A nascent riboswitch helix orchestrates robust transcriptional regulation through signal integration.
Riboswitch
/ genetics
Gene Expression Regulation, Bacterial
Nucleic Acid Conformation
Transcription, Genetic
Lactococcus lactis
/ genetics
DNA-Directed RNA Polymerases
/ metabolism
RNA, Bacterial
/ metabolism
Manganese
/ metabolism
Transcription Factors
/ metabolism
Bacterial Proteins
/ metabolism
Single Molecule Imaging
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
10 May 2024
10 May 2024
Historique:
received:
09
01
2024
accepted:
29
04
2024
medline:
11
5
2024
pubmed:
11
5
2024
entrez:
10
5
2024
Statut:
epublish
Résumé
Widespread manganese-sensing transcriptional riboswitches effect the dependable gene regulation needed for bacterial manganese homeostasis in changing environments. Riboswitches - like most structured RNAs - are believed to fold co-transcriptionally, subject to both ligand binding and transcription events; yet how these processes are orchestrated for robust regulation is poorly understood. Through a combination of single-molecule and bulk approaches, we discover how a single Mn
Identifiants
pubmed: 38729929
doi: 10.1038/s41467-024-48409-8
pii: 10.1038/s41467-024-48409-8
doi:
Substances chimiques
Riboswitch
0
DNA-Directed RNA Polymerases
EC 2.7.7.6
RNA, Bacterial
0
Manganese
42Z2K6ZL8P
Transcription Factors
0
Bacterial Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
3955Informations de copyright
© 2024. The Author(s).
Références
Bakkeren, E., Diard, M. & Hardt, W.-D. Evolutionary causes and consequences of bacterial antibiotic persistence. Nat. Rev. Microbiol. 18, 479–490 (2020).
pubmed: 32461608
doi: 10.1038/s41579-020-0378-z
Sherwood, A. V. & Henkin, T. M. Riboswitch-Mediated Gene Regulation: Novel RNA Architectures Dictate Gene Expression Responses. Annu. Rev. Microbiol. 70, 361–374 (2016).
pubmed: 27607554
doi: 10.1146/annurev-micro-091014-104306
Kavita, K. & Breaker, R. R. Discovering riboswitches: the past and the future. Trends Biochem. Sci. 48, 119–141 (2023).
pubmed: 36150954
doi: 10.1016/j.tibs.2022.08.009
Bédard, A.-S. V., Hien, E. D. M. & Lafontaine, D. A. Riboswitch regulation mechanisms: RNA, metabolites and regulatory proteins. Biochim. Biophys. Acta Gene Regul. Mech. 1863, 194501 (2020).
pubmed: 32036061
doi: 10.1016/j.bbagrm.2020.194501
Chauvier, A. & Walter, N. G. Regulation of bacterial gene expression by non-coding RNA: It is all about time! Cell Chem. Biol. 31, 71–85 (2024).
pubmed: 38211587
doi: 10.1016/j.chembiol.2023.12.011
Ray-Soni, A., Bellecourt, M. J. & Landick, R. Mechanisms of Bacterial Transcription Termination: All Good Things Must End. Annu. Rev. Biochem. 85, 319–347 (2016).
pubmed: 27023849
doi: 10.1146/annurev-biochem-060815-014844
Chauvier, A. et al. Transcriptional pausing at the translation start site operates as a critical checkpoint for riboswitch regulation. Nat. Commun. 8, 13892 (2017).
pubmed: 28071751
pmcid: 5234074
doi: 10.1038/ncomms13892
Hollands, K. et al. Riboswitch control of Rho-dependent transcription termination. Proc. Natl Acad. Sci. USA 109, 5376–5381 (2012).
pubmed: 22431636
pmcid: 3325659
doi: 10.1073/pnas.1112211109
Hollands, K., Sevostiyanova, A. & Groisman, E. A. Unusually long-lived pause required for regulation of a Rho-dependent transcription terminator. Proc. Natl Acad. Sci. USA 111, E1999–E2007 (2014).
