Breaking antimicrobial resistance by disrupting extracytoplasmic protein folding
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, United Kingdom
- Department of Molecular Biosciences, University of Texas at Austin, United States
- Department of Microbiology, Faculty of Biology, Universidad de Sevilla, Spain
- Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, United Kingdom
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, United Kingdom
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, France
- EA7361 “Structure, Dynamics, Function and Expression of Broad-spectrum β-lactamases", Paris-Sud University, LabEx Lermit, Faculty of Medicine, France
- French National Reference Centre for Antibiotic Resistance, France
- Laboratoire de Microbiologie, Institut de Biologie, Université de Neuchâtel, Switzerland
- John Ring LaMontagne Center for Infectious Diseases, University of Texas at Austin, United States
Figures
Figure 1 with 9 supplements
Several antimicrobial resistance mechanisms depend on disulfide bond formation.
(A) DsbA introduces disulfide bonds into extracytoplasmic proteins containing two or more cysteine residues. After each round of oxidative protein folding, DsbA is regenerated by the quinone …
Figure 1—figure supplement 1
Phylogenetic analysis of MCR- and EptA-like enzymes found in Proteobacteria.
A phylogenetic tree was built based on the alignment of 781 sequences from Proteobacteria. The assignment of each sequence to a specific group was done using Hidden Markov Models built from …
Figure 1—figure supplement 2
DsbA dependence is conserved within phylogenetic groups of disulfide-bond-containing β-lactamases.
β-lactam MIC values for E. coli MC1000 expressing disulfide-bond-containing β-lactamases belonging to the same phylogenetic family (Supplementary file 1) are substantially reduced in the absence of …
Figure 1—figure supplement 3
SHV-27 function is dependent on DsbA at temperatures higher than 37°C.
The ESBL SHV-27 differs from the canonical SHV-1 enzyme by a single amino acid substitution (D156G) (Corkill et al., 2001). At 37°C deletion of dsbA does not affect the cefuroxime MIC for E. coli …
Figure 1—figure supplement 4
Complementation of dsbA restores the β-lactam MIC values for E. coli MC1000 dsbA expressing β-lactamases.
Re-insertion of dsbA at the attTn7 site of the chromosome restores the β-lactam MIC values for E. coli MC1000 dsbA harboring (A) pDM1-blaGES-1 (ceftazidime MIC), (B) pDM1-blaOXA-4 (cefuroxime MIC), …
Figure 1—figure supplement 5
Complementation of dsbA restores the colistin MIC values for E. coli MC1000 dsbA expressing MCR enzymes.
Re-insertion of dsbA at the attTn7 site of the chromosome restores the colistin MIC values for E. coli MC1000 dsbA harboring (A) pDM1-mcr-1 (B) pDM1-mcr-3 (C) pDM1-mcr-4 (D) pDM1-mcr-5 (E) pDM1-mcr-8…
Figure 1—figure supplement 6
Gentamicin MIC values for E. coli MC1000 strains expressing MCR enzymes.
Deletion of dsbA does not affect the gentamicin MIC values for E. coli MC1000 strains expressing MCR enzymes, confirming that absence of DsbA does not compromise the general ability of this strain …
Figure 1—figure supplement 7
Deletion of dsbA has no effect on membrane permeability in E. coli MC1000.
(A) Outer membrane integrity assays. (left) The bacterial outer membrane acts as a selective permeability barrier to hydrophobic molecules. Deletion of dsbA has no effect on the outer membrane …
Figure 1—figure supplement 8
Complementation of dsbA restores efflux-pump substrate MIC values for E. coli MG1655 dsbA.
Re-insertion of dsbA at the attTn7 site of the chromosome restores (A) erythromycin, (B) chloramphenicol and (C) nalidixic acid MIC values for MG1655 dsbA. Graphs show MIC values (µg/mL) from two …
Figure 1—figure supplement 9
Deletion of dsbA has no effect on membrane permeability in E. coli MG1655.
(A) Outer membrane integrity assays. (left) The bacterial outer membrane acts as a selective permeability barrier to hydrophobic molecules. Deletion of dsbA has no effect on the outer membrane …
Figure 2
β-lactamase enzymes from most classes become unstable in the absence of DsbA.
