The Interdomain Linker of AAV-2 Rep68 Is an Integral Part of Its Oligomerization Domain: Role of a Conserved SF3 Helicase Residue in Oligomerization

English version České info

The four Rep proteins of adeno-associated virus (AAV) orchestrate all aspects of its viral life cycle, including transcription regulation, DNA replication, virus assembly, and site-specific integration of the viral genome into the human chromosome 19. All Rep proteins share a central SF3 superfamily helicase domain. In other SF3 members this domain is sufficient to induce oligomerization. However, the helicase domain in AAV Rep proteins (i.e. Rep40/Rep52) as shown by its monomeric characteristic, is not able to mediate stable oligomerization. This observation led us to hypothesize the existence of an as yet undefined structural determinant that regulates Rep oligomerization. In this document, we described a detailed structural comparison between the helicase domains of AAV-2 Rep proteins and those of the other SF3 members. This analysis shows a major structural difference residing in the small oligomerization sub-domain (OD) of Rep helicase domain. In addition, secondary structure prediction of the linker connecting the helicase domain to the origin-binding domain (OBD) indicates the potential to form α-helices. We demonstrate that mutant Rep40 constructs containing different lengths of the linker are able to form dimers, and in the presence of ATP/ADP, larger oligomers. We further identified an aromatic linker residue (Y224) that is critical for oligomerization, establishing it as a conserved signature motif in SF3 helicases. Mutation of this residue critically affects oligomerization as well as completely abolishes the ability to produce infectious virus. Taken together, our data support a model where the linker residues preceding the helicase domain fold into an α-helix that becomes an integral part of the helicase domain and is critical for the oligomerization and function of Rep68/78 proteins through cooperative interaction with the OBD and helicase domains.

Vyšlo v časopise: The Interdomain Linker of AAV-2 Rep68 Is an Integral Part of Its Oligomerization Domain: Role of a Conserved SF3 Helicase Residue in Oligomerization. PLoS Pathog 8(6): e32767. doi:10.1371/journal.ppat.1002764
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1002764

Souhrn

Zdroje

1. GreenMRRoederRG 1980 Transcripts of the adeno associated virus genome: mapping of the major RNAs. J Virol 36 79 92

2. LusbyEWBernsKI 1982 Mapping of the 5′ termini of two adeno-associated virus 2 RNAs in the left half of the genome. J Virol 41 518 526

3. SrivastavaALusbyEWBernsKI 1983 Nucleotide sequence and organization of the adeno-associated virus 2 genome. J Virol 45 555 564

4. YoonMSmithDHWardPMedranoFJAggarwalAK 2001 Amino-terminal domain exchange redirects origin-specific interactions of adeno-associated virus rep78 in vitro. J Virol 75 3230 3239

5. CathomenTColleteDWeitzmanMD 2000 A chimeric protein containing the N-terminus domain of the adeno-associated virus Rep protein recognizes its target site in an in vivo assay. J Virol 74 2372 2383

6. DavisMDWuJOwensRA 2000 Mutational analysis of adeno-associated virus type 2 Rep68 protein endonuclease activity on partially single-stranded substrates. J Virol 74 2936 2942

7. ImDSMuzyczkaN 1990 The AAV origin binding protein Rep68 is an ATP-dependent site-specific endonuclease with DNA helicase activity. Cell 61 447 457

8. ChioriniJAWienerSMOwensRAKyostioSRKotinRM 1994 Sequence requirements for stable binding and function of Rep68 on the adeno-associated virus type 2 inverted terminal repeats. J Virol 68 7448 7457

9. KyostioSRWonderlingRSOwensRA 1995 Negative regulation of the adeno-associated virus (AAV) P5 promoter involves both the P5 rep binding site and the consensus ATP-binding motif of the AAV Rep68 protein. J Virol 69 6787 6796

10. HickmanABRonningDRKotinRMDydaF 2002 Structural unity among viral origin binding proteins: crystal structure of the nuclease domain of adeno-associated virus Rep. Mol Cell 10 327 337

11. LuoXSanfordDGBullockPABachovchinW 1996 Structure of the origin specific DNA binding domain from simian virus 40 T-antigen. J Virol 3 1034 1039

12. EnemarkEJChenGVaughnDEStenlundAJoshua- TorL 2000 Crystal structure of the DNA binding domain of the replication initiation protein E1 from papillomavirus. Mol Cell 6 149 158