pubmed: 24778260
pmcid: 4024889
doi: 10.1073/pnas.1319193111
Martin, J. E. & Waters, L. S. Regulation of Bacterial Manganese Homeostasis and Usage During Stress Responses and Pathogenesis. Front. Mol. Biosci. 9, 945724 (2022).
pubmed: 35911964
pmcid: 9334652
doi: 10.3389/fmolb.2022.945724
Dambach, M. et al. The Ubiquitous yybP-ykoY Riboswitch Is a Manganese-Responsive Regulatory Element. Mol. Cell 57, 1099–1109 (2015).
pubmed: 25794618
pmcid: 4376352
doi: 10.1016/j.molcel.2015.01.035
Price, I. R., Gaballa, A., Ding, F., Helmann, J. D. & Ke, A. Mn(2+)-Sensing Mechanisms of yybP-ykoY Orphan Riboswitches. Mol. Cell 57, 1110–1123 (2015).
pubmed: 25794619
pmcid: 4703321
doi: 10.1016/j.molcel.2015.02.016
Suddala, K. C. et al. Local-to-global signal transduction at the core of a Mn2+ sensing riboswitch. Nat. Commun. 10, 4304 (2019).
pubmed: 31541094
pmcid: 6754395
doi: 10.1038/s41467-019-12230-5
Bachas, S. T. & Ferré-D’Amaré, A. R. Convergent Use of Heptacoordination for Cation Selectivity by RNA and Protein Metalloregulators. Cell Chem. Biol. 25, 962–973.e5 (2018).
pubmed: 29805037
pmcid: 6097924
doi: 10.1016/j.chembiol.2018.04.016
Sung, H.-L. & Nesbitt, D. J. Single-Molecule FRET Kinetics of the Mn2+ Riboswitch: Evidence for Allosteric Mg2+ Control of ‘Induced-Fit’ vs ‘Conformational Selection’ Folding Pathways. J. Phys. Chem. B 123, 2005–2015 (2019).
pubmed: 30739441
doi: 10.1021/acs.jpcb.8b11841
Scull, C. E., Dandpat, S. S., Romero, R. A. & Walter, N. G. Transcriptional Riboswitches Integrate Timescales for Bacterial Gene Expression Control. Front. Mol. Biosci. 7, 607158 (2020).
pubmed: 33521053
doi: 10.3389/fmolb.2020.607158
Wickiser, J. K., Winkler, W. C., Breaker, R. R. & Crothers, D. M. The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol. Cell 18, 49–60 (2005).
pubmed: 15808508
doi: 10.1016/j.molcel.2005.02.032
Suddala, K. C., Wang, J., Hou, Q. & Walter, N. G. Mg(2+) shifts ligand-mediated folding of a riboswitch from induced-fit to conformational selection. J. Am. Chem. Soc. 137, 14075–14083 (2015).
pubmed: 26471732
pmcid: 5098500
doi: 10.1021/jacs.5b09740
Suddala, K. C. et al. Hierarchical mechanism of amino acid sensing by the T-box riboswitch. Nat. Commun. 9, 1896 (2018).
pubmed: 29760498
pmcid: 5951919
doi: 10.1038/s41467-018-04305-6
Yadav, R., Widom, J. R., Chauvier, A. & Walter, N. G. An anionic ligand snap-locks a long-range interaction in a magnesium-folded riboswitch. Nat. Commun. 13, 207 (2022).
pubmed: 35017489
pmcid: 8752731
doi: 10.1038/s41467-021-27827-y
Widom, J. R. et al. Ligand Modulates Cross-Coupling between Riboswitch Folding and Transcriptional Pausing. Mol. Cell 72, 541–552.e6 (2018).
pubmed: 30388413
pmcid: 6565381
doi: 10.1016/j.molcel.2018.08.046
Chauvier, A. et al. Monitoring RNA dynamics in native transcriptional complexes. Proc. Natl Acad. Sci. USA 118, e2106564118 (2021).
