1
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Subedi K, Roy PC, Saiz B, Basile F, Wall D. Cell-cell transfer of adaptation traits benefits kin and actor in a cooperative microbe. Proc Natl Acad Sci U S A 2024; 121:e2402559121. [PMID: 39012831 DOI: 10.1073/pnas.2402559121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 06/14/2024] [Indexed: 07/18/2024] Open
Abstract
Microbes face many physical, chemical, and biological insults from their environments. In response, cells adapt, but whether they do so cooperatively is poorly understood. Here, we use a model social bacterium, Myxococcus xanthus, to ask whether adapted traits are transferable to naïve kin. To do so we isolated cells adapted to detergent stresses and tested for trait transfer. In some cases, strain-mixing experiments increased sibling fitness by transferring adaptation traits. This cooperative behavior depended on a kin recognition system called outer membrane exchange (OME) because mutants defective in OME could not transfer adaptation traits. Strikingly, in mixed stressed populations, the transferred trait also benefited the adapted (actor) cells. This apparently occurred by alleviating a detergent-induced stress response in kin that otherwise killed actor cells. Additionally, this adaptation trait when transferred also conferred resistance against a lipoprotein toxin delivered to targeted kin. Based on these and other findings, we propose a model for stress adaptation and how OME in myxobacteria promotes cellular cooperation in response to environmental stresses.
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Affiliation(s)
- Kalpana Subedi
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071
- Department of Chemistry, University of Wyoming, Laramie, WY 82071
| | - Pravas C Roy
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071
| | - Brandon Saiz
- Department of Chemistry, University of Wyoming, Laramie, WY 82071
| | - Franco Basile
- Department of Chemistry, University of Wyoming, Laramie, WY 82071
| | - Daniel Wall
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071
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2
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Wei L, Han Y, Zheng J, Xu X, Zhu L. Accelerated dissemination of antibiotic resistant genes via conjugative transfer driven by deficient denitrification in biochar-based biofiltration systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 934:173268. [PMID: 38754503 DOI: 10.1016/j.scitotenv.2024.173268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/25/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
Biofiltration systems harbored and disseminated antibiotic resistance genes (ARGs), when confronting antibiotic-contained wastewater. Biochar, a widely used environmental remediation material, can mitigate antibiotic stress on adjoining microbes by lowering the availability of sorbed antibiotics, and enhance the attachment of denitrifiers. Herein, bench-scale biofiltration systems, packed with commercial biochars, were established to explore the pivotal drivers affecting ARG emergence. Results showed that biofiltration columns, achieving higher TN removal and denitrification capacity, showed a significant decrease in ARG accumulation (p < 0.05). The relative abundance of ARGs (0.014 ± 0.0008) in the attached biofilms decreased to 1/5-folds of that in the control group (0.065 ± 0.004). Functional analysis indicated ARGs' accumulation was less attributed to ARG activation or horizontal gene transfer (HGT) driven by sorbed antibiotics. Most denitrifiers, like Bradyrhizobium, Geothrix, etc., were found to be enriched and host ARGs. Nitrosative stress from deficient denitrification was demonstrated to be the dominant driver for affecting ARG accumulation and dissemination. Metagenomic and metaproteomic analysis revealed that nitrosative stress promoted the conjugative HGT of ARGs mainly via increasing the transmembrane permeability and enhancing the amino acid transport and metabolism, such as cysteine, methionine, and valine metabolism. Overall, this study highlighted the risks of deficient denitrification in promoting ARG transfer and transmission in biofiltration systems and natural ecosystems.
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Affiliation(s)
- Lecheng Wei
- Institute of Environment Pollution Control and Treatment, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; Innovation Center of Yangtze River Delta, Zhejiang University
| | - Yutong Han
- Institute of Environment Pollution Control and Treatment, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; Innovation Center of Yangtze River Delta, Zhejiang University
| | - Jingjing Zheng
- Institute of Environment Pollution Control and Treatment, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; Innovation Center of Yangtze River Delta, Zhejiang University
| | - Xiangyang Xu
- Institute of Environment Pollution Control and Treatment, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058, China; Zhejiang Provincial Engineering Laboratory of Water Pollution Control, Hangzhou 310058, China
| | - Liang Zhu
- Institute of Environment Pollution Control and Treatment, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058, China; Zhejiang Provincial Engineering Laboratory of Water Pollution Control, Hangzhou 310058, China; Innovation Center of Yangtze River Delta, Zhejiang University.
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3
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Guo X, Zhao X, Lu X, Zhao L, Zeng Q, Chen F, Zhang Z, Xu M, Feng S, Fan T, Wei W, Zhang X, Pang J, You X, Song D, Wang Y, Jiang J. A deep learning-driven discovery of berberine derivatives as novel antibacterial against multidrug-resistant Helicobacter pylori. Signal Transduct Target Ther 2024; 9:183. [PMID: 38972904 PMCID: PMC11228022 DOI: 10.1038/s41392-024-01895-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 05/17/2024] [Accepted: 06/14/2024] [Indexed: 07/09/2024] Open
Abstract
Helicobacter pylori (H. pylori) is currently recognized as the primary carcinogenic pathogen associated with gastric tumorigenesis, and its high prevalence and resistance make it difficult to tackle. A graph neural network-based deep learning model, employing different training sets of 13,638 molecules for pre-training and fine-tuning, was aided in predicting and exploring novel molecules against H. pylori. A positively predicted novel berberine derivative 8 with 3,13-disubstituted alkene exhibited a potency against all tested drug-susceptible and resistant H. pylori strains with minimum inhibitory concentrations (MICs) of 0.25-0.5 μg/mL. Pharmacokinetic studies demonstrated an ideal gastric retention of 8, with the stomach concentration significantly higher than its MIC at 24 h post dose. Oral administration of 8 and omeprazole (OPZ) showed a comparable gastric bacterial reduction (2.2-log reduction) to the triple-therapy, namely OPZ + amoxicillin (AMX) + clarithromycin (CLA) without obvious disturbance on the intestinal flora. A combination of OPZ, AMX, CLA, and 8 could further decrease the bacteria load (2.8-log reduction). More importantly, the mono-therapy of 8 exhibited comparable eradication to both triple-therapy (OPZ + AMX + CLA) and quadruple-therapy (OPZ + AMX + CLA + bismuth citrate) groups. SecA and BamD, playing a major role in outer membrane protein (OMP) transport and assembling, were identified and verified as the direct targets of 8 by employing the chemoproteomics technique. In summary, by targeting the relatively conserved OMPs transport and assembling system, 8 has the potential to be developed as a novel anti-H. pylori candidate, especially for the eradication of drug-resistant strains.
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Affiliation(s)
- Xixi Guo
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, China
| | - Xiaosa Zhao
- School of Information Science and Technology, Northeast Normal University, Changchun, 130117, China
| | - Xi Lu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, China
| | - Liping Zhao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, China
| | - Qingxuan Zeng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, China
| | - Fenbei Chen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, China
| | - Zhimeng Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, China
| | - Mengyi Xu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, China
| | - Shijiao Feng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, China
| | - Tianyun Fan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, China
| | - Wei Wei
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, China
| | - Xin Zhang
- Department of Pharmacy, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, 272029, Shandong, China
| | - Jing Pang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, China.
| | - Xuefu You
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, China.
| | - Danqing Song
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, China.
| | - Yanxiang Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, China.
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, 230601, Anhui, China.
| | - Jiandong Jiang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, China
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4
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Watanabe N, Savchenko A. Molecular insights into the initiation step of the Rcs signaling pathway. Structure 2024:S0969-2126(24)00221-1. [PMID: 38964336 DOI: 10.1016/j.str.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/05/2024] [Accepted: 06/07/2024] [Indexed: 07/06/2024]
Abstract
The Rcs pathway is repressed by the inner membrane protein IgaA under non-stressed conditions. This repression is hypothesized to be relieved by the binding of the outer membrane-anchored RcsF to IgaA. However, the precise mechanism by which RcsF binding triggers the signaling remains unclear. Here, we present the 1.8 Å resolution crystal structure capturing the interaction between IgaA and RcsF. Our comparative structural analysis, examining both the bound and unbound states of the periplasmic domain of IgaA (IgaAp), highlights rotational flexibility within IgaAp. Conversely, the conformation of RcsF remains unchanged upon binding. Our in vivo and in vitro studies do not support the model of a stable complex involving RcsF, IgaAp, and RcsDp. Instead, we demonstrate that the elements beyond IgaAp play a role in the interaction between IgaA and RcsD. These findings collectively allow us to propose a potential mechanism for the signaling across the inner membrane through IgaA.
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Affiliation(s)
- Nobuhiko Watanabe
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada; Center for Structural Biology for Infectious Diseases (CSBID) Chicago, IL, USA
| | - Alexei Savchenko
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada; Center for Structural Biology for Infectious Diseases (CSBID) Chicago, IL, USA.
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5
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Gerken H, Shetty D, Kern B, Kenney LJ, Misra R. Effects of pleiotropic ompR and envZ alleles of Escherichia coli on envelope stress and antibiotic sensitivity. J Bacteriol 2024; 206:e0017224. [PMID: 38809006 DOI: 10.1128/jb.00172-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 05/06/2024] [Indexed: 05/30/2024] Open
Abstract
The EnvZ-OmpR two-component system of Escherichia coli regulates the expression of the ompF and ompC porin genes in response to medium osmolarity. However, certain mutations in envZ confer pleiotropy by affecting the expression of genes of the iron and maltose regulons not normally controlled by EnvZ-OmpR. In this study, we obtained two novel envZ and ompR pleiotropic alleles, envZT15P and ompRL19Q, among revertants of a mutant with heightened envelope stress and an outer membrane (OM) permeability defect. Unlike envZ, pleiotropic mutations in ompR have not been described previously. The mutant alleles reduced the expression of several outer membrane proteins (OMPs), overcame the temperature-sensitive growth defect of a protease-deficient (ΔdegP) strain, and lowered envelope stress and OM permeability defects in a background lacking the BamB protein of an essential β-barrel assembly machinery complex. Biochemical analysis showed OmpRL19Q, like wild-type OmpR, is readily phosphorylated by EnvZ, but the EnvZ-dependent dephosphorylation of OmpRL19Q~P was drastically impaired compared to wild-type OmpR. This defect would lead to a prolonged half-life for OmpRL19Q~P, an outcome remarkably similar to what we had previously described for EnvZR397L, resulting in pleiotropy. By employing null alleles of the OMP genes, it was determined that the three pleiotropic alleles lowered envelope stress by reducing OmpF and LamB levels. The absence of LamB was principally responsible for lowering the OM permeability defect, as assessed by the reduced sensitivity of a ΔbamB mutant to vancomycin and rifampin. Possible mechanisms by which novel EnvZ and OmpR mutants influence EnvZ-OmpR interactions and activities are discussed.IMPORTANCEMaintenance of the outer membrane (OM) integrity is critical for the survival of Gram-negative bacteria. Several envelope homeostasis systems are activated when OM integrity is perturbed. Through the isolation and characterization of novel pleiotropic ompR/envZ alleles, this study highlights the involvement of the EnvZ-OmpR two-component system in lowering envelope stress and the OM permeability defect caused by the loss of proteins that are involved in OM biogenesis, envelope homeostasis, and structural integrity.
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Affiliation(s)
- Henri Gerken
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Dasvit Shetty
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Brea Kern
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Linda J Kenney
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
- Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Rajeev Misra
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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6
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Ravi J, Anantharaman V, Chen SZ, Brenner EP, Datta P, Aravind L, Gennaro ML. The phage shock protein (PSP) envelope stress response: discovery of novel partners and evolutionary history. mSystems 2024; 9:e0084723. [PMID: 38809013 PMCID: PMC11237479 DOI: 10.1128/msystems.00847-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 03/20/2024] [Indexed: 05/30/2024] Open
Abstract
Bacterial phage shock protein (PSP) systems stabilize the bacterial cell membrane and protect against envelope stress. These systems have been associated with virulence, but despite their critical roles, PSP components are not well characterized outside proteobacteria. Using comparative genomics and protein sequence-structure-function analyses, we systematically identified and analyzed PSP homologs, phyletic patterns, domain architectures, and gene neighborhoods. This approach underscored the evolutionary significance of the system, revealing that its core protein PspA (Snf7 in ESCRT outside bacteria) was present in the last universal common ancestor and that this ancestral functionality has since diversified into multiple novel, distinct PSP systems across life. Several novel partners of the PSP system were identified: (i) the Toastrack domain, likely facilitating assembly of sub-membrane stress-sensing and signaling complexes, (ii) the newly defined HTH-associated α-helical signaling domain-PadR-like transcriptional regulator pair system, and (iii) multiple independent associations with ATPase, CesT/Tir-like chaperone, and Band-7 domains in proteins thought to mediate sub-membrane dynamics. Our work also uncovered links between the PSP components and other domains, such as novel variants of SHOCT-like domains, suggesting roles in assembling membrane-associated complexes of proteins with disparate biochemical functions. Results are available at our interactive web app, https://jravilab.org/psp.IMPORTANCEPhage shock proteins (PSP) are virulence-associated, cell membrane stress-protective systems. They have mostly been characterized in Proteobacteria and Firmicutes. We now show that a minimal PSP system was present in the last universal common ancestor that evolved and diversified into newly identified functional contexts. Recognizing the conservation and evolution of PSP systems across bacterial phyla contributes to our understanding of stress response mechanisms in prokaryotes. Moreover, the newly discovered PSP modularity will likely prompt new studies of lineage-specific cell envelope structures, lifestyles, and adaptation mechanisms. Finally, our results validate the use of domain architecture and genetic context for discovery in comparative genomics.
