Caps on Eukaryotic mRNAs

Yasuhiro Furuichi, GeneCare Research Institute Co. Ltd., Kamakura, Japan

Published online: July 2014

DOI: 10.1002/9780470015902.a0000891.pub3

Abstract

A 5′‐terminal cap is added to most eukaryotic cellular and viral messenger ribonucleic acids (mRNAs) at an early stage of transcription. Capping is essential and modulates several subsequent events in gene expression including pre‐mRNA splicing, 3′‐poly(A) addition, overall stability, nuclear exit to cytoplasm, protein synthesis, and mRNA turnover initiated by decapping. These and other effects involve cap‐binding proteins that recognise the m7GpppN cap structure. Capping proceeds by a similar series of enzymatic steps in a wide range of systems, but differences exist between metazoans and unicellular eukaryotes and viruses, pointing to capping enzymes as potential targets for the development of selective drugs against some fungal, viral and parasitic infections. Moreover, the unique structural features of caps enable us to define the initiation sites and promoter regions of gene transcription, and provide a basis for advanced sequencer‐mediated high‐throughput genome‐wide profiling of gene expression in a wide range of cell types.

Key Concepts:

  • mRNA caps are now known to be essential components of gene expression in eukaryotic organisms.

  • The history of the discovery of the presence of 5′ caps on messenger RNA and its subsequent scientific flowering is a good example of how a seemingly small biochemical observation can lead to the deeper understanding of a wide range of fundamental molecular biological phenomena.

  • Evolution has resulted in wide variations in capping structure and function among organisms ranging from viruses to humans; the selective forces underlying such variation requires more research.

  • Research that has documented viral‐specific capping reactions in viruses should prove to be a fertile source of research leading to new and novel anti‐viral agents.

  • The ‘cap‐snatching’ strategies of influenza viruses is a remarkable example of an apparent adaptation to enhance infectivity and is a particularly compelling target for therapeutic intervention.

  • The NMD mRNA surveillance pathway, which includes a pioneer round of translation with cap‐binding proteins, results in a striking decrease of defective mRNA in cells of patients with genetic diseases containing premature termination codons.

  • Methylation of genomic DNA and mRNA is now widely accepted as a major pathway of the regulation of both transcription and translation in eukaryotes.

  • Protein synthesis is a major field of gene expression where many players work for mRNA capping, decapping, decoding, quality control of gene transcripts and peptide elongation.

  • Micro RNAs are now widely accepted as major players in the translational control of protein synthesis.

  • The analysis of cap‐trapped sequences by high‐throughput sequencers enables one to carry out a genome‐wide identification of promoters together with quantification of their expression, thus elucidating a promoter‐based network of transcriptional regulation.

Keywords: RNA capping and decapping; RNA methylation; cap‐binding proteins; translation; mRNA stability; CAGE (cap analysis of gene expression); next‐generation sequencer

Figure 1.

Cap structure. Cap 2 m7GpppNmpNmp – showing the m7guanosine linked to the 5′‐end of the primary transcript via a 5′–5′ triphosphate linkage.

Figure 2.

Mechanism of cap formation.
Figure 3.

Viral variations: Vesicular stomatitis virus (VSV) mRNA capping by RNA–GDP polyribonucleotidyl transfer and utilisation of m7GTP in Semliki Forest virus (SFV) mRNA capping.

Figure 4.

Initiation of influenza virus mRNA synthesis by cap‐snatching. Courtesy R. Krug.

Figure 5.

Models of (a) cap recognition and mRNA attachment to ribosomes and (b) of ribosome recycling facilitated by the interaction of polyA‐ and cap‐binding proteins. Panel (b) courtesy of N. Sonenberg.

Figure 6.

Schematic representation of cap‐related procedures for full‐size cDNA cloning using the 5′‐5′ linkage in cap structure (a) and a high‐throughput profiling of cap‐trapped transcripts using the free 2′‐ and 3′‐OH groups in the cap m7G ribose (b).