pubmed: 34740970
pmcid: 8609307
doi: 10.1073/pnas.2106564118
Chauvier, A., Ajmera, P., Yadav, R. & Walter, N. G. Dynamic competition between a ligand and transcription factor NusA governs riboswitch-mediated transcription regulation. Proc. Natl Acad. Sci. USA 118, e2109026118 (2021).
pubmed: 34782462
pmcid: 8617461
doi: 10.1073/pnas.2109026118
Hua, B. et al. Real-time monitoring of single ZTP riboswitches reveals a complex and kinetically controlled decision landscape. Nat. Commun. 11, 4531 (2020).
pubmed: 32913225
pmcid: 7484762
doi: 10.1038/s41467-020-18283-1
Chauvier, A. et al. Structural basis for control of bacterial RNA polymerase pausing by a riboswitch and its ligand. Nat. Struct. Mol. Biol. 30, 902–913 (2023).
pubmed: 37264140
doi: 10.1038/s41594-023-01002-x
Al-Hashimi, H. M. & Walter, N. G. RNA dynamics: it is about time. Curr. Opin. Struct. Biol. 18, 321–329 (2008).
pubmed: 18547802
pmcid: 2580758
doi: 10.1016/j.sbi.2008.04.004
Landick, R. Transcriptional Pausing as a Mediator of Bacterial Gene Regulation. Annu. Rev. Microbiol 75, 291–314 (2021).
pubmed: 34348029
doi: 10.1146/annurev-micro-051721-043826
Chatterjee, S., Chauvier, A., Dandpat, S. S., Artsimovitch, I. & Walter, N. G. A translational riboswitch coordinates nascent transcription-translation coupling. Proc. Natl Acad. Sci. USA 118, e2023426118 (2021).
pubmed: 33850018
pmcid: 8072259
doi: 10.1073/pnas.2023426118
Perdrizet, G. A. et al. Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch. Proc. Natl Acad. Sci. USA 109, 3323–3328 (2012).
pubmed: 22331895
pmcid: 3295289
doi: 10.1073/pnas.1113086109
Wong, T. N., Sosnick, T. R. & Pan, T. Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures. Proc. Natl Acad. Sci. USA 104, 17995–18000 (2007).
pubmed: 17986617
pmcid: 2084285
doi: 10.1073/pnas.0705038104
Mandell, Z. F. et al. Comprehensive transcription terminator atlas for Bacillus subtilis. Nat. Microbiol 7, 1918–1931 (2022).
pubmed: 36192538
pmcid: 10024249
doi: 10.1038/s41564-022-01240-7
Yakhnin, A. V. & Babitzke, P. NusA-stimulated RNA polymerase pausing and termination participates in the Bacillus subtilis trp operon attenuation mechanism invitro. Proc. Natl Acad. Sci. USA 99, 11067–11072 (2002).
pubmed: 12161562
pmcid: 123211
doi: 10.1073/pnas.162373299
Yakhnin, A. V. & Babitzke, P. Mechanism of NusG-stimulated pausing, hairpin-dependent pause site selection and intrinsic termination at overlapping pause and termination sites in the Bacillus subtilis trp leader. Mol. Microbiol. 76, 690–705 (2010).
pubmed: 20384694
pmcid: 2919817
doi: 10.1111/j.1365-2958.2010.07126.x
Larson, M. H. et al. A pause sequence enriched at translation start sites drives transcription dynamics in vivo. Science 344, 1042–1047 (2014).
pubmed: 24789973
pmcid: 4108260
doi: 10.1126/science.1251871
Zhang, J. & Landick, R. A Two-Way Street: Regulatory Interplay between RNA Polymerase and Nascent RNA Structure. Trends Biochem. Sci. 41, 293–310 (2016).
pubmed: 26822487
pmcid: 4911296
doi: 10.1016/j.tibs.2015.12.009
Artsimovitch, I. & Landick, R. Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals. Proc. Natl Acad. Sci. USA 97, 7090–7095 (2000).
