Thermodynamic analysis of DNA binding by a Bacillus single stranded DNA binding protein

BMC Biochemistry

Volumn 13, Issue 1, 2012, Pages

  Biswas Fiss, Esther E ^a,b   Kukiratirat, Jirayu ^a   Biswas, Subhasis B ^a  

^a UNIVERSITY OF MEDICINE AND DENTISTRY OF NEW JERSEY   (United States)

^b THOMAS JEFFERSON UNIVERSITY   (United States)

Author keywords

DNA replication; Fluorescence anisotropy; Protein DNA complex; Single stranded DNA binding protein (SSB); ssDNA binding

Indexed keywords

AMINO ACID; BACTERIAL DNA; BACTERIAL PROTEIN; DNA POLYMERASE; SINGLE STRANDED DNA BINDING PROTEIN; DNA BINDING PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BACILLUS ANTHRACIS; BINDING AFFINITY; CONTROLLED STUDY; DNA BINDING; DNA RECOMBINATION; DNA REPAIR; DNA REPLICATION; DNA TEMPLATE; FLUORESCENCE RESONANCE ENERGY TRANSFER; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HYDROPHOBICITY; MOLECULAR CLONING; MOLECULAR EVOLUTION; NONHUMAN; PROKARYOTE; PROTEIN ASSEMBLY; PROTEIN STRUCTURE; THERMODYNAMICS; BACILLUS; CHEMICAL STRUCTURE; CHEMISTRY; GEL CHROMATOGRAPHY; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MOLECULAR GENETICS; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN BINDING; SEQUENCE HOMOLOGY;

BACILLUS (BACTERIUM); BACILLUS ANTHRACIS; BACTERIA (MICROORGANISMS); PROKARYOTA;

AMINO ACID SEQUENCE; BACILLUS; BACTERIAL PROTEINS; CHROMATOGRAPHY, GEL; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; DNA, BACTERIAL; DNA-BINDING PROTEINS; ELECTROPHORESIS, POLYACRYLAMIDE GEL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; SEQUENCE HOMOLOGY, AMINO ACID; THERMODYNAMICS;

EID: 84862174388     PISSN: None     EISSN: 14712091     Source Type: Journal    
DOI: 10.1186/1471-2091-13-10     Document Type: Article

References (53)

