Skip to main content

Single-Stranded DNA-Binding Proteins in the Archaea

  • Protocol
  • First Online:
Book cover Single Stranded DNA Binding Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2281))

Abstract

Single-stranded (ss) DNA-binding proteins are found in all three domains of life where they play vital roles in nearly all aspects of DNA metabolism by binding to and stabilizing exposed ssDNA and acting as platforms onto which DNA-processing activities can assemble. The ssDNA-binding factors SSB and RPA are extremely well conserved across bacteria and eukaryotes, respectively, and comprise one or more OB-fold ssDNA-binding domains. In the third domain of life, the archaea, multiple types of ssDNA-binding protein are found with a variety of domain architectures and subunit compositions, with OB-fold ssDNA-binding domains being a characteristic of most, but not all. This chapter summarizes current knowledge of the distribution, structure, and biological function of the archaeal ssDNA-binding factors, highlighting key features shared between clades and those that distinguish the proteins of different clades from one another. The likely cellular functions of the proteins are discussed and gaps in current knowledge identified.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 149.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Marceau AH (2012) Functions of single-strand DNA-binding proteins in DNA replication, recombination, and repair. Methods Mol Biol 922:1–21

    CAS  PubMed  Google Scholar 

  2. Theobald DL, Mitton-Fry RM, Wuttke DS (2003) Nucleic acid recognition by OB-fold proteins. Annu Rev Biophys Biomol Struct 32:115–133

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Bianco PR (2017) The tale of SSB. Prog Biophys Mol Biol 127:111–118

    Article  CAS  PubMed  Google Scholar 

  4. Eggington JM, Haruta N, Wood EA, Cox MM (2004) The single-stranded DNA-binding protein of Deinococcus radiodurans. BMC Microbiol 4:2

    Article  PubMed  PubMed Central  Google Scholar 

  5. 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 U S A 101:8575–8580

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Iftode C, Daniely Y, Borowiec JA (1999) Replication protein A (RPA): the eukaryotic SSB. Crit Rev Biochem Mol Biol 34:141–180

    Article  CAS  PubMed  Google Scholar 

  7. Wold MS (1997) Replication protein A: a heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism. Annu Rev Biochem 66:61–92

    Article  CAS  PubMed  Google Scholar 

  8. Prakash A, Borgstahl GE (2012) The structure and function of replication protein A in DNA replication. Subcell Biochem 62:171–196

    Article  CAS  PubMed  Google Scholar 

  9. Fan J, Pavletich NP (2012) Structure and conformational change of a replication protein A heterotrimer bound to ssDNA. Genes Dev 26:2337–2347

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Kemp MG, Mason AC, Carreira A, Reardon JT, Haring SJ, Borgstahl GE, Kowalczykowski SC, Sancar A, Wold MS (2010) An alternative form of replication protein A expressed in normal human tissues supports DNA repair. J Biol Chem 285:4788–4797

    Article  CAS  PubMed  Google Scholar 

  11. Haring SJ, Humphreys TD, Wold MS (2010) A naturally occurring human RPA subunit homolog does not support DNA replication or cell-cycle progression. Nucleic Acids Res 38:846–858

    Article  CAS  PubMed  Google Scholar 

  12. Mason AC, Haring SJ, Pryor JM, Staloch CA, Gan TF, Wold MS (2009) An alternative form of replication protein A prevents viral replication in vitro. J Biol Chem 284:5324–5331

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Flynn RL, Zou L (2010) Oligonucleotide/oligosaccharide-binding fold proteins: a growing family of genome guardians. Crit Rev Biochem Mol Biol 45:266–275

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Li Y, Bolderson E, Kumar R, Muniandy PA, Xue Y, Richard DJ, Seidman M, Pandita TK, Khanna KK, Wang W (2009) HSSB1 and hSSB2 form similar multiprotein complexes that participate in DNA damage response. J Biol Chem 284:23525–23531

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Richard DJ, Bolderson E, Cubeddu L, Wadsworth RI, Savage K, Sharma GG, Nicolette ML, Tsvetanov S, McIlwraith MJ, Pandita RK et al (2008) Single-stranded DNA-binding protein hSSB1 is critical for genomic stability. Nature 453:677–681