(A) Protein levels of disulfide-bond-containing Ambler class A and B β-lactamases are drastically reduced when these enzymes are expressed in E. coli MC1000 dsbA; the amount of the control enzyme …
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Figure 2—source data 1
Original files of the full raw unedited immunoblots used to prepare Figure 2A.
‘Top Panel’ in the file name refers to immunoblots carried out using a Strep-Tactin-AP conjugate, while ‘Bottom Panel’ refers to immunoblots carried out using an anti-DnaK 8E2/2 antibody. ‘Left’ and ‘Right’ in the file names refer to the part of the immunoblot to the left or to the right of the vertical black line shown in the final figure, respectively.
- https://cdn.elifesciences.org/articles/57974/elife-57974-fig2-data1-v2.zip
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Figure 2—source data 2
Uncropped immunoblots used to prepare Figure 2A.
The figure included in the paper is shown in the center and relevant bands used for each part of the figure are marked with color-coded boxes on the uncropped immunoblots.
- https://cdn.elifesciences.org/articles/57974/elife-57974-fig2-data2-v2.zip
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Figure 2—source data 3
Original files of the full raw unedited immunoblots used to prepare Figure 2B.
‘Top Panel’ in the file name refers to immunoblots carried out using a Strep-Tactin-AP conjugate or a Strep-Tactin-HRP conjugate, while ‘Bottom Panel’ refers to immunoblots carried out using an anti-DnaK 8E2/2 antibody. ‘Left’, ‘Middle’, and ‘Right’ in the file names refer to the part of the immunoblot to the left, in-between, or to the right of the vertical black lines shown in the final figure, respectively.
- https://cdn.elifesciences.org/articles/57974/elife-57974-fig2-data3-v2.zip
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Figure 2—source data 4
Uncropped immunoblots used to prepare Figure 2B.
The figure included in the paper is shown in the center and relevant bands used for each part of the figure are marked with color-coded boxes on the uncropped immunoblots.
- https://cdn.elifesciences.org/articles/57974/elife-57974-fig2-data4-v2.zip
Figure 3
MCR enzymes become unstable in the absence of DsbA.
(A) The amounts of MCR proteins are drastically reduced when they are expressed in E. coli MC1000 dsbA; the red arrow indicates the position of the MCR-specific bands. Protein levels of …
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Figure 3—source data 1
Original files of the full raw unedited immunoblots used to prepare Figure 3A for which a Strep-Tactin-AP conjugate and an anti-DnaK 8E2/2 antibody were used.
The file names indicate the lanes of the immunoblot included in the paper that each of these files corresponds to.
- https://cdn.elifesciences.org/articles/57974/elife-57974-fig3-data1-v2.zip
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Figure 3—source data 2
Uncropped immunoblots used to prepare Figure 3A.
The figure included in the paper is shown at the top and relevant bands used for each part of the figure are marked with color-coded boxes on the uncropped immunoblots.
- https://cdn.elifesciences.org/articles/57974/elife-57974-fig3-data2-v2.zip
Figure 4
RND efflux pump function is impaired in the absence of DsbA due to accumulation of unfolded AcrA resulting from insufficient DegP activity (A, B, C).
(A) In the absence of DsbA the pool of active DegP is reduced. In E. coli MG1655 (lane 1), DegP is detected as a single band, corresponding to the intact active enzyme. In E. coli MG1655 dsbA (lane …
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Figure 4—source data 1
Original files of the full raw unedited immunoblots used to prepare Figure 4A.
‘Top Panel’ in the file name refers to immunoblots carried out using an anti-HtrA1 (DegP) antibody, while ‘Bottom Panel’ refers to immunoblots carried out using an anti-DnaK 8E2/2 antibody. ‘Left’ and ‘Right’ in the file names refer to the part of the immunoblot to the left or to the right of the vertical black line shown in the final figure, respectively.
- https://cdn.elifesciences.org/articles/57974/elife-57974-fig4-data1-v2.zip
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Figure 4—source data 2
Uncropped immunoblots used to prepare Figure 4A.
The figure included in the paper is shown in the center and relevant bands used for each part of the figure are marked with color-coded boxes on the uncropped immunoblots.
- https://cdn.elifesciences.org/articles/57974/elife-57974-fig4-data2-v2.zip
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Figure 4—source data 3
Original files of the full raw unedited immunoblots used to prepare Figure 4B.