1. Mechanisms of single-stranded DNA-binding protein functioning in cellular DNA metabolism. Pestryakov PE, Lavrik OI, Biochemistry (Mosc) 2008 73 13 1388 1404 10.1134/S0006297908130026
2. From RPA to BRCA2: lessons from single-stranded DNA binding by the OB-fold. Bochkarev A, Bochkareva E, Curr Opin Struct Biol 2004 14 1 36 42 10.1016/j.sbi.2004.01.001 15102447
3. Replication protein A (RPA): the eukaryotic SSB. Iftode C, Daniely Y, Borowiec JA, Crit Rev Biochem Mol Biol 1999 34 3 141 180 10.1080/ 10409239991209255 10473346
4. Protein-nucleic acid interactions in bacteriophage phi 29 DNA replication. Salas M, Freire R, Soengas MS, Esteban JA, Mendez J, Bravo A, Serrano M, Blasco MA, Lazaro JM, Blanco L, et al. FEMS Microbiol Rev 1995 17 1-2 73 82 7669351
5. The single-stranded DNA-binding protein of Escherichia coli. Meyer RR, Laine PS, Microbiol Rev 1990 54 4 342 380 2087220
6. Sequences of the ssb gene and protein. Sancar A, Williams KR, Chase JW, Rupp WD, Proc Natl Acad Sci USA 1981 78 7 4274 4278 10.1073/pnas.78.7.4274 6270666
7. Cloning of uvrA, lexC and ssb genes of Escherichia coli. Sancar A, Rupp WD, Biochem Biophys Res Commun 1979 90 1 123 129 10.1016/0006-291X(79)91598-5 387033
8. Initiation of simian virus 40 DNA replication in vitro: large-tumor-antigen- and origin-dependent unwinding of the template. Wold MS, Li JJ, Kelly TJ, Proc Natl Acad Sci USA 1987 84 11 3643 3647 10.1073/pnas.84.11. 3643 3035543
9. Single-stranded DNA binding proteins required for DNA replication. Chase JW, Williams KR, Annu Rev Biochem 1986 55 103 136 10.1146/annurev.bi.55.070186. 000535 3527040
10. Functions of human replication protein A (RPA): from DNA replication to DNA damage and stress responses. Zou Y, Liu Y, Wu X, Shell SM, J Cell Physiol 2006 208 2 267 273 10.1002/jcp.20622 16523492
11. SSB as an organizer/mobilizer of genome maintenance complexes. Shereda RD, Kozlov AG, Lohman TM, Cox MM, Keck JL, Crit Rev Biochem Mol Biol 2008 43 5 289 318 10.1080/10409230802341296 18937104
12. The Escherichia coli dnaB replication protein is a DNA helicase. LeBowitz JH, McMacken R, J Biol Chem 1986 261 10 4738 4748 3007474
13. Modulation of enzymatic activities of Escherichia coli DnaB helicase by single-stranded DNA-binding proteins. Biswas EE, Chen PH, Biswas SB, Nucleic Acids Res 2002 30 13 2809 2816 10.1093/nar/gkf384 12087164
14. Enzymatic recognition of DNA replication origins. Stayton MM, Bertsch L, Biswas S, Burgers P, Dixon N, Flynn JE, Fuller R, Kaguni J, Kobori J, Kodaira M, et al. Cold Spring Harb Symp Quant Biol 1983 47 Pt 2 693 700 6345074
15. Complexes of Escherichia coli primase with the replication origin of G4 phage DNA. Stayton MM, Kornberg A, J Biol Chem 1983 258 21 13205 13212 6355106
16. Cryptic single-stranded-DNA binding activities of the phage lambda P and Escherichia coli DnaC replication initiation proteins facilitate the transfer of E. coli DnaB helicase onto DNA. Learn BA, Um SJ, Huang L, McMacken R, Proc Natl Acad Sci USA 1997 94 4 1154 1159 10.1073/pnas.94.4.1154 9037022
17. Regulation of dnaB function in DNA replication in Escherichia coli by dnaC and lambda P gene products. Biswas SB, Biswas EE, J Biol Chem 1987 262 16 7831 7838 3034907
18. RPA not that different from SSB. Krejci L, Sung P, Structure 2002 10 5 601 602 10.1016/S0969-2126(02)00765-7 12015141
19. A distinctive single-strand DNA-binding protein from the Archaeon Sulfolobus solfataricus. Haseltine CA, Kowalczykowski SC, Mol Microbiol 2002 43 6 1505 1515 10.1046/j.1365-2958.2002.02807.x 11971263
20. Functional analysis of multiple single-stranded DNA-binding proteins from Methanosarcina acetivorans and their effects on DNA synthesis by DNA polymerase BI. Robbins JB, Murphy MC, White BA, Mackie RI, Ha T, Cann IK, J Biol Chem 2004 279 8 6315 6326 14676214
21. Identification and properties of the crenarchaeal single-stranded DNA binding protein from Sulfolobus solfataricus. Wadsworth RI, White MF, Nucleic Acids Res 2001 29 4 914 920 10.1093/nar/29.4.914 11160923
22. Salt dependent binding of T4 gene 32 protein to single and double-stranded DNA: single molecule force spectroscopy measurements. Pant K, Karpel RL, Rouzina I, Williams MC, J Mol Biol 2005 349 2 317 330 10.1016/j.jmb.2005.03.065 15890198
23. The effect of the T7 and Escherichia coli DNA-binding proteins at the replication fork of bacteriophage T7. Nakai H, Richardson CC, J Biol Chem 1988 263 20 9831 9839 2838482
24. A mutation in E. coli SSB protein (W54S) alters intra-tetramer negative cooperativity and inter-tetramer positive cooperativity for single-stranded DNA binding. Ferrari ME, Fang J, Lohman TM, Biophys Chem 1997 64 1-3 235 251 9127948
25. Linkage of pH, anion and cation effects in protein-nucleic acid equilibria. Escherichia coli SSB protein-single stranded nucleic acid interactions. Overman LB, Lohman TM, J Mol Biol 1994 236 1 165 178 10.1006/jmbi.1994.1126 8107102
26. Dynamic Structural Rearrangements Between DNA Binding Modes of E. coli SSB Protein. Roy R, Kozlov AG, Lohman TM, Ha T, J Mol Biol 2007 369 5 1244 1257 10.1016/j.jmb.2007.03.079 17490681
27. Visualization of SSB-ssDNA complexes active in the assembly of stable RecA-DNA filaments. Griffith JD, Harris LD, Register J, Cold Spring Harb Symp Quant Biol 1984 49 553 559 10.1101/SQB.1984.049.01.062 6397310
