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Mechanism of RNA Packaging Motor

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Book cover Viral Molecular Machines

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 726))

Abstract

P4 proteins are hexameric RNA packaging ATPases of dsRNA bacteriophages of the Cystoviridae family. P4 hexamers are integral part of the inner polymerase core and play several essential roles in the virus replication cycle. P4 proteins are structurally related to the hexameric helicases and translocases of superfamily 4 (SF4) and other RecA-like ATPases. Recombinant P4 proteins retain their 5’ to 3’ helicase and translocase activity in vitro and thus serve as a model system for studying the mechanism of action of hexameric ring helicases and RNA translocation. This review summarizes the different roles that P4 proteins play during virus assembly, genome packaging, and transcription. Structural and mechanistic details of P4 action are laid out to and subsequently compared with those of the related hexameric helicases and other packaging motors.

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Abbreviations

AMPcPP:

[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-­hydroxyphosphoryl]methylphosphonic acid

AMPPNP:

Adenylyl-imidodiphosphate

ASCE:

Additional strand conserved E

LTAg:

Simian virus 40 large T antigen

PC:

Procapsid

Pi :

Inorganic phosphate

γP:

Gamma phosphate in ATP

SF:

Superfamily

References

  • Adelman JL, Jeong YJ, Liao JC, Patel G, Kim DE, Oster G, Patel SS (2006) Mechanochemistry of transcription termination factor Rho. Mol Cell 22:611–621

    Article  PubMed  CAS  Google Scholar 

  • Allin C, Ahmadian MR, Wittinghofer A, Gerwert K (2001) Monitoring the GAP catalyzed H-Ras GTPase reaction at atomic resolution in real time. Proc Natl Acad Sci USA 98:7754–7759

    Article  PubMed  CAS  Google Scholar 

  • Bamford DH, Ojala PM, Frilander M, Walin L, Bamford JKH (1995) Isolation, purification, and function of assembly intermediates and subviral particles of bacteriophages PRD1 and phi6. In: Adolph KW (ed) Methods in molecular genetics. Academic, San Diego, pp 455–474

    Google Scholar 

  • Butcher SJ, Dokland T, Ojala PM, Bamford DH, Fuller SD (1997) Intermediates in the assembly pathway of the double-stranded RNA virus phi6. EMBO J 16:4477–4487

    Article  PubMed  CAS  Google Scholar 

  • Crampton DJ, Mukherjee S, Richardson CC (2006) DNA-induced switch from independent to sequential dTTP hydrolysis in the bacteriophage T7 DNA helicase. Mol Cell 21:165–174

    Article  PubMed  CAS  Google Scholar 

  • Donmez I, Patel SS (2006) Mechanisms of a ring shaped helicase. Nucleic Acids Res 34:4216–4224

    Article  PubMed  CAS  Google Scholar 

  • Enemark EJ, Joshua-Tor L (2006) Mechanism of DNA translocation in a replicative hexameric helicase. Nature 442:270–275

    Article  PubMed  CAS  Google Scholar 

  • Enemark EJ, Joshua-Tor L (2008) On helicases and other motor proteins. Curr Opin Struct Biol 18:243–257

    Article  PubMed  CAS  Google Scholar 

  • Erzberger JP, Berger JM (2006) Evolutionary relationship and structural mechanisms of AAA+ proteins. In: Rees DC (ed) Annual reviews of biophysics and biomolecular structure. Annual Reviews, Palo Alto, pp 93–114

    Google Scholar 

  • Frilander M, Gottlieb P, Strassman J, Bamford DH, Mindich L (1992) Dependence of minus-strand synthesis on complete genomic packaging in the double-stranded RNA bacteriophage phi 6. J Virol 66:5013–5017

    PubMed  CAS  Google Scholar 

  • Gai D, Zhao R, Li D, Finkielstein CV, Chen XS (2004) Mechanisms of conformational change for a replicative hexameric helicase of SV40 large tumor antigen. Cell 119:47–60

    Article  PubMed  CAS  Google Scholar 

  • Gottlieb P, Strassman J, Frucht A, Qiao XY, Mindich L (1991) In vitro packaging of the bacteriophage phi 6 ssRNA genomic precursors. Virology 181:589–594

    Article  PubMed  CAS  Google Scholar 

  • Gottlieb P, Strassman J, Mindich L (1992a) Protein P4 of the bacteriophage phi 6 procapsid has a nucleoside triphosphate-binding site with associated nucleoside triphosphate phosphohydrolase activity. J Virol 66:6220–6222

