1
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Maybin M, Ranade AM, Schombel U, Gisch N, Mamat U, Meredith TC. IS 1-mediated chromosomal amplification of the arn operon leads to polymyxin B resistance in Escherichia coli B strains. mBio 2024:e0063424. [PMID: 38904391 DOI: 10.1128/mbio.00634-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/14/2024] [Indexed: 06/22/2024] Open
Abstract
Polymyxins [colistin and polymyxin B (PMB)] comprise an important class of natural product lipopeptide antibiotics used to treat multidrug-resistant Gram-negative bacterial infections. These positively charged lipopeptides interact with lipopolysaccharide (LPS) located in the outer membrane and disrupt the permeability barrier, leading to increased uptake and bacterial cell death. Many bacteria counter polymyxins by upregulating genes involved in the biosynthesis and transfer of amine-containing moieties to increase positively charged residues on LPS. Although 4-deoxy-l-aminoarabinose (Ara4N) and phosphoethanolamine (PEtN) are highly conserved LPS modifications in Escherichia coli, different lineages exhibit variable PMB susceptibilities and frequencies of resistance for reasons that are poorly understood. Herein, we describe a mechanism prevalent in E. coli B strains that depends on specific insertion sequence 1 (IS1) elements that flank genes involved in the biosynthesis and transfer of Ara4N to LPS. Spontaneous and transient chromosomal amplifications mediated by IS1 raise the frequency of PMB resistance by 10- to 100-fold in comparison to strains where a single IS1 element located 90 kb away from the end of the arn operon has been deleted. Amplification involving IS1 becomes the dominant resistance mechanism in the absence of PEtN modification. Isolates with amplified arn operons gradually lose their PMB-resistant phenotype with passaging, consistent with classical PMB heteroresistance behavior. Analysis of the whole genome transcriptome profile showed altered expression of genes residing both within and outside of the duplicated chromosomal segment, suggesting complex phenotypes including PMB resistance can result from tandem amplification events.IMPORTANCEPhenotypic variation in susceptibility and the emergence of resistant subpopulations are major challenges to the clinical use of polymyxins. While a large database of genes and alleles that can confer polymyxin resistance has been compiled, this report demonstrates that the chromosomal insertion sequence (IS) content and distribution warrant consideration as well. Amplification of large chromosomal segments containing the arn operon by IS1 increases the Ara4N content of the lipopolysaccharide layer in Escherichia coli B lineages using a mechanism that is orthogonal to transcriptional upregulation through two-component regulatory systems. Altogether, our work highlights the importance of IS elements in modulating gene expression and generating diverse subpopulations that can contribute to phenotypic polymyxin B heteroresistance.
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Affiliation(s)
- Michael Maybin
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Aditi M Ranade
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ursula Schombel
- Division of Bioanalytical Chemistry, Priority Research Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Nicolas Gisch
- Division of Bioanalytical Chemistry, Priority Research Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Uwe Mamat
- Division of Cellular Microbiology, Priority Research Area Infections, Research Center Borstel, Leibniz Lung Center, Leibniz Research Alliance INFECTIONS, Borstel, Germany
| | - Timothy C Meredith
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
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2
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Gao X, Han J, Zhu L, Nychas GJE, Mao Y, Yang X, Liu Y, Jiang X, Zhang Y, Dong P. The Effect of the PhoP/PhoQ System on the Regulation of Multi-Stress Adaptation Induced by Acid Stress in Salmonella Typhimurium. Foods 2024; 13:1533. [PMID: 38790833 PMCID: PMC11121531 DOI: 10.3390/foods13101533] [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: 04/14/2024] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Acidic stress in beef cattle slaughtering abattoirs can induce the acid adaptation response of in-plant contaminated Salmonella. This may further lead to multiple resistance responses threatening public health. Therefore, the acid, heat, osmotic and antibiotic resistances of Salmonella typhimurium (ATCC14028) were evaluated after a 90 min adaption in a pH = 5.4 "mild acid" Luria-Bertani medium. Differences in such resistances were also determined between the ∆phoP mutant and wild-type Salmonella strains to confirm the contribution of the PhoP/PhoQ system. The transcriptomic differences between the acid-adapted and ∆phoP strain were compared to explore the role of the PhoP/Q two-component system in regulating multi-stress resistance. Acid adaptation was found to increase the viability of Salmonella to lethal acid, heat and hyperosmotic treatments. In particular, acid adaptation significantly increased the resistance of Salmonella typhimurium to Polymyxin B, and such resistance can last for 21 days when the adapted strain was stored in meat extract medium at 4 °C. Transcriptomics analysis revealed 178 up-regulated and 274 down-regulated genes in the ∆phoP strain. The Salmonella infection, cationic antimicrobial peptide (CAMP) resistance, quorum sensing and two-component system pathways were down-regulated, while the bacterial tricarboxylic acid cycle pathways were up-regulated. Transcriptomics and RT-qPCR analyses revealed that the deletion of the phoP gene resulted in the down-regulation of the expression of genes related to lipid A modification and efflux pumps. These changes in the gene expression result in the change in net negative charge and the mobility of the cell membrane, resulting in enhanced CAMP resistance. The confirmation of multiple stress resistance under acid adaptation and the transcriptomic study in the current study may provide valuable information for the control of multiple stress resistance and meat safety.