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Affiliation(s)
- Janani Ravi
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Vivek Anantharaman
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, USA
| | - Samuel Zorn Chen
- Computer Science Engineering Undergraduate Program, Michigan State University, East Lansing, Michigan, USA
| | - Evan Pierce Brenner
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Pratik Datta
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - L. Aravind
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, USA
| | - Maria Laura Gennaro
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey, USA
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7
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Rai AK, Sawasato K, Bennett HC, Kozlova A, Sparagna GC, Bogdanov M, Mitchell AM. Genetic evidence for functional diversification of gram-negative intermembrane phospholipid transporters. PLoS Genet 2024; 20:e1011335. [PMID: 38913742 PMCID: PMC11226057 DOI: 10.1371/journal.pgen.1011335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 07/05/2024] [Accepted: 06/07/2024] [Indexed: 06/26/2024] Open
Abstract
The outer membrane of gram-negative bacteria is a barrier to chemical and physical stress. Phospholipid transport between the inner and outer membranes has been an area of intense investigation and, in E. coli K-12, it has recently been shown to be mediated by YhdP, TamB, and YdbH, which are suggested to provide hydrophobic channels for phospholipid diffusion, with YhdP and TamB playing the major roles. However, YhdP and TamB have different phenotypes suggesting distinct functions. It remains unclear whether these functions are related to phospholipid metabolism. We investigated a synthetic cold sensitivity caused by deletion of fadR, a transcriptional regulator controlling fatty acid degradation and unsaturated fatty acid production, and yhdP, but not by ΔtamB ΔfadR or ΔydbH ΔfadR. Deletion of tamB recuses the ΔyhdP ΔfadR cold sensitivity further demonstrating the phenotype is related to functional diversification between these genes. The ΔyhdP ΔfadR strain shows a greater increase in cardiolipin upon transfer to the non-permissive temperature and genetically lowering cardiolipin levels can suppress cold sensitivity. These data also reveal a qualitative difference between cardiolipin synthases in E. coli, as deletion of clsA and clsC suppresses cold sensitivity but deletion of clsB does not. Moreover, increased fatty acid saturation is necessary for cold sensitivity and lowering this level genetically or through supplementation of oleic acid suppresses the cold sensitivity of the ΔyhdP ΔfadR strain. Together, our data clearly demonstrate that the diversification of function between YhdP and TamB is related to phospholipid metabolism. Although indirect regulatory effects are possible, we favor the parsimonious hypothesis that YhdP and TamB have differential phospholipid-substrate transport preferences. Thus, our data provide a potential mechanism for independent control of the phospholipid composition of the inner and outer membranes in response to changing conditions based on regulation of abundance or activity of YhdP and TamB.
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Affiliation(s)
- Ashutosh K. Rai
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
| | - Katsuhiro Sawasato
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Haley C. Bennett
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
| | - Anastasiia Kozlova
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Genevieve C. Sparagna
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Mikhail Bogdanov
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Angela M. Mitchell
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
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8
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Rai AK, Sawasato K, Bennett HC, Kozlova A, Sparagna GC, Bogdanov M, Mitchell AM. Genetic evidence for functional diversification of gram-negative intermembrane phospholipid transporters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.21.545913. [PMID: 37745482 PMCID: PMC10515749 DOI: 10.1101/2023.06.21.545913] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The outer membrane of Gram-negative bacteria is a barrier to chemical and physical stress. Phospholipid transport between the inner and outer membranes has been an area of intense investigation and, in E. coli K-12, it has recently been shown to be mediated by YhdP, TamB, and YdbH, which are suggested to provide hydrophobic channels for phospholipid diffusion, with YhdP and TamB playing the major roles. However, YhdP and TamB have different phenotypes suggesting distinct functions. We investigated these functions using synthetic cold sensitivity (at 30 °C) caused by deletion of yhdP and fadR, a transcriptional regulator controlling fatty acid degradation and unsaturated fatty acid production, but not by ΔtamB ΔfadR or ΔydbH ΔfadR,. Deletion of tamB suppresses the ΔyhdP ΔfadR cold sensitivity suggesting this phenotype is related to phospholipid transport. The ΔyhdP ΔfadR strain shows a greater increase in cardiolipin upon transfer to the non-permissive temperature and genetically lowering cardiolipin levels can suppress cold sensitivity. These data also reveal a qualitative difference between cardiolipin synthases in E. coli, as deletion of clsA and clsC suppresses cold sensitivity but deletion of clsB does not despite lower cardiolipin levels. In addition to increased cardiolipin, increased fatty acid saturation is necessary for cold sensitivity and lowering this level genetically or through supplementation of oleic acid suppresses the cold sensitivity of the ΔyhdP ΔfadR strain. Although indirect effects are possible, we favor the parsimonious hypothesis that YhdP and TamB have differential substrate transport preferences, most likely with YhdP preferentially transporting more saturated phospholipids and TamB preferentially transporting more unsaturated phospholipids. We envision cardiolipin contributing to this transport preference by sterically clogging TamB-mediated transport of saturated phospholipids. Thus, our data provide a potential mechanism for independent control of the phospholipid composition of the inner and outer membranes in response to changing conditions.
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Affiliation(s)
- Ashutosh K. Rai
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Katsuhiro Sawasato
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Haley C. Bennett
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Anastasiia Kozlova
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Genevieve C. Sparagna
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Mikhail Bogdanov
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Angela M. Mitchell
- Department of Biology, Texas A&M University, College Station, Texas, USA
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9
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Correa Velez KE, Alam M, Baalousha MA, Norman RS. Wildfire Ashes from the Wildland-Urban Interface Alter Vibrio vulnificus Growth and Gene Expression. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:8169-8181. [PMID: 38690750 DOI: 10.1021/acs.est.3c08658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Climate change-induced stressors are contributing to the emergence of infectious diseases, including those caused by marine bacterial pathogens such as Vibrio spp. These stressors alter Vibrio temporal and geographical distribution, resulting in increased spread, exposure, and infection rates, thus facilitating greater Vibrio-human interactions. Concurrently, wildfires are increasing in size, severity, frequency, and spread in the built environment due to climate change, resulting in the emission of contaminants of emerging concern. This study aimed to understand the potential effects of urban interface wildfire ashes on Vibrio vulnificus (V. vulnificus) growth and gene expression using transcriptomic approaches. V. vulnificus was exposed to structural and vegetation ashes and analyzed to identify differentially expressed genes using the HTSeq-DESeq2 strategy. Exposure to wildfire ash altered V. vulnificus growth and gene expression, depending on the trace metal composition of the ash. The high Fe content of the vegetation ash enhanced bacterial growth, while the high Cu, As, and Cr content of the structural ash suppressed growth. Additionally, the overall pattern of upregulated genes and pathways suggests increased virulence potential due to the selection of metal- and antibiotic-resistant strains. Therefore, mixed fire ashes transported and deposited into coastal zones may lead to the selection of environmental reservoirs of Vibrio strains with enhanced antibiotic resistance profiles, increasing public health risk.
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Affiliation(s)
- Karlen Enid Correa Velez
- Department of Environmental Health Sciences, University of South Carolina, 921 Assembly St., Suite 401, Columbia, South Carolina 29208, United States
- NIEHS Center for Oceans and Human Health and Climate Change Interactions, University of South Carolina, 921 Assembly St., Suite 401, Columbia, South Carolina 29208, United States
| | - Mahbub Alam
- Department of Environmental Health Sciences, University of South Carolina, 921 Assembly St., Suite 401, Columbia, South Carolina 29208, United States
- Center for Environmental Nanoscience and Risk, University of South Carolina, 921 Assembly St., Suite 401, Columbia, South Carolina 29208, United States
| | - Mohammed A Baalousha
- Department of Environmental Health Sciences, University of South Carolina, 921 Assembly St., Suite 401, Columbia, South Carolina 29208, United States
- Center for Environmental Nanoscience and Risk, University of South Carolina, 921 Assembly St., Suite 401, Columbia, South Carolina 29208, United States
| | - R Sean Norman
- Department of Environmental Health Sciences, University of South Carolina, 921 Assembly St., Suite 401, Columbia, South Carolina 29208, United States
- NIEHS Center for Oceans and Human Health and Climate Change Interactions, University of South Carolina, 921 Assembly St., Suite 401, Columbia, South Carolina 29208, United States
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10
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Zhang Q, Zhou H, Jiang P, Wu L, Xiao X. Silver nanoparticles facilitate phage-borne resistance gene transfer in planktonic and microplastic-attached bacteria. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133942. [PMID: 38452675 DOI: 10.1016/j.jhazmat.2024.133942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 02/17/2024] [Accepted: 02/29/2024] [Indexed: 03/09/2024]
Abstract
The spread of bacteriophage-borne antibiotic resistance genes (ARGs) poses a realistic threat to human health. Nanomaterials, as important emerging pollutants, have potential impacts on ARGs dissemination in aquatic environments. However, little is known about its role in transductive transfer of ARGs mediated by bacteriophage in the presence of microplastics. Therefore, this study comprehensively investigated the influence of silver nanoparticles (AgNPs) on the transfer of bacteriophage-encoded ARGs in planktonic Escherichia coli and microplastic-attached biofilm. AgNPs exposure facilitated the phage transduction in planktonic and microplastic-attached bacteria at ambient concentration of 0.1 mg/L. Biological binding mediated by phage-specific recognition, rather than physical aggregation conducted by hydrophilicity and ζ-potential, dominated the bacterial adhesion of AgNPs. The aggregated AgNPs in turn resulted in elevated oxidative stress and membrane destabilization, which promoted the bacteriophage infection to planktonic bacteria. AgNPs exposure could disrupt colanic acid biosynthesis and then reduce the thickness of biofilm on microplastics, contributing to the transfer of phage-encoded ARGs. Moreover, the roughness of microplastics also affected the performance of AgNPs on the transductive transfer of ARGs in biofilms. This study reveals the compound risks of nanomaterials and microplastics in phage-borne ARGs dissemination and highlights the complexity in various environmental scenarios.
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Affiliation(s)
- Qiurong Zhang
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Huixian Zhou
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Ping Jiang
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Lijun Wu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Xiang Xiao
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China.
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11
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Luo K, Hu X, Li Y, Guo M, Liu X, Zhang Y, Zhuo W, Yang B, Wang X, Shi C. Revealing the mechanism of citral induced entry of Vibrio vulnificus into viable but not culturable (VBNC) state based on transcriptomics. Int J Food Microbiol 2024; 416:110656. [PMID: 38461733 DOI: 10.1016/j.ijfoodmicro.2024.110656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/24/2024] [Accepted: 02/27/2024] [Indexed: 03/12/2024]
Abstract
Citral has attracted much attention as a safe and effective plant-derived bacteriostatic agent. However, the ability of citral to induce the formation of VBNC state in Vibrio vulnificus has not been evaluated. In the present study, V. vulnificus was shown to be induced to form the VBNC state at 4.5 h and 3 h of citral treatment at 4MIC and 6MIC. Moreover, the citral-induced VBNC state of V. vulnificus maintained some respiratory chain activity and was able to recover well in both APW media, APW media supplemented with 5 % (v/v) Tween 80 and 2 mg/mL sodium pyruvate. Field emission and transmission electron microscopy showed that the external structure of the citral-induced VBNC V. vulnificus cells was shortened to short rods, with folded cell membrane, rough cell surface, and dense cytoplasm and loose nuclear material in the internal cell structure. In addition, the possible molecular mechanisms of citral-induced formation and recovery of V. vulnificus in the VBNC state were explored by transcriptomics. Transcriptome analyses revealed that 1118 genes were significantly altered upon entry into the VBNC state, and 1052 genes were changed after resuscitation. Most of the physiological activities related to energy production were inhibited in the citral-induced VBNC state of V. vulnificus; however, the bacteria retained its pathogenicity. The citral-induced resuscitation of V. vulnificus in the VBNC state selectively restored the activity of some genes related to bacterial growth and reproduction. Meanwhile, the expression levels of other genes may have been influenced by citral-induced resuscitation after the formation of the VBNC state. In conclusion, this study evaluated and analyzed the ability and possible mechanism of citral on the formation of VBNC state and the recovery of VBNC state of V. vulnificus, and made a comprehensive assessment for the safety of citral application in food production.
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Affiliation(s)
- Kunyao Luo
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China; Northwest A&F University Shenzhen Research Institute, Shenzhen, Guangdong 518057, China
| | - Xinquan Hu
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanzheng Li
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Meixian Guo
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xing Liu
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yingying Zhang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Weiwei Zhuo
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Baowei Yang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xin Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chao Shi
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China; Northwest A&F University Shenzhen Research Institute, Shenzhen, Guangdong 518057, China; Shaanxi Engineering Research Centre of Dairy Products Quality, Safety and Health, China.
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12
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Saenkham-Huntsinger P, Ritter M, Donati GL, Mitchell AM, Subashchandrabose S. The inner membrane protein YhiM links copper and CpxAR envelope stress responses in uropathogenic E. coli. mBio 2024; 15:e0352223. [PMID: 38470052 PMCID: PMC11005409 DOI: 10.1128/mbio.03522-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/13/2024] [Indexed: 03/13/2024] Open
Abstract
Urinary tract infection (UTI) is a ubiquitous infectious condition, and uropathogenic Escherichia coli (UPEC) is the predominant causative agent of UTI. Copper (Cu) is implicated in innate immunity, including against UPEC. Cu is a trace element utilized as a co-factor, but excess Cu is toxic due to mismetalation of non-cognate proteins. E. coli precisely regulates Cu homeostasis via efflux systems. However, Cu import mechanisms into the bacterial cell are not clear. We hypothesized that Cu import defective mutants would exhibit increased resistance to Cu. This hypothesis was tested in a forward genetic screen with transposon (Tn5) insertion mutants in UPEC strain CFT073, and we identified 32 unique Cu-resistant mutants. Transposon and defined mutants lacking yhiM, which encodes a hypothetical inner membrane protein, were more resistant to Cu than parental strain. Loss of YhiM led to decreased cellular Cu content and increased expression of copA, encoding a Cu efflux pump. The CpxAR envelope stress response system was activated in the ΔyhiM mutant as indicated by increased expression of cpxP. Transcription of yhiM was regulated by CueR and CpxR, and the CpxAR system was essential for increased Cu resistance in the ΔyhiM mutant. Importantly, activation of CpxAR system in the ΔyhiM mutant was independent of NlpE, a known activator of this system. YhiM was required for optimal fitness of UPEC in a mouse model of UTI. Our findings demonstrate that YhiM is a critical mediator of Cu homeostasis and links bacterial adaptation to Cu stress with the CpxAR-dependent envelope stress response in UPEC.IMPORTANCEUPEC is a common bacterial infection. Bacterial pathogens are exposed to host-derived Cu during infection, including UTI. Here, we describe detection of genes involved in Cu homeostasis in UPEC. A UPEC mutant lacking YhiM, a membrane protein, exhibited dramatic increase in resistance to Cu. Our study demonstrates YhiM as a nexus between Cu stress and the CpxAR-dependent envelope stress response system. Importantly, our findings establish NlpE-independent activation of CpxAR system during Cu stress in UPEC. Collectively, YhiM emerges as a critical mediator of Cu homeostasis in UPEC and highlights the interlinked nature of bacterial adaptation to survival during Cu and envelope stress.
