Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts.
DNA polymerase III
DNA polymerases
DNA viruses
RNA polymerase
anti-phage systems
nicotinamide dinucleotide
nucleotides
transcription
virus evolution
Journal
Viruses
ISSN: 1999-4915
Titre abrégé: Viruses
Pays: Switzerland
ID NLM: 101509722
Informations de publication
Date de publication:
05 Jan 2021
05 Jan 2021
Historique:
received:
24
11
2020
revised:
31
12
2020
accepted:
31
12
2020
entrez:
20
1
2021
pubmed:
21
1
2021
medline:
9
3
2021
Statut:
epublish
Résumé
Jumbo phages have attracted much attention by virtue of their extraordinary genome size and unusual aspects of biology. By performing a comparative genomics analysis of 224 jumbo phages, we suggest an objective inclusion criterion based on genome size distributions and present a synthetic overview of their manifold adaptations across major biological systems. By means of clustering and principal component analysis of the phyletic patterns of conserved genes, all known jumbo phages can be classified into three higher-order groups, which include both myoviral and siphoviral morphologies indicating multiple independent origins from smaller predecessors. Our study uncovers several under-appreciated or unreported aspects of the DNA replication, recombination, transcription and virion maturation systems. Leveraging sensitive sequence analysis methods, we identify novel protein-modifying enzymes that might help hijack the host-machinery. Focusing on host-virus conflicts, we detect strategies used to counter different wings of the bacterial immune system, such as cyclic nucleotide- and NAD
Identifiants
pubmed: 33466489
pii: v13010063
doi: 10.3390/v13010063
pmc: PMC7824862
pii:
doi:
Types de publication
Journal Article
Research Support, N.I.H., Intramural
Langues
eng
Sous-ensembles de citation
IM
Références
Biochem Biophys Res Commun. 2005 Oct 7;335(4):1217-23
pubmed: 16112649
Neuron. 2017 Mar 22;93(6):1334-1343.e5
pubmed: 28334607
Curr Opin Microbiol. 2010 Apr;13(2):142-9
pubmed: 20211578
J Mol Biol. 2006 Apr 21;358(1):16-37
pubmed: 16497325
Viruses. 2020 Sep 23;12(10):
pubmed: 32977622
Nat Struct Mol Biol. 2004 Feb;11(2):157-62
pubmed: 14730355
Adv Virus Res. 2019;103:167-202
pubmed: 30635076
Genome Dyn. 2007;3:48-65
pubmed: 18753784
Hum Mol Genet. 1999 Jul;8(7):1201-7
pubmed: 10369865
Biochemistry. 2010 Jul 27;49(29):6143-54
pubmed: 20545305
Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):19961-6
pubmed: 22135460
Cell. 2007 Sep 7;130(5):824-36
pubmed: 17803906
Genetics. 1998 Apr;148(4):1539-50
pubmed: 9560373
Nature. 2007 Oct 4;449(7162):616-20
pubmed: 17873859
Proc Natl Acad Sci U S A. 2011 May 3;108(18):7403-7
pubmed: 21502523
Q Rev Biophys. 2008 Feb;41(1):41-101
pubmed: 18755053
Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8298-305
pubmed: 11459967
J Virol. 2016 Oct 28;90(22):10284-10298
pubmed: 27605673
Cell. 1996 Sep 6;86(5):835-43
pubmed: 8797829
