Pathway · 20 proteins
RNA maturation
Ribonucleases and modifying enzymes help produce functional RNA.
How it works
- Primary transcripts can require end processing, cleavage and chemical modification.
- Different enzymes mature rRNA and tRNA, and process or degrade other RNAs.
- Correct processing supports RNA function; RNA turnover recovers material and helps regulate the RNA pool. These activities form several routes, not one universal processing line.
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 |
|---|---|---|---|---|---|
| tRNA (guanine-N(7)-)-methyltransferase | 2.1.1.33 | guanosine(46) in tRNA + S-adenosyl-L-methionine = N(7)-methylguanosine(46) in tRNA + S-adenosyl-L-homocysteine | — | 297 | Step named |
| tRNA dimethylallyltransferase | 2.5.1.75 | adenosine(37) in tRNA + dimethylallyl diphosphate = N(6)-dimethylallyladenosine(37) in tRNA + diphosphate | Mg(2+) | 305 | Step named |
| Ribosomal RNA small subunit methyltransferase I | 2.1.1.198 | cytidine(1402) in 16S rRNA + S-adenosyl-L-methionine = 2'-O-methylcytidine(1402) in 16S rRNA + S-adenosyl-L-homocysteine + H(+) | — | 221 | Step named |
| Endoribonuclease YbeY | 3.1.-.- | — | Zn(2+) | 150 | Step named |
| tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | guanosine(37) in tRNA + S-adenosyl-L-methionine = N(1)-methylguanosine(37) in tRNA + S-adenosyl-L-homocysteine + H(+) | — | 257 | Step named |
| Ribosomal RNA small subunit methyltransferase G | 2.1.1.- | — | — | 196 | Step named |
| Ribosomal RNA small subunit methyltransferase E | 2.1.1.193 | uridine(1498) in 16S rRNA + S-adenosyl-L-methionine = N(3)-methyluridine(1498) in 16S rRNA + S-adenosyl-L-homocysteine + H(+) | — | 229 | Step named |
| tRNA (guanosine(18)-2'-O)-methyltransferase | 2.1.1.34 | guanosine(18) in tRNA + S-adenosyl-L-methionine = 2'-O-methylguanosine(18) in tRNA + S-adenosyl-L-homocysteine + H(+) | — | 211 | Step named |
| Ribosomal RNA small subunit methyltransferase A | 2.1.1.182 | adenosine(1518)/adenosine(1519) in 16S rRNA + 4 S-adenosyl-L-methionine = N(6)-dimethyladenosine(1518)/N(6)-dimethyladenosine(1519) in 16S rRNA + 4 S-adenosyl-L-homocysteine + 4 H(+) | — | 248 | Step named |
| Ribosomal RNA small subunit methyltransferase H | 2.1.1.199 | cytidine(1402) in 16S rRNA + S-adenosyl-L-methionine = N(4)-methylcytidine(1402) in 16S rRNA + S-adenosyl-L-homocysteine + H(+) | — | 294 | Step named |
| rRNA methylase | — | — | — | 240 | System only |
| MnmC-like methyltransferase domain-containing protein | — | — | — | 308 | System only |
| tRNA (adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.220 | adenosine(58) in tRNA + S-adenosyl-L-methionine = N(1)-methyladenosine(58) in tRNA + S-adenosyl-L-homocysteine + H(+) | — | 248 | Step named |
| A-adding tRNA nucleotidyltransferase | 2.7.7.- | a tRNA with a 3' CC end + ATP = a tRNA with a 3' CCA end + diphosphate | Mg(2+) | 824 | Step named |
| PUA domain-containing protein | — | — | — | 380 | System only |
| Radical SAM core domain-containing protein | — | — | [4Fe-4S] cluster | 317 | System only |
| Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | 2.1.1.74 | uridine(54) in tRNA + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NADH + H(+) = 5-methyluridine(54) in tRNA + (6S)-5,6,7,8-tetrahydrofolate + NAD(+) | — | 445 | Step named |
| tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG | — | — | — | 617 | Step named |
| tRNA modification GTPase MnmE | 3.6.-.- | — | K(+), Mg(2+) | 448 | Step named |
| Ribonuclease PH | 2.7.7.56 | tRNA(n+1) + phosphate = tRNA(n) + a ribonucleoside 5'-diphosphate | — | 255 | 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 |
|---|---|---|---|---|---|
| tRNA-2-methylthio-N(6)-dimethylallyladenosine synthaseHome: RNA maturation | 2.8.4.3 | N(6)-dimethylallyladenosine(37) in tRNA + (sulfur carrier)-SH + AH2 + 2 S-adenosyl-L-methionine = 2-methylsulfanyl-N(6)-dimethylallyladenosine(37) in tRNA + (sulfur carrier)-H + 5'-deoxyadenosine + L-methionine + A + S-adenosyl-L-homocysteine + 2 H(+) | [4Fe-4S] cluster | 440 | Step named |
| Threonylcarbamoyladenosine tRNA methylthiotransferase MtaBHome: RNA maturation | 2.8.4.5 | N(6)-L-threonylcarbamoyladenosine(37) in tRNA + (sulfur carrier)-SH + AH2 + 2 S-adenosyl-L-methionine = 2-methylsulfanyl-N(6)-L-threonylcarbamoyladenosine(37) in tRNA + (sulfur carrier)-H + 5'-deoxyadenosine + L-methionine + A + S-adenosyl-L-homocysteine + 2 H(+) | [4Fe-4S] cluster | 410 | Step named |
| Methyltransferase small domain-containing proteinHome: RNA maturation | — | — | — | 239 | System only |
| tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferaseHome: RNA maturation | 2.1.1.215 | guanosine(26)/guanosine(27) in tRNA + 4 S-adenosyl-L-methionine = N(2)-dimethylguanosine(26)/N(2)-dimethylguanosine(27) in tRNA + 4 S-adenosyl-L-homocysteine + 4 H(+) | Zn(2+) | 392 | Step named |
| Ribonuclease 3Home: RNA processing and turnover | 3.1.26.3 | Endonucleolytic cleavage to 5'-phosphomonoester. | Mg(2+) | 221 | Step named |
| HemolysinHome: Not yet placed in a pathway | — | — | — | 258 | Unspecified |
Origins
How could RNA be trimmed and modified before the proteins that do it today existed?
How it was discovered
- 1981Tom Cech and colleagues report an RNA that cuts itself; shortly afterwards Sidney Altman shows that RNase P, which trims transfer RNA, has a catalytic RNA.Zubay, Origins of Life on Earth and in the Cosmos, p. 269
Naturalistic proposal
The discovery of self-splicing RNA and of RNase P showed that RNA can catalyse reactions. This encouraged the idea that RNA once did the jobs proteins do now.
Design analysis
In the cell, the enzymes that trim and chemically modify transfer and ribosomal RNA are proteins made by translation, and translation itself needs mature RNA. Each depends on the other.
From the books: Zubay, Origins of Life on Earth and in the Cosmos, p. 269; Ribas de Pouplana (ed.), The Genetic Code and the Origin of Life, PDF p. 120.
The wider question for this part of the cell: origins for building proteins and folding them.
Sources
- Atlas pathway grouping from the VF5 reference-genome system map (Deckert et al. 1998; Braakman & Smith 2014)
Other pathways in this group: Ribosomal subunits · Translation interface · Translation cycle · Protein translocation · Protein turnover · Folding and stabilization · Recycling and rescue · Early folding support · Protein targeting · Ribosome · Protein export · Not yet placed in a pathway