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Affiliation(s)
- Xu Gao
- Lab of Beef Processing and Quality Control, Shandong Agricultural University, Taian 271018, China; (X.G.); (L.Z.); (G.-J.E.N.); (Y.M.); (X.Y.); (Y.L.); (X.J.); (Y.Z.)
- International Joint Research Lab (China and Greece) of Digital Transformation as an Enabler for Food Safety and Sustainability, Taian 271018, China
| | - Jina Han
- Shandong Provincial Key Laboratory of Poultry Diseases Diagnosis and Immunology, Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan 250023, China;
| | - Lixian Zhu
- Lab of Beef Processing and Quality Control, Shandong Agricultural University, Taian 271018, China; (X.G.); (L.Z.); (G.-J.E.N.); (Y.M.); (X.Y.); (Y.L.); (X.J.); (Y.Z.)
- International Joint Research Lab (China and Greece) of Digital Transformation as an Enabler for Food Safety and Sustainability, Taian 271018, China
| | - George-John E. Nychas
- Lab of Beef Processing and Quality Control, Shandong Agricultural University, Taian 271018, China; (X.G.); (L.Z.); (G.-J.E.N.); (Y.M.); (X.Y.); (Y.L.); (X.J.); (Y.Z.)
- International Joint Research Lab (China and Greece) of Digital Transformation as an Enabler for Food Safety and Sustainability, Taian 271018, China
- Department of Food Science and Human Nutrition, Agricultural University of Athens, 11855 Athens, Greece
| | - Yanwei Mao
- Lab of Beef Processing and Quality Control, Shandong Agricultural University, Taian 271018, China; (X.G.); (L.Z.); (G.-J.E.N.); (Y.M.); (X.Y.); (Y.L.); (X.J.); (Y.Z.)
- International Joint Research Lab (China and Greece) of Digital Transformation as an Enabler for Food Safety and Sustainability, Taian 271018, China
| | - Xiaoyin Yang
- Lab of Beef Processing and Quality Control, Shandong Agricultural University, Taian 271018, China; (X.G.); (L.Z.); (G.-J.E.N.); (Y.M.); (X.Y.); (Y.L.); (X.J.); (Y.Z.)
- International Joint Research Lab (China and Greece) of Digital Transformation as an Enabler for Food Safety and Sustainability, Taian 271018, China
| | - Yunge Liu
- Lab of Beef Processing and Quality Control, Shandong Agricultural University, Taian 271018, China; (X.G.); (L.Z.); (G.-J.E.N.); (Y.M.); (X.Y.); (Y.L.); (X.J.); (Y.Z.)
- International Joint Research Lab (China and Greece) of Digital Transformation as an Enabler for Food Safety and Sustainability, Taian 271018, China
| | - Xueqing Jiang
- Lab of Beef Processing and Quality Control, Shandong Agricultural University, Taian 271018, China; (X.G.); (L.Z.); (G.-J.E.N.); (Y.M.); (X.Y.); (Y.L.); (X.J.); (Y.Z.)
- International Joint Research Lab (China and Greece) of Digital Transformation as an Enabler for Food Safety and Sustainability, Taian 271018, China
| | - Yimin Zhang
- Lab of Beef Processing and Quality Control, Shandong Agricultural University, Taian 271018, China; (X.G.); (L.Z.); (G.-J.E.N.); (Y.M.); (X.Y.); (Y.L.); (X.J.); (Y.Z.)
- International Joint Research Lab (China and Greece) of Digital Transformation as an Enabler for Food Safety and Sustainability, Taian 271018, China
| | - Pengcheng Dong
- Lab of Beef Processing and Quality Control, Shandong Agricultural University, Taian 271018, China; (X.G.); (L.Z.); (G.-J.E.N.); (Y.M.); (X.Y.); (Y.L.); (X.J.); (Y.Z.)
- International Joint Research Lab (China and Greece) of Digital Transformation as an Enabler for Food Safety and Sustainability, Taian 271018, China
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3
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Oluwole A, Hernández-Rocamora VM, Cao Y, Li X, Vollmer W, Robinson CV, Bolla JR. Real-Time Biosynthetic Reaction Monitoring Informs the Mechanism of Action of Antibiotics. J Am Chem Soc 2024; 146:7007-7017. [PMID: 38428018 PMCID: PMC10941186 DOI: 10.1021/jacs.4c00081] [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: 01/05/2024] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 03/03/2024]
Abstract
The rapid spread of drug-resistant pathogens and the declining discovery of new antibiotics have created a global health crisis and heightened interest in the search for novel antibiotics. Beyond their discovery, elucidating mechanisms of action has necessitated new approaches, especially for antibiotics that interact with lipidic substrates and membrane proteins. Here, we develop a methodology for real-time reaction monitoring of the activities of two bacterial membrane phosphatases, UppP and PgpB. We then show how we can inhibit their activities using existing and newly discovered antibiotics such as bacitracin and teixobactin. Additionally, we found that the UppP dimer is stabilized by phosphatidylethanolamine, which, unexpectedly, enhanced the speed of substrate processing. Overall, our results demonstrate the potential of native mass spectrometry for real-time biosynthetic reaction monitoring of membrane enzymes, as well as their in situ inhibition and cofactor binding, to inform the mode of action of emerging antibiotics.
