KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal S9.6 DNA:RNA Hybrid antibody | Millipore | MABE1095 |
| Rabbit polyclonal anti-DnaC Antibody | Smits et al., 2010 | N/A |
| Rabbit polyclonal anti-Gfp antibody | Merrikh et al., 2015 | N/A |
| Mouse monoclonal anti-Myc antibody (clone 9E10) | Invitrogen | 13–2500 |
| Mouse monoclonal anti-RpoB antibody (clone 8RB13) | Thermo | MA125425 |
| Bacterial and virus strains | ||
| B. subtilis phe trp | Brehm et al., 1973 | HM1 |
| B. subtilis phe trp thrC::Pxis-lacZ (HO) ICEBs1(0) | Merrikh et al., 2015 | HM211 |
| B. subtilis phe trp thrC::Pxis-lacZ (HO) | Merrikh et al., 2015 | HM640 |
| B. subtilis phe trp amyE::Pspank(hy)-lacZ (HO) | Lang et al., 2017 | HM1300 |
| B. subtilis phe trp amyE::Pspank(hy)-lacZ (CD) | Lang et al., 2017 | HM1416 |
| B. subtilis phe trp thrC::Pxis-lacZ (HO) ICEBs1(0) amyE::Pspank(hy)-sspB parC::parC-ssrA | This study | HM1450 |
| B. subtilis phe trp thrC::Pxis-lacZ (HO) amyE::Pspank(hy)-sspB parC::parC-ssrA | This study | HM1467 |
| B. subtilis phe trp thrC::Pxis-lacZ (CD) amyE::Pspank(hy)-sspB parC::parC-ssrA | This study | HM1468 |
| B. subtilis phe trp thrC::Pxis-lacZ (CD) ICEBs1(0) amyE::Pspank(hy)-sspB parC::parC-ssrA | This study | HM1469 |
| B. subtilis phe trp thrC::Pxis-lacZ (CD) amyE::Pspank(hy)-sspB gyrB::gyrB-ssrA | This study | HM1949 |
| B. subtilis phe trp thrC::Pxis-lacZ (CD) ICEBs1(0) amyE::Pspank(hy)-sspB gyrB::gyrB-ssrA | This study | HM1950 |
| B. subtilis phe trp thrC::Pxis-lacZ (HO) amyE::Pspank(hy)-sspB gyrB::gyrB-ssrA | This study | HM1951 |
| B. subtilis phe trp thrC::Pxis-lacZ (HO) ICEBs1(0) amyE::Pspank(hy)-sspB gyrB::gyrB-ssrA | This study | HM1952 |
| B. subtilis phe trp amyE::Pspank(hy)-lacZ (HO) ΔrnhC::MLS | Lang et al., 2017 | HM2043 |
| B. subtilis phe trp amyE::Pspank(hy)-lacZ (CD) ΔrnhC::MLS | Lang et al., 2017 | HM2044 |
| B. subtilis phe trp thrC::Pxis-lacZ (HO) ICEBs1(0) amyE::Pspank(hy)-sspB gyrB::gyrB(R138L)-ssrA | This study | HM2420 |
| B. subtilis phe trp thrC::Pxis-lacZ (CD) ICEBs1(0) amyE::Pspank(hy)-sspBgyrB::gyrB(R138L)-ssrA | This study | HM2421 |
| B. subtilis phe trp thrC::Pxis-lacZ (HO) ICEBs1(0) amyE::Pspank(hy)-sspBgyrB::gyrB-myc-ssrA | This study | HM2442 |
| B. subtilis phe trp thrC::Pxis-lacZ (HO) ICEBs1(0) amyE::Pspank(hy)-sspB gyrB::parC-myc-ssrA | This study | HM2444 |
| B. subtilis phe trp ΔrnhC::MLS | Lang et al., 2017 | HM2655 |
| B. subtilis amyE::Pspank(hy)-lacZ (HO) lacA::Pspank(hy)-3xmyc-gfp | This study | HM3019 |
| B. subtilis amyE::Pspank(hy)-lacZ (CD) lacA::Pspank(hy)-3xmyc-gfp | This study | HM3020 |
