Elowitz MB, Levine AJ, Siggia ED, Swain PS. Stochastic gene expression in a single cell. Science. 2002;297:1183–6.
Golding I, Paulsson J, Zawilski SM, Cox EC. Real-time kinetics of gene activity in individual bacteria. Cell. 2005;123:1025–36.
Swain PS, Elowitz MB, Siggia ED. Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc Natl Acad Sci USA. 2002;99:12795–800.
Raj A, van Oudenaarden A. Nature, nurture, or chance: stochastic gene expression and its consequences. Cell. 2008;135:216–26.
Gordon AJ, Halliday JA, Blankschien MD, Burns PA, Yatagai F, Herman C. Transcriptional infidelity promotes heritable phenotypic change in a bistable gene network. PLoS Biol. 2009;7:e44.
Meyerovich M, Mamou G, Ben-Yehuda S. Visualizing high error levels during gene expression in living bacterial cells. Proc Natl Acad Sci USA. 2010;107:11543–8.
Atkins JF, Loughran G, Bhatt PR, Firth AE, Baranov PV. Ribosomal frameshifting and transcriptional slippage: from genetic steganography and cryptography to adventitious use. Nucleic Acids Res. 2016;44:7007–78.
Casadesús J, Low D. Epigenetic gene regulation in the bacterial world. Microbiol Mol Biol Rev. 2006;70:830–56.
Atkins JF, Gesteland RF. Recoding: expansion of decoding rules enriches gene expression. Nucleic acids and molecular biology, vol. 24. Berlin: Springer; 2010.
Gordon AJ, Satory D, Halliday JA, Herman C. Lost in transcription: transient errors in information transfer. Curr Opin Microbiol. 2015;24:80–7.
Penno C, Sharma V, Coakley A, O’Connell Motherway M, van Sinderen D, Lubkowska L, Kireeva ML, Kashlev M, Baranov PV, Atkins JF. Productive mRNA stem loop-mediated transcriptional slippage: crucial features in common with intrinsic terminators. Proc Natl Acad Sci USA. 2015;112:E1984–93.
Satory D, Gordon AJ, Halliday JA, Herman C. Epigenetic switches: can infidelity govern fate in microbes? Curr Opin Microbiol. 2011;14:212–7.
Anikin M, Molodtsov V, Temiakov D, McAllister WT. Transcript slippage and recoding. In: Atkins JF, Gesteland RF, editors. Recoding: expansion of decoding rules enriches gene expression, vol. 24. New York: Springer; 2010.
Sharma V, Firth AE, Antonov I, Fayet O, Atkins JF, Borodovsky M, Baranov PV. A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment. Mol Biol Evol. 2011;28:3195–211.
Turnbough CL. Regulation of gene expression by reiterative transcription. Curr Opin Microbiol. 2011;14:142–7.
Wons E, Furmanek-Blaszk B, Sektas M. RNA editing by T7 RNA polymerase bypasses InDel mutations causing unexpected phenotypic changes. Nucleic Acids Res. 2015;43:3950–63.
Banavali NK. Partial base flipping is sufficient for strand slippage near DNA duplex termini. J Am Chem Soc. 2013;135:8274–82.
Neher RA, Gerland U. Dynamics of force-induced DNA slippage. Phys Rev Lett. 2004;93:198102.
Arnott S, Chandrasekaran R, Hall IH, Puigjaner LC. Heteronomous DNA. Nucleic Acids Res. 1983;11:4141–55.
Klug A, Jack A, Viswamitra MA, Kennard O, Shakked Z, Steitz TA. A hypothesis on a specific sequence-dependent conformation of DNA and its relation to the binding of the lac-repressor protein. J Mol Biol. 1979;131:669–80.
Nelson HC, Finch JT, Luisi BF, Klug A. The structure of an oligo(dA).oligo(dT) tract and its biological implications. Nature. 1987;330:221–6.
Rhodes D, Klug A. Sequence-dependent helical periodicity of DNA. Nature. 1981;292:378–80.
Yoon C, Privé GG, Goodsell DS, Dickerson RE. Structure of an alternating-B DNA helix and its relationship to A-tract DNA. Proc Natl Acad Sci USA. 1988;85:6332–6.
Kvaratskhelia M, Budihas SR, Le Grice SF. Pre-existing distortions in nucleic acid structure aid polypurine tract selection by HIV-1 reverse transcriptase. J Biol Chem. 2002;277:16689–96.
