Chemokines kill bacteria without triggering antimicrobial resistance by binding anionic phospholipids
Data files
May 22, 2025 version files 14.53 MB
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Figure_1A.prism
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Figure_1B.pzfx
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Figure_3C.pzfx
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Figure_3D.pzfx
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Figure_4B_FACS_files.zip
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Figure_4B.wsp
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Figure_4C.pzfx
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Figure_4D.pzfx
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Figure_4E.pzfx
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Figure_4F.prism
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Figure_4H.pzfx
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Figure_5A.pzfx
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Figure_5B.pzfx
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Figure_5C.pzfx
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Figure_5D_FACS_files.zip
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Figure_5D_quantification.pzfx
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Figure_5D.wsp
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Figure_6A.prism
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Figure_6C.xlsx
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Figure_6D.pzfx
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Figure_6E.prism
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Figure_7C.pzfx
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Figure_7D.pzfx
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Figure_7E.pzfx
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Figure_S3A.pzfx
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Figure_S3B.prism
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Figure_S4.prism
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Figure_S5.prism
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Figure_S6A.prism
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Figure_S6B.prism
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Figure_S7.pzfx
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README.md
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Abstract
Classically, chemokines coordinate leukocyte trafficking; however, many chemokines also possess direct antibacterial activity. Yet, the bacterial killing mechanism of chemokines and the biochemical properties that define which members of the chemokine superfamily are antimicrobial remain poorly understood. We report that the antimicrobial activity of chemokines is defined by their ability to bind phosphatidylglycerol and cardiolipin, two anionic phospholipids commonly found in the bacterial plasma membrane. We show that only chemokines able to bind these two phospholipids kill bacteria and that they exert rapid bacteriostatic and bactericidal effects with a higher potency than the antimicrobial peptide beta-defensin 3. Both biochemical and genetic interference with the chemokine-cardiolipin interaction impaired microbial growth arrest, bacterial killing, and membrane disruption by chemokines. Moreover, unlike conventional antibiotics, E. coli failed to develop resistance when placed under increasing antimicrobial chemokine pressure in vitro. Thus, we have identified cardiolipin and phosphatidylglycerol as novel binding partners for chemokines responsible for chemokine antimicrobial action.
https://doi.org/10.5061/dryad.dbrv15fc5
Description of the data and file structure
These are Excel, Prism files, and original FACS files containing the raw numerical data used to generate the final figures and FACS plots in the manuscript. The imaging data can also be found in the accompanying dataset 10.5061/dryad.m63xsj4c8.
Files and variables
File: Figure_1A.prism
Description: Antimicrobial assays. Surviving number of E. coli colonies 2 h after treatment with increasing doses of protein/chemokine. Columns, treatment protein name. Rows, protein concentration in µM.
File: Figure_3D.pzfx
Description: Antimicrobial assays. Surviving number S. aureus colonies 2 h after treatment with 5 µg/ml of CXCL9 or CXCL11 in the presence of liposomes containing 30% of cardiolipin (CL), phosphatidylglycerol (PG) or phosphatidylethanolamine (PE). Columns, type of liposome. Rows, liposome concentration in µM.
File: Figure_1B.pzfx
Description: Antimicrobial assays. Surviving number of E. coli and S. aureus colonies 2 h after treatment with increasing doses of protein/chemokine. Columns, type (genera) of bacteria. Rows, chemokine concentration in µg/ml.
File: Figure_3C.pzfx
Description: Antimicrobial assays. Surviving number of E. coli colonies 2 h after treatment with 5 µg/ml of CCL20 or CXCL11 in the presence of liposomes containing 30% of cardiolipin (CL), phosphatidylglycerol (PG) or phosphatidylethanolamine (PE). Columns, type of liposome. Rows, liposome concentration in µM.
File: Figure_4C.pzfx
Description: Bacteria binding assays. Quantification of the median fluorescence intensity of the binding of fluorescently-labeled chemokines to W3110 and BKT12 strains of E. coli. Columns, E. coli strain name. Rows, chemokine name.
File: Figure_4E.pzfx
Description: Antimicrobial assays. Surviving number of colonies for W3110 and BKT12 E. coli strains after combination and simultaneous incubation for 2 h with buffer alone or 1.2 µM of chemokine. Columns, E. coli strain name. Rows, treatment/chemokine name.
