Single-stranded DNA-binding proteins [SSBs] - sources and applications in molecular biology

• Autorzy: Kur J. , Olszewski M. , Dlugolecka A. , Filipkowski P.
• Języki publikacji: EN

Abstrakty

EN

Single-stranded DNA-binding proteins (SSBs) play essential roles in DNA replication, recombination, and repair in bacteria, archaea and eukarya. The SSBs share a common core ssDNA-binding domain with a conserved OB (oligonucleotide/oligosaccharide binding) fold. This ssDNA-binding domain was presumably present in the common ancestor to all three major branches of life. In recent years, there has been an increasing interest in SSBs because they are useful for molecular biology methods and for analytical purposes. In this review, we concentrate on recent advances in the discovery of new sources of SSBs as well as certain aspects of their applications in analytical sciences.

Słowa kluczowe

EN

Thermus thermophilus; Thermus aquaticus; DNA replication; single-stranded DNA binding protein; recombination; bacteria; Escherichia coli; polymerase chain reaction; molecular biology

• Wydawca: -
• Czasopismo: Acta Biochimica Polonica
• Rocznik: 2005
• Tom: 52
• Numer: 3
• Opis fizyczny: p.569-574,ref.

Twórcy

autor

Kur J.

• Gdansk University of Technology, Gdansk, Poland

autor

Olszewski M.

autor

Dlugolecka A.

autor

Filipkowski P.