Genome Biol. 2003;4(12):R81
pubmed: 14659018
J Bacteriol. 2017 Apr 11;199(9):
pubmed: 28167526
J Mol Biol. 2020 Jun 26;432(14):4139-4153
pubmed: 32454153
Crit Rev Microbiol. 2018 May;44(3):304-317
pubmed: 28885059
Nucleic Acids Res. 2016 Oct 14;44(18):8525-8555
pubmed: 27536007
J Bacteriol. 1990 Apr;172(4):2079-87
pubmed: 2156810
Arch Virol. 1994;137(1-2):185-90
pubmed: 7979992
Biol Direct. 2012 Nov 14;7:40
pubmed: 23151069
Curr Opin Microbiol. 2016 Apr;30:22-29
pubmed: 26773214
Protein Sci. 2020 Apr;29(4):883-892
pubmed: 31886915
Nat Microbiol. 2020 Jan;5(1):48-55
pubmed: 31819217
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W197-201
pubmed: 18463136
Nucleic Acids Res. 2015 Dec 15;43(22):10633-54
pubmed: 26590262
Nucleic Acids Res. 1999 Dec 1;27(23):4658-70
pubmed: 10556324
Nucleic Acids Res. 2013 Sep;41(16):7635-55
pubmed: 23814188
Cell Cycle. 2009 Jun 1;8(11):1698-710
pubmed: 19411852
Mol Cell. 2019 Mar 21;73(6):1282-1291.e8
pubmed: 30792174
Nat Rev Immunol. 2014 Aug;14(8):521-8
pubmed: 25033909
Virus Res. 2006 Apr;117(1):156-84
pubmed: 16494962
Genes Dev. 2003 Dec 1;17(23):2889-901
pubmed: 14633974
Biochim Biophys Acta. 2010 Mar-Apr;1799(3-4):302-18
pubmed: 19878744
J Biol Chem. 2019 Jun 28;294(26):10211-10235
pubmed: 31092555
Biol Direct. 2015 May 15;10:21
pubmed: 25976611
Mol Biol Cell. 2019 Jan 1;30(1):146-159
pubmed: 30403545
Viruses. 2020 Sep 02;12(9):
pubmed: 32887488
Mol Biosyst. 2012 Oct 30;8(12):3142-65
pubmed: 23044854
J Biol Chem. 2015 Aug 21;290(34):20734-42
pubmed: 26152727
J Mol Biol. 1998 Feb 6;275(5):725-30
pubmed: 9480764
Mol Biosyst. 2009 Dec;5(12):1636-60
pubmed: 20023723
J Mol Biol. 2006 Sep 1;361(5):1003-34
pubmed: 16889794
J Bacteriol. 2020 Nov 19;202(24):
pubmed: 32868406
Front Cell Infect Microbiol. 2012 Jun 29;2:89
pubmed: 22919680
Cell. 1993 Oct 8;75(1):147-54
pubmed: 8402894
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W244-8
pubmed: 15980461
Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3083-8
pubmed: 19204287
J Biol Chem. 1999 Jan 29;274(5):2637-44
pubmed: 9915792
Biol Direct. 2012 Jun 25;7:18
pubmed: 22731697
Biochim Biophys Acta. 2012 Jan;1823(1):83-91
pubmed: 21781991
Science. 2019 Aug 23;365(6455):799-803
pubmed: 31439793
PLoS One. 2013 Apr 09;8(4):e60717
pubmed: 23593293
Mutat Res. 2000 Feb 16;459(1):43-53
pubmed: 10677682
Nucleic Acids Res. 1998 Aug 15;26(16):3746-52
pubmed: 9685491
Protein Eng. 1990 May;3(6):461-7
pubmed: 2196557
Structure. 2012 Jul 3;20(7):1189-200
pubmed: 22658750
Trends Microbiol. 2020 Dec;28(12):959-967
pubmed: 33158732
Genome Res. 2001 Aug;11(8):1365-74
pubmed: 11483577
Nat Commun. 2016 Aug 22;7:12227
pubmed: 27548043
Adv Virus Res. 2012;82:339-49
pubmed: 22420857
EcoSal Plus. 2018 Aug;8(1):
pubmed: 30066669
Proc Natl Acad Sci U S A. 2013 Aug 6;110(32):13114-9
pubmed: 23878220
Curr Opin Struct Biol. 2004 Dec;14(6):757-64
pubmed: 15582400
Genome Inform. 2009 Oct;23(1):205-11
pubmed: 20180275