    Article  CAS  PubMed  Google Scholar 

  16. Wu Y, Lu J, Kang T (2016) Human single-stranded DNA binding proteins: guardians of genome stability. Acta Biochim Biophys Sin Shanghai 48:671–677

    Article  CAS  PubMed  Google Scholar 

  17. Taib, N. and Gribaldo, S. (2020). SSB/RPA distribution in the Archaea—dataset. https://data.mendeley.com/datasets/gc4xm4jn5x/draft?a=cdfb530e-9551-45e2-a180-d3e94ea82074

  18. 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 U S A 95:14634–14639

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Chédin 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

    Article  PubMed  Google Scholar 

  20. Skowyra A, MacNeill SA (2012) Identification of essential and non-essential single-stranded DNA-binding proteins in a model archaeal organism. Nucleic Acids Res 40:1077–1090

    Article  CAS  PubMed  Google Scholar 

  21. Stroud A, Liddell S, Allers T (2012) Genetic and biochemical identification of a novel single-stranded DNA-binding complex in Haloferax volcanii. Front Microbiol 3:224

    Article  PubMed  PubMed Central  Google Scholar 

  22. Komori K, Ishino Y (2001) Replication protein A in Pyrococcus furiosus is involved in homologous DNA recombination. J Biol Chem 276:25654–25660

    Google Scholar 

  23. Nagata M, Ishino S, Yamagami T, Ishino Y (2019) Replication protein A complex in Thermococcus kodakarensis interacts with DNA polymerases and helps their effective strand synthesis. Biosci Biotechnol Biochem 83:695–704

    Article  CAS  PubMed  Google Scholar 

  24. Adam PS, Borrel G, Brochier-Armanet C, Gribaldo S (2017) The growing tree of Archaea: new perspectives on their diversity, evolution and ecology. ISME J 11:2407–2425

    Article  PubMed  PubMed Central  Google Scholar 

  25. Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, Sutton GG, Blake JA, FitzGerald LM, Clayton RA, Gocayne JD et al (1996) Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273:1058–1073

    Article  CAS  PubMed  Google Scholar 

  26. Sarmiento F, Mrazek J, Whitman WB (2013) Genome-scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Methanococcus maripaludis. Proc Natl Acad Sci U S A 110:4726–4731

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Kelman Z, Pietrokovski S, Hurwitz J (1999) Isolation and characterization of a split B-type DNA polymerase from the archaeon Methanobacterium thermoautotrophicum ΔH. J Biol Chem 274:28751–28761

    Article  CAS  PubMed  Google Scholar 

  28. Woodman IL, Brammer K, Bolt EL (2011) Physical interaction between archaeal DNA repair helicase Hel308 and replication protein A (RPA). DNA Repair (Amst) 10:306–313

    Article  CAS  Google Scholar 

  29. Robbins JB, McKinney MC, Guzman CE, Sriratana B, Fitz-Gibbon S, Ha T, Cann IK (2005) The Euryarchaeota, Nature’s medium for engineering of single-stranded DNA-binding proteins. J Biol Chem 280:15325–15339

    Google Scholar 

  30. Robbins JB, Murphy MC, White BA, Mackie RI, Ha T, Cann IK (2004) Functional analysis of multiple single-stranded DNA-binding proteins from Methanosarcina acetivorans and their effects on DNA synthesis by DNA polymerase BI. J Biol Chem 279:6315–6326

    Article  CAS  PubMed  Google Scholar 

  31. Lin Y, Robbins JB, Nyannor EK, Chen YH, Cann IK (2005) A CCCH zinc finger conserved in a replication protein A homolog found in diverse Euryarchaeotes. J Bacteriol 187:7881–7889

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Lin Y, Guzman CE, McKinney MC, Nair SK, Ha T, Cann IK (2006) Methanosarcina acetivorans flap endonuclease 1 activity is inhibited by a cognate single-stranded-DNA-binding protein. J Bacteriol 188:6153–6167

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Lin Y, Lin LJ, Sriratana P, Coleman K, Ha T, Spies M, Cann IK (2008) Engineering of functional replication protein a homologs based on insights into the evolution of oligonucleotide/oligosaccharide-binding folds. J Bacteriol 190:5766–5780

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Farkas JA, Picking JW, Santangelo TJ (2013) Genetic techniques for the archaea. Annu Rev Genet 47:539–561

