Pathway · 3 proteins
RNA processing and turnover
RNases process or degrade RNA substrates.
How it works
- RNase III, PH, Rne/Rng, Y and R annotations represent different RNA-processing or degradation activities. RNA structure, ends and associated proteins influence which enzyme can act.
- Endoribonucleases cut within suitable RNA substrates, while exonucleolytic activities remove residues from an accessible end. Processing can generate functional RNA, whereas turnover removes selected transcripts or fragments.
- A list of RNases is not one universal degradation sequence. Their substrate preferences, localization and partner dependence must be resolved before assigning an order to a particular RNA.
Grouped by the atlas’s curated pathway map. The table order is not a proven reaction order.
Its proteins
| Protein | EC | Reaction (UniProt) | Metal or cluster | Amino acids | Certainty |
|---|---|---|---|---|---|
| Ribonuclease Y | 3.1.-.- | — | — | 558 | Step named |
| Ribonuclease R | 3.1.13.1 | Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates. | — | 705 | Step named |
| Ribonuclease 3 | 3.1.26.3 | Endonucleolytic cleavage to 5'-phosphomonoester. | Mg(2+) | 221 | Step named |
Also part of this pathway
These proteins are described under another pathway, but also take part here.
| Protein | EC | Reaction (UniProt) | Metal or cluster | Amino acids | Certainty |
|---|---|---|---|---|---|
| Ribonuclease PHHome: RNA maturation | 2.7.7.56 | tRNA(n+1) + phosphate = tRNA(n) + a ribonucleoside 5'-diphosphate | — | 255 | Step named |
| Cytoplasmic axial filament proteinHome: Not yet placed in a pathway | — | — | Mg(2+) | 458 | Unspecified |
Origins
How were RNA molecules trimmed, and broken down when no longer needed, before these enzymes existed?
RNA can store information, catalyse reactions and take part in processing and editing, which is the basis of the RNA world hypothesis.
A chapter in Ribas de Pouplana's book finds no conclusive evidence that self-splicing and ribozyme-based RNA processing were activities of the first cells.
In the cell, messenger RNAs must be destroyed on time, or the cell could never stop making a protein. RNA turnover is part of control, not only of cleaning up.
From the books: Ruiz-Mirazo et al., Prebiotic Systems Chemistry, PDF p. 43; Ribas de Pouplana (ed.), The Genetic Code and the Origin of Life, p. 36.
The wider question for this part of the cell: origins for reading genes into rna.
Sources
- Atlas pathway grouping from the VF5 reference-genome system map (Deckert et al. 1998; Braakman & Smith 2014)
Other pathways in this group: Transcription · DNA replication · Not yet placed in a pathway