J Mol Biol. 1995 Apr 7;247(4):636-47
pubmed: 7723020
Cell Host Microbe. 2019 Feb 13;25(2):184-194
pubmed: 30763533
Proc Natl Acad Sci U S A. 1975 Jan;72(1):122-6
pubmed: 1090929
Nucleic Acids Res. 2005 Jan 31;33(2):650-60
pubmed: 15684411
BMC Genomics. 2015 Aug 07;16:582
pubmed: 26250905
Mol Microbiol. 2010 Oct;78(1):1-4
pubmed: 20545861
Biol Chem. 2019 Oct 25;400(11):1443-1464
pubmed: 31120853
J Struct Biol. 2012 Sep;179(3):299-319
pubmed: 22210308
Bioinformatics. 2008 Dec 1;24(23):2780-1
pubmed: 18818215
Nucleic Acids Res. 2002 Dec 1;30(23):5229-43
pubmed: 12466548
Virology. 2007 Jun 5;362(2):245-56
pubmed: 17291557
Nucleic Acids Res. 2015 Dec 2;43(21):10411-20
pubmed: 26490960
Nat Rev Mol Cell Biol. 2017 Aug;18(8):495-506
pubmed: 28512351
ISME J. 2014 Sep;8(9):1949-52
pubmed: 24599069
Annu Rev Virol. 2015 Nov;2(1):351-78
pubmed: 26958920
Annu Rev Microbiol. 2020 Sep 8;74:387-407
pubmed: 32660384
Elife. 2020 Feb 26;9:
pubmed: 32101166
Nat Microbiol. 2019 Apr;4(4):693-700
pubmed: 30692672
J Bacteriol. 2020 Dec 18;203(2):
pubmed: 32868402
Front Microbiol. 2018 Aug 14;9:1861
pubmed: 30154772
Adv Virus Res. 2012;82:119-53
pubmed: 22420853
Proc Natl Acad Sci U S A. 2009 Sep 8;106(36):15394-9
pubmed: 19706397
Nucleic Acids Res. 1998 Sep 15;26(18):4205-13
pubmed: 9722641
Proteins. 2002 Jul 1;48(1):1-14
pubmed: 12012333
J Biol Chem. 2011 Mar 11;286(10):7727-31
pubmed: 21224389
Res Microbiol. 2018 Nov;169(9):505-514
pubmed: 29777834
Mol Biosyst. 2012 Jun;8(6):1661-77
pubmed: 22399070
Environ Microbiol. 2010 Nov;12(11):3035-56
pubmed: 20662890
Curr Opin Struct Biol. 2012 Oct;22(5):540-9
pubmed: 22819665
Cell Cycle. 2008 May 15;7(10):1467-72
pubmed: 18418069
Nucleic Acids Res. 2018 Nov 2;46(19):10474-10488
pubmed: 30169742
Annu Rev Biochem. 2001;70:369-413
pubmed: 11395412
J Mol Microbiol Biotechnol. 1999 Nov;1(2):303-5
pubmed: 10943560
Proc Natl Acad Sci U S A. 1978 Apr;75(4):1783-7
pubmed: 273909
Virol J. 2010 Oct 28;7:290
pubmed: 21029434
J Biol Chem. 2011 Feb 11;286(6):4117-22
pubmed: 21098490
Proc Natl Acad Sci U S A. 2018 Jun 26;115(26):E6048-E6055
pubmed: 29891656
Annu Rev Genomics Hum Genet. 2000;1:99-116
pubmed: 11701626
J Biol Chem. 2007 Feb 2;282(5):2821-31
pubmed: 17158460
Structure. 2007 Oct;15(10):1316-24
pubmed: 17937920
mBio. 2017 Oct 17;8(5):
pubmed: 29042498
Mol Microbiol. 2019 Jan;111(1):221-236
pubmed: 30315706
Mol Microbiol. 1995 Feb;15(3):415-20
pubmed: 7540246
Structure. 2014 Feb 4;22(2):315-25
pubmed: 24389024
Virol J. 2010 Oct 28;7:289
pubmed: 21029433
Curr Opin Struct Biol. 2002 Jun;12(3):392-9
pubmed: 12127460
Nature. 2019 Feb;566(7743):259-263
pubmed: 30728498
Microbiology (Reading). 2011 Mar;157(Pt 3):859-867
pubmed: 21163841
Biochemistry (Mosc). 1998 Apr;63(4):399-406
pubmed: 9556522
Genome Res. 2000 Jan;10(1):5-16
pubmed: 10645945
Proc Natl Acad Sci U S A. 2012 May 15;109(20):7711-6
pubmed: 22538818
Curr Opin Virol. 2011 Oct;1(4):298-303
pubmed: 22034588
