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Padhy I, Dwibedy SK, Mohapatra SS. A molecular overview of the polymyxin-LPS interaction in the context of its mode of action and resistance development. Microbiol Res 2024; 283:127679. [PMID: 38508087 DOI: 10.1016/j.micres.2024.127679] [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: 07/31/2023] [Revised: 03/03/2024] [Accepted: 03/06/2024] [Indexed: 03/22/2024]
Abstract
With the rising incidences of antimicrobial resistance (AMR) and the diminishing options of novel antimicrobial agents, it is paramount to decipher the molecular mechanisms of action and the emergence of resistance to the existing drugs. Polymyxin, a cationic antimicrobial lipopeptide, is used to treat infections by Gram-negative bacterial pathogens as a last option. Though polymyxins were identified almost seventy years back, their use has been restricted owing to toxicity issues in humans. However, their clinical use has been increasing in recent times resulting in the rise of polymyxin resistance. Moreover, the detection of "mobile colistin resistance (mcr)" genes in the environment and their spread across the globe have complicated the scenario. The mechanism of polymyxin action and the development of resistance is not thoroughly understood. Specifically, the polymyxin-bacterial lipopolysaccharide (LPS) interaction is a challenging area of investigation. The use of advanced biophysical techniques and improvement in molecular dynamics simulation approaches have furthered our understanding of this interaction, which will help develop polymyxin analogs with better bactericidal effects and lesser toxicity in the future. In this review, we have delved deeper into the mechanisms of polymyxin-LPS interactions, highlighting several models proposed, and the mechanisms of polymyxin resistance development in some of the most critical Gram-negative pathogens.
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Affiliation(s)
- Indira Padhy
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India
| | - Sambit K Dwibedy
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India
| | - Saswat S Mohapatra
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India.
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2
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Baijal K, Abramchuk I, Herrera CM, Mah TF, Trent MS, Lavallée-Adam M, Downey M. Polyphosphate kinase regulates LPS structure and polymyxin resistance during starvation in E. coli. PLoS Biol 2024; 22:e3002558. [PMID: 38478588 PMCID: PMC10962826 DOI: 10.1371/journal.pbio.3002558] [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: 08/09/2023] [Revised: 03/25/2024] [Accepted: 02/21/2024] [Indexed: 03/26/2024] Open
Abstract
Polyphosphates (polyP) are chains of inorganic phosphates that can reach over 1,000 residues in length. In Escherichia coli, polyP is produced by the polyP kinase (PPK) and is thought to play a protective role during the response to cellular stress. However, the molecular pathways impacted by PPK activity and polyP accumulation remain poorly characterized. In this work, we used label-free mass spectrometry to study the response of bacteria that cannot produce polyP (Δppk) during starvation to identify novel pathways regulated by PPK. In response to starvation, we found 92 proteins significantly differentially expressed between wild-type and Δppk mutant cells. Wild-type cells were enriched for proteins related to amino acid biosynthesis and transport, while Δppk mutants were enriched for proteins related to translation and ribosome biogenesis, suggesting that without PPK, cells remain inappropriately primed for growth even in the absence of the required building blocks. From our data set, we were particularly interested in Arn and EptA proteins, which were down-regulated in Δppk mutants compared to wild-type controls, because they play a role in lipid A modifications linked to polymyxin resistance. Using western blotting, we confirm differential expression of these and related proteins in K-12 strains and a uropathogenic isolate, and provide evidence that this mis-regulation in Δppk cells stems from a failure to induce the BasRS two-component system during starvation. We also show that Δppk mutants unable to up-regulate Arn and EptA expression lack the respective L-Ara4N and pEtN modifications on lipid A. In line with this observation, loss of ppk restores polymyxin sensitivity in resistant strains carrying a constitutively active basR allele. Overall, we show a new role for PPK in lipid A modification during starvation and provide a rationale for targeting PPK to sensitize bacteria towards polymyxin treatment. We further anticipate that our proteomics work will provide an important resource for researchers interested in the diverse pathways impacted by PPK.
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Affiliation(s)
- Kanchi Baijal
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Cellular & Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Iryna Abramchuk
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Carmen M. Herrera
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Thien-Fah Mah
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
| | - M. Stephen Trent
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Mathieu Lavallée-Adam
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael Downey
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Cellular & Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
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3
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Liu H, Wang Y, Zhang Z, Qi H, Zhang Y, Li W, Shi Q, Xie X. Nutrient condition modulates the antibiotic tolerance of Pseudomonas aeruginosa. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166749. [PMID: 37659534 DOI: 10.1016/j.scitotenv.2023.166749] [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: 06/14/2023] [Revised: 08/06/2023] [Accepted: 08/30/2023] [Indexed: 09/04/2023]
Abstract
The variation in nutrient content across diverse environments has a significant impact on the survival and metabolism of microorganisms. In this study, we examined the influence of nutrients on the antibiotic tolerance of the PAO1 strain of Pseudomonas aeruginosa. Our findings indicate that under nutrient-rich conditions, this strain exhibited relatively high tolerance to ceftazidime, chloramphenicol, and tetracycline, but not aminoglycosides and fluoroquinolones. Transcriptome analysis revealed that genes associated with antibiotic tolerance were expressed more efficiently in nutrient-rich media, including ribosomal protein genes and multidrug efflux pump genes, which conferred higher tetracycline tolerance to the strain. Furthermore, the genes responsible for translation, biosynthesis, and oxidative phosphorylation were suppressed when nutrients were limited, resulting in decreased metabolic activity and lower sensitivity to ciprofloxacin. Artificial interference with ATP synthesis utilizing arsenate confirmed that the curtailment of energy provision bolstered the observed tolerance to ciprofloxacin. In general, our results indicate that this strain of P. aeruginosa tends to activate its intrinsic resistance mechanisms in nutrient-rich environments, thereby enhancing resistance to certain antibiotics. Conversely, in nutrient-limited environments, the strain is more likely to enter a dormant state, which enables it to tolerate antibiotics to which it would otherwise be sensitive. These findings further suggest that antibiotics released in environments with varying eutrophication levels may have divergent effects on the development of bacterial antibiotic resistance.
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Affiliation(s)
- Huizhong Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Yingsi Wang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Zhiqing Zhang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Hong Qi
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Yu Zhang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Wenru Li
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Qingshan Shi
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Xiaobao Xie
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
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Ostroumova OS, Efimova SS. Lipid-Centric Approaches in Combating Infectious Diseases: Antibacterials, Antifungals and Antivirals with Lipid-Associated Mechanisms of Action. Antibiotics (Basel) 2023; 12:1716. [PMID: 38136750 PMCID: PMC10741038 DOI: 10.3390/antibiotics12121716] [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: 10/31/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
One of the global challenges of the 21st century is the increase in mortality from infectious diseases against the backdrop of the spread of antibiotic-resistant pathogenic microorganisms. In this regard, it is worth targeting antibacterials towards the membranes of pathogens that are quite conservative and not amenable to elimination. This review is an attempt to critically analyze the possibilities of targeting antimicrobial agents towards enzymes involved in pathogen lipid biosynthesis or towards bacterial, fungal, and viral lipid membranes, to increase the permeability via pore formation and to modulate the membranes' properties in a manner that makes them incompatible with the pathogen's life cycle. This review discusses the advantages and disadvantages of each approach in the search for highly effective but nontoxic antimicrobial agents. Examples of compounds with a proven molecular mechanism of action are presented, and the types of the most promising pharmacophores for further research and the improvement of the characteristics of antibiotics are discussed. The strategies that pathogens use for survival in terms of modulating the lipid composition and physical properties of the membrane, achieving a balance between resistance to antibiotics and the ability to facilitate all necessary transport and signaling processes, are also considered.
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Affiliation(s)
- Olga S. Ostroumova
- Laboratory of Membrane and Ion Channel Modeling, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg 194064, Russia;
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Liang Z, Huang L, Liu H, Zheng Y, Feng J, Shi Z, Chen Y, Lv M, Zhou J, Zhang L, Chen S. Characterization of the Arn lipopolysaccharide modification system essential for zeamine resistance unveils its new roles in Dickeya oryzae physiology and virulence. MOLECULAR PLANT PATHOLOGY 2023; 24:1480-1494. [PMID: 37740253 PMCID: PMC10632790 DOI: 10.1111/mpp.13386] [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: 04/20/2023] [Revised: 07/14/2023] [Accepted: 08/22/2023] [Indexed: 09/24/2023]
Abstract
The zeamines produced by Dickeya oryzae are potent polyamine antibiotics and phytotoxins that are essential for bacterial virulence. We recently showed that the RND efflux pump DesABC in D. oryzae confers partial resistance to zeamines. To fully elucidate the bacterial self-protection mechanisms, in this study we used transposon mutagenesis to identify the genes encoding proteins involved in zeamine resistance in D. oryzae EC1. This led to the identification of a seven-gene operon, arnEC1 , that encodes enzyme homologues associated with lipopolysaccharide modification. Deletion of the arnEC1 genes in strain EC1 compromised its zeamine resistance 8- to 16-fold. Further deletion of the des gene in the arnEC1 mutant background reduced zeamine resistance to a level similar to that of the zeamine-sensitive Escherichia coli DH5α. Intriguingly, the arnEC1 mutants showed varied bacterial virulence on rice, potato, and Chinese cabbage. Further analyses demonstrated that ArnBCATEC1 are involved in maintenance of the bacterial nonmucoid morphotype by repressing the expression of capsular polysaccharide genes and that ArnBEC1 is a bacterial virulence determinant, influencing transcriptional expression of over 650 genes and playing a key role in modulating bacterial motility and virulence. Taken together, these findings decipher a novel zeamine resistance mechanism in D. oryzae and document new roles of the Arn enzymes in modulation of bacterial physiology and virulence.
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Affiliation(s)
- Zhibin Liang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Luhao Huang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
| | - Huidi Liu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Ying Zheng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
| | - Jiani Feng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
| | - Zurong Shi
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
- School of Biological EngineeringHuainan Normal UniversityHuainanChina
| | - Yufan Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
- Research Center of Chinese Herbal Resource Science and EngineeringGuangzhou University of Chinese MedicineGuangzhouChina
| | - Mingfa Lv
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
- College of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jianuan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Lian‐Hui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Shaohua Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
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Muñoz-Escudero D, Breazeale SD, Lee M, Guan Z, Raetz CRH, Sousa MC. Structure and Function of ArnD. A Deformylase Essential for Lipid A Modification with 4-Amino-4-deoxy-l-arabinose and Polymyxin Resistance. Biochemistry 2023; 62:2970-2981. [PMID: 37782650 PMCID: PMC10914315 DOI: 10.1021/acs.biochem.3c00293] [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: 10/04/2023]
Abstract
Covalent modification of lipid A with 4-deoxy-4-amino-l-arabinose (Ara4N) mediates resistance to cationic antimicrobial peptides and polymyxin antibiotics in Gram-negative bacteria. The proteins required for Ara4N biosynthesis are encoded in the pmrE and arnBCADTEF loci, with ArnT ultimately transferring the amino sugar from undecaprenyl-phospho-4-deoxy-4-amino-l-arabinose (C55P-Ara4N) to lipid A. However, Ara4N is N-formylated prior to its transfer to undecaprenyl-phosphate by ArnC, requiring a deformylase activity downstream in the pathway to generate the final C55P-Ara4N donor. Here, we show that deletion of the arnD gene in an Escherichia coli mutant that constitutively expresses the arnBCADTEF operon leads to accumulation of the formylated ArnC product undecaprenyl-phospho-4-deoxy-4-formamido-l-arabinose (C55P-Ara4FN), suggesting that ArnD is the downstream deformylase. Purification of Salmonella typhimurium ArnD (stArnD) shows that it is membrane-associated. We present the crystal structure of stArnD revealing a NodB homology domain structure characteristic of the metal-dependent carbohydrate esterase family 4 (CE4). However, ArnD displays several distinct features: a 44 amino acid insertion, a C-terminal extension in the NodB fold, and sequence divergence in the five motifs that define the CE4 family, suggesting that ArnD represents a new family of carbohydrate esterases. The insertion is responsible for membrane association as its deletion results in a soluble ArnD variant. The active site retains a metal coordination H-H-D triad, and in the presence of Co2+ or Mn2+, purified stArnD efficiently deformylates C55P-Ara4FN confirming its role in Ara4N biosynthesis. Mutations D9N and H233Y completely inactivate stArnD implicating these two residues in a metal-assisted acid-base catalytic mechanism.
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Affiliation(s)
- Daniel Muñoz-Escudero
- Department of Molecular Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309
| | - Steven D. Breazeale
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710
| | - Myeongseon Lee
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710
| | | | - Marcelo C. Sousa
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309
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Materon IC, Palzkill T. Structural biology of MCR-1-mediated resistance to polymyxin antibiotics. Curr Opin Struct Biol 2023; 82:102647. [PMID: 37399693 PMCID: PMC10527939 DOI: 10.1016/j.sbi.2023.102647] [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: 04/01/2023] [Revised: 05/30/2023] [Accepted: 06/07/2023] [Indexed: 07/05/2023]
Abstract
Polymyxins, a last resort antibiotic, target the outer membrane of pathogens and are used to address the increasing prevalence of multidrug-resistant Gram-negative bacteria. The plasmid-encoded enzyme MCR-1 confers polymyxin resistance to bacteria by modifying the outer membrane. Transferable resistance to polymyxins is a major concern; therefore, MCR-1 is an important drug target. In this review, we discuss recent structural and mechanistic aspects of MCR-1 function, its variants and homologs, and how they are relevant to polymyxin resistance. Specifically, we discuss work on polymyxin-mediated disruption of the outer and inner membranes, computational studies on the catalytic mechanism of MCR-1, mutagenesis and structural analysis concerning residues important for substrate binding in MCR-1, and finally, advancements in inhibitors targeting MCR-1.
