Δg-based prediction and experimental confirmation of SYCRP1-binding sites on the Synechocystis genome

FEBS Journal

Volumn 275, Issue 19, 2008, Pages 4786-4795

  Omagari, Katsumi ^a   Yoshimura, Hidehisa ^b   Suzuki, Takayuki ^b   Takano, Mitunori ^c   Ohmori, Masayuki ^b,d   Sarai, Akinori ^e  

^a NAGOYA CITY UNIV MEDICAL SCHOOL   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c WASEDA UNIVERSITY   (Japan)

^d CHUO UNIVERSITY   (Japan)

^e KYUSHU INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

Additivity; Binding free energy change; DNA binding sites; Prediction; Regulatory protein

Indexed keywords

BACTERIAL PROTEIN; BINDING PROTEIN; PROTEIN SYCRP1; UNCLASSIFIED DRUG; CYCLIC AMP RECEPTOR; SYCRP1 PROTEIN, SYNECHOCYSTIS;

ARTICLE; BASE PAIRING; BINDING SITE; CONSENSUS SEQUENCE; CONTROLLED STUDY; GENE SEQUENCE; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN BINDING; SYNECHOCYSTIS; BACTERIAL GENOME; CHEMISTRY; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; POINT MUTATION; THERMODYNAMICS;

SYNECHOCYSTIS; SYNECHOCYSTIS SP.;

BACTERIAL PROTEINS; BASE SEQUENCE; BINDING SITES; GENOME, BACTERIAL; MOLECULAR SEQUENCE DATA; POINT MUTATION; RECEPTORS, CYCLIC AMP; SYNECHOCYSTIS; THERMODYNAMICS;

EID: 51749086005     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2008.06618.x     Document Type: Article

References (29)

1. Yoshimura H, Hisabori T, Yanagisawa S Ohmori M (2000) Identification and characterization of a novel cAMP receptor protein in the cyanobacterium Synechocystis sp. PCC 6803. J Biol Chem 275, 6241 6245.
2. Yoshimura H, Yanagisawa S, Kanehisa M Ohmori M (2002) Screening for the target gene of cyanobacterial cAMP receptor protein SYCRP1. Mol Microbiol 43, 843 853.
3. Yoshimura H, Yanagisawa S, Kanehisa M Ohmori M (2002) A cAMP receptor protein, SYCRP1, is responsible for the cell motility of Synechocystis sp. PCC 6803. Plant Cell Physiol 43, 460 463.
4. Ohmori M Okamoto S (2004) Photoresponsive cAMP signal transduction in cyanobacteria. Photochem, Photobiol Sci 3, 503 511.
5. Terauchi K Ohmori M (2004) Blue light stimulates cyanobacterial motility via a cAMP signal transduction system. Mol Microbiol 52, 303 309.
6. Sarai A Kono H 2003) DNA-Protein Interactions: Target predictions. In Handbook of Computational Biology (Crabbe MJC Konopka AK, eds) pp. 241 278. Marcel Dekker Inc., New York.
7. Stormo GD Fields DS (1998) Specificity, free energy and information content in protein-DNA interactions. Trends Biochem Sci 23, 109 113.
8. Frech K, Quandt K Werner T (1997) Finding protein-binding sites in DNA sequences: the next generation. Trends Biochem Sci 22, 103 104.
9. Kono H Sarai A (1999) Structure-based prediction of DNA target sites by regulatory proteins. Proteins 35, 114 131.
10. Deng QL, Ishii S Sarai A (1996) Binding site analysis of c-Myb: screening of potential binding sites by using the mutation matrix derived from systematic binding affinity measurements. Nucleic Acids Res 24, 766 774.
11. 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.
12. 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.
13. Tanikawa J, Yasukawa T, Enari M, Ogata K, Nishimura Y, Ishii S Sarai A (1993) Recognition of specific DNA sequences by the c-myb protooncogene product: role of three repeat units in the DNA-binding domain. Proc Natl Acad Sci USA 90, 9320 9324.
14. Hao D, Yamasaki K, Sarai A Ohme-Takagi M (2002) Determinants in the sequence specific binding of two plant transcription factors, CBF1 and NtERF2, to the DRE and GCC motifs. Biochemistry 41, 4202 4208.
15. Gunasekera A, Ebright YW Ebright RH (1992) DNA sequence determinants for binding of the Escherichia coli catabolite gene activator protein. J Biol Chem 267, 14713 14720.
16. Omagari K, Yoshimura H, Takano M, Hao D, Ohmori M, Sarai A Suyama A (2004) Systematic single base-pair substitution analysis of DNA binding by the cAMP receptor protein in cyanobacterium Synechocystis sp. PCC 6803. FEBS Lett 563, 55 58.
17. Cameron AD Redfield RJ (2006) Non-canonical CRP sites control competence regulons in Escherichia coli and many other gamma-proteobacteria. Nucleic Acids Res 34, 6001 6014.
18. Pyles EA, Chin AJ Lee JC (1998) Escherichia coli cAMP receptor protein-DNA complexes. 1. Energetic contributions of half-sites and flanking sequences in DNA recognition. Biochemistry 37, 5194 5200.
19. Parkinson G, Wilson C, Gunasekera A, Ebright YW, Ebright RE Berman HM (1996) Structure of the CAP-DNA complex at 2.5 angstroms resolution: a complete picture of the protein-DNA interface. J Mol Biol 260, 395 408.
20. Shanblatt SH Revzin A (1986) The binding of catabolite activator protein and RNA polymerase to the Escherichia coli galactose and lactose promoters probed by alkylation interference studies. J Biol Chem 261, 10885 10890.
21. Man TK Stormo GD (2001) Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay. Nucleic Acids Res 29, 2471 2478.
22. Bulyk ML, Johnson PL Church GM (2002) Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res 30, 1255 1261.
23. Benos PV, Bulyk ML Stormo GD (2002) Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res 30, 4442 4451.
24. Benos PV, Lapedes AS Stormo GD (2002) Is there a code for protein-DNA recognition? Probab(ilistical)ly... Bioessays 24, 466 475.
25. Berggrun A Sauer RT (2001) Contributions of distinct quaternary contacts to cooperative operator binding by Mnt repressor. Proc Natl Acad Sci USA 98, 2301 2305.
26. Jin Y, Mead J, Li T, Wolberger C Vershon AK (1995) Altered DNA recognition and bending by insertions in the alpha 2 tail of the yeast a1/alpha 2 homeodomain heterodimer. Science 270, 290 293.
27. Li T, Stark MR, Johnson AD Wolberger C (1995) Crystal structure of the MATa1/MAT alpha 2 homeodomain heterodimer bound to DNA. Science 270, 262 269.
28. Gromiha MM, Siebers JG, Selvaraj S, Kono H Sarai A (2004) Intermolecular and intramolecular readout mechanisms in protein-DNA recognition. J Mol Biol 337, 285 294.
29. Gill SC von Hippel PH (1989 Calculation of protein extinction coefficients from amino acid sequence data. Anal Biochem 182, 319 326 (erratum appears in Anal Biochem189, 283).