Architecture of the herpesvirus genomepackaging complex and implications for DNA translocation
Yunxiang Yang1,2, Pan Yang1, Nan Wang1, Zhonghao Chen1, Dan Su2, Z. Hong Zhou3, Zihe Rao1,4,5(), Xiangxi Wang1()
1. CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China 2. State Key Laboratory of Biotherapy, West China Hospital, Collaborative Innovation Center for Biotherapy, Sichuan University, Chengdu 610041, China 3. Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA 4. Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China 5. State Key Laboratory of Medicinal Chemical Biology and College of Life Science, Nankai University, Tianjin 300353, China
Genome packaging is a fundamental process in a viral life cycle and a prime target of antiviral drugs. Herpesviruses use an ATP-driven packaging motor/terminase complex to translocate and cleave concatemeric dsDNA into procapsids but its molecular architecture and mechanism are unknown. We report atomic structures of a herpesvirus hexameric terminase complex in both the apo and ADP•BeF3-bound states. Each subunit of the hexameric ring comprises three components—the ATPase/terminase pUL15 and two regulator/fixer proteins, pUL28 and pUL33—unlike bacteriophage terminases. Distal to the nuclease domains, six ATPase domains form a central channel with conserved basicpatches conducive to DNA binding and trans-acting arginine fingers are essential to ATP hydrolysis and sequential DNA translocation. Rearrangement of the nuclease domains mediated by regulatory domains converts DNA translocation mode to cleavage mode. Our structures favor a sequential revolution model for DNA translocation and suggest mechanisms for concerted domain rearrangements leading to DNA cleavage.
. [J]. Protein & Cell, 2020, 11(5): 339-351.
Yunxiang Yang, Pan Yang, Nan Wang, Zhonghao Chen, Dan Su, Z. Hong Zhou, Zihe Rao, Xiangxi Wang. Architecture of the herpesvirus genomepackaging complex and implications for DNA translocation. Protein Cell, 2020, 11(5): 339-351.
K Adelman, B Salmon, JD Baines (2001) Herpes simplex virus DNA packaging sequences adopt novel structures that are specifically recognized by a component of the cleavage and packaging machinery. Proc Natl Acad Sci USA 98:3086–3091 https://doi.org/10.1073/pnas.061555698
2
PV Afonine, RW Grosse-Kunstleve, N Echols, JJ Headd, NW Moriarty, M Mustyakimov, TC Terwilliger, A, Urzhumtsev PH Zwart, PD Adams (2012) Towards automated crystallographic structure refinement with phenix. refine. Acta Crystallogr Sect D Biol Crystallogr 68:352–367 https://doi.org/10.1107/S0907444912001308
E Bogner (2002) Human cytomegalovirus terminase as a target for antiviral chemotherapy. Rev Med Virol 12:115–127 https://doi.org/10.1002/rmv.344
5
E Bogner, K Radsak, MF Stinski (1998) The gene product of human cytomegalovirus open reading frame UL56 binds the pac motif and has specific nuclease activity. J Virol 72:2259–2264 https://doi.org/10.1128/JVI.72.3.2259-2264.1998
6
W Chen, H Xiao, X Wang, S Song, Z Han, X Li, F Yang, L Wang, J Song, H Liu, L Cheng (2020) Structural changes of a bacteriophage upon DNA packaging and maturation. Protein Cell. https://doi.org/10.1007/s13238-020-00715-9
7
X Dai, ZH Zhou (2018) Structure of the herpes simplex virus 1 capsid with associated tegument protein complexes. Science 360:eaao7298 https://doi.org/10.1126/science.aao7298
8
P Emsley, K Cowtan (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60:2126–2132 https://doi.org/10.1107/S0907444904019158
9
T Grant, A Rohou, N Grigorieff (2018) cisTEM, user friendly software for single-particle image processing. Elife 7:e35383 https://doi.org/10.7554/eLife.35383
10