‘Top Panel’ in the file name refers to immunoblots carried out using an anti-AcrA antibody, while ‘Bottom Panel’ refers to immunoblots carried out using an anti-DnaK 8E2/2 antibody. ‘Left’ and ‘Right’ in the file names refer to the part of the immunoblot to the left or to the right of the vertical black line shown in the final figure, respectively.
- https://cdn.elifesciences.org/articles/57974/elife-57974-fig4-data3-v2.zip
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Figure 4—source data 4
Uncropped immunoblots used to prepare Figure 4B.
The figure included in the paper is shown in the center and relevant bands used for each part of the figure are marked with color-coded boxes on the uncropped immunoblots.
- https://cdn.elifesciences.org/articles/57974/elife-57974-fig4-data4-v2.zip
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Figure 4—source data 5
Original files of the full raw unedited immunoblots used to prepare Figure 4C.
‘Top Panel’ in the file name refers to immunoblots carried out using an anti-TolC antibody, while ‘Bottom Panel’ refers to immunoblots carried out using an anti-DnaK 8E2/2 antibody. ‘Left’ and ‘Right’ in the file names refer to the part of the immunoblot to the left or to the right of the vertical black line shown in the final figure, respectively.
- https://cdn.elifesciences.org/articles/57974/elife-57974-fig4-data5-v2.zip
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Figure 4—source data 6
Uncropped immunoblots used to prepare Figure 4C.
The figure included in the paper is shown in the center and relevant bands used for each part of the figure are marked with color-coded boxes on the uncropped immunoblots.
- https://cdn.elifesciences.org/articles/57974/elife-57974-fig4-data6-v2.zip
Figure 5 with 3 supplements
Chemical inhibition of the DSB system impedes DsbA function in E. coli MC1000 and phenocopies the β-lactam and colistin MIC changes that were observed using a dsbA mutant.
(A) Chemical inhibition of the DSB system impedes flagellar motility in E. coli MC1000. A functional DSB system is necessary for flagellar motility in E. coli because folding of the P-ring component …
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Figure 5—source data 1
Original file of the full raw unedited immunoblot used to prepare Figure 5C, for which an anti-DsbA antibody was used.
- https://cdn.elifesciences.org/articles/57974/elife-57974-fig5-data1-v2.zip
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Figure 5—source data 2
Uncropped immunoblot used to prepare Figure 5C.
The figure included in the paper is shown at the bottom and relevant bands used for each part of the figure are marked with a red box on the uncropped immunoblot.
- https://cdn.elifesciences.org/articles/57974/elife-57974-fig5-data2-v2.zip
Figure 5—figure supplement 1
Gentamicin MIC values for E. coli MC1000 strains expressing MCR enzymes.
Chemical inhibition of the DSB system does not affect the gentamicin MIC values for E. coli MC1000 strains expressing MCR enzymes, confirming that inactivation of DsbA does not compromise the …
Figure 5—figure supplement 2
Chemical inhibition of the DSB system or deletion of dsbA does not compromise the growth of E. coli MC1000.
Growth curves of (A) E. coli MC1000 with and without chemical inhibition of the DSB system and (B) E. coli MC1000 and its dsbA mutant show that bacterial growth remains unaffected by the DSB system …
Figure 5—figure supplement 3
Changes in MIC values observed using the DSB system inhibitor are due solely to inhibition of the DSB system.
(A) E. coli MC1000 harboring pDM1-blaKPC-3 has an imipenem MIC value of 24 μg/mL. Upon chemical inhibition of the DSB system the imipenem MIC for this strain drops to 4 μg/mL, and accordingly the …
Figure 6
Chemical inhibition of the DSB system sensitizes multidrug-resistant clinical isolates to currently available β-lactam antibiotics.
(A) Addition of a small-molecule inhibitor of DsbB results in sensitization of a K. pneumoniae clinical isolate to imipenem. (B) Chemical inhibition of the DSB system in the presence of imipenem …
Figure 7
Chemical inhibition of the DSB system sensitizes multidrug-resistant clinical isolates to colistin.
