Effects of individual base-pairs on in vivo target search and destruction kinetics of bacterial small RNA.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
08 02 2021
08 02 2021
Historique:
received:
16
09
2020
accepted:
11
01
2021
entrez:
9
2
2021
pubmed:
10
2
2021
medline:
17
2
2021
Statut:
epublish
Résumé
Base-pairing interactions mediate many intermolecular target recognition events. Even a single base-pair mismatch can cause a substantial difference in activity but how such changes influence the target search kinetics in vivo is unknown. Here, we use high-throughput sequencing and quantitative super-resolution imaging to probe the mutants of bacterial small RNA, SgrS, and their regulation of ptsG mRNA target. Mutations that disrupt binding of a chaperone protein, Hfq, and are distal to the mRNA annealing region still decrease the rate of target association, k
Identifiants
pubmed: 33558533
doi: 10.1038/s41467-021-21144-0
pii: 10.1038/s41467-021-21144-0
pmc: PMC7870926
doi:
Substances chimiques
Nucleotides
0
RNA, Bacterial
0
RNA, Messenger
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
874Subventions
Organisme : NIGMS NIH HHS
ID : R35 GM139557
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM112659
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM092830
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM122569
Pays : United States
Organisme : Howard Hughes Medical Institute
Pays : United States
Organisme : NIH HHS
ID : S10 OD021567
Pays : United States
Références
Malkova, A. & Ira, G. Break-induced replication: functions and molecular mechanism. Curr. Opin. Genet. Dev. 23, 271–279 (2013).
Geisler, S. & Coller, J. RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts. Nat. Rev. Mol. Cell Biol. 14, 699–712 (2013).
Storz, G., Vogel, J. & Wassarman, K. M. Regulation by small RNAs in bacteria: expanding frontiers. Mol. Cell 43, 880–891 (2011).
pubmed: 21925377
pmcid: 3176440
doi: 10.1016/j.molcel.2011.08.022
Wiedenheft, B., Sternberg, S. H. & Doudna, J. A. RNA-guided genetic silencing systems in bacteria and archaea. Nature 482, 331–338 (2012).
Askari, F. K. & McDonnell, W. M. Antisense-oligonucleotide therapy. N. Engl. J. Med. 334, 316–318 (1996).
pubmed: 8532029
doi: 10.1056/NEJM199602013340508
Singh, D. et al. Real-time observation of DNA target interrogation and product release by the RNA-guided endonuclease CRISPR Cpf1 (Cas12a). Proc. Natl Acad. Sci. USA 115, 5444–5449 (2018).
pubmed: 29735714
doi: 10.1073/pnas.1718686115
pmcid: 6003496
Singh, D., Sternberg, S. H., Fei, J., Doudna, J. A. & Ha, T. Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9. Nat. Commun. 7, 1–8 (2016).
doi: 10.1038/ncomms12778
Globyte, V., Lee, S. H., Bae, T., Kim, J. & Joo, C. CRISPR /Cas9 searches for a protospacer adjacent motif by lateral diffusion. EMBO J. 38, e99466 (2019).
Globyte, V., Kim, S. H. & Joo, C. Single-Molecule View of Small RNA–Guided Target Search and Recognition. Annu. Rev. Biophys. 47, 569–593 (2018).
pubmed: 29595998
doi: 10.1146/annurev-biophys-070317-032923
Ragunathan, K., Liu, C. & Ha, T. RecA filament sliding on DNA facilitates homology search. Elife 2012, e00067 (2012).