Tuberculosis (Edinb). 2015 Jul;95(4):385-94
pubmed: 25999286
Biol Direct. 2008 Oct 04;3:39
pubmed: 18834537
Genetics. 1962 Feb;47:179-86
pubmed: 13889186
Arch Biochem Biophys. 2005 Jan 1;433(1):129-43
pubmed: 15581572
Mol Microbiol. 2012 Apr;84(2):324-39
pubmed: 22429790
J Mol Biol. 1989 Oct 20;209(4):667-81
pubmed: 2685327
Nucleic Acids Res. 2005 Jul 15;33(12):3875-96
pubmed: 16027112
Proc Natl Acad Sci U S A. 2000 Aug 1;97(16):8926-31
pubmed: 10890916
Mol Microbiol. 1995 Aug;17(3):405-10
pubmed: 8559059
BMC Genomics. 2002 Mar 21;3:8
pubmed: 11914131
Structure. 1998 Feb 15;6(2):183-93
pubmed: 9519409
Front Microbiol. 2017 Jan 24;8:44
pubmed: 28174560
Microbiol Mol Biol Rev. 2003 Mar;67(1):86-156, table of contents
pubmed: 12626685
Nature. 2020 Jan;577(7789):244-248
pubmed: 31819262
Nucleic Acids Res. 2000 Sep 15;28(18):3417-32
pubmed: 10982859
Nat Struct Biol. 2001 May;8(5):467-72
pubmed: 11323725
Nucleic Acids Res. 2019 Dec 16;47(22):11826-11838
pubmed: 31722405
Front Microbiol. 2020 Sep 07;11:2072
pubmed: 33013756
Curr Opin Microbiol. 2007 Aug;10(4):388-95
pubmed: 17703991
Proc Natl Acad Sci U S A. 1996 Sep 17;93(19):10268-73
pubmed: 8816789
Virology. 2020 Apr;543:7-12
pubmed: 32056848
J Bacteriol. 2017 Jul 11;199(15):
pubmed: 28559295
Biochemistry. 2006 Jan 10;45(1):272-82
pubmed: 16388603
J Virol. 2011 May;85(10):4812-21
pubmed: 21367903
Prog Mol Biol Transl Sci. 2011;101:25-104
pubmed: 21507349
Cell Rep. 2020 Sep 15;32(11):108133
pubmed: 32937129
Biochem Soc Trans. 2004 Apr;32(Pt 2):231-5
pubmed: 15046578
Virology. 2016 Aug;495:185-96
pubmed: 27236306
Arch Virol. 2020 Feb;165(2):303-311
pubmed: 31786689
Compr Physiol. 2012 Jan;2(1):779-803
pubmed: 23728985
Biochim Biophys Acta. 2000 May 23;1478(2):211-20
pubmed: 10825532
J Biol Chem. 2009 Nov 27;284(48):33654-61
pubmed: 19801667
J Bacteriol. 2004 Nov;186(21):7032-68
pubmed: 15489417
Nat Struct Mol Biol. 2020 Feb;27(2):202-209
pubmed: 32042153
J Biol Chem. 2010 Jan 1;285(1):473-82
pubmed: 19901023
J Virol. 1982 Jan;41(1):345-7
pubmed: 7086957
J Mol Biol. 1972 Nov 14;71(2):113-25
pubmed: 4629016
J Mol Biol. 2013 Jun 26;425(12):2164-73
pubmed: 23528827
Front Genet. 2014 Apr 30;5:102
pubmed: 24817877
Nat Commun. 2015 Jul 06;6:7548
pubmed: 26144253
Clin Exp Immunol. 2018 Oct;194(1):9-16
pubmed: 30030848
Front Microbiol. 2018 Sep 12;9:2169
pubmed: 30258425
Cell. 2006 Sep 8;126(5):881-92
pubmed: 16959568
Nature. 2019 Mar;567(7747):194-199
pubmed: 30787435
Nature. 2017 Aug 31;548(7669):543-548
pubmed: 28722012
BMC Bioinformatics. 2004 Aug 19;5:113
pubmed: 15318951
Trends Biochem Sci. 1998 Dec;23(12):469-72
pubmed: 9868367
Curr Top Microbiol Immunol. 2015;384:3-32
pubmed: 25027823
Proc Natl Acad Sci U S A. 2009 Oct 20;106(42):17921-6
pubmed: 19805122
Science. 2019 Jan 11;363(6423):
pubmed: 30467178
BMC Struct Biol. 2003 Jan 28;3:1
pubmed: 12553882
Mol Microbiol. 2015 Sep;97(5):898-910
pubmed: 26031711
Bioinformatics. 2012 Sep 1;28(17):2223-30
