Appendix 1—key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| strain, strain background (Escherichia coli) | BTH101 | Karimova et al., 1998 doi: 10.1073/pnas.95.10.5752 | F– cya-99 araD139 galE15 galK16 rpsL(StrR) hsdR2 mcrA1 mcrB1 relA1 | |
| strain, strain background (E. coli) | BL21 (DE3) | New England Biolabs | B F– ompT gal | |
| strain, strain background (E. coli) | MG1655; WT | Lab collection | Wild-type | |
| strain, strain background (E. coli) | nirDE50K | This paper | MG1655 nirDE50K | |
| strain, strain background (E. coli) | ΔnirD | This paper | MG1655 nirD::FRT; P1 from KEIO collection (resistance cassette has been flipped out) (Baba et al., 2006) | |
| strain, strain background (E. coli) | ΔrelA | Germain et al., 2019 doi: 10.1038/s41467-019-13764-4 | MG1655 relA::FRT | |
| strain, strain background (E. coli) | ΔrelA spoT | This paper | MG1655 relA::FRT spoT207::cat; P1 transduction from CF1693 (Baba et al., 2006) in MG1655 relA::FRT | |
| recombinant DNA reagent | pBbS2k-rfp | Lee et al., 2011 doi: 10.1186/1754-1611-5-12 | KanR, Ptet, rfp | |
| recombinant DNA reagent | pBbS2k-relA | This paper | KanR, Ptet, relA; primers 16/17; Maisonneuve lab | |
| recombinant DNA reagent | pBbS2k-relA (sd4) | This paper | KanR, Ptet, sd4, relA; primers 163/17; Maisonneuve lab | |
| recombinant DNA reagent | pBbS2k-relAN-terminal | This paper | KanR, Ptet, relAN-terminal; primers 16/557; Maisonneuve lab | |
| recombinant DNA reagent | pEG25 | Germain et al., 2019 doi: 10.1038/s41467-019-13764-4 | AmpR, PT5-lac | |
| recombinant DNA reagent | pEG25-nirD | This paper | AmpR, PT5-lac, nirD; primers 386/387; Maisonneuve lab | |
| recombinant DNA reagent | pEG25-spoT (sd8U) | Germain et al., 2019 doi: 10.1038/s41467-019-13764-4 | AmpR, PT5-lac, sd8U, spoT | |
| recombinant DNA reagent | pEG25-nirDE50K | This paper | AmpR, PT5-lac, nirDE50K; primers 386/387; Maisonneuve lab | |
| recombinant DNA reagent | pEG25-nirD (WTsd) | This paper | AmpR, PT5-lac, WTsd, nirD; primers 555/387; Maisonneuve lab | |
| recombinant DNA reagent | pEG25-nirBD (WTsd) | This paper | AmpR, PT5-lac, WTsd, nirBD; primers 553/544; Maisonneuve lab | |
| recombinant DNA reagent | pEG25-relAN-terminal | Germain et al., 2019 doi: 10.1038/s41467-019-13764-4 | AmpR, PT5-lac, relAN-terminal | |
| recombinant DNA reagent | pKD46 | Datsenko and Wanner, 2000 doi: 10.1073/pnas.120163297 | AmpR, Para, λ Red | |
| recombinant DNA reagent | pKT25 | Karimova et al., 1998 doi: 10.1073/pnas.95.10.5752 | KanR | |
| recombinant DNA reagent | pKT25-zip | Karimova et al., 1998 doi: 10.1073/pnas.95.10.5752 | KanR, zip | |
| recombinant DNA reagent | pKT25-relA | Germain et al., 2019 doi: 10.1038/s41467-019-13764-4 | KanR, relA | |
| recombinant DNA reagent | pKT25-spoT | Germain et al., 2019 doi: 10.1038/s41467-019-13764-4 | KanR, spoT | |
| recombinant DNA reagent | pKT25-nirB | This paper | KanR, nirB; primers 617/618; Maisonneuve lab | |
| recombinant DNA reagent | pKT25-relA1-663 | This paper | KanR, relA1-663; primers 497/502; Maisonneuve lab | |
| recombinant DNA reagent | pKT25-relA1-580 | This paper | KanR, relA1-580; primers 497/501; Maisonneuve lab | |