Lee, J. Y. et al. Base triplet stepping by the Rad51/RecA family of recombinases. Science 349, 977–981 (2015).
pubmed: 26315438
pmcid: 4580133
doi: 10.1126/science.aab2666
Qi, Z. et al. DNA sequence alignment by microhomology sampling during homologous recombination. Cell 160, 856–869 (2015).
pubmed: 25684365
pmcid: 4344887
doi: 10.1016/j.cell.2015.01.029
Jones, D. L. et al. Kinetics of dCas9 target search in Escherichia coli. Science 357, 1420–1424 (2017).
pubmed: 28963258
pmcid: 6150439
doi: 10.1126/science.aah7084
Richards, G. R. & Vanderpool, C. K. Molecular call and response: the physiology of bacterial small RNAs. Biochim. Biophys. Acta 1809, 525–531 (2011).
pubmed: 21843668
pmcid: 3186873
doi: 10.1016/j.bbagrm.2011.07.013
Desnoyers, G., Bouchard, M. P. & Massé, E. New insights into small RNA-dependent translational regulation in prokaryotes. Trends Genet. 29, 92–98 (2013).
pubmed: 23141721
doi: 10.1016/j.tig.2012.10.004
Massé, E., Vanderpool, C. K. & Gottesman, S. Effect of RyhB small RNA on global iron use in Escherichia coli. J. Bacteriol. 187, 6962–6971 (2005).
pubmed: 16199566
pmcid: 1251601
doi: 10.1128/JB.187.20.6962-6971.2005
Lease, R. A., Smith, D., McDonough, K. & Belfort, M. The small noncoding DsrA RNA is an acid resistance regulator in Escherichia coli. J. Bacteriol. 186, 6179–6185 (2004).
pubmed: 15342588
pmcid: 515158
doi: 10.1128/JB.186.18.6179-6185.2004
Domenech, P., Honoré, N., Heym, B. & Cole, S. T. Role of OxyS of Mycobacterium tuberculosis in oxidative stress: Overexpression confers increased sensitivity to organic hydroperoxides. Microbes Infect. 3, 713–721 (2001).
pubmed: 11489419
doi: 10.1016/S1286-4579(01)01422-8
Zhang, A. et al. Global analysis of small RNA and mRNA targets of Hfq. Mol. Microbiol. 50, 1111–1124 (2003).
pubmed: 14622403
doi: 10.1046/j.1365-2958.2003.03734.x
Bobrovskyy, M. & Vanderpool, C. K. The small RNA SgrS: roles in metabolism and pathogenesis of enteric bacteria. Front. Cell. Infect. Microbiol. 4, 61 (2014).
Richards, G. R., Patel, M. V., Lloyd, C. R. & Vanderpool, C. K. Depletion of glycolytic intermediates plays a key role in glucose-phosphate stress in escherichia coli. J. Bacteriol. 195, 4816–4825 (2013).
pubmed: 23995640
pmcid: 3807488
doi: 10.1128/JB.00705-13
Bobrovskyy, M. et al. Determinants of target prioritization and regulatory hierarchy for the bacterial small RNA SgrS. Mol. Microbiol. 112, 1199–1218 (2019).
Rice, J. B. & Vanderpool, C. K. The small RNA SgrS controls sugar-phosphate accumulation by regulating multiple PTS genes. Nucleic Acids Res. 39, 3806–3819 (2011).
pubmed: 21245045
pmcid: 3089445
doi: 10.1093/nar/gkq1219
Kawamoto, H., Koide, Y., Morita, T. & Aiba, H. Base-pairing requirement for RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq. Mol. Microbiol. 61, 1013–1022 (2006).
pubmed: 16859494
doi: 10.1111/j.1365-2958.2006.05288.x
Panja, S. & Woodson, S. A. Hfq proximity and orientation controls RNA annealing. Nucleic Acids Res. 40, 8690–8697 (2012).
