TABLE 1.
A list of bacterial proteases with examples of their substrates.
| Protease | ATPase partner | Adaptor or regulator | Substrates | Degron location | Sequence | References |
| ClpP | ClpX (E. coli) | SspB | ssrA-tagged proteins | C-terminus | AANDENYALAA | Gottesman et al., 1998 |
| RseA1–108 (cleaved) | C-terminus | VRPWAAQLTQMGVAA | Flynn et al., 2004 | |||
| – | MuA | C-terminus | RRKKAI | Harshey et al., 1985; Levchenko et al., 1995 | ||
| – | FtsZ | C-terminus | AKEPDYLDIPAFLRKQAD | Camberg et al., 2009 | ||
| RssB | RpoS (σS) | N-terminus | KVHDLNEDAEFDENGVE VFDEKALVEQEP | Stüdemann et al., 2003 | ||
| – | λO | N-terminus | TNTAKILNFGR | Flynn et al., 2003 | ||
| – | Dps | N-terminus | STAKLVKSKAT | Flynn et al., 2003 | ||
| – | OmpA | N-terminus | MKKTAAIAIAV | Flynn et al., 2003 | ||
| ClpX (B. subtilis) | – | Poly-Ala-tagged proteins | C-terminus | Poly-Ala | Lytvynenko et al., 2019 | |
| YjbH | Spx | C-terminus | FLPRKVRSFQLRE | Awad et al., 2019 | ||
| CmpA | SpoIVA | n.d. | n.d. | Tan et al., 2015 | ||
| ClpX (C. crescentus) | CpdR/RcdA/PopA | CtrA | N-terminus | DPNEQVNAA | Domian et al., 1997; Joshi et al., 2015 | |
| CpdR/RcdA | TacA | C-terminus | TLEEIERDLIQH | Joshi et al., 2015 | ||
| CpdR | PdeA | C-terminus | GAAPVKARG | Rood et al., 2012 | ||
| SocA | SocB | n.d. | n.d. | Aakre et al., 2013 | ||
| ClpA (E. coli) | ClpS | N-degron pathway | N-terminus | L, F, W, Y | Dougan et al., 2002; Ninnis et al., 2009; Schuenemann et al., 2009 | |
| ClpC (B. subtilis) | MecA | ComK | C-terminus | FMLYPKEERTMIYD FILRELGERY | Prepiak and Dubnau, 2007 | |
| ComS | N-terminus | IILYPR | Ogura et al., 1999; Prepiak and Dubnau, 2007 | |||
| McsB | CtsR | Internal (tagged Arg) | pArg | Trentini et al., 2016 | ||
| MgsR | Internal (tagged Arg) | pArg | Lilge et al., 2020 | |||
| Lon | Lon AAA+ domain | – | RcsA (E. coli) | n.d. | n.d. | Stout et al., 1991; Gur and Sauer, 2009 |
| – | SulA (E. coli) | C-terminus | ASSHATRQLSGLKIHSNLYH | Ishii et al., 2000; Gur and Sauer, 2009 | ||
| – | Y2853 (Y. pestis) | C-terminus | PLTATSYPIIH | Puri and Karzai, 2017 | ||
| – | UmuD (E. coli) | N-terminus | FPLFSDLVQCGFPSP | Gonzalez et al., 1998 | ||
| – | ZntR (E. coli) | N-terminus | n.d. | Pruteanu et al., 2007 | ||
| – | Unfolded proteins | Internal | Hydrophobic amino acids | Gur and Sauer, 2008b | ||
| – | DnaA (C. crescentus) | N-terminus | MSLSLWQQCLARL QDELPATEF | Liu et al., 2019 | ||
| – | SoxS (E. coli) | N-terminus | SHQKIIQDLIAWIDEHIDQ | Shah and Wolf, 2006 | ||
| HspQ | YmoA (Y. pestis) | n.d. | n.d. | Puri and Karzai, 2017 | ||
| – | PerR (B. subtilis) | Internal, oxidation | NNLRVFR | Ahn and Baker, 2016 | ||
| FtsH (E. coli) | FtsH AAA+ domain | n.d. | LpxC | C-terminus | LAFKAPSAVLA | Führer et al., 2006 |
| λCIII | λCII | C-terminus | RSEQIQMEF | Kobiler et al., 2002 | ||
| n.d. | RpoH (σ32) | n.d. | n.d. | Herman et al., 1995, 2003 | ||
| – | YfgM | N-terminus | EIYENENDQVEAV | Bittner et al., 2015 | ||
| – | YccA | N-terminus | VSSSHDRT | Kihara et al., 1999 | ||
| – | SecY | n.d. | n.d. | Kihara et al., 1995 | ||
| HslV (ClpQ) (E. coli) | HslU (ClpY) | – | RcsA | n.d. | n.d. | Chang et al., 2016 |
| – | SulA | Internal | GFIMRP | Chang et al., 2019 | ||
| – | YbaB | n.d. | n.d. | Tsai et al., 2017 | ||
| – | RpoH (σ32) | n.d. | n.d. | Kanemori et al., 1997 | ||
| 20S Proteasome (M. tuberculosis) | Mpa | – | Pup-tagged proteins | Internal (tagged Lys) | MAQEQTKRGGGGGDD DDIAGSTAAGQERREKLTE ETDDLLDEIDDVLEENAE DFVRAYVQKGGQ | Cole et al., 1998 |
| – | Bpa | Unstructured proteins | Internal | Hydrophobic amino acids | Delley et al., 2014 | |
| Cpa | – | n.d. | n.d. | n.d. | Ziemski et al., 2018 |
n.d., not determined.