(A) Addition of a small-molecule inhibitor of DsbB to a colistin-resistant clinical E. coli isolate expressing MCR-1 results in sensitization to colistin. (B) Chemical inhibition of the DSB system …
Figure 8
Absence of the principal DsbA analogue (DsbA1) from P. aeruginosa clinical isolates expressing OXA enzymes sensitizes them to existing β-lactam antibiotics and dramatically increases the survival of infected G. mellonella larvae that undergo antibiotic treatment.
(A) Absence of DsbA1 sensitizes the P. aeruginosa PA43417 clinical isolate expressing OXA-198 to the first-line antibiotic piperacillin. (B) Absence of DsbA1 sensitizes the P. aeruginosa PAe191 …
Tables
Table 1
Overview of the β-lactamase enzymes investigated in this study.
Enzymes GES-1, –2 and –11 as well as KPC-2 and –3 belong to the same phylogenetic cluster (GES-42 and KPC-44, respectively, see Supplementary file 1). All other tested enzymes belong to distinct …
| Enzyme | Amblerclass | Cysteine positions | Mobile | Spectrum | Inhibition |
|---|---|---|---|---|---|
| L2-1 | A | C82 C136 C233 | no | ESBL | yes |
| GES-1 | A | C63 C233 | yes | ESBL | yes |
| GES-2 | A | C63 C233 | yes | ESBL | yes |
| GES-11 | A | C63 C233 | yes | Carbapenemase | yes |
| SHV-27 | A | C73 C119 | no | ESBL | yes |
| OXA-4 | D | C43 C63 | yes | ESBL | yes |
| OXA-10 | D | C44 C51 | yes | ESBL | no (Aubert et al., 2001) |
| OXA-198 | D | C116 C119 | yes | Carbapenemase | no (El Garch et al., 2011) |
| FRI-1 | A | C68 C238 | yes | Carbapenemase | no (Dortet et al., 2015) |
| L1-1 | B3 | C239 C267 | no | Carbapenemase | no (Palzkill, 2013) |
| KPC-2 | A | C68 C237 | yes | Carbapenemase | no (Papp-Wallace et al., 2010) |
| KPC-3 | A | C68 C237 | yes | Carbapenemase | no (Papp-Wallace et al., 2010) |
| SME-1 | A | C72 C242 | no | Carbapenemase | yes |
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Genetic reagent(Escherichia coli) | DH5α | Hanahan and Glover, 1985 | F– endA1 glnV44 thi-1 recA1 relA1 gyrA96 deoR nupG purB20 φ80dlacZ∆M15 ∆(lacZYA-argF)U169 hsdR17(rK–mK+) λ– | - |
| Genetic reagent(Escherichia coli) | CC118λpir | Herrero et al., 1990 | araD Δ(ara, leu) ΔlacZ74 phoA20 galK thi-1 rspE rpoB argE recA1 λpir | - |
| Genetic reagent(Escherichia coli) | HB101 | Boyer and Roulland-Dussoix, 1969 | supE44 hsdS20 recA13 ara-14 proA2 lacY1 galK2 rpsL20 xyl-5 mtl-1 | - |
| Genetic reagent(Escherichia coli) | MC1000 | Casadaban and Cohen, 1980 | araD139 ∆(ara, leu)7697 ∆lacX74 galU galK strA | - |
| Genetic reagent(Escherichia coli) | MC1000 dsbA | Kadokura et al., 2004 | dsbA::aphA, KanR | - |
| Genetic reagent(Escherichia coli) | MC1000 dsbA attTn7::Ptac-dsbA | This study | dsbA::aphA attTn7::dsbA, KanR | Can be obtained from the Mavridou lab |
| Genetic reagent(Escherichia coli) | MG1655 | Blattner et al., 1997 | K-12 F– λ– ilvG– rfb-50 rph-1 | - |
| Genetic reagent(Escherichia coli) | MG1655 dsbA | This study | dsbA::aphA, KanR | Can be obtained from the Mavridou lab |
| Genetic reagent(Escherichia coli) | MG1655 dsbA attTn7::Ptac-dsbA | This study | dsbA::aphA attTn7::dsbA, KanR | Can be obtained from the Mavridou lab |
| Genetic reagent(Escherichia coli) | MG1655 acrA | This study | acrA | Can be obtained from the Mavridou lab |
| Genetic reagent(Escherichia coli) | MG1655 tolC | This study | tolC | Can be obtained from the Mavridou lab |
| Genetic reagent(Escherichia coli) | MG1655 degP | This study | degP::strAB, StrR | Can be obtained from the Mavridou lab |
| Strain, strain background (Escherichia coli) | BM16 | Dortet et al., 2014 | blaTEM-1bblaKPC-2 | Human clinical strain |
| Strain, strain background (Escherichia coli) | LIL-1 | Dortet et al., 2014 | blaTEM-1blaOXA-9 blaKPC-2 | Human clinical strain |
