Table 1.
Documented DBP-sRNA regulons are captured by node 1 of the ID-sRnA approach.
| sRNA | sRNA Function | DBP | DBP Function | Suggested DBP Effect | DESeq Evidence | Reference of DBP Binding Site |
|---|---|---|---|---|---|---|
| ArrS | Stabilizes gadE maturation, Regulates acid response | GadE | Regulates acid response | Activator | –ΔgadE | Ma, J Bacteriol (2004) |
| CyaR | Represses porin synthesis and group behavior | Crp | Catabolism of secondary carbon sources | Activator | –Δcrp/Glucose, –Δcrp/Glycerol | Johnson, J Mol Biol (2008) |
| Represses porin synthesis and group behavior | CpxR | Regulates envelope stress response | Repressor | -H2O2 | Vogt, J Bacteriol (2014) | |
| GadF | unknown, generated from 3’ UTR of gadE | Crp | Catabolism of secondary carbon sources | Repressor, Dual | ++Δcrp/glucose, ++Δcrp/fructose, ++Δcrp/Glycerol, ++Acetate | Hirakawa, J Bacteriol (2006) |
| ArcA | Regulates anaerobic metabolism | Activator | +Anaerobic | Deng, Front Microbiol (2013) | ||
| H-NS | Nucleoid-Associated | Repressor | ++Δhns | Krin, BMC Microbiol (2010) | ||
| GadY | Activates acid response | RpoS | Stationary phase regulator | Activator | –ΔrpoS, +MidStat | Opdyke, J Bacteriol (2004) |
| IsrB | Contains peptide coding sequence | Crp | Catabolism of secondary carbon sources | Repressor | –Fructose, –Acetate | Hemm, J Bacteriol (2010) |
| McaS | Regulates flagellar motility and biofilm formation | Crp | Catabolism of secondary carbon sources | Activator | –Δcrp/Glucose, –Δcrp/Glycerol | Thomason, Mol Microbiol (2012) |
| MgrR | Represses modified lipopolysaccharide | PhoP | PhoPQ two-component system | Activator | ++Low Mg | Moon, Mol Microbiol (2009) |
| RnpB | Subunit of ribonuclease | Fis | Nucleoid-Associated | Activator | –Δfis | Choi, Mol Cells (2005) |
| RyhB | Represses production of iron-containing proteins | Fur | Iron regulator | Repressor | ++Δfur/Fe+, -Anaerobic | Chen, NAR (2007) |
| Spot42 | Represses galactokinase degradation | Crp | Catabolism of secondary carbon sources | Activator, Dual | –Δcrp/Glucose, –Acetate, –Fructose, –Glycerol | Polayes, J Bacteriol (1988) |
| SroD | Unknown, generated from 3’ UTR | FadR | Fatty acid regulator | Repressor | ++ΔfadR | Feng, PLoS One (2012) |
| SsrS | Represses polymerase and σ70 activity | Fis | Nucleod Associated | Activator | –Δfis | Neusser, Biol Chem (2008) |
Of 39 sRNAs with well-characterized transcriptional regulators, 12 were captured as high-confidence DBPs by the integrative approach. Bold factors are documented in a recent sRNA review (Hör et al., 2020). Characters (+/-) indicate log2 fold change strength with double characters (++/–) signifying greater/less than |1.5|.