PX Guo, CL Zhang, CP Chen, K Garver, M Trottier (1998) Inter-RNA interaction of phage phi 29 pRNA to form a hexameric complex for viral DNA transportation. Mol Cell 2:149–155 https://doi.org/10.1016/S1097-2765(00)80124-0
11
PX Guo, C Schwartz, J Haak, ZY Zhao (2013) Discovery of a new motion mechanism of biomotors similar to the earth revolving around the sun without rotation. Virology 446:133–143 https://doi.org/10.1016/j.virol.2013.07.025
BJ Hilbert, JA Hayes, NP Stone, CM Duffy, B, Sankaran BA Kelch (2015) Structure and mechanism of the ATPase that powers viral genome packaging. Proc Natl Acad Sci USA 112:E3792–E3799 https://doi.org/10.1073/pnas.1506951112
14
BJ Hilbert, JA Hayes, NP Stone, RG Xu, BA Kelch (2017) The large terminase DNA packaging motor grips DNA with its ATPase domain for cleavage by the flexible nuclease domain. Nucleic Acids Res 45:3591–3605 https://doi.org/10.1093/nar/gkw1356
15
T Hugel, J Michaelis, CL Hetherington, PJ Jardine, S Grimes, JM Walter, W Faik, DL Anderson, C Bustamante (2007) Experimental test of connector rotation during DNA packaging into bacteriophage phi 29 capsids. PLoS Biol 5:558–567 https://doi.org/10.1371/journal.pbio.0050059
16
JS Hwang, E Bogner (2002) ATPase activity of the terminase subunit pUL56 of human cytomegalovirus. J Biol Chem 277:6943–6948 https://doi.org/10.1074/jbc.M108984200
17
DN Mastronarde (2005) Automated electron microscope tomography using robust prediction of specimen movements. J Struct Biol 152:36–51 https://doi.org/10.1016/j.jsb.2005.07.007
18
DP Melendez, RR Razonable (2015) Letermovir and inhibitors of the terminase complex: a promising new class of investigational antiviral drugs against human cytomegalovirus. Infect Drug Resist 8:269–277 https://doi.org/10.2147/IDR.S79131
JM Miller, EJ Enemark (2016) Fundamental Characteristics of AAA+ Protein Family Structure and Function. Archaea 2016:9294307 https://doi.org/10.1155/2016/9294307
21
WC Nan Wang, L Zhu, R Feng, J Wang, D Zhu, X Zhang, H Liu, Z Rao, X Wang (2020) Structures of the portal vertex reveal essential protein-protein interactions for Herpesvirus assembly and maturation. Protein Cell https://doi.org/10.1007/s13238-020-00711-z
22
EF Pettersen, TD Goddard, CC Huang, GS Couch, DM Greenblatt, EC Meng, TE Ferrin (2004) UCSF Chimera—a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612 https://doi.org/10.1002/jcc.20084
23
R Ren, S Ghassabi Kondalaji, GD Bowman (2019) The Chd1 chromatin remodeler forms long-lived complexes with nucleosomes in the presence of ADP.BeF3 (-) and transition state analogs. J Biol Chem 294:18181–18191 https://doi.org/10.1074/jbc.RA119.009782
24
AE Reynolds, Y Fan, JD Baines (2000) Characterization of the U(L) 33 gene product of herpes simplex virus 1. Virology 266:310–318 https://doi.org/10.1006/viro.1999.0090
25
SH Scheres (2012) RELION: implementation of a Bayesian approach to cryo-EM structure determination. J Struct Biol 180:519–530 https://doi.org/10.1016/j.jsb.2012.09.006
26
B Scholz, S Rechter, JC Drach, LB Townsend, E Bogner (2003) Identification of the ATP-binding site in the terminase subunit pUL56 of human cytomegalovirus. Nucleic Acids Res 31:1426–1433 https://doi.org/10.1093/nar/gkg229
27
S Selvarajan Sigamani, H Zhao, YN Kamau, JD Baines, L Tang (2013) The structure of the herpes simplex virus DNA-packaging terminase pUL15 nuclease domain suggests an evolutionary lineage among eukaryotic and prokaryotic viruses. J Virol 87:7140–7148 https://doi.org/10.1128/JVI.00311-13
28
SY Sun, K Kondabagil, PM Gentz, MG Rossmann, VB Rao (2007) The structure of the ATPase that powers DNA packaging into bacteriophage t4 procapsids. Mol Cell 25:943–949 https://doi.org/10.1016/j.molcel.2007.02.013