| Strain, strain background (Escherichia coli) | CNR1790 | Dortet et al., 2018 | blaTEM-15 mcr-1 | Human clinical strain |
| Strain, strain background (Escherichia coli) | CNR20140385 | Dortet et al., 2018 | blaOXA-48mcr-1 | Human clinical strain |
| Strain, strain background (Escherichia coli) | WI2 (ST1288) | Beyrouthy et al., 2017 | blaOXA-48blaKPC-28 mcr-1 | Human clinical strain |
| Strain, strain background (Escherichia coli) | 1073944 (ST117) | Wise et al., 2018 | mcr-1 | Human clinical strain |
| Strain, strain background (Escherichia coli) | 41,489 | Dortet et al., 2018 | mcr-1 | Human clinical strain |
| Strain, strain background (Escherichia coli) | - | Dortet et al., 2018 | mcr-1 | Human clinical strain |
| Strain, strain background (Escherichia coli) | 1256822 (ST48) | Wise et al., 2018 | mcr-1.5 | Human clinical strain |
| Strain, strain background (Escherichia coli) | 27,841 (ST744) | Haenni et al., 2018 | blaCTX-M-55mcr-3.2 | Environmental strain from livestock |
| Strain, strain background (Escherichia coli) | 1144230 (ST641) | Wise et al., 2018 | blaCMY-2mcr-5 | Human clinical strain |
| Strain, strain background (Klebsiella pneumoniae) | ST234 | Nordmann et al., 2012 | blaSHV-27blaKPC-2 | Human clinical strain |
| Strain, strain background (Citrobacter freundii) | BM19 | Dortet et al., 2014 | blaKPC-2 | Human clinical strain |
| Strain, strain background (Enterobacter cloacae) | DUB | Dortet et al., 2015 | blaFRI-1 | Human clinical strain |
| Strain, strain background (Pseudomonas aeruginosa) | PA43417 | El Garch et al., 2011 | blaOXA-198 | Human clinical strain |
| Genetic reagent (Pseudomonas aeruginosa) | PA43417 | This study | dsbA1 blaOXA-198 | Can be obtained from the Mavridou lab |
| Strain, strain background (Pseudomonas aeruginosa) | PAe191 | Mugnier et al., 1998 | blaOXA-19 | Human clinical strain |
| Genetic reagent (Pseudomonas aeruginosa) | PAe191 | This study | dsbA1 blaOXA-19 | Can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1 (plasmid) | Lab stock | GenBank MN128719 | pDM1 vector, p15A ori, Ptac promoter, MCS, TetR |
| Recombinant DNA reagent | pDM1-blaL2-1 (plasmid) | This study | - | blaL2-1 cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-blaGES-1 (plasmid) | This study | - | blaGES-1 cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-blaGES-2 (plasmid) | This study | - | blaGES-2 cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-blaGES-11 (plasmid) | This study | - | blaGES-11 cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-blaSHV-27 (plasmid) | This study | - | blaSHV-27 cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-blaOXA-4 (plasmid) | This study | - | blaOXA-4 cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-blaOXA-10 (plasmid) | This study | - | blaOXA-10 cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-blaOXA-198 (plasmid) | This study | - | blaOXA-198 cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-blaFRI-1 (plasmid) | This study | - | blaFRI-1 cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-blaL1-1 (plasmid) | This study | - | blaL1-1 cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-blaKPC-2 (plasmid) | This study | - | blaKPC-2 cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-blaKPC-3 (plasmid) | This study | - | blaKPC-3 cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-blaSME-1 (plasmid) | This study | - | blaSME-1 cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-mcr-1 (plasmid) | This study | - | mcr-1 cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-mcr-3 (plasmid) | This study | - | mcr-3 cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-mcr-4 (plasmid) | This study | - | mcr-4 cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-mcr-5 (plasmid) | This study | - | mcr-5 cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-mcr-8 (plasmid) | This study | - | mcr-8 cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-blaL2-1-StrepII (plasmid) | This study | - | blaL2-1 encoding L2-1 with a C-terminal StrepII tag cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-blaGES-1-StrepII (plasmid) | This study | - | blaGES-1 encoding GES-1 with a C-terminal StrepII tag cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-StrepII-blaOXA-4 (plasmid) | This study | - | blaOXA-4 encoding OXA-4 with an N-terminal StrepII tag cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-blaOXA-10-StrepII (plasmid) | This study | - | blaOXA-10 encoding OXA-10 with a C-terminal StrepII tag cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-blaOXA-198-StrepII (plasmid) | This study | - | blaOXA-198 encoding OXA-198 with a C-terminal StrepII tag cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-blaFRI-1-StrepII (plasmid) | This study | - | blaFRI-1 encoding FRI-1 with a C-terminal StrepII tag cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-blaL1-1-StrepII (plasmid) | This study | - | blaL1-1 encoding L1-1 with a C-terminal StrepII tag cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-blaKPC-3-StrepII (plasmid) | This study | - | blaKPC-3 encoding KPC-3 with a C-terminal StrepII tag cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-mcr-1-StrepII (plasmid) | This study | - | blaMCR-1 encoding MCR-1 with a C-terminal StrepII tag cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-mcr-3-StrepII (plasmid) | This study | - | blaMCR-3 encoding MCR-3 with a C-terminal StrepII tag cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-mcr-4-StrepII (plasmid) | This study | - | blaMCR-4 encoding MCR-4 with a C-terminal StrepII tag cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-mcr-5-StrepII (plasmid) | This study | - | blaMCR-5 encoding MCR-5 with a C-terminal StrepII tag cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pDM1-mcr-8-StrepII (plasmid) | This study | - | blaMCR-8 encoding MCR-8 with a C-terminal StrepII tag cloned into pDM1, TetR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pGRG25 (plasmid) | McKenzie and Craig, 2006 | - | Encodes a Tn7 transposon and tnsABCD under the control of ParaB, thermosensitive pSC101 ori, AmpR |
| Recombinant DNA reagent | pGRG25-Ptac::dsbA (plasmid) | This study | - | Ptac::dsbA fragment cloned within the Tn7 of pGRG25; when inserted into the chromosome and the plasmid cured, the strain expresses DsbA upon IPTG induction, AmpR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pSLTS (plasmid) | Kim et al., 2014 | - | Thermosensitive pSC101ori, ParaB for λ-Red, PtetR for I-SceI, AmpR |
| Recombinant DNA reagent | pUltraGFP-GM (plasmid) | Mavridou et al., 2016 | - | Constitutive sfGFP expression from a strong Biofab promoter, p15A ori, (template for the accC cassette), GentR |
| Recombinant DNA reagent | pKD4 (plasmid) | Datsenko and Wanner, 2000 | - | Conditional oriRγ ori, (template for the aphA cassette), AmpR |
| Recombinant DNA reagent | pCB112 (plasmid) | Paradis-Bleau et al., 2014 | - | Inducible lacZ expression under the control of the Plac promoter, pBR322 ori, CamR |
| Recombinant DNA reagent | pKNG101 (plasmid) | Kaniga et al., 1991 | - | Gene replacement suicide vector, oriR6K, oriTRK2, sacB, (template for the strAB cassette), StrR |
| Recombinant DNA reagent | pKNG101-dsbA1 (plasmid) | This study | - | PCR fragment containing the regions upstream and downstream P. aeruginosa dsbA1 cloned in pKNG101; when inserted into the chromosome the strain is a merodiploid for dsbA1 mutant, StrR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pRK600 (plasmid) | Kessler et al., 1992 | - | Helper plasmid, ColE1 ori, mobRK2, traRK2, CamR |