28. Escherichia coli single-strand binding protein organizes single-stranded DNA in nucleosome-like units. Chrysogelos S, Griffith J, Proc Natl Acad Sci USA 1982 79 19 5803 5807 10.1073/pnas.79.19.5803 6764531
29. Phylogenetic and functional analysis of the bacteriophage P1 single-stranded DNA-binding protein. Bendtsen JD, Nilsson AS, Lehnherr H, J Virol 2002 76 19 9695 9701 10.1128/JVI.76.19.9695-9701.2002 12208948
30. Multiple independent horizontal transfers of informational genes from bacteria to plasmids and phages: implications for the origin of bacterial replication machinery. Moreira D, Mol Microbiol 2000 35 1 1 5 10.1046/j.1365-2958.2000.01692.x 10632872
31. Differential expression of two paralogous genes of Bacillus subtilis encoding single-stranded DNA binding protein. Lindner C, Nijland R, van Hartskamp M, Bron S, Hamoen LW, Kuipers OP, J Bacteriol 2004 186 4 1097 1105 10.1128/JB.186.4.1097-1105.2004 14762004
32. Differential single-stranded DNA binding properties of the paralogous SsbA and SsbB proteins from Streptococcus pneumoniae. Grove DE, Willcox S, Griffith JD, Bryant FR, J Biol Chem 2005 280 12 11067 11073 10.1074/jbc. M414057200 15647253
33. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR, et al. Nature 2003 423 6935 81 86 10.1038/nature01586 12721629
34. Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis. Takami H, Nakasone K, Takaki Y, Maeno G, Sasaki R, Masui N, Fuji F, Hirama C, Nakamura Y, Ogasawara N, et al. Nucleic Acids Res 2000 28 21 4317 4331 10.1093/nar/28.21. 4317 11058132
35. Interaction of E. coli single-stranded DNA binding protein (SSB) with exonuclease I. The carboxy-terminus of SSB is the recognition site for the nuclease. Genschel J, Curth U, Urbanke C, Biol Chem 2000 381 3 183 192 10782989
36. In vitro and in vivo function of the C-terminus of Escherichia coli single-stranded DNA binding protein. Curth U, Genschel J, Urbanke C, Greipel J, Nucleic Acids Res 1996 24 14 2706 2711 10.1093/nar/24.14.2706 8759000
37. Roles of functional loops and the C-terminal segment of a single-stranded DNA binding protein elucidated by X-Ray structure analysis. Matsumoto T, Morimoto Y, Shibata N, Kinebuchi T, Shimamoto N, Tsukihara T, Yasuoka N, J Biochem 2000 127 2 329 335 10.1093/oxfordjournals.jbchem.a022611 10731701
38. OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. Murzin AG, EMBO J 1993 12 3 861 867 8458342
39. Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined by multiwavelength x-ray diffraction on the selenomethionyl protein at 2.9-A resolution. Raghunathan S, Ricard CS, Lohman TM, Waksman G, Proc Natl Acad Sci USA 1997 94 13 6652 6657 10.1073/pnas.94.13.6652 9192620
40. Affinity and sequence specificity of DNA binding and site selection for primer synthesis by Escherichia coli primase. Khopde S, Biswas EE, Biswas SB, Biochemistry 2002 41 50 14820 14830 10.1021/bi026711m 12475230
41. Salt dependence of DNA binding by Thermus aquaticus and Escherichia coli DNA polymerases. Datta K, LiCata VJ, J Biol Chem 2003 278 8 5694 5701 10.1074/jbc.M208133200 12466277
42. Structure of the DNA binding domain of E. coli SSB bound to ssDNA. Raghunathan S, Kozlov AG, Lohman TM, Waksman G, Nat Struct Biol 2000 7 8 648 652 10.1038/77943 10932248
43. Protein structure homology modeling using SWISS-MODEL workspace. Bordoli L, Kiefer F, Arnold K, Benkert P, Battey J, Schwede T, Nat Protoc 2009 4 1 1 13 19131951
44. The SWISS-MODEL Repository and associated resources. Kiefer F, Arnold K, Kunzli M, Bordoli L, Schwede T, Nucleic Acids Res 2009 37 Database issue 387 D392 18931379
45. Characterization of the structural and functional defect in the Escherichia coli single-stranded DNA binding protein encoded by the ssb-1 mutant gene. Expression of the ssb-1 gene under lambda pL regulation. Williams KR, Murphy JB, Chase JW, J Biol Chem 1984 259 19 11804 11811 6384214
46. Crystal structure of the Deinococcus radiodurans single-stranded DNA-binding protein suggests a mechanism for coping with DNA damage. Bernstein DA, Eggington JM, Killoran MP, Misic AM, Cox MM, Keck JL, Proc Natl Acad Sci USA 2004 101 23 8575 8580 10.1073/pnas.0401331101 15159541
47. Single-stranded DNA-binding protein complex from Helicobacter pylori suggests an ssDNA-binding surface. Chan KW, Lee YJ, Wang CH, Huang H, Sun YJ, J Mol Biol 2009 388 3 508 519 10.1016/j.jmb.2009.03.022 19285993
48. Escherichia coli single-stranded DNA-binding protein: multiple DNA-binding modes and cooperativities. Lohman TM, Ferrari ME, Annu Rev Biochem 1994 63 527 570 10.1146/annurev.bi.63.070194.002523 7979247
49. Kornberg A, Baker TA, DNA Replication Freeman, New York, NY 1992
50. A temperature-sensitive single-stranded DNA-binding protein from Escherichia coli. Meyer RR, Glassberg J, Scott JV, Kornberg A, J Biol Chem 1980 255 7 2897 2901 6244299
51. Discovery, characterization and comparison of inhibitors of Bacillus anthracis and Staphylococcus aureus replicative DNA helicases. Aiello D, Barnes MH, Biswas EE, Biswas SB, Gu S, Williams JD, Bowlin TL, Moir DT, Bioorg Med Chem 2009 17 4466 4476 10.1016/j.bmc.2009.05.014 19477652
52. Fluorescence anisotropy controlled by light quenching. Gryczynski I, Gryczynski Z, Lakowicz JR, Photochem Photobiol 1998 67 6 641 646 10.1111/j.1751-1097.1998.tb09467.x 9648529
53. Lakowicz JR, Principles of Fluorescence Spectroscopy Springer Sciences + Business Media, LLC, New York 2006