| B. subtilis phe trp amyE::Pspank(hy)-lacZ (HO) gyrA::gyrA-gfp | This study | HM3863 |
| B. subtilis phe trp amyE::Pspank(hy)-lacZ (CD) gyrA::gyrA-gfp | This study | HM3864 |
| B. subtilis phe trp gyrB(R138L) | Samadpour and Merrikh, 2018 | HM3387 |
| B. subtilis phe trp ΔrnhC::MLS gyrB(R138L) | This study | HM4064 |
| B. subtilis phe trp ΔrnhC::MLS gyrB(R138L) amyE::Pspank(hy)-lacZ (HO) | This study | HM4065 |
| B. subtilis phe trp ΔrnhC::MLS gyrB(R138L) amyE::Pspank(hy)-lacZ (CD) | This study | HM4066 |
| B. subtilis phe trp amyE::Pspank(hy)-lacZ (HO) parC::parC-3xMyc | This study | HM4074 |
| B. subtilis phe trp amyE::Pspank(hy)-lacZ (CD) parC::parC-3xMyc | This study | HM4075 |
| Chemicals, peptides, and recombinant proteins | ||
| EcoRV-HF | NEB | R0195 |
| HindIII-HF | NEB | R0104 |
| EcoRI-HF | NEB | R0101 |
| DraI | NEB | R0129 |
| RNase H | NEB | M0297 |
| Protein A Sepharose | GE | GE17-0780-01 |
| Critical commercial assays | ||
| Nextera XT DNA Library Preparation Kit | Illumina | FC-131–1024 |
| NEBNext DNA Library Prep master Mix Set | NEB | E6040 |
| GeneJET PCR Purification Kit | Thermo | K0701 |
| iScript supermix | Bio-Rad | 1708840 |
| iTaq Universal SYBR Green master mix | Bio-Rad | 1725121 |
| GeneJet Genomic DNA purication Kit | Thermo | K0721 |
| Deposited data | ||
| All sequencing DATA uploaded to the Sequence Read Archive | NCBI SRA | Bioproject PRJNA691533 |
| Oligonucleotides | ||
| GACATCCTCTGACAATCCTAGAG | This study | HM86 |
| GGCAGTCACCTTAGAGTGCCCAAC | This study | HM87 |
| GGCTTTCGCTACCTGGAGAG | Lang et al., 2017 | HM188 |
| GACGAAGCCGCCCTGTAAAC | Lang et al., 2017 | HM189 |
| CCGTCTGACCCGATCTTTTA | Lang et al., 2017 | HM192 |
| GTCATGCTGAATGTCGTGCT | Lang et al., 2017 | HM193 |
| AAGGCACATGGCTGAATATCG | Lang et al., 2017 | HM910 |
| ACACCAGACCAACTGGTAATGG | Lang et al., 2017 | HM911 |
| TTATGGATCCTGAAGGGTGAAGATGAACTG | This study | HM1690 |
| TTATTCTAGATTGTTCTGTATGAAGGCGCCAAAC | This study | HM1691 |
| ttatgaattcTATCGTAGAGGGTGACTCTG | This study | HM2282 |
| TTATTCTAGAGATGTCAAGATTTTTAACGTATCTC | This study | HM2283 |
| Recombinant DNA | ||
| pGCS::parC | This study | pHM186 |
| pGCS::gyrB | This study | pHM260 |
| Software and algorithms | ||
| SAMtools | Li et al., 2009 | http://www.htslib.org/ |
| Bowtie 2 | Langmead and Salzberg, 2012 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| Prism 7 | Graphpad | https://www.graphpad.com/scientific-software/prism/ |
| DeepTools | Ramírez et al., 2014 | https://deeptools.readthedocs.io/en/develop/ |
| IGV | Robinson et al., 2011 | http://software.broadinstitute.org/software/igv/ |
| HOMER | Heinz et al., 2010 | http://homer.ucsd.edu/homer/ |