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Affiliation(s)
- Isabel Cristina Materon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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Kompes G, Duvnjak S, Reil I, Hendriksen RS, Sørensen LH, Zdelar-Tuk M, Habrun B, Cvetnić L, Bagarić A, Špičić S. First Report and Characterization of the mcr-1 Positive Multidrug-Resistant Escherichia coli Strain Isolated from Pigs in Croatia. Microorganisms 2023; 11:2442. [PMID: 37894098 PMCID: PMC10609023 DOI: 10.3390/microorganisms11102442] [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: 07/31/2023] [Revised: 08/21/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
The emergence and rapid spread of the plasmid-mediated colistin-resistant mcr-1 gene introduced a serious threat to public health. In 2021, a multi-drug resistant, mcr-1 positive Escherichia coli EC1945 strain, was isolated from pig caecal content in Croatia. Antimicrobial susceptibility testing and whole genome sequencing were performed. Bioinformatics tools were used to determine the presence of resistance genes, plasmid Inc groups, serotype, sequence type, virulence factors, and plasmid reconstruction. The isolated strain showed phenotypic and genotypic resistance to nine antimicrobial classes. It was resistant to colistin, gentamicin, ampicillin, cefepime, cefotaxime, ceftazidime, sulfamethoxazole, chloramphenicol, nalidixic acid, and ciprofloxacin. Antimicrobial resistance genes included mcr-1, blaTEM-1B, blaCTX-M-1, aac(3)-IId, aph(3')-Ia, aadA5, sul2, catA1, gyrA (S83L, D87N), and parC (A56T, S80I). The mcr-1 gene was located within the conjugative IncX4 plasmid. IncI1, IncFIB, and IncFII plasmids were also detected. The isolate also harbored 14 virulence genes and was classified as ST744 and O101:H10. ST744 is a member of the ST10 group which includes commensal, extraintestinal pathogenic E. coli isolates that play a crucial role as a reservoir of genes. Further efforts are needed to identify mcr-1-carrying E. coli isolates in Croatia, especially in food-producing animals to identify such gene reservoirs.
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Affiliation(s)
- Gordan Kompes
- Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (G.K.); (M.Z.-T.); (B.H.); (L.C.); (A.B.); (S.Š.)
| | - Sanja Duvnjak
- Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (G.K.); (M.Z.-T.); (B.H.); (L.C.); (A.B.); (S.Š.)
| | - Irena Reil
- Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (G.K.); (M.Z.-T.); (B.H.); (L.C.); (A.B.); (S.Š.)
| | - Rene S. Hendriksen
- Research Group for Global Capacity Building, National Food Institute, Technical University of Denmark, Kemitorvet, 2800 Lyngby, Denmark; (R.S.H.); (L.H.S.)
| | - Lauge Holm Sørensen
- Research Group for Global Capacity Building, National Food Institute, Technical University of Denmark, Kemitorvet, 2800 Lyngby, Denmark; (R.S.H.); (L.H.S.)
| | - Maja Zdelar-Tuk
- Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (G.K.); (M.Z.-T.); (B.H.); (L.C.); (A.B.); (S.Š.)
| | - Boris Habrun
- Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (G.K.); (M.Z.-T.); (B.H.); (L.C.); (A.B.); (S.Š.)
| | - Luka Cvetnić
- Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (G.K.); (M.Z.-T.); (B.H.); (L.C.); (A.B.); (S.Š.)
| | - Antonela Bagarić
- Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (G.K.); (M.Z.-T.); (B.H.); (L.C.); (A.B.); (S.Š.)
| | - Silvio Špičić
- Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (G.K.); (M.Z.-T.); (B.H.); (L.C.); (A.B.); (S.Š.)
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Gadar K, de Dios R, Kadeřábková N, Prescott TAK, Mavridou DAI, McCarthy RR. Disrupting iron homeostasis can potentiate colistin activity and overcome colistin resistance mechanisms in Gram-Negative Bacteria. Commun Biol 2023; 6:937. [PMID: 37704838 PMCID: PMC10499790 DOI: 10.1038/s42003-023-05302-2] [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: 01/26/2023] [Accepted: 08/29/2023] [Indexed: 09/15/2023] Open
Abstract
Acinetobacter baumannii is a Gram-negative priority pathogen that can readily overcome antibiotic treatment through a range of intrinsic and acquired resistance mechanisms. Treatment of carbapenem-resistant A. baumannii largely relies on the use of colistin in cases where other treatment options have been exhausted. However, the emergence of resistance against this last-line drug has significantly increased amongst clinical strains. In this study, we identify the phytochemical kaempferol as a potentiator of colistin activity. When administered singularly, kaempferol has no effect on growth but does impact biofilm formation. Nonetheless, co-administration of kaempferol with sub-inhibitory concentrations of colistin exposes bacteria to a metabolic Achilles heel, whereby kaempferol-induced dysregulation of iron homeostasis leads to bacterial killing. We demonstrate that this effect is due to the disruption of Fenton's reaction, and therefore to a lethal build-up of toxic reactive oxygen species in the cell. Furthermore, we show that this vulnerability can be exploited to overcome both intrinsic and acquired colistin resistance in clinical strains of A. baumannii and E. coli in vitro and in the Galleria mellonella model of infection. Overall, our findings provide a proof-of-principle demonstration that targeting iron homeostasis is a promising strategy for enhancing the efficacy of colistin and overcoming colistin-resistant infections.
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Affiliation(s)
- Kavita Gadar
- Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UB8 3PH, UK
| | - Rubén de Dios
- Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UB8 3PH, UK
| | - Nikol Kadeřábková
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | | | - Despoina A I Mavridou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
- John Ring LaMontagne Centre for Infectious Diseases, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Ronan R McCarthy
- Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UB8 3PH, UK.
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Sivasankar C, Hewawaduge C, Lee JH. Screening of lipid-A related genes and development of low-endotoxicity live-attenuated Salmonella gallinarum by arnT deletion that elicits immune responses and protection against fowl typhoid in chickens. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 145:104707. [PMID: 37044268 DOI: 10.1016/j.dci.2023.104707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 05/27/2023]
Abstract
In the present study, lipid-A gene mutants of Salmonella gallinarum (SG) were screened, and the arnT mutant exhibited optimal acidic and oxidative-stress and macrophage-survival. Modifying lipid-A by arnT-deletion resulted in significantly reduced endotoxicity, virulence, and mortality. Therefore, the arnT-deleted vaccine-candidate strain JOL2841 was constructed and demonstrated to be safe due to appropriate clearance by the chicken immune system. The reduced-endotoxicity of JOL2841 was evident from the downregulation of TNFα and IL-1β inflammatory cytokines, no inflammatory signs in organ gross-examination, and histopathological analysis. The IgY and IgA antibody titres, CD4, and CD8 T-cell population improvements, and IL-4, IL-2, and INFγ expression decipher the profound Th2 and Th1 immunogenicity. Consequently, JOL2841 exhibited prominent protection against wild-type SG challenge, as revealed by organ pathogen-load determination, organ gross-examination, and histopathological examination. Overall, the study represented the first report of arnT deficient SG resulted in negligible endotoxicity, low-virulence, safety and coordinated elicitation of humoral and cell-mediated immune response in chickens.
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Affiliation(s)
- Chandran Sivasankar
- College of Veterinary Medicine, Jeonbuk National University, Iksan Campus, 54596, Republic of Korea
| | - Chamith Hewawaduge
- College of Veterinary Medicine, Jeonbuk National University, Iksan Campus, 54596, Republic of Korea
| | - John Hwa Lee
- College of Veterinary Medicine, Jeonbuk National University, Iksan Campus, 54596, Republic of Korea.
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Gomez SA, Sanz MB, Rapoport M, Sucin G, Corallo TA, Poklepovich T, Campos J, Ceriana P, de Mendieta JM, Prieto M, Pasteran F, Corso A. Novel Metallo-β-Lactamase blaCVI-1 Isolated from a Chromobaterium violaceum Clinical Strain Resistant to Colistin. Pathogens 2023; 12:961. [PMID: 37513808 PMCID: PMC10385785 DOI: 10.3390/pathogens12070961] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/08/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
OBJECTIVE We aimed to describe a colistin (COL)-resistant (R) Chromobacterium violaceum (Cvi) isolate from a septic patient in Argentina expressing a previously unknown gene, blaCVI-1. METHODS In 2019, a 12 year old child was injured with a thorn in a lagoon. The child was hospitalized due to sepsis and multiple abscesses. Cvi was isolated from skin and soft tissue and tracheal aspirate. The patient was successfully treated with imipenem (IMI) plus amikacin. Antimicrobial susceptibility was assessed by disk diffusion, broth microdilution, and the E-test. Carbapenemase activity was assayed by double-disk synergy and microbiological tests. Resistance, virulence, and additional gene searches were performed by in silico analysis of sequences obtained by whole-genome sequencing (WGS). A maximum likelihood phylogenetic tree was built with public Cvi genomes. RESULTS R was seen for IMI and COL. Expression of a metallo-β-lactamase was confirmed. Genome analysis revealed blaCVI-1, a subclass B2 metallo-β-lactamase with 62.66% ID with CphA from A. hydrophila (WP081086394). R to COL could be attributed to the arnC and arnT genes. Virulence factors required for invasion and toxicity were also found. No plasmids were detected. The phylogeny tree showed two main clades with geographical distinction, and the isolate studied here stands alone in a branch closely related to two clinical isolates from the USA. CONCLUSIONS This is the second report of infection by Cvi in Argentina. This pathogen carried a new gene, blaCVI-1, a metallo-β-lactamase that can be detected by routine methods. Prompt suspicion of C. violaceum infection is crucial to treating this rare pathogen rapidly and properly.
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Affiliation(s)
- Sonia A Gomez
- Servicio Antimicrobianos, INEI-ANLIS "Dr. Carlos G. Malbrán", National and Regional Reference Laboratory in Antimicrobial Resistance (NRRLAR), Buenos Aires C1282AFF, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1425FQB, Argentina
| | - María Belén Sanz
- Servicio Antimicrobianos, INEI-ANLIS "Dr. Carlos G. Malbrán", National and Regional Reference Laboratory in Antimicrobial Resistance (NRRLAR), Buenos Aires C1282AFF, Argentina
| | - Melina Rapoport
- Servicio Antimicrobianos, INEI-ANLIS "Dr. Carlos G. Malbrán", National and Regional Reference Laboratory in Antimicrobial Resistance (NRRLAR), Buenos Aires C1282AFF, Argentina
| | - Graciela Sucin
- Sector de Bacteriología, Hosp. Pediátrico "Dr. Avelino Castelán", Resistencia H3508, Argentina
| | - Teresa A Corallo
- Sector de Bacteriología, Hosp. Pediátrico "Dr. Avelino Castelán", Resistencia H3508, Argentina
| | - Tomás Poklepovich
- Plataforma de Genómica y Bioinformática, INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires CP1281, Argentina
| | - Josefina Campos
- Plataforma de Genómica y Bioinformática, INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires CP1281, Argentina
| | - Paola Ceriana
- Servicio Antimicrobianos, INEI-ANLIS "Dr. Carlos G. Malbrán", National and Regional Reference Laboratory in Antimicrobial Resistance (NRRLAR), Buenos Aires C1282AFF, Argentina
| | - Juan Manuel de Mendieta
- Servicio Antimicrobianos, INEI-ANLIS "Dr. Carlos G. Malbrán", National and Regional Reference Laboratory in Antimicrobial Resistance (NRRLAR), Buenos Aires C1282AFF, Argentina
| | - Mónica Prieto
- Servicio Bacteriología Especial INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires CP1281, Argentina
| | - Fernando Pasteran
- Servicio Antimicrobianos, INEI-ANLIS "Dr. Carlos G. Malbrán", National and Regional Reference Laboratory in Antimicrobial Resistance (NRRLAR), Buenos Aires C1282AFF, Argentina
| | - Alejandra Corso
- Servicio Antimicrobianos, INEI-ANLIS "Dr. Carlos G. Malbrán", National and Regional Reference Laboratory in Antimicrobial Resistance (NRRLAR), Buenos Aires C1282AFF, Argentina
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12
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Baijal K, Abramchuk I, Herrera CM, Stephen Trent M, Lavallée-Adam M, Downey M. Proteomics analysis reveals a role for E. coli polyphosphate kinase in membrane structure and polymyxin resistance during starvation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.546892. [PMID: 37461725 PMCID: PMC10350021 DOI: 10.1101/2023.07.06.546892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Polyphosphates (polyP) are chains of inorganic phosphates that can reach over 1000 residues in length. In Escherichia coli, polyP is produced by the polyP kinase (PPK) and is thought to play a protective role during the response to cellular stress. However, the molecular pathways impacted by PPK activity and polyP accumulation remain poorly characterized. In this work we used label-free mass spectrometry to study the response of bacteria that cannot produce polyP (∆ppk) during starvation to identify novel pathways regulated by PPK. In response to starvation, we found 92 proteins significantly differentially expressed between wild-type and ∆ppk mutant cells. Wild-type cells were enriched for proteins related to amino acid biosynthesis and transport, while Δppk mutants were enriched for proteins related to translation and ribosome biogenesis, suggesting that without PPK, cells remain inappropriately primed for growth even in the absence of required building blocks. From our dataset, we were particularly interested in Arn and EptA proteins, which were downregulated in ∆ppk mutants compared to wild-type controls, because they play a role in lipid A modifications linked to polymyxin resistance. Using western blotting, we confirm differential expression of these and related proteins, and provide evidence that this mis-regulation in ∆ppk cells stems from a failure to induce the BasS/BasR two-component system during starvation. We also show that ∆ppk mutants unable to upregulate Arn and EptA expression lack the respective L-Ara4N and pEtN modifications on lipid A. In line with this observation, loss of ppk restores polymyxin sensitivity in resistant strains carrying a constitutively active basR allele. Overall, we show a new role for PPK in lipid A modification during starvation and provide a rationale for targeting PPK to sensitize bacteria towards polymyxin treatment. We further anticipate that our proteomics work will provide an important resource for researchers interested in the diverse pathways impacted by PPK.