13. SingletonMRDillinghamMSWigleyDB 2007 Structure and mechanism of helicases and nucleic acid translocases. Annu Rev Biochem 76 23 50

14. SedmanJStenlundA 1998 The papillomavirus E1 protein forms a DNA-dependent hexameric complex with ATPase and DNA helicase activities. J Virol 72 6893 6897

15. EnermarkEJoshua-TorL 2006 Mechanism of DNA translocation in a replicative hexameric helicase. Nature 442 270 275

16. Ruiz-MasoJALopez-ZumelCMenendezMEspinosaMdel SolarG 2004 Structural features of the initiator of replication protein RepB encoded by the promiscuous plasmid pMV158. Biochim Biophys Acta 1696 113 119

17. SmithRHKotinRM 1998 The Rep52 gene product of adeno-associated virus is a DNA helicase with 3′-to-5′ polarity. J Virol 72 4874 4881

18. Mansilla-SotoJYoon-RobartsMRiceWJAryaSEscalanteCR 2009 DNA structure modulates the oligomerization properties of the AAV initiator protein Rep68. PLoS Pathog 5 e1000513

19. DaweiLZhaoRLilyestromWGaiDZhangR 2003 Structure of the replicative helicase of the oncoprotein SV40 large tumour antigen. Nature 423 512 518

20. DignamSSCollacoRFBieszczadJNeedhamPTrempeJP 2007 Coupled ATP and DNA binding of adeno-associated virus Rep40 helicase. Biochemistry 46 568 576

21. SchuckP 2000 Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling. Biophys J 78 1606 1619

22. KarSRKingsburyJSLewisMSLaueTMSchuckP 2000 Analysis of transport experiments using pseudo-absorbance data. Anal Biochem 285 135 142

23. CorreiaJJStaffordWF 2009 Extracting Equilibrium Constants from Kinetically Limited Reacting Systems. In: Methods Enzymol. Academic Press. 455 419 446

24. JamesJAAggarwalAKLindenRMEscalanteCR 2004 Structure of adeno-associated virus type 2 Rep40-ADP complex: insight into nucleotide recognition and catalysis by superfamily 3 helicases. Proc Natl Acad Sci U S A 101 12455 12460

25. KlemmJDRouldMAAuroraRHerrWPaboCO 1994 Crystal Structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules. Cell 77 21 23

26. Panne DMTHarrison S.C 2004 Crystal Structure of ATF-2/c-Jun and IRF-3 bound to the interferon-B enhancer. EMBO J 23 4384 4393

27. KimDEChivianDBakerD 2004 Protein Structure prediction and analysis using the Robetta server. Nucleic Acids Res 32 W526 531

28. BoerDRRuiz-MasoJALopez-BlancoAGVives-LlacerMChaconP 2009 Plasmid replication initiator RepB forms a hexamer reminescent of ring helicases and has mobile nuclease domains. EMBO J 28 1666 1678

29. WalkerSLWonderlingRSOwensRA 1997 Mutational Analysis of the Adeno-Associated Virus Rep68 Protein: Identification of Critical Residues Necesssary for Site-Specific Endonuclease Activity. J Virol 71 2722 2730

30. MagginJEJamesJAChappieJSDydaFHickmanAB 2012 The amino Acid Linker between the Endonuclease and Helicase Domains of Adeno-Associated virus Type 5 Rep Plays a Critical Role in DNA-Dependent Oligomerization. J Virol 86 3337 3346

31. PackmanLCPerhamRN 1982 Quaternary structure of the pyruvate dehydrogenase multienzyme complex of Bacillus sterearothermophilus studied by a new reversible cross-linking procedure with bis(imidoesters). Biochemistry 21 5171 5175

32. EmsleyPLohkampBScootWGCowtanK 2010 Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66 486 501

33. SchrodingerLLC 2010 PyMOL The PyMOL Molecular Graphics System. Version 1.3. Schrodinger,LLC

34. PettersenEFGoddardTDHuangCCCouchGSGreenblattDM 2004 UCSF Chimera - A Visualization System for Exploratory Research and Analysis. J Comput Chem 25 1605 1612

35. HolmLRosenströmP 2010 Dali server: conservation mapping in 3D. Nucleic Acids Res 38 W545 549

36. RostBYachdavGLiuJ 1997 The PredictProtein Server. Nucleic Acids Res 32 W321 W326