| Recombinant DNA reagent | pMA-T mcr-3 (plasmid) | This study | - | GeneArt cloning vector containing mcr-3, ColE1 ori, (template for mcr-3), AmpR; can be obtained from the Mavridou lab |
| Recombinant DNA reagent | pMK-T mcr-8 (plasmid) | This study | - | GeneArt cloning vector containing mcr-8, ColE1 ori, (template for mcr-8), KanR; can be obtained from the Mavridou lab |
| Chemical compound, drug | Ampicillin | Melford | A40040-10.0 | - |
| Chemical compound, drug | Piperacillin | Melford | P55100-1.0 | - |
| Chemical compound, drug | Cefuroxime | Melford | C56300-1.0 | - |
| Chemical compound, drug | Ceftazidime | Melford | C59200-5.0 | - |
| Chemical compound, drug | Imipenem | Cambridge Bioscience | CAY16039-100 mg | - |
| Chemical compound, drug | Aztreonam | Cambridge Bioscience | CAY19784-100 mg | - |
| Chemical compound, drug | Kanamycin | Gibco | 11815032 | - |
| Chemical compound, drug | Gentamicin | VWR | A1492.0025 | - |
| Chemical compound, drug | Streptomycin | ACROS Organics | AC612240500 | - |
| Chemical compound, drug | Tetracycline | Duchefa Biochemie | T0150.0025 | - |
| Chemical compound, drug | Colistin sulphate | Sigma | C4461-1G | - |
| Chemical compound, drug | Tazobactam | Sigma | T2820-10MG | - |
| Chemical compound, drug | Isopropyl β-D-1-thiogalactopyranoside (IPTG) | Melford | I56000-25.0 | - |
| Chemical compound, drug | KOD Hotstart DNA Polymerase | Sigma | 71086–3 | - |
| Chemical compound, drug | Nitrocefin | Abcam | ab145625-25mg | - |
| Chemical compound, drug | 1-N-phenylnaphthylamine (NPN) | Acros Organics | 147160250 | - |
| Chemical compound, drug | 4-acetamido-4ˊ-maleimidyl-stilbene-2,2ˊ-disulfonic acid (AMS) | ThermoFisher Scientific | A485 | - |
| Chemical compound, drug | 4,5-dichloro-2-(2-chlorobenzyl)pyridazin-3-one | Enamine | EN300-173996 | - |
| Commercial assay or kit | BugBuster Mastermix | Sigma | 71456–3 | - |
| Commercial assay or kit | Novex ECL HRP chemiluminescent substrate reagent kit | ThermoFisher Scientific | WP20005 | - |
| Commercial assay or kit | SigmaFast BCIP/NBT tablets | Sigma | B5655-25TAB | - |
| Commercial assay or kit | Immobilon Crescendo chemiluminescent reagent | Sigma | WBLUR0100 | - |
| Commercial assay or kit | ETEST - Amoxicillin | Biomerieux | 412,242 | - |
| Commercial assay or kit | ETEST - Cefuroxime | Biomerieux | 412,304 | - |
| Commercial assay or kit | ETEST - Ceftazidime | Biomerieux | 412,292 | - |
| Commercial assay or kit | ETEST - Imipenem | Biomerieux | 412,373 | - |
| Commercial assay or kit | ETEST - Aztreonam | Biomerieux | 412,258 | - |
| Commercial assay or kit | ETEST - Gentamicin | Biomerieux | 412,367 | - |
| Commercial assay or kit | ETEST - Erythromycin | Biomerieux | 412,333 | - |
| Commercial assay or kit | ETEST - Chloramphenicol | Biomerieux | 412,308 | - |
| Commercial assay or kit | ETEST - Nalidixic acid | Biomerieux | 516,540 | - |
| Commercial assay or kit | ETEST - Ciprofloxacin | Biomerieux | 412,310 | - |
| Commercial assay or kit | ETEST - Nitrofurantoin | Biomerieux | 530,440 | - |
| Commercial assay or kit | ETEST - Trimethoprim | Biomerieux | 412,482 | - |
| Antibody | Strep-Tactin-HRP conjugate (mouse monoclonal) | Iba Lifesciences | NC9523094 | (1:3,000) in 3 w/v % BSA/TBS-T |
| Antibody | Strep-Tactin-AP conjugate (mouse monoclonal) | Iba Lifesciences | NC0485490 | (1:3,000) in 3 w/v % BSA/TBS-T |
| Antibody | anti-DsbA(rabbit polyclonal) | Beckwith lab | - | (1:1,000) in 5 w/v % skimmed milk/TBS-T |
| Antibody | anti-AcrA(rabbit polyclonal) | Koronakis lab | - | (1:10,000) in 5 w/v % skimmed milk/TBS-T |
