The 5' cap is a specially altered nucleotide end to the 5' end of precursor messenger RNA as found in eukaryotes and, as a special exception, caliciviruses, of which norovirus is one. The process of 5' capping is vital to creating mature messenger RNA which is then able to undergo translation. Capping ensures the messenger RNA's stability while it undergoes translation in the process of protein synthesis, and is a highly regulated process which occurs in the nucleus.
5' cap structure
The 5' cap is found on the 5' end of an mRNA molecule and consists of a guanine nucleotide connected to the mRNA via an unusual 5' to 5' triphosphate linkage. This guanosine is methylated on the 7 position directly after capping in vitro by a methyl transferase. It is referred to as a 7-methylguanosine cap, abbreviated m7G.
Further modifications include the possible methylation of the 2' hydroxy-groups of the first 3 ribose sugars of the 5' end of the mRNA. The methylation of both 2' hydroxy-groups is shown on the diagram.
Functionally the 5' cap looks like the 3' end of an RNA molecule (the 5' carbon of the cap ribose is bonded, and the 3' unbonded). This provides significant resistance to 5' exonucleases.
The starting point is the unaltered 5' end of an RNA molecule. This features a final nucleotide followed by three phosphate groups attached to the 5' carbon.
- One of the terminal phosphate groups is removed (by a phosphatase), leaving two terminal phosphates.
- GTP is added to the terminal phosphates (by a guanylyl transferase), losing two phosphate groups (from the GTP) in the process. This results in the 5' to 5' triphosphate linkage.
- The guanine is methylated (by a methyl transferase).
- Other methyltransferases are optionally used to carry out methylation of 5' proximal nucleotides.
5' capping targeting
The required nuclear Capping Enzyme Complex (CEC) required for capping is found bound to the RNA polymerase II before transcription starts. As soon as the 5' end of the new transcript emerges the enzymes transfer to it and begin the capping process (this is a similar kind of mechanism to ensure capping as for polyadenylation).
The enzymes for capping can only bind to RNA polymerase II ensuring specificity to only these transcripts, which are almost entirely mRNA.
5' cap function
The 5' cap has 4 main functions:
- Regulation of nuclear export.
- Prevention of degradation by exonucleases.
- Promotion of translation (see ribosome and translation).
- Promotion of 5' proximal intron excision.
Degradation of the mRNA by 5' exonucleases is prevented (as mentioned above) by functionally looking like a 3' end. This increases the half-life of the mRNA, essential in eukaryotes as the export process takes significant time.
While actively being translated the cap is bound by the translation initiation factor eIF-4E which recruits eIF-4G and thus the ribosome. The CBC is also involved in this process, recruiting the initiation factors. Decapping of an mRNA is catalyzed by the decapping complex made up of at least dcp1 and dcp2 which must compete with eIF-4E to bind the cap. Thus the 5' cap is a marker of an actively translating mRNA and is used by cells to regulate mRNA half-lives in response to new stimuli. Undesirable mRNAs are sent to P-bodies for temporary storage or decapping, the details of which are still being resolved.
The mechanism of 5' proximal intron excision promotion is not well understood, but the 5' cap appears to loop round and interact with the spliceosome in the splicing process, promoting intron excision.
-  PubMed Medical Subject Heading -RNA Caps