Sarafianos SG, Das K, Tantillo C, Clark AD, Ding J, Whitcomb JM, Boyer PL, Hughes SH, Arnold E. Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA. EMBO J. 2001;20:1449–61.
Molodtsov V, Anikin M, McAllister WT. The presence of an RNA:DNA hybrid that is prone to slippage promotes termination by T7 RNA polymerase. J Mol Biol. 2014;426:3095–107.
Kashkina E, Anikin M, Brueckner F, Pomerantz RT, McAllister WT, Cramer P, Temiakov D. Template misalignment in multisubunit RNA polymerases and transcription fidelity. Mol Cell. 2006;24:257–66.
Pomerantz RT, Temiakov D, Anikin M, Vassylyev DG, McAllister WT. A mechanism of nucleotide misincorporation during transcription due to template-strand misalignment. Mol Cell. 2006;24:245–55.
Tsuchihashi Z, Brown PO. Sequence requirements for efficient translational frameshifting in the Escherichia coli dnaX gene and the role of an unstable interaction between tRNA(Lys) and an AAG lysine codon. Genes Dev. 1992;6:511–9.
Larsen B, Wills NM, Nelson C, Atkins JF, Gesteland RF. Nonlinearity in genetic decoding: homologous DNA replicase genes use alternatives of transcriptional slippage or translational frameshifting. Proc Natl Acad Sci USA. 2000;97:1683–8.
Turnbough CL, Switzer RL. Regulation of pyrimidine biosynthetic gene expression in bacteria: repression without repressors. Microbiol Mol Biol Rev. 2008;72:266–300.
Baranov PV, Hammer AW, Zhou J, Gesteland RF, Atkins JF. Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression. Genome Biol. 2005;6:R25.
Gordon AJ, Satory D, Halliday JA, Herman C. Heritable change caused by transient transcription errors. PLoS Genet. 2013;9:e1003595.
Rockah-Shmuel L, Tóth-Petróczy Á, Sela A, Wurtzel O, Sorek R, Tawfik DS. Correlated occurrence and bypass of frame-shifting insertion-deletions (InDels) to give functional proteins. PLoS Genet. 2013;9:e1003882.
Tamas I, Wernegreen JJ, Nystedt B, Kauppinen SN, Darby AC, Gomez-Valero L, Lundin D, Poole AM, Andersson SG. Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts. Proc Natl Acad Sci USA. 2008;105:14934–9.
Wernegreen JJ, Kauppinen SN, Degnan PH. Slip into something more functional: selection maintains ancient frameshifts in homopolymeric sequences. Mol Biol Evol. 2010;27:833–9.
Wagner LA, Weiss RB, Driscoll R, Dunn DS, Gesteland RF. Transcriptional slippage occurs during elongation at runs of adenine or thymine in Escherichia coli. Nucleic Acids Res. 1990;18:3529–35.
Groebe DR, Uhlenbeck OC. Characterization of RNA hairpin loop stability. Nucleic Acids Res. 1988;16:11725–35.
Xiong XF, Reznikoff WS. Transcriptional slippage during the transcription initiation process at a mutant lac promoter in vivo. J Mol Biol. 1993;231:569–80.
Traverse CC, Ochman H. Genome-wide spectra of transcription insertions and deletions reveal that slippage depends on RNA:DNA hybrid complementarity. MBio. 2017;8:e01230.
Murakami KS. Structural biology of bacterial RNA polymerase. Biomolecules. 2015;5:848–64.
Miller WG, Lindow SE. An improved GFP cloning cassette designed for prokaryotic transcriptional fusions. Gene. 1997;191:149–53.
Sambrook J, Fritsch EF, Maniatis T. Molecular cloning. A laboratory manual. Cold Spring Harbor: Cold Spring Harbor Laboratory Press; 1989.
Vinella D, Potrykus K, Murphy H, Cashel M. Effects on growth by changes of the balance between GreA, GreB, and DksA suggest mutual competition and functional redundancy in Escherichia coli. J Bacteriol. 2012;194:261–73.
Guzman LM, Belin D, Carson MJ, Beckwith J. Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. J Bacteriol. 1995;177:4121–30.
Furmanek-Blaszk B, Boratynski R, Zolcinska N, Sektas M. M1.MboII and M2.MboII type IIS methyltransferases: different specificities, the same target. Microbiology. 2009;155:1111–21.
Zhou K, Zhou L, Lim Q, Zou R, Stephanopoulos G, Too HP. Novel reference genes for quantifying transcriptional responses of Escherichia coli to protein overexpression by quantitative PCR. BMC Mol Biol. 2011;12:18.
