mRNA-Mediated Duplexes Play Dual Roles in the Regulation of Bidirectional Ribosomal Frameshifting
Abstract
:1. Introduction
2. Results
2.1. Distinct Upstream Duplexes Stimulate +1 Frameshifting and Attenuate −1 Frameshifting in an In Vitro 70S Translation System
2.2. A Downstream mPK Plays Opposite Roles in +1 and −1 Frameshifting Regulation
2.3. An Unusual −1 Frameshifting Event is Triggered in a +1 Frameshift-Prone Sequence by Downstream Structures in the Absence of RF2
2.4. Efficient Non-Canonical −1 Frameshifting Requires an Identical Nucleotide Bridging E- and P-Sites in Addition to a Downstream Structure
2.5. Stable mRNA Structures Flanking the mRNA-Binding Channel of an Elongation Ribosome Counteract Each Other’s Frameshifting Activity
2.6. Co-Existence of +1 and −1 Frameshifting by Modulating the Stabilities of Structures Flanking the mRNA-Binding Channel of an Elongation Ribosome
2.7. Ribosomal Flanking mRNA Structures also Modulate Bidirectional Frameshifting When an A-site Occupying Codon Becomes a Hungry Codon
3. Discussion
3.1. Upstream Hairpin Juxtaposing E-Site as the Functional Mimicry of Internal SD Mediated Duplex
3.2. Mechanisms of the Non-Canonical −1 Frameshifting in +1 Frameshift-Prone CUUUGA Site
3.3. Stable mRNA Structure Unwinding and Refolding in CAG Trinucleotide Repeat Expansion
4. Materials and Methods
4.1. Plasmids, Reporter Design and Construction
4.2. Recombinant DNAs and Mutagenesis
4.3. In Vitro Radioactivity-Based Frameshifting Assay
4.4. Immunoprecipitation
4.5. In-Gel Digestion and Mass Spectrometry
Supplementary Materials
Author Contributions
Funding
Acknowledgement
Conflicts of Interest
References
- Takyar, S.; Hickerson, R.P.; Noller, H.F. mRNA helicase activity of the ribosome. Cell 2005, 120, 49–58. [Google Scholar] [CrossRef] [PubMed]
- Qu, X.; Wen, J.D.; Lancaster, L.; Noller, H.F.; Bustamante, C.; Tinoco, I., Jr. The ribosome uses two active mechanisms to unwind messenger RNA during translation. Nature 2011, 475, 118–121. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Chamorro, M.; Parkin, N.; Varmus, H.E. An RNA pseudoknot and an optimal heptameric shift site are required for highly efficient ribosomal frameshifting on a retroviral messenger RNA. Proc. Natl. Acad. Sci. USA 1992, 89, 713–717. [Google Scholar] [CrossRef] [PubMed]
- Yu, C.H.; Noteborn, M.H.; Pleij, C.W.; Olsthoorn, R.C. Stem-loop structures can effectively substitute for an RNA pseudoknot in -1 ribosomal frameshifting. Nucleic Acids Res. 2011, 39, 8952–8959. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Harger, J.W.; Meskauskas, A.; Dinman, J.D. An ‘integrated model’ of programmed ribosomal frameshifting. Trends Biochem. Sci. 2002, 27, 448–454. [Google Scholar] [CrossRef]
- Plant, E.P.; Jacobs, K.L.M.; Harger, J.W.; Meskauskas, A.; Jacobs, J.L.; Baxter, J.L.; Petrov, A.N.; Dinman, J.D. The 9-A solution: How mRNA pseudoknots promote efficient programmed −1 ribosomal frameshifting. RNA 2003, 9, 168–174. [Google Scholar] [CrossRef]
- Farabaugh, P.J. Programmed translational frameshifting. Microbiol. Rev. 1996, 60, 103–134. [Google Scholar] [CrossRef] [PubMed]
- Namy, O.; Rousset, J.-P.; Napthine, S.; Brierley, I. Reprogrammed Genetic Decoding in Cellular Gene Expression. Mol. Cell 2004, 13, 157–168. [Google Scholar] [CrossRef]
- Atkins, J.F.; Loughran, G.; Bhatt, P.R.; Firth, A.E.; Baranov, P.V. Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use. Nucleic Acids Res. 2016, 44, 7007–7078. [Google Scholar] [CrossRef]
- Belcourt, M.F.; Farabaugh, P.J. Ribosomal frameshifting in the yeast retrotransposon Ty: TRNAs induce slippage on a 7 nucleotide minimal site. Cell 1990, 62, 339–352. [Google Scholar] [CrossRef]
- Baranov, P.V. P-site tRNA is a crucial initiator of ribosomal frameshifting. RNA 2004, 10, 221–230. [Google Scholar] [CrossRef] [Green Version]
- Larsen, B.; Wills, N.M.; Gesteland, R.F.; Atkins, J.F. rRNA-mRNA base pairing stimulates a programmed −1 ribosomal frameshift. J. Bacteriol. 1994, 176, 6842–6851. [Google Scholar] [CrossRef]