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Affiliation(s)
- Abraham
O. Oluwole
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| | - Víctor M. Hernández-Rocamora
- Centre
for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, U.K.
| | - Yihui Cao
- Department
of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Xuechen Li
- Department
of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Waldemar Vollmer
- Centre
for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, U.K.
- Institute
for Molecular Bioscience, University of
Queensland, Carmody Road, Brisbane, Queensland 4072, Australia
| | - Carol V. Robinson
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| | - Jani R. Bolla
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
- Department
of Biology, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K.
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4
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Noel HR, Keerthi S, Ren X, Winkelman JD, Troutman JM, Palmer LD. Genetic synergy between Acinetobacter baumannii undecaprenyl phosphate biosynthesis and the Mla system impacts cell envelope and antimicrobial resistance. mBio 2024; 15:e0280423. [PMID: 38364179 PMCID: PMC10936186 DOI: 10.1128/mbio.02804-23] [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: 10/16/2023] [Accepted: 01/17/2024] [Indexed: 02/18/2024] Open
Abstract
Acinetobacter baumannii is a Gram-negative bacterial pathogen that poses a major health concern due to increasing multidrug resistance. The Gram-negative cell envelope is a key barrier to antimicrobial entry and includes an inner and outer membrane. The maintenance of lipid asymmetry (Mla) system is the main homeostatic mechanism by which Gram-negative bacteria maintain outer membrane asymmetry. Loss of the Mla system in A. baumannii results in attenuated virulence and increased susceptibility to membrane stressors and some antibiotics. We recently reported two strain variants of the A. baumannii type strain ATCC 17978: 17978VU and 17978UN. Here, ∆mlaF mutants in the two ATCC 17978 strains display different phenotypes for membrane stress resistance, antibiotic resistance, and pathogenicity in a murine pneumonia model. Although allele differences in obgE were previously reported to synergize with ∆mlaF to affect growth and stringent response, obgE alleles do not affect membrane stress resistance. Instead, a single-nucleotide polymorphism (SNP) in the essential gene encoding undecaprenyl pyrophosphate (Und-PP) synthase, uppS, results in decreased enzymatic rate and decrease in total Und-P levels in 17978UN compared to 17978VU. The UppSUN variant synergizes with ∆mlaF to reduce capsule and lipooligosaccharide (LOS) levels, increase susceptibility to membrane stress and antibiotics, and reduce persistence in a mouse lung infection. Und-P is a lipid glycan carrier required for the biosynthesis of A. baumannii capsule, cell wall, and glycoproteins. These findings uncover synergy between Und-P and the Mla system in maintaining the A. baumannii cell envelope and antibiotic resistance.IMPORTANCEAcinetobacter baumannii is a critical threat to global public health due to its multidrug resistance and persistence in hospital settings. Therefore, novel therapeutic approaches are urgently needed. We report that a defective undecaprenyl pyrophosphate synthase (UppS) paired with a perturbed Mla system leads to synthetically sick cells that are more susceptible to clinically relevant antibiotics and show reduced virulence in a lung infection model. These results suggest that targeting UppS or undecaprenyl species and the Mla system may resensitize A. baumannii to antibiotics in combination therapies. This work uncovers a previously unknown synergistic relationship in cellular envelope homeostasis that could be leveraged for use in combination therapy against A. baumannii.
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Affiliation(s)
- Hannah R. Noel
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
| | - Sowmya Keerthi
- Department of Chemistry, University of North Carolina Charlotte, Charlotte, North Carolina, USA
| | - Xiaomei Ren
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
| | | | - Jerry M. Troutman
- Department of Chemistry, University of North Carolina Charlotte, Charlotte, North Carolina, USA
| | - Lauren D. Palmer
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
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5
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Noel HR, Keerthi S, Ren X, Winkelman JD, Troutman JM, Palmer LD. Genetic synergy in Acinetobacter baumannii undecaprenyl biosynthesis and maintenance of lipid asymmetry impacts outer membrane and antimicrobial resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.556980. [PMID: 37790371 PMCID: PMC10542541 DOI: 10.1101/2023.09.22.556980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Acinetobacter baumannii is a Gram-negative healthcare-associated pathogen that poses a major health concern due to increasing multidrug resistance. The Gram-negative cell envelope is a key barrier to antimicrobial entry and includes an inner and outer membrane. The outer membrane has an asymmetric composition that is important for structural integrity and barrier to the environment. Therefore, Gram-negative bacteria have mechanisms to uphold this asymmetry such as the maintenance of lipid asymmetry system (Mla), which removes glycerophospholipids from the outer leaflet of the outer membrane and transports them to the inner membrane. Loss of this system in A. baumannii results in attenuated virulence and increased susceptibility to membrane stressors and some antibiotics. We recently reported two strain variants of the A. baumannii type strain ATCC 17978, 17978VU and 17978UN. We show here that ΔmlaF mutants in the two strains display different phenotypes for membrane stress resistance, antibiotic resistance, and pathogenicity in a murine pneumonia model. We used comparative genetics to identify interactions between ATCC 17978 strain alleles and mlaF to uncover the cause behind the phenotypic differences. Although allele differences in obgE were previously reported to synergize with ΔmlaF to affect growth and stringent response, we show that obgE alleles do not affect membrane stress resistance. Instead, a single nucleotide polymorphism (SNP) in the essential gene encoding undecaprenyl pyrophosphate (Und-PP) synthase, uppS, synergizes with ΔmlaF to increase susceptibility to membrane stress and antibiotics, and reduce persistence in a mouse lung infection. Und-P is a lipid glycan carrier known to be required for biosynthesis of A. baumannii capsule, cell wall, and glycoproteins. Our data suggest that in the absence of the Mla system, the cellular level of Und-P is critical for envelope integrity, antibiotic resistance, and lipooligosaccharide abundance. These findings uncover synergy between Und-P and the Mla system in maintaining the A. baumannii outer membrane and stress resistance.