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Affiliation(s)
- Panatda Saenkham-Huntsinger
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Matthew Ritter
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - George L. Donati
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Angela M. Mitchell
- Department of Biology, College of Science, Texas A&M University, College Station, Texas, USA
| | - Sargurunathan Subashchandrabose
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
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13
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Willdigg JR, Patel Y, Arquilevich BE, Subramanian C, Frank MW, Rock CO, Helmann JD. The Bacillus subtilis cell envelope stress-inducible ytpAB operon modulates membrane properties and contributes to bacitracin resistance. J Bacteriol 2024; 206:e0001524. [PMID: 38323910 PMCID: PMC10955860 DOI: 10.1128/jb.00015-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 02/08/2024] Open
Abstract
Antibiotics that inhibit peptidoglycan synthesis trigger the activation of both specific and general protective responses. σM responds to diverse antibiotics that inhibit cell wall synthesis. Here, we demonstrate that cell wall-inhibiting drugs, such as bacitracin and cefuroxime, induce the σM-dependent ytpAB operon. YtpA is a predicted hydrolase previously proposed to generate the putative lysophospholipid antibiotic bacilysocin (lysophosphatidylglycerol), and YtpB is the branchpoint enzyme for the synthesis of membrane-localized C35 terpenoids. Using targeted lipidomics, we reveal that YtpA is not required for the production of lysophosphatidylglycerol. Nevertheless, ytpA was critical for growth in a mutant strain defective for homeoviscous adaptation due to a lack of genes for the synthesis of branched chain fatty acids and the Des phospholipid desaturase. Consistently, overexpression of ytpA increased membrane fluidity as monitored by fluorescence anisotropy. The ytpA gene contributes to bacitracin resistance in mutants additionally lacking the bceAB or bcrC genes, which directly mediate bacitracin resistance. These epistatic interactions support a model in which σM-dependent induction of the ytpAB operon helps cells tolerate bacitracin stress, either by facilitating the flipping of the undecaprenyl phosphate carrier lipid or by impacting the assembly or function of membrane-associated complexes involved in cell wall homeostasis.IMPORTANCEPeptidoglycan synthesis inhibitors include some of our most important antibiotics. In Bacillus subtilis, peptidoglycan synthesis inhibitors induce the σM regulon, which is critical for intrinsic antibiotic resistance. The σM-dependent ytpAB operon encodes a predicted hydrolase (YtpA) and the enzyme that initiates the synthesis of C35 terpenoids (YtpB). Our results suggest that YtpA is critical in cells defective in homeoviscous adaptation. Furthermore, we find that YtpA functions cooperatively with the BceAB and BcrC proteins in conferring intrinsic resistance to bacitracin, a peptide antibiotic that binds tightly to the undecaprenyl-pyrophosphate lipid carrier that sustains peptidoglycan synthesis.
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Affiliation(s)
| | - Yesha Patel
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | | | - Chitra Subramanian
- Department of Host Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Matthew W. Frank
- Department of Host Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Charles O. Rock
- Department of Host Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - John D. Helmann
- Department of Microbiology, Cornell University, Ithaca, New York, USA
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14
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Méndez AAE, Argüello JM, Soncini FC, Checa SK. Scs system links copper and redox homeostasis in bacterial pathogens. J Biol Chem 2024; 300:105710. [PMID: 38309504 PMCID: PMC10907172 DOI: 10.1016/j.jbc.2024.105710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 02/05/2024] Open
Abstract
The bacterial envelope is an essential compartment involved in metabolism and metabolites transport, virulence, and stress defense. Its roles become more evident when homeostasis is challenged during host-pathogen interactions. In particular, the presence of free radical groups and excess copper in the periplasm causes noxious reactions, such as sulfhydryl group oxidation leading to enzymatic inactivation and protein denaturation. In response to this, canonical and accessory oxidoreductase systems are induced, performing quality control of thiol groups, and therefore contributing to restoring homeostasis and preserving survival under these conditions. Here, we examine recent advances in the characterization of the Dsb-like, Salmonella-specific Scs system. This system includes the ScsC/ScsB pair of Cu+-binding proteins with thiol-oxidoreductase activity, an alternative ScsB-partner, the membrane-linked ScsD, and a likely associated protein, ScsA, with a role in peroxide resistance. We discuss the acquisition of the scsABCD locus and its integration into a global regulatory pathway directing envelope response to Cu stress during the evolution of pathogens that also harbor the canonical Dsb systems. The evidence suggests that the canonical Dsb systems cannot satisfy the extra demands that the host-pathogen interface imposes to preserve functional thiol groups. This resulted in the acquisition of the Scs system by Salmonella. We propose that the ScsABCD complex evolved to connect Cu and redox stress responses in this pathogen as well as in other bacterial pathogens.
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Affiliation(s)
- Andrea A E Méndez
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - José M Argüello
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Fernando C Soncini
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - Susana K Checa
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina.
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15
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Hansson A, Karlsen EA, Stensen W, Svendsen JSM, Berglin M, Lundgren A. Preventing E. coli Biofilm Formation with Antimicrobial Peptide-Functionalized Surface Coatings: Recognizing the Dependence on the Bacterial Binding Mode Using Live-Cell Microscopy. ACS APPLIED MATERIALS & INTERFACES 2024; 16:6799-6812. [PMID: 38294883 PMCID: PMC10875647 DOI: 10.1021/acsami.3c16004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/02/2024]
Abstract
Antimicrobial peptides (AMPs) can kill bacteria by destabilizing their membranes, yet translating these molecules' properties into a covalently attached antibacterial coating is challenging. Rational design efforts are obstructed by the fact that standard microbiology methods are ill-designed for the evaluation of coatings, disclosing few details about why grafted AMPs function or do not function. It is particularly difficult to distinguish the influence of the AMP's molecular structure from other factors controlling the total exposure, including which type of bonds are formed between bacteria and the coating and how persistent these contacts are. Here, we combine label-free live-cell microscopy, microfluidics, and automated image analysis to study the response of surface-bound Escherichia coli challenged by the same small AMP either in solution or grafted to the surface through click chemistry. Initially after binding, the grafted AMPs inhibited bacterial growth more efficiently than did AMPs in solution. Yet, after 1 h, E. coli on the coated surfaces increased their expression of type-1 fimbriae, leading to a change in their binding mode, which diminished the coating's impact. The wealth of information obtained from continuously monitoring the growth, shape, and movements of single bacterial cells allowed us to elucidate and quantify the different factors determining the antibacterial efficacy of the grafted AMPs. We expect this approach to aid the design of elaborate antibacterial material coatings working by specific and selective actions, not limited to contact-killing. This technology is needed to support health care and food production in the postantibiotic era.
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Affiliation(s)
- Adam Hansson
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg 40530, Sweden
- Department
of Chemistry and Materials, RISE Research
Institutes of Sweden, Borås 50115, Sweden
| | - Eskil André Karlsen
- Amicoat
A/S, Sykehusvegen 23, Tromsø 9019, Norway
- Department
of Chemistry, UiT The Arctic University
of Norway, Tromsø 9037, Norway
| | - Wenche Stensen
- Department
of Chemistry, UiT The Arctic University
of Norway, Tromsø 9037, Norway
| | - John S. M. Svendsen
- Amicoat
A/S, Sykehusvegen 23, Tromsø 9019, Norway
- Department
of Chemistry, UiT The Arctic University
of Norway, Tromsø 9037, Norway
| | - Mattias Berglin
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg 40530, Sweden
- Department
of Chemistry and Materials, RISE Research
Institutes of Sweden, Borås 50115, Sweden
| | - Anders Lundgren
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg 40530, Sweden
- Centre
for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg 41346, Sweden
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16
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Qin Z, Peng K, Feng Y, Wang Y, Huang B, Tian Z, Ouyang P, Huang X, Chen D, Lai W, Geng Y. Transcriptome reveals the role of the htpG gene in mediating antibiotic resistance through cell envelope modulation in Vibrio mimicus SCCF01. Front Microbiol 2024; 14:1295065. [PMID: 38239724 PMCID: PMC10794384 DOI: 10.3389/fmicb.2023.1295065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/04/2023] [Indexed: 01/22/2024] Open
Abstract
HtpG, a bacterial homolog of the eukaryotic 90 kDa heat-shock protein (Hsp90), represents the simplest member of the heat shock protein family. While the significance of Hsp90 in fungal and cancer drug resistance has been confirmed, the role of HtpG in bacterial antibiotic resistance remains largely unexplored. This research aims to investigate the impact of the htpG gene on antibiotic resistance in Vibrio mimicus. Through the creation of htpG gene deletion and complementation strains, we have uncovered the essential role of htpG in regulating the structural integrity of the bacterial cell envelope. Our transcriptomics analysis demonstrates that the deletion of htpG increases the sensitivity of V. mimicus to antimicrobial peptides, primarily due to upregulated lipopolysaccharide synthesis, reduced glycerophospholipid content, and weakened efflux pumps activity. Conversely, reduced sensitivity to β-lactam antibiotics in the ΔhtpG strain results from decreased peptidoglycan synthesis and dysregulated peptidoglycan recycling and regulation. Further exploration of specific pathway components is essential for a comprehensive understanding of htpG-mediated resistance mechanisms, aiding in the development of antimicrobial agents. To our knowledge, this is the first effort to explore the relationship between htpG and drug resistance in bacteria.
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Affiliation(s)
- Zhenyang Qin
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Kun Peng
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yang Feng
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yilin Wang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bowen Huang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ziqi Tian
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ping Ouyang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaoli Huang
- Department of Aquaculture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Defang Chen
- Department of Aquaculture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Weimin Lai
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yi Geng
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
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17
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Storek KM, Sun D, Rutherford ST. Inhibitors targeting BamA in gram-negative bacteria. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119609. [PMID: 37852326 DOI: 10.1016/j.bbamcr.2023.119609] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/08/2023] [Accepted: 09/19/2023] [Indexed: 10/20/2023]
Abstract
Antibiotic resistance has led to an increase in the number of patient hospitalizations and deaths. The situation for gram-negative bacteria is especially dire as the last new class of antibiotics active against these bacteria was introduced to the clinic over 60 years ago, thus there is an immediate unmet need for new antibiotic classes able to overcome resistance. The outer membrane, a unique and essential structure in gram-negative bacteria, contains multiple potential antibacterial targets including BamA, an outer membrane protein that folds and inserts transmembrane β-barrel proteins. BamA is essential and conserved, and its outer membrane location eliminates a barrier that molecules must overcome to access this target. Recently, antibacterial small molecules, natural products, peptides, and antibodies that inhibit BamA activity have been reported, validating the druggability of this target and generating potential leads for antibiotic development. This review will describe these BamA inhibitors, highlight their key attributes, and identify challenges with this potential target.
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Affiliation(s)
- Kelly M Storek
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Dawei Sun
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Steven T Rutherford
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA.
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18
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Lang M, Carvalho A, Baharoglu Z, Mazel D. Aminoglycoside uptake, stress, and potentiation in Gram-negative bacteria: new therapies with old molecules. Microbiol Mol Biol Rev 2023; 87:e0003622. [PMID: 38047635 PMCID: PMC10732077 DOI: 10.1128/mmbr.00036-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023] Open
Abstract
SUMMARYAminoglycosides (AGs) are long-known molecules successfully used against Gram-negative pathogens. While their use declined with the discovery of new antibiotics, they are now classified as critically important molecules because of their effectiveness against multidrug-resistant bacteria. While they can efficiently cross the Gram-negative envelope, the mechanism of AG entry is still incompletely understood, although this comprehension is essential for the development of new therapies in the face of the alarming increase in antibiotic resistance. Increasing antibiotic uptake in bacteria is one strategy to enhance effective treatments. This review aims, first, to consolidate old and recent knowledge about AG uptake; second, to explore the connection between AG-dependent bacterial stress and drug uptake; and finally, to present new strategies of potentiation of AG uptake for more efficient antibiotic therapies. In particular, we emphasize on the connection between sugar transport and AG potentiation.
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Affiliation(s)
- Manon Lang
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
| | - André Carvalho
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
| | - Zeynep Baharoglu
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
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19
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Liu Z, Guan J, Chen Z, Tai C, Deng Z, Chao Y, Ou HY. CpxR promotes the carbapenem antibiotic resistance of Klebsiella pneumoniae by directly regulating the expression and the dissemination of blaKPC on the IncFII conjugative plasmid. Emerg Microbes Infect 2023; 12:2256427. [PMID: 37672539 PMCID: PMC10524804 DOI: 10.1080/22221751.2023.2256427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 09/01/2023] [Indexed: 09/08/2023]
Abstract
Klebsiella pneumoniae is an important human pathogen known for its resistance to carbapenem antibiotics, especially the increasing carbapenem-resistant hypervirulent variants. The carbapenem resistance is mainly caused by the carbapenemase gene blaKPC which was commonly found on the IncFII transferable plasmids in K. pneumoniae ST11 isolates in regions of China. However, the mechanisms of the plasmid-carrying blaKPC regulation by the host strain are not clear. To investigate the chromosome-encoded two-component system (TCS) that regulates the carbapenem resistance of K. pneumoniae caused by blaKPC, twenty-four TCSs of a carbapenem-resistant classical K. pneumoniae ST11 clinical isolate were knocked out. The deletion mutation of the TCS regulator cpxR exhibited increased sensitivity to carbapenem, which could be restored by complementation with cpxR in trans. Electrophoretic mobility shift, isothermal titration calorimetry and DNase I footprinting results revealed that CpxR directly bound to the promoter DNA of blaKPC and the binding was abolished by disrupting the DNA-binding domain in CpxR. The subsequent in vivo assays using the lacZ reporter system and qPCR showed that CpxR upregulates the transcription of blaKPC. Notably, CpxR was also found to activate the transfer of the blaKPC-carrying IncFII plasmid between the hypervirulent K. pneumoniae and E. coli isolates, in which CpxR promoted the transcription of the tra operon via binding to its promoter region. These results provide an important insight into the regulation of the host factor CpxR in the plasmid-carrying carbapenemase gene in the classical and hypervirulent K. pneumoniae.
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Affiliation(s)
- Zhiyuan Liu
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- The Center for Microbes, Development and Health (CMDH), CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Jiahao Guan
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Zhaoyan Chen
- Intensive Care Unit, First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
| | - Cui Tai
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yanjie Chao
- The Center for Microbes, Development and Health (CMDH), CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Hong-Yu Ou
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
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20
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Wu F, Ren F, Xie X, Meng J, Wu X. The implication of viability and pathogenicity by truncated lipopolysaccharide in Yersinia enterocolitica. Appl Microbiol Biotechnol 2023; 107:7165-7180. [PMID: 37728625 DOI: 10.1007/s00253-023-12785-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/21/2023]
Abstract
The fast envelope stress responses play a key role in the transmission and pathogenesis of Yersinia enterocolitica, one of the most common foodborne pathogens. Our previous study showed that deletion of the waaF gene, essential for the biosynthesis of lipopolysaccharide (LPS) core polysaccharides, led to the formation of a truncated LPS structure and induced cell envelope stress. This envelope stress may disturb the intracellular signal transduction, thereby affecting the physiological functions of Y. enterocolitica. In this study, truncated LPS caused by waaF deletion was used as a model of envelope stress in Y. enterocolitica. We investigated the mechanisms of envelope stress responses and the cellular functions affected by truncated LPS. Transcriptome analysis and phenotypic validation showed that LPS truncation reduced flagellar assembly, bacterial chemotaxis, and inositol phosphate metabolism, presenting lower pathogenicity and viability both in vivo and in vitro environments. Further 4D label-free phosphorylation analysis confirmed that truncated LPS perturbed multiple intracellular signal transduction pathways. Specifically, a comprehensive discussion was conducted on the mechanisms by which chemotactic signal transduction and Rcs system contribute to the inhibition of chemotaxis. Finally, the pathogenicity of Y. enterocolitica with truncated LPS was evaluated in vitro using IPEC-J2 cells as models, and it was found that truncated LPS exhibited reduced adhesion, invasion, and toxicity of Y. enterocolitica to IPEC-J2 cells. Our research provides an understanding of LPS in the regulation of Y. enterocolitica viability and pathogenicity and, thus, opening new avenues to develop novel food safety strategies or drugs to prevent and control Y. enterocolitica infections. KEY POINTS: • Truncated LPS reduces flagellar assembly, chemotaxis, and inositol phosphate metabolism in Y. enterocolitica. • Truncated LPS reduces adhesion, invasion, and toxicity of Y. enterocolitica to IPEC-J2 cells. • Truncated LPS regulates intracellular signal transduction of Y. enterocolitica.
