This document discusses the 5' terminal m7G cap structure found on eukaryotic messenger RNA. It summarizes that the cap evolved in eukaryotes to serve as an alternative to the prokaryotic Shine-Dalgarno sequence for directing ribosomes to mRNA. The structure of the cap involves a 5' to 5' triphosphate bridge and methyl group on the guanine nitrogen. Capping occurs co-transcriptionally within 30 nucleotides of the 5' end. The cap protects mRNA from degradation, marks the translation start site, and facilitates translation initiation and splicing.

1. 5’terminal m7G cap
of messenger RNA:
structure and function
By Sukanya Varape
Roll No. 1385

2. Why the cap was evolved only in Eukaryotes?
Loss of Shine- Dulgarno base pairing in eukaryotes which is a means of
directing the ribosome to the mRNA
Eukaryote use ‘cap’ as an alternative signal for directing translational
machinery to the mRNA
Appearance of 5’exorionuclease only in eukaryotes
Existence of capping enzymes only in eukaryotes
Specificity of Guanylytransferase

3. Structure of 7-
methyl
guanosine
cap
5’ to 5’ triphosphate bridge( phosphoanhydride bonds)
Methyl group on N-7 position

4. Co-transcriptional capping
Carboxy-terminal
domain
~30 nucleotide
Addition of guanine in
opposite direction

5. Structure and mechanism of the RNA triphosphatase enzymes
Mechanically and structurally they are diverse
Two families
The divalent-cation-dependent RNA triphosphatase-
Found in protozoa, eukaryotic viruses and fungi
The metal-independent class of triphosphatase enzyme-
Found in metazoa and plants

6. Structure and mechanism of the RNA
guanylyltransferase enzymes
Lysine side chain
It have two structural domains
N-terminal nucleotidyl transferae
C-terminal OB fold domain
It resembles DNA and RNA ligases

7. Structure and mechanism of the mRNA cap
(guanine-N7) methyltransferase
It’s structure has revealed that, enzyme contains
separate ligand- binding pocket for AdoMet(methyl
donor) and cap guanine(methyl acceptor)

8. Types of caps

9. The exception
RNA dependent RNA polymerase of Vesicular Stomatitis
Virus(VSV) incorporates GDP into the cap structure

10. Functions of m7G cap
Essential for the growth of eukaryotic cells
Marks the translational start site
Protects mRNA from degradation by 5’exoribonucleases
Methyl group facilitate translation
Participate in mRNA splicing and enhances its accuracy
Binds to nuclear cap binding complex to facilitate mRNA transport to
cytoplasm
Specificity of Gunylytransferase ensures that the caps are added only to the
intact transcripts and not to endolyticaly cleaved once.

11. Up regulators:
1.Myc
2.E2F1-cell proliferation transcription factor
3.Importin alpha
Down regulators:
1.Cdc34-ubiquitin-conjugating enzyme
2.SAHH-S-adenosylhomocystine hydrolyase

12. 1.Specificity
2.Potency

13. mammalian cells contain a surveillance machinery anchored by the DXO and
Xrn2 factors that will rapidly degrade incorrectly capped pre-mRNAs
Possible Target proteins:
1. Viral TAT protein
2. Mammalian PMIT enzyme

14. mRNAs with short poly-A tails are captured poorly by oligo-dT based methods
Recombinant human cap-binding protein eIF4E was used to capture mRNAs
on the basis of the 5’ cap structure
With mRNA capture by the 5’ 7-methyl guanosine cap provides a more
complete view of the transcriptome and can be used to assay changes in
mRNA poly-A tail length on a genome-wide scale.

15. Based preparation and sequencing of concatamers of DNA tags deriving from
the initial 20 nucleotides from 5’ end mRNAs CAGE
Allows high-throughout gene expression analysis and the profiling of
transcriptional start points (TSP), including promoter usage Analysis

16. References
Amiya k. Banerjee, 5'-Terminal Cap Structure in Eukaryotic Messenger Ribonucleic
Acids, MICROBIOLOGICAL REVIEWS, vol.2 June 1980
Stewart Shuman, What messenger RNA Capping tells us about the eukaryotic
evolution, Nature reviews, MolCellBio, Vol. 3 Aug. 2002
Meigang Gu and Christopher D Lima, Processing the message: structural insights into
capping and decapping mRNA, Current Opinion in Structural Biology, 15:99–106, 2005
Victoria H. COWLING, Regulation of mRNA cap methylation, Biochem. J. (2010) 425,
295–302
Tomoaki Ogino and Amiya K. Banerjee Unconventional Mechanism of mRNACapping
by the RNA-Dependent RNA Polymerase of Vesicular Stomatitis Virus Molecular Cell 25,
85–97, January 12, 2007
Jeffrey Wilusz, Putting an ‘End’ to HIV mRNAs: capping and polyadenylation as
potential therapeutic targets, Wilusz AIDS Research and Therapy 2013, 10:31
François Ferron, Etienne Decroly, Barbara Selisko, Bruno Canard, The viral RNA
capping machinery as a target for antiviral drugs, Antiviral Research 96 (2012) 21–31
Michael D. Blower et al, Combining Different mRNA Capture Methods to Analyze the
Transcriptome: Analysis of the Xenopus laevis Transcriptome, PLOS ONE ,October
2013, Volume 8, Issue 10
Toshiyuki Shiraki, Cap analysis gene expression for high-throughput analysis of
transcriptional starting point and identification of promoter usage, PNAS December 23,
2003 vol. 100 no. 26

17. Anne-Claude Gingras, Nature Reviews Molecular Cell Biology AOP, published
online 14 october 2009