sci USA 93: 8858-8862.
6. Martin RG, Gillette WK, Rhee S, Rosner JL (1999) Structural requirements for marbox function in transcriptional activation of mar/sox/rob regulon promoters in Escherichia coli: sequence, orientation and spatial relationship to the core promoter. Mol Microbiol 34: 431-441.
7. Hawley DK, McClure WR (1983) Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res 11: 2237-2255.
8. McClure WR (1985) Mechanism and control of transcription initiation in prokaryotes. Annu Rev Biochem 54: 171-204.
9. Browning DF, Busby SJ (2004) The regulation of bacterial transcription initiation. Nat Rev Microbiol 2: 57-65.
10. Bintu L, Buchler N, Garcia H, Gerland U, Hwa T, et al. (2005) Transcriptional regulation by the numbers: models. Current opinion in genetics & development 15: 116-124.
11. Shultzaberger RK, Chen Z, Lewis KA, Schneider TD (2007) Anatomy of Escherichia coli s70 promoters. Nucleic Acids Res 35: 771-788.
12. Gertz J, Siggia E, Cohen B (2008) Analysis of combinatorial cis-regulation in synthetic and genomic promoters.
13. Mustonen V, Kinney J, Callan C, Lassig M (2008) Energy-dependent fitness: A quantitative model for the evolution of yeast transcription factor binding sites. Proceedings of the National Academy of Sciences 105: 12376.
14. Fry C, Farnham P (1999) Context-dependent transcriptional regulation.
15. Hochschild A, Dove S (1998) Protein-Protein Contacts Minireview that Activate and Repress Prokaryotic Transcription. Cell 92: 597-600.
16. Roy S, Garges S, Adhya S (1998) Activation and repression of transcription by differential contact: two sides of a coin.
17. Kim J, Shapiro D (1996) In simple synthetic promoters YY1-induced DNA bending is important in transcription activation and repression. Nucleic acids research 24: 4341.
18. Sheridan S, Benham C, Hatfield G (1998) Activation of gene expression by a novel DNA structural transmission mechanism that requires supercoilinginduced DNA duplex destabilization in an upstream activating sequence. Journal of Biological Chemistry 273: 21298-21308.
19. Martin R, Gillette W, Martin N, Rosner J (2002) Complex formation between activator and RNA polymerase as the basis for transcriptional activation by MarA and SoxS in Escherichia coli. Molecular Microbiology 43: 355-370.
20. Shultzaberger RK, Chiang DY, Moses AM, Eisen MB (2007) Determining physical constraints in transcriptional initiation complexes using DNA sequence analysis. PLoS ONE 2: e1199. doi:10.1371/journal.pone.0001199.
21. Mandecki W, Reznikoff WS (1982) A lac promotor with a changed distance between 210 and 235 regions. Nucleic Acids Res 10: 903-912.
22. Martin R, Jair K, Wolf R, Rosner J (1996) Autoactivation of the marRAB multiple antibiotic resistance operon by the MarA transcriptional activator in Escherichia coli. Journal of bacteriology 178: 2216-2223.
23. Schneider TD, Stormo GD, Gold L, Ehrenfeucht A (1986) Information content of binding sites on nucleotide sequences. J Mol Biol 188: 415-431.
24. Schneider TD (1991) Theory of molecular machines. II. Energy dissipation from molecular machines. J Theor Biol 148: 125-137.
25. Dekel E, Alon U (2005) Optimality and evolutionary tuning of the expression level of a protein. Nature 436: 588-592.
26. Nguyen T, Phan Q, Duong L, Bertrand K, Lenski R (1989) Effects of carriage and expression of the TnlO tetracycline-resistance operon on the fitness of Escherichia coli K12. Molecular Biology and Evolution 6: 213-225.
27. Lenski R, Souza V, Duong L, Phan Q, Nguyen T, et al. (1994) Epistatic effects of promoter and repressor functions of the Tn10 tetracycline-resistance operon on the fitness of Escherichia coli. Molecular Ecology 3: 127-135.
28. Ellinger T, Behnke D, Bujard H, Gralla J (1994) Stalling of Escherichia coli RNA polymerase in the+ 6 to+ 12 region in vivo is associated with tight binding to consensus promoter elements. Journal of molecular biology 239: 455-465.
29. Fenton MS, Lee SJ, Gralla JD (2000) Escherichia coli promoter opening and 210 recognition: mutational analysis of s70. EMBO J 19: 1130-1137.
30. Sclavi B, Zaychikov E, Rogozina A, Walther F, Buckle M, et al. (2005) Real-time characterization of intermediates in the pathway to open complex formation by Escherichia coli RNA polymerase at the T7A1 promoter. Proc Natl Acad Sci USA 102: 4706-4711.
31. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning, A Laboratory Manual. Cold Spring Harbor New York: Cold Spring Harbor Laboratory, second edition.
32. Zheng L, Baumann U, Reymond J (2004) An efficient one-step site-directed and site-saturation mutagenesis protocol. Nucleic acids research 32: e115.
33. Schneider TD, Stephens RM (1990) Sequence logos: A new way to display consensus sequences. Nucleic Acids Res 18: 6097-6100.
34. Shultzaberger RK, Schneider TD (1999) Using sequence logos and information analysis of Lrp DNA binding sites to investigate discrepancies between natural selection and SELEX. Nucleic Acids Res 27: 882-887.