- Chen, J.; Petrov, A.; Johansson, M.; Tsai, A.; O’Leary, S.E.; Puglisi, J.D. Dynamic pathways of −1 translational frameshifting. Nature 2014, 512, 328–332. [Google Scholar] [CrossRef] [Green Version]
- Caliskan, N.; Katunin, V.I.; Belardinelli, R.; Peske, F.; Rodnina, M.V. Programmed −1 frameshifting by kinetic partitioning during impeded translocation. Cell 2014, 157, 1619–1631. [Google Scholar] [CrossRef]
- Weiss, R.B.; Dunn, D.M.; Dahlberg, A.E.; Atkins, J.F.; Gesteland, R.F. Reading frame switch caused by base-pair formation between the 3’ end of 16S rRNA and the mRNA during elongation of protein synthesis in Escherichia coli. EMBO J. 1988, 7, 1503–1507. [Google Scholar] [CrossRef]
- Li, G.W.; Oh, E.; Weissman, J.S. The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature 2012, 484, 538–541. [Google Scholar] [CrossRef]
- Su, M.C.; Chang, C.T.; Chu, C.H.; Tsai, C.H.; Chang, K.Y. An atypical RNA pseudoknot stimulator and an upstream attenuation signal for −1 ribosomal frameshifting of SARS coronavirus. Nucleic Acids Res. 2005, 33, 4265–4275. [Google Scholar] [CrossRef] [PubMed]
- Cho, C.P.; Lin, S.C.; Chou, M.Y.; Hsu, H.T.; Chang, K.Y. Regulation of programmed ribosomal frameshifting by co-translational refolding RNA hairpins. PLoS ONE 2013, 8, e62283. [Google Scholar] [CrossRef]
- Hu, H.T.; Cho, C.P.; Lin, Y.H.; Chang, K.Y. A general strategy to inhibiting viral −1 frameshifting based on upstream attenuation duplex formation. Nucleic Acids Res. 2016, 44, 256–266. [Google Scholar] [CrossRef]
- Ude, S.; Lassak, J.; Starosta, A.L.; Kraxenberger, T.; Wilson, D.N.; Jung, K. Translation Elongation Factor EF-P Alleviates Ribosome Stalling at Polyproline Stretches. Science 2013, 339, 82–85. [Google Scholar] [CrossRef]
- Meydan, S.; Klepacki, D.; Karthikeyan, S.; Margus, T.; Thomas, P.; Jones, J.E.; Khan, Y.; Briggs, J.; Dinman, J.D.; Vazquez-Laslop, N.; Mankin, A.S. Programmed Ribosomal Frameshifting Generates a Copper Transporter and a Copper Chaperone from the Same Gene. Mol. Cell 2017, 65, 207–219. [Google Scholar] [CrossRef] [Green Version]
- Grentzmann, G.; Ingram, J.A.; Kelly, P.J.; Gesteland, R.F.; Atkins, J.F. A dual-luciferase reporter system for studying recoding signals. RNA 1998, 4, 479–486. [Google Scholar]
- Brierley, I.; Digard, P.; Inglis, S.C. Characterization of an efficient coronavirus ribosomal frameshifting signal: Requirement for an RNA pseudoknot. Cell 1989, 57, 537–547. [Google Scholar] [CrossRef]
- Marquez, V.; Wilson, D.N.; Tate, W.P.; Triana-Alonso, F.; Nierhaus, K.H. Maintaining the ribosomal reading frame: The influence of the E site during translational regulation of release factor 2. Cell 2004, 118, 45–55. [Google Scholar] [CrossRef]
- Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31, 3406–3415. [Google Scholar] [CrossRef] [Green Version]
- Kim, Y.-G.; Maas, S.; Rich, A. Comparative mutational analysis of cis-acting RNA signals for translational frameshifting in HIV-1 and HTLV-2. Nucleic Acids Res. 2001, 29, 1125–1131. [Google Scholar] [CrossRef] [Green Version]
- Léger, M.; Dulude, D.; Steinberg, S.V.; Brakier-Gingras, L. The three transfer RNAs occupying the A, P and E sites on the ribosome are involved in viral programmed −1 ribosomal frameshift. Nucleic Acids Res. 2007, 35, 5581–5592. [Google Scholar] [CrossRef]
- Lainé, S.; Thouard, A.; Komar, A.A.; Rossignol, J.M. Ribosome can resume the translation in both +1 or −1 frames after encountering an AGA cluster in Escherichia coli. Gene 2008, 412, 95–101. [Google Scholar] [CrossRef]
- Girstmair, H.; Saffert, P.; Rode, S.; Czech, A.; Holland, G.; Bannert, N.; Ignatova, Z. Depletion of cognate charged transfer RNA causes translational frameshifting within the expanded CAG stretch in huntingtin. Cell Rep. 2013, 3, 148–159. [Google Scholar] [CrossRef]
