Abstract
Methylated RNA nucleotides were recently discovered to be highly abundant in RNAs. The effects of these methylations were mainly attributed to altered mRNA stabilities, protein-binding affinities, or RNA structures. The direct impact of RNA modifications on the performance of the ribosome has not been investigated so far. In this chapter, we describe an approach that allows introducing RNA modifications site-specifically into coding sequences of mRNAs and determining their effect on the translation machinery in a well-defined bacterial in vitro system.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
El Yacoubi B, Bailly M, de Crecy-Lagard V (2012) Biosynthesis and function of posttranscriptional modifications of transfer RNAs. Annu Rev Genet 46:69–95
Nedialkova DD, Leidel SA (2015) Optimization of codon translation rates via tRNA modifications maintains proteome integrity. Cell 161(7):1606–1618
Wilson DN, Nierhaus KH (2007) The weird and wonderful world of bacterial ribosome regulation. Crit Rev Biochem Mol Biol 42(3):187–219
Pan T (2013) N6-methyl-adenosine modification in messenger and long non-coding RNA. Trends Biochem Sci 38(4):204–209
Edelheit S, Schwartz S, Mumbach MR, Wurtzel O, Sorek R (2013) Transcriptome-wide mapping of 5-methylcytidine RNA modifications in bacteria, archaea, and yeast reveals m5C within archaeal mRNAs. PLoS Genet 9(6):e1003602
Squires JE, Patel HR, Nousch M, Sibbritt T, Humphreys DT, Parker BJ, Suter CM, Preiss T (2012) Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. Nucleic Acids Res 40(11):5023–5033
Carlile TM, Rojas-Duran MF, Zinshteyn B, Shin H, Bartoli KM, Gilbert WV (2014) Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature 515:143–146
Lovejoy AF, Riordan DP, Brown PO (2014) Transcriptome-wide mapping of pseudouridines: pseudouridine synthases modify specific mRNAs in S. cerevisiae. PLoS One 9(10):e110799
Hoernes TP, Erlacher MD (2016) Translating the epitranscriptome. WIREs RNA 2016. doi:10.1002/wrna.1375
Li X, Xiong X, Wang K, Wang L, Shu X, Ma S, Yi C (2016) Transcriptome-wide mapping reveals reversible and dynamic N(1)-methyladenosine methylome. Nat Chem Biol 12(5):311–316
Dominissini D, Nachtergaele S, Moshitch-Moshkovitz S, Peer E, Kol N, Ben-Haim MS, Dai Q, Di Segni A, Salmon-Divon M, Clark WC et al (2016) The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA. Nature 530(7591):441–446
Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SR (2012) Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell 149(7):1635–1646
Fu Y, Dominissini D, Rechavi G, He C (2014) Gene expression regulation mediated through reversible m(6)A RNA methylation. Nat Rev Genet 15(5):293–306
Jia G, Fu Y, Zhao X, Dai Q, Zheng G, Yang Y, Yi C, Lindahl T, Pan T, Yang YG, He C (2011) N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat Chem Biol 7(12):885–887
Deng X, Chen K, Luo GZ, Weng X, Ji Q, Zhou T, He C (2015) Widespread occurrence of N6-methyladenosine in bacterial mRNA. Nucleic Acids Res 43:6557–6567
Vitali P, Basyuk E, Le Meur E, Bertrand E, Muscatelli F, Cavaille J, Huttenhofer A (2005) ADAR2-mediated editing of RNA substrates in the nucleolus is inhibited by C/D small nucleolar RNAs. J Cell Biol 169(5):745–753
Wang Y, Li Y, Toth JI, Petroski MD, Zhang Z, Zhao JC (2014) N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells. Nat Cell Biol 16(2):191–198