    Article  CAS  PubMed  Google Scholar 

  35. Winter JA, Patoli B, Bunting KA (2012) DNA binding in high salt: analysing the salt dependence of replication protein A3 from the halophile Haloferax volcanii. Archaea 2012:719092

    PubMed  PubMed Central  Google Scholar 

  36. Delpech F, Collien Y, Mahou P, Beaurepaire E, Myllykallio H, Lestini R (2018) Snapshots of archaeal DNA replication and repair in living cells using super-resolution imaging. Nucleic Acids Res 46:10757–10770

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Karan R, DasSarma P, Balcer-Kubiczek E, Weng RR, Liao CC, Goodlett DR, Ng WV, Dassarma S (2014) Bioengineering radioresistance by overproduction of RPA, a mammalian-type single-stranded DNA-binding protein, in a halophilic archaeon. Appl Microbiol Biotechnol 98:1737–1747

    Article  CAS  PubMed  Google Scholar 

  38. McCready S, Muller JA, Boubriak I, Berquist BR, Ng WL, Dassarma S (2005) UV irradiation induces homologous recombination genes in the model archaeon, Halobacterium sp. NRC-1. Saline Syst 1:3

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  39. Webb KM, Yu J, Robinson CK, Noboru T, Lee YC, DiRuggiero J (2013) Effects of intracellular Mn on the radiation resistance of the halophilic archaeon Halobacterium salinarum. Extremophiles 17:485–497

    Article  CAS  PubMed  Google Scholar 

  40. Whitehead K, Kish A, Pan M, Kaur A, Reiss DJ, King N, Hohmann L, DiRuggiero J, Baliga NS (2006) An integrated systems approach for understanding cellular responses to gamma radiation. Mol Syst Biol 2:47

    Article  PubMed  PubMed Central  Google Scholar 

  41. DeVeaux LC, Muller JA, Smith J, Petrisko J, Wells DP, DasSarma S (2007) Extremely radiation-resistant mutants of a halophilic archaeon with increased single-stranded DNA-binding protein (RPA) gene expression. Radiat Res 168:507–514

    Article  CAS  PubMed  Google Scholar 

  42. Evans JJ, Gygli PE, McCaskill J, DeVeaux LC (2018) Divergent roles of RPA homologs of the model archaeon Halobacterium salinarum in survival of DNA damage. Genes (Basel) 9:223

    Article  CAS  Google Scholar 

  43. Pluchon PF, Fouqueau T, Creze C, Laurent S, Briffotaux J, Hogrel G, Palud A, Henneke G, Godfroy A, Hausner W et al (2013) An extended network of genomic maintenance in the archaeon Pyrococcus abyssi highlights unexpected associations between eucaryotic homologs. PLoS One 8:e79707

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Li Z, Santangelo TJ, Cubonova L, Reeve JN, Kelman Z (2010) Affinity purification of an archaeal DNA replication protein network. MBio 1:e00221–e00210

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Pugh RA, Lin Y, Eller C, Leesley H, Cann IK, Spies M (2008) Ferroplasma acidarmanus RPA2 facilitates efficient unwinding of forked DNA substrates by monomers of FacXPD helicase. J Mol Biol 383:982–998

    Article  CAS  PubMed  Google Scholar 

  46. Guy L, Ettema TJ (2011) The archaeal 'TACK' superphylum and the origin of eukaryotes. Trends Microbiol 19:580–587

    Article  CAS  PubMed  Google Scholar 

  47. Haseltine CA, Kowalczykowski SC (2002) A distinctive single-strand DNA-binding protein from the archaeon Sulfolobus solfataricus. Mol Microbiol 43:1505–1515

    Article  CAS  PubMed  Google Scholar 

  48. Wadsworth RI, White MF (2001) Identification and properties of the crenarchaeal single-stranded DNA binding protein from Sulfolobus solfataricus. Nucleic Acids Res 29:914–920

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Kerr ID, Wadsworth RI, Blankenfeldt W, Staines AG, White MF, Naismith JH (2001) Overexpression, purification, crystallization and data collection of a single-stranded DNA-binding protein from Sulfolobus solfataricus. Acta Crystallogr D Biol Crystallogr 57:1290–1292