| recombinant DNA reagent | pKT25-relA1-470 | This paper | KanR, relA1-470; primers 497/500; Maisonneuve lab | |
| recombinant DNA reagent | pKT25-relAN-terminal | This paper | KanR, relAN-terminal; primers 497/499; Maisonneuve lab | |
| recombinant DNA reagent | pKT25-relA1-181 | This paper | KanR, relA1-181; primers 497/498; Maisonneuve lab | |
| recombinant DNA reagent | pKT25-relA181-744 | This paper | KanR, relA181-744; primers 531/533; Maisonneuve lab | |
| recombinant DNA reagent | pKT25-spoTN-terminal | Germain et al., 2019 doi: 10.1038/s41467-019-13764-4 | KanR, relAN-terminal | |
| recombinant DNA reagent | pUT18C | Karimova et al., 1998 doi: 10.1073/pnas.95.10.5752 | AmpR | |
| recombinant DNA reagent | pUT18C-zip | Karimova et al., 1998 doi: 10.1073/pnas.95.10.5752 | AmpR, zip | |
| recombinant DNA reagent | pUT18C-nirD | This paper | AmpR, nirD; primers 441/443; Maisonneuve lab | |
| recombinant DNA reagent | pUT18C-nirDE50K | This paper | AmpR, nirDE50K; primers 441/443; Maisonneuve lab | |
| recombinant DNA reagent | pET28a(+) | Germain et al., 2019 doi: 10.1038/s41467-019-13764-4 | KanR, Trx, His | |
| recombinant DNA reagent | pET28a(+)-nirD | This paper | KanR, Trx, His, TEV, nirD; primers 558/544; Maisonneuve lab | |
| recombinant DNA reagent | pET28a(+)-nirDE50K | This paper | KanR, Trx, His, TEV, nirDE50K; primers 558/544; Maisonneuve lab | |
| recombinant DNA reagent | pWRG99 | Blank et al., 2011 doi: 10.1371/journal.pone.0015763 | pKD46 with Ptet, I-SceI | |
| recombinant DNA reagent | pWRG100 |
Karimova et al., 1998 doi: 10.1073/pnas.95.10.5752 doi: 10.1371/journal.pone.0015763 |
pKD3 with I-SceI recognition site | |
| sequence-based reagent | Primer 16 | This paper | CCCCGAATTCGTCGACTCAAGGAGGTTTTATAAATGGTTGCGGTAAGAAGTGCA; restriction enzyme EcoRI; Maisonneuve lab | |
| sequence-based reagent | Primer 17 | This paper | CCCCGGATCCCTAACTCCCGTGCAACCGAC; restriction enzyme BamHI; Maisonneuve lab | |
| sequence-based reagent | Primer 163 | This paper | CCCCGAATTCGTCGACTCAAGGATTAAATGGTTGCGGTAAGAAGTGCA; restriction enzyme EcoRI; Maisonneuve lab | |
| sequence-based reagent | Primer 386 | This paper | CCCCGAATTCGTCGACTCAAGGAGGTTTTATAAATGAGCCAGTGGAAAGACAT; restriction enzyme EcoRI; Maisonneuve lab | |
| sequence-based reagent | Primer 387 | This paper | CCCCGGATCCTTAACCGCGCAGCTGCACCA; restriction enzyme BamHI; Maisonneuve lab | |
| sequence-based reagent | Primer 441 | This paper | CCCCTCTAGAAATGAGCCAGTGGAAAGACAT; restriction enzyme XbaI; Maisonneuve lab | |
| sequence-based reagent | Primer 443 | This paper | CCCCGGTACCTTAACCGCGCAGCTGCACCA; restriction enzyme KpnI; Maisonneuve lab | |
| sequence-based reagent | Primer 497 | This paper | CCCCTCTAGAAATGGTTGCGGTAAGAAGTGC; restriction enzyme XbaI; Maisonneuve lab | |
| sequence-based reagent | Primer 498 | This paper | CCCCGGTACCGATGTTGGTACACTCTTTTG; restriction enzyme KpnI; Maisonneuve lab | |
| sequence-based reagent | Primer 499 | This paper | CCCCGGTACCTTCGTCGAGCATTTCGCCGG; restriction enzyme KpnI; Maisonneuve lab | |
| sequence-based reagent | Primer 500 | This paper | CCCCGGTACCGTTCGGCTGTTTCTGGGTGA; restriction enzyme KpnI; Maisonneuve lab | |