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References

Adams JM and Cory S (1975) Modified nucleosides and bizarre 5′‐termini in mouse myeloma mRNA. Nature 255: 28–33.

Braun JE, Truffault V, Boland A et al. (2012) A direct interaction between DCP1 and XRN1 couples mRNA decapping to 5′ exonucleolytic degradation. Nature Structural & Molecular Biology 12: 1324–1331.

Cheng H, Dufu K, Lee C‐S et al. (2006) Human mRNA export machinery recruited to the 5′ end of mRNA. Cell 127: 1389–1400.

Chu C and Shatkin AJ (2008) Apoptosis and autophagy induction in mammalian cells by small interfering RNA knockdown of mRNA capping enzymes. Molecular Cell Biology 19: 5829–5836.

Coller J and Parker R (2004) Eukaryotic mRNA decapping. Annual Review of Biochemistry 73: 861–890.

Fabian MR and Sonenberg N (2012) The mechanics of miRNA‐mediated gene silencing: a look under the hood of miRISC. Nature Structural & Molecular Biology 19: 586–593.

Fabian MR, Sonenberg N and Filipowicz W (2010) Regulation of mRNA translation and stability by microRNAs. Annual Review of Biochemistry 79: 351–379.

Feoktistova K, Tuvshintogs E, Do A and Fraser CS (2013) Human eIF4E promotes mRNA restructuring by stimulating eIF4A helicase activity. Proceedings of the National Academy of Sciences of the USA 110: 13339–13344.

Filipowicz W, Furuichi Y, Sierra JM et al. (1976) A protein binding the methylated 5′‐terminal sequence, m7GpppN, of eukaryotic messenger RNA. Proceedings of the National Academy of Sciences of the USA 73: 1559–1563.

Forrest AR, Kawaji H, Rehli M et al. (2014) A promotor level mammalian expression atlas. Nature 507: 462–470.

Furuichi Y (1974) “Methylation‐coupled” transcription by virus‐associated transcriptase of cytoplasmic polyhedrosis virus containing double‐stranded RNA. Nucleic Acids Research 1: 809.

Furuichi Y, LaFiandra A and Shatkin AJ (1977) 5′‐Terminal structure and mRNA stability. Nature 266: 235–239.

Furuichi Y and Miura K (1975) A blocked structure at the 5′ terminus of mRNA from cytoplasmic polyhedrosis virus. Nature 253: 374–375.

Furuichi Y, Morgan M, Muthukrishnan S and Shatkin AJ (1975a) Reovirus messenger RNA contains a methylated, blocked 5′‐terminal structure: m‐7G(5′)ppp(5′)G‐MpCp‐. Proceedings of the National Academy of Sciences of the USA 72: 362–366.

Furuichi Y, Morgan M, Shatkin AJ et al. (1975b) Methylated, blocked 5 termini in HeLa cell mRNA. Proceedings of the National Academy of Sciences of the USA 72: 1904–1908.

Furuichi Y, Muthukrishnan S, Tomasz J and Shatkin AJ (1976) Mechanism of formation of reovirus mRNA 5′‐terminal blocked and methylated sequence, m7GpppGmpC. Journal of Biological Chemistry 251: 5043–5053.

Furuichi Y and Shatkin AJ (2000) Viral and cellular mRNA capping: past and prospects. Advances in Virus Research 55: 135–184.

Furuichi Y, Shatkin AJ, Stavnezer E and Bishop JM (1975c) Blocked, methylated 5′‐terminal sequence in avian sarcoma virus RNA. Nature 257: 618–620.

Gingras A‐C, Raught B and Sonenberg N (1999) elF4 Initiation factors: effectors of mRNA recruitment to ribosomes and regulators of translation. Annual Review of Biochemistry 68: 913–963.

Gonatopoulos‐Pournatzis T and Cowling VH (2014) Cap‐ binding complex (CBC). Biochemical Journal 457: 231–242.

Gupta KC and Roy P (1981) Stimulation of transcription by S‐adenosyl‐L‐homocysteine and virion‐encapsidated methyl donor in spring viraemia of carp virus. Journal of General Virology 53: 183–187.