pubmed: 10860976
pmcid: 16504
doi: 10.1073/pnas.97.13.7090
Huang, Y.-H. et al. Structure-Based Mechanisms of a Molecular RNA Polymerase/Chaperone Machine Required for Ribosome Biosynthesis. Mol. Cell 79, 1024–1036.e5 (2020).
pubmed: 32871103
doi: 10.1016/j.molcel.2020.08.010
Vogel, U. & Jensen, K. F. NusA is required for ribosomal antitermination and for modulation of the transcription elongation rate of both antiterminated RNA and mRNA. J. Biol. Chem. 272, 12265–12271 (1997).
pubmed: 9139668
doi: 10.1074/jbc.272.19.12265
Said, N. et al. Structural basis for λN-dependent processive transcription antitermination. Nat. Microbiol. 2, 17062 (2017).
pubmed: 28452979
doi: 10.1038/nmicrobiol.2017.62
Krupp, F. et al. Structural Basis for the Action of an All-Purpose Transcription Anti-termination Factor. Mol. Cell 74, 143–157.e5 (2019).
pubmed: 30795892
doi: 10.1016/j.molcel.2019.01.016
Gusarov, I. & Nudler, E. Control of Intrinsic Transcription Termination by N and NusA: The Basic Mechanisms. Cell 107, 437–449 (2001).
pubmed: 11719185
doi: 10.1016/S0092-8674(01)00582-7
Mondal, S., Yakhnin, A. V., Sebastian, A., Albert, I. & Babitzke, P. NusA-dependent transcription termination prevents misregulation of global gene expression. Nat. Microbiol 1, 15007 (2016).
pubmed: 27571753
pmcid: 5358096
doi: 10.1038/nmicrobiol.2015.7
Zhou, J., Ha, K. S., La Porta, A., Landick, R. & Block, S. M. Applied force provides insight into transcriptional pausing and its modulation by transcription factor NusA. Mol. Cell 44, 635–646 (2011).
pubmed: 22099310
pmcid: 3227225
doi: 10.1016/j.molcel.2011.09.018
Guo, X. et al. Structural Basis for NusA Stabilized Transcriptional Pausing. Mol. Cell 69, 816–827.e4 (2018).
pubmed: 29499136
pmcid: 5842316
doi: 10.1016/j.molcel.2018.02.008
Ha, K. S., Toulokhonov, I., Vassylyev, D. G. & Landick, R. The NusA N-terminal domain is necessary and sufficient for enhancement of transcriptional pausing via interaction with the RNA exit channel of RNA polymerase. J. Mol. Biol. 401, 708–725 (2010).
pubmed: 20600118
pmcid: 3682478
doi: 10.1016/j.jmb.2010.06.036
Toulokhonov, I. & Landick, R. The flap domain is required for pause RNA hairpin inhibition of catalysis by RNA polymerase and can modulate intrinsic termination. Mol. Cell 12, 1125–1136 (2003).
pubmed: 14636572
doi: 10.1016/S1097-2765(03)00439-8
Pan, T., Artsimovitch, I., Fang, X. W., Landick, R. & Sosnick, T. R. Folding of a large ribozyme during transcription and the effect of the elongation factor NusA. Proc. Natl Acad. Sci. USA 96, 9545–9550 (1999).
pubmed: 10449729
pmcid: 22245
doi: 10.1073/pnas.96.17.9545
Prasch, S. et al. RNA-binding specificity of E. coli NusA. Nucleic Acids Res. 37, 4736–4742 (2009).
pubmed: 19515940
pmcid: 2724277
doi: 10.1093/nar/gkp452
Mah, T. F., Kuznedelov, K., Mushegian, A., Severinov, K. & Greenblatt, J. The alpha subunit of E. coli RNA polymerase activates RNA binding by NusA. Genes Dev. 14, 2664–2675 (2000).
pubmed: 11040219
pmcid: 316996
doi: 10.1101/gad.822900
Ma, C. et al. RNA polymerase-induced remodelling of NusA produces a pause enhancement complex. Nucleic Acids Res. 43, 2829–2840 (2015).