Bibliografia

• Alani E, Thresher R, Griffith JD, Kolodner RD (1992) Characterization of DNA-binding and strand-exchange stimulation properties of y-RPA, a yeast single-strand-DNA-binding protein. J Mol Biol 227: 54–71.
• Alberts BM, Frey L (1970) T4 bacteriophage gene 32: a structural protein in the replication and recombination of DNA. Nature 227: 1313–1318.
• Bernstein DA, Eggington JM, Killoran MP, Misic AM, Cox MM, Keck JL (2004) Crystal structure of the Deinococcus radiodurans single-stranded DNA-binding protein suggests a mechanism for coping with DNA damage. Proc Natl Acad Sci USA 101: 8575–8580.
• Bochkarev A, Pfuetzner RA, Edwards AM, Frappier L (1997) Structure of the single-stranded DNA-binding domain of replication protein A bound to DNA. Nature 385: 176–181.
• Bochkareva E, Frappier L, Edwards AM, Bochkarev A (1998) The RPA32 subunit of human replication protein A contains a single-stranded DNA-binding domain. J Biol Chem 273: 3932–3936.
• Brockman JM, Frutos AG, Corn RM (1999) A multistep chemical modification procedure to create DNA arrays on gold surfaces for the study of protein–DNA interactions with surface plasmon resonance imaging. J Am Chem Soc 121: 8044–8051.
• Bujalowski W, Overman LB, Lohman TM (1988) Binding mode transitions of Escherichia coli single strand binding protein–single-stranded DNA complexes. Cation, anion, pH, and binding density effects. J Biol Chem 163: 4629–4640.
• Chedin F, Seitz EM, Kowalczykowski SC (1998) Novel homologs of replication protein A in archaea: implications for the evolution of ssDNA–binding proteins. Trends Biochem Sci 23: 273–277.
• Curth U, Genschel J, Urbanke C, Greipel J (1996) In vitro and in vivo function of the C-terminus of Escherichia coli single-stranded DNA binding protein. Nucleic Acids Res 24: 2706–2711.
• Dąbrowski S, Kur J (1999) Cloning, overexpression, and purification of the recombinant His-tagged SSB protein of Escherichia coli and use in polymerase chain reactionamplification. Protein Exrp Purif 16: 96–102.
• Dąbrowski S, Olszewski M, Piątek R, Brillowska-Dąbrowska A, Konopa G, Kur J (2002a) Identification and characterization of single-stranded-DNA-binding proteins from Thermus thermophilus and Thermus aquaticus— new arrangement of binding domains. Microbiology 148: 3307–3315.
• Dąbrowski S, Olszewski M, Piątek R, Kur J (2002b) Novel thermostable ssDNA-binding proteins from Thermus thermophilus and T. aquaticus — expression and purification. Protein Expr Purif 26: 131–138.
• Drabovich A, Krylov SN (2004) Single-stranded-DNAbinding protein facilitates gel-free analysis of polymerase chain reaction products in capillary electrophoresis. J. Chromatogr A 1051: 171–175.
• Eggington JM, Haruta N, Wood EA, Cox MM (2004) The single-stranded DNA-binding protein of Deinococcus radiodurans. BMC Microbiol 4: 2.
• Genschel J, Litz L, Thole H, Roemling U, Urbanke C (1996) Isolation, sequencing and overproduction of the singlestranded DNA binding protein from Pseudomonas aeruginosa PAO. Gene 182: 137–143.
• Greipel J, Urbanke C, Mass G (1989) The single-stranded DNA binding protein of Escherichia coli. Physicochemical properties and biological functions. In Protein–Nucleic Acid Interaction, Saenger W, Heinemann U, eds, pp 61–86. Macmillan, London.
• Henricksen LA, Carter T, Dutta A, Wold MS (1996) Phosphorylation of human replication protein A by the DNA-dependent protein kinase is involved in the modulation of DNA replication. Nucleic Acids Res 24: 3107–3112.
• Kelly RC, von Hippel PH (1976) DNA “melting” proteins. III. Fluorescence “mapping” of the nucleic acid binding site of bacteriophage T4 gene 32-protein. J Biol Chem 251: 7229–7239.
• Kelly TJ, Simancek P, Brush GS (1998) Identification and characterization of a single-stranded DNA-binding protein from the archaeon Methanococcus jannaschii. Proc Natl Acad Sci USA 95: 14634–14639.
• Kerman K, Morita Y, Takamura Y, Ozsoz M, Tamiva E (2004) Modification of Escherichia coli single-stranded DNA binding protein with gold nanoparticles for electrochemical detection of DNA hybridization. Anal Chimica Acta 510: 169–174.
• Lin YL, Shivji KK, Chen C, Kolodner R, Wood RD, Dutta A (1998) The evolutionarily conserved zinc finger motif in the largest subunit of human replication protein A is required for DNA replication and mismatch repair but not for nucleotide excision repair. J Biol Chem 273: 1453–1461.
• Lindner C, Nijland R, van Hartskamp M, Bron S, Hamoen LW, Kuipers OP (2004) Differential expression of two paralogous genes of Bacillus subtilis encoding singlestranded DNA binding protein. J Bacteriol 186: 1097–1105.