    PubMed  CAS  Google Scholar 

  • Gottlieb P, Strassman J, Qiao X, Frilander M, Frucht A, Mindich L (1992b) In vitro packaging and replication of individual genomic segments of bacteriophage phi 6 RNA. J Virol 66:2611–2616

    PubMed  CAS  Google Scholar 

  • Gottlieb P, Qiao X, Strassman J, Frilander M, Mindich L (1994) Identification of the packaging regions within the genomic RNA segments of bacteriophage phi 6. Virology 200:42–47

    Article  PubMed  CAS  Google Scholar 

  • Huiskonen JT, Butcher SJ (2007) Membrane-containing viruses with icosahedrally symmetric capsids. Curr Opin Struct Biol 17:229–236

    Article  PubMed  CAS  Google Scholar 

  • Huiskonen JT, de Haas F, Bubeck D, Bamford DH, Fuller SD, Butcher SJ (2006) Structure of the bacteriophage phi6 nucleocapsid suggests a mechanism for sequential RNA packaging. Structure 14:1039–1048

    Article  PubMed  CAS  Google Scholar 

  • Huiskonen JT, Jaalinoja HT, Briggs JA, Fuller SD, Butcher SJ (2007) Structure of a hexameric RNA packaging motor in a viral polymerase complex. J Struct Biol 158:156–164

    Article  PubMed  CAS  Google Scholar 

  • Iyer LM, Leipe DD, Koonin EV, Aravind L (2004) Evolutionary history and higher order classification of AAA+ ATPases. J Struct Biol 146:11–31

    Article  PubMed  CAS  Google Scholar 

  • Jaalinoja HT, Huiskonen JT, Butcher SJ (2007) Electron cryomicroscopy comparison of the architectures of the enveloped bacteriophages phi6 and phi8. Structure 15:157–167

    Article  PubMed  Google Scholar 

  • Juuti JT, Bamford DH, Tuma R, Thomas GJ Jr (1998) Structure and NTPase activity of the RNA-translocating protein (P4) of bacteriophage phi 6. J Mol Biol 279:347–359

    Article  PubMed  CAS  Google Scholar 

  • Kainov DE, Pirttimaa M, Tuma R, Butcher SJ, Thomas GJ Jr, Bamford DH, Makeyev EV (2003) RNA packaging device of double-stranded RNA bacteriophages, possibly as simple as hexamer of P4 protein. J Biol Chem 278:48084–48091

    Article  PubMed  CAS  Google Scholar 

  • Kainov DE, Lisal J, Bamford DH, Tuma R (2004) Packaging motor from double-stranded RNA bacteriophage phi12 acts as an obligatory passive conduit during transcription. Nucleic Acids Res 32:3515–3521

    Article  PubMed  CAS  Google Scholar 

  • Kainov DE, Tuma R, Mancini EJ (2006) Hexameric molecular motors: P4 packaging ATPase unravels the mechanism. Cell Mol Life Sci 63:1095–1105

    Article  PubMed  CAS  Google Scholar 

  • Kainov DE, Mancini EJ, Telenius J, Lisal J, Grimes JM, Bamford DH, Stuart DI, Tuma R (2008) Structural basis of mechanochemical coupling in a hexameric molecular motor. J Biol Chem 283:3607–3617

    Article  PubMed  CAS  Google Scholar 

  • Levin MK, Patel SS (2003) Helicases as molecular motors. In: Schliwa M (ed) Molecular motors. Wiley-VCH, Weinheim, pp 179–203

    Google Scholar 

  • Liao JC, Jeong YJ, Kim DE, Patel SS, Oster G (2005) Mechanochemistry of T7 DNA helicase. J Mol Biol 350:452–475

    Article  PubMed  CAS  Google Scholar 

  • Lisal J, Tuma R (2005) Cooperative mechanism of RNA packaging motor. J Biol Chem 280:23157–23164

    Article  PubMed  CAS  Google Scholar 

  • Lisal J, Kainov DE, Bamford DH, Thomas GJ Jr, Tuma R (2004) Enzymatic mechanism of RNA translocation in double-stranded RNA bacteriophages. J Biol Chem 279:1343–1350

    Article  PubMed  CAS  Google Scholar 

  • Lisal J, Lam T, Kainov DE, Emmett MR, Marshall AG, Tuma R (2005) Functional visualization of viral molecular motor by hydrogen-deuterium exchange reveals transient states. Nat Struct Mol Biol 12:460–466

