Within and Beyond the Nucleotide Addition Cycle of Viral RNA-dependent RNA Polymerases.
RNA virus
RNA-dependent RNA polymerase
cleavage
misincorporation
nucleotide addition cycle
nucleotide analog
translocation
Journal
Frontiers in molecular biosciences
ISSN: 2296-889X
Titre abrégé: Front Mol Biosci
Pays: Switzerland
ID NLM: 101653173
Informations de publication
Date de publication:
2021
2021
Historique:
received:
25
11
2021
accepted:
21
12
2021
entrez:
27
1
2022
pubmed:
28
1
2022
medline:
28
1
2022
Statut:
epublish
Résumé
Nucleotide addition cycle (NAC) is a fundamental process utilized by nucleic acid polymerases when carrying out nucleic acid biosynthesis. An induced-fit mechanism is usually taken by these polymerases upon NTP/dNTP substrate binding, leading to active site closure and formation of a phosphodiester bond. In viral RNA-dependent RNA polymerases, the post-chemistry translocation is stringently controlled by a structurally conserved motif, resulting in asymmetric movement of the template-product duplex. This perspective focuses on viral RdRP NAC and related mechanisms that have not been structurally clarified to date. Firstly, RdRP movement along the template strand in the absence of catalytic events may be relevant to catalytic complex dissociation or proofreading. Secondly, pyrophosphate or non-cognate NTP-mediated cleavage of the product strand 3'-nucleotide can also play a role in reactivating paused or arrested catalytic complexes. Furthermore, non-cognate NTP substrates, including NTP analog inhibitors, can not only alter NAC when being misincorporated, but also impact on subsequent NACs. Complications and challenges related to these topics are also discussed.
Identifiants
pubmed: 35083282
doi: 10.3389/fmolb.2021.822218
pii: 822218
pmc: PMC8784604
doi:
Types de publication
Journal Article
Langues
eng
Pagination
822218Informations de copyright
Copyright © 2022 Gong.
Déclaration de conflit d'intérêts
The author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Références
PLoS One. 2013 May 08;8(5):e60272
pubmed: 23667424
Cell. 2004 Feb 6;116(3):381-91
pubmed: 15016373
Cell. 2020 Sep 17;182(6):1560-1573.e13
pubmed: 32783916
J Antimicrob Chemother. 2017 Mar 1;72(3):727-734
pubmed: 28069884
Nature. 2020 Mar;579(7798):270-273
pubmed: 32015507
PLoS Pathog. 2013;9(8):e1003549
pubmed: 23950717
Front Microbiol. 2019 Aug 22;10:1945
pubmed: 31507560
Cell. 2004 Mar 19;116(6):803-16
pubmed: 15035983
Mol Cell. 2018 Mar 1;69(5):802-815.e5
pubmed: 29499135
J Mol Biol. 2019 Sep 20;431(20):4030-4039
pubmed: 30978344
J Biol Chem. 1981 Mar 25;256(6):2777-86
pubmed: 7009597
J Biol Chem. 2008 Mar 21;283(12):7705-12
pubmed: 18184655
PLoS Pathog. 2013;9(12):e1003760
pubmed: 24348241
Nature. 2021 Aug;596(7873):590-596
pubmed: 34293799
Nat Struct Mol Biol. 2021 Sep;28(9):740-746
pubmed: 34381216
Cell. 2006 Feb 10;124(3):507-20
pubmed: 16469698
Proc Natl Acad Sci U S A. 2021 May 11;118(19):
pubmed: 33883267
Nat Commun. 2020 Jul 17;11(1):3590
pubmed: 32681014
J Biol Chem. 2021 Jul;297(1):100770
pubmed: 33989635
Science. 1998 Nov 27;282(5394):1669-75
pubmed: 9831551
J Mol Biol. 1994 Apr 29;238(2):145-58
pubmed: 8158645
Mol Cell. 2019 Jul 25;75(2):298-309.e4
pubmed: 31103420
J Biol Chem. 2000 Jun 9;275(23):17677-82
pubmed: 10748208
Elife. 2021 Oct 07;10:
pubmed: 34617885
Cell. 2004 Feb 6;116(3):393-404
pubmed: 15016374
Cell. 2020 May 14;181(4):877-893.e21
pubmed: 32304664
Antiviral Res. 2010 Aug;87(2):125-48
pubmed: 19945487