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Affiliation(s)
- Kanchi Baijal
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Cellular & Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Iryna Abramchuk
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Carmen M. Herrera
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - M. Stephen Trent
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Mathieu Lavallée-Adam
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael Downey
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Cellular & Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
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13
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Coluccia M, Besaury L. Acidobacteria members harbour an abundant and diverse carbohydrate-active enzymes (cazyme) and secreted proteasome repertoire, key factors for potential efficient biomass degradation. Mol Genet Genomics 2023:10.1007/s00438-023-02045-x. [PMID: 37335345 DOI: 10.1007/s00438-023-02045-x] [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: 12/05/2022] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
The Acidobacteria phylum is a very abundant group (20-30% of microbial communities in soil ecosystems); however, little is known about these microorganisms and their ability to degrade the biomass and lignocellulose due to the difficulty of culturing them. We, therefore, bioinformatically studied the content of lignocellulolytic enzymes (total and predicted secreted enzymes) and secreted peptidases in an in silico library containing 41 Acidobacteria genomes. The results showed a high abundance and diversity of total and secreted Carbohydrate-Active enzymes (cazyme) families among the Acidobacteria compared to known previous degraders. Indeed, the relative abundance of cazymes in some genomes represented more than 6% of the gene coding proteins with at least 300 cazymes. The same observation was made with the predicted secreted peptidases with several families of secreted peptidases, which represented at least 1.5% of the gene coding proteins in several genomes. These results allowed us to highlight the lignocellulolytic potential of the Acidobacteria phylum in the degradation of lignocellulosic biomass, which could explain its high abundance in the environment.
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Affiliation(s)
- Marion Coluccia
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France
| | - Ludovic Besaury
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France.
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14
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Schumann A, Cohn AR, Gaballa A, Wiedmann M. Escherichia coli B-Strains Are Intrinsically Resistant to Colistin and Not Suitable for Characterization and Identification of mcr Genes. Microbiol Spectr 2023; 11:e0089423. [PMID: 37199645 PMCID: PMC10269513 DOI: 10.1128/spectrum.00894-23] [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: 03/02/2023] [Accepted: 04/24/2023] [Indexed: 05/19/2023] Open
Abstract
Antimicrobial resistance is an increasing threat to human and animal health. Due to the rise of multi-, extensive, and pandrug resistance, last resort antibiotics, such as colistin, are extremely important in human medicine. While the distribution of colistin resistance genes can be tracked through sequencing methods, phenotypic characterization of putative antimicrobial resistance (AMR) genes is still important to confirm the phenotype conferred by different genes. While heterologous expression of AMR genes (e.g., in Escherichia coli) is a common approach, so far, no standard methods for heterologous expression and characterization of mcr genes exist. E. coli B-strains, designed for optimum protein expression, are frequently utilized. Here, we report that four E. coli B-strains are intrinsically resistant to colistin (MIC 8-16 μg/mL). The three tested B-strains that encode T7 RNA polymerase show growth defects when transformed with empty or mcr-expressing pET17b plasmids and grown in the presence of IPTG; K-12 or B-strains without T7 RNA polymerase do not show these growth defects. E. coli SHuffle T7 express carrying empty pET17b also skips wells in colistin MIC assays in the presence of IPTG. These phenotypes could explain why B-strains were erroneously reported as colistin susceptible. Analysis of existing genome data identified one nonsynonymous change in each pmrA and pmrB in all four E. coli B-strains; the E121K change in PmrB has previously been linked to intrinsic colistin resistance. We conclude that E. coli B-strains are not appropriate heterologous expression hosts for identification and characterization of mcr genes. IMPORTANCE Given the rise in multidrug, extensive drug, and pandrug resistance in bacteria and the increasing use of colistin to treat human infections, occurrence of mcr genes threatens human health, and characterization of these resistance genes becomes more important. We show that three commonly used heterologous expression strains are intrinsically resistant to colistin. This is important because these strains have previously been used to characterize and identify new mobile colistin resistance (mcr) genes. We also show that expression plasmids (i.e., pET17b) without inserts cause cell viability defects when carried by B-strains with T7 RNA polymerase and grown in the presence of IPTG. Our findings are important as they will facilitate improved selection of heterologous strains and plasmid combinations for characterizing AMR genes, which will be particularly important with a shift to Culture-independent diagnostic tests where bacterial isolates become increasingly less available for characterization.
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Affiliation(s)
- Anna Schumann
- Department of Food Science, Cornell University, Ithaca, New York, USA
- Graduate Field of Biomedical and Biological Sciences, Cornell University, Ithaca, New York, USA
| | - Alexa R. Cohn
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Ahmed Gaballa
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York, USA
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15
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Yang H, Sherman ME, Koo CJ, Treaster LM, Smith JP, Gallaher SG, Goodlett DR, Sweet CR, Ernst RK. Structure Determination of Lipid A with Multiple Glycosylation Sites by Tandem MS of Lithium-Adducted Negative Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1047-1055. [PMID: 37184080 DOI: 10.1021/jasms.3c00014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
FLATn is a tandem mass spectrometric technique that can be used to rapidly generate spectral information applicable for structural elucidation of lipids like lipid A from Gram-negative bacterial species from a single bacterial colony. In this study, we extend the scope and capability of FLATn by tandem MS fragmentation of lithium-adducted molecular lipid A anions and fragments (FLATn-Li) that provides additional structural and diagnostic data from FLATn samples allowing for the discrimination of terminal phosphate modifications in a variety of pathogenic and environmental species. Using FLATn-Li, we elucidated the lipid A structure from several bacterial species, including novel structures from arctic bacterioplankton of the Duganella and Massilia genera that favor 4-amino-4-deoxy-l-arabinopyranose (Ara4N) modification at the 1-phosphate position and that demonstrate double glycosylation with Ara4N at the 1 and 4' phosphate positions simultaneously. The structures characterized in this work demonstrate that some environmental psychrophilic species make extensive use of this structural lipid A modification previously characterized as a pathogenic adaptation and the structural basis of resistance to cationic antimicrobial peptides. This observation extends the role of phosphate modification(s) in environmental species adaptation and suggests that Ara4N modification can functionally replace the positive charge of the phosphoethanolamine modification that is more typically found attached to the 1-phosphate position of modified lipid A.
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Affiliation(s)
- Hyojik Yang
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, United States of America
| | - Matthew E Sherman
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, United States of America
| | - Caitlyn J Koo
- Chemistry Department, United States Naval Academy, Annapolis, Maryland 21402, United States of America
- School of Medicine, Uniformed Services University, Bethesda, Maryland 20814, United States of America
| | - Logan M Treaster
- Chemistry Department, United States Naval Academy, Annapolis, Maryland 21402, United States of America
- School of Medicine, University of Kansas, Kansas City, Kansas 66160, United States of America
| | - Joseph P Smith
- Oceanography Department, United States Naval Academy, Annapolis, Maryland 21402, United States of America
| | - Shawn G Gallaher
- Oceanography Department, United States Naval Academy, Annapolis, Maryland 21402, United States of America
| | - David R Goodlett
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
- Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7Z8, Canada
| | - Charles R Sweet
- Chemistry Department, United States Naval Academy, Annapolis, Maryland 21402, United States of America
| | - Robert K Ernst
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, United States of America
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16
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Pětrošová H, Mikhael A, Culos S, Giraud-Gatineau A, Gomez AM, Sherman ME, Ernst RK, Cameron CE, Picardeau M, Goodlett DR. Lipid A structural diversity among members of the genus Leptospira. Front Microbiol 2023; 14:1181034. [PMID: 37303810 PMCID: PMC10248169 DOI: 10.3389/fmicb.2023.1181034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/02/2023] [Indexed: 06/13/2023] Open
Abstract
Lipid A is the hydrophobic component of bacterial lipopolysaccharide and an activator of the host immune system. Bacteria modify their lipid A structure to adapt to the surrounding environment and, in some cases, to evade recognition by host immune cells. In this study, lipid A structural diversity within the Leptospira genus was explored. The individual Leptospira species have dramatically different pathogenic potential that ranges from non-infectious to life-threatening disease (leptospirosis). Ten distinct lipid A profiles, denoted L1-L10, were discovered across 31 Leptospira reference species, laying a foundation for lipid A-based molecular typing. Tandem MS analysis revealed structural features of Leptospira membrane lipids that might alter recognition of its lipid A by the host innate immune receptors. Results of this study will aid development of strategies to improve diagnosis and surveillance of leptospirosis, as well as guide functional studies on Leptospira lipid A activity.
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Affiliation(s)
- Helena Pětrošová
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
- University of Victoria Genome British Columbia Proteomics Center, University of Victoria, Victoria, BC, Canada
| | - Abanoub Mikhael
- University of Victoria Genome British Columbia Proteomics Center, University of Victoria, Victoria, BC, Canada
| | - Sophie Culos
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | | | - Alloysius M. Gomez
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Matthew E. Sherman
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, MD, United States
| | - Robert K. Ernst
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, MD, United States
| | - Caroline E. Cameron
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, United States
| | - Mathieu Picardeau
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Biology of Spirochetes Unit, Paris, France
| | - David R. Goodlett
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
- University of Victoria Genome British Columbia Proteomics Center, University of Victoria, Victoria, BC, Canada
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17
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Purcell AB, Simpson BW, Trent MS. Impact of the cAMP-cAMP Receptor Protein Regulatory Complex on Lipopolysaccharide Modifications and Polymyxin B Resistance in Escherichia coli. J Bacteriol 2023; 205:e0006723. [PMID: 37070977 PMCID: PMC10210979 DOI: 10.1128/jb.00067-23] [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: 02/15/2023] [Accepted: 03/17/2023] [Indexed: 04/19/2023] Open
Abstract
Gram-negative bacteria have a unique cell surface that can be modified to maintain bacterial fitness in diverse environments. A well-defined example is the modification of the lipid A component of lipopolysaccharide (LPS), which promotes resistance to polymyxin antibiotics and antimicrobial peptides. In many organisms, such modifications include the addition of the amine-containing constituents 4-amino-4-deoxy-l-arabinose (l-Ara4N) and phosphoethanolamine (pEtN). Addition of pEtN is catalyzed by EptA, which uses phosphatidylethanolamine (PE) as its substrate donor, resulting in production of diacylglycerol (DAG). DAG is then quickly recycled into glycerophospholipid (GPL) synthesis by the DAG kinase A (DgkA) to produce phosphatidic acid, the major GPL precursor. Previously, we hypothesized that loss of DgkA recycling would be detrimental to the cell when LPS is heavily modified. Instead, we found that DAG accumulation inhibits EptA activity, preventing further degradation of PE, the predominant GPL of the cell. However, DAG inhibition of pEtN addition results in complete loss of polymyxin resistance. Here, we selected for suppressors to find a mechanism of resistance independent of DAG recycling or pEtN modification. Disrupting the gene encoding the adenylate cyclase, cyaA, fully restored antibiotic resistance without restoring DAG recycling or pEtN modification. Supporting this, disruptions of genes that reduce CyaA-derived cAMP formation (e.g., ptsI) or disruption of the cAMP receptor protein, Crp, also restored resistance. We found that loss of the cAMP-CRP regulatory complex was necessary for suppression and that resistance arises from a substantial increase in l-Ara4N-modified LPS, bypassing the need for pEtN modification. IMPORTANCE Gram-negative bacteria can alter the structure of their LPS to promote resistance to cationic antimicrobial peptides, including polymyxin antibiotics. Polymyxins are considered last-resort antibiotics for treatment against multidrug-resistant Gram-negative organisms. Here, we explore how changes in general metabolism and carbon catabolite repression pathways can alter LPS structure and influence polymyxin resistance.
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Affiliation(s)
- Alexandria B. Purcell
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Brent W. Simpson
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - M. Stephen Trent
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
- Department of Microbiology, College of Arts and Sciences, University of Georgia, Athens, Georgia, USA
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18
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Lucena ACR, Ferrarini MG, de Oliveira WK, Marcon BH, Morello LG, Alves LR, Faoro H. Modulation of Klebsiella pneumoniae Outer Membrane Vesicle Protein Cargo under Antibiotic Treatment. Biomedicines 2023; 11:1515. [PMID: 37371610 DOI: 10.3390/biomedicines11061515] [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: 02/17/2023] [Revised: 04/14/2023] [Accepted: 05/14/2023] [Indexed: 06/29/2023] Open
Abstract
Klebsiella pneumoniae is a nosocomial pathogen and an important propagator of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains. Like other Gram-negative bacteria, they secrete outer membrane vesicles (OMVs) that distribute virulence and resistance factors. Here, we subjected a K. pneumoniae-XDR to subinhibitory concentrations of meropenem, amikacin, polymyxin B, and a combination of these agents to evaluate changes in the protein cargo of OMVs through liquid chromatography-tandem mass spectrometry (LC-MS/MS). Genome sequencing of the clinical isolate K. pneumoniae strain HCD1 (KpHCD1) revealed the presence of 41 resistance genes and 159 virulence factors. We identified 64 proteins in KpHCD1-OMVs modulated with different antibiotic treatments involved in processing genetic information, environmental information, cell envelope formation, energy metabolism, and drug resistance. The OMV proteome expression profile suggests that OMVs may be associated with pathogenicity, survival, stress response, and resistance dissemination.
