Single-molecule insights into torsion and roadblocks in bacterial transcript elongation.
Journal
Transcription
ISSN: 2154-1272
Titre abrégé: Transcription
Pays: United States
ID NLM: 101530967
Informations de publication
Date de publication:
08 2021
08 2021
Historique:
pubmed:
2
11
2021
medline:
7
5
2022
entrez:
1
11
2021
Statut:
ppublish
Résumé
During transcription, RNA polymerase (RNAP) translocates along the helical template DNA while maintaining high transcriptional fidelity. However, all genomes are dynamically twisted, writhed, and decorated by bound proteins and motor enzymes. In prokaryotes, proteins bound to DNA, specifically or not, frequently compact DNA into conformations that may silence genes by obstructing RNAP. Collision of RNAPs with these architectural proteins, may result in RNAP stalling and/or displacement of the protein roadblock. It is important to understand how rapidly transcribing RNAPs operate under different levels of supercoiling or in the presence of roadblocks. Given the broad range of asynchronous dynamics exhibited by transcriptional complexes, single-molecule assays, such as atomic force microscopy, fluorescence detection, optical and magnetic tweezers, etc. are well suited for detecting and quantifying activity with adequate spatial and temporal resolution. Here, we summarize current understanding of the effects of torsion and roadblocks on prokaryotic transcription, with a focus on single-molecule assays that provide real-time detection and readout.
Identifiants
pubmed: 34719335
doi: 10.1080/21541264.2021.1997315
pmc: PMC8632135
doi:
Substances chimiques
DNA
9007-49-2
DNA-Directed RNA Polymerases
EC 2.7.7.6
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
219-231Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM084070
Pays : United States
Références
Cell. 1988 May 6;53(3):433-40
pubmed: 2835168
PLoS Genet. 2011 Jun;7(6):e1002123
pubmed: 21698131
EMBO Rep. 2007 Mar;8(3):271-8
pubmed: 17290289
Nat Struct Mol Biol. 2010 Jun;17(6):745-52
pubmed: 20453861
Nucleic Acids Res. 2006;34(16):4642-52
pubmed: 16963779
Chromosoma. 1976 Dec 16;59(2):89-101
pubmed: 795620
Cell. 2013 May 23;153(5):1168-1168.e1
pubmed: 23706746
Proc Natl Acad Sci U S A. 2016 Jan 19;113(3):602-7
pubmed: 26733675
Nucleic Acids Res. 2021 Jan 11;49(1):15-24
pubmed: 33330935
Nat Rev Mol Cell Biol. 2006 Aug;7(8):580-8
pubmed: 16936698
Nucleic Acids Res. 2022 Mar 21;50(5):2826-2835
pubmed: 35188572
Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15402-7
pubmed: 25319264
Methods. 2016 Aug 1;105:3-15
pubmed: 27371121
Biochemistry. 2003 Sep 16;42(36):10718-25
pubmed: 12962496
J Biol Chem. 1999 Jun 4;274(23):16659-64
pubmed: 10347234
Biophys J. 2012 Oct 17;103(8):1753-61
pubmed: 23083719
Annu Rev Biochem. 1992;61:199-223
pubmed: 1497310
Nat Struct Mol Biol. 2008 Feb;15(2):146-54
pubmed: 18193062
Nucleic Acids Res. 2018 May 18;46(9):4417-4424
pubmed: 29538766
Nucleic Acids Res. 2018 Mar 16;46(5):2370-2379
pubmed: 29365152
Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):6106-11
pubmed: 22474350
Nucleic Acids Res. 2021 Nov 18;49(20):11550-11559
pubmed: 34723343
J Bacteriol. 1999 Oct;181(20):6361-70
pubmed: 10515926
Nat Commun. 2016 Mar 30;7:11055
pubmed: 27025941
Science. 2011 Sep 9;333(6048):1445-9
pubmed: 21903814