Proc Natl Acad Sci U S A. 2007 May 29;104(22):9463-8
pubmed: 17517631
DNA Repair (Amst). 2019 Sep;81:102652
pubmed: 31326363
Proc Natl Acad Sci U S A. 2010 Jun 15;107(24):10884-9
pubmed: 20534494
Proc Natl Acad Sci U S A. 1993 Jul 15;90(14):6498-502
pubmed: 8341661
Annu Rep Med Chem. 2021;57:109-132
pubmed: 34728865
Nature. 2014 Dec 18;516(7531):355-60
pubmed: 25409142
Nat Struct Biol. 1999 Oct;6(10):937-43
pubmed: 10504728
Virus Res. 2018 Jan 15;244:181-193
pubmed: 29175107
Cell. 2021 Jun 24;184(13):3474-3485.e11
pubmed: 34143953
Nat Commun. 2020 May 25;11(1):2605
pubmed: 32451382
mBio. 2018 Nov 27;9(6):
pubmed: 30482837
Enzymes. 2021;49:63-82
pubmed: 34696839
Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10352-7
pubmed: 17553968
Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):13910-3
pubmed: 10570172
J Mol Biol. 2019 Jun 28;431(14):2528-2542
pubmed: 31029704
Cell. 2005 Dec 16;123(6):977-9
pubmed: 16360025
Science. 2009 May 29;324(5931):1203-6
pubmed: 19478184
Nucleic Acids Res. 2021 Sep 7;49(15):8811-8821
pubmed: 34365500
Nature. 2014 Dec 18;516(7531):361-6
pubmed: 25409151
J Biol Chem. 2020 Nov 20;295(47):16156-16165
pubmed: 32967965
J Mol Biol. 1997 Jan 10;265(1):8-19
pubmed: 8995520
Proc Natl Acad Sci U S A. 2013 Jan 29;110(5):E348-57
pubmed: 23307808
Nat Commun. 2019 May 28;10(1):2342
pubmed: 31138817
Virus Res. 2017 Apr 15;234:4-20
pubmed: 28163093
EMBO J. 1998 Dec 15;17(24):7514-25
pubmed: 9857206
Nucleic Acids Res. 2009 Oct;37(18):6042-53
pubmed: 19700770
Angew Chem Int Ed Engl. 2018 Aug 20;57(34):10826-10841
pubmed: 29978534
Cell. 2021 Jan 7;184(1):184-193.e10
pubmed: 33232691
Proc Natl Acad Sci U S A. 2007 Aug 7;104(32):12955-61
pubmed: 17670940
mBio. 2018 Mar 6;9(2):
pubmed: 29511076
Proc Natl Acad Sci U S A. 2010 Dec 28;107(52):22505-10
pubmed: 21148772
J Biol Chem. 2020 Apr 10;295(15):4773-4779
pubmed: 32094225
N Engl J Med. 2020 Dec 31;383(27):2598-2600
pubmed: 33264539
Nat Commun. 2021 Jan 12;12(1):279
pubmed: 33436624
Antiviral Res. 2013 Nov;100(2):446-54
pubmed: 24084488
Cell Rep. 2021 Oct 26;37(4):109882
pubmed: 34653416
N Engl J Med. 2013 Jan 3;368(1):34-44
pubmed: 23281974
Nat Med. 2000 Dec;6(12):1375-9
pubmed: 11100123
Proc Natl Acad Sci U S A. 1998 Nov 10;95(23):13471-6
pubmed: 9811824
Proc Natl Acad Sci U S A. 2000 Apr 11;97(8):3838-43
pubmed: 10760255
Science. 1999 Apr 23;284(5414):611-5
pubmed: 10213678
Bioorg Med Chem Lett. 2012 Apr 15;22(8):2705-7
pubmed: 22446091
Enzymes. 2021;49:39-62
pubmed: 34696838
Nature. 2001 Mar 8;410(6825):235-40
pubmed: 11242087
EMBO J. 2004 Sep 1;23(17):3462-71
pubmed: 15306852
Nucleic Acids Res. 2000 Nov 1;28(21):4147-56
pubmed: 11058111
Cell. 2015 Jul 16;162(2):314-327
pubmed: 26144317
Enzymes. 2021;49:215-233
pubmed: 34696833
Cell. 2006 Dec 1;127(5):941-54
pubmed: 17129781
Proc Natl Acad Sci U S A. 2014 Sep 16;111(37):E3900-9
pubmed: 25197083
Nucleic Acids Res. 2018 Nov 16;46(20):10840-10854
pubmed: 30239956
PLoS One. 2013 Jul 10;8(7):e68347
pubmed: 23874596
Proc Natl Acad Sci U S A. 2001 Jun 5;98(12):6895-900
pubmed: 11371613
Curr Top Microbiol Immunol. 2000;242:55-84
pubmed: 10592656
Annu Rep Med Chem. 2021;57:1-47
pubmed: 34728864
Lancet. 2016 Jul 30;388(10043):498-503
pubmed: 27209148
Mol Cell. 2018 Mar 1;69(5):816-827.e4
pubmed: 29499136
Proc Natl Acad Sci U S A. 2016 Jul 12;113(28):E4005-14
pubmed: 27339134
Science. 2015 Feb 13;347(6223):771-5
pubmed: 25678663
Cell. 2020 Jul 23;182(2):417-428.e13
pubmed: 32526208
J Biol Chem. 2020 May 15;295(20):6785-6797
pubmed: 32284326