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Affiliation(s)
- Hannah R. Noel
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA
| | - Sowmya Keerthi
- Department of Chemistry, University of North Carolina Charlotte, Charlotte, NC, USA
| | - Xiaomei Ren
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA
| | | | - Jerry M. Troutman
- Department of Chemistry, University of North Carolina Charlotte, Charlotte, NC, USA
| | - Lauren D. Palmer
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA
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6
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Wilhelm L, Ducret A, Grangeasse C. New insights into the Undecaprenol monophosphate recycling pathway of Streptococcus pneumoniae. FEMS Microbiol Lett 2023; 370:fnad109. [PMID: 37849218 DOI: 10.1093/femsle/fnad109] [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: 07/21/2023] [Revised: 10/08/2023] [Accepted: 10/16/2023] [Indexed: 10/19/2023] Open
Abstract
Recycling of undecaprenol pyrophosphate is critical to regenerate the pool of undecaprenol monophosphate required for cell wall biosynthesis. Undecaprenol pyrophosphate is dephosphorylated by membrane-associated undecaprenyl pyrophosphate phosphatases such as UppP or type 2 Phosphatidic Acid Phosphatases (PAP2) and then transferred across the cytoplasmic membrane by Und-P flippases such as PopT (DUF368-containing protein) or UptA (a DedA family protein). While the deletion of uppP in S. pneumoniae has been reported to increase susceptibility to bacitracin and reduce infectivity in a murine infection model, the presence of PAP2 family proteins or Und-P flippases and their potential interplay with UppP in S. pneumoniae remained unknown. In this report, we identified two PAP2 family proteins and a DUF368-containing protein and investigated their roles together with that of UppP in cell growth, cell morphology and susceptibility to bacitracin in S. pneumoniae. Our results suggest that the undecaprenol monophosphate recycling pathway in S. pneumoniae could result from a functional redundancy between UppP, the PAP2-family protein Spr0434 and the DUF368-containing protein Spr0889.
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Affiliation(s)
- Linus Wilhelm
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université de Lyon, CNRS, 69007 Lyon, France
| | - Adrien Ducret
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université de Lyon, CNRS, 69007 Lyon, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université de Lyon, CNRS, 69007 Lyon, France
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Naidu V, Bartczak A, Brzoska AJ, Lewis P, Eijkelkamp BA, Paulsen IT, Elbourne LDH, Hassan KA. Evolution of RND efflux pumps in the development of a successful pathogen. Drug Resist Updat 2023; 66:100911. [PMID: 36592567 DOI: 10.1016/j.drup.2022.100911] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
AIMS This study examined the origins and evolution of the AdeABC, AdeFGH and AdeIJK efflux pumps in the Acinetobacter genus, including human and animal pathogens and species from non-clinical environments. METHODS Comparative genome analyses were performed using the reference sequences for 70 Acinetobacter species to identify putative orthologs of AdeABC, AdeFGH and AdeIJK and their regulators. Sequence similarities and the genomic locations of coding sequences were correlated with phylogeny to infer modes of evolution. Intraspecies variation was assessed in species of interest using up to 236 complete genome sequences. Mutants overproducing adeIJK in A. baylyi were examined to identify regulators of this system in a non A. baumannii species. RESULTS The results indicate that adeIJK has been a stable part of Acinetobacter genomes since the genesis of this genus, whereas adeABC and adeFGH were carried by less than half of the species, but showed some lineage specificity. The organisation and local genetic contexts of adeABC loci were particularly variable to the sub-species level, suggesting frequent recombination. Cognate regulatory systems were almost always found in the genomes of species encoding pumps. Mutations in adeN, which encodes a repressor of adeIJK, were selected by antibiotic exposure in A. baylyi, similar to previous findings in pathogenic lineages. CONCLUSIONS The multidrug efflux capacity of clinical Acinetobacter strains stems from accessory and core genetic features. AdeIJK is likely to have ancient core function(s) that have promoted its maintenance, whereas recent antibiotic use may be driving the evolution of the AdeABC pump.
