Table 1.
Genes encoding ribonucleases and related proteins for RNA processing or degradation in the γ‐proteobacterium Escherichia coli, the firmicute Bacillus subtilis, the unicellular cyanobacterium Synechocystis PCC 6803, and the filamentous cyanobacterium Anabaena PCC 7120.
| Genes from different bacteria | ||||||
|---|---|---|---|---|---|---|
| Protein | Activity and known functions | Escherichia coli | Bacillus subtilis | Synechocystis PCC 6803 | Anabaena PCC 7120 | |
| Endoribonucleases | ||||||
| RNase E/G | Cleaving ssRNA, participating in bulk RNA degradation | rne; rng | / | slr1129 (rne) | alr4331 (rne) | |
| RNase Y | Cleaving ssRNA, participating in bulk RNA degradation | / | rny | / | / | |
| RNase III | Cleaving dsRNAs, participating rRNA maturation and bulk RNA degradation | rnc | rnc | slr1646; slr0346 | alr0280; all4107 | |
| Mini‐III | Cleaving dsRNAs, mainly participating in 23S rRNA maturation | / | mrnC | slr0954 | alr1158 | |
| RNase HI | Cleaving the RNA strand in RNA–DNA hybrids | rnhA | / | slr0080 | alr0142 | |
| RNase HII | Cleaving the RNA strand in RNA–DNA hybrids | rnhB | rnhB | slr1130 | alr4332 | |
| RNase HIII | Cleaving the RNA strand in RNA–DNA hybrids | / | rnhC | / | / | |
| YbeY | Cleaving ssRNAs, mainly participating in 16S rRNA maturation | ybeY | ybeY | slr0053 | all0271 | |
| RNase P | Cleaving tRNA precursors to produce the mature 5ʹ ends | rnpA, rnpB | rnpA, rnpB | slr1469 (rnpA), rnpB | alr3413 (rnpA), rnpB | |
| RNase Z/BN | Cleaving tRNA precursors to produce the 3ʹ end for CAA addition | rbn | rnz | slr0050 | alr5152 | |
| RNase M5 | Cleaving specifically at a double‐strand region in 5S rRNA precursor to produce mature 3ʹ and 5ʹ ends | / | rnmV | / | / | |
| Cas6 | Cleaving specifically within the CRISPR repeats for the maturation of crRNAs | cas6 | cas6 | slr7014 (cas6‐1); slr7068 (cas6‐2a) | alr1482; alr1566 | |
| Exoribonucleases | ||||||
| PNPase | Degrading ssRNAs from 3ʹ by phosphorolysis, polyadenylating ssRNAs | pnp | pnp | sll1043 | all4396 | |
| RNase J | Hydrolyzing ssRNAs from 5ʹ end or cleaving it at internal sites | / | rnj1; rnj2 | slr0551 (rnj) | all3678 (rnj) | |
| RNase R/II | Hydrolyzing ssRNAs from 3ʹ end, participating in bulk RNA degradation | rnb; rnr | rnr | sll1290; sll1910 | all4450; alr1240 | |
| Orn | Oligoribonuclease, hydrolyzing short oligoribonucleotides into single ribonucleotides | b4162 | / | / | / | |
| nanoRNase | Oligoribonuclease, hydrolyzing short oligoribonucleotides into single ribonucleotides | / | nrnA; nrnB | / | / | |
| RNase PH | Degrading ssRNAs from 3ʹ end by phosphorolysis, mainly producing mature tRNA 3ʹ ends | rph | rph | / | alr0069 | |
| RNase D | Hydrolyzing ssRNAs from 3ʹ end, participating in tRNA maturation | rnd | / | sll0320 | all1697; all3791 | |
| RNase T | Hydrolyzing ssRNAs from 3ʹ end, mainly participating in the maturation of tRNAs, 5S RNA and 23S rRNA | rnt | / | / | / | |
| Auxiliary proteins | ||||||
| RNA helicase | Unwinding secondary structures of double‐strand RNA segments | rhlE; rhlB; deaD/csdA; dbpA; srmB | cshA; cshB; deaD/yxiN; and yfmL | slr0083 (crhR) | alr1223 (crhB); alr4718 (crhC) | |
| Hfq | Binding to sRNAs and mRNAs, facilitating the base pairing between sRNAs and their mRNA targets | hfq | hfq | ssr3341 (hfq) | asl2047 (hfq) | |
| ProQ | Binding mainly to mRNAs, acting as an RNA chaperone | proQ | / | / | / | |
| RppH | RNA 5ʹ pyrophosphohydrolase, converting 5ʹ triphosphate to 5ʹ monophosphate | rppH | rppH | / | / | |
crRNA, CRISPR RNA; dsRNA, double‐stranded RNA; mRNA, messenger RNA; sRNA, small RNA; ssRNA, single‐stranded RNA; tRNA, transfer RNA.