Zuzanna, W. & Mikolaj, O. Hfq assists small RNAs in binding to the coding sequence of ompD mRNA and in rearranging its structure. RNA 22, 979–994 (2016).
doi: 10.1261/rna.055251.115
Ishikawa, H., Otaka, H., Maki, K., Morita, T. & Aiba, H. The functional Hfq-binding module of bacterial sRNAs consists of a double or single hairpin preceded by a U-rich sequence and followed by a 3′ poly(U) tail. RNA 18, 1062–1074 (2012).
pubmed: 22454537
pmcid: 3334693
doi: 10.1261/rna.031575.111
Morita, T., Nishino, R. & Aiba, H. Role of the terminator hairpin in the biogenesis of functional Hfq-binding sRNAs. RNA 23, 1419–1431 (2017).
pubmed: 28606943
pmcid: 5558911
doi: 10.1261/rna.060756.117
Otaka, H., Ishikawa, H., Morita, T. & Aiba, H. PolyU tail of rho-independent terminator of bacterial small RNAs is essential for Hfq action. Proc. Natl Acad. Sci. USA 108, 13059–13064 (2011).
pubmed: 21788484
doi: 10.1073/pnas.1107050108
pmcid: 3156202
Horler, R. S. P. & Vanderpool, C. K. Homologs of the small RNA SGRS are broadly distributed in enteric bacteria but have diverged in size and sequence. Nucleic Acids Res. 37, 5465–5476 (2009).
pubmed: 19531735
pmcid: 2760817
doi: 10.1093/nar/gkp501
Maki, K., Uno, K., Morita, T. & Aiba, H. RNA, but not protein partners, is directly responsible for translational silencing by a bacterial Hfq-binding small RNA. Proc. Natl Acad. Sci. USA 105, 10332–10337 (2008).
pubmed: 18650387
doi: 10.1073/pnas.0803106105
pmcid: 2492515
Soper, T. J. & Woodson, S. A. The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA. RNA 14, 1907–1917 (2008).
Maki, K., Morita, T., Otaka, H. & Aiba, H. A minimal base-pairing region of a bacterial small RNA SgrS required for translational repression of ptsG mRNA. Mol. Microbiol. 76, 782–792 (2010).
pubmed: 20345651
doi: 10.1111/j.1365-2958.2010.07141.x
Fei, J. et al. Determination of in vivo target search kinetics of regulatory noncoding RNA. Science 347, 1371–1374 (2015).
pubmed: 25792329
pmcid: 4410144
doi: 10.1126/science.1258849
Arluison, V. et al. Spectroscopic observation of RNA chaperone activities of Hfq in post-transcriptional regulation by a small non-coding RNA. Nucleic Acids Res. 35, 999–1006 (2007).
Hwang, W., Arluison, V. & Hohng, S. Dynamic competition of DsrA and rpoS fragments for the proximal binding site of Hfq as a means for efficient annealing. Nucleic Acids Res. 39, 5131–5139 (2011).
Rutherford, S. T., Valastyan, J. S., Taillefumier, T., Wingreen, N. S. & Bassler, B. L. Comprehensive analysis reveals how single nucleotides contribute to noncoding RNA function in bacterial quorum sensing. Proc. Natl. Acad. Sci. USA 112, E6038–E6047 (2015).
Kinney, J. B., Murugan, A., Callan, C. G. & Cox, E. C. Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proc. Natl Acad. Sci. USA 107, 9158–9163 (2010).
pubmed: 20439748
doi: 10.1073/pnas.1004290107
pmcid: 2889059
Peterman, N., Lavi-Itzkovitz, A. & Levine, E. Large-scale mapping of sequence-function relations in small regulatory RNAs reveals plasticity and modularity. Nucleic Acids Res. 42, 12177–12188 (2014).
pubmed: 25262352
pmcid: 4231740
doi: 10.1093/nar/gku863
Bobrovskyy, M. & Vanderpool, C. K. Diverse mechanisms of post-transcriptional repression by the small RNA regulator of glucose-phosphate stress. Mol. Microbiol. 99, 254–273 (2016).
pubmed: 26411266
doi: 10.1111/mmi.13230
Wadler, C. S. & Vanderpool, C. K. A dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide. Proc. Natl Acad. Sci. USA 104, 20454–20459 (2007).
pubmed: 18042713
doi: 10.1073/pnas.0708102104
pmcid: 2154452
Balasubramanian, D. & Vanderpool, C. K. Deciphering the interplay between two independent functions of the small RNA regulator SgrS in Salmonella. J. Bacteriol. 195, 4620–4630 (2013).
