TABLE 1.
Bacterial strains and plasmids.
| Strain/plasmid | Relevant characteristics | Source/references |
| Agrobacterium tumefaciens | ||
| C58 (EML530) | Wild-type virulence strain containing pTiC58 and pAtC58 | Eugene Nester |
| C58:△atu4333 (EML1073) | atu4333 (tssL) in-frame deletion mutant of C58 background | (Ma et al., 2012) |
| Escherichia coli | ||
| DH10B | Host for DNA cloning | Invitrogen |
| BW25113 | Wild-type strain of the Keio Collection. rrnB DElacZ4787 HsdR514 DE(araBAD)567 DE(rhaBAD)568 rph-1. | (Baba et al., 2006) |
| Keio collection | Systematic single-gene knockout mutants of E. coli BW25113 | (Baba et al., 2006) |
| JW0427 | BW25113 clpP:kan | (Baba et al., 2006) |
| JW0866 | BW25113 clpA:kan | (Baba et al., 2006) |
| JW0428 | BW25113 clpX:kan | (Baba et al., 2006) |
| EML5395 | DH10B harboring pNptII | This study |
| EML5393 | BW25113 wild-type harboring pNptII | This study |
| BL21(DE3) | Host for protein expression | (Studier and Moffatt, 1986) |
| Plasmids | ||
| pTrc200HA | SpR, pTrc200 harboring C-terminal influenza hemagglutinin (HA) epitope, Ptrc, lacIq, pVS1 origin | Laboratory collection |
| pRL662 | GmR, a non-transferable broad-host range vector derived from pBBR1MCS2 | (Vergunst et al., 2000) |
| pET22b(+) | ApR, E. coli overexpression vector harboring C-terminal 6xHis epitope | Novagen |
| pRL-rpsL | GmR, pRL662 expressing BW25113 rpsL gene | This study |
| pRL-galk | GmR, pRL662 expressing BW25113 galK gene | This study |
| pRL-nupG | GmR, pRL662 expressing BW25113 nupG gene | This study |
| pRL-rpsLStr | GmR, pRL662 expressing DH10B rpsLStr gene | This study |
| pNptII | KmR, GmR, pRL662 expressing nptII gene | This study |
| pClpP-HA | SpR, pTrc200HA expressing ClpP-HA fusion protein | This study |
| pClpA-HA | SpR, pTrc200HA expressing ClpA-HA fusion protein | This study |
| pClpPS111A-HA | SpR, pTrc200HA expressing ClpP-HA fusion protein with S111A substitution | This study |
| pClpPH136A-HA | SpR, pTrc200HA expressing ClpP-HA fusion protein with H136A substitution | This study |
| pClpPD185A-HA | SpR, pTrc200HA expressing ClpP-HA fusion protein with D185A substitution | This study |
| pClpPR26A-HA | SpR, pTrc200HA expressing ClpP-HA fusion protein with R26A substitution | This study |
| pClpPD32A-HA | SpR, pTrc200HA expressing ClpP-HA fusion protein with D32A substitution | This study |
| pClpX-ΔN-ter | Plasmid used for purifying ClpX-ΔN | Robert T. Sauer |
| pGFP-ssrA | Plasmid used for purifying GFP-ssrA | Robert T. Sauer |
| pClpP-tev-His | ApR, pET22b(+) expressing ClpP-tev-His, in which ClpP protein is fused with a TEV protease cleavage site and a His-tag in its C-terminal | Robert T. Sauer |
| pClpPS111A-tev-His | ApR, pET22b(+) expressing ClpP-tev-His with ClpP S111A substitution | This study |
| pClpPH136A-tev-His | ApR, pET22b(+) expressing ClpP-tev-His with ClpP H136A substitution | This study |
| pClpPD185A-tev-His | ApR, pET22b(+) expressing ClpP-tev-His with ClpP D185A substitution | This study |