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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
  1. 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.