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Affiliation(s)
- Fan Wu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Bioengineering, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Fengyun Ren
- Laboratory of Nutrient Resources and Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, Tianjin, 300308, China
| | - Xixian Xie
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Bioengineering, Tianjin University of Science and Technology, Tianjin, 300457, China.
| | - Jiao Meng
- Laboratory of Nutrient Resources and Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, Tianjin, 300308, China.
| | - Xin Wu
- Laboratory of Nutrient Resources and Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, Tianjin, 300308, China
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21
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Miano A, Rychel K, Lezia A, Sastry A, Palsson B, Hasty J. High-resolution temporal profiling of E. coli transcriptional response. Nat Commun 2023; 14:7606. [PMID: 37993418 PMCID: PMC10665441 DOI: 10.1038/s41467-023-43173-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 11/02/2023] [Indexed: 11/24/2023] Open
Abstract
Understanding how cells dynamically adapt to their environment is a primary focus of biology research. Temporal information about cellular behavior is often limited by both small numbers of data time-points and the methods used to analyze this data. Here, we apply unsupervised machine learning to a data set containing the activity of 1805 native promoters in E. coli measured every 10 minutes in a high-throughput microfluidic device via fluorescence time-lapse microscopy. Specifically, this data set reveals E. coli transcriptome dynamics when exposed to different heavy metal ions. We use a bioinformatics pipeline based on Independent Component Analysis (ICA) to generate insights and hypotheses from this data. We discovered three primary, time-dependent stages of promoter activation to heavy metal stress (fast, intermediate, and steady). Furthermore, we uncovered a global strategy E. coli uses to reallocate resources from stress-related promoters to growth-related promoters following exposure to heavy metal stress.
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Affiliation(s)
- Arianna Miano
- Department of Bioengineering, University of California San Diego, 9500 Gliman Dr, La Jolla, CA, USA.
| | - Kevin Rychel
- Department of Bioengineering, University of California San Diego, 9500 Gliman Dr, La Jolla, CA, USA
| | - Andrew Lezia
- Department of Bioengineering, University of California San Diego, 9500 Gliman Dr, La Jolla, CA, USA
| | - Anand Sastry
- Department of Bioengineering, University of California San Diego, 9500 Gliman Dr, La Jolla, CA, USA
| | - Bernhard Palsson
- Department of Bioengineering, University of California San Diego, 9500 Gliman Dr, La Jolla, CA, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs, Lyngby, Denmark
| | - Jeff Hasty
- Department of Bioengineering, University of California San Diego, 9500 Gliman Dr, La Jolla, CA, USA
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, 9500 Gliman Dr, La Jolla, CA, USA
- Synthetic Biology Institute, University of California San Diego, 9500 Gliman Dr, La Jolla, CA, USA
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22
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Wiesmann CL, Wang NR, Zhang Y, Liu Z, Haney CH. Origins of symbiosis: shared mechanisms underlying microbial pathogenesis, commensalism and mutualism of plants and animals. FEMS Microbiol Rev 2023; 47:fuac048. [PMID: 36521845 PMCID: PMC10719066 DOI: 10.1093/femsre/fuac048] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/17/2023] Open
Abstract
Regardless of the outcome of symbiosis, whether it is pathogenic, mutualistic or commensal, bacteria must first colonize their hosts. Intriguingly, closely related bacteria that colonize diverse hosts with diverse outcomes of symbiosis have conserved host-association and virulence factors. This review describes commonalities in the process of becoming host associated amongst bacteria with diverse lifestyles. Whether a pathogen, commensal or mutualist, bacteria must sense the presence of and migrate towards a host, compete for space and nutrients with other microbes, evade the host immune system, and change their physiology to enable long-term host association. We primarily focus on well-studied taxa, such as Pseudomonas, that associate with diverse model plant and animal hosts, with far-ranging symbiotic outcomes. Given the importance of opportunistic pathogens and chronic infections in both human health and agriculture, understanding the mechanisms that facilitate symbiotic relationships between bacteria and their hosts will help inform the development of disease treatments for both humans, and the plants we eat.
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Affiliation(s)
- Christina L Wiesmann
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Nicole R Wang
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Yue Zhang
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Zhexian Liu
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Cara H Haney
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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23
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Ramezanifard R, Golubeva YA, Palmer AD, Slauch JM. TamAB is regulated by PhoPQ and functions in outer membrane homeostasis during Salmonella pathogenesis. J Bacteriol 2023; 205:e0018323. [PMID: 37728604 PMCID: PMC10601761 DOI: 10.1128/jb.00183-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/12/2023] [Indexed: 09/21/2023] Open
Abstract
Salmonella survive and replicate in macrophages, which normally kill bacteria by exposing them to a variety of harsh conditions and antimicrobial effectors, many of which target the bacterial cell envelope. The PhoPQ two-component system responds to the phagosome environment and induces factors that protect the outer membrane, allowing adaptation and growth in the macrophage. We show that PhoPQ induces the transcription of the tamAB operon both in vitro and in macrophages. The TamA protein is structurally similar to BamA, an essential protein in the Bam complex that assembles β-barrel proteins in the outer membrane, while TamB is an AsmA-family protein implicated in lipid transport between the inner and outer membranes. We show that the Bam machinery is stressed in vitro under low Mg2+, low pH conditions that mimic the phagosome. Not surprisingly, mutations affecting Bam function confer significant virulence defects. Although loss of TamAB alone confers no virulence defect, a tamAB deletion confers a synthetic phenotype in bam mutant backgrounds in animals and macrophages, and in vitro upon treatment with vancomycin or sodium dodecyl sulfate. Mutations affecting YhdP, which functions in partial redundancy with TamB, also confer synthetic phenotypes with bam mutations in the animal, but this interaction is not evident in vitro. Thus, in the harsh phagocytic environment of the macrophage, the outer membrane Bam machinery is compromised, and the TamAB system, and perhaps other PhoPQ-regulated factors, is induced to compensate. It is most likely that TamAB and other systems assist the Bam complex indirectly by affecting outer membrane properties. IMPORTANCE The TamAB system has been implicated in both outer membrane protein localization and phospholipid transport between the inner and outer membranes. We show that the β-barrel protein assembly complex, Bam, is stressed under conditions thought to mimic the macrophage phagosome. TamAB expression is controlled by the PhoPQ two-component system and induced in macrophages. This system somehow compensates for the Bam complex as evidenced by the fact that mutations affecting the two systems confer synthetic phenotypes in animals, macrophages, and in vitro in the presence of vancomycin or SDS. This study has implications concerning the role of TamAB in outer membrane homeostasis. It also contributes to our understanding of the systems necessary for Salmonella to adapt and reproduce within the macrophage phagosome.
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Affiliation(s)
- Rouhallah Ramezanifard
- Department of Microbiology, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
| | - Yekaterina A. Golubeva
- Department of Microbiology, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
| | - Alexander D. Palmer
- Department of Microbiology, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
| | - James M. Slauch
- Department of Microbiology, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
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24
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Rousseau CJ, Fraikin N, Zedek S, Van Melderen L. Are envelope stress responses essential for persistence to β-lactams in Escherichia coli? Antimicrob Agents Chemother 2023; 67:e0032923. [PMID: 37787525 PMCID: PMC10583663 DOI: 10.1128/aac.00329-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 08/05/2023] [Indexed: 10/04/2023] Open
Abstract
Bacterial persistence to antibiotics defines the ability of small sub-populations of sensitive cells within an isogenic population to survive high doses of bactericidal antibiotics. Here, we investigated the importance of the five main envelope stress responses (ESRs) of Escherichia coli in persistence to five bactericidal β-lactam antibiotics by combining classical time-kill curve experiments and single-cell analysis using time-lapse microscopy. We showed that the survival frequency of mutants for the Bae, Cpx, Psp, and Rcs systems treated with different β-lactams is comparable to that of the wild-type strain, indicating that these ESRs do not play a direct role in persistence to β-lactams. Since the σE-encoding gene is essential, we could not directly test its role. Using fluorescent reporters to monitor the activation of ESRs, we observed that σE is induced by high doses of meropenem. However, the dynamics of σE activation during meropenem treatment did not reveal any difference in persister cells compared to the bulk of the population, indicating that σE activation is not a hallmark of persistence. The Bae, Cpx, Psp, and Rcs responses were neither induced by ampicillin nor by meropenem. However, pre-induction of the Rcs system by polymyxin B increased survival to meropenem in an Rcs-dependent manner, suggesting that this ESR might confer some yet uncharacterized advantages during meropenem treatment or at the post-antibiotic recovery step. Altogether, our data suggest that ESRs are not key actors in E. coli persistence to β-lactams in the conditions we tested.
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Affiliation(s)
- Clothilde J. Rousseau
- Bacterial Genetics and Physiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Nathan Fraikin
- Bacterial Genetics and Physiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Safia Zedek
- Bacterial Genetics and Physiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Laurence Van Melderen
- Bacterial Genetics and Physiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium
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25
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Li J, Lu H, Wang A, Wen X, Huang Y, Li Q. The fates of antibiotic resistance genes and their association with cell membrane permeability in response to peroxydisulfate during composting. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118659. [PMID: 37478721 DOI: 10.1016/j.jenvman.2023.118659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/18/2023] [Accepted: 07/15/2023] [Indexed: 07/23/2023]
Abstract
The aims of this study were to use metagenomics to reveal the fates of antibiotic resistance genes (ARGs) during composting under the regulation of peroxydisulfate and clarify the relationship between ARGs and cell membrane permeability. Results showed that peroxydisulfate increased cell membrane permeability by effectively regulating the expression of outer membrane protein and lipopolysaccharide related genes. Besides, it reduced polysaccharides and proteins in extracellular polymer substances by 36% and 58%, respectively, making it easier for intracellular ARGs (i-ARGs) to reach the extracellular environment, among which the absolute intracellular abundance of mphK, Erm(31), and tet(44) decreased to 1.2, 1.0, and 0.89 fold of the control, respectively. Finally, variation partitioning analysis showed that i-ARGs dominated the removal of ARGs. These results revealed that the removal of i-ARGs by activated peroxydisulfate was the key to the removal of ARGs and increased cell membrane permeability played a key role for peroxydisulfate to remove i-ARGs during composting.
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Affiliation(s)
- Jixuan Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Heng Lu
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Ao Wang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Xiaoli Wen
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Yite Huang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Qunliang Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China.
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26
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Xu T, Fang D, Li F, Wang Z, Liu Y. A Dietary Source of High Level of Fluoroquinolone Tolerance in mcr-Carrying Gram-Negative Bacteria. RESEARCH (WASHINGTON, D.C.) 2023; 6:0245. [PMID: 37808177 PMCID: PMC10557118 DOI: 10.34133/research.0245] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/14/2023] [Indexed: 10/10/2023]
Abstract
The emergence of antibiotic tolerance, characterized by the prolonged survival of bacteria following antibiotic exposure, in natural bacterial populations, especially in pathogens carrying antibiotic resistance genes, has been an increasing threat to public health. However, the major causes contributing to the formation of antibiotic tolerance and underlying molecular mechanisms are yet poorly understood. Herein, we show that potassium sorbate (PS), a widely used food additive, triggers a high level of fluoroquinolone tolerance in bacteria carrying mobile colistin resistance gene mcr. Mechanistic studies demonstrate that PS treatment results in the accumulation of intracellular fumarate, which activates bacterial two-component system and decreases the expression level of outer membrane protein OmpF, thereby reducing the uptake of ciprofloxacin. In addition, the supplementation of PS inhibits aerobic respiration, reduces reactive oxygen species production and alleviates DNA damage caused by bactericidal antibiotics. Furthermore, we demonstrate that succinate, an intermediate product of the tricarboxylic acid cycle, overcomes PS-mediated ciprofloxacin tolerance. In multiple animal models, ciprofloxacin treatment displays failure outcomes in PS preadministrated animals, including comparable survival and bacterial loads with the vehicle group. Taken together, our works offer novel mechanistic insights into the development of antibiotic tolerance and uncover potential risks associated with PS use.
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Affiliation(s)
- Tianqi Xu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine,
Yangzhou University, Yangzhou 225009, China
| | - Dan Fang
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine,
Yangzhou University, Yangzhou 225009, China
| | - Fulei Li
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine,
Yangzhou University, Yangzhou 225009, China
| | - Zhiqiang Wang
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine,
Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China,
Yangzhou University, Yangzhou 225009, China
| | - Yuan Liu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine,
Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China,
Yangzhou University, Yangzhou 225009, China
- Institute of Comparative Medicine,
Yangzhou University, Yangzhou 225009, China
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27
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Browne K, Kuppusamy R, Walsh WR, Black DS, Willcox MDP, Kumar N, Chen R. Antimicrobial Peptidomimetics Prevent the Development of Resistance against Gentamicin and Ciprofloxacin in Staphylococcus and Pseudomonas Bacteria. Int J Mol Sci 2023; 24:14966. [PMID: 37834415 PMCID: PMC10573972 DOI: 10.3390/ijms241914966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/30/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023] Open
Abstract
Bacteria readily acquire resistance to traditional antibiotics, resulting in pan-resistant strains with no available treatment. Antimicrobial resistance is a global challenge and without the development of effective antimicrobials, the foundation of modern medicine is at risk. Combination therapies such as antibiotic-antibiotic and antibiotic-adjuvant combinations are strategies used to combat antibiotic resistance. Current research focuses on antimicrobial peptidomimetics as adjuvant compounds, due to their promising activity against antibiotic-resistant bacteria. Here, for the first time we demonstrate that antibiotic-peptidomimetic combinations mitigate the development of antibiotic resistance in Staphylococcus aureus and Pseudomonas aeruginosa. When ciprofloxacin and gentamicin were passaged individually at sub-inhibitory concentrations for 10 days, the minimum inhibitory concentrations (MICs) increased up to 32-fold and 128-fold for S. aureus and P. aeruginosa, respectively. In contrast, when antibiotics were passaged in combination with peptidomimetics (Melimine, Mel4, RK758), the MICs of both antibiotics and peptidomimetics remained constant, indicating these combinations were able to mitigate the development of antibiotic-resistance. Furthermore, antibiotic-peptidomimetic combinations demonstrated synergistic activity against both Gram-positive and Gram-negative bacteria, reducing the concentration needed for bactericidal activity. This has significant potential clinical applications-including preventing the spread of antibiotic-resistant strains in hospitals and communities, reviving ineffective antibiotics, and lowering the toxicity of antimicrobial chemotherapy.