- Curran, J.F. Analysis of effects of tRNA:message stability on frameshift frequency at the Escherichia coli RF2 programmed frameshift site. Nucleic Acids Res. 1993, 21, 1837–1843. [Google Scholar] [CrossRef] [Green Version]
- Sanders, C.L.; Curran, J.F. Genetic analysis of the E site during RF2 programmed frameshifting. RNA 2007, 13, 1483–1491. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Devaraj, A.; Fredrick, K. Short spacing between the Shine-Dalgarno sequence and P codon destabilizes codon-anticodon pairing in the P site to promote +1 programmed frameshifting. Mol. Microbiol. 2010, 78, 1500–1509. [Google Scholar] [CrossRef] [PubMed]
- Chen, C.; Zhang, H.; Broitman, S.L.; Reiche, M.; Farrell, I.; Cooperman, B.S.; Goldman, Y.E. Dynamics of translation by single ribosomes through mRNA secondary structures. Nat. Struct. Mol. Biol. 2013, 20, 582–588. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Liao, P.Y.; Choi, Y.S.; Dinman, J.D.; Lee, K.H. The many paths to frameshifting: Kinetic modelling and analysis of the effects of different elongation steps on programmed −1 ribosomal frameshifting. Nucleic Acids Res. 2011, 39, 300–312. [Google Scholar] [CrossRef]
- Frank, J.; Gao, H.; Sengupta, J.; Gao, N.; Taylor, D.J. The process of mRNA–tRNA translocation. Proc. Natl. Acad. Sci. USA 2007, 104, 19671–19678. [Google Scholar] [CrossRef] [PubMed]
- Ratje, A.H.; Loerke, J.; Mikolajka, A.; Brünner, M.; Hildebrand, P.W.; Starosta, A.L.; Dönhöfer, A.; Connell, S.R.; Fucini, P.; Mielke, T.; et al. Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites. Nature 2010, 468, 713–716. [Google Scholar] [CrossRef]
- Zhou, J.; Lancaster, L.; Donohue, J.P.; Noller, H.F. Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation. Science 2013, 340, 1236086. [Google Scholar] [CrossRef] [PubMed]
- Noller, H.F.; Lancaster, L.; Zhou, J.; Mohan, S. The ribosome moves: RNA mechanics and translocation. Nat. Struct. Mol. Biol. 2017, 24, 1021–1027. [Google Scholar] [CrossRef]
- Kim, H.-K.; Liu, F.; Fei, J.; Bustamante, C.; Gonzalez, R.L.; Tinoco, I. A frameshifting stimulatory stem loop destabilizes the hybrid state and impedes ribosomal translocation. Proc. Natl. Acad. Sci. USA 2014, 111, 5538–5543. [Google Scholar] [CrossRef] [Green Version]
- Toulouse, A.; Au-Yeung, F.; Gaspar, C.; Roussel, J.; Dion, P.; Rouleau, G.A. Ribosomal frameshifting on MJD-1 transcripts with long CAG tracts. Hum. Mol. Genet. 2005, 14, 2649–2660. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- De Mezer, M.; Wojciechowska, M.; Napierala, M.; Sobczak, K.; Krzyzosiak, W.J. Mutant CAG repeats of Huntingtin transcript fold into hairpins, form nuclear foci and are targets for RNA interference. Nucleic Acids Res. 2011, 39, 3852–3863. [Google Scholar] [CrossRef] [Green Version]
- Saffert, P.; Adamla, F.; Schieweck, R.; Atkins, J.F.; Ignatova, Z. An Expanded CAG Repeat in Huntingtin Causes +1 Frameshifting. J. Biol. Chem. 2016, 291, 18505–18513. [Google Scholar] [CrossRef]
- Casimiro, D.R.; Toy-Palmer, A.; Blake, R.C., II; Dyson, H.J. Gene Synthesis, high-Level expression, and mutagenesis of Thiobacillus ferrooxidans Rusticyanin: His 85 Is a Ligand to the Blue Copper Center. Biochemistry 1995, 34, 6640–6648. [Google Scholar] [CrossRef]
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Huang, W.-P.; Cho, C.-P.; Chang, K.-Y. mRNA-Mediated Duplexes Play Dual Roles in the Regulation of Bidirectional Ribosomal Frameshifting. Int. J. Mol. Sci. 2018, 19, 3867. https://doi.org/10.3390/ijms19123867
Huang W-P, Cho C-P, Chang K-Y. mRNA-Mediated Duplexes Play Dual Roles in the Regulation of Bidirectional Ribosomal Frameshifting. International Journal of Molecular Sciences. 2018; 19(12):3867. https://doi.org/10.3390/ijms19123867
Chicago/Turabian StyleHuang, Wan-Ping, Che-Pei Cho, and Kung-Yao Chang. 2018. "mRNA-Mediated Duplexes Play Dual Roles in the Regulation of Bidirectional Ribosomal Frameshifting" International Journal of Molecular Sciences 19, no. 12: 3867. https://doi.org/10.3390/ijms19123867