Pfaffl MW. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001;29:e45.
Furmanek B, Sektas M, Wons E, Kaczorowski T. Molecular characterization of the DNA methyltransferase M1.NcuI from Neisseria cuniculi ATCC 14688. Res Microbiol. 2007;158:164–74.
Dopf J, Horiagon TM. Deletion mapping of the Aequorea victoria green fluorescent protein. Gene. 1996;173:39–44.
Li X, Zhang G, Ngo N, Zhao X, Kain SR, Huang CC. Deletions of the Aequorea victoria green fluorescent protein define the minimal domain required for fluorescence. J Biol Chem. 1997;272:28545–9.
Wons E, Koscielniak D, Szadkowska M, Sektas M. Evaluation of GFP reporter utility for analysis of transcriptional slippage during gene expression. Microb Cell Fact. 2018;17:150.
McAllister WT, Raskin CA. The phage RNA polymerases are related to DNA polymerases and reverse transcriptases. Mol Microbiol. 1993;10:1–6.
Tabor S, Richardson CC. A bacteriophage T7 RNA polymerase/promoter system for controlled exclusive expression of specific genes. Proc Natl Acad Sci USA. 1985;82:1074–8.
Proshkin S, Rahmouni AR, Mironov A, Nudler E. Cooperation between translating ribosomes and RNA polymerase in transcription elongation. Science. 2010;328:504–8.
de Smit MH, Verlaan PW, van Duin J, Pleij CW. Intracistronic transcriptional polarity enhances translational repression: a new role for Rho. Mol Microbiol. 2008;69:1278–89.
Stanssens P, Remaut E, Fiers W. Inefficient translation initiation causes premature transcription termination in the lacZ gene. Cell. 1986;44:711–8.
Chevrier-Miller M, Jacques N, Raibaud O, Dreyfus M. Transcription of single-copy hybrid lacZ genes by T7 RNA polymerase in Escherichia coli: mRNA synthesis and degradation can be uncoupled from translation. Nucleic Acids Res. 1990;18:5787–92.
Lopez PJ, Iost I, Dreyfus M. The use of a tRNA as a transcriptional reporter: the T7 late promoter is extremely efficient in Escherichia coli but its transcripts are poorly expressed. Nucleic Acids Res. 1994;22:2434.
Pasman Z, von Hippel PH. Regulation of rho-dependent transcription termination by NusG is specific to the Escherichia coli elongation complex. Biochemistry. 2000;39:5573–85.
Studier FW. Bacteriophage T7. Science. 1972;176:367–76.
Parks AR, Court C, Lubkowska L, Jin DJ, Kashlev M, Court DL. Bacteriophage λ N protein inhibits transcription slippage by Escherichia coli RNA polymerase. Nucleic Acids Res. 2014;42:5823–9.
Zwiefka A, Kohn H, Widger WR. Transcription termination factor rho: the site of bicyclomycin inhibition in Escherichia coli. Biochemistry. 1993;32:3564–70.
Saxena S, Gowrishankar J. Modulation of Rho-dependent transcription termination in Escherichia coli by the H–NS family of proteins. J Bacteriol. 2011;193:3832–41.
Joyce SA, Dreyfus M. In the absence of translation, RNase E can bypass 5′ mRNA stabilizers in Escherichia coli. J Mol Biol. 1998;282:241–54.
Iost I, Guillerez J, Dreyfus M. Bacteriophage T7 RNA polymerase travels far ahead of ribosomes in vivo. J Bacteriol. 1992;174:619–22.
Komissarova N, Becker J, Solter S, Kireeva M, Kashlev M. Shortening of RNA:DNA hybrid in the elongation complex of RNA polymerase is a prerequisite for transcription termination. Mol Cell. 2002;10:1151–62.
Penno C, Sansonetti P, Parsot C. Frameshifting by transcriptional slippage is involved in production of MxiE, the transcription activator regulated by the activity of the type III secretion apparatus in Shigella flexneri. Mol Microbiol. 2005;56:204–14.
Zhou YN, Lubkowska L, Hui M, Court C, Chen S, Court DL, Strathern J, Jin DJ, Kashlev M. Isolation and characterization of RNA polymerase rpoB mutations that alter transcription slippage during elongation in Escherichia coli. J Biol Chem. 2013;288:2700–10.
Chamberlin MJ. Comparative properties of DNA, RNA, and hybrid homopolymer pairs. Fed Proc. 1965;24:1446–57.