Humphreys DT, Westman BJ, Martin DI and Preiss T (2005) MicroRNAs control translation initiation by inhibiting eukaryotic initiation factor 4E/cap and poly(A) tail function. Proceedings of the National Academy of Sciences of the USA 102: 16961–16966.

Kanamori‐Katayama M, Itoh M, Kawaji H et al. (2011) Unamplified cap analysis of gene expression on a single‐molecule sequencer. Genome Research 21: 1150–1159.

Kozak M (1978) How do eukaryotic ribosomes select initiation regions in messenger RNA? Cell 15: 1109–1123.

Kozak M (1989) The scanning model for translation: an update. Cell Biology 108: 229–241.

Krug RM (1989) The Influenza Viruses. NewYork, NY: Plenum Press.

Lee AS, Burdeinick‐Kerr R and Whelan SP (2013) A ribosome‐specialized translation initiation pathway is required for cap‐dependent translation of vesicular stomatitis virus mRNAs. Proceedings of the National Academy of Sciences of the USA 110: 324–329.

Lewis JD and Izaurralde E (1997) The role of the cap structure in RNA processing and nuclear export. European Journal of Biochemistry 247: 461–469.

Maquat LE, Hwang J, Sato H and Tang Y (2010) CBP80‐promoted mRNP rearrangements during the pioneer round of translation, nonsense‐mediated mRNA decay, and thereafter. Cold Spring Harbor Symposia on Quantitative Biology 75: 127–134.

Martineau Y, Azar R, Bousquet C and Pyronnet S (2013) Anti‐oncogenic potential of the eIF4E‐binding proteins. Oncogene 32: 671–677.

Maruyama K and Sugano S (1994) Oligo‐capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene 138: 171–174.

Mathonnet G, Fabian MR, Svitkin YV et al. (2007) MicroRNA inhibition of translation initiation in vitro by targeting the cap‐binding complex eIF4F. Science 317: 1764–1767.

Miura K, Watanabe K and Sugiura M (1974) 5′‐Terminal nucleotide sequences of the double‐stranded RNA of silkworm cytoplasmic polyhedrosis virus. Journal of Molecular Biology 86: 31–48.

Nagarajan VK, Jones CI, Newbury SF and Green PJ (2013) XRN 5′→3′ exoribonucleases: structure, mechanisms and functions. Biochimica et Biophysica Acta 1829: 590–603.

Nuss DL, Furuichi Y, Koch G and Shatkin AJ (1975) Detection in HeLa cell extracts of a 7‐methyl guanosine specific enzyme activity that cleaves m7GpppNm. Cell 6: 21–27.

Ogino T, Yadav SP and Banerjee AK (2010) Histidine‐mediated RNA transfer to GDP for unique mRNA capping by vesicular stomatitis virus RNA polymerase. Proceedings of the National Academy of Sciences of the USA 107: 3463–3468.

Otsuka Y, Kedersha NL and Schoenberg DR (2009) Identification of a cytoplasmic complex that adds a cap onto 5′‐monophosphate RNA. Molecular Cell Biology 29: 2155–2167.

Parrish S, Resch W and Moss B (2007) Vaccinia virus D10 protein has mRNA decapping activity, providing a mechanism for control of host and viral gene expression. Proceedings of the National Academy of Sciences of the USA 104: 2139–2144

Pillutla RC, Shimamoto A, Furuichi Y and Shatkin AJ (1998) Human mRNA capping enzyme (RNGTT) and cap methyltransferase (RNMT) map to 6q16 and 18p11.22‐p11.23, respectively. Genomics 54: 351–353.

Ricci EP, Limousin T, Soto‐Rifo R et al. (2013) miRNA repression of translation in vitro takes place during 43S ribosomal scanning. Nucleic Acids Research 41: 586–598.

Richter JD and Sonenberg N (2005) Regulation of cap‐dependent translation by eIF4E inhibitory proteins. Nature 433: 477–480.