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Affiliation(s)
- Varsha Naidu
- College of Science, Engineering and Environment, University of Newcastle, Callaghan, NSW, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, North Ryde, NSW, Australia
| | - Amelia Bartczak
- College of Science, Engineering and Environment, University of Newcastle, Callaghan, NSW, Australia
| | - Anthony J Brzoska
- College of Science, Engineering and Environment, University of Newcastle, Callaghan, NSW, Australia
| | - Peter Lewis
- College of Science, Engineering and Environment, University of Newcastle, Callaghan, NSW, Australia; Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia; Hunter Biological Solutions, Newcastle, NSW, Australia
| | - Bart A Eijkelkamp
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Ian T Paulsen
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, North Ryde, NSW, Australia; School of Natural Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Liam D H Elbourne
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, North Ryde, NSW, Australia; School of Natural Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Karl A Hassan
- College of Science, Engineering and Environment, University of Newcastle, Callaghan, NSW, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, North Ryde, NSW, Australia.
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8
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Zang M, Ascari A, Adams FG, Alquethamy S, Eijkelkamp BA. Characterizing the role of phosphatidylglycerol-phosphate phosphatases in Acinetobacter baumannii cell envelope biogenesis and antibiotic resistance. Cell Surf 2022; 9:100092. [PMID: 36545493 PMCID: PMC9760654 DOI: 10.1016/j.tcsw.2022.100092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
The dissemination of multi-drug resistant Acinetobacter baumannii threatens global healthcare systems and necessitates the development of novel therapeutic options. The Gram-negative bacterial cell envelope provides a first defensive barrier against antimicrobial assault. Essential components of this multi-layered complex are the phospholipid-rich membranes. Phosphatidylglycerol phosphate (PGP) phosphatases are responsible for a key step in the biosynthesis of a major phospholipid species, phosphatidylglycerol (PG), but these enzymes have also been implicated in the biogenesis of other cell envelope components. Our bioinformatics analyses identified two putative PGP candidates in the A. baumannii genome, PgpA and PgpB. Phospholipid analyses of isogenic pgpA mutants in two distinct A. baumannii strains revealed a shift in the desaturation levels of phosphatidylethanolamine (PE) phospholipid species, possibly due to the activation of the phospholipid desaturase DesA. We also investigated the impact of the inner membrane phosphatases on other cell envelope components, which revealed a role of PgpB in the maintenance of the A. baumannii peptidoglycan layer, and consequently carbapenem resistance. Collectively, this work provides novel insights into the roles of PGP phosphatases on the global lipidomic landscape of A. baumannii and their interconnectivity with the biogenesis of other cell envelope components. The non-essentiality of these candidates exemplifies metabolic versatility of A. baumannii, which is believed to be key to its success as global pathogen.
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Affiliation(s)
- Maoge Zang
- Molecular Sciences and Technology, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Alice Ascari
- Molecular Sciences and Technology, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia,Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
| | - Felise G. Adams
- Molecular Sciences and Technology, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Saleh Alquethamy
- Molecular Sciences and Technology, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Bart A. Eijkelkamp
- Molecular Sciences and Technology, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia,Corresponding author.
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9
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Afolayan AO, Aboderin AO, Oaikhena AO, Odih EE, Ogunleye VO, Adeyemo AT, Adeyemo AT, Bejide OS, Underwood A, Argimón S, Abrudan M, Egwuenu A, Ihekweazu C, Aanensen DM, Okeke IN. An ST131 clade and a phylogroup A clade bearing an O101-like O-antigen cluster predominate among bloodstream Escherichia coli isolates from South-West Nigeria hospitals. Microb Genom 2022; 8:mgen000863. [PMID: 36748556 PMCID: PMC9837563 DOI: 10.1099/mgen.0.000863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/15/2022] [Indexed: 12/23/2022] Open
Abstract
Escherichia coli bloodstream infections are typically attributed to a limited number of lineages that carry virulence factors associated with invasiveness. In Nigeria, the identity of circulating clones is largely unknown and surveillance of their antimicrobial resistance has been limited. We verified and whole-genome sequenced 68 2016-2018 bloodstream E. coli isolates from three sentinel sites in South-Western Nigeria and susceptibility tested 67 of them. Resistance to antimicrobials commonly used in Nigeria was high, with 67 (100 %), 62 (92.5 %), 53 (79.1 %) and 37 (55.2 %) showing resistance to trimethoprim, ampicillin, ciprofloxacin and aminoglycosides, respectively. Thirty-five (51 %) isolates carried extended-spectrum β-lactamase genes and 32 (91 %) of these were multidrug resistant. All the isolates were susceptible to carbapenems and colistin. The strain set included globally disseminated high-risk clones from sequence type (ST)12 (2), ST131 (12) and ST648 (4). Twenty-three (33.8 %) of the isolates clustered within two clades. The first of these consisted of ST131 strains, comprising O16:H5 and O25:H4 sub-lineages. The second was an ST10-ST167 complex clade comprising strains carrying O-antigen and capsular genes of likely Klebsiella origin, identical to those of avian pathogenic E. coli Sanji, and serotyped in silico as O89, O101 or ONovel32, depending on the tool used. Four temporally associated ST90 strains from one sentinel were closely related enough to suggest that at least some of them represented a retrospectively detected outbreak cluster. Our data implicate a broad repertoire of E. coli isolates associated with bloodstream infections in South-West Nigeria. Continued genomic surveillance is valuable for tracking clones of importance and for outbreak identification.