• Lohman TM, Overman LB (1985) Two binding modes in Escherichia coli single strand binding protein–single stranded DNA complexes. Modulation by NaCl concentration. J Biol Chem 260: 3394–3603.
• Lohman TM, Bujalowski W (1994) Effects of base composition on the negative cooperativity and binding mode transitions of Escherichia coli SSB-single-stranded DNA complexes. Biochemistry 33: 6167–6176.
• Matsumoto T, Morimoto Y, Shibata N, Kinebuchi T, Shimamoto N, Tsukihara T, Yasuoka N (2000) Roles of functional loops and the C-terminal segment of a single- stranded DNA binding protein elucidated by X-ray structure analysis. J Biochem (Tokyo) 127: 329–335.
• Meyer RR, Laine PS (1990) The single-stranded DNA-binding protein of Escherichia coli. Microbiol Rev 54: 342–380.
• Meyer RR, Glassberg J, Kornberg A (1979) An Escherichia coli mutant defective in single-strand binding protein is defective in DNA replication. Proc Natl Acad Sci USA 76: 1702–1705.
• Moore SP, Erdile T, Kelly T, Fishel R (1991) The human homologous pairing protein HPP-1 is specifically stimulated by the cognate single-stranded binding protein hRP-A. Proc Natl Acad Sci USA 88: 9067–9071.
• Murzin AG (1993) OB (oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. EMBO J 12: 861–867.
• Olszewski M, Rębała K, Szczerkowska Z, Kur J (2005) Application of SSB-like protein from Thermus aquaticus in multiplex PCR of human Y-STR markers identification. Mol Cell Probes 19: 203–205.
• Perales C, Cava F, Meijer WJJ, Berenguer J (2003) Enhancement of DNA, cDNA synthesis and fidelity at high temperatures by a dimeric single-stranded DNA-binding protein. Nucleic Acids Res 31: 6473–6480.
• Pfuetzner RA, Bochkarev A, Frappier L, Edwards AM (1997) Replication protein A. Characterization and crystallization of the DNA binding domain. J Biol Chem 272: 430–434.
• Purnaparte K, Varshney U (1999) Cloning, over-expression and biochemical characterization of the single-stranded DNA binding protein from Mycobacterium tuberculosis. Eur J Biochem 264: 591–598.
• Richard DJ, Bell SD, White MF (2004) Physical and functional interaction of the archaeal single-stranded DNAbinding protein SSB with RNA polymerase. Nucleic Acids Res 32: 1065–1074.
• Raghunathan S, Kozlov AG, Lohman TM, Waksman G (2000) Structure of the DNA binding domain of E. Coli SSB bound to ssDNA. Nat Struct Biol 7: 648–652.
• Rapley R (1994) Enhancing PCR amplification and sequencing using DNA-binding proteins. Mol Biotechnol 2: 295–298.
• Sancar A, Williams K, Chase J, Rupp W (1981) Sequences of the ssb gene and protein. Proc Natl Acad Sci USA 78: 4274–4278.
• Sigal N, Delius H, Kornberg T, Gefter ML, Alberts B (1972) A DNA unwinding protein isolated from Escherichia coli: its interaction with DNA and DNA polymerase. Proc Natl Acad Sci USA 69: 3537–3541.
• Shamoo Y, Friedman AM, Parsons MR, Konigsberg WH, Steits TA (1995) Crystal structure of a replication fork single-stranded DNA binding protein (T4 gp 32) complexes to DNA. Nature 376: 362–366.
• Stassen AP, Folmer RH, Hilbers CW, Konings RN (1995) Single-stranded DNA-binding protein encoded by the filamentous bacteriophage M13: structural and functional characteristics. Mol Biol Rep 20: 109–127.
• Wadsworth RIM, White MF (2001) Identification and properties of the crenarchaeal single-stranded DNA binding protein from Sulfolobus solfataricus. Nucleic Acids Res 29: 914–920.
• Webster G, Genschel J, Curth U, Urbanke C, Kang C, Hilgenfeld R (1997) A common core for binding singlestranded DNA: structural comparison of the singlestranded DNA-binding proteins (SSB) from E. coli and human mitochondria. FEBS Lett 411: 313–316.
• Weiner JH, Bertsch LL, Kornberg A (1975) The deoxyribonucleic acid unwinding protein of Escherichia coli. Properties and functions in replication. J Biol Chem 250: 1972–1980.
• Williams KR, Koningsberg W (1978) Structural changes in the T4 gene 32 protein induced by DNA and polynucleotides. J Biol Chem 253: 2463–2470.
• Williams KR, Spicer EK, LoPresti MB, Guggenheimer RA, Chase JW (1983) Limited proteolysis studies on the Escherichia coli single-stranded DNA binding protein. Evidence for a functionally homologous domain in both the Escherichia coli and T4 DNA binding proteins. J Biol Chem 258: 3346–3355.
• Witte G, Urbanke C, Curth U (2005) Single-stranded DNAbinding protein of Deinococcus radiodurans: a biophysical characterization. Nucleic Acids Res 33: 1662–1670.
• Wold MS (1997) Replication protein A: a heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism. Annu Rev Biochem 66: 61–92.