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Affiliation(s)
- Katrina Browne
- School of Chemistry, University of New South Wales (UNSW) Sydney, Sydney 2052, Australia
- Surgical and Orthopaedic Research Laboratories (SORL), Prince of Wales Clinical School, Prince of Wales Hospital, University of New South Wales (UNSW), Randwick 2031, Australia
| | - Rajesh Kuppusamy
- School of Chemistry, University of New South Wales (UNSW) Sydney, Sydney 2052, Australia
- School of Optometry and Vision Science, University of New South Wales (UNSW) Sydney, Sydney 2052, Australia
| | - William R. Walsh
- Surgical and Orthopaedic Research Laboratories (SORL), Prince of Wales Clinical School, Prince of Wales Hospital, University of New South Wales (UNSW), Randwick 2031, Australia
| | - David StC Black
- School of Chemistry, University of New South Wales (UNSW) Sydney, Sydney 2052, Australia
| | - Mark D. P. Willcox
- School of Optometry and Vision Science, University of New South Wales (UNSW) Sydney, Sydney 2052, Australia
| | - Naresh Kumar
- School of Chemistry, University of New South Wales (UNSW) Sydney, Sydney 2052, Australia
| | - Renxun Chen
- School of Chemistry, University of New South Wales (UNSW) Sydney, Sydney 2052, Australia
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28
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Li G, Huang J, Cai Q, Wei Z, Pen G, Li Z, Wang J, Zhai L. Analysis of Osmotic Tolerance, Physiological Characteristics, and Gene Expression of Salmonella enterica subsp . enterica Serotype Derby. ACS OMEGA 2023; 8:36088-36099. [PMID: 37810736 PMCID: PMC10551921 DOI: 10.1021/acsomega.3c04257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/22/2023] [Indexed: 10/10/2023]
Abstract
Salmonella is an important foodborne pathogen, and recent epidemiological studies have shown high infection rates of Salmonella enterica subsp. enterica serotype Derby (S.Derby) in poultry in western China and other regions. S.Derby presents increasing concerns with the development of resistance to hypertonic environments; however, there are few reports investigating the mechanism of resistance. Therefore, in this study, we examined hypertonic adaptation in S.Derby at the physiological and molecular levels. The K-B paper method, wiping glass bead method, crystal violet staining, and RT-PCR combined with comparative genomics analysis were employed to characterize virulence, drug resistance, biofilm formation, and changes in gene expression of genes related to hypertonic adaptation in S.Derby. Hypertonic-adapted S.Derby exhibited resistance to OXA, AMP, PEN, and CEP antibiotics, and biofilm-forming ability was 1.25 times that of nonadapted S.Derby. RT-PCR results showed that compared with nonadapted S.Derby, the expression of virulence-related genes in hypertonic-adapted S.Derby increased by 2-3 times, that of biofilm-related genes increased by 2-4 times, and that of OXA, AMP, PEN, and CEP-related drug resistance genes was relatively high. Four hypertonic tolerance-related genes (otsA, proV, proW, omsV) were preliminarily identified in S.Derby. The expression of proW was always relatively high in hypertonic-adapted S.Derby, the expression of otsA gradually became higher than that of proW with increasing time of osmotic stress, and the expression of proV and omsV was only high in non-hypertonic-adapted S.Derby.
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Affiliation(s)
- Ganghui Li
- Key Laboratory
of Food Processing
and Safety, College of Food Engineering, Anhui University of Science and Technology, Chuzhou 233100, China
| | - Ju Huang
- Key Laboratory
of Food Processing
and Safety, College of Food Engineering, Anhui University of Science and Technology, Chuzhou 233100, China
| | - Qiuhui Cai
- Key Laboratory
of Food Processing
and Safety, College of Food Engineering, Anhui University of Science and Technology, Chuzhou 233100, China
| | - Zhaohui Wei
- Key Laboratory
of Food Processing
and Safety, College of Food Engineering, Anhui University of Science and Technology, Chuzhou 233100, China
| | - Gang Pen
- Key Laboratory
of Food Processing
and Safety, College of Food Engineering, Anhui University of Science and Technology, Chuzhou 233100, China
| | - Zhen Li
- Key Laboratory
of Food Processing
and Safety, College of Food Engineering, Anhui University of Science and Technology, Chuzhou 233100, China
| | - Junying Wang
- Key Laboratory
of Food Processing
and Safety, College of Food Engineering, Anhui University of Science and Technology, Chuzhou 233100, China
| | - Ligong Zhai
- Key Laboratory
of Food Processing
and Safety, College of Food Engineering, Anhui University of Science and Technology, Chuzhou 233100, China
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29
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Bustamante JA, Ceron JS, Gao IT, Ramirez HA, Aviles MV, Bet Adam D, Brice JR, Cuellar RA, Dockery E, Jabagat MK, Karp DG, Lau JKO, Li S, Lopez-Magaña R, Moore RR, Morin BKR, Nzongo J, Rezaeihaghighi Y, Sapienza-Martinez J, Tran TTK, Huang Z, Duthoy AJ, Barnett MJ, Long SR, Chen JC. A protease and a lipoprotein jointly modulate the conserved ExoR-ExoS-ChvI signaling pathway critical in Sinorhizobium meliloti for symbiosis with legume hosts. PLoS Genet 2023; 19:e1010776. [PMID: 37871041 PMCID: PMC10659215 DOI: 10.1371/journal.pgen.1010776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/20/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023] Open
Abstract
Sinorhizobium meliloti is a model alpha-proteobacterium for investigating microbe-host interactions, in particular nitrogen-fixing rhizobium-legume symbioses. Successful infection requires complex coordination between compatible host and endosymbiont, including bacterial production of succinoglycan, also known as exopolysaccharide-I (EPS-I). In S. meliloti EPS-I production is controlled by the conserved ExoS-ChvI two-component system. Periplasmic ExoR associates with the ExoS histidine kinase and negatively regulates ChvI-dependent expression of exo genes, necessary for EPS-I synthesis. We show that two extracytoplasmic proteins, LppA (a lipoprotein) and JspA (a lipoprotein and a metalloprotease), jointly influence EPS-I synthesis by modulating the ExoR-ExoS-ChvI pathway and expression of genes in the ChvI regulon. Deletions of jspA and lppA led to lower EPS-I production and competitive disadvantage during host colonization, for both S. meliloti with Medicago sativa and S. medicae with M. truncatula. Overexpression of jspA reduced steady-state levels of ExoR, suggesting that the JspA protease participates in ExoR degradation. This reduction in ExoR levels is dependent on LppA and can be replicated with ExoR, JspA, and LppA expressed exogenously in Caulobacter crescentus and Escherichia coli. Akin to signaling pathways that sense extracytoplasmic stress in other bacteria, JspA and LppA may monitor periplasmic conditions during interaction with the plant host to adjust accordingly expression of genes that contribute to efficient symbiosis. The molecular mechanisms underlying host colonization in our model system may have parallels in related alpha-proteobacteria.
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Affiliation(s)
- Julian A. Bustamante
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Josue S. Ceron
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Ivan Thomas Gao
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Hector A. Ramirez
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Milo V. Aviles
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Demsin Bet Adam
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Jason R. Brice
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Rodrigo A. Cuellar
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Eva Dockery
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Miguel Karlo Jabagat
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Donna Grace Karp
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Joseph Kin-On Lau
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Suling Li
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Raymondo Lopez-Magaña
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Rebecca R. Moore
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Bethany Kristi R. Morin
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Juliana Nzongo
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Yasha Rezaeihaghighi
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Joseph Sapienza-Martinez
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Tuyet Thi Kim Tran
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Zhenzhong Huang
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Aaron J. Duthoy
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Melanie J. Barnett
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Sharon R. Long
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Joseph C. Chen
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
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30
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Abstract
Small regulatory RNA (sRNAs) are key mediators of posttranscriptional gene control in bacteria. Assisted by RNA-binding proteins, a single sRNA often modulates the expression of dozens of genes, and thus sRNAs frequently adopt central roles in regulatory networks. Posttranscriptional regulation by sRNAs comes with several unique features that cannot be achieved by transcriptional regulators. However, for optimal network performance, transcriptional and posttranscriptional control mechanisms typically go hand-in-hand. This view is reflected by the ever-growing class of mixed network motifs involving sRNAs and transcription factors, which are ubiquitous in biology and whose regulatory properties we are beginning to understand. In addition, sRNA activity can be antagonized by base-pairing with sponge RNAs, adding yet another layer of complexity to these networks. In this article, we summarize the regulatory concepts underlying sRNA-mediated gene control in bacteria and discuss how sRNAs shape the output of a network, focusing on several key examples.
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Affiliation(s)
- Kai Papenfort
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany;
- Microverse Cluster, Friedrich Schiller University Jena, Jena, Germany
| | - Sahar Melamed
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel;
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31
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Njenga R, Boele J, Öztürk Y, Koch HG. Coping with stress: How bacteria fine-tune protein synthesis and protein transport. J Biol Chem 2023; 299:105163. [PMID: 37586589 PMCID: PMC10502375 DOI: 10.1016/j.jbc.2023.105163] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023] Open
Abstract
Maintaining a functional proteome under different environmental conditions is challenging for every organism, in particular for unicellular organisms, such as bacteria. In order to cope with changing environments and stress conditions, bacteria depend on strictly coordinated proteostasis networks that control protein production, folding, trafficking, and degradation. Regulation of ribosome biogenesis and protein synthesis are cornerstones of this cellular adaptation in all domains of life, which is rationalized by the high energy demand of both processes and the increased resistance of translationally silent cells against internal or external poisons. Reduced protein synthesis ultimately also reduces the substrate load for protein transport systems, which are required for maintaining the periplasmic, inner, and outer membrane subproteomes. Consequences of impaired protein transport have been analyzed in several studies and generally induce a multifaceted response that includes the upregulation of chaperones and proteases and the simultaneous downregulation of protein synthesis. In contrast, generally less is known on how bacteria adjust the protein targeting and transport machineries to reduced protein synthesis, e.g., when cells encounter stress conditions or face nutrient deprivation. In the current review, which is mainly focused on studies using Escherichia coli as a model organism, we summarize basic concepts on how ribosome biogenesis and activity are regulated under stress conditions. In addition, we highlight some recent developments on how stress conditions directly impair protein targeting to the bacterial membrane. Finally, we describe mechanisms that allow bacteria to maintain the transport of stress-responsive proteins under conditions when the canonical protein targeting pathways are impaired.
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Affiliation(s)
- Robert Njenga
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany; Faculty of Biology, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Julian Boele
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Yavuz Öztürk
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Hans-Georg Koch
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany.
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32
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Zhang C, Kong Y, Xiang Q, Ma Y, Guo Q. Bacterial memory in antibiotic resistance evolution and nanotechnology in evolutionary biology. iScience 2023; 26:107433. [PMID: 37575196 PMCID: PMC10415926 DOI: 10.1016/j.isci.2023.107433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023] Open
Abstract
Bacterial memory refers to the phenomenon in which past experiences influence current behaviors in response to changing environments. It serves as a crucial process that enables adaptation and evolution. We first summarize the state-of-art approaches regarding history-dependent behaviors that impact growth dynamics and underlying mechanisms. Then, the phenotypic and genotypic origins of memory and how encoded memory modulates drug tolerance/resistance are reviewed. We also provide a summary of possible memory effects induced by antimicrobial nanoparticles. The regulatory networks and genetic underpinnings responsible for memory building partially overlap with nanoparticle and drug exposures, which may raise concerns about the impact of nanotechnology on adaptation. Finally, we provide a perspective on the use of nanotechnology to harness bacterial memory based on its unique mode of actions on information processing and transmission in bacteria. Exploring bacterial memory mechanisms provides valuable insights into acclimation, evolution, and the potential applications of nanotechnology in harnessing memory.
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Affiliation(s)
- Chengdong Zhang
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Yan Kong
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Qingxin Xiang
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Yayun Ma
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Quanyi Guo
- School of Environment, Beijing Normal University, Beijing 100875, China
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33
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Han YY, Wang JT, Cheng WC, Chen KL, Chi Y, Teng LJ, Wang JK, Wang YL. SERS-based rapid susceptibility testing of commonly administered antibiotics on clinically important bacteria species directly from blood culture of bacteremia patients. World J Microbiol Biotechnol 2023; 39:282. [PMID: 37589866 PMCID: PMC10435613 DOI: 10.1007/s11274-023-03717-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/28/2023] [Indexed: 08/18/2023]
Abstract
Bloodstream infections are a growing public health concern due to emerging pathogens and increasing antimicrobial resistance. Rapid antibiotic susceptibility testing (AST) is urgently needed for timely and optimized choice of antibiotics, but current methods require days to obtain results. Here, we present a general AST protocol based on surface-enhanced Raman scattering (SERS-AST) for bacteremia caused by eight clinically relevant Gram-positive and Gram-negative pathogens treated with seven commonly administered antibiotics. Our results show that the SERS-AST protocol achieves a high level of agreement (96% for Gram-positive and 97% for Gram-negative bacteria) with the widely deployed VITEK 2 diagnostic system. The protocol requires only five hours to complete per blood-culture sample, making it a rapid and effective alternative to conventional methods. Our findings provide a solid foundation for the SERS-AST protocol as a promising approach to optimize the choice of antibiotics for specific bacteremia patients. This novel protocol has the potential to improve patient outcomes and reduce the spread of antibiotic resistance.
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Affiliation(s)
- Yin-Yi Han
- Department of Anesthesiology, National Taiwan University Hospital, 7 Zhongshan S. Road, Taipei, 100225, Taiwan.
- Department of Surgery, National Taiwan University Hospital, 7 Zhongshan S. Road, Taipei, 100225, Taiwan.