pubmed: 25690895
pmcid: 4357713
doi: 10.1093/nar/gkv108
Chauvier, A., Nadon, J.-F., Grondin, J. P., Lamontagne, A.-M. & Lafontaine, D. A. Role of a hairpin-stabilized pause in the Escherichia coli thiC riboswitch function. RNA Biol. 16, 1066–1073 (2019).
pubmed: 31081713
pmcid: 6602414
doi: 10.1080/15476286.2019.1616354
Lemay, J.-F. et al. Comparative study between transcriptionally- and translationally-acting adenine riboswitches reveals key differences in riboswitch regulatory mechanisms. PLoS Genet. 7, e1001278 (2011).
pubmed: 21283784
pmcid: 3024265
doi: 10.1371/journal.pgen.1001278
Rinaldi, A. J., Lund, P. E., Blanco, M. R. & Walter, N. G. The Shine-Dalgarno sequence of riboswitch-regulated single mRNAs shows ligand-dependent accessibility bursts. Nat. Commun. 7, 8976 (2016).
pubmed: 26781350
pmcid: 4735710
doi: 10.1038/ncomms9976
Chauvier, A., Cabello-Villegas, J. & Walter, N. G. Probing RNA structure and interaction dynamics at the single molecule level. Methods 162–163, 3–11 (2019).
pubmed: 30951833
pmcid: 7944401
doi: 10.1016/j.ymeth.2019.04.002
Xue, Y. et al. Observation of structural switch in nascent SAM-VI riboswitch during transcription at single-nucleotide and single-molecule resolution. Nat. Commun. 14, 2320 (2023).
pubmed: 37087479
pmcid: 10122661
doi: 10.1038/s41467-023-38042-2
Zhao, B., Guffy, S. L., Williams, B. & Zhang, Q. An excited state underlies gene regulation of a transcriptional riboswitch. Nat. Chem. Biol. 13, 968–974 (2017).
pubmed: 28719589
pmcid: 5562522
doi: 10.1038/nchembio.2427
Toulokhonov, I., Artsimovitch, I. & Landick, R. Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins. Science 292, 730–733 (2001).
pubmed: 11326100
doi: 10.1126/science.1057738
Jayasinghe, O. T., Mandell, Z. F., Yakhnin, A. V., Kashlev, M. & Babitzke, P. Transcriptome-Wide Effects of NusA on RNA Polymerase Pausing in Bacillus subtilis. J. Bacteriol. 204, e0053421 (2022).
pubmed: 35258320
doi: 10.1128/jb.00534-21
Rodgers, M. L. & Woodson, S. A. Transcription Increases the Cooperativity of Ribonucleoprotein Assembly. Cell 179, 1370–1381.e12 (2019).
pubmed: 31761536
pmcid: 6886681
doi: 10.1016/j.cell.2019.11.007
Schmidt, A. et al. The quantitative and condition-dependent Escherichia coli proteome. Nat. Biotechnol. 34, 104–110 (2016).
pubmed: 26641532
doi: 10.1038/nbt.3418
Mooney, R. A. et al. Regulator trafficking on bacterial transcription units in vivo. Mol. Cell 33, 97–108 (2009).
pubmed: 19150431
pmcid: 2747249
doi: 10.1016/j.molcel.2008.12.021
Helmling, C. et al. Life times of metastable states guide regulatory signaling in transcriptional riboswitches. Nat. Commun. 9, 944 (2018).
pubmed: 29507289
pmcid: 5838219
doi: 10.1038/s41467-018-03375-w
Zhu, C. et al. Transcription factors modulate RNA polymerase conformational equilibrium. Nat. Commun. 13, 1546 (2022).
pubmed: 35318334
pmcid: 8940904
doi: 10.1038/s41467-022-29148-0
Abdelkareem, M. et al. Structural Basis of Transcription: RNA Polymerase Backtracking and Its Reactivation. Mol. Cell 75, 298–309.e4 (2019).