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Affiliation(s)
- Ayorinde O. Afolayan
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo State, Nigeria
| | - A. Oladipo Aboderin
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Osun State, Nigeria
| | - Anderson O. Oaikhena
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo State, Nigeria
| | - Erkison Ewomazino Odih
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo State, Nigeria
| | - Veronica O. Ogunleye
- Department of Medical Microbiology and Parasitology, University College Hospital, Ibadan, Oyo State, Nigeria
| | - Adeyemi T. Adeyemo
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Osun State, Nigeria
| | - Abolaji T. Adeyemo
- Department of Medical Microbiology and Parasitology, University of Osun Teaching Hospital, Osogbo, Osun State, Nigeria
| | - Oyeniyi S. Bejide
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo State, Nigeria
| | - Anthony Underwood
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, UK
- Wellcome Genome Campus, Hinxton, UK
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, UK
- Wellcome Genome Campus, Hinxton, UK
| | - Monica Abrudan
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, UK
- Wellcome Genome Campus, Hinxton, UK
| | | | | | - David M. Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, UK
- Wellcome Genome Campus, Hinxton, UK
| | - Iruka N. Okeke
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo State, Nigeria
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10
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Mullally C, Stubbs KA, Thai VC, Anandan A, Bartley S, Scanlon MJ, Jarvis GA, John CM, Lim KYL, Sullivan CM, Sarkar-Tyson M, Vrielink A, Kahler CM. Novel small molecules that increase the susceptibility of Neisseria gonorrhoeae to cationic antimicrobial peptides by inhibiting lipid A phosphoethanolamine transferase. J Antimicrob Chemother 2022; 77:2441-2447. [PMID: 35770844 PMCID: PMC9410672 DOI: 10.1093/jac/dkac204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/19/2022] [Indexed: 11/14/2022] Open
Abstract
Objectives Neisseria gonorrhoeae is an exclusively human pathogen that commonly infects the urogenital tract resulting in gonorrhoea. Empirical treatment of gonorrhoea with antibiotics has led to multidrug resistance and the need for new therapeutics. Inactivation of lipooligosaccharide phosphoethanolamine transferase A (EptA), which attaches phosphoethanolamine to lipid A, results in attenuation of the pathogen in infection models. Small molecules that inhibit EptA are predicted to enhance natural clearance of gonococci via the human innate immune response. Methods A library of small-fragment compounds was tested for the ability to enhance susceptibility of the reference strain N. gonorrhoeae FA1090 to polymyxin B. The effect of these compounds on lipid A synthesis and viability in models of infection were tested. Results Three compounds, 135, 136 and 137, enhanced susceptibility of strain FA1090 to polymyxin B by 4-fold. Pre-treatment of bacterial cells with all three compounds resulted in enhanced killing by macrophages. Only lipid A from bacterial cells exposed to compound 137 showed a 17% reduction in the level of decoration of lipid A with phosphoethanolamine by MALDI-TOF MS analysis and reduced stimulation of cytokine responses in THP-1 cells. Binding of 137 occurred with higher affinity to purified EptA than the starting material, as determined by 1D saturation transfer difference NMR. Treatment of eight MDR strains with 137 increased susceptibility to polymyxin B in all cases. Conclusions Small molecules have been designed that bind to EptA, inhibit addition of phosphoethanolamine to lipid A and can sensitize N. gonorrhoeae to killing by macrophages.