29
S Sun, K, Kondabagil B Draper, TI Alam, VD Bowman, Z Zhang, S Hegde, A Fokine, MG Rossmann, VB Rao (2008) The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces. Cell 135:1251–1262 https://doi.org/10.1016/j.cell.2008.11.015
X Wang, W Peng, J Ren, Z Hu, J Xu, Z Lou, X Li, W Yin, X Shen, C Porta (2012) A sensor-adaptor mechanism for enterovirus uncoating from structures of EV71. Nat Struct Mol Biol 19:424–429 https://doi.org/10.1038/nsmb.2255
32
X Wang, J Ren, Q Gao, Z Hu, Y Sun, X Li, DJ Rowlands, W Yin, J Wang, DI Stuartet al.(2015) Hepatitis A virus and the origins of picornaviruses. Nature 517:85–88 https://doi.org/10.1038/nature13806
33
J Wang, S, Yuan D Zhu, H Tang, N Wang, W Chen, Q Gao, Y Li, H Liu, X Zhanget al. (2018) Structure of the herpes simplex virus type 2 C-capsid with capsid-vertex-specific component. Nat Commun 9:3668 https://doi.org/10.1038/s41467-018-06078-4
34
N Wang, D, Zhao J Wang, Y Zhang, M Wang, Y Gao, F Li, Z Bu, Z, Rao X Wang(2019) Architecture of African swine fever virus and implications for viral assembly. Science 366:640–644. https://doi.org/10.1007/s13238-020-00711-z
35
CA White, ND Stow, AH Patel, M Hughes, VG Preston (2003) Herpes simplex virus type 1 portal protein UL6 interacts with the putative terminase subunits UL15 and UL28. J Virol 77:6351–6358 https://doi.org/10.1128/JVI.77.11.6351-6358.2003
36
RG Xu, HT Jenkins, AA Antson, SJ Greive (2017a) Structure of the large terminase from a hyperthermophilic virus reveals a unique mechanism for oligomerization and ATP hydrolysis. Nucleic acids research 45(22):13029–13042 https://doi.org/10.1093/nar/gkx947
37
RG Xu, HT Jenkins, M Chechik, EV Blagova, A Lopatina, E Klimuk, L Minakhin, K Severinov, SJ Greive, AA Antson (2017b) Viral genome packaging terminase cleaves DNA using the canonical RuvC-like two-metal catalysis mechanism. Nucleic Acids Res 45:3580–3590 https://doi.org/10.1093/nar/gkw1354
38
K Yang, AP Poon, B Roizman, JD Baines (2008) Temperaturesensitive mutations in the putative herpes simplex virus type 1 terminase subunits pUL15 and pUL33 preclude viral DNA cleavage/packaging and interaction with pUL28 at the nonpermissive temperature. J Virol 82:487–494 https://doi.org/10.1128/JVI.01875-07
39
SA Yuan, JL Wang, DJ Zhu, N Wang, Q Gao, WY Chen, H Tang, JZ Wang, XZ Zhang, HR Liuet al. (2018) Cryo-EM structure of a herpesvirus capsid at 3.1 angstrom. Science 360:48–60 https://doi.org/10.1126/science.aao7283
F Zhang, S Lemieux, XL Wu, D St-Arnaud, CT McMurray, F Major, D Anderson (1998) Function of hexameric RNA in packaging of bacteriophage phi 29 DNA in vitro. Mol Cell 2:141–147 https://doi.org/10.1016/S1097-2765(00)80123-9
42
H Zhao, TE Christensen, YN Kamau, L Tang (2013a) Structures of the phage Sf6 large terminase provide new insights into DNA translocation and cleavage. Proc Natl Acad Sci U S A 110:8075–8080 https://doi.org/10.1073/pnas.1301133110
43
ZY Zhao, E Khisamutdinov, C Schwartz, PX Guo (2013b) Mechanism of One-Way Traffic of Hexameric Phi29 DNA Packaging Motor with Four Electropositive Relaying Layers Facilitating Antiparallel Revolution. ACS Nano 7:4082–4092 https://doi.org/10.1021/nn4002775
44
D Zhu, X Wang, Q Fang, JL Van Etten, MG Rossmann, Z Rao, X Zhang (2018a) Pushing the resolution limit by correcting the Ewald sphere effect in single-particle Cryo-EM reconstructions. Nat Commun 9:1552 https://doi.org/10.1038/s41467-018-04051-9
45
L Zhu, Y Sun, J Fan, B Zhu, L Cao, Q Gao, Y Zhang, H Liu, Z Rao, X Wang (2018b) Structures of Coxsackievirus A10 unveil the molecular mechanisms of receptor binding and viral uncoating. Nat Commun 9:4985 https://doi.org/10.1038/s41467-018-07531-0