pubmed: 31103420
pmcid: 7611809
doi: 10.1016/j.molcel.2019.04.029
Kang, J. Y. et al. Structural Basis for Transcript Elongation Control by NusG Family Universal Regulators. Cell 173, 1650–1662.e14 (2018).
pubmed: 29887376
pmcid: 6003885
doi: 10.1016/j.cell.2018.05.017
Kang, J. Y. et al. RNA Polymerase Accommodates a Pause RNA Hairpin by Global Conformational Rearrangements that Prolong Pausing. Mol. Cell 69, 802–815.e1 (2018).
pubmed: 29499135
pmcid: 5903582
doi: 10.1016/j.molcel.2018.01.018
Bushhouse, D. Z. & Lucks, J. B. Tuning strand displacement kinetics enables programmable ZTP riboswitch dynamic range in vivo. Nucleic Acids Res. 51, 2891–2903 (2023).
pubmed: 36864761
pmcid: 10085676
doi: 10.1093/nar/gkad110
Cheng, L. et al. Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch. Nucleic Acids Res. 50, 12001–12018 (2022).
pubmed: 35348734
pmcid: 9756952
doi: 10.1093/nar/gkac102
Strobel, E. J., Cheng, L., Berman, K. E., Carlson, P. D. & Lucks, J. B. A ligand-gated strand displacement mechanism for ZTP riboswitch transcription control. Nat. Chem. Biol. 15, 1067–1076 (2019).
pubmed: 31636437
pmcid: 6814202
doi: 10.1038/s41589-019-0382-7
Lai, D., Proctor, J. R. & Meyer, I. M. On the importance of cotranscriptional RNA structure formation. RNA 19, 1461–1473 (2013).
pubmed: 24131802
pmcid: 3851714
doi: 10.1261/rna.037390.112
Liu, S.-R., Hu, C.-G. & Zhang, J.-Z. Regulatory effects of cotranscriptional RNA structure formation and transitions. Wiley Interdiscip. Rev. RNA 7, 562–574 (2016).
pubmed: 27028291
doi: 10.1002/wrna.1350
Li, X. & Manley, J. L. Cotranscriptional processes and their influence on genome stability. Genes Dev. 20, 1838–1847 (2006).
pubmed: 16847344
doi: 10.1101/gad.1438306
Frieda, K. L. & Block, S. M. Direct observation of cotranscriptional folding in an adenine riboswitch. Science 338, 397–400 (2012).
pubmed: 23087247
pmcid: 3496414
doi: 10.1126/science.1225722
Helmling, C. et al. NMR Structural Profiling of Transcriptional Intermediates Reveals Riboswitch Regulation by Metastable RNA Conformations. J. Am. Chem. Soc. 139, 2647–2656 (2017).
pubmed: 28134517
doi: 10.1021/jacs.6b10429
Heppell, B. et al. Molecular insights into the ligand-controlled organization of the SAM-I riboswitch. Nat. Chem. Biol. 7, 384–392 (2011).
pubmed: 21532599
doi: 10.1038/nchembio.563
Ellinger, E. et al. Riboswitches as therapeutic targets: promise of a new era of antibiotics. Expert Opin. Ther. Targets 27, 433–445 (2023).
pubmed: 37364239
doi: 10.1080/14728222.2023.2230363
Landick, R., Wang, D. & Chan, C. L. Quantitative analysis of transcriptional pausing by Escherichia coli RNA polymerase: his leader pause site as paradigm. Meth. Enzymol. 274, 334–353 (1996).
doi: 10.1016/S0076-6879(96)74029-6
Suddala, K. C. & Walter, N. G. Riboswitch structure and dynamics by smFRET microscopy. Meth. Enzymol. 549, 343–373 (2014).
doi: 10.1016/B978-0-12-801122-5.00015-5
Blanco, M. & Walter, N. G. Analysis of complex single-molecule FRET time trajectories. Meth. Enzymol. 472, 153–178 (2010).
doi: 10.1016/S0076-6879(10)72011-5