病毒基因组包装马达

doi:10.3969/j.issn.0253-9608.2023.01.002

摘要/Abstract

摘要： 病毒只有通过侵入宿主细胞，占用后者的马达蛋白并耗尽其能量才能完成复制，而基因组的包装是其复制过程的重要一环。双链DNA或双链RNA病毒必须借助生物马达施力将无序的新生遗传物质注入衣壳内形成有序的类晶体结构后才算完成了复制。文章简单介绍了包装马达的结构、功能及其工作机制，并从能量效率角度推断其力学化学是不可逆的。

关键词: 病毒, 基因组, 包装马达, 末端酶, 生物马达, ATP酶

Abstract: The virus cannot replicate itself until it has infected host cell and irritated relative biomotorsto exhaust latter’s ATP. The packaging of the viral genome, however, is the key step of viral replication. The dsDNA or dsRNA virus has to utilize hydrolysis energy of ATP by a biomotor to inject its nascent disordered genome into the preformed capsid to form a crystal-like structure before it completes replication. Here, we briefly introduce the structure, function and working mechanism of the packaging motor, and infer that its mechanochemical coupling is irreversible from the perspective of efficiency.

戴立强, 舒咬根. 病毒基因组包装马达[J]. 自然杂志, 2023, 45(1): 17-21.

DAI Liqiang, SHU Yaogen. Viral genome packaging motor[J]. Chinese Journal of Nature, 2023, 45(1): 17-21.

参考文献

[1] 舒咬根, 欧阳钟灿. 生物分子马达 [J]. 物理, 2007, 36: 735.
[2] 黎明, 舒咬根. 生物分子马达[M]// 国家自然科学基金委员会, 中国科学院编. 中国学科发展战略•软凝聚态物理学. 北京: 科学出
版社, 2020.
[3] YILDIZ A, TOMISHIGE M, VALE R D, et al. Kinesin walks handover-hand [J]. Science, 2004, 303: 676-678.
[4] CARTER N J, CROSS R. Mechanics of the kinesin step [J]. Nature, 2005, 435: 308-312.
[5] LI M, OUYANG Z C, SHU Y G. Advances in the study of the mechanochemical coupling of kinesin I [J]. JMPB, 2018, 32:
1840001.
[6] HARRINGTON W F, RODGERS M E. Myosin [J]. Annu Rev Biochem, 1984, 53: 35-73.
[7] BURGESS S A, WALKER M L, SAKAKIBARA H, et al. Dynein structure and power stroke [J]. Nature, 2003, 421: 715-718.
[8] SUBRAMANYA H S, BIRD L E, BRANNIGAN J A, et al. Crystal structure of a DExx box DNA helicase [J]. Nature, 1996, 384: 379-
383.
[9] SHU Y G, SONG Y S, OUYANG Z C, et al. A general theory of kinetics and thermodynamics of steady-state copolymerization [J]. J Phys: Condens Mat, 2015, 27: 235105.
[10] SONG Y S, SHU Y G, ZHOU X, et al. Proofreading of DNA polymerase: a new kinetic model with higher-order terminal effects
[J]. J Phys: Condens Mat, 2017, 29: 025101.
[11] SMALE S T, KADONAGA J T. The RNA polymerase II core promoter [J]. Annu Rev Biochem, 2003, 72: 449-479.
[12] SHU Y G, LAI P Y. Systematic kinetics study of FoF1-ATPase: analytic results and comparison with experiments [J]. J Phys Chem B, 2008, 112: 13453.
[13] DAI L, XU Y, SU X, et al. Revealing atomic scale molecular diffusion of a plant transcription factor WRKY domain protein along
DNA [J]. PNAS, 2021, 118: e2102621118.
[14] 舒咬根, 欧阳钟灿. 转动分子马达：ATP合酶[J]. 自然杂志, 2007, 29: 249-254.
[15] SOWA Y, BERRY R M. Bacterial flagellar motor [J]. Q Rev Biophys, 2008, 41: 103-132.

[16] BUCK K W. Replication of tobacco mosaic virus RNA [J]. Philos Trans R Soc Lond B: Biol Sci, 1999, 354: 613-627.

