Caps on Eukaryotic mRNAs

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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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]