- Department of Traumatology, National Taiwan University Hospital, 7 Zhongshan S. Road, Taipei, 100225, Taiwan.
| | - Jann-Tay Wang
- Division of Infectious Diseases, Department of Internal Medicine, National Taiwan University Hospital, 7 Zhongshan S. Road, Taipei, 100225, Taiwan
- Taiwan National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli, 35053, Taiwan
| | - Wei-Chih Cheng
- Institute of Atomic and Molecular Sciences, Academia Sinica, 1 Roosevelt Road Sec. 4, Taipei, 10617, Taiwan
| | - Ko-Lun Chen
- Institute of Atomic and Molecular Sciences, Academia Sinica, 1 Roosevelt Road Sec. 4, Taipei, 10617, Taiwan
| | - Yi Chi
- Institute of Atomic and Molecular Sciences, Academia Sinica, 1 Roosevelt Road Sec. 4, Taipei, 10617, Taiwan
| | - Lee-Jene Teng
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, 1, Roosevelt Road Sec. 4, Taipei, 10048, Taiwan
| | - Juen-Kai Wang
- Institute of Atomic and Molecular Sciences, Academia Sinica, 1 Roosevelt Road Sec. 4, Taipei, 10617, Taiwan.
- Center for Condensed Matter Sciences, National Taiwan University, 1 Roosevelt Road Sec. 4, Taipei, 106319, Taiwan.
| | - Yuh-Lin Wang
- Institute of Atomic and Molecular Sciences, Academia Sinica, 1 Roosevelt Road Sec. 4, Taipei, 10617, Taiwan.
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34
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Hogan AM, Rahman ASMZ, Motnenko A, Natarajan A, Maydaniuk DT, León B, Batun Z, Palacios A, Bosch A, Cardona ST. Profiling cell envelope-antibiotic interactions reveals vulnerabilities to β-lactams in a multidrug-resistant bacterium. Nat Commun 2023; 14:4815. [PMID: 37558695 PMCID: PMC10412643 DOI: 10.1038/s41467-023-40494-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/28/2023] [Indexed: 08/11/2023] Open
Abstract
The cell envelope of Gram-negative bacteria belonging to the Burkholderia cepacia complex (Bcc) presents unique restrictions to antibiotic penetration. As a consequence, Bcc species are notorious for causing recalcitrant multidrug-resistant infections in immunocompromised individuals. Here, we present the results of a genome-wide screen for cell envelope-associated resistance and susceptibility determinants in a Burkholderia cenocepacia clinical isolate. For this purpose, we construct a high-density, randomly-barcoded transposon mutant library and expose it to 19 cell envelope-targeting antibiotics. By quantifying relative mutant fitness with BarSeq, followed by validation with CRISPR-interference, we profile over a hundred functional associations and identify mediators of antibiotic susceptibility in the Bcc cell envelope. We reveal connections between β-lactam susceptibility, peptidoglycan synthesis, and blockages in undecaprenyl phosphate metabolism. The synergy of the β-lactam/β-lactamase inhibitor combination ceftazidime/avibactam is primarily mediated by inhibition of the PenB carbapenemase. In comparison with ceftazidime, avibactam more strongly potentiates the activity of aztreonam and meropenem in a panel of Bcc clinical isolates. Finally, we characterize in Bcc the iron and receptor-dependent activity of the siderophore-cephalosporin antibiotic, cefiderocol. Our work has implications for antibiotic target prioritization, and for using additional combinations of β-lactam/β-lactamase inhibitors that can extend the utility of current antibacterial therapies.
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Affiliation(s)
- Andrew M Hogan
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Anna Motnenko
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Aakash Natarajan
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Dustin T Maydaniuk
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Beltina León
- CINDEFI, CONICET-CCT La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Zayra Batun
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Armando Palacios
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Alejandra Bosch
- CINDEFI, CONICET-CCT La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Silvia T Cardona
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada.
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35
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Bekale LA, Sharma D, Bacacao B, Chen J, Santa Maria PL. Eradication of Bacterial Persister Cells By Leveraging Their Low Metabolic Activity Using Adenosine Triphosphate Coated Gold Nanoclusters. NANO TODAY 2023; 51:101895. [PMID: 37575958 PMCID: PMC10421611 DOI: 10.1016/j.nantod.2023.101895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Bacteria first develop tolerance after antibiotic exposure; later genetic resistance emerges through the population of tolerant bacteria. Bacterial persister cells are the multidrug-tolerant subpopulation within an isogenic bacteria culture that maintains genetic susceptibility to antibiotics. Because of this link between antibiotic tolerance and resistance and the rise of antibiotic resistance, there is a pressing need to develop treatments to eradicate persister cells. Current anti persister cell strategies are based on the paradigm of "awakening" them from their low metabolic state before attempting eradication with traditional antibiotics. Herein, we demonstrate that the low metabolic activity of persister cells can be exploited for eradication over their metabolically active counterparts. We engineered gold nanoclusters coated with adenosine triphosphate (AuNC@ATP) as a benchmark nanocluster that kills persister cells over exponential growth bacterial cells and prove the feasibility of this new concept. Finally, using AuNC@ATP as a new research tool, we demonstrated that it is possible to prevent the emergence of antibiotic-resistant superbugs with an anti-persister compound. Eradicating persister cells with AuNC@ATP in an isogenic culture of bacteria stops the emergence of superbug bacteria mediated by the sub-lethal dose of conventional antibiotics. Our findings lay the groundwork for developing novel nano-antibiotics targeting persister cells, which promise to prevent the emergence of superbugs and prolong the lifespan of currently available antibiotics.
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Affiliation(s)
- Laurent A. Bekale
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, 801 Welch Road Stanford, CA 94305-5739, USA
| | - Devesh Sharma
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, 801 Welch Road Stanford, CA 94305-5739, USA
| | - Brian Bacacao
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, 801 Welch Road Stanford, CA 94305-5739, USA
| | - Jing Chen
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, 801 Welch Road Stanford, CA 94305-5739, USA
| | - Peter L. Santa Maria
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, 801 Welch Road Stanford, CA 94305-5739, USA
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36
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Huang C, Li W, Chen J. Stringent Response Factor DksA Contributes to Fatty Acid Degradation Function to Influence Cell Membrane Stability and Polymyxin B Resistance of Yersinia enterocolitica. Int J Mol Sci 2023; 24:11951. [PMID: 37569327 PMCID: PMC10418728 DOI: 10.3390/ijms241511951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
DksA is a proteobacterial regulator that binds directly to the secondary channel of RNA polymerase with (p)ppGpp and is responsible for various bacterial physiological activities. While (p)ppGpp is known to be involved in the regulation and response of fatty acid metabolism pathways in many foodborne pathogens, the role of DksA in this process has yet to be clarified. This study aimed to characterize the function of DksA on fatty acid metabolism and cell membrane structure in Yersinia enterocolitica. Therefore, comparison analysis of gene expression, growth conditions, and membrane permeabilization among the wide-type (WT), DksA-deficient mutant (YEND), and the complemented strain was carried out. It confirmed that deletion of DksA led to a more than four-fold decrease in the expression of fatty acid degradation genes, including fadADEIJ. Additionally, YEND exhibited a smaller growth gap compared to the WT strain at low temperatures, indicating that DksA is not required for the growth of Y. enterocolitica in cold environments. Given that polymyxin B is a cationic antimicrobial peptide that targets the cell membrane, the roles of DksA under polymyxin B exposure were also characterized. It was found that DksA positively regulates the integrity of the inner and outer membranes of Y. enterocolitica under polymyxin B, preventing the leakage of intracellular nucleic acids and proteins and ultimately reducing the sensitivity of Y. enterocolitica to polymyxin B. Taken together, this study provides insights into the functions of DksA and paves the way for novel fungicide development.
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Affiliation(s)
| | | | - Jingyu Chen
- Beijing Laboratory for Food Quality and Safety, College of Food Science & Nutritional Engineering, China Agricultural University, 17 Qinghua East Rd., Beijing 100083, China
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37
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Qian M, Ismail BB, He Q, Zhang X, Yang Z, Ding T, Ye X, Liu D, Guo M. Inhibitory mechanisms of promising antimicrobials from plant byproducts: A review. Compr Rev Food Sci Food Saf 2023; 22:2523-2590. [PMID: 37070214 DOI: 10.1111/1541-4337.13152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 03/16/2023] [Accepted: 03/16/2023] [Indexed: 04/19/2023]
Abstract
Plant byproducts and waste present enormous environmental challenges and an opportunity for valorization and industrial application. Due to consumer demands for natural compounds, the evident paucity of novel antimicrobial agents against foodborne pathogens, and the urgent need to improve the arsenal against infectious diseases and antimicrobial resistance (AMR), plant byproduct compounds have attracted significant research interest. Emerging research highlighted their promising antimicrobial activity, yet the inhibitory mechanisms remain largely unexplored. Therefore, this review summarizes the overall research on the antimicrobial activity and inhibitory mechanisms of plant byproduct compounds. A total of 315 natural antimicrobials from plant byproducts, totaling 1338 minimum inhibitory concentrations (MIC) (in μg/mL) against a broad spectrum of bacteria, were identified, and a particular emphasis was given to compounds with high or good antimicrobial activity (typically <100 μg/mL MIC). Moreover, the antimicrobial mechanisms, particularly against bacterial pathogens, were discussed in-depth, summarizing the latest research on using natural compounds to combat pathogenic microorganisms and AMR. Furthermore, safety concerns, relevant legislation, consumer perspective, and current gaps in the valorization of plant byproducts-derived compounds were comprehensively discussed. This comprehensive review covering up-to-date information on antimicrobial activity and mechanisms represents a powerful tool for screening and selecting the most promising plant byproduct compounds and sources for developing novel antimicrobial agents.
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Affiliation(s)
- Mengyan Qian
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou, China
| | - Balarabe B Ismail
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou, China
- Department of Food Science and Technology, Bayero University Kano, Kano, Nigeria
| | - Qiao He
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou, China
| | - Xinhui Zhang
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou, China
| | - Zhehao Yang
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou, China
| | - Tian Ding
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou, China
- Fuli Institute of Food Science, Zhejiang University, Hangzhou, China
- Ningbo Research Institute, Zhejiang University, Ningbo, China
| | - Xingqian Ye
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou, China
- Fuli Institute of Food Science, Zhejiang University, Hangzhou, China
- Ningbo Research Institute, Zhejiang University, Ningbo, China
| | - Donghong Liu
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou, China
- Fuli Institute of Food Science, Zhejiang University, Hangzhou, China
- Ningbo Research Institute, Zhejiang University, Ningbo, China
| | - Mingming Guo
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou, China
- Fuli Institute of Food Science, Zhejiang University, Hangzhou, China
- Ningbo Research Institute, Zhejiang University, Ningbo, China
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38
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Seidel M, Skotnicka D, Glatter T, Søgaard-Andersen L. During heat stress in Myxococcus xanthus, the CdbS PilZ domain protein, in concert with two PilZ-DnaK chaperones, perturbs chromosome organization and accelerates cell death. PLoS Genet 2023; 19:e1010819. [PMID: 37339150 DOI: 10.1371/journal.pgen.1010819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/07/2023] [Indexed: 06/22/2023] Open
Abstract
C-di-GMP is a bacterial second messenger that regulates diverse processes in response to environmental or cellular cues. The nucleoid-associated protein (NAP) CdbA in Myxococcus xanthus binds c-di-GMP and DNA in a mutually exclusive manner in vitro. CdbA is essential for viability, and CdbA depletion causes defects in chromosome organization, leading to a block in cell division and, ultimately, cell death. Most NAPs are not essential; therefore, to explore the paradoxical cdbA essentiality, we isolated suppressor mutations that restored cell viability without CdbA. Most mutations mapped to cdbS, which encodes a stand-alone c-di-GMP binding PilZ domain protein, and caused loss-of-function of cdbS. Cells lacking CdbA and CdbS or only CdbS were fully viable and had no defects in chromosome organization. CdbA depletion caused post-transcriptional upregulation of CdbS accumulation, and this CdbS over-accumulation was sufficient to disrupt chromosome organization and cause cell death. CdbA depletion also caused increased accumulation of CsdK1 and CsdK2, two unusual PilZ-DnaK chaperones. During CdbA depletion, CsdK1 and CsdK2, in turn, enabled the increased accumulation and toxicity of CdbS, likely by stabilizing CdbS. Moreover, we demonstrate that heat stress, possibly involving an increased cellular c-di-GMP concentration, induced the CdbA/CsdK1/CsdK2/CdbS system, causing a CsdK1- and CsdK2-dependent increase in CdbS accumulation. Thereby this system accelerates heat stress-induced chromosome mis-organization and cell death. Collectively, this work describes a unique system that contributes to regulated cell death in M. xanthus and suggests a link between c-di-GMP signaling and regulated cell death in bacteria.
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Affiliation(s)
- Michael Seidel
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Dorota Skotnicka
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Timo Glatter
- Core Facility for Mass Spectrometry & Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Lotte Søgaard-Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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39
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Choi U, Park SH, Lee HB, Son JE, Lee CR. Coordinated and Distinct Roles of Peptidoglycan Carboxypeptidases DacC and DacA in Cell Growth and Shape Maintenance under Stress Conditions. Microbiol Spectr 2023; 11:e0001423. [PMID: 37098975 PMCID: PMC10269652 DOI: 10.1128/spectrum.00014-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 04/09/2023] [Indexed: 04/27/2023] Open
Abstract
Peptidoglycan (PG) is an essential bacterial architecture pivotal for shape maintenance and adaptation to osmotic stress. Although PG synthesis and modification are tightly regulated under harsh environmental stresses, few related mechanisms have been investigated. In this study, we aimed to investigate the coordinated and distinct roles of the PG dd-carboxypeptidases (DD-CPases) DacC and DacA in cell growth under alkaline and salt stresses and shape maintenance in Escherichia coli. We found that DacC is an alkaline DD-CPase, the enzyme activity and protein stability of which are significantly enhanced under alkaline stress. Both DacC and DacA were required for bacterial growth under alkaline stress, whereas only DacA was required for growth under salt stress. Under normal growth conditions, only DacA was necessary for cell shape maintenance, while under alkaline stress conditions, both DacA and DacC were necessary for cell shape maintenance, but their roles were distinct. Notably, all of these roles of DacC and DacA were independent of ld-transpeptidases, which are necessary for the formation of PG 3-3 cross-links and covalent bonds between PG and the outer membrane lipoprotein Lpp. Instead, DacC and DacA interacted with penicillin-binding proteins (PBPs)-dd-transpeptidases-mostly in a C-terminal domain-dependent manner, and these interactions were necessary for most of their roles. Collectively, our results demonstrate the coordinated and distinct novel roles of DD-CPases in bacterial growth and shape maintenance under stress conditions and provide novel insights into the cellular functions of DD-CPases associated with PBPs. IMPORTANCE Most bacteria have a peptidoglycan architecture for cell shape maintenance and protection against osmotic challenges. Peptidoglycan dd-carboxypeptidases control the amount of pentapeptide substrates, which are used in the formation of 4-3 cross-links by the peptidoglycan synthetic dd-transpeptidases, penicillin-binding proteins (PBPs). Seven dd-carboxypeptidases exist in Escherichia coli, but the physiological significance of their redundancy and their roles in peptidoglycan synthesis are poorly understood. Here, we showed that DacC is an alkaline dd-carboxypeptidase for which both protein stability and enzyme activity are significantly enhanced at high pH. Strikingly, dd-carboxypeptidases DacC and DacA physically interacted with PBPs, and these interactions were necessary for cell shape maintenance as well as growth under alkaline and salt stresses. Thus, cooperation between dd-carboxypeptidases and PBPs may allow E. coli to overcome various stresses and to maintain cell shape.