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Affiliation(s)
- Aline Castro Rodrigues Lucena
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
| | - Mariana Galvão Ferrarini
- Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, CNRS, Université de Lyon, Université Lyon 1, 69622 Villeurbanne, France
| | - Willian Klassen de Oliveira
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
| | - Bruna Hilzendeger Marcon
- Laboratory for Basic Biology of Stem Cells, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
| | - Luis Gustavo Morello
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
| | - Lysangela Ronalte Alves
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
- CHU de Quebec Research Center, Department of Microbiology, Infectious Disease and Immunology, University Laval, Quebec, QC G1V 0A6, Canada
| | - Helisson Faoro
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
- CHU de Quebec Research Center, Department of Microbiology, Infectious Disease and Immunology, University Laval, Quebec, QC G1V 0A6, Canada
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Seethalakshmi PS, Rajeev R, Prabhakaran A, Kiran GS, Selvin J. The menace of colistin resistance across globe: Obstacles and opportunities in curbing its spread. Microbiol Res 2023; 270:127316. [PMID: 36812837 DOI: 10.1016/j.micres.2023.127316] [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: 05/01/2022] [Revised: 11/27/2022] [Accepted: 02/01/2023] [Indexed: 02/11/2023]
Abstract
Colistin-resistance in bacteria is a big concern for public health, since it is a last resort antibiotic to treat infectious diseases of multidrug resistant and carbapenem resistant Gram-negative pathogens in clinical settings. The emergence of colistin resistance in aquaculture and poultry settings has escalated the risks associated with colistin resistance in environment as well. The staggering number of reports pertaining to the rise of colistin resistance in bacteria from clinical and non-clinical settings is disconcerting. The co-existence of colistin resistant genes with other antibiotic resistant genes introduces new challenges in combatting antimicrobial resistance. Some countries have banned the manufacture, sale and distribution of colistin and its formulations for food producing animals. However, to tackle the issue of antimicrobial resistance, a one health approach initiative, inclusive of human, animal, and environmental health needs to be developed. Herein, we review the recent reports in colistin resistance in bacteria of clinical and non-clinical settings, deliberating on the new findings obtained regarding the development of colistin resistance. This review also discusses the initiatives implemented globally in mitigating colistin resistance, their strength and weakness.
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Affiliation(s)
- P S Seethalakshmi
- Department of Microbiology, Pondicherry University, Puducherry 605014, India.
| | - Riya Rajeev
- Department of Microbiology, Pondicherry University, Puducherry 605014, India.
| | | | - George Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Puducherry 605014, India.
| | - Joseph Selvin
- Department of Microbiology, Pondicherry University, Puducherry 605014, India.
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20
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Bilsing FL, Anlauf MT, Hachani E, Khosa S, Schmitt L. ABC Transporters in Bacterial Nanomachineries. Int J Mol Sci 2023; 24:ijms24076227. [PMID: 37047196 PMCID: PMC10094684 DOI: 10.3390/ijms24076227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/18/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Members of the superfamily of ABC transporters are found in all domains of life. Most of these primary active transporters act as isolated entities and export or import their substrates in an ATP-dependent manner across biological membranes. However, some ABC transporters are also part of larger protein complexes, so-called nanomachineries that catalyze the vectorial transport of their substrates. Here, we will focus on four bacterial examples of such nanomachineries: the Mac system providing drug resistance, the Lpt system catalyzing vectorial LPS transport, the Mla system responsible for phospholipid transport, and the Lol system, which is required for lipoprotein transport to the outer membrane of Gram-negative bacteria. For all four systems, we tried to summarize the existing data and provide a structure-function analysis highlighting the mechanistical aspect of the coupling of ATP hydrolysis to substrate translocation.
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21
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Fivenson EM, Rohs PD, Vettiger A, Sardis MF, Torres G, Forchoh A, Bernhardt TG. A role for the Gram-negative outer membrane in bacterial shape determination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.03.527047. [PMID: 36778245 PMCID: PMC9915748 DOI: 10.1101/2023.02.03.527047] [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] [Indexed: 02/07/2023]
Abstract
The cell envelope of Gram-negative bacteria consists of three distinct layers: the cytoplasmic membrane, a cell wall made of peptidoglycan (PG), and an asymmetric outer membrane (OM) composed of phospholipid in the inner leaflet and lipopolysaccharide (LPS) glycolipid in the outer leaflet. The PG layer has long been thought to be the major structural component of the envelope protecting cells from osmotic lysis and providing them with their characteristic shape. In recent years, the OM has also been shown to be a load-bearing layer of the cell surface that fortifies cells against internal turgor pressure. However, whether the OM also plays a role in morphogenesis has remained unclear. Here, we report that changes in LPS synthesis or modification predicted to strengthen the OM can suppress the growth and shape defects of Escherichia coli mutants with reduced activity in a conserved PG synthesis machine called the Rod system (elongasome) that is responsible for cell elongation and shape determination. Evidence is presented that OM fortification in the shape mutants restores the ability of MreB cytoskeletal filaments to properly orient the synthesis of new cell wall material by the Rod system. Our results are therefore consistent with a role for the OM in the propagation of rod shape during growth in addition to its well-known function as a diffusion barrier promoting the intrinsic antibiotic resistance of Gram-negative bacteria. SIGNIFICANCE The cell wall has traditionally been thought to be the main structural determinant of the bacterial cell envelope that resists internal turgor and determines cell shape. However, the outer membrane (OM) has recently been shown to contribute to the mechanical strength of Gram-negative bacterial envelopes. Here, we demonstrate that changes to OM composition predicted to increase its load bearing capacity rescue the growth and shape defects of Escherichia coli mutants defective in the major cell wall synthesis machinery that determines rod shape. Our results therefore reveal a previously unappreciated role for the OM in bacterial shape determination in addition to its well-known function as a diffusion barrier that protects Gram-negative bacteria from external insults like antibiotics.
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Affiliation(s)
- Elayne M. Fivenson
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Patricia D.A. Rohs
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Andrea Vettiger
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Marios F. Sardis
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Grasiela Torres
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Alison Forchoh
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Thomas G. Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
- Howard Hughes Medical Institute, Boston, United States
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22
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Modi SK, Gaur S, Sengupta M, Singh MS. Mechanistic insights into nanoparticle surface-bacterial membrane interactions in overcoming antibiotic resistance. Front Microbiol 2023; 14:1135579. [PMID: 37152753 PMCID: PMC10160668 DOI: 10.3389/fmicb.2023.1135579] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 03/30/2023] [Indexed: 05/09/2023] Open
Abstract
Antimicrobial Resistance (AMR) raises a serious concern as it contributes to the global mortality by 5 million deaths per year. The overall impact pertaining to significant membrane changes, through broad spectrum drugs have rendered the bacteria resistant over the years. The economic expenditure due to increasing drug resistance poses a global burden on healthcare community and must be dealt with immediate effect. Nanoparticles (NP) have demonstrated inherent therapeutic potential or can serve as nanocarriers of antibiotics against multidrug resistant (MDR) pathogens. These carriers can mask the antibiotics and help evade the resistance mechanism of the bacteria. The targeted delivery can be fine-tuned through surface functionalization of Nanocarriers using aptamers, antibodies etc. This review covers various molecular mechanisms acquired by resistant bacteria towards membrane modification. Mechanistic insight on 'NP surface-bacterial membrane' interactions are crucial in deciding the role of NP as therapeutic. Finally, we highlight the potential accessible membrane targets for designing smart surface-functionalized nanocarriers which can act as bacteria-targeted robots over the existing clinically available antibiotics. As the bacterial strains around us continue to evolve into resistant versions, nanomedicine can offer promising and alternative tools in overcoming AMR.
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Affiliation(s)
- Suraj Kumar Modi
- Department of Biotechnology, Bennett University, Greater Noida, Uttar Pradesh, India
- Centre of Excellence for Nanosensors and Nanomedicine, Bennett University, Greater Noida, Uttar Pradesh, India
| | - Smriti Gaur
- Department of Biotechnology, Bennett University, Greater Noida, Uttar Pradesh, India
| | - Mrittika Sengupta
- Department of Biotechnology, Bennett University, Greater Noida, Uttar Pradesh, India
- Centre of Excellence for Nanosensors and Nanomedicine, Bennett University, Greater Noida, Uttar Pradesh, India
- Mrittika Sengupta, ;
| | - Manu Smriti Singh
- Department of Biotechnology, Bennett University, Greater Noida, Uttar Pradesh, India
- Centre of Excellence for Nanosensors and Nanomedicine, Bennett University, Greater Noida, Uttar Pradesh, India
- *Correspondence: Manu Smriti Singh, ;
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23
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Lipid Microenvironment Modulates the Pore-Forming Ability of Polymyxin B. Antibiotics (Basel) 2022; 11:antibiotics11101445. [PMID: 36290103 PMCID: PMC9598075 DOI: 10.3390/antibiotics11101445] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022] Open
Abstract
The ability of polymyxin B, an antibiotic used to treat infections caused by multidrug-resistant Gram-negative bacteria as a last-line therapeutic option, to form ion pores in model membranes composed of various phospholipids and lipopolysaccharides was studied. Our data demonstrate that polymyxin B predominantly interacts with negatively charged lipids. Susceptibility decreases as follows: Kdo2-Lipid A >> DOPG ≈ DOPS >> DPhPG ≈ TOCL ≈ Lipid A. The dimer and hexamer of polymyxin B are involved in the pore formation in DOPG(DOPS)- and Kdo2-Lipid A-enriched bilayers, respectively. The pore-forming ability of polymyxin B significantly depends on the shape of membrane lipids, which indicates that the antibiotic produces toroidal lipopeptide-lipid pores. Small amphiphilic molecules diminishing the membrane dipole potential and inducing positive curvature stress were shown to be agonists of pore formation by polymyxin B and might be used to develop innovative lipopeptide-based formulations.
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24
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Burata OE, Yeh TJ, Macdonald CB, Stockbridge RB. Still rocking in the structural era: A molecular overview of the small multidrug resistance (SMR) transporter family. J Biol Chem 2022; 298:102482. [PMID: 36100040 PMCID: PMC9574504 DOI: 10.1016/j.jbc.2022.102482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/24/2022] [Accepted: 09/07/2022] [Indexed: 11/20/2022] Open
Abstract
The small multidrug resistance (SMR) family is composed of widespread microbial membrane proteins that fulfill different transport functions. Four functional SMR subtypes have been identified, which variously transport the small, charged metabolite guanidinium, bulky hydrophobic drugs and antiseptics, polyamines, and glycolipids across the membrane bilayer. The transporters possess a minimalist architecture, with ∼100-residue subunits that require assembly into homodimers or heterodimers for transport. In part because of their simple construction, the SMRs are a tractable system for biochemical and biophysical analysis. Studies of SMR transporters over the last 25 years have yielded deep insights for diverse fields, including membrane protein topology and evolution, mechanisms of membrane transport, and bacterial multidrug resistance. Here, we review recent advances in understanding the structures and functions of SMR transporters. New molecular structures of SMRs representing two of the four functional subtypes reveal the conserved structural features that have permitted the emergence of disparate substrate transport functions in the SMR family and illuminate structural similarities with a distantly related membrane transporter family, SLC35/DMT.
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Affiliation(s)
- Olive E Burata
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Trevor Justin Yeh
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Randy B Stockbridge
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA; Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA; Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
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25
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Marciano DC, Wang C, Hsu TK, Bourquard T, Atri B, Nehring RB, Abel NS, Bowling EA, Chen TJ, Lurie PD, Katsonis P, Rosenberg SM, Herman C, Lichtarge O. Evolutionary action of mutations reveals antimicrobial resistance genes in Escherichia coli. Nat Commun 2022; 13:3189. [PMID: 35680894 PMCID: PMC9184624 DOI: 10.1038/s41467-022-30889-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 05/24/2022] [Indexed: 11/08/2022] Open
Abstract
Since antibiotic development lags, we search for potential drug targets through directed evolution experiments. A challenge is that many resistance genes hide in a noisy mutational background as mutator clones emerge in the adaptive population. Here, to overcome this noise, we quantify the impact of mutations through evolutionary action (EA). After sequencing ciprofloxacin or colistin resistance strains grown under different mutational regimes, we find that an elevated sum of the evolutionary action of mutations in a gene identifies known resistance drivers. This EA integration approach also suggests new antibiotic resistance genes which are then shown to provide a fitness advantage in competition experiments. Moreover, EA integration analysis of clinical and environmental isolates of antibiotic resistant of E. coli identifies gene drivers of resistance where a standard approach fails. Together these results inform the genetic basis of de novo colistin resistance and support the robust discovery of phenotype-driving genes via the evolutionary action of genetic perturbations in fitness landscapes.
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Affiliation(s)
- David C Marciano
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Chen Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Teng-Kuei Hsu
- The Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Thomas Bourquard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Benu Atri
- Structural and Computational Biology & Molecular Biophysics Program, Baylor College of Medicine, Houston, TX, 77030, USA
- Clara Analytics Inc., 451 El Camino Real #201, Santa Clara, CA, 95050, USA
| | - Ralf B Nehring
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- The Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nicholas S Abel
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Elizabeth A Bowling
- The Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Taylor J Chen
- Integrative Molecular & Biomedical Biosciences Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pamela D Lurie
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- The Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Integrative Molecular & Biomedical Biosciences Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Structural and Computational Biology & Molecular Biophysics Program, Baylor College of Medicine, Houston, TX, 77030, USA.