    Article  CAS  PubMed  Google Scholar 

  50. Kerr ID, Wadsworth RI, Cubeddu L, Blankenfeldt W, Naismith JH, White MF (2003) Insights into ssDNA recognition by the OB fold from a structural and thermodynamic study of Sulfolobus SSB protein. EMBO J 22:2561–2570

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Gamsjaeger R, Kariawasam R, Gimenez AX, Touma C, McIlwain E, Bernardo RE, Shepherd NE, Ataide SF, Dong Q, Richard DJ et al (2015) The structural basis of DNA binding by the single-stranded DNA-binding protein from Sulfolobus solfataricus. Biochem J 465:337–346

    Article  CAS  PubMed  Google Scholar 

  52. Rolfsmeier ML, Haseltine CA (2010) The single-stranded DNA binding protein of Sulfolobus solfataricus acts in the presynaptic step of homologous recombination. J Mol Biol 397:31–45

    Article  CAS  PubMed  Google Scholar 

  53. Morten MJ, Gamsjaeger R, Cubeddu L, Kariawasam R, Peregrina J, Penedo JC, White MF (2017) High-affinity RNA binding by a hyperthermophilic single-stranded DNA-binding protein. Extremophiles 21:369–379

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Gamsjaeger R, Kariawasam R, Touma C, Kwan AH, White MF, Cubeddu L (2014) Backbone and side-chain 1H, 13C and 15N resonance assignments of the OB domain of the single stranded DNA binding protein from Sulfolobus solfataricus and chemical shift mapping of the DNA-binding interface. Biomol NMR Assign 8:243–246

    Google Scholar 

  55. Morten MJ, Peregrina JR, Figueira-Gonzalez M, Ackermann K, Bode BE, White MF, Penedo JC (2015) Binding dynamics of a monomeric SSB protein to DNA: a single-molecule multi-process approach. Nucleic Acids Res 43:10907–10924

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Cubeddu L, White MF (2005) DNA damage detection by an archaeal single-stranded DNA-binding protein. J Mol Biol 353:507–516

    Article  CAS  PubMed  Google Scholar 

  57. Richard DJ, Bell SD, White MF (2004) Physical and functional interaction of the archaeal single-stranded DNA-binding protein SSB with RNA polymerase. Nucleic Acids Res 32:1065–1074

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Napoli A, Valenti A, Salerno V, Nadal M, Garnier F, Rossi M, Ciaramella M (2005) Functional interaction of reverse gyrase with single-strand binding protein of the archaeon Sulfolobus. Nucleic Acids Res 33:564–576

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Zhang C, Phillips APR, Wipfler RL, Olsen GJ, Whitaker RJ (2018) The essential genome of the crenarchaeal model Sulfolobus islandicus. Nat Commun 9:4908

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  60. Suzuki S, Kurosawa N (2019) Robust growth of archaeal cells lacking a canonical single-stranded DNA-binding protein. FEMS Microbiol Lett 366:fnz124

    Article  CAS  PubMed  Google Scholar 

  61. Paytubi S, McMahon SA, Graham S, Liu H, Botting CH, Makarova KS, Koonin EV, Naismith JH, White MF (2012) Displacement of the canonical single-stranded DNA-binding protein in the Thermoproteales. Proc Natl Acad Sci U S A 109:E398–E405

    Article  CAS  PubMed  Google Scholar 

  62. Ghalei H, von Moeller H, Eppers D, Sohmen D, Wilson DN, Loll B, Wahl MC (2014) Entrapment of DNA in an intersubunit tunnel system of a single-stranded DNA-binding protein. Nucleic Acids Res 42:6698–6708

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. 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

    Google Scholar 

  64. Zimmermann L, Stephens A, Nam SZ, Rau D, Kubler J, Lozajic M, Gabler F, Soding J, Lupas AN, Alva V (2017) A completely reimplemented MPI Bioinformatics Toolkit with a new HHpred server at its core. J Mol Biol 430:2237–2243

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Stuart A. MacNeill .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Taib, N., Gribaldo, S., MacNeill, S.A. (2021). Single-Stranded DNA-Binding Proteins in the Archaea. In: Oliveira, M.T. (eds) Single Stranded DNA Binding Proteins. Methods in Molecular Biology, vol 2281. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1290-3_2

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-1290-3_2

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1289-7

  • Online ISBN: 978-1-0716-1290-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics