Pathway · 4 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-2-methylthio-N(6)-dimethylallyladenosine synthase | 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 MtaB | 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 protein | — | — | — | 239 | System only |
| tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | 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 |
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 3Home: RNA processing and turnover | 3.1.26.3 | Endonucleolytic cleavage to 5'-phosphomonoester. | Mg(2+) | 221 | Step named |
| tRNA (guanine-N(7)-)-methyltransferaseHome: RNA maturation | 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 dimethylallyltransferaseHome: RNA maturation | 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 IHome: RNA maturation | 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 YbeYHome: RNA maturation | 3.1.-.- | — | Zn(2+) | 150 | Step named |
| tRNA (guanine-N(1)-)-methyltransferaseHome: RNA maturation | 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 GHome: RNA maturation | 2.1.1.- | — | — | 196 | Step named |
| Ribosomal RNA small subunit methyltransferase EHome: RNA maturation | 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)-methyltransferaseHome: RNA maturation | 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 AHome: RNA maturation | 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 HHome: RNA maturation | 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 methylaseHome: RNA maturation | — | — | — | 240 | System only |
| MnmC-like methyltransferase domain-containing proteinHome: RNA maturation | — | — | — | 308 | System only |
| tRNA (adenine(58)-N(1))-methyltransferase TrmIHome: RNA maturation | 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 nucleotidyltransferaseHome: RNA maturation | 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 proteinHome: RNA maturation | — | — | — | 380 | System only |
| Radical SAM core domain-containing proteinHome: RNA maturation | — | — | [4Fe-4S] cluster | 317 | System only |
| Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFOHome: RNA maturation | 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 MnmGHome: RNA maturation | — | — | — | 617 | Step named |
| tRNA modification GTPase MnmEHome: RNA maturation | 3.6.-.- | — | K(+), Mg(2+) | 448 | Step named |
| Ribonuclease PHHome: RNA maturation | 2.7.7.56 | tRNA(n+1) + phosphate = tRNA(n) + a ribonucleoside 5'-diphosphate | — | 255 | 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
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.
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 making the twenty amino acids.
Sources
- Atlas pathway grouping from the VF5 reference-genome system map (Deckert et al. 1998; Braakman & Smith 2014)
Other pathways in this group: Aromatic amino acids · Branched-chain amino acids · Aspartate-family branches · Nitrogen assimilation · Folate-linked carbon transfer · Arginine biosynthesis · Cysteine and methionine metabolism · Histidine metabolism · Lysine biosynthesis · Arginine and proline metabolism · Phenylalanine, tyrosine and tryptophan biosynthesis · Not yet placed in a pathway