Table 3. Overview of trans-encoded antisense RNAs from low GC Gram-positive bacteria.
| sRNA (nt) | target RNA(s) | Biological function | Mechanism of action | Control of expression/ specific characteristic |
|---|---|---|---|---|
| Bacillus subtilis | ||||
| SR1 (205) | ahrC | arginine catabolism | TI | CcpN, CcpA |
| gapA operon* | sugar metabolism | SR1P/GapA* | ||
| FsrA (84) | sdhCAB, citB | succinate dehydrogenase | TI | Fur, iron; some targets need FbpA, B, or C |
| gltA | glutamate synthase (iron-sulfur) | |||
| lutABC | iron-sulfur oxidase | |||
| dctP | dicarboxylate permease | |||
| yvfW, leuCD | ||||
| RsaE (114) | cstAa, sucCa, galKa central metabolisma | TI | exponential phase | |
| Staphylococcus aureus | ||||
| RNAIII (514) | hla | α hemolysin | TA | AgrC/AgrA |
| rot | repressor of toxins Host-pathogen interactions |
TIb and RD | stationary phase | |
| sa1000/sa2261 | fibrinogen BP, ABC transporter | |||
| spa | protein A | |||
| coa | coagulase | |||
| lytM | peptidoglycan hydrolase | |||
| map | MCH class II analogous protein | TA? | ||
| RsaE (96) | opp-3B/3A, sucC, sA0873 | central metabolism | TI | pre-stationary phase, heat-shock |
| SprA (202) | sa2216# | ABC transporter? | Post-translational? | strain-specific |
| SprD (142) | sbi | immune response | TI, RD | growth phase |
| Psm-mec (157) | agrA | virulence regulator | TI, RD independent of TI | |
| Art A (345) | sarT | transcriptional regulator of hla | RD | ArgA |
| Streptococcus pyogenes | ||||
| Pel RNA (459) | speB, | cysteine protease | post-transcriptional | Multiple transcription regulators and conditioned media |
| emm, sic, nga | M- and -related proteins | transcriptional control | ||
| FasX (205) | ska | streptokinase | RNA stabilization | FasBCA, luxS |
| sagS | streptolysin | ? | aa starvation | |
| fbp54 | fibronectin binding protein | ? | ||
| mrp | fibrogene binding protein | ? | ||
| RivX (289,237,189) | mga | virulence | TA? | CovR/CovS |
| tracrRNA (171,89) | crRNA precursor | CRISPR maturation | RNA processing | Csn1b |
| S. pneumoniae | ||||
| srn206 (120) | comD | sensor histidine kinase, competence | TI? | |
| csRNA1–5 (87–151) |
comC | competence | TI? | All 5 homologous sRNAs are regulated by CiaRH |
| spr0081 | ABC transporter | |||
| spr0159 | DNA binding protein | |||
| spr0551 | branched chain aa transport | |||
| spr1097 | formate/nitrite transporter | |||
| Clostridium perfringens | ||||
| VR (386) | pfoA, vrr, virT, virU, ccp | collagenase, toxin genes | RNA processing | VirR/VirS |
| CE1446/CE1447 | TA? | |||
| VirX(?) | pfoA, plc, colA | α, κ, τ enterotoxin production | TA? | independent of VirR/VirS |
| spo0A σE, σF, σK | sporulation | encodes 51 aa peptide VirX | ||
| Listeria monocytogenes | ||||
| LhrA (268) | lmo0850 | protein of unknown function | TI and RD | Hfq required for stability and target binding |
| chiA | two chitinases | TI | ||
| lmo0302 | protein of unknown function | TI | ||
| SreA (228) | prfA | virulence master regulator | TI | SAM RS, blood |
| lmo0049 = agrD | quorum sensing molecule | TA? | ||
| SreB (179) | prfA, lmo2230 | arsenate reductase homol. | ? | |
| RilB | lmo2104/2105# | iron transport proteins | ? | |
| RilE | comEA/FA, lmo0945# | competence factors | ? | |
| RliI | lmo1035# | phosphotransferase system | ? | |
| Rli23, 25, 35 | lmo0172# | transposases | ||
| Rli45 | rli46# | ? | ||
| Rli29 | lmo9471# | ? | ||
| Rli30 | lmo0506# | ? | ||
Only sRNAs are listed for which target genes have been identified or #proposed. aIn analogy to S. aureus RsaE, which interacts via C-rich loops with SD sequences, targets have been predicted. bRequired for processing of the sRNA/target RNA duplex by RNase III *SR1 acts on gapA as a peptide encoding mRNA, i.e., SR1P interacts with GapA, thereby stabilizing gapA mRNA. TI, translation inhibition; TA, translation activation; RD, mRNA degradation. Control of expression: All proteins and growth conditions known to regulate sRNA expression are listed. It is not indicated whether these factors promote or inhibit sRNA expression. For more details, see text. RS, riboswitch.