File: Figure_4F.prism
Description: Antimicrobial assays. Surviving percentage of colonies for BW25113 and JW1241 E. coli strains 2 h after treatment with 1.2 µM of chemokine. Columns, E. coli strain name. Rows, treatment/chemokine name.
File: Figure_4D.pzfx
Description: Antimicrobial assays. Surviving percentage of colonies for W3110 and BKT12 E. coli strains 2 h after treatment with 1.2 µM of chemokine. Columns, E. coli strain name.
File: Figure_4H.pzfx
Description: Outer membrane permeabilization assay. Kinetics of the percentage of N-phenyl-1-phenylnapthylamine (NPN) fluorescence in W3110 and BKT12 E. coli strains treated (columns) with buffer alone, protamine, polymyxin B (PolB) or the chemokines CXCL9 and CXCL8, relative to the maximum fluorescence read measured after PolB treatment. Rows, time in minutes.
File: Figure_5B.pzfx
Description: Bacterial plasma membrane integrity assay. Kinetics of the percentage of W3110 and BKT12 E. coli strains positive for SYTOX after treatment with 1.2 µM of human beta-defensin 3 (hBD3) or chemokines. Columns, E. coli strain name. Rows, time in minutes.
File: Figure_5A.pzfx
Description: Bacterial growth assay. Kinetics of the growth of W3110 and BKT12 E. coli strains in the presence of buffer alone or 1.2 µM of human beta-defensin 3 (hBD3) or chemokines. Columns, E. coli strain name treated with buffer or chemokine. Rows, time in minutes.
File: Figure_5D_quantification.pzfx
Description: Bacterial plasma membrane integrity assay. Quantification of the percentage of SYTOX-positive W3110 and BKT12 E. coli strains 20 min after treatment with 4.8 µM of protamine or chemokines. Columns, E. coli strain name. Rows, treatment/chemokine name (Ptm, protamine).
File: Figure_5C.pzfx
Description: Bacterial growth and killing assay. Quantification of the percentage of live (SYTOX-negative) and killed (SYTOX-positive) W3110 and BKT12 E. coli strains 1 h and 2 h after treatment with increasing doses of CXCL11 or CCL21. Columns, E. coli strain name live or killed. Rows, chemokine concentration in µM.
File: Figure_6A.prism
Description: Calcein leakage assays. Kinetics of the percentage of calcein released from phophatidylethanolamine (PE) /phosphatidylglycerol (PG) /cardiolipin (CL) (70/25/5 mass ratio) liposomes in the presence of 1.2 µM protamine or chemokine relative to the maximum release detected after addition of Triton X-100. Columns, treatment/chemokine name. Rows, time in minutes.
File: Figure_6C.xlsx
Description: Liposome SAXS assays. Peak positions (√) for the cubic phases (Pn3m, lm3m, and la3d) and mean negative gaussian curvature (k) detected by SAXS of phosphatidylglycerol/phosphatidylethamolamine (20:80 mass ratio) liposomes in the presence of increasing chemokine:liposome ratios. Blank cells indicate the absence of a cubic phase. Columns, type of cubic phase. Rows, chemokine name and chemokine:liposome ratio.
File: Figure_6D.pzfx
Description: Calcein leakage assays. Kinetics of the percentage of calcein released from phophatidylethanolamine (PE) /phosphatidylglycerol (PG) /cardiolipin (CL) (70/25/5 mass ratio), PE/PG (70/30 mass ratio) or PE/phosphatidylcholine (PC) (70/30 mass ratio) liposomes in the presence of 1.2 µM protamine or chemokine relative to the maximum release detected after addition of Triton X-100. Columns, type of liposome. Rows, time in minutes.
File: Figure_7C.pzfx
Description: Minimum inhibitory concentration assay. Percentage of E. coli viability determined using the BacTiter-Glo kit after 18 h incubation with increasing doses of recombinant CCL20-His protein. Column, E. coli strain name. Rows, protein concentration in µM.
File: Figure_6E.prism
Description: Calcein leakage assays. Quantification of the percentage of calcein released from phophatidylethanolamine (PE) /phosphatidylglycerol (PG) /cardiolipin (CL) (70/25/5 mass ratio), PE/PG (70/30 mass ratio) or PE/phosphatidylcholine (PC) (70/30 mass ratio) liposomes 20 min after addition of increasing doses of protamine or the chemokines CCL21 and CXCL9 relative to the maximum release detected after addition of Triton X-100. Columns, type of liposome. Rows, protein concentration in µM.