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.
- Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX, 77030, USA.
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26
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Valvano MA. Remodelling of the Gram-negative bacterial Kdo 2-lipid A and its functional implications. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35394417 DOI: 10.1099/mic.0.001159] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The lipopolysaccharide (LPS) is a characteristic molecule of the outer leaflet of the Gram-negative bacterial outer membrane, which consists of lipid A, core oligosaccharide, and O antigen. The lipid A is embedded in outer membrane and provides an efficient permeability barrier, which is particularly important to reduce the permeability of antibiotics, toxic cationic metals, and antimicrobial peptides. LPS, an important modulator of innate immune responses ranging from localized inflammation to disseminated sepsis, displays a high level of structural and functional heterogeneity, which arise due to regulated differences in the acylation of the lipid A and the incorporation of non-stoichiometric modifications in lipid A and the core oligosaccharide. This review focuses on the current mechanistic understanding of the synthesis and assembly of the lipid A molecule and its most salient non-stoichiometric modifications.
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Affiliation(s)
- Miguel A Valvano
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, BT9 7BL, UK
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27
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Garcia-Vello P, Di Lorenzo F, Zucchetta D, Zamyatina A, De Castro C, Molinaro A. Lipopolysaccharide lipid A: A promising molecule for new immunity-based therapies and antibiotics. Pharmacol Ther 2022; 230:107970. [PMID: 34454000 DOI: 10.1016/j.pharmthera.2021.107970] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/24/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022]
Abstract
Lipopolysaccharides (LPS) are the main components of the external leaflet of the Gram-negative outer membrane and consist of three different moieties: lipid A, core oligosaccharide, and O-polysaccharide. The lipid A is a glucosamine disaccharide with different levels of acylation and phosphorylation, beside carrying, in certain cases, additional substituents on the sugar backbone. It is also the main immunostimulatory part of the LPS, as its recognition by the host immune system represents a fundamental event for detection of perilous microorganisms. Moreover, an uncontrolled immune response caused by a large amount of circulating LPS can lead to dramatic outcomes for human health, such as septic shock. The immunostimulant properties of an LPS incredibly vary depending on lipid A chemical structure, and for this reason, natural and synthetic variants of the lipid A are under study to develop new drugs that mimic or antagonise its natural effects. Here, we review past and recent findings on the lipid A as an antibiotic target and immune-therapeutic molecule, with a special attention on the crucial role of the chemical structure and its exploitation for conceiving novel strategies for treatment of several immune-related pathologies.
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Affiliation(s)
- Pilar Garcia-Vello
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy.
| | - Flaviana Di Lorenzo
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy
| | - Daniele Zucchetta
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Alla Zamyatina
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Cristina De Castro
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy.
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28
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Murtha AN, Kazi MI, Schargel RD, Cross T, Fihn C, Cattoir V, Carlson EE, Boll JM, Dörr T. High-level carbapenem tolerance requires antibiotic-induced outer membrane modifications. PLoS Pathog 2022; 18:e1010307. [PMID: 35130322 PMCID: PMC8853513 DOI: 10.1371/journal.ppat.1010307] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/17/2022] [Accepted: 01/26/2022] [Indexed: 12/22/2022] Open
Abstract
Antibiotic tolerance is an understudied potential contributor to antibiotic treatment failure and the emergence of multidrug-resistant bacteria. The molecular mechanisms governing tolerance remain poorly understood. A prominent type of β-lactam tolerance relies on the formation of cell wall-deficient spheroplasts, which maintain structural integrity via their outer membrane (OM), an asymmetric lipid bilayer consisting of phospholipids on the inner leaflet and a lipid-linked polysaccharide (lipopolysaccharide, LPS) enriched in the outer monolayer on the cell surface. How a membrane structure like LPS, with its reliance on mere electrostatic interactions to maintain stability, is capable of countering internal turgor pressure is unknown. Here, we have uncovered a novel role for the PhoPQ two-component system in tolerance to the β-lactam antibiotic meropenem in Enterobacterales. We found that PhoPQ is induced by meropenem treatment and promotes an increase in 4-amino-4-deoxy-L-aminoarabinose [L-Ara4N] modification of lipid A, the membrane anchor of LPS. L-Ara4N modifications likely enhance structural integrity, and consequently tolerance to meropenem, in several Enterobacterales species. Importantly, mutational inactivation of the negative PhoPQ regulator mgrB (commonly selected for during clinical therapy with the last-resort antibiotic colistin, an antimicrobial peptide [AMP]) results in dramatically enhanced tolerance, suggesting that AMPs can collaterally select for meropenem tolerance via stable overactivation of PhoPQ. Lastly, we identify histidine kinase inhibitors (including an FDA-approved drug) that inhibit PhoPQ-dependent LPS modifications and consequently potentiate meropenem to enhance lysis of tolerant cells. In summary, our results suggest that PhoPQ-mediated LPS modifications play a significant role in stabilizing the OM, promoting survival when the primary integrity maintenance structure, the cell wall, is removed. Treating an infection with an antibiotic often fails, resulting in a tremendous public health burden. One understudied likely reason for treatment failure is the development of “antibiotic tolerance”, the ability of bacteria to survive normally lethal exposure to an antibiotic. Here, we describe a molecular mechanism promoting tolerance. A bacterial stress sensor (PhoPQ) is activated in response to antibiotic (meropenem) treatment and consequently strengthens a bacterial protective “shell” to enhance survival. We also identify inhibitors of this mechanism, opening the door to developing compounds that help antibiotics work better against tolerant bacteria.
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Affiliation(s)
- Andrew N. Murtha
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| | - Misha I. Kazi
- Department of Biology, University of Texas Arlington, Arlington, Texas, United States of America
| | - Richard D. Schargel
- Department of Biology, University of Texas Arlington, Arlington, Texas, United States of America
| | - Trevor Cross
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| | - Conrad Fihn
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Vincent Cattoir
- Department of Clinical Microbiology and National Reference Center for Antimicrobial Resistance (Lab Enterococci), Rennes University Hospital, Rennes, France; Inserm Unit U1230, University of Rennes 1, Rennes, France
| | - Erin E. Carlson
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Molecular Pharmacology and Therapeutics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Joseph M. Boll
- Department of Biology, University of Texas Arlington, Arlington, Texas, United States of America
- * E-mail: (JMB); (TD)
| | - Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, New York, United States of America
- * E-mail: (JMB); (TD)
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29
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Colistin Interaction and Surface Changes Associated with mcr-1 Conferred Plasmid Mediated Resistance in E. coli and A. veronii Strains. Pharmaceutics 2022; 14:pharmaceutics14020295. [PMID: 35214028 PMCID: PMC8880236 DOI: 10.3390/pharmaceutics14020295] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/02/2022] [Accepted: 01/16/2022] [Indexed: 02/05/2023] Open
Abstract
Colistin, a polycationic antimicrobial peptide, is one of the last-resort antibiotics for treating infections caused by carbapenem-resistant Gram-negative bacteria. The antibacterial activity of colistin occurs through electrostatic interaction between the polycationic peptide group of colistin and the negatively charged phosphate groups of lipid A membrane. This study investigated the interaction of colistin with the outer membrane and surface constituents of resistant and susceptible strains of Escherichia coli and Aeromonas veronii harboring mcr-1 resistance gene. Bacterial membrane and lipopolysaccharide used in this study were isolated from susceptible as well as colistin-resistant strains of E. coli and A. veronii. Interaction of colistin with the bacterial surface was studied by deoxycholate and lysozyme sensitivity test, N-phenyl-1-naphthylamine (NPN) uptake assay, Atomic force microscopy (AFM), Zeta potential measurements and 1H NMR. The binding affinity of colistin was found to be lower with outer membrane from resistant strains in comparison with the susceptible strains. Colistin exposure enhances the outer membrane permeability of the susceptible strains to deoxycholate and lysozyme. However, on the other hand, colistin dose of 256 µg/mL did not permeabilize the outer membrane of resistant bacteria. The NPN permeability in resistant strains was greater in comparison with susceptible strains. Atomic force microscopy images depicted smooth, featherless and deformed membranes in treated susceptible cells. Contrary to the above, resistant treated cells displayed surface roughness topography even at 256 µg/mL colistin concentration. Surface charge alterations were confirmed by Zeta potential measurements as a function of the growth phase. Mid-logarithmic phase susceptible strains showed a greater negative charge than resistant strains upon exposure to colistin. However, there was no statistical variation in the Zeta potential measurements between resistant and susceptible strains at the stationary phase. NMR analysis revealed line broadening in susceptible strains with increasing colistin: LPS aggregates mass ratio. Moreover, resistant strains did not show line broadening for the outer membrane, even at the highest mass ratio. The findings of this study suggest that the resistant strains of E. coli and A. veronii can block the electrostatic contact between the cationic peptide and anionic lipid A component that drives the first phase of colistin action, thereby preventing hydrophobically driven second-tier action of colistin on the outer lipopolysaccharide layer.
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30
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Tiwari V, Panta PR, Billiot CE, Douglass MV, Herrera CM, Trent MS, Doerrler WT. A Klebsiella pneumoniae DedA family membrane protein is required for colistin resistance and for virulence in wax moth larvae. Sci Rep 2021; 11:24365. [PMID: 34934166 PMCID: PMC8692421 DOI: 10.1038/s41598-021-03834-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/10/2021] [Indexed: 12/15/2022] Open
Abstract
Ineffectiveness of carbapenems against multidrug resistant pathogens led to the increased use of colistin (polymyxin E) as a last resort antibiotic. A gene belonging to the DedA family encoding conserved membrane proteins was previously identified by screening a transposon library of K. pneumoniae ST258 for sensitivity to colistin. We have renamed this gene dkcA (dedA of Klebsiella required for colistin resistance). DedA family proteins are likely membrane transporters required for viability of Escherichia coli and Burkholderia spp. at alkaline pH and for resistance to colistin in a number of bacterial species. Colistin resistance is often conferred via modification of the lipid A component of bacterial lipopolysaccharide with aminoarabinose (Ara4N) and/or phosphoethanolamine. Mass spectrometry analysis of lipid A of the ∆dkcA mutant shows a near absence of Ara4N in the lipid A, suggesting a requirement for DkcA for lipid A modification with Ara4N. Mutation of K. pneumoniae dkcA resulted in a reduction of the colistin minimal inhibitory concentration to approximately what is found with a ΔarnT strain. We also identify a requirement of DkcA for colistin resistance that is independent of lipid A modification, instead requiring maintenance of optimal membrane potential. K. pneumoniae ΔdkcA displays reduced virulence in Galleria mellonella suggesting colistin sensitivity can cause loss of virulence.
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Affiliation(s)
- Vijay Tiwari
- grid.64337.350000 0001 0662 7451Department of Biological Sciences, Louisiana State University, Baton Rouge, LA USA
| | - Pradip R. Panta
- grid.64337.350000 0001 0662 7451Department of Biological Sciences, Louisiana State University, Baton Rouge, LA USA
| | - Caitlin E. Billiot
- grid.64337.350000 0001 0662 7451Department of Biological Sciences, Louisiana State University, Baton Rouge, LA USA
| | - Martin V. Douglass
- grid.213876.90000 0004 1936 738XDepartment of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA USA
| | - Carmen M. Herrera
- grid.213876.90000 0004 1936 738XDepartment of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA USA
| | - M. Stephen Trent
- grid.213876.90000 0004 1936 738XDepartment of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA USA
| | - William T. Doerrler
- grid.64337.350000 0001 0662 7451Department of Biological Sciences, Louisiana State University, Baton Rouge, LA USA
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31
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Diacylglycerol kinase A is essential for polymyxin resistance provided by EptA, MCR-1 and other lipid A phosphoethanolamine transferases. J Bacteriol 2021; 204:e0049821. [PMID: 34843376 DOI: 10.1128/jb.00498-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gram-negative bacteria utilize glycerophospholipids (GPLs) as phospho-form donors to modify various surface structures. These modifications play important roles in bacterial fitness in diverse environments influencing cell motility, recognition by the host during infection, and antimicrobial resistance. A well-known example is the modification of the lipid A component of lipopolysaccharide by the phosphoethanolamine (pEtN) transferase EptA that utilizes phosphatidyethanoalmine (PE) as the phospho-form donor. Addition of pEtN to lipid A promotes resistance to cationic antimicrobial peptides (CAMPs), including the polymyxin antibiotics like colistin. A consequence of pEtN modification is the production of diacylglycerol (DAG) that must be recycled back into GPL synthesis via the diacylglycerol kinase A (DgkA). DgkA phosphorylates DAG forming phosphatidic acid, the precursor for GPL synthesis. Here we report that deletion of dgkA in polymyxin-resistant E. coli results in a severe reduction of pEtN modification and loss of antibiotic resistance. We demonstrate that inhibition of EptA is regulated post-transcriptionally and is not due to EptA degradation during DAG accumulation. We also show that the inhibition of lipid A modification by DAG is a conserved feature of different Gram-negative pEtN transferases. Altogether, our data suggests that inhibition of EptA activity during DAG accumulation likely prevents disruption of GPL synthesis helping to maintain cell envelope homeostasis.