| Antibody | anti-TolC(rabbit polyclonal) | Koronakis lab | - | (1:5,000) in 5 w/v % skimmed milk/TBS-T |
| Antibody | anti-HtrA1 (DegP)(rabbit polyclonal) | Abcam | ab231195 | (1:1,000) in 5 w/v % skimmed milk/TBS-T |
| Antibody | anti-DnaK 8E2/2(mouse monoclonal) | Enzo Life Sciences | ADI-SPA-880-D | (1:10,000) in 5% w/v skimmed milk/TBS-T |
| Antibody | anti-rabbit IgG-AP conjugate (goat polyclonal) | Sigma | A3687-.25ML | (1:6,000) in 5% w/v skimmed milk/TBS-T |
| Antibody | anti-rabbit IgG-HRP conjugate (goat polyclonal) | Sigma | A0545-1ML | (1:6,000) in 5% w/v skimmed milk/TBS-T |
| Antibody | anti-mouse IgG-AP conjugate (goat polyclonal) | Sigma | A3688-.25ML | (1:6,000) in 5% w/v skimmed milk/TBS-T |
| Antibody | anti-mouse IgG-HRP conjugate (goat polyclonal) | Sigma | A4416-.5ML | (1:6,000) in 5% w/v skimmed milk/TBS-T |
| Software, algorithm | FlowJo | Tree Star | - | version 10.0.6 |
| Software, algorithm | Adobe Photoshop CS4 | Adobe | - | extended version 11.0 |
| Software, algorithm | Prism | GraphPad | - | version 8.0.2 |
| Software, algorithm | blastp | Altschul et al., 1990 | - | version 2.2.28+ |
| Software, algorithm | USEARCH | Edgar, 2010 | - | version 7.0 |
| Software, algorithm | MUSCLE | Edgar, 2004 | - | - |
| Software, algorithm | FastTree | Price et al., 2010 | - | version 2.1.7 |
| Software, algorithm | HMMER | Finn et al., 2015 | - | version 3.1b2 |
Additional files
-
Supplementary file 1
Analysis of the cysteine content and phylogeny of all identified β-lactamases.
6,649 unique β-lactamase protein sequences were clustered with a 90% identity threshold and the centroid of each cluster was used as a phylogenetic cluster identified for each sequence (“Phylogenetic cluster” column). All sequences were searched for the presence of cysteine residues (“Total number of cysteines” and “Positions of all cysteines” columns). Proteins with two or more cysteines after the first 30 amino acids of their primary sequence (cells shaded in grey in the “Number of cysteines after position 30” column) are potential substrates of the DSB system for organisms where oxidative protein folding is carried out by DsbA and provided that translocation of the β-lactamase outside the cytoplasm is performed by the Sec system. The first 30 amino acids of each sequence were excluded to avoid considering cysteines that are part of the signal sequence mediating the translocation of these enzymes outside the cytoplasm. Cells shaded in grey in the “Reported in pathogens” column mark β-lactamases that are found in pathogens or organisms capable of causing opportunistic infections. The Ambler class of each enzyme is indicated in the “Ambler class column” and each class (A, B1, B2, B3, C and D) is highlighted with a different color.
- https://cdn.elifesciences.org/articles/57974/elife-57974-supp1-v2.xlsx
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Supplementary file 2
MIC data used to generate Figure 1B, Figure 1—figure supplement 2, and Figure 5B.
Cells that are shaded in grey represent strain-antibiotic combinations that were not tested. The aminoglycoside antibiotic gentamicin serves as a control for all strains. For the “Supplementary File 2a” tab, values are representative of three biological experiments each conducted as a single technical repeat, and for the “Supplementary File 2b” tab, values are representative of two biological experiments each conducted as a single technical repeat.
- https://cdn.elifesciences.org/articles/57974/elife-57974-supp2-v2.xlsx
-
Supplementary file 3
Supplementary tables 1-6 and relevant citations.
- https://cdn.elifesciences.org/articles/57974/elife-57974-supp3-v2.docx
-
Transparent reporting form
- https://cdn.elifesciences.org/articles/57974/elife-57974-transrepform1-v2.docx
