Table 1.
Major ribonucleases acting on single-stranded (ss) or double-stranded (ds) regions of RNA and ancillary RNA-modifying enzymes (pyrophosphohydrolase, RppH; poly(A) polymerase I, PAPI; and DEAD-box RNA helicases) involved in RNA turnover in bacteria.
| Endoribonucleases | |||
|---|---|---|---|
| Name | Essential for cell survival |
Description of the reaction catalyzed |
Specific functions in vivo |
| RNase E/G | Yes | Cleavage of A/U-rich ss regions of RNA yielding 5'-monophosphorylated products; 5'-end-dependent hydrolase | Ribosomal and transfer RNA processing, initiation of decay of non-coding and mRNAs, turnover of messenger, non-coding and stable RNA decay intermediates |
| RNase III | Yes | Endonucleolytic cleavage of ds regions of RNA yielding 5'-monophosphorylated products | Ribosomal and transfer RNA processing and mRNA processing and decay |
| RNases J1/J2* | RNaseJ1/Yes | Endonucleolytic cleavage of ss regions of RNA yielding 5'-monophosphorylated products; 5'-end-dependent hydrolase | RNA processing and decay in B. subtilis |
| RNase Y | Yes | Endonucleolytic cleavage of ss regions of RNA yielding 5'-monophosphorylated products; 5'-end-dependent hydrolase | Degradation of B. subtilis transcripts containing SAM-dependent riboswitches |
| Exoribonucleases | |||
| Name | Essential for cell survival |
Description of the reaction catalyzed |
Specific functions in vivo |
| RNase PH | No | tRNA nucleotidyltransferase | Exonucleolytic trimming of the 3'-termini of tRNA precursors |
| PNPase | No | (i) Phosphorolytic 3' to 5' exoribonuclease and (ii) 3'-terminal oligonucleotide polymerase activities |
3' to 5' decay of ssRNA |
| RNase II | Yes | Exonucleolytic cleavage in the 3' to 5' direction to yield ribonucleoside 5'-monophosphates | Removal of 3'-terminal nucleotides in monomeric tRNA precursors, 3' to 5' exonucleolytic decay of unstructured RNAs |
| RNase R | No | Exonucleolytic cleavage in the 3' to 5' direction to yield ribonucleoside 5'-monophosphates | 3' to 5' exonucleolytic decay of structured RNAs (e.g. mRNA and rRNA) |
| RNase J1/J2* | Yes | Exonucleolytic cleavage in the 5' to 3' direction to yield nucleoside 5'-monophosphates | 5' to 3' exonucleolytic decay of B. subtilis RNAs |
| Oligoribo-nuclease | yes | Exonucleolytic cleavage of short oligonucleotides to yield nucleoside 5'-phosphates | Completion of the last steps of RNA decay |
| Ancillary RNA-modifying enzymes | |||
| Name | Essential for cell survival |
Description of the reaction catalyzed |
Specific functions in vivo |
| RppH | No | Removal of pyrophosphate groups from the 5'-end of triphosphorylated RNAs | Facilitation of endoribonucleolytic cleavages of primary transcripts by RNase E/G |
| PAPI | No | Addition of adenosines to the 3'-end of RNA | Facilitation of 3' to 5' exonuclolytic decay of structured RNAs by adding 3' poly(A) tails |
| DEAD-box helicases | No | ATP-dependent unwinding of ds regions of RNAs |
Facilitation of the PNPase- dependent decay of structured RNAs |
The presented classification of the enzymes and their functions in vivo were adopted from several enzyme databases (KEGG, http://www.genome.jp; EXPASY, http://us.expasy.org/enzyme/; and IntEnz, http://www.ebi.ac.uk/intenz/.*RNases J1/J2 possess both exo- and endoribonucleolytic activities.