File: Figure_7D.pzfx
Description: Antimicrobial resistance assay. Fold change of the minimum inhibitory concentration (MIC) of ampicillin (Amp), tetracycline (Tet) and recombinant CCL20-His protein relative to their initial MIC after maintenance of E. coli cultures for 14 days in the presence of sublethal (0.5 x MIC) doses of the antimicrobial compounds. Columns, treatment/antimicrobial compound name. Rows, time in days.
File: Figure_7E.pzfx
Description: Antimicrobial assays. Quantification (%) of the viability of the E. coli W3110 strains generated in Figure 7D, preconditioning for 14 days with ampicillin (Amp), tetracycline (Tet) and recombinant CCL20-His, 18 h after treatment with a dose corresponding to the initial minimum inhibitory concentration of each antimicrobial compound. Columns, E. coli strain name. Rows, treatment/antimicrobial compound name.
File: Figure_S4.prism
Description: Bacterial growth assay. Kinetics of the growth of W3110 and BKT12 E. coli strains in the presence of buffer alone or 1.2 µM of protamine. Columns, E. coli strain name treated with protamine or buffer. Rows, time in minutes.
File: Figure_S6B.prism
Description: Calcein leakage assays. Kinetics of the percentage of calcein released from phophatidylethanolamine (PE) /phosphatidylglycerol (PG) /cardiolipin (CL) (70/25/5 mass ratio), PE/PG (70/30 mass ratio) or PE/phosphatidylcholine (PC) (70/30 mass ratio) liposomes in the presence of 0.15 µM protamine or chemokine relative to the maximum release detected after addition of Triton X-100. Columns, type of liposome. Rows, time in minutes.
File: Figure_S3A.pzfx
Description: Antimicrobial assays. Surviving percentage of E. coli colonies after 2 h treatment with 1.2 µM of CCL20, CXCL9 or human beta-defensin 3 (hBD3) in the presence of 0.85 or 85 mM NaCl. Columns, NaCl concentration in mM. Rows, treatment/chemokine name.
File: Figure_S7.pzfx
Description: Antimicrobial assays. Surviving percentage of colonies for E. coli W3110 strain or the ampicillin-resistant strain (W3110-Amp) generated in Figure 7D after 2 h treatment with buffer alone, 1.2 µM of CXCL8 or CXCL9, or 5 µg/ml of ampicillin (Amp). Columns, E. coli strain name. Rows, treatment/chemokine name.
File: Figure_S5.prism
Description: Bacterial plasma membrane integrity assay. Quantification of the percentage of SYTOX-positive W3110 and BKT12 E. coli strains 90 min after treatment with 4.8 µM of protamine (Ptm) or chemokines. Columns, E. coli strain name. Rows, treatment/chemokine name.
File: Figure_S3B.prism
Description: Antimicrobial assays. Surviving percentage of E. coli colonies 2 h after treatment with increasing doses of protein/chemokine in the presence of 85 mM NaCl. Columns, treatment/chemokine name. hBD3, human beta-defensing 3. Rows, protein concentration in µM.
File: Figure_S6A.prism
Description: Antimicrobial assays. Percentage of E. coli viability determined using the BacTiter-Glo kit after 2 h incubation with buffer alone or 1.2 µM of CCL5 or CCL19. Columns, treatment/chemokine name.
File: Figure_5D.wsp
Description: Bacterial plasma membrane integrity assay. FlowJo file with the analysis performed to generate the contour plots of Figure 5D. Bacteria are stained with SYTO24 (FITC filter) and SYTOX-Orange (PE filter).
File: Figure_4B.wsp
Description: Bacteria binding assay. FlowJo file with the analysis performed to generate the chemokine binding histograms of Figure 4B. Bacteria are stained with SYTO24 (FITC filter), SYTOX-Orange (PE filter) and AZ647-labeled chemokines (APC filter). Figure 4B shows chemokine binding to live bacteria (positive for SYTO24+, negative for SYTOX-Orange).
File: Figure_4B_FACS_files.zip
Description: Flow cytometry acquisition files used to generate Figure 4B. These are needed for Figure_4B.wsp.
File: Figure_5D_FACS_files.zip
Description: Flow cytometry acquisition files used to generate Figure 5D. These are needed for Figure_5D.wsp.