Shatkin AJ (1976) Capping of eucaryotic mRNAs. Cell 9: 645–653.

Shuman S (2001) Structure, mechanism and evolution of the mRNA capping apparatus. Progress in Nucleic Acid Research and Molecular Biology 66: 1–40.

Sonenberg N and Hinnebusch AG (2009) Regulation of translation initiation in eukaryotes: mechanisms and biological targets. Cell 136: 731–745.

Sonenberg N, Morgan MA, Merrick WC and Shatkin AJ (1978) A polypeptide in eukaryotic initiation factors that crosslinks specifically to the 5′‐terminal cap in mRNA. Proceedings of the National Academy of Sciences of the USA 75: 4843–4847.

Standart N and Jackson RJ (2007) MicroRNAs repress translation of m7Gppp‐capped target mRNAs in vitro by inhibiting initiation and promoting deadenylation. Genes & Development 21: 1975–1982.

Suzuki Y and Sugano S (2003) Construction of a full‐length enriched and 5′‐end enriched cDNA library using the oligo capping method. Methods in Molecular Biology 221: 73–91.

Topisirovic I, Svitkin YV, Sonenberg N and Shatkin AJ (2010) Cap and cap‐binding proteins in the control of gene expression. Wiley Interdisciplinary Reviews: RNA 2: 277–298.

Wang Z, Jiao X, Carr‐Schmid A and Kiledjian M (2002) The hDcp2 protein is a mammalian mRNA decapping enzyme. Proceedings of the National Academy of Sciences of the USA 99: 12663–12668.

Yamabe Y, Sugimoto M, Satoh M et al. (1997) Down‐regulation of the defective transcripts of the Werner's syndrome gene in the cells of patients. Biochemical and Biophysical Research Communications 236: 1

Further Reading

Anderson R, Gebhard C, Miguel‐Escalada I et al. (2014) An atlas of active enhancers across human cell types and tissues. Nature 507: 455–461.

Furuichi Y (1981) Allosteric stimulatory effect of S‐adenosylmethionine on the RNA polymerase in cytoplasmic polyhedrosis virus. A model for the positive control of eukaryotic transcription. Journal of Biological Chemistry 256: 483–493.

Holcik M and Sonenberg N (2005) Translational control in stress and apoptosis. Nature Reviews Molecular Cell Biology 6: 318–327.

Huntzinger E, Kuzuoglu‐Öztürk D, Braun JE et al. (2013) The interactions of GW182 proteins with PABP and deadenylases are required for both translational repression and degradation of miRNA targets. Nucleic Acids Research 41: 978–994.

Liu H and Kiledjian M (2006) Decapping the message: a beginning or an end. Biochemical Society Transactions 34: 35–38.

Meijer HA, Kong YW, Lu WT et al. (2013) Translational repression and eIF4A2 activity are critical for microRNA‐mediated gene regulation. Science 340: 82–85.

Popp MW and Maquat LE (2013) Organizing principles of mammalian nonsense‐mediated mRNA decay. Annual Review of Genetics 47: 139–165.

Valencia‐Sanchez MA, Liu J, Hannon GJ and Parker R (2006) Control of translation and mRNA degradation by miRNAs and siRNAs. Genes and Development 20: 515–524.

Wahl MC, Will CL and Luhrmann R (2009) The splicesome: design principles of a dynamic RNP machine. Cell 136: 701–718.

Related Sub-Topics:

Nucleic Acid Structure | Nucleic Acids: Structure, Function, Metabolism | Transcriptional Regulation | Enzymes: Structure and Action Mechanism | Biomolecular Interactions | Translation and Protein Synthesis | Other Biomolecules: Structure, Function, Metabolism | Posttranscriptional Modification | RNA Structure and Function | Translation of RNA | Transcription | Transcription of DNA
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Article Title: Caps on Eukaryotic mRNAs
 
How to Cite close
Furuichi, Yasuhiro(Jul 2014) Caps on Eukaryotic mRNAs. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000891.pub3]