Huang Y, Chen C, Russu IM. Dynamics and stability of individual base pairs in two homologous RNA–DNA hybrids. Biochemistry. 2009;48:3988–97.
Martin FH, Tinoco I. DNA–RNA hybrid duplexes containing oligo(dA:rU) sequences are exceptionally unstable and may facilitate termination of transcription. Nucleic Acids Res. 1980;8:2295–9.
Steitz TA. The structural basis of the transition from initiation to elongation phases of transcription, as well as translocation and strand separation, by T7 RNA polymerase. Curr Opin Struct Biol. 2004;14:4–9.
Borukhov S, Lee J, Laptenko O. Bacterial transcription elongation factors: new insights into molecular mechanism of action. Mol Microbiol. 2005;55:1315–24.
Roghanian M, Zenkin N, Yuzenkova Y. Bacterial global regulators DksA/ppGpp increase fidelity of transcription. Nucleic Acids Res. 2015;43:1529–36.
Satory D, Gordon AJ, Wang M, Halliday JA, Golding I, Herman C. DksA involvement in transcription fidelity buffers stochastic epigenetic change. Nucleic Acids Res. 2015;43:10190–9.
Zhang Y, Mooney RA, Grass JA, Sivaramakrishnan P, Herman C, Landick R, Wang JD. DksA guards elongating RNA polymerase against ribosome-stalling-induced arrest. Mol Cell. 2014;53:766–78.
Bonner G, Lafer EM, Sousa R. Characterization of a set of T7 RNA polymerase active site mutants. J Biol Chem. 1994;269:25120–8.
Gueguen E, Wills NM, Atkins JF, Cascales E. Transcriptional frameshifting rescues Citrobacter rodentium type VI secretion by the production of two length variants from the prematurely interrupted tssM gene. PLoS Genet. 2014;10:e1004869.
Penno C, Hachani A, Biskri L, Sansonetti P, Allaoui A, Parsot C. Transcriptional slippage controls production of type III secretion apparatus components in Shigella flexneri. Mol Microbiol. 2006;62:1460–8.
Wenthzel AM, Stancek M, Isaksson LA. Growth phase dependent stop codon readthrough and shift of translation reading frame in Escherichia coli. FEBS Lett. 1998;421:237–42.
Yurieva O, Skangalis M, Kuriyan J, O’Donnell M. Thermus thermophilis dnaX homolog encoding gamma- and tau-like proteins of the chromosomal replicase. J Biol Chem. 1997;272:27131–9.
Penno C, Parsot C. Transcriptional slippage in mxiE controls transcription and translation of the downstream mxiD gene, which encodes a component of the Shigella flexneri type III secretion apparatus. J Bacteriol. 2006;188:1196–8.
Strathern JN, Jin DJ, Court DL, Kashlev M. Isolation and characterization of transcription fidelity mutants. Biochim Biophys Acta. 2012;1819:694–9.
Kashkina E, Anikin M, Brueckner F, Lehmann E, Kochetkov SN, McAllister WT, Cramer P, Temiakov D. Multisubunit RNA polymerases melt only a single DNA base pair downstream of the active site. J Biol Chem. 2007;282:21578–82.
Cheeran A, Babu Suganthan R, Swapna G, Bandey I, Achary MS, Nagarajaram HA, Sen R. Escherichia coli RNA polymerase mutations located near the upstream edge of an RNA:DNA hybrid and the beginning of the RNA-exit channel are defective for transcription antitermination by the N protein from lambdoid phage H-19B. J Mol Biol. 2005;352:28–43.
Kent T, Kashkina E, Anikin M, Temiakov D. Maintenance of RNA–DNA hybrid length in bacterial RNA polymerases. J Biol Chem. 2009;284:13497–504.
Sidorenkov I, Komissarova N, Kashlev M. Crucial role of the RNA:DNA hybrid in the processivity of transcription. Mol Cell. 1998;2:55–64.
Nudler E, Mustaev A, Lukhtanov E, Goldfarb A. The RNA–DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase. Cell. 1997;89:33–41.
Chamberlin MJ. New models for the mechanism of transcription elongation and its regulation. Harvey Lect. 1992;88:1–21.
Blank A, Gallant JA, Burgess RR, Loeb LA. An RNA polymerase mutant with reduced accuracy of chain elongation. Biochemistry. 1986;25:5920–8.