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Affiliation(s)
- Umji Choi
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
| | - Si Hyoung Park
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
| | - Han Byeol Lee
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
| | - Ji Eun Son
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
| | - Chang-Ro Lee
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
- The Natural Science Research Institute, Myongji University, Yongin, Gyeonggido, Republic of Korea
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40
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Frantz R, Gwozdzinski K, Gisch N, Doijad SP, Hudel M, Wille M, Abu Mraheil M, Schwudke D, Imirzalioglu C, Falgenhauer L, Ehrmann M, Chakraborty T. A Single Residue within the MCR-1 Protein Confers Anticipatory Resilience. Microbiol Spectr 2023; 11:e0359222. [PMID: 37071007 PMCID: PMC10269488 DOI: 10.1128/spectrum.03592-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 03/21/2023] [Indexed: 04/19/2023] Open
Abstract
The envelope stress response (ESR) of Gram-negative enteric bacteria senses fluctuations in nutrient availability and environmental changes to avert damage and promote survival. It has a protective role toward antimicrobials, but direct interactions between ESR components and antibiotic resistance genes have not been demonstrated. Here, we report interactions between a central regulator of ESR viz., the two-component signal transduction system CpxRA (conjugative pilus expression), and the recently described mobile colistin resistance protein (MCR-1). Purified MCR-1 is specifically cleaved within its highly conserved periplasmic bridge element, which links its N-terminal transmembrane domain with the C-terminal active-site periplasmic domain, by the CpxRA-regulated serine endoprotease DegP. Recombinant strains harboring cleavage site mutations in MCR-1 are either protease resistant or degradation susceptible, with widely differing consequences for colistin resistance. Transfer of the gene encoding a degradation-susceptible mutant to strains that lack either DegP or its regulator CpxRA restores expression and colistin resistance. MCR-1 production in Escherichia coli imposes growth restriction in strains lacking either DegP or CpxRA, effects that are reversed by transactive expression of DegP. Excipient allosteric activation of the DegP protease specifically inhibits growth of isolates carrying mcr-1 plasmids. As CpxRA directly senses acidification, growth of strains at moderately low pH dramatically increases both MCR-1-dependent phosphoethanolamine (PEA) modification of lipid A and colistin resistance levels. Strains expressing MCR-1 are also more resistant to antimicrobial peptides and bile acids. Thus, a single residue external to its active site induces ESR activity to confer resilience in MCR-1-expressing strains to commonly encountered environmental stimuli, such as changes in acidity and antimicrobial peptides. Targeted activation of the nonessential protease DegP can lead to the elimination of transferable colistin resistance in Gram-negative bacteria. IMPORTANCE The global presence of transferable mcr genes in a wide range of Gram-negative bacteria from clinical, veterinary, food, and aquaculture environments is disconcerting. Its success as a transmissible resistance factor remains enigmatic, because its expression imposes fitness costs and imparts only moderate levels of colistin resistance. Here, we show that MCR-1 triggers regulatory components of the envelope stress response, a system that senses fluctuations in nutrient availability and environmental changes, to promote bacterial survival in low pH environments. We identify a single residue within a highly conserved structural element of mcr-1 distal to its catalytic site that modulates resistance activity and triggers the ESR. Using mutational analysis, quantitative lipid A profiling and biochemical assays, we determined that growth in low pH environments dramatically increases colistin resistance levels and promotes resistance to bile acids and antimicrobial peptides. We exploited these findings to develop a targeted approach that eliminates mcr-1 and its plasmid carriers.
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Affiliation(s)
- Renate Frantz
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| | - Konrad Gwozdzinski
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| | - Nicolas Gisch
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Swapnil Prakash Doijad
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| | - Martina Hudel
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Maria Wille
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Mobarak Abu Mraheil
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Dominik Schwudke
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Partner Site: Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Airway Research Center North, Partner Site: Research Center Borstel, Borstel, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- Hessian University Competence Center for Hospital Hygiene, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| | - Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
- Hessian University Competence Center for Hospital Hygiene, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| | - Michael Ehrmann
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- Hessian University Competence Center for Hospital Hygiene, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
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Ghandour R, Papenfort K. Small regulatory RNAs in Vibrio cholerae. MICROLIFE 2023; 4:uqad030. [PMID: 37441523 PMCID: PMC10335731 DOI: 10.1093/femsml/uqad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023]
Abstract
Vibrio cholerae is a major human pathogen causing the diarrheal disease, cholera. Regulation of virulence in V. cholerae is a multifaceted process involving gene expression changes at the transcriptional and post-transcriptional level. Whereas various transcription factors have been reported to modulate virulence in V. cholerae, small regulatory RNAs (sRNAs) have now been established to also participate in virulence control and the regulation of virulence-associated processes, such as biofilm formation, quorum sensing, stress response, and metabolism. In most cases, these sRNAs act by base-pairing with multiple target transcripts and this process typically requires the aid of an RNA-binding protein, such as the widely conserved Hfq protein. This review article summarizes the functional roles of sRNAs in V. cholerae, their underlying mechanisms of gene expression control, and how sRNAs partner with transcription factors to modulate complex regulatory programs. In addition, we will discuss regulatory principles discovered in V. cholerae that not only apply to other Vibrio species, but further extend into the large field of RNA-mediated gene expression control in bacteria.
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Affiliation(s)
- Rabea Ghandour
- Friedrich Schiller University Jena, Institute of Microbiology, 07745 Jena, Germany
| | - Kai Papenfort
- Corresponding author. Institute of Microbiology, General Microbiology, Friedrich Schiller University Jena, Winzerlaer Straße 2, 07745 Jena, Germany. Tel: +49-3641-949-311; E-mail:
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Fernandes M, González-Ballesteros N, da Costa A, Machado R, Gomes AC, Rodríguez-Argüelles MC. Antimicrobial and anti-biofilm activity of silver nanoparticles biosynthesized with Cystoseira algae extracts. J Biol Inorg Chem 2023; 28:439-450. [PMID: 37083842 PMCID: PMC10149473 DOI: 10.1007/s00775-023-01999-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 04/06/2023] [Indexed: 04/22/2023]
Abstract
Antimicrobial resistance is an ever-growing global concern to public health with no clear or immediate solution. Silver nanoparticles (AgNPs) have long been proposed as efficient agents to fight the growing number of antibiotic-resistant strains. However, the synthesis of these particles is often linked to high costs and the use of toxic, hazardous chemicals, with environmental and health impact. In this study, we successfully produced AgNPs by green synthesis with the aid of the extract of two brown algae-Cystoseira baccata (CB) and Cystoseira tamariscifolia (CT)-and characterized their physico-chemical properties. The NPs produced in both cases (Ag@CB and Ag@CT) present similar sizes, with mean diameters of around 22 nm. The antioxidant activity of the extracts and the NPs was evaluated, with the extracts showing important antioxidant activity. The bacteriostatic and bactericidal properties of both Ag@CB and Ag@CT were tested and compared with gold NPs produced in the same algae extracts as previously reported. AgNPs demonstrated the strongest bacteriostatic and bactericidal properties, at concentrations as low as 2.16 µg/mL against Pseudomonas aeruginosa and Escherichia coli. Finally, the capacity of these samples to prevent the formation of biofilms characteristic of infections with a poorer outcome was assessed, obtaining similar results. This work points towards an alternative for the treatment of bacterial infections, even biofilm-inducing, with the possibility of minimizing the risk of drug resistance, albeit the necessary caution implied using metallic NPs.
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Affiliation(s)
- Mário Fernandes
- Centre of Molecular and Environmental Biology (CBMA)/Aquatic Research Network (ARNET) Associate Laboratory, Department of Biology, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- Institute of Science and Innovation for Sustainability (IB-S), Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | | | - André da Costa
- Centre of Molecular and Environmental Biology (CBMA)/Aquatic Research Network (ARNET) Associate Laboratory, Department of Biology, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- Institute of Science and Innovation for Sustainability (IB-S), Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Raúl Machado
- Centre of Molecular and Environmental Biology (CBMA)/Aquatic Research Network (ARNET) Associate Laboratory, Department of Biology, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- Institute of Science and Innovation for Sustainability (IB-S), Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Andreia C Gomes
- Centre of Molecular and Environmental Biology (CBMA)/Aquatic Research Network (ARNET) Associate Laboratory, Department of Biology, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
- Institute of Science and Innovation for Sustainability (IB-S), Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
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43
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Hwang Y, Harshey RM. A Second Role for the Second Messenger Cyclic-di-GMP in E. coli: Arresting Cell Growth by Altering Metabolic Flow. mBio 2023; 14:e0061923. [PMID: 37036337 PMCID: PMC10127611 DOI: 10.1128/mbio.00619-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 03/20/2023] [Indexed: 04/11/2023] Open
Abstract
c-di-GMP primarily controls motile to sessile transitions in bacteria. Diguanylate cyclases (DGCs) catalyze the synthesis of c-di-GMP from two GTP molecules. Typically, bacteria encode multiple DGCs that are activated by specific environmental signals. Their catalytic activity is modulated by c-di-GMP binding to autoinhibitory sites (I-sites). YfiN is a conserved inner membrane DGC that lacks these sites. Instead, YfiN activity is directly repressed by periplasmic YfiR, which is inactivated by redox stress. In Escherichia coli, an additional envelope stress causes YfiN to relocate to the mid-cell to inhibit cell division by interacting with the division machinery. Here, we report a third activity for YfiN in E. coli, where cell growth is inhibited without YfiN relocating to the division site. This action of YfiN is only observed when the bacteria are cultured on gluconeogenic carbon sources, and is dependent on absence of the autoinhibitory sites. Restoration of I-site function relieves the growth-arrest phenotype, and disabling this function in a heterologous DGC causes acquisition of this phenotype. Arrested cells are tolerant to a wide range of antibiotics. We show that the likely cause of growth arrest is depletion of cellular GTP from run-away synthesis of c-di-GMP, explaining the dependence of growth arrest on gluconeogenic carbon sources that exhaust more GTP during production of glucose. This is the first report of c-di-GMP-mediated growth arrest by altering metabolic flow. IMPORTANCE The c-di-GMP signaling network in bacteria not only controls a variety of cellular processes such as motility, biofilms, cell development, and virulence, but does so by a dizzying array of mechanisms. The DGC YfiN singularly represents the versatility of this network in that it not only inhibits motility and promotes biofilms, but also arrests growth in Escherichia coli by relocating to the mid-cell and blocking cell division. The work described here reveals that YfiN arrests growth by yet another mechanism in E. coli, changing metabolic flow. This function of YfiN, or of DGCs without autoinhibitory I-sites, may contribute to antibiotic tolerant persisters in relevant niches such as the gut where gluconeogenic sugars are found.
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Affiliation(s)
- YuneSahng Hwang
- Department of Molecular Biosciences and LaMontagne Center for Infectious Diseases, University of Texas at Austin, Austin, Texas, USA
| | - Rasika M. Harshey
- Department of Molecular Biosciences and LaMontagne Center for Infectious Diseases, University of Texas at Austin, Austin, Texas, USA
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Aurass P, Kim S, Pinedo V, Cava F, Isberg RR. Identification of Genes Required for Long-Term Survival of Legionella pneumophila in Water. mSphere 2023; 8:e0045422. [PMID: 36988466 PMCID: PMC10117105 DOI: 10.1128/msphere.00454-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/24/2023] [Indexed: 03/30/2023] Open
Abstract
Long-term survival of Legionella pneumophila in aquatic environments is thought to be important for facilitating epidemic outbreaks. Eliminating bacterial colonization in plumbing systems is the primary strategy that depletes this reservoir and prevents disease. To uncover L. pneumophila determinants facilitating survival in water, a Tn-seq strategy was used to identify survival-defective mutants during 50-day starvation in tap water at 42°C. The mutants with the most drastic survival defects carried insertions in electron transport chain genes, indicating that membrane energy charge and/or ATP synthesis requires the generation of a proton gradient by the respiratory chain to maintain survival in the presence of water stress. In addition, periplasmically localized proteins that are known (EnhC) or hypothesized (lpg1697) to stabilize the cell wall against turnover were essential for water survival. To test that the identified mutations disrupted water survival, candidate genes were knocked down by CRISPRi. The vast majority of knockdown strains with verified transcript depletion showed remarkably low viability after 50-day incubations. To demonstrate that maintenance of cell wall integrity was an important survival determinant, a deletion mutation in lpg1697, in a gene encoding a predicted l,d-transpeptidase domain, was analyzed. The loss of this gene resulted in increased osmolar sensitivity and carbenicillin hypersensitivity relative to the wild type, as predicted for loss of an l,d-transpeptidase. These results indicate that the L. pneumophila envelope has been evolutionarily selected to allow survival under conditions in which the bacteria are subjected to long-term exposure to starvation and low osmolar conditions. IMPORTANCE Water is the primary vector for transmission of L. pneumophila to humans, and the pathogen is adapted to persist in this environment for extended periods of time. Preventing survival of L. pneumophila in water is therefore critical for prevention of Legionnaires' disease. We analyzed dense transposon mutation pools for strains with severe survival defects during a 50-day water incubation at 42°C. By tracking the associated transposon insertion sites in the genome, we defined a distinct essential gene set for water survival and demonstrate that a predicted peptidoglycan cross-linking enzyme, lpg1697, and components of the electron transport chain are required to ensure survival of the pathogen. Our results indicate that select characteristics of the cell wall and components of the respiratory chain of L. pneumophila are primary evolutionary targets being shaped to promote its survival in water.
