title: Bacterial replication, transcription and translation: mechanistic insights from single-molecule biochemical studies.
abstract: Decades of research have resulted in a remarkably detailed understanding of the molecular mechanisms of bacterial DNA replication, transcription and translation. Our understanding of the kinetics and physical mechanisms that drive these processes forward has been expanded by the ability of single-molecule in vitro techniques, such as force spectroscopy and single-molecule Förster (fluorescence) resonance energy transfer (smFRET), to capture short-lived intermediate states in complex pathways. Furthermore, these technologies have revealed novel mechanisms that support enzyme processivity and govern the assembly of large multicomponent complexes. Here, we summarize the application of in vitro single-molecule studies to the analysis of fundamental bacterial processes, with a focus on the most recent functional insights that have been gained from fluorescence-based methods.
authors.affiliation: Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands.
authors.forename: Andrew
authors.initials: A
authors.lastname: Robinson
authors.forename: Antoine M
authors.initials: AM
authors.lastname: van Oijen
mesh_terms: D018407:Bacterial Physiological Phenomena / Q000235:genetics*; D004261:DNA Replication; D004269:DNA, Bacterial / Q000096:biosynthesis* / Q000235:genetics*; D031541:Fluorescence Resonance Energy Transfer / Q000379:methods*; D014176:Protein Biosynthesis; D014158:Transcription, Genetic
chemical_list: D004269:DNA, Bacterial
references.citation: Nat Struct Mol Biol. 2010 Dec;17(12):1470-7
references.pmid: 21057527
references.citation: Proc Natl Acad Sci U S A. 2011 Oct 11;108(41):16980-5
references.pmid: 21969541
references.citation: Proc Natl Acad Sci U S A. 2005 Mar 1;102(9):3254-9
references.pmid: 15728347
references.citation: Nat Rev Genet. 2013 Jan;14(1):9-22
references.pmid: 23150038
references.citation: Science. 2012 Oct 26;338(6106):528-31
references.pmid: 23112333
references.citation: Nature. 2009 Dec 17;462(7275):940-3
references.pmid: 19924126
references.citation: Annu Rev Biophys. 2010;39:491-513
references.pmid: 20192783
references.citation: FEBS Lett. 2010 Jun 18;584(12):2596-605
references.pmid: 20388515
references.citation: Nat Struct Mol Biol. 2012 May 06;19(6):609-15
references.pmid: 22562136
references.citation: Nat Chem Biol. 2010 Jan;6(1):54-62
references.pmid: 19946275
references.citation: Cell. 2011 Feb 18;144(4):480-97
references.pmid: 21335233
references.citation: J Biol Chem. 1980 May 10;255(9):4290-3
references.pmid: 6989836
references.citation: Proc Natl Acad Sci U S A. 2009 Aug 11;106(32):13236-41
references.pmid: 19666586
references.citation: Mol Cell. 2007 Aug 17;27(4):527-38
references.pmid: 17707226
references.citation: Nucleic Acids Res. 2012 Aug;40(15):7375-83
references.pmid: 22581769
references.citation: Cell. 2012 Jul 20;150(2):389-401
references.pmid: 22817898
references.citation: Nat Methods. 2012 Oct;9(10):987-92
references.pmid: 22961247
references.citation: Annu Rev Biochem. 2011;80:403-36
references.pmid: 21675919
references.citation: Nat Chem Biol. 2009 Dec;5(12):904-12
references.pmid: 19838204
references.citation: Cell Mol Life Sci. 2009 Feb;66(3):423-36
references.pmid: 19011758
references.citation: Nature. 2006 Feb 2;439(7076):621-4
references.pmid: 16452983
references.citation: Mol Cell. 2011 May 6;42(3):367-77
references.pmid: 21549313
references.citation: Nat Struct Mol Biol. 2012 Sep;19(9):957-63
references.pmid: 22902368
references.citation: J Mol Biol. 2010 Sep 3;401(5):743-56
references.pmid: 20600127
references.citation: Nat Struct Mol Biol. 2010 Jul;17(7):793-800
references.pmid: 20562856
references.citation: Curr Drug Targets. 2012 Mar;13(3):352-72
references.pmid: 22206257
references.citation: Cold Spring Harb Perspect Biol. 2010 Jan;2(1):a000331
references.pmid: 20182599
references.citation: Nature. 2011 Jul 20;475(7356):308-15
references.pmid: 21776076
references.citation: Science. 2010 Apr 23;328(5977):498-501
references.pmid: 20413500
references.citation: Nat Rev Microbiol. 2004 Jan;2(1):57-65
references.pmid: 15035009
references.citation: Curr Opin Struct Biol. 2009 Feb;19(1):103-9
references.pmid: 19223173