J Bacteriol. 1992 Nov;174(22):7121-7
pubmed: 1429435
Methods Mol Biol. 2018;1703:63-73
pubmed: 29177733
Nucleic Acids Res. 1997 Feb 15;25(4):873-6
pubmed: 9016640
Front Biosci. 2007 May 01;12:4409-23
pubmed: 17485385
Nature. 2006 Aug 17;442(7104):836-9
pubmed: 16862122
Nat Struct Mol Biol. 2004 Nov;11(11):1092-100
pubmed: 15502847
Phys Rev Lett. 2010 Oct 8;105(15):158101
pubmed: 21230940
Nat Methods. 2007 Mar;4(3):223-5
pubmed: 17322891
Nucleic Acids Res. 2021 Nov 18;49(20):11778-11786
pubmed: 34718727
Cell. 2006 Jun 16;125(6):1083-94
pubmed: 16777599
Genetica. 1999;106(1-2):57-62
pubmed: 10710710
Nucleic Acids Res. 2014 Aug;42(14):8861-72
pubmed: 25034688
Proc Natl Acad Sci U S A. 2015 Jun 16;112(24):7495-500
pubmed: 26023188
Biophys J. 2007 Oct 15;93(8):2726-31
pubmed: 17573434
Protein Sci. 2017 Jul;26(7):1427-1438
pubmed: 28295806
Nat Commun. 2018 Jul 26;9(1):2930
pubmed: 30050038
Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Dec;74(6 Pt 1):061907
pubmed: 17280096
Sci Rep. 2016 Feb 09;6:20513
pubmed: 26856421
J Bacteriol. 2013 Mar;195(6):1109-19
pubmed: 23292776
Annu Rev Biophys Biomol Struct. 2005;34:201-19
pubmed: 15869388
Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Dec;72(6 Pt 1):061902
pubmed: 16485969
Environ Microbiol. 2014 Mar;16(3):734-45
pubmed: 23869858
Science. 2013 Feb 15;339(6121):816-9
pubmed: 23413354
Mol Cell. 2006 Feb 3;21(3):417-25
pubmed: 16455496
PLoS Genet. 2019 Dec 12;15(12):e1008456
pubmed: 31830036
Methods. 2016 Oct 1;108:4-13
pubmed: 27402355
Nat Methods. 2010 Dec;7(12):977-80
pubmed: 20953173
Nucleic Acids Res. 2012 Sep;40(16):7728-38
pubmed: 22718983
Nucleic Acids Res. 2009 May;37(9):2789-95
pubmed: 19276206
Proc Natl Acad Sci U S A. 2009 Apr 28;106(17):6986-91
pubmed: 19359479
Nucleic Acids Res. 2008 May;36(8):2505-13
pubmed: 18310101
Eur J Biochem. 2002 Mar;269(6):1662-9
pubmed: 11895436
Nat Methods. 2008 Jun;5(6):491-505
pubmed: 18511917
DNA Res. 2006 Aug 31;13(4):141-53
pubmed: 17046956
Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1996 Mar;53(3):2984-2987
pubmed: 9964592
Proc Natl Acad Sci U S A. 1993 Mar 1;90(5):1917-21
pubmed: 8446609
Cell. 1983 Aug;34(1):105-13
pubmed: 6309403
Macromolecules. 2012 Apr 10;45(7):3188-3196
pubmed: 23526178
Nucleic Acids Res. 2008 Jul;36(12):4204-10
pubmed: 18573800
Nat Commun. 2021 Feb 16;12(1):1053
pubmed: 33594049
Nat Struct Mol Biol. 2013 Mar;20(3):396-403
pubmed: 23416947
Phys Rev Lett. 2011 Sep 2;107(10):108102
pubmed: 21981534
Science. 2006 Nov 17;314(5802):1139-43
pubmed: 17110577
Biopolymers. 2011 Feb;95(2):144-50
pubmed: 20882535
Genes Dev. 2000 Jan 15;14(2):212-23
pubmed: 10652275
Biophys Rev. 2016 Nov;8(Suppl 1):75-87
pubmed: 28275417
Cell. 2014 Jul 17;158(2):314-326
pubmed: 25036631
Science. 1996 Mar 29;271(5257):1835-7
pubmed: 8596951
Nucleic Acids Res. 2021 Apr 19;49(7):e39
pubmed: 33511418
PLoS One. 2016 Jul 25;11(7):e0159527
pubmed: 27455049
Methods Mol Biol. 2011;778:229-41
pubmed: 21809210
Science. 1995 Jan 20;267(5196):378-80
pubmed: 7824935
Biochim Biophys Acta. 2012 Jul;1819(7):830-5
pubmed: 22387214
Front Biosci. 2003 Jan 01;8:d210-21
pubmed: 12456359
Nucleic Acids Res. 2017 Jul 7;45(12):e109
pubmed: 28398514
Eur Biophys J. 1998;27(1):55-61
pubmed: 9463890
Proc Natl Acad Sci U S A. 2004 Apr 6;101(14):4776-80