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Affiliation(s)
- Philipp Aurass
- Department of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Seongok Kim
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Victor Pinedo
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Ralph R. Isberg
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
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Wang W, Cao Y, Li J, Lu S, Ge H, Pan S, Pan X, Wang L. The impact of osmotic stresses on the biofilm formation, immunodetection, and morphology of Aeromonas hydrophila. Microbiol Res 2023; 269:127301. [PMID: 36689842 DOI: 10.1016/j.micres.2023.127301] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/29/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
Aeromonas hydrophila (Ah) is a zoonotic pathogen of great importance to aquaculture and human health. This study systematically evaluated the impact of salinity, sugar, ammonia nitrogen, and nitric nitrogen levels on the fitness of Ah by using Luria-Bertani (LB) broth supplemented with different concentrations of NaCl, sucrose, NH4Cl, urea, NaNO2 or NaNO3. Results showed that the static biofilm formation of Ah was higher at 28 °C compared to 37 °C (P < 0.05). At 28 °C, as the NaCl (>1 %) and sucrose levels increased, the Ah biofilm formation and the binding between Ah cells and monoclonal antibodies (mAbs, for immunodetection) decreased. Elevated ammonia nitrogen and nitric nitrogen levels generated no significant impact on Ah biofilm formation or immunodetection (P > 0.05). The expression of mAbs-targeted Omp remained unchanged under high NaCl or sucrose conditions. Further analysis showed that high sucrose conditions led to the over-expression of the extracellular polysaccharides (PS) and promoted the formation of capsule-like structures. These over-expressed PS and capsule structures might be one reason explaining the inhibited immunodetection efficacy. Results generated from this study provide crucial insights for the design of recovery and detection protocols for Ah present in food or environmental samples.
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Affiliation(s)
- Wenbin Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, Jiangsu, China; Key Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture and Rural Affairs; Key Laboratory of Fish Health and Nutrition of Zhejiang Province; Zhejiang Institute of Freshwater Fisheries, Huzhou, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, Jiangsu, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, Jiangsu, China
| | - Ye Cao
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, Jiangsu, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, Jiangsu, China
| | - Jing Li
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, Jiangsu, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, Jiangsu, China
| | - Shuaichen Lu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, Jiangsu, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, Jiangsu, China
| | - Hongxing Ge
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, Jiangsu, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, Jiangsu, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, Jiangsu, China
| | - Saikun Pan
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, Jiangsu, China; Key Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture and Rural Affairs; Key Laboratory of Fish Health and Nutrition of Zhejiang Province; Zhejiang Institute of Freshwater Fisheries, Huzhou, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, Jiangsu, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, Jiangsu, China
| | - Xiaoyi Pan
- Key Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture and Rural Affairs; Key Laboratory of Fish Health and Nutrition of Zhejiang Province; Zhejiang Institute of Freshwater Fisheries, Huzhou, China.
| | - Luxin Wang
- Department of Food Science and Technology, University of California Davis, Davis, CA 95616, USA.
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Liang Z, Lin Q, Wang Q, Huang L, Liu H, Shi Z, Cui Z, Zhou X, Gao YG, Zhou J, Zhang LH, Deng Y. Gram-negative bacteria resist antimicrobial agents by a DzrR-mediated envelope stress response. BMC Biol 2023; 21:62. [PMID: 36978084 PMCID: PMC10052836 DOI: 10.1186/s12915-023-01565-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND Envelope stress responses (ESRs) are critical for adaptive resistance of Gram-negative bacteria to envelope-targeting antimicrobial agents. However, ESRs are poorly defined in a large number of well-known plant and human pathogens. Dickeya oryzae can withstand a high level of self-produced envelope-targeting antimicrobial agents zeamines through a zeamine-stimulated RND efflux pump DesABC. Here, we unraveled the mechanism of D. oryzae response to zeamines and determined the distribution and function of this novel ESR in a variety of important plant and human pathogens. RESULTS In this study, we documented that a two-component system regulator DzrR of D. oryzae EC1 mediates ESR in the presence of envelope-targeting antimicrobial agents. DzrR was found modulating bacterial response and resistance to zeamines through inducing the expression of RND efflux pump DesABC, which is likely independent on DzrR phosphorylation. In addition, DzrR could also mediate bacterial responses to structurally divergent envelope-targeting antimicrobial agents, including chlorhexidine and chlorpromazine. Significantly, the DzrR-mediated response was independent on the five canonical ESRs. We further presented evidence that the DzrR-mediated response is conserved in the bacterial species of Dickeya, Ralstonia, and Burkholderia, showing that a distantly located DzrR homolog is the previously undetermined regulator of RND-8 efflux pump for chlorhexidine resistance in B. cenocepacia. CONCLUSIONS Taken together, the findings from this study depict a new widely distributed Gram-negative ESR mechanism and present a valid target and useful clues to combat antimicrobial resistance.
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Affiliation(s)
- Zhibin Liang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Qiqi Lin
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Qingwei Wang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Luhao Huang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
| | - Huidi Liu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Zurong Shi
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
- School of Biological Engineering, HuaiNan Normal University, Huainan, 232038, China
| | - Zining Cui
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Xiaofan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yong-Gui Gao
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 639798, Singapore
| | - Jianuan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Lian-Hui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
| | - Yizhen Deng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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47
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Solmi L, Rossi FR, Romero FM, Bach-Pages M, Preston GM, Ruiz OA, Gárriz A. Polyamine-mediated mechanisms contribute to oxidative stress tolerance in Pseudomonas syringae. Sci Rep 2023; 13:4279. [PMID: 36922543 PMCID: PMC10017717 DOI: 10.1038/s41598-023-31239-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023] Open
Abstract
Bacterial phytopathogens living on the surface or within plant tissues may experience oxidative stress because of the triggered plant defense responses. Although it has been suggested that polyamines can defend bacteria from this stress, the mechanism behind this action is not entirely understood. In this study, we investigated the effects of oxidative stress on the polyamine homeostasis of the plant pathogen Pseudomonas syringae and the functions of these compounds in bacterial stress tolerance. We demonstrated that bacteria respond to H2O2 by increasing the external levels of the polyamine putrescine while maintaining the inner concentrations of this compound as well as the analogue amine spermidine. In line with this, adding exogenous putrescine to media increased bacterial tolerance to H2O2. Deletion of arginine decarboxylase (speA) and ornithine decarboxylate (speC), prevented the synthesis of putrescine and augmented susceptibility to H2O2, whereas targeting spermidine synthesis alone through deletion of spermidine synthase (speE) increased the level of extracellular putrescine and enhanced H2O2 tolerance. Further research demonstrated that the increased tolerance of the ΔspeE mutant correlated with higher expression of H2O2-degrading catalases and enhanced outer cell membrane stability. Thus, this work demonstrates previously unrecognized connections between bacterial defense mechanisms against oxidative stress and the polyamine metabolism.
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Affiliation(s)
- Leandro Solmi
- Instituto Tecnológico de Chascomús (CONICET-UNSAM), Avenida Intendente Marino Km 8.2, Chascomús, CP7130, Buenos Aires, Argentina.,Escuela de Bio y Nanotecnologías (UNSAM), Buenos Aires, Argentina
| | - Franco R Rossi
- Instituto Tecnológico de Chascomús (CONICET-UNSAM), Avenida Intendente Marino Km 8.2, Chascomús, CP7130, Buenos Aires, Argentina.,Escuela de Bio y Nanotecnologías (UNSAM), Buenos Aires, Argentina
| | - Fernando M Romero
- Instituto Tecnológico de Chascomús (CONICET-UNSAM), Avenida Intendente Marino Km 8.2, Chascomús, CP7130, Buenos Aires, Argentina.,Escuela de Bio y Nanotecnologías (UNSAM), Buenos Aires, Argentina
| | | | - Gail M Preston
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Oscar A Ruiz
- Instituto Tecnológico de Chascomús (CONICET-UNSAM), Avenida Intendente Marino Km 8.2, Chascomús, CP7130, Buenos Aires, Argentina.,Escuela de Bio y Nanotecnologías (UNSAM), Buenos Aires, Argentina
| | - Andrés Gárriz
- Instituto Tecnológico de Chascomús (CONICET-UNSAM), Avenida Intendente Marino Km 8.2, Chascomús, CP7130, Buenos Aires, Argentina. .,Escuela de Bio y Nanotecnologías (UNSAM), Buenos Aires, Argentina.
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Cho SH, Dekoninck K, Collet JF. Envelope-Stress Sensing Mechanism of Rcs and Cpx Signaling Pathways in Gram-Negative Bacteria. J Microbiol 2023; 61:317-329. [PMID: 36892778 DOI: 10.1007/s12275-023-00030-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 03/10/2023]
Abstract
The global public health burden of bacterial antimicrobial resistance (AMR) is intensified by Gram-negative bacteria, which have an additional membrane, the outer membrane (OM), outside of the peptidoglycan (PG) cell wall. Bacterial two-component systems (TCSs) aid in maintaining envelope integrity through a phosphorylation cascade by controlling gene expression through sensor kinases and response regulators. In Escherichia coli, the major TCSs defending cells from envelope stress and adaptation are Rcs and Cpx, which are aided by OM lipoproteins RcsF and NlpE as sensors, respectively. In this review, we focus on these two OM sensors. β-Barrel assembly machinery (BAM) inserts transmembrane OM proteins (OMPs) into the OM. BAM co-assembles RcsF, the Rcs sensor, with OMPs, forming the RcsF-OMP complex. Researchers have presented two models for stress sensing in the Rcs pathway. The first model suggests that LPS perturbation stress disassembles the RcsF-OMP complex, freeing RcsF to activate Rcs. The second model proposes that BAM cannot assemble RcsF into OMPs when the OM or PG is under specific stresses, and thus, the unassembled RcsF activates Rcs. These two models may not be mutually exclusive. Here, we evaluate these two models critically in order to elucidate the stress sensing mechanism. NlpE, the Cpx sensor, has an N-terminal (NTD) and a C-terminal domain (CTD). A defect in lipoprotein trafficking results in NlpE retention in the inner membrane, provoking the Cpx response. Signaling requires the NlpE NTD, but not the NlpE CTD; however, OM-anchored NlpE senses adherence to a hydrophobic surface, with the NlpE CTD playing a key role in this function.
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Affiliation(s)
- Seung-Hyun Cho
- WELBIO-Walloon Excellence in Life Sciences and Biotechnology, 1200, Brussels, Belgium. .,de Duve Institute, Université Catholique de Louvain, 1200, Brussels, Belgium.
| | - Kilian Dekoninck
- WELBIO-Walloon Excellence in Life Sciences and Biotechnology, 1200, Brussels, Belgium.,de Duve Institute, Université Catholique de Louvain, 1200, Brussels, Belgium.,University of California, Berkeley, CA, 94720, USA
| | - Jean-Francois Collet
- WELBIO-Walloon Excellence in Life Sciences and Biotechnology, 1200, Brussels, Belgium.,de Duve Institute, Université Catholique de Louvain, 1200, Brussels, Belgium
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Öztürk FY, Darcan C, Kariptaş E. The Determination, Monitoring, Molecular Mechanisms and Formation of Biofilm in E. coli. Braz J Microbiol 2023; 54:259-277. [PMID: 36577889 PMCID: PMC9943865 DOI: 10.1007/s42770-022-00895-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 12/16/2022] [Indexed: 12/30/2022] Open
Abstract
Biofilms are cell assemblies embedded in an exopolysaccharide matrix formed by microorganisms of a single or many different species. This matrix in which they are embedded protects the bacteria from external influences and antimicrobial effects. The biofilm structure that microorganisms form to protect themselves from harsh environmental conditions and survive is found in nature in many different environments. These environments where biofilm formation occurs have in common that they are in contact with fluids. The gene expression of bacteria in complex biofilm differs from that of bacteria in the planktonic state. The differences in biofilm cell expression are one of the effects of community life. Means of quorum sensing, bacteria can act in coordination with each other. At the same time, while biofilm formation provides many benefits to bacteria, it has positive and negative effects in many different areas. Depending on where they occur, biofilms can cause serious health problems, contamination risks, corrosion, and heat and efficiency losses. However, they can also be used in water treatment plants, bioremediation, and energy production with microbial fuel cells. In this review, the basic steps of biofilm formation and biofilm regulation in the model organism Escherichia coli were discussed. Finally, the methods by which biofilm formation can be detected and monitored were briefly discussed.
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Affiliation(s)
- Fırat Yavuz Öztürk
- Department of Molecular Biology and Genetic, Faculty of Arts and Science, Bilecik Seyh Edebali University, Bilecik, Turkey.
| | - Cihan Darcan
- Department of Molecular Biology and Genetic, Faculty of Arts and Science, Bilecik Seyh Edebali University, Bilecik, Turkey
| | - Ergin Kariptaş
- Department of Medical Microbiology, Faculty of Medicine, Samsun University, Samsun, Turkey
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Pinel-Cabello M, Jauregui R, Jroundi F, Geffers R, Jarek M, Link A, Vilchez-Vargas R, Merroun ML. Genetic mechanisms for Se(VI) reduction and synthesis of trigonal 1-D nanostructures in Stenotrophomonas bentonitica: Perspectives in eco-friendly nanomaterial production and bioremediation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 862:160635. [PMID: 36476772 DOI: 10.1016/j.scitotenv.2022.160635] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/15/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Selenate (Se(VI)) is one of the most soluble and toxic species of Se. Microbial Se(VI) reduction is an efficient tool for bioremediation strategies. However, this process is limited to a few microorganisms, and its molecular basis remains unknown. We present detailed Se(VI)-resistance mechanisms under 50 and 200 mM, in Stenotrophomonas bentonitica BII-R7, coupling enzymatic reduction of Se(VI) to formation of less toxic trigonal Se (t-Se). The results reveal a concentration-dependent response. Despite the lack of evidence of Se(VI)-reduction to Se(0) under 50 mM Se(VI), many genes were highly induced, indicating that Se(VI)-resistance could be based on intracellular reduction to Se(IV), mainly through molybdenum-dependent enzymes (e.g. respiratory nitrate reductase), and antioxidant activity by enzymes like glutathione peroxidase. Although exposure to 200 mM provoked a sharp drop in gene expression, a time-dependent process of reduction and formation of amorphous (a), monoclinic (m) and t-Se nanostructures was unravelled: a-Se nanospheres were initially synthesized intracellularly, which would transform into m-Se and finally into t-Se nanostructures during the following phases. This is the first work describing an intracellular Se(VI) reduction and biotransformation process to long-term stable and insoluble t-Se nanomaterials. These results expand the fundamental understanding of Se biogeochemical cycling, and the effectiveness of BII-R7 for bioremediation purposes.
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Affiliation(s)
| | - Ruy Jauregui
- AgResearch Grasslands Research Centre, Tennent Drive, Palmerston North, New Zealand
| | - Fadwa Jroundi
- Department of Microbiology, University of Granada, Granada, Spain
| | - Robert Geffers
- Genome Analytics, Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
| | - Michael Jarek
- Genome Analytics, Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, University of Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
| | - Ramiro Vilchez-Vargas
- Department of Gastroenterology, Hepatology and Infectious Diseases, University of Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
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