[17] VALEGÅRD K, MURRAY J B, STOCKLEY P G, et al. Crystal structure of an RNA bacteriophage coat protein-operator complex
[J]. Nature, 1994, 371: 623-626.
[18] RAO V B, FEISS M. The bacteriophage DNA packaging motor [J]. Annu Rev Genet, 2008, 42: 647-681.
[19] CASJENS S R. The DNA-packaging nanomotor of tailed
bacteriophages [J]. Nat Rev Microbiol, 2011, 9: 647-657.
[20] EARNSHAW W C, CASJENS S R. DNA packaging by the doublestranded DNA bacteriophages [J]. Cell, 1980, 21: 319-331.
[21] SMITH D E, TANS S J, SMITH S B, et al. The bacteriophage φ29 portal motor can package DNA against a large internal force [J]. Nature, 2001, 413: 748-752.
[22] CAPPELLO G, PIEROBON P, SYMONDS C, et al. Myosin V stepping mechanism [J]. PNAS, 2007, 104: 15328.
[23] SIMPSON A A, TAO Y, LEIMANP G, et al. Structure of the bacteriophage φ29 DNA packaging motor [J]. Nature, 2000, 408:
745-750.
[24] OLIA A S, PREVELIGE P E JR, JOHNSON J E, et al. Threedimensional structure of a viral genome-delivery portal vertex [J].
Nat Struct Mol Biol, 2011, 18: 597-603.
[25] KANAMARU S, KONDABAGIL K, ROSSMANN M G, et al. The functional domains of bacteriophage T4 terminase [J]. J Biol Chem, 2004, 279: 40795-40801.
[26] SUN S, KONDABAGIL K, DRAPER B, et al. The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces [J]. Cell, 2008, 135: 1251-1262.
[27] YANG Y X, YANG P, WANG N, et al. Architecture of the herpesvirus genome packaging complex and implications for DNA
translocation [J]. Protein Cell, 2020, 11: 339-351.
[28] GUO P X, DRIVER D, ZHAO Z Y, et al. Controlling the revolving and rotating motion direction of asymmetric hexameric nanomotor by arginine finger and channel chirality [J]. ACS Nano, 2019, 13: 6207-6223.
[29] SHU Y G, CHENG X L. Direct structural evidence supporting a revolving mechanism in DNA packaging motors [J]. Biophys Rep,
2020, 6: 155-158.
[30] HENDRIX R W. Symmetry mismatch and DNA packaging in large bacteriophages [J]. PNAS, 1978, 75: 4779-4783.
[31] GUASCH A, POUS J, IBARRA B, et al. Detailed architecture of a DNA translocating machine: the high-resolution structure of the bacteriophage φ29 connector particle [J]. J Mol Biol, 2002, 315: 663-676.
[32] LEBEDEV A A, KRAUSEM H, ISIDROA L, et al. Structural framework for DNA translocation via the viral portal protein [J].
EMBOJ, 2007, 26: 1984-1994.
[33] HUGEL T, MICHAELIS J, HETHERINGTON C L, et al. Experimental test of connector rotation during DNA packaging into
bacteriophage φ29 capsids [J]. PLoS Biol, 2007, 5: e59.
[34] MITCHELL M S, MATSUZAKI S, IMAI S, et al. Sequence analysis of bacteriophage T4 DNA packaging/terminase genes 16
and 17 reveals a common ATPase center in the large subunit of viral terminases [J]. Nucleic Acids Res, 2002, 30: 4009-4021.
[35] GUO P, PETERSON C, ANDERSON D. Prohead and DNA-gp3-dependent ATPase activity of the DNA packaging protein gp16 of
bacteriophage φ29 [J]. J Mol Biol, 1987, 197: 229-236.
[36] MORITA M, TASAKA M, FUJISAWA H. DNA packaging ATPase of bacteriophage T3 [J]. Virology, 1993, 193: 748-752.
[37] YASUDA R, NOJI H, KINOSITAJR K, et al. F1-ATPase is a highly efficient molecular motor that rotates with discrete 120 steps [J]. Cell, 1998, 93: 1117-1124.
[38] SHU Y G, OUYANG Z C. Biomotor is not a heat engine [J]. Biophys Rev Lett, 2022, 17: 43-50.
[39] NADAL M, MAS P J, BLANCO A G, et al. Structure and inhibition of herpesvirus DNA packaging terminase nuclease domain [J].
PNAS, 2010, 107: 16078-16083.
[40] FENG Y X, ZHANG Y C, YING C F, et al. Nanopore-based fourthgeneration DNA sequencing technology [J]. Genomics, Proteomics & Bioinformatics, 2015, 13: 4-16.
[41] SCHNEIDER G, DEKKER C. DNA sequencing with nanopores [J]. Nat Biotechnol, 2012, 30: 326-328.
[42] WENDELL D, JING P, GENG J, et al. Translocation of doublestranded DNA through membrane-adapted phi29 motor protein
nanopores [J]. Nature Nanotechnology, 2009, 4: 765-772.