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Scarbrough BA, Eade CR, Reid AJ, Williams TC, Troutman JM. Lipopolysaccharide Is a 4-Aminoarabinose Donor to Exogenous Polyisoprenyl Phosphates through the Reverse Reaction of the Enzyme ArnT. ACS OMEGA 2021; 6:25729-25741. [PMID: 34632229 PMCID: PMC8495848 DOI: 10.1021/acsomega.1c04036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Indexed: 05/11/2023]
Abstract
Modification of the lipid A portion of LPS with cationic monosaccharides provides resistance to polymyxins, which are often employed as a last resort to treat multidrug-resistant bacterial infections. Here, we describe the use of fluorescent polyisoprenoids, liquid chromatography-mass spectrometry, and bacterial genetics to probe the activity of membrane-localized proteins that utilize the 55-carbon lipid carrier bactoprenyl phosphate (BP). We have discovered that a substantial background reaction occurs when B-strain E. coli cell membrane fractions are supplemented with exogenous BP. This reaction involves proteins associated with the arn operon, which is necessary for the covalent modification of lipid A with the cationic 4-aminoarabinose (Ara4N). Using a series of arn operon gene deletion mutants, we identified that the modification was dependent on ArnC, which is responsible for forming BP-linked Ara4N, or ArnT, which transfers Ara4N to lipid A. Surprisingly, we found that the majority of the Ara4N-modified isoprenoid was due to the reverse reaction catalyzed by ArnT and demonstrate this using heat-inactivated membrane fractions, isolated lipopolysaccharide fractions, and analyses of a purified ArnT. This work provides methods that will facilitate thorough and rapid investigation of bacterial outer membrane remodeling and the evaluation of polyisoprenoid precursors required for covalent glycan modifications.
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Affiliation(s)
- Beth A. Scarbrough
- Nanoscale
Science Program, The University of North
Carolina at Charlotte, Charlotte, North Carolina 28223-0001, United States
| | - Colleen R. Eade
- Department
of Chemistry, The University of North Carolina
at Charlotte, Charlotte, North Carolina 28223-0001, United States
| | - Amanda J. Reid
- Nanoscale
Science Program, The University of North
Carolina at Charlotte, Charlotte, North Carolina 28223-0001, United States
| | - Tiffany C. Williams
- Department
of Chemistry, The University of North Carolina
at Charlotte, Charlotte, North Carolina 28223-0001, United States
| | - Jerry M. Troutman
- Department
of Chemistry, The University of North Carolina
at Charlotte, Charlotte, North Carolina 28223-0001, United States
- Nanoscale
Science Program, The University of North
Carolina at Charlotte, Charlotte, North Carolina 28223-0001, United States
- . Phone: 704-687-5180
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33
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Lipopolysaccharide of the Yersinia pseudotuberculosis Complex. Biomolecules 2021; 11:biom11101410. [PMID: 34680043 PMCID: PMC8533242 DOI: 10.3390/biom11101410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/27/2021] [Accepted: 09/21/2021] [Indexed: 11/16/2022] Open
Abstract
Lipopolysaccharide (LPS), localized in the outer leaflet of the outer membrane, serves as the major surface component of the Gram-negative bacterial cell envelope responsible for the activation of the host's innate immune system. Variations of the LPS structure utilized by Gram-negative bacteria promote survival by providing resistance to components of the innate immune system and preventing recognition by TLR4. This review summarizes studies of the biosynthesis of Yersinia pseudotuberculosis complex LPSs, and the roles of their structural components in molecular mechanisms of yersiniae pathogenesis and immunogenesis.
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Yin W, Ling Z, Dong Y, Qiao L, Shen Y, Liu Z, Wu Y, Li W, Zhang R, Walsh TR, Dai C, Li J, Yang H, Liu D, Wang Y, Gao GF, Shen J. Mobile Colistin Resistance Enzyme MCR-3 Facilitates Bacterial Evasion of Host Phagocytosis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2101336. [PMID: 34323389 PMCID: PMC8456205 DOI: 10.1002/advs.202101336] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/12/2021] [Indexed: 05/10/2023]
Abstract
Mobile colistin resistance enzyme MCR-3 is a phosphoethanolamine transferase modifying lipid A in Gram-negative bacteria. MCR-3 generally mediates low-level (≤8 mg L-1 ) colistin resistance among Enterobacteriaceae, but occasionally confers high-level (>128 mg L-1 ) resistance in aeromonads. Herein, it is determined that MCR-3, together with another lipid A modification mediated by the arnBCADTEF operon, may be responsible for high-level colistin resistance in aeromonads. Lipid A is the critical site of pathogens for Toll-like receptor 4 recognizing. However, it is unknown whether or how MCR-3-mediated lipid A modification affects the host immune response. Compared with the wild-type strains, increased mortality is observed in mice intraperitoneally-infected with mcr-3-positive Aeromonas salmonicida and Escherichia coli strains, along with sepsis symptoms. Further, mcr-3-positive strains show decreased clearance rates than wild-type strains, leading to bacterial accumulation in organs. The increased mortality is tightly associated with the increased tissue hypoxia, injury, and post-inflammation. MCR-3 expression also impairs phagocytosis efficiency both in vivo and in vitro, contributing to the increased persistence of mcr-3-positive bacteria in tissues compared with parental strains. This study, for the first time, reveals a dual function of MCR-3 in bacterial resistance and pathogenicity, which calls for caution in treating the infections caused by mcr-positive pathogens.
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Affiliation(s)
- Wenjuan Yin
- Beijing Key Laboratory of Detection Technology for Animal‐Derived Food SafetyCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193China
- College of Basic Medical ScienceKey Laboratory of Pathogenesis Mechanism and Control of Inflammatory‐Autoimmune Diseases of Hebei ProvinceHebei UniversityBaoding071002China
| | - Zhuoren Ling
- Beijing Key Laboratory of Detection Technology for Animal‐Derived Food SafetyCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193China
| | - Yanjun Dong
- Department of Basic Veterinary MedicineCollege of Veterinary MedicineChina Agricultural UniversityHaidianBeijing100193China
| | - Lu Qiao
- Beijing Key Laboratory of Detection Technology for Animal‐Derived Food SafetyCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193China
| | - Yingbo Shen
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of Sciences (CAS)Beijing100101China
| | - Zhihai Liu
- Beijing Key Laboratory of Detection Technology for Animal‐Derived Food SafetyCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193China
- Agricultural Bio‐Pharmaceutical LaboratoryCollege of Chemistry and Pharmaceutical SciencesQingdao Agricultural UniversityQingdao266109China
| | - Yifan Wu
- Beijing Key Laboratory of Detection Technology for Animal‐Derived Food SafetyCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193China
| | - Wan Li
- Beijing Key Laboratory of Detection Technology for Animal‐Derived Food SafetyCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193China
| | - Rong Zhang
- The Second Affiliated Hospital of Zhejiang UniversityZhejiang UniversityHangzhou310009China
| | | | - Chongshan Dai
- Beijing Key Laboratory of Detection Technology for Animal‐Derived Food SafetyCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193China
| | - Juan Li
- State Key Laboratory of Infectious Disease Prevention and ControlNational Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionChangpingBeijing102206China
| | - Hui Yang
- NHC Key Laboratory of Food Safety Risk AssessmentChina National Center for Food Safety Risk AssessmentNo. 7 Panjiayuan NanliBeijing100021China
| | - Dejun Liu
- Beijing Key Laboratory of Detection Technology for Animal‐Derived Food SafetyCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193China
| | - Yang Wang
- Beijing Key Laboratory of Detection Technology for Animal‐Derived Food SafetyCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193China
| | - George Fu Gao
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of Sciences (CAS)Beijing100101China
- College of Veterinary MedicineChina Agricultural UniversityHaidianBeijing100193China
| | - Jianzhong Shen
- Beijing Key Laboratory of Detection Technology for Animal‐Derived Food SafetyCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193China
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35
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Mohapatra SS, Dwibedy SK, Padhy I. Polymyxins, the last-resort antibiotics: Mode of action, resistance emergence, and potential solutions. J Biosci 2021. [PMID: 34475315 PMCID: PMC8387214 DOI: 10.1007/s12038-021-00209-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Infections caused by multi-drug resistant (MDR) bacterial pathogens are a leading cause of mortality and morbidity across the world. Indiscriminate use of broad-spectrum antibiotics has seriously affected this situation. With the diminishing discovery of novel antibiotics, new treatment methods are urgently required to combat MDR pathogens. Polymyxins, the cationic lipopeptide antibiotics, discovered more than half a century ago, are considered to be the last-line of antibiotics available at the moment. This antibiotic shows a great bactericidal effect against Gram-negative bacteria. Polymyxins primarily target the bacterial membrane and disrupt them, causing lethality. Because of their membrane interacting mode of action, polymyxins cause nephrotoxicity and neurotoxicity in humans, limiting their usability. However, recent modifications in their chemical structure have been able to reduce the toxic effects. The development of better dosing regimens has also helped in getting better clinical outcomes in the infections caused by MDR pathogens. Since the mid-1990s the use of polymyxins has increased manifold in clinical settings, resulting in the emergence of polymyxin-resistant strains. The risk posed by the polymyxin-resistant nosocomial pathogens such as the Enterobacteriaceae group, Pseudomonas aeruginosa, and Acinetobacter baumannii, etc. is very serious considering these pathogens are resistant to almost all available antibacterial drugs. In this review article, the mode of action of the polymyxins and the genetic regulatory mechanism responsible for the emergence of resistance are discussed. Specifically, this review aims to update our current understanding in the field and suggest possible solutions that can be pursued for future antibiotic development. As polymyxins primarily target the bacterial membranes, resistance to polymyxins arises primarily by the modification of the lipopolysaccharides (LPS) in the outer membrane (OM). The LPS modification pathways are largely regulated by the bacterial two-component signal transduction (TCS) systems. Therefore, targeting or modulating the TCS signalling mechanisms can be pursued as an alternative to treat the infections caused by polymyxin-resistant MDR pathogens. In this review article, this aspect is also highlighted.
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Affiliation(s)
- Saswat S Mohapatra
- Molecular Microbiology Lab, Department of Bioscience and Bioinformatics, Khallikote University, Konisi, Berhampur, 761 008 Odisha India
| | - Sambit K Dwibedy
- Molecular Microbiology Lab, Department of Bioscience and Bioinformatics, Khallikote University, Konisi, Berhampur, 761 008 Odisha India
| | - Indira Padhy
- Molecular Microbiology Lab, Department of Bioscience and Bioinformatics, Khallikote University, Konisi, Berhampur, 761 008 Odisha India
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36
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Augusto LA, Bourgeois-Nicolaos N, Breton A, Barreault S, Alonso EH, Gera S, Faraut-Derouin V, Semaan N, De Luca D, Chaby R, Doucet-Populaire F, Tissières P. Presence of 2-hydroxymyristate on endotoxins is associated with death in neonates with Enterobacter cloacae complex septic shock. iScience 2021; 24:102916. [PMID: 34409274 PMCID: PMC8361193 DOI: 10.1016/j.isci.2021.102916] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/11/2021] [Accepted: 07/27/2021] [Indexed: 11/29/2022] Open
Abstract
Enterobacter cloacae complex species are involved in infections among critically ill patients. After a recent E.cloacae outbreak of fulminant neonatal septic shock, we conducted a study to determine whether septic shock severity and its lethal consequence are related to structural features of the endotoxin (lipopolysaccharide [LPS]) of the strains isolated from hospitalized infants and more specifically its lipid A region. It appeared that the LPSs are very heterogeneous, carrying fifteen different molecular species of lipid A. The virulence was correlated with a structural feature identified by matrix-assisted laser desorption ionization–time of flight mass spectrometry and gas chromatography coupled with mass spectrometry: the presence of 2-hydroxymyristic acid as a secondary substituent in lipid A. This is the first published evidence linking LPS structural moiety to neonatal sepsis outcome and opens the possibility of using this fatty acid marker as a detection tool for high-risk patients, which could help reduce their mortality. Fifteen different molecular species of lipid A is found in E. cloacae complex 2-Hydroxymyristate moiety on Lipid A is a virulence marker of the E. cloacae complex Presence of 2-hydroxymyristate is associated with mortality in neonatal sepsis
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Affiliation(s)
- Luis A Augusto
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Nadège Bourgeois-Nicolaos
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.,Department of Bacteriology-Hygiene, AP-HP Paris-Saclay, Hôpital Antoine Béclère, Clamart Cedex, France
| | - Aude Breton
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Simon Barreault
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.,Department of Pediatrics Intensive Care and Neonatal Medicine, AP-HP Université Paris -Saclay, Bicêtre Hospital, Paris, France
| | - Enrique Hernandez Alonso
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Stuti Gera
- Department of Bacteriology-Hygiene, AP-HP Paris-Saclay, Hôpital Antoine Béclère, Clamart Cedex, France
| | - Véronique Faraut-Derouin
- Department of Bacteriology-Hygiene, AP-HP Paris-Saclay, Hôpital Antoine Béclère, Clamart Cedex, France
| | - Nada Semaan
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.,Department of Pediatrics Intensive Care and Neonatal Medicine, AP-HP Université Paris -Saclay, Bicêtre Hospital, Paris, France
| | - Daniele De Luca
- Department of Neonatal Intensive Care, AP-HP Université Paris -Saclay, Hôpital Antoine Béclère, Clamart, France
| | - Richard Chaby
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Florence Doucet-Populaire
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.,Department of Bacteriology-Hygiene, AP-HP Paris-Saclay, Hôpital Antoine Béclère, Clamart Cedex, France
| | - Pierre Tissières
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.,Department of Pediatrics Intensive Care and Neonatal Medicine, AP-HP Université Paris -Saclay, Bicêtre Hospital, Paris, France.,FHU Sepsis, AP-HP/Université Paris-Saclay/Inserm, Le Kremlin-Bicêtre, France
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37
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The Xanthomonas RaxH-RaxR Two-Component Regulatory System Is Orthologous to the Zinc-Responsive Pseudomonas ColS-ColR System. Microorganisms 2021; 9:microorganisms9071458. [PMID: 34361895 PMCID: PMC8306577 DOI: 10.3390/microorganisms9071458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 01/08/2023] Open
Abstract
Genome sequence comparisons to infer likely gene functions require accurate ortholog assignments. In Pseudomonas spp., the sensor-regulator ColS-ColR two-component regulatory system responds to zinc and other metals to control certain membrane-related functions, including lipid A remodeling. In Xanthomonas spp., three different two-component regulatory systems, RaxH-RaxR, VgrS-VgrR, and DetS-DetR, have been denoted as ColS-ColR in several different genome annotations and publications. To clarify these assignments, we compared the sensor periplasmic domain sequences and found that those from Pseudomonas ColS and Xanthomonas RaxH share a similar size as well as the location of a Glu-X-X-Glu metal ion-binding motif. Furthermore, we determined that three genes adjacent to raxRH are predicted to encode enzymes that remodel the lipid A component of lipopolysaccharide. The modifications catalyzed by lipid A phosphoethanolamine transferase (EptA) and lipid A 1-phosphatase (LpxE) previously were detected in lipid A from multiple Xanthomonas spp. The third gene encodes a predicted lipid A glycosyl transferase (ArnT). Together, these results indicate that the Xanthomonas RaxH-RaxR system is orthologous to the Pseudomonas ColS-ColR system that regulates lipid A remodeling. To avoid future confusion, we recommend that the terms ColS and ColR no longer be applied to Xanthomonas spp., and that the Vgr, Rax, and Det designations be used instead.