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Affiliation(s)
- Christopher Mullally
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Science, University of Western Australia, Perth, Australia
| | - Keith A Stubbs
- School of Molecular Sciences, University of Western Australia, Perth, Australia
| | - Van C Thai
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Science, University of Western Australia, Perth, Australia
| | - Anandhi Anandan
- School of Molecular Sciences, University of Western Australia, Perth, Australia
| | - Stephanie Bartley
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Science, University of Western Australia, Perth, Australia
| | - Martin J Scanlon
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Gary A Jarvis
- Center for Immunochemistry, Veterans Affairs Medical Center, San Francisco, USA.,Department of Laboratory Medicine, University of California, San Francisco, USA
| | - Constance M John
- Center for Immunochemistry, Veterans Affairs Medical Center, San Francisco, USA.,Department of Laboratory Medicine, University of California, San Francisco, USA
| | - Katherine Y L Lim
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Science, University of Western Australia, Perth, Australia
| | - Courtney M Sullivan
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Science, University of Western Australia, Perth, Australia
| | - Mitali Sarkar-Tyson
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Science, University of Western Australia, Perth, Australia
| | - Alice Vrielink
- School of Molecular Sciences, University of Western Australia, Perth, Australia
| | - Charlene M Kahler
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Science, University of Western Australia, Perth, Australia.,Telethon Kids Institute, Perth Children's Hospital, Perth, Australia
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11
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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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12
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Chen X, Tian J, Luo C, Wang X, Li X, Wang M. Cell Membrane Remodeling Mediates Polymyxin B Resistance in Klebsiella pneumoniae: An Integrated Proteomics and Metabolomics Study. Front Microbiol 2022; 13:810403. [PMID: 35222333 PMCID: PMC8866958 DOI: 10.3389/fmicb.2022.810403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 01/14/2022] [Indexed: 11/26/2022] Open
Abstract
Polymyxin B (PB) is introduced into the clinic as the last-line therapy against carbapenem-resistant Klebsiella pneumoniae (CRKP). Unfortunately, increased resistance to PB in Klebsiella pneumoniae (K. pneumoniae) has threatened global health. Resistance of K. pneumoniae to PB was induced by passaging in serial concentrations of PB and determined by microbroth dilution method. Growth characteristics of induced strains including growth curve, reversibility of resistance, and biofilm formation (crystal violet staining method) were measured. This study employed TMT-labeled quantitative proteomics and LC-MS/MS metabolomics analysis to investigate the key biological processes associated with PB resistance in K. pneumoniae. A total of 315 differentially expressed proteins (DEPs) were identified, of which 133 were upregulated and 182 were downregulated in the PB-resistant K. pneumoniae. KEGG enrichment analysis revealed that the DEPs were mainly involved in ATP-binding cassette (ABC) transporters and cationic antimicrobial peptide (CAMP) resistance. Proteins related to central carbon metabolism were inhibited in the PB-resistant K. pneumoniae, but proteins mediating LPS modification were activated. Transcriptional levels of CAMP resistance-related proteins were significantly different between PB-susceptible and -resistant K. pneumoniae. PB treatment led to an increase in reactive oxygen species (ROS) levels of K. pneumoniae. Metabolomics data demonstrated that 23 metabolites were significantly upregulated in PB-resistant K. pneumoniae and 5 were downregulated. The differential metabolites were mainly lipids, including glycerophospholipids, sphingolipids, and fatty acids. Exposure to PB resulted in increased level of phospholipid transport gene mlaF in K. pneumoniae. Our study suggested that membrane remodeling and inhibited central carbon metabolism are conducive to the development of PB resistance in K. pneumoniae.
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13
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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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14
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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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15
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Kravchenko U, Gogoleva N, Kalubaka N, Kruk A, Diubo Y, Gogolev Y, Nikolaichik Y. The PhoPQ Two-Component System Is the Major Regulator of Cell Surface Properties, Stress Responses and Plant-Derived Substrate Utilisation During Development of Pectobacterium versatile-Host Plant Pathosystems. Front Microbiol 2021; 11:621391. [PMID: 33519782 PMCID: PMC7843439 DOI: 10.3389/fmicb.2020.621391] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/24/2020] [Indexed: 11/19/2022] Open
Abstract
Pectobacterium versatile (formerly P. carotovorum) is a recently defined species of soft rot enterobacteria capable of infecting many plant hosts and damaging different tissues. Complex transcriptional regulation of virulence properties can be expected for such a versatile pathogen. However, the relevant information is available only for related species and is rather limited. The PhoPQ two-component system, originally described in pectobacteria as PehRS, was previously shown to regulate a single gene, pehA. Using an insertional phoP mutant of Pectobacterium versatile (earlier-P. carotovorum), we demonstrate that PhoP regulates at least 115 genes with a majority of them specific for pectobacteria. The functions performed by PhoP-controlled genes include degradation, transport and metabolism of plant-derived carbon sources (polygalacturonate, arabinose-containing polysaccharides and citrate), modification of bacterial cell envelope and stress resistance. We also demonstrated PhoP involvement in establishing the order of plant cell wall decomposition and utilisation of the corresponding breakdown products. Based on experimental data and in silico analysis, we defined a PhoP binding site motif and provided proof for its universality in enteric bacteria. Scanning P. versatile genome for the locations of this motif suggested a much larger PhoP regulon enriched with the genes important for a plant pathogen, which makes PhoP a global virulence regulator. Potential PhoP targets include many regulatory genes and PhoP control over one of them, expI, was confirmed experimentally, highlighting the link between the PhoPQ two-component and quorum sensing systems. High concentrations of calcium and magnesium ions were found to abolish the PhoPQ-dependent transcription activation but did not relieve repression. Reduced PhoP expression and minimisation of PhoP dependence of regulon members' expression in P. versatile cells isolated from potato tuber tissues suggest that PhoPQ system is a key switch of expression levels of multiple virulence-related genes fine-tuned to control the development of P. versatile-host plant pathosystem.