references.citation: Nucleic Acids Res. 2007;35(9):2813-24
references.pmid: 17355988
references.citation: Science. 2010 Jul 30;329(5991):533-8
references.pmid: 20671182
references.citation: Curr Opin Struct Biol. 2012 Feb;22(1):110-8
references.pmid: 22155178
references.citation: Biochemistry. 2010 Nov 16;49(45):9732-8
references.pmid: 20886842
references.citation: Anal Chem. 2012 Sep 18;84(18):7607-12
references.pmid: 22950646
references.citation: Science. 2003 Aug 29;301(5637):1235-8
references.pmid: 12947199
references.citation: Biochemistry. 2006 Jul 4;45(26):7990-7
references.pmid: 16800624
references.citation: Nature. 2010 Dec 16;468(7326):978-82
references.pmid: 21124318
references.citation: EMBO Rep. 2010 Apr;11(4):312-6
references.pmid: 20224578
references.citation: Science. 2003 Jan 31;299(5607):682-6
references.pmid: 12560545
references.citation: Science. 2006 Nov 17;314(5802):1144-7
references.pmid: 17110578
references.citation: Nature. 2009 Jan 15;457(7227):336-9
references.pmid: 19029884
references.citation: Nat Rev Microbiol. 2007 May;5(5):343-54
references.pmid: 17435790
references.citation: Genes Dev. 2011 Jun 15;25(12):1205-31
references.pmid: 21685361
references.citation: Mol Cell. 2011 Jul 22;43(2):161-3
references.pmid: 21777806
references.citation: Nature. 2010 Apr 15;464(7291):1012-7
references.pmid: 20393556
references.citation: Biophys J. 2010 Nov 3;99(9):3002-9
references.pmid: 21044598
references.citation: Science. 2006 Nov 17;314(5802):1139-43
references.pmid: 17110577
references.citation: Science. 2012 Jan 20;335(6066):328-31
references.pmid: 22194411
references.citation: Nature. 2011 Oct 02;478(7368):209-13
references.pmid: 21964332
references.citation: Mol Cell. 2011 Feb 4;41(3):249-62
references.pmid: 21292158
references.citation: Cell. 2012 Feb 17;148(4):679-89
references.pmid: 22341441
references.citation: Biochemistry. 2010 Nov 2;49(43):9171-80
references.pmid: 20818825
references.citation: Nature. 2012 Jul 19;487(7407):390-3
references.pmid: 22722848
references.citation: Annu Rev Biochem. 2008;77:149-76
references.pmid: 18410247
references.citation: Nat Struct Mol Biol. 2011 Dec 11;19(1):113-6
references.pmid: 22157955
references.citation: Microbiol Mol Biol Rev. 2010 Jun;74(2):273-97
references.pmid: 20508250
references.citation: Nat Rev Microbiol. 2012 Jun 06;10(7):449-58
references.pmid: 22669220
references.citation: Science. 2012 Aug 3;337(6094):591-5
references.pmid: 22859489
references.citation: Science. 2000 Aug 11;289(5481):905-20
references.pmid: 10937989
references.citation: Mol Cell. 2005 Nov 11;20(3):347-56
references.pmid: 16285917
references.citation: Nucleic Acids Res. 2009 Mar;37(4):e27
references.pmid: 19155275
references.citation: Proc Natl Acad Sci U S A. 2011 Mar 1;108(9):3584-9
references.pmid: 21245349
references.citation: Science. 2008 Oct 17;322(5900):442-6
references.pmid: 18927393
references.citation: Annu Rev Biophys. 2012;41:1-19
references.pmid: 22577819
references.citation: EMBO J. 2011 May 4;30(9):1830-40
references.pmid: 21441898
references.citation: Proc Natl Acad Sci U S A. 2009 Dec 29;106(52):22175-80
references.pmid: 20018723
references.citation: Nature. 2009 Dec 17;462(7275):854-5
references.pmid: 20016583
references.citation: Proc Natl Acad Sci U S A. 2007 Mar 27;104(13):5312-7
references.pmid: 17369350
references.citation: Annu Rev Biochem. 2010;79:381-412
references.pmid: 20235828
references.citation: Biophys J. 2012 Feb 8;102(3):532-41
references.pmid: 22325276
references.citation: J Biol Chem. 2000 Jan 14;275(2):855-60
references.pmid: 10625618
references.citation: Mol Microbiol. 2012 Apr;84(1):6-16
references.pmid: 22417087
references.citation: Nucleic Acids Res. 2006 Jul 11;34(12):3409-20
references.pmid: 16835309
references.citation: Nature. 2011 Jul 06;475(7354):118-21
references.pmid: 21734708
references.citation: Proc Natl Acad Sci U S A. 2010 Feb 2;107(5):1900-5
references.pmid: 20080681
references.citation: Crit Rev Biochem Mol Biol. 2012 Jul-Aug;47(4):334-48
references.pmid: 22515367
references.citation: Mol Cell. 2013 Feb 7;49(3):547-57
references.pmid: 23260658
references.citation: Nat Commun. 2011 Aug 23;2:439
references.pmid: 21863006
references.citation: Microbiol Mol Biol Rev. 2005 Mar;69(1):101-23
references.pmid: 15755955