Bochkareva A, Yuzenkova Y, Tadigotla VR, Zenkin N. Factor-independent transcription pausing caused by recognition of the RNA–DNA hybrid sequence. EMBO J. 2012;31:630–9.
Vassylyev DG, Vassylyeva MN, Perederina A, Tahirov TH, Artsimovitch I. Structural basis for transcription elongation by bacterial RNA polymerase. Nature. 2007;448:157–62.
Belogurov GA, Artsimovitch I. Regulation of transcript elongation. Annu Rev Microbiol. 2015;69:49–69.
Huang J, Brieba LG, Sousa R. Misincorporation by wild-type and mutant T7 RNA polymerases: identification of interactions that reduce misincorporation rates by stabilizing the catalytically incompetent open conformation. Biochemistry. 2000;39:11571–80.
Peters JM, Vangeloff AD, Landick R. Bacterial transcription terminators: the RNA 3′-end chronicles. J Mol Biol. 2011;412:793–813.
Landick R, Yanofsky C. Stability of an RNA secondary structure affects in vitro transcription pausing in the trp operon leader region. J Biol Chem. 1984;259:11550–5.
Yarchuk O, Iost I, Dreyfus M. The relation between translation and mRNA degradation in the lacZ gene. Biochimie. 1991;73:1533–41.
Peters JM, Mooney RA, Kuan PF, Rowland JL, Keles S, Landick R. Rho directs widespread termination of intragenic and stable RNA transcription. Proc Natl Acad Sci USA. 2009;106:15406–11.
Strauß M, Vitiello C, Schweimer K, Gottesman M, Rösch P, Knauer SH. Transcription is regulated by NusA:NusG interaction. Nucleic Acids Res. 2016;44:5971–82.
Mohanty BK, Kushner SR. The majority of Escherichia coli mRNAs undergo post-transcriptional modification in exponentially growing cells. Nucleic Acids Res. 2006;34:5695–704.
Hansen MT, Bennett PM, von Meyenburg K. Intracistronic polarity during dissociation of translation from transcription in Escherichia coli. J Mol Biol. 1973;77:589–604.
Goldberg LA. Degradation of abnormal proteins in Escherichia coli. Proc Natl Acad Sci. 1972;69:422–6.
Cannistraro VJ, Subbarao MN, Kennell D. Specific endonucleolytic cleavage sites for decay of Escherichia coli mRNA. J Mol Biol. 1986;192:257–74.
Das A. How the phage lambda N gene product suppresses transcription termination: communication of RNA polymerase with regulatory proteins mediated by signals in nascent RNA. J Bacteriol. 1992;174:6711–6.
Rees WA, Weitzel SE, Das A, von Hippel PH. Regulation of the elongation-termination decision at intrinsic terminators by antitermination protein N of phage lambda. J Mol Biol. 1997;273:797–813.
DeVito J, Das A. Control of transcription processivity in phage lambda: Nus factors strengthen the termination-resistant state of RNA polymerase induced by N antiterminator. Proc Natl Acad Sci USA. 1994;91:8660–4.
Franklin NC, Doelling JH. Overexpression of N antitermination proteins of bacteriophages lambda, 21, and P22: loss of N protein specificity. J Bacteriol. 1989;171:2513–22.
Rees WA, Weitzel SE, Yager TD, Das A, von Hippel PH. Bacteriophage lambda N protein alone can induce transcription antitermination in vitro. Proc Natl Acad Sci USA. 1996;93:342–6.
Coenye T, Vandamme P. Characterization of mononucleotide repeats in sequenced prokaryotic genomes. DNA Res. 2005;12:221–33.
Traverse CC, Ochman H. A genome-wide assay specifies only GreA as a transcription fidelity factor. G3 (Bethesda). 2018;8:2257–64.
James K, Gamba P, Cockell SJ, Zenkin N. Misincorporation by RNA polymerase is a major source of transcription pausing in vivo. Nucleic Acids Res. 2017;45:1105–13.
Bubunenko MG, Court CB, Rattray AJ, Gotte DR, Kireeva ML, Irizarry-Caro JA, Li X, Jin DJ, Court DL, Strathern JN, Kashlev M. A Cre transcription fidelity reporter identifies GreA as a major RNA proofreading factor in Escherichia coli. Genetics. 2017;206:179–87. https://doi.org/10.1534/genetics.116.198960
Imashimizu M, Oshima T, Lubkowska L, Kashlev M. Direct assessment of transcription fidelity by high-resolution RNA sequencing. Nucleic Acids Res. 2013;41:9090–104.