Morita, T., Ueda, M., Kubo, K. & Aiba, H. Insights into transcription termination of Hfq-binding sRNAs of Escherichia coli and characterization of readthrough products. RNA 21, 1490–1501 (2015).
pubmed: 26106215
pmcid: 4509938
doi: 10.1261/rna.051870.115
De Lay, N., Schu, D. J. & Gottesman, S. Bacterial small RNA-based negative regulation: Hfq and its accomplices. J. Biol. Chem. 288, 7996–8003 (2013).
pubmed: 23362267
pmcid: 3605619
doi: 10.1074/jbc.R112.441386
Sun, Y. & Vanderpool, C. K. Physiological consequences of multiple-target regulation by the small RNA SgrS in escherichia coli. J. Bacteriol. 195, 4804–4815 (2013).
pubmed: 23873911
pmcid: 3807494
doi: 10.1128/JB.00722-13
Rice, J. B., Balasubramanian, D. & Vanderpool, C. K. Small RNA binding-site multiplicity involved in translational regulation of a polycistronic mRNA. Proc. Natl. Acad. Sci. USA 109, E2691–E2698 (2012).
Wadler, C. S. & Vanderpool, C. K. Characterization of homologs of the small rna sgrs reveals diversity in function. Nucleic Acids Res. 37, 5477–5485 (2009).
pubmed: 19620214
pmcid: 2760806
doi: 10.1093/nar/gkp591
Gottesman, S. & Storz, G. Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harb. Perspect. Biol. 3, a003798 (2011).
Aiba, H. Mechanism of RNA silencing by Hfq-binding small RNAs. Curr. Opin. Microbiol. 10, 134–139 (2007).
pubmed: 17383928
doi: 10.1016/j.mib.2007.03.010
Sauer, E. & Weichenrieder, O. Structural basis for RNA 3′-end recognition by Hfq. Proc. Natl Acad. Sci. USA 108, 13065–13070 (2011).
pubmed: 21737752
doi: 10.1073/pnas.1103420108
pmcid: 3156190
Panja, S., Schu, D. J. & Woodson, S. A. Conserved arginines on the rim of Hfq catalyze base pair formation and exchange. Nucleic Acids Res. 41, 7536–7546 (2013).
Panja, S., Paul, R., Greenberg, M. M. & Woodson, S. A. Light-triggered RNA annealing by an RNA chaperone. Angew. Chem. Int. Ed. 54, 7281–7284 (2015).
doi: 10.1002/anie.201501658
Mann, M., Wright, P. R. & Backofen, R. IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions. Nucleic Acids Res. 45, W435–W439 (2017).
pubmed: 28472523
pmcid: 5570192
doi: 10.1093/nar/gkx279
Wright, P. R. et al. CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains. Nucleic Acids Res. 42, W119–W123 (2014).
Busch, A., Richter, A. S. & Backofen, R. IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics 24, 2849–2856 (2008).
pubmed: 18940824
pmcid: 2639303
doi: 10.1093/bioinformatics/btn544
Raden, M. et al. Freiburg RNA tools: a central online resource for RNA-focused research and teaching. Nucleic Acids Res. 46, W25–W29 (2018).
pubmed: 29788132
pmcid: 6030932
doi: 10.1093/nar/gky329
Morita, T., Maki, K. & Aiba, H. RNase E-based ribonucleoprotein complexes: mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs. Genes Dev. 19, 2176–2186 (2005).
pubmed: 16166379
pmcid: 1221888
doi: 10.1101/gad.1330405
Bruce, H. A. et al. Analysis of the natively unstructured RNA/protein-recognition core in the Escherichia coli RNA degradosome and its interactions with regulatory RNA/Hfq complexes. Nucleic Acids Res. 46, 387–402 (2018).