Wang X, Zhao BS, Roundtree IA, Lu Z, Han D, Ma H, Weng X, Chen K, Shi H, He C (2015) N(6)-methyladenosine modulates messenger RNA translation efficiency. Cell 161(6):1388–1399
Liu N, Dai Q, Zheng G, He C, Parisien M, Pan T (2015) N(6)-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions. Nature 518(7540):560–564
Kariko K, Muramatsu H, Keller JM, Weissman D (2012) Increased erythropoiesis in mice injected with submicrogram quantities of pseudouridine-containing mRNA encoding erythropoietin. Mol Ther 20(5):948–953
Kariko K, Muramatsu H, Ludwig J, Weissman D (2011) Generating the optimal mRNA for therapy: HPLC purification eliminates immune activation and improves translation of nucleoside-modified, protein-encoding mRNA. Nucleic Acids Res 39(21):e142
Kariko K, Muramatsu H, Welsh FA, Ludwig J, Kato H, Akira S, Weissman D (2008) Incorporation of pseudouridine into mRNA yields superior nonimmunogenic vector with increased translational capacity and biological stability. Mol Ther 16(11):1833–1840
Heilman KL, Leach RA, Tuck MT (1996) Internal 6-methyladenine residues increase the in vitro translation efficiency of dihydrofolate reductase messenger RNA. Int J Biochem Cell Biol 28(7):823–829
Simms CL, Hudson BH, Mosior JW, Rangwala AS, Zaher HS (2014) An active role for the ribosome in determining the fate of oxidized mRNA. Cell Rep 9(4):1256–1264
Hudson BH, Zaher HS (2015) O6-Methylguanosine leads to position-dependent effects on ribosome speed and fidelity. RNA 21(9):1648–1659
Hoernes TP, Clementi N, Faserl K, Glasner H, Breuker K, Lindner H, Hüttenhofer H, Erlacher MD (2016) Nucleotide modifications within bacterial messenger RNAs regulate their translation and are able to rewire the genetic code. Nucleic Acids Res 44(2):852–862
Schägger H (2006) Tricine-SDS-PAGE. Nat Protoc 1(1):16–22 doi:nprot.2006.4
Vazquez-Laslop N, Thum C, Mankin AS (2008) Molecular mechanism of drug-dependent ribosome stalling. Mol Cell 30(2):190–202
Lang K, Micura R (2008) The preparation of site-specifically modified riboswitch domains as an example for enzymatic ligation of chemically synthesized RNA fragments. Nat Protoc 3(9):1457–1466
Shimizu Y, Inoue A, Tomari Y, Suzuki T, Yokogawa T, Nishikawa K, Ueda T (2001) Cell-free translation reconstituted with purified components. Nat Biotechnol 19(8):751–755
Erlacher MD, Chirkova A, Voegele P, Polacek N (2011) Generation of chemically engineered ribosomes for atomic mutagenesis studies on protein biosynthesis. Nat Protoc 6(5):580–592
Schmid K, Thuring K, Keller P, Ochel A, Kellner S, Helm M (2015) Variable presence of 5-methylcytosine in commercial RNA and DNA. RNA Biol 12(10):1152–1158
Bommer U, Burkhardt N, Jünemann R, Spahn CM, Triana-Alonso FJ, Nierhaus KH (1997) Ribosomes and polysomes. Subcellular fractionation—a practical approach. IRL Press, Washington, DC, pp 271–301
Acknowledgment
This work was supported by the FWF (P 22658-B12 and P 28494-BBL to M.E.)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer Science+Business Media LLC
About this protocol
Cite this protocol
Hoernes, T.P., Erlacher, M.D. (2017). Methylated mRNA Nucleotides as Regulators for Ribosomal Translation. In: Lusser, A. (eds) RNA Methylation. Methods in Molecular Biology, vol 1562. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6807-7_19
Download citation
DOI: https://doi.org/10.1007/978-1-4939-6807-7_19
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-6805-3
Online ISBN: 978-1-4939-6807-7
eBook Packages: Springer Protocols