    Article  PubMed  CAS  Google Scholar 

  • Lisal J, Kainov DE, Lam TT, Emmett MR, Wei H, Gottlieb P, Marshall AG, Tuma R (2006) Interaction of packaging motor with the polymerase complex of dsRNA bacteriophage. Virology 351:73–79

    Article  PubMed  CAS  Google Scholar 

  • Mancini EJ, Tuma R (2008) Structure and function of P4, a dsRNA virus packaging motor. In: Patton JT (ed) Segmented double-stranded RNA viruses: structure and molecular biology. Caister Academic, Norfolk, UK, pp 259–272

    Google Scholar 

  • Mancini EJ, Kainov DE, Grimes JM, Tuma R, Bamford DH, Stuart DI (2004a) Atomic snapshots of an RNA packaging motor reveal conformational changes linking ATP hydrolysis to RNA translocation. Cell 118:743–755

    Article  PubMed  CAS  Google Scholar 

  • Mancini EJ, Kainov DE, Wei H, Gottlieb P, Tuma R, Bamford DH, Stuart DI, Grimes JM (2004b) Production, crystallization and preliminary X-ray crystallographic studies of the bacteriophage phi 12 packaging motor. Acta Crystallogr D 60:588–590

    Article  PubMed  Google Scholar 

  • Meier C, Mancini EJ, Bamford DH, Walsh MA, Stuart DI, Grimes JM (2005) Overcoming the false-minima problem in direct methods: structure determination of the packaging enzyme P4 from bacteriophage phi13. Acta Crystallogr D 61:1238–1244

    Article  PubMed  Google Scholar 

  • Mindich L (1999) Precise packaging of the three genomic segments of the double-stranded RNA bacteriophage phi6. Microbiol Mol Biol Rev 63:149–160

    PubMed  CAS  Google Scholar 

  • Mindich L (2004) Packaging, replication and recombination of the segmented genome of bacteriophage Phi6 and its relatives. Virus Res 101:83–92

    Article  PubMed  CAS  Google Scholar 

  • Mindich L, Sinclair JF, Cohen J (1976) The morphogenesis of bacteriophage phi6: particles formed by nonsense mutants. Virology 75:224–231

    Article  PubMed  CAS  Google Scholar 

  • Mitchell MS, Matsuzaki S, Imai S, Rao VB (2002) Sequence analysis of bacteriophage T4 DNA packaging/terminase genes 16 and 17 reveals a common ATPase center in the large subunit of viral terminases. Nucleic Acids Res 30:4009–4021

    Article  PubMed  CAS  Google Scholar 

  • Nemecek D, Heymann JB, Qiao J, Mindich L, Steven AC (2010) Cryo-electron tomography of bacteriophage phi6 procapsids shows random occupancy of the binding sites for RNA polymerase and packaging NTPase. J Struct Biol 171:389–396

    Article  PubMed  CAS  Google Scholar 

  • Paatero AO, Mindich L, Bamford DH (1998) Mutational analysis of the role of nucleoside triphosphatase P4 in the assembly of the RNA polymerase complex of bacteriophage phi6. J Virol 72:10058–10065

    PubMed  CAS  Google Scholar 

  • Pirttimaa MJ, Bamford DH (2000) RNA secondary structures of the bacteriophage phi6 packaging regions. RNA 6:880–889

    Article  PubMed  CAS  Google Scholar 

  • Poranen MM, Tuma R (2004) Self-assembly of double-stranded RNA bacteriophages. Virus Res 101:93–100

    Article  PubMed  CAS  Google Scholar 

  • Poranen MM, Paatero AO, Tuma R, Bamford DH (2001) Self-assembly of a viral molecular machine from purified protein and RNA constituents. Mol Cell 7:845–854

    Article  PubMed  CAS  Google Scholar 

  • Poranen MM, Tuma R, Bamford DH (2008) Dissecting the assembly pathway of bacterial dsRNA viruses: infectious nucleocapsids produced by self-assembly. In: Patton JT (ed) Segmented double-stranded RNA viruses: structure and molecular biology. Caister Academic, Norfolk, UK, pp 115–132

    Google Scholar 

  • Qiao X, Qiao J, Mindich L (1997) Stoichiometric packaging of the three genomic segments of double-stranded RNA bacteriophage phi6. Proc Natl Acad Sci USA 94:4074–4079