pubmed: 29136196
doi: 10.1093/nar/gkx1083
Caillet, J., Baron, B., Boni, I. V., Caillet-Saguy, C. & Hajnsdorf, E. Identification of protein-protein and ribonucleoprotein complexes containing Hfq. Sci. Rep. 9, 1–12 (2019).
doi: 10.1038/s41598-019-50562-w
Updegrove, T. B., Zhang, A. & Storz, G. Hfq: the flexible RNA matchmaker. Curr. Opin. Microbiol. 30, 133–138 (2016).
pubmed: 26907610
pmcid: 4821791
doi: 10.1016/j.mib.2016.02.003
Schu, D. J., Zhang, A., Gottesman, S. & Storz, G. Alternative Hfq‐ sRNA interaction modes dictate alternative mRNA recognition. EMBO J. 34, 2557–2573 (2015).
Dimastrogiovanni, D. et al. Recognition of the small regulatory RNA RydC by the bacterial Hfq protein. Elife 3, e05375 (2014).
Geissmann, T. A. & Touati, D. Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulator. EMBO J. 23, 396–405 (2004).
pubmed: 14739933
pmcid: 1271764
doi: 10.1038/sj.emboj.7600058
Peng, Y., Curtis, J. E., Fang, X. & Woodson, S. A. Structural model of an mRNA in complex with the bacterial chaperone Hfq. Proc. Natl Acad. Sci. USA 111, 17134–17139 (2014).
pubmed: 25404287
doi: 10.1073/pnas.1410114111
pmcid: 4260595
Storz, G., Opdyke, J. A. & Zhang, A. Controlling mRNA stability and translation with small, noncoding RNAs. Curr. Opin. Microbiol. 7, 140–144 (2004).
pubmed: 15063850
doi: 10.1016/j.mib.2004.02.015
Valentin-Hansen, P., Eriksen, M. & Udesen, C. The bacterial Sm-like protein Hfq: A key player in RNA transactions. Mol. Microbiol. 51, 1525–1533 (2004).
pubmed: 15009882
doi: 10.1111/j.1365-2958.2003.03935.x
Miller, J. H. Experiments in Molecular Genetics (Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 1972).
Yu, D. et al. An efficient recombination system for chromosome engineering in Escherichia coli. Proc. Natl Acad. Sci. USA 97, 5978–5983 (2000).
pubmed: 10811905
doi: 10.1073/pnas.100127597
pmcid: 18544
Mandin, P. & Gottesman, S. A genetic approach for finding small RNAs regulators of genes of interest identifies RybC as regulating the DpiA/DpiB two-component system. Mol. Microbiol. 72, 551–565 (2009).
pubmed: 19426207
pmcid: 2714224
doi: 10.1111/j.1365-2958.2009.06665.x
Levine, E., Zhang, Z., Kuhlman, T. & Hwa, T. Quantitative characteristics of gene regulation by small RNA. PLoS Biol. 5, e229 (2007).
Aiba, H., Adhya, S. & de Crombrugghe, B. Evidence for two functional gal promoters in intact Escherichia coli cells. J. Biol. Chem. 256, 11905–11910 (1981).
pubmed: 6271763
doi: 10.1016/S0021-9258(19)68491-7
Majdalani, N., Chen, S., Murrow, J., St. John, K. & Gottesman, S. Regulation of RpoS by a novel small RNA: the characterization of RprA. Mol. Microbiol. 39,1382–1394 (2001).
Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nature Methods 9, 671–675 (2012).
Rust, M. J., Bates, M. & Zhuang, X. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat. Methods 3, 793–795 (2006).
pubmed: 16896339
pmcid: 2700296
doi: 10.1038/nmeth929
Huang, B., Wang, W., Bates, M. & Zhuang, X. Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 319, 810–813 (2008).
pubmed: 18174397
pmcid: 2633023
doi: 10.1126/science.1153529