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.
From: Composition and conservation of the mRNA-degrading machinery 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 |