| sequence-based reagent | Primer 501 | This paper | CCCCGGTACCAAGTTGCTTCAGCGCGGCGG; restriction enzyme KpnI; Maisonneuve lab | |
| sequence-based reagent | Primer 502 | This paper | CCCCGGTACCGGCGGAGTAGCTCTCACCCC; restriction enzyme KpnI; Maisonneuve lab | |
| sequence-based reagent | Primer 531 | This paper | CCCCTCTAGAATACGCACCGCTGGCTAACCG; restriction enzyme XbaI; Maisonneuve lab | |
| sequence-based reagent | Primer 533 | This paper | CCCCGGTACCCTAACTCCCGTGCAACCGAC; restriction enzyme KpnI; Maisonneuve lab | |
| sequence-based reagent | Primer 544 | This paper | CCCCAAGCTTTTAACCGCGCAGCTGCACCA; restriction enzyme HindIII; Maisonneuve lab | |
| sequence-based reagent | Primer 553 | This paper | CCCCGAATTCAATAGAAAAGAAATCGAGGCAAAAATGAGCAAAGTCAGACTCGC; restriction enzyme EcoRI; Maisonneuve lab | |
| sequence-based reagent | Primer 555 | This paper | CCCCGAATTCAGTAACTCTGGTGGAGGACAACGCATGAGCCAGTGGAAAGACAT; restriction enzyme EcoRI; Maisonneuve lab | |
| sequence-based reagent | Primer 557 | This paper | CCCCGGATCCTTATTCGTCGAGCATTTCGCCGG; restriction enzyme BamHI; Maisonneuve lab | |
| sequence-based reagent | Primer 558 | This paper | CCCCGGATCCGAGAACCTGTACTTCCAATCAATGAGCCAGTGGAAAGACAT; restriction enzyme BamHI; Maisonneuve lab | |
| sequence-based reagent | Primer 617 | This paper | CCCCTCTAGAAATGAGCAAAGTCAGACTCGC; restriction enzyme XbaI; Maisonneuve lab | |
| sequence-based reagent | Primer 618 | This paper | CCCCGGTACCTCATGCGTTGTCCTCCACCA; restriction enzyme KpnI; Maisonneuve lab | |
| sequence-based reagent | Primer 629 | This paper | ATGAGCCAGTGGAAAGACATCTGCAAAATCGATGACATCCTGCCTGAAACCGCCTTACGCCCCGCCCTGC; Maisonneuve lab | |
| sequence-based reagent | Primer 630 | This paper | TTAACCGCGCAGCTGCACCACGCCGTCTTTCACTCGCGCTTCGTAATGTTCTAGACTATATTACCCTGTT; Maisonneuve lab | |
| sequence-based reagent | Primer 655 | This paper | ATGAGCCAGTGGAAAGACAT; Maisonneuve lab | |
| sequence-based reagent | Primer 656 | This paper | TTAACCGCGCAGCTGCACCA; Maisonneuve lab | |
| chemical compound, drug | [α32P]GTP | PerkinElmer | Catalog number: BLU006H250UC | |
| chemical compound, drug | 32P | PerkinElmer | Catalog number: NEX053H001MC | |
| chemical compound, drug | EZ-Link NHS-PEG4-Biotin | Thermo Scientific | Catalog number: 21330 | |
| software, algorithm | BLItz Pro Software | https://www.sartorius.com/en/products/protein-analysis | ||
| software, algorithm | MicroCal PEAQ-ITC Analysis Software | Malvern Panalytical | https://www.malvernpanalytical.com/fr/products/product-range/microcal-range/microcal-itc-range/microcal-peaq-itc | |
| software, algorithm | Prism 5.0 software | GraphPad | https://www.graphpad.com/scientific-software/prism/ | |
| other | HiLoad 16/600 Superdex 200 column | GE Healthcare | Catalog number: GE28-9893-35 | |
| other | HiPrep 26/10 Desalting column | GE Healthcare | Catalog number: GE17-5087-01 | |
| other | HisTrap column | GE Healthcare | Catalog number: GE17-5248-02 | |
| other | Streptavidin Biosensors | FortéBio | Catalog number: 18-5117 | |
| other | Superdex 200 10/300 GL | GE Healthcare | Catalog number: GE28-9909-44 | |
| other | Zeba Spin Desalting column | Thermo Scientific | Catalog number: 89882 |