pubmed: 22796954
Annu Rev Biochem. 2016 Jun 2;85:431-54
pubmed: 26844395
Sci Rep. 2018 Mar 14;8(1):4486
pubmed: 29540765
Nucleic Acids Res. 2001 Mar 1;29(5):1175-84
pubmed: 11222767
Nucleic Acids Res. 2016 Jan 4;44(D1):D279-85
pubmed: 26673716
Proc Natl Acad Sci U S A. 1972 Oct;69(10):3009-13
pubmed: 4342972
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
pubmed: 9254694
PLoS Genet. 2016 May 23;12(5):e1006080
pubmed: 27214040
PLoS One. 2010 Mar 10;5(3):e9490
pubmed: 20224823
Trends Biochem Sci. 2005 Jun;30(6):275-9
pubmed: 15950866
Nature. 2013 Aug 15;500(7462):350-353
pubmed: 23925114
Nature. 2020 Feb;578(7795):425-431
pubmed: 32051592
Proc Natl Acad Sci U S A. 2000 Jul 18;97(15):8278-83
pubmed: 10880568
Mol Cell Oncol. 2014 Oct 29;1(2):e960754
pubmed: 27308331
Nucleic Acids Res. 2009 Feb;37(3):858-65
pubmed: 19103665
Biochem Biophys Res Commun. 2010 Jul 30;398(3):500-5
pubmed: 20599695
PLoS One. 2016 May 05;11(5):e0154899
pubmed: 27148748
Genes Dev. 2003 Jul 15;17(14):1768-78
pubmed: 12832395
Front Microbiol. 2017 Mar 14;8:403
pubmed: 28352259
Proc Natl Acad Sci U S A. 2008 Apr 1;105(13):5046-51
pubmed: 18362338
Bioessays. 2016 Jan;38(1):27-40
pubmed: 26660621
Structure. 2008 Sep 10;16(9):1417-27
pubmed: 18786404
Cell. 2004 Apr 2;117(1):57-68
pubmed: 15066282
Biochemistry. 2016 Feb 23;55(7):989-1002
pubmed: 26818562
Cell Cycle. 2008 Jan 1;7(1):120-1
pubmed: 18204304
FEMS Microbiol Rev. 2005 Apr;29(2):231-62
pubmed: 15808743
Nucleic Acids Res. 2019 Mar 18;47(5):2377-2388
pubmed: 30576517
Nucleic Acids Res. 2012 Sep 1;40(17):8568-78
pubmed: 22730290
J Biol Chem. 2005 Jun 3;280(22):21561-9
pubmed: 15781450
Mol Cell. 2013 Jul 25;51(2):226-35
pubmed: 23747010
J Virol. 2001 Dec;75(23):11720-34
pubmed: 11689653
Mol Biol Cell. 2017 Nov 1;28(22):2924-2931
pubmed: 29084910
Protein Sci. 2005 Nov;14(11):2849-61
pubmed: 16251366
Sci Rep. 2019 Nov 13;9(1):16679
pubmed: 31723182
Nature. 2016 May 11;533(7603):353-8
pubmed: 27193681
Chem Rev. 2016 Oct 26;116(20):12655-12687
pubmed: 27319741
J Bacteriol. 2005 Apr;187(8):2774-82
pubmed: 15805524
J Gen Microbiol. 1989 Mar;135(3):499-502
pubmed: 2559940
PLoS Pathog. 2015 Jun 11;11(6):e1004847
pubmed: 26066799
PLoS One. 2013 Sep 06;8(9):e74477
pubmed: 24040257
J Virol. 1975 Jul;16(1):1-4
pubmed: 805845
J Biol Chem. 2011 Sep 2;286(35):30867-77
pubmed: 21705802
Bacteriophage. 2014 Jan 1;4(1):e28281
pubmed: 24616838
Int J Mol Sci. 2019 Apr 23;20(8):
pubmed: 31018531
Biol Chem. 1998 Jan;379(1):51-8
pubmed: 9504717
Genome Biol. 2003;4(2):R11
pubmed: 12620121
Mol Microbiol. 2020 Jan;113(1):222-236
pubmed: 31665539
J Bacteriol. 1980 Jul;143(1):50-8
pubmed: 6772635
Mol Cell. 2015 Mar 19;57(6):984-994
pubmed: 25728768
Nucleic Acids Res. 2004 Oct 05;32(17):5260-79
pubmed: 15466593
Curr Biol. 2018 Feb 5;28(3):421-430.e4
pubmed: 29395922
J Mol Evol. 1995 Feb;40(2):136-54
pubmed: 7699720
J Biol Chem. 2017 Nov 17;292(46):18832-18847
pubmed: 28972145