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38
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Park J, Kim M, Shin B, Kang M, Yang J, Lee TK, Park W. A novel decoy strategy for polymyxin resistance in Acinetobacter baumannii. eLife 2021; 10:66988. [PMID: 34180396 PMCID: PMC8324293 DOI: 10.7554/elife.66988] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/27/2021] [Indexed: 12/17/2022] Open
Abstract
Modification of the outer membrane charge by a polymyxin B (PMB)-induced PmrAB two-component system appears to be a dominant phenomenon in PMB-resistant Acinetobacter baumannii. PMB-resistant variants and many clinical isolates also appeared to produce outer membrane vesicles (OMVs). Genomic, transcriptomic, and proteomic analyses revealed that upregulation of the pmr operon and decreased membrane-linkage proteins (OmpA, OmpW, and BamE) are linked to overproduction of OMVs, which also promoted enhanced biofilm formation. The addition of OMVs from PMB-resistant variants into the cultures of PMB-susceptible A. baumannii and the clinical isolates protected these susceptible bacteria from PMB. Taxonomic profiling of in vitro human gut microbiomes under anaerobic conditions demonstrated that OMVs completely protected the microbial community against PMB treatment. A Galleria mellonella-infection model with PMB treatment showed that OMVs increased the mortality rate of larvae by protecting A. baumannii from PMB. Taken together, OMVs released from A. baumannii functioned as decoys against PMB. Wrapped in a thick, protective outer membrane, Acinetobacter baumannii bacteria can sometimes cause serious infections when they find their way into human lungs and urinary tracts. Antibiotics are increasingly ineffective against this threat, which forces physicians to resort to polymyxin B, an old, positively-charged drug that ‘sticks’ to the negatively-charged proteins and fatty components at the surface of A. baumannii. Scientists have noticed that when bacteria are exposed to lethal drugs, they often react by releasing vesicles, small ‘sacs’ made of pieces of the outer membranes which can contain DNA or enzymes. How this strategy protects the cells against antibiotics such as polymyxin B remains poorly understood. To investigate this question, Park et al. examined different strains of A. baumannii, showing that bacteria resistant to polymyxin B had lower levels of outer membrane proteins but would release more vesicles. Adding vesicles from resistant strains to non-resistant A. baumannii cultures helped cells to survive the drugs. In fact, this protective effect extended to other species, shielding whole communities of bacteria against polymyxin B. In vivo, the vesicles protected bacteria in moth larvae infected with A. baumannii, leading to a higher death rate in the animals. Experiments showed that the negatively-charged vesicles worked as decoys, trapping the positively-charged polymyxin B away from its target. Taken together, the findings by Park et al. highlight a new strategy that allows certain strains of bacteria to protect themselves from antibiotics, while also benefitting the rest of the microbial community.
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Affiliation(s)
- Jaeeun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Misung Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Bora Shin
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Mingyeong Kang
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Jihye Yang
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Tae Kwon Lee
- Department of Environmental Engineering, Yonsei University, Wonju, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
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39
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Kazi MI, Perry BW, Card DC, Schargel RD, Ali HB, Obuekwe VC, Sapkota M, Kang KN, Pellegrino MW, Greenberg DE, Castoe TA, Boll JM. Discovery and characterization of New Delhi metallo-β-lactamase-1 inhibitor peptides that potentiate meropenem-dependent killing of carbapenemase-producing Enterobacteriaceae. J Antimicrob Chemother 2021; 75:2843-2851. [PMID: 32591801 DOI: 10.1093/jac/dkaa242] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/20/2020] [Accepted: 05/06/2020] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Metallo-β-lactamases (MBLs) are an emerging class of antimicrobial resistance enzymes that degrade β-lactam antibiotics, including last-resort carbapenems. Infections caused by carbapenemase-producing Enterobacteriaceae (CPE) are increasingly prevalent, but treatment options are limited. While several serine-dependent β-lactamase inhibitors are formulated with commonly prescribed β-lactams, no MBL inhibitors are currently approved for combinatorial therapies. New compounds that target MBLs to restore carbapenem activity against CPE are therefore urgently needed. Herein we identified and characterized novel synthetic peptide inhibitors that bound to and inhibited NDM-1, which is an emerging β-lactam resistance mechanism in CPE. METHODS We leveraged Surface Localized Antimicrobial displaY (SLAY) to identify and characterize peptides that inhibit NDM-1, which is a primary carbapenem resistance mechanism in CPE. Lead inhibitor sequences were chemically synthesized and MBCs and MICs were calculated in the presence/absence of carbapenems. Kinetic analysis with recombinant NDM-1 and select peptides tested direct binding and supported NDM-1 inhibitor mechanisms of action. Inhibitors were also tested for cytotoxicity. RESULTS We identified approximately 1700 sequences that potentiated carbapenem-dependent killing against NDM-1 Escherichia coli. Several also enhanced meropenem-dependent killing of other CPE. Biochemical characterization of a subset indicated the peptides penetrated the bacterial periplasm and directly bound NDM-1 to inhibit enzymatic activity. Additionally, each demonstrated minimal haemolysis and cytotoxicity against mammalian cell lines. CONCLUSIONS Our approach advances a molecular platform for antimicrobial discovery, which complements the growing need for alternative antimicrobials. We also discovered lead NDM-1 inhibitors, which serve as a starting point for further chemical optimization.
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Affiliation(s)
- Misha I Kazi
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Daren C Card
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Richard D Schargel
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Hana B Ali
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Victor C Obuekwe
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Madhab Sapkota
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Katie N Kang
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Mark W Pellegrino
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - David E Greenberg
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Joseph M Boll
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
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40
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Tian X, Manat G, Gasiorowski E, Auger R, Hicham S, Mengin-Lecreulx D, Boneca IG, Touzé T. LpxT-Dependent Phosphorylation of Lipid A in Escherichia coli Increases Resistance to Deoxycholate and Enhances Gut Colonization. Front Microbiol 2021; 12:676596. [PMID: 34017319 PMCID: PMC8129183 DOI: 10.3389/fmicb.2021.676596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/09/2021] [Indexed: 11/13/2022] Open
Abstract
The cell surface of Gram-negative bacteria usually exhibits a net negative charge mostly conferred by lipopolysaccharides (LPS). This property sensitizes bacterial cells to cationic antimicrobial peptides, such as polymyxin B, by favoring their binding to the cell surface. Gram-negative bacteria can modify their surface to counteract these compounds such as the decoration of their LPS by positively charged groups. For example, in Escherichia coli and Salmonella, EptA and ArnT add amine-containing groups to the lipid A moiety. In contrast, LpxT enhances the net negative charge by catalyzing the synthesis of tri-phosphorylated lipid A, whose function is yet unknown. Here, we report that E. coli has the intrinsic ability to resist polymyxin B upon the simultaneous activation of the two component regulatory systems PhoPQ and PmrAB by intricate environmental cues. Among many LPS modifications, only EptA- and ArnT-dependent decorations were required for polymyxin B resistance. Conversely, the acquisition of polymyxin B resistance compromised the innate resistance of E. coli to deoxycholate, a major component of bile. The inhibition of LpxT by PmrR, under PmrAB-inducing conditions, specifically accounted for the acquired susceptibility to deoxycholate. We also report that the kinetics of intestinal colonization by the E. coli lpxT mutant was impaired as compared to wild-type in a mouse model of infection and that lpxT was upregulated at the temperature of the host. Together, these findings highlight an important function of LpxT and suggest that a tight equilibrium between EptA- and LpxT-dependent decorations, which occur at the same position of lipid A, is critical for the life style of E. coli.
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Affiliation(s)
- Xudong Tian
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Guillaume Manat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Elise Gasiorowski
- Institut Pasteur, Unité Biologie et Génétique de la Paroi Bactérienne, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Rodolphe Auger
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Samia Hicham
- Institut Pasteur, Unité Biologie et Génétique de la Paroi Bactérienne, Paris, France
| | - Dominique Mengin-Lecreulx
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Ivo Gomperts Boneca
- Institut Pasteur, Unité Biologie et Génétique de la Paroi Bactérienne, Paris, France
| | - Thierry Touzé
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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41
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The MCR-3 inside linker appears as a facilitator of colistin resistance. Cell Rep 2021; 35:109135. [PMID: 34010644 DOI: 10.1016/j.celrep.2021.109135] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 12/23/2020] [Accepted: 04/23/2021] [Indexed: 01/08/2023] Open
Abstract
An evolving family of mobile colistin resistance (MCR) enzymes is threatening public health. However, the molecular mechanism by which the MCR enzyme as a rare member of lipid A-phosphoethanolamine (PEA) transferases gains the ability to confer phenotypic colistin resistance remains enigmatic. Here, we report an unusual example that genetic duplication and amplification produce a functional variant (Ah762) of MCR-3 in certain Aeromonas species. The lipid A-binding cavity of Ah762 is functionally defined. Intriguingly, we locate a hinge linker of Ah762 (termed Linker 59) that determines the MCR. Genetic and biochemical characterization reveals that Linker 59 behaves as a facilitator to render inactive MCR variants to regain the ability of colistin resistance. Along with molecular dynamics (MD) simulation, isothermal titration calorimetry (ITC) suggests that this facilitator guarantees the formation of substrate phosphatidylethanolamine (PE)-accessible pocket within MCR-3-like enzymes. Therefore, our finding defines an MCR-3 inside facilitator for colistin resistance.
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Abstract
Antibiotic resistance is a major global health challenge and, worryingly, several key Gram negative pathogens can become resistant to most currently available antibiotics. Polymyxins have been revived as a last-line therapeutic option for the treatment of infections caused by multidrug-resistant Gram negative bacteria, in particular Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacterales. Polymyxins were first discovered in the late 1940s but were abandoned soon after their approval in the late 1950s as a result of toxicities (e.g., nephrotoxicity) and the availability of "safer" antibiotics approved at that time. Therefore, knowledge on polymyxins had been scarce until recently, when enormous efforts have been made by several research teams around the world to elucidate the chemical, microbiological, pharmacokinetic/pharmacodynamic, and toxicological properties of polymyxins. One of the major achievements is the development of the first scientifically based dosage regimens for colistin that are crucial to ensure its safe and effective use in patients. Although the guideline has not been developed for polymyxin B, a large clinical trial is currently being conducted to optimize its clinical use. Importantly, several novel, safer polymyxin-like lipopeptides are developed to overcome the nephrotoxicity, poor efficacy against pulmonary infections, and narrow therapeutic windows of the currently used polymyxin B and colistin. This review discusses the latest achievements on polymyxins and highlights the major challenges ahead in optimizing their clinical use and discovering new-generation polymyxins. To save lives from the deadly infections caused by Gram negative "superbugs," every effort must be made to improve the clinical utility of the last-line polymyxins. SIGNIFICANCE STATEMENT: Antimicrobial resistance poses a significant threat to global health. The increasing prevalence of multidrug-resistant (MDR) bacterial infections has been highlighted by leading global health organizations and authorities. Polymyxins are a last-line defense against difficult-to-treat MDR Gram negative pathogens. Unfortunately, the pharmacological information on polymyxins was very limited until recently. This review provides a comprehensive overview on the major achievements and challenges in polymyxin pharmacology and clinical use and how the recent findings have been employed to improve clinical practice worldwide.
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Affiliation(s)
- Sue C Nang
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia (S.C.N., M.A.K.A., J.L.); Department of Pharmacology and Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia (T.V.); and Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana (Q.T.Z.)
| | - Mohammad A K Azad
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia (S.C.N., M.A.K.A., J.L.); Department of Pharmacology and Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia (T.V.); and Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana (Q.T.Z.)
| | - Tony Velkov
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia (S.C.N., M.A.K.A., J.L.); Department of Pharmacology and Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia (T.V.); and Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana (Q.T.Z.)
| | - Qi Tony Zhou
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia (S.C.N., M.A.K.A., J.L.); Department of Pharmacology and Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia (T.V.); and Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana (Q.T.Z.)
| | - Jian Li
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia (S.C.N., M.A.K.A., J.L.); Department of Pharmacology and Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia (T.V.); and Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana (Q.T.Z.)