    Article  PubMed  CAS  Google Scholar 

  • Qiao X, Qiao J, Mindich L (2003) Analysis of specific binding involved in genomic packaging of the double-stranded-RNA bacteriophage phi6. J Bacteriol 185:6409–6414

    Article  PubMed  CAS  Google Scholar 

  • Rabhi M, Tuma R, Boudvillain M (2010) RNA remodeling by hexameric RNA helicases. RNA Biol 7:16–27

    Article  Google Scholar 

  • Rao VB, Feiss M (2008) The bacteriophage DNA packaging motor. Annu Rev Genet 42:647–681

    Article  PubMed  CAS  Google Scholar 

  • Sawaya MR, Guo S, Tabor S, Richardson CC, Ellenberger T (1999) Crystal structure of the helicase domain from the replicative helicase-primase of bacteriophage T7. Cell 99:167–177

    Article  PubMed  CAS  Google Scholar 

  • Scheffzek K, Ahmadian MR, Kabsch W, Wiesmuller L, Lautwein A, Schmitz F, Wittinghofer A (1997) The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants. Science 277:333–338

    Article  PubMed  CAS  Google Scholar 

  • Singleton MR, Sawaya MR, Ellenberger T, Wigley DB (2000) Crystal structure of T7 gene 4 ring helicase indicates a mechanism for sequential hydrolysis of nucleotides. Cell 101:589–600

    Article  PubMed  CAS  Google Scholar 

  • Singleton MR, Dillingham MS, Wigley DB (2007) Structure and mechanism of helicases and nucleic acid translocases. Annu Rev Biochem 76:23–50

    Article  PubMed  CAS  Google Scholar 

  • Skordalakes E, Berger JM (2003) Structure of the Rho transcription terminator: mechanism of mRNA recognition and helicase loading. Cell 114:135–146

    Article  PubMed  CAS  Google Scholar 

  • Sun S, Kondabagil K, Gentz PM, Rossmann MG, Rao VB (2007) The structure of the ATPase that powers DNA packaging into bacteriophage T4 procapsids. Mol Cell 25:943–949

    Article  PubMed  CAS  Google Scholar 

  • Sun S, Kondabagil K, Draper B, Alam TI, Bowman VD, Zhang Z, Hegde S, Fokine A, Rossmann MG, Rao VB (2008) The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces. Cell 135:1251–1262

    Article  PubMed  CAS  Google Scholar 

  • Telenius J, Wallin AE, Straka M, Zhang H, Mancini EJ, Tuma R (2008) RNA packaging motor: from structure to quantum mechanical modeling and sequential-stochastic mechanism. Comput Math Methods Med 9:351–369

    Article  Google Scholar 

  • Thomsen ND, Berger JM (2009) Running in reverse: the structural basis for translocation polarity in hexameric helicases. Cell 139:523–534

    Article  PubMed  CAS  Google Scholar 

  • Tuma R (2008) Icosahedral enveloped dsRNA bacterial viruses. In: Mahy BWJ, Regenmortel MHVV (eds) Encyclopedia of virology. Elsevier, Oxford, pp 6–13

    Chapter  Google Scholar 

  • Tuma R (2010) Hexameric viral RNA helicases. In: Jankowsky E (ed) RNA helicases. RSC, Cambridge, UK, pp 213–242

    Chapter  Google Scholar 

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Author information

Authors and Affiliations

  1. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, OX3 7BN, UK

    Erika J. Mancini

  2. The Astbury Centre for Structural Molecular Biology, Institute of Cellular and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK

    Roman Tuma

Authors
  1. Erika J. Mancini
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  2. Roman Tuma
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Corresponding authors

Correspondence to Erika J. Mancini or Roman Tuma .

Editor information

Editors and Affiliations

  1. Dept. Biological Sciences, Purdue University, W. State St. 915, West Lafayette, 47907-2054, Indiana, USA

    Michael G. Rossmann

  2. Dept. Biology, Catholic University of America, Washington, 20064, District of Columbia, USA

    Venigalla B. Rao

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Mancini, E.J., Tuma, R. (2012). Mechanism of RNA Packaging Motor. In: Rossmann, M., Rao, V. (eds) Viral Molecular Machines. Advances in Experimental Medicine and Biology, vol 726. Springer, Boston, MA. https://doi.org/10.1007/978-1-4614-0980-9_27

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