Bacterial and Virus Strains |
Clostridioides difficile R20291
|
Stabler et al., 2009 |
|
Clostridioides difficile hsmR::CT |
This study |
|
Clostridioides difficile hsmA::CT |
This study |
|
Bacillus subtilis JH BS2 |
Francis et al., 2013 |
|
Escherichia coli DH5α |
Hanahan, 1983 |
|
Escherichia coli MG1655 |
Blattner et al., 1997 |
|
Escherichia coli BL21(DE3) |
Jeong et al., 2009 |
|
Staphylococcus aureus RN4220 |
Kreiswirth et al., 1983 |
|
Staphylococcus aureus Newman |
Duthie and Lorenz, 1952 |
|
Staphylococcus aureus ΔhrtB
|
Attia et al., 2010 |
|
Staphylococcus aureus ΔΔsod |
Kehl-Fie et al., 2011 |
|
Staphylococcus aureus ΔkatA
|
Choby et al., 2018 |
|
|
|
|
Chemicals, Peptides, and Recombinant Proteins |
Hemin from porcine |
Sigma-Aldirch |
Cat#51280–5G |
Protoporphyrin IX |
Sigma-Aldrich |
Cat#P8293–1G |
Paraquat dichloride hydrate |
Sigma-Aldrich |
Cat#36541–100MG |
Vancomycin |
Fisher Scientific |
Cat#BP2958 |
Metronidazole |
Fisher Scientific |
Cat#AC210340050 |
Iron (II) sulfate |
Sigma-Aldrich |
Cat#215422–250 |
RQ1 DNase |
Thermo Fisher Scientific |
Cat#M6106 |
Ribolock RNase inhibitor |
Promega |
Cat#EO0381 |
M-MLV reverse transcriptase |
Thermo Fisher Scientific |
Cat#M1705 |
iQ SYBER green supermix |
Biorad |
Cat#1708880 |
HisPur cobalt Resin |
Thermo Fisher Scientific |
Cat#25230 |
HsmR |
This paper |
|
HsmR H50A |
This paper |
|
Cefoperazone |
Sigma-Aldrich |
Cat#C4292 |
SYBR-safe |
Invitrogen |
Cat#S33102
|
Dihydrorhodamine 123 |
Invitrogen |
Cat#DS2806 |
|
|
|
Critical Commercial Assays |
Thrombin Cleancleave kit |
Sigma-Aldrich |
Cat#RECOMT-1KT |
RNeasy Mini Kit |
Qiagen |
Cat#74104 |
Ribo-Zero rRNA removal kit |
Illumina |
Cat#2003715 |
TruSeq RNA library prep kit v2 |
Illumina |
Cat#RS-122–2001 |
|
|
|
Deposited Data |
Raw RNA-sequence data |
This Study |
PRJNA576216 |
|
|
|
Experimental Models: Organisms/Strains |
C57BL/6J mice |
The Jackson Laboratory |
Cat #664 |
|
|
|
Oligonucleotides |
Primers for cloning and qRT-PCR: Table S1
|
|
|
|
|
|
Recombinant DNA |
Plasmids for complementation and expression: Table S2
|
|
|
|
|
|
Software and Algorithms |
TargeTronics algorithm |
Targetrons |
|
PATRIC database |
PATRIC |
Version 3.5.43 |
iTOL |
iTOL |
Version 4 |
PubSEED |
The SEED |
Version 2.0 |
GeneGraphics |
Katlabs |
|
Prism |
Graph Pad |
Version 8.2 |
CLC Genomics Workbench |
Qiagen |
Version 20.0.1 |
HMMER |
EMBL-EBI |
Version 2.41.1 |
MODELLER |
University of California San Francisco |
Version 9.24 |
Canvas X16 |
Canvas |
Version 16 |