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Ben-Chetrit E, Mc Gann P, Maybank R, Stam J, Assous MV, Katz DE. Colistin-resistant Klebsiella pneumoniae bloodstream infection: old drug, bad bug. Arch Microbiol 2021; 203:2999-3006. [PMID: 33774687 DOI: 10.1007/s00203-021-02289-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/14/2021] [Accepted: 03/16/2021] [Indexed: 11/24/2022]
Abstract
Multi-drug-resistant (MDR) Enterobacteriaceae pose a global threat to hospitalized patients. We report a series of colistin-resistant Klebsiella pneumoniae blood isolates from Israel and explore their resistance mechanisms using whole genome sequencing (WGS). Patients with colistin-resistant K. pneumoniae bloodstream infection (BSI) were identified during the period between 2006 and 2018. Demographic and clinical data were collected, and antibiotic susceptibility testing (AST) was performed using three commercial platforms. Long and short read sequencing were performed on a PacBio RS II (Pacific Biosciences) and an Illumina Miseq (Illumina), respectively. Thirteen patients with colistin-resistant K. pneumoniae BSI were identified, and seven isolates from seven different patients were successfully revived. Patient records indicated that five of the patients were previously treated with colistin. AST indicated that six of the seven isolates were colistin resistant and four of these isolates were resistant to carbapenems. WGS assigned the isolates to four distinct clusters that corresponded to in silico-derived multi-locus sequence types (MLST). Three isolates carried blaKPC-3 on two different plasmids and one carried blaOXA-48 on a novel IncL/M plasmid. All colistin-resistant isolates carried a variety of different mutations that inactivated the mgrB gene. We report the first comprehensive analysis of a series of colistin-resistant K. pneumoniae from Israel. A diverse set of isolates were obtained and colistin resistance was found to be attributed to different mechanisms that ablated the mgrB gene. Notably, carbapenemase genes were identified in four isolates and were carried on novel plasmids.
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Affiliation(s)
- Eli Ben-Chetrit
- Shaare Zedek Medical Center, Department of Infectious Diseases, Jerusalem, Israel.,Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Patrick Mc Gann
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Rosslyn Maybank
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Jason Stam
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Marc V Assous
- Shaare Zedek Medical Center, Department of Microbiology, Jerusalem, Israel
| | - David E Katz
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel. .,Shaare Zedek Medical Center, Division of Internal Medicine, Jerusalem, Israel.
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Avila-Calderón ED, Ruiz-Palma MDS, Aguilera-Arreola MG, Velázquez-Guadarrama N, Ruiz EA, Gomez-Lunar Z, Witonsky S, Contreras-Rodríguez A. Outer Membrane Vesicles of Gram-Negative Bacteria: An Outlook on Biogenesis. Front Microbiol 2021; 12:557902. [PMID: 33746909 PMCID: PMC7969528 DOI: 10.3389/fmicb.2021.557902] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 02/04/2021] [Indexed: 12/14/2022] Open
Abstract
Outer membrane vesicles (OMVs) from Gram-negative bacteria were first described more than 50 years ago. However, the molecular mechanisms involved in biogenesis began to be studied only in the last few decades. Presently, the biogenesis and molecular mechanisms for their release are not completely known. This review covers the most recent information on cellular components involved in OMV biogenesis, such as lipoproteins and outer membrane proteins, lipopolysaccharide, phospholipids, quorum-sensing molecules, and flagella.
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Affiliation(s)
- Eric Daniel Avila-Calderón
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México City, Mexico.,Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional, CINVESTAV-IPN, México City, Mexico
| | - María Del Socorro Ruiz-Palma
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México City, Mexico.,División Químico Biológicas, Universidad Tecnológica de Tecámac, Tecámac, Mexico
| | - Ma Guadalupe Aguilera-Arreola
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México City, Mexico
| | - Norma Velázquez-Guadarrama
- Unidad de Investigación en enfermedades infecciosas, Hospital Infantil de México Federico Gómez, Ciudad de México, Mexico
| | - Enrico A Ruiz
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México City, Mexico
| | - Zulema Gomez-Lunar
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México City, Mexico
| | - Sharon Witonsky
- Center for One Health Research, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States.,Large Animal Clinical Sciences, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States
| | - Araceli Contreras-Rodríguez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México City, Mexico
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Kawahara K. Variation, Modification and Engineering of Lipid A in Endotoxin of Gram-Negative Bacteria. Int J Mol Sci 2021; 22:2281. [PMID: 33668925 PMCID: PMC7956469 DOI: 10.3390/ijms22052281] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/20/2021] [Accepted: 02/22/2021] [Indexed: 12/12/2022] Open
Abstract
Lipid A of Gram-negative bacteria is known to represent a central role for the immunological activity of endotoxin. Chemical structure and biosynthetic pathways as well as specific receptors on phagocytic cells had been clarified by the beginning of the 21st century. Although the lipid A of enterobacteria including Escherichia coli share a common structure, other Gram-negative bacteria belonging to various classes of the phylum Proteobacteria and other taxonomical groups show wide variety of lipid A structure with relatively decreased endotoxic activity compared to that of E. coli. The structural diversity is produced from the difference of chain length of 3-hydroxy fatty acids and non-hydroxy fatty acids linked to their hydroxyl groups. In some bacteria, glucosamine in the backbone is substituted by another amino sugar, or phosphate groups bound to the backbone are modified. The variation of structure is also introduced by the enzymes that can modify electrostatic charges or acylation profiles of lipid A during or after its synthesis. Furthermore, lipid A structure can be artificially modified or engineered by the disruption and introduction of biosynthetic genes especially those of acyltransferases. These technologies may produce novel vaccine adjuvants or antagonistic drugs derived from endotoxin in the future.
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Affiliation(s)
- Kazuyoshi Kawahara
- Department of Biosciences, College of Science and Engineering, Kanto Gakuin University, Yokohama, Kanagawa 236-8501, Japan
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46
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Mohapatra SS, Dwibedy SK, Padhy I. Polymyxins, the last-resort antibiotics: Mode of action, resistance emergence, and potential solutions. J Biosci 2021; 46:85. [PMID: 34475315 PMCID: PMC8387214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/03/2021] [Indexed: 04/04/2024]
Abstract
Infections caused by multi-drug resistant (MDR) bacterial pathogens are a leading cause of mortality and morbidity across the world. Indiscriminate use of broad-spectrum antibiotics has seriously affected this situation. With the diminishing discovery of novel antibiotics, new treatment methods are urgently required to combat MDR pathogens. Polymyxins, the cationic lipopeptide antibiotics, discovered more than half a century ago, are considered to be the last-line of antibiotics available at the moment. This antibiotic shows a great bactericidal effect against Gram-negative bacteria. Polymyxins primarily target the bacterial membrane and disrupt them, causing lethality. Because of their membrane interacting mode of action, polymyxins cause nephrotoxicity and neurotoxicity in humans, limiting their usability. However, recent modifications in their chemical structure have been able to reduce the toxic effects. The development of better dosing regimens has also helped in getting better clinical outcomes in the infections caused by MDR pathogens. Since the mid1990s the use of polymyxins has increased manifold in clinical settings, resulting in the emergence of polymyxin-resistant strains. The risk posed by the polymyxin-resistant nosocomial pathogens such as the Enterobacteriaceae group, Pseudomonas aeruginosa, and Acinetobacter baumannii, etc. is very serious considering these pathogens are resistant to almost all available antibacterial drugs. In this review article, the mode of action of the polymyxins and the genetic regulatory mechanism responsible for the emergence of resistance are discussed. Specifically, this review aims to update our current understanding in the field and suggest possible solutions that can be pursued for future antibiotic development. As polymyxins primarily target the bacterial membranes, resistance to polymyxins arises primarily by the modification of the lipopolysaccharides (LPS) in the outer membrane (OM). The LPS modification pathways are largely regulated by the bacterial two-component signal transduction (TCS) systems. Therefore, targeting or modulating the TCS signalling mechanisms can be pursued as an alternative to treat the infections caused by polymyxin-resistant MDR pathogens. In this review article, this aspect is also highlighted.
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Affiliation(s)
- Saswat S Mohapatra
- Molecular Microbiology Lab, Department of Bioscience and Bioinformatics, Khallikote University, Konisi, Berhampur, 761 008 Odisha India
| | - Sambit K Dwibedy
- Molecular Microbiology Lab, Department of Bioscience and Bioinformatics, Khallikote University, Konisi, Berhampur, 761 008 Odisha India
| | - Indira Padhy
- Molecular Microbiology Lab, Department of Bioscience and Bioinformatics, Khallikote University, Konisi, Berhampur, 761 008 Odisha India
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Zdorovenko EL, Kadykova AA, Shashkov AS, Varbanets LD, Bulyhina TV, Toukach PV. Structure and Biological Properties of the O-specific Polysaccharide and Lipid a from Pantoea
agglomerans P324. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721010124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Kim M, Park J, Park W. Genomic and phenotypic analyses of multidrug-resistant Acinetobacter baumannii NCCP 16007 isolated from a patient with a urinary tract infection. Virulence 2020; 12:150-164. [PMID: 33372826 PMCID: PMC7781626 DOI: 10.1080/21505594.2020.1867421] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Polymyxin B (PMB) is increasingly used as a last-line antibiotic; however, the emergence of PMB resistance is a serious threat to global health. Here, a total of 40 Acinetobacter baumannii clinical isolates were collected to screen for PMB-resistant strains. Several clinical isolates including NCCP 16007 were far more resistant to PMB (MIC: 128-256 μg/ml) than the ATCC 17978 strain (MIC: 2 μg/ml) and appeared to possess resistance to broad-spectrum antibiotics including meropenem and 12 others. Four highly PMB-resistant strains possessed point mutations in the histidine kinase PmrB, leading to an increased expression of pmrC encoding a phosphoethanolamine transferase. Whole-genome analyses revealed that the NCCP 16007 stain had acquired two additional copies of the pmrC gene with phage integrase and 13 antibiotic resistance genes (ARGs) from other pathogens, including Klebsiella pneumoniae and Pseudomonas aeruginosa. The GC ratios of the ARGs (50-60%) were higher than that of the chromosomal backbone (39.06%), further supporting the horizontal gene transfer of ARGs. Comparative genomics with other multidrug-resistant A. baumannii strains revealed that the NCCP 16007 strain has many additional ARGs and has lost several virulence factors including Csu pili and heme oxygenase but exhibited high pathogenicity in Galleria mellonella-infection models. The observation of condensed biofilm through confocal and scanning electron microscopy suggested that the NCCP 16007 strain may possess high adhesion capacity during urinary tract infection. Therefore, our genomic and phenotypic analyses suggested that the multidrug-resistant A. baumannii NCCP 16007 strain possesses high genome plasticity, natural transformation ability, and pathogenicity.
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Affiliation(s)
- Misung Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University , Seoul, Republic of Korea
| | - Jaeeun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University , Seoul, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University , Seoul, Republic of Korea
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Adak T, Morales DL, Cook AJ, Grigg JC, Murphy MEP, Tanner ME. ArnD is a deformylase involved in polymyxin resistance. Chem Commun (Camb) 2020; 56:6830-6833. [PMID: 32432293 DOI: 10.1039/d0cc02241a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The modification of lipid A with cationic 4-amino-4-deoxy-l-arabinose residues serves to confer resistance against cationic peptide antibiotics in Gram-negative bacteria. In this work, the enzyme ArnD is shown to act as a metal-dependent deformylase in the biosynthesis of this carbohydrate.
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Affiliation(s)
- Taniya Adak
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada.
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50
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Outer Membrane Lipid Secretion and the Innate Immune Response to Gram-Negative Bacteria. Infect Immun 2020; 88:IAI.00920-19. [PMID: 32253250 DOI: 10.1128/iai.00920-19] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria is an asymmetric lipid bilayer that consists of inner leaflet phospholipids and outer leaflet lipopolysaccharides (LPS). The asymmetric character and unique biochemistry of LPS molecules contribute to the OM's ability to function as a molecular permeability barrier that protects the bacterium against hazards in the environment. Assembly and regulation of the OM have been extensively studied for understanding mechanisms of antibiotic resistance and bacterial defense against host immunity; however, there is little knowledge on how Gram-negative bacteria release their OMs into their environment to manipulate their hosts. Discoveries in bacterial lipid trafficking, OM lipid homeostasis, and host recognition of microbial patterns have shed new light on how microbes secrete OM vesicles (OMVs) to influence inflammation, cell death, and disease pathogenesis. Pathogens release OMVs that contain phospholipids, like cardiolipins, and components of LPS molecules, like lipid A endotoxins. These multiacylated lipid amphiphiles are molecular patterns that are differentially detected by host receptors like the Toll-like receptor 4/myeloid differentiation factor 2 complex (TLR4/MD-2), mouse caspase-11, and human caspases 4 and 5. We discuss how lipid ligands on OMVs engage these pattern recognition receptors on the membranes and in the cytosol of mammalian cells. We then detail how bacteria regulate OM lipid asymmetry, negative membrane curvature, and the phospholipid-to-LPS ratio to control OMV formation. The goal is to highlight intersections between OM lipid regulation and host immunity and to provide working models for how bacterial lipids influence vesicle formation.
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