pubmed: 15037753
Proc Natl Acad Sci U S A. 2020 May 19;117(20):10856-10864
pubmed: 32371489
Nature. 2001 Jan 4;409(6816):113-5
pubmed: 11343125
J Mol Biol. 2015 Jul 3;427(13):2305-18
pubmed: 25902201
Nucleic Acids Res. 2012 May;40(10):4306-19
pubmed: 22275524
PLoS Genet. 2012;8(3):e1002615
pubmed: 22457642
Nucleic Acids Res. 1987 Jul 10;15(13):5339-51
pubmed: 3299270
Curr Opin Struct Biol. 2012 Feb;22(1):80-7
pubmed: 22172540
Nature. 2003 Jul 17;424(6946):338-41
pubmed: 12867987
Mol Cell. 2005 Nov 11;20(3):347-56
pubmed: 16285917
Chem Rev. 2020 Jan 8;120(1):36-78
pubmed: 31661246
J Biol Chem. 2000 Mar 17;275(11):8103-13
pubmed: 10713132
Nucleic Acids Res. 2019 Jan 10;47(1):210-220
pubmed: 30445553
Nat Struct Mol Biol. 2013 Mar;20(3):387-95
pubmed: 23416946
Biophys J. 1998 Apr;74(4):2016-28
pubmed: 9545060
Methods Mol Biol. 2009;582:71-89
pubmed: 19763943
Curr Opin Microbiol. 2002 Apr;5(2):135-41
pubmed: 11934608
Nature. 1991 Aug 1;352(6334):444-8
pubmed: 1861724
Biophys J. 2019 Mar 5;116(5):760-771
pubmed: 30795872
Biomicrofluidics. 2014 Jun 12;8(3):034113
pubmed: 25379073
EMBO J. 2003 Sep 15;22(18):4719-27
pubmed: 12970184
Cell. 2019 Sep 19;179(1):106-119.e16
pubmed: 31539491
Science. 2009 Jul 31;325(5940):626-8
pubmed: 19644123
Biochem Soc Trans. 2013 Apr;41(2):542-7
pubmed: 23514151
Mol Cell. 2012 Nov 30;48(4):560-71
pubmed: 23084832
Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Dec;88(6):062722
pubmed: 24483501
Proc Natl Acad Sci U S A. 2009 Dec 29;106(52):22175-80
pubmed: 20018723
Phys Rev Lett. 2010 Jan 29;104(4):048301
pubmed: 20366742
Biochemistry. 1978 Dec 26;17(26):5798-804
pubmed: 365234
Mol Microbiol. 2004 Mar;51(5):1471-81
pubmed: 14982639
PLoS Biol. 2013;11(6):e1001591
pubmed: 23853547
Methods Enzymol. 2003;371:207-18
pubmed: 14712702
Proc Natl Acad Sci U S A. 2013 Oct 22;110(43):17386-91
pubmed: 24101469
Nucleic Acids Res. 1998 Jan 15;26(2):669-75
pubmed: 9421532
EMBO J. 2004 Oct 27;23(21):4330-41
pubmed: 15470498
Biophys Rev. 2016 Sep;8(3):209-220
pubmed: 28510224
Biophys J. 2005 Mar;88(3):1692-701
pubmed: 15653717
Phys Rev Lett. 2010 Jun 25;104(25):258103
pubmed: 20867418
Science. 2013 Jun 28;340(6140):1580-3
pubmed: 23812716
Front Microbiol. 2018 Aug 27;9:2019
pubmed: 30210483
Proc Natl Acad Sci U S A. 2019 Dec 26;116(52):26534-26539
pubmed: 31806753
Nucleic Acids Res. 1999 Jul 1;27(13):2814-24
pubmed: 10373601
Proc Natl Acad Sci U S A. 1987 Oct;84(20):7024-7
pubmed: 2823250
Phys Rev Lett. 2008 Apr 11;100(14):148301
pubmed: 18518075
Science. 1992 Nov 13;258(5085):1122-6
pubmed: 1439819
RNA. 2019 Nov;25(11):1457-1469
pubmed: 31320398
Proc Natl Acad Sci U S A. 2010 Mar 16;107(11):4985-90
pubmed: 20194794
Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11373-7
pubmed: 14500788
Proc Natl Acad Sci U S A. 2007 Sep 11;104(37):14670-5
pubmed: 17804808
Phys Rev Lett. 2009 Feb 20;102(7):078301
pubmed: 19257716
EMBO J. 1992 Feb;11(2):667-72
pubmed: 1537341
Nucleic Acids Res. 2010 Nov;38(20):7089-99
pubmed: 20601682
Proc Natl Acad Sci U S A. 2002 Sep 17;99(19):12126-31
pubmed: 12167668
Proc Natl Acad Sci U S A. 1997 Sep 30;94(20):10606-11
pubmed: 9380682
Nat Rev Microbiol. 2010 Mar;8(3):185-95
pubmed: 20140026
Nano Lett. 2009 Apr;9(4):1720-5
pubmed: 19301859
Curr Opin Microbiol. 2020 Jun;55:26-33
pubmed: 32120333