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Affiliation(s)
- Uljana Kravchenko
- Department of Molecular Biology, Belarusian State University, Minsk, Belarus
| | - Natalia Gogoleva
- Federal Research Center “Kazan Scientific Center of RAS”, Kazan Institute of Biochemistry and Biophysics, Kazan, Russia
- Laboratory of Extreme Biology, Kazan Federal University Institute of Fundamental Medicine and Biology, Kazan, Russia
| | - Nastassia Kalubaka
- Department of Molecular Biology, Belarusian State University, Minsk, Belarus
| | - Alla Kruk
- Department of Molecular Biology, Belarusian State University, Minsk, Belarus
| | - Yuliya Diubo
- Department of Molecular Biology, Belarusian State University, Minsk, Belarus
| | - Yuri Gogolev
- Federal Research Center “Kazan Scientific Center of RAS”, Kazan Institute of Biochemistry and Biophysics, Kazan, Russia
- Department of Biochemistry, Biotechnology and Pharmacology, Kazan Federal University Institute of Fundamental Medicine and Biology, Kazan, Russia
| | - Yevgeny Nikolaichik
- Department of Molecular Biology, Belarusian State University, Minsk, Belarus
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16
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Gallardo A, Ugarte-Ruiz M, Hernández M, Miguela-Villoldo P, Rodríguez-Lázaro D, Domínguez L, Quesada A. Involvement of hpap2 and dgkA Genes in Colistin Resistance Mediated by mcr Determinants. Antibiotics (Basel) 2020; 9:antibiotics9090531. [PMID: 32842668 PMCID: PMC7559476 DOI: 10.3390/antibiotics9090531] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 08/19/2020] [Accepted: 08/21/2020] [Indexed: 11/16/2022] Open
Abstract
Plasmid-mediated colistin resistance (mcr) determinants are challenging the efficacy of polymyxins against Gram-negative pathogens. Among 10 mcr genes described so far, the major determinants mcr-1 and mcr-3 are found closely linked to hpap2 or dgkA genes, encoding a hypothetical phosphatidic acid phosphatase of type 2 (PAP2) and a diacylglycerol kinase, respectively, whose functions are still unknown. In this study, mcr-1, mcr-1–hpap2, mcr-3, and mcr-3–dgkA were expressed in Escherichia coli, and recombinant strains were analyzed to detect antimicrobial susceptibility and changes in the expression of genes involved in phospholipid metabolism. The mcr-1 or mcr-3 single genes were enough to drive growth on colistin selective media, although co-expression of linked genes conferred maximal antibiotic resistance. Expression of mcr determinants downregulated endogenous genes involved in lipopolysaccharide (LPS) modification or phospholipid recycling, although to different extents of repression: strong for arnB, ybjG, and pmrR; medium for eptA, lpxT, and dgkA; small for bacA and pgpB. Four of these genes (bacA, lpxT, pgpB, and ybjG) encode undecaprenyl pyrophosphate (UPP) phosphatases. In these conditions, cells presented resistance against bacitracin, an antibiotic that sequesters UPP from PAP2 enzymes. The hpap2 and dgkA genes might play a role in colistin resistance by compensating for phospholipid metabolism functions altered during LPS modification by colistin resistance determinants.
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Affiliation(s)
- Alejandro Gallardo
- Departamento de Bioquímica, Facultad de Veterinaria, Universidad de Extremadura, Av. de la Universidad s/n, 10003 Cáceres, Spain;
| | - María Ugarte-Ruiz
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, 28040 Madrid, Spain; (M.U.-R.); (P.M.-V.); (L.D.)
| | - Marta Hernández
- Laboratorio de Biología Molecular y Microbiología, Instituto Tecnológico Agrario de Castilla y León, 47071 Valladolid, Spain;
| | - Pedro Miguela-Villoldo
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, 28040 Madrid, Spain; (M.U.-R.); (P.M.-V.); (L.D.)
| | - David Rodríguez-Lázaro
- Unidad de Microbiología, Departamento de Biotecnología y Ciencia de los Alimentos, Universidad de Burgos, 09001 Burgos, Spain;
| | - Lucas Domínguez
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, 28040 Madrid, Spain; (M.U.-R.); (P.M.-V.); (L.D.)
| | - Alberto Quesada
- Departamento de Bioquímica, Facultad de Veterinaria, Universidad de Extremadura, Av. de la Universidad s/n, 10003 Cáceres, Spain;
- INBIO G + C, Universidad de Extremadura, 10003 Cáceres, Spain
- Correspondence: ; Tel.: +34-927251334
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17
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Tian X, Auger R, Manat G, Kerff F, Mengin-Lecreulx D, Touzé T. Insight into the dual function of lipid phosphate phosphatase PgpB involved in two essential cell-envelope metabolic pathways in Escherichia coli. Sci Rep 2020; 10:13209. [PMID: 32764655 PMCID: PMC7413402 DOI: 10.1038/s41598-020-70047-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 07/16/2020] [Indexed: 11/09/2022] Open
Abstract
Ubiquitous PAP2 lipid phosphatases are involved in a wide array of central physiological functions. PgpB from Escherichia coli constitutes the archetype of this subfamily of membrane proteins. It displays a dual function by catalyzing the biosynthesis of two essential lipids, the phosphatidylglycerol (PG) and the undecaprenyl phosphate (C55-P). C55-P constitutes a lipid carrier allowing the translocation of peptidoglycan subunits across the plasma membrane. PG and C55-P are synthesized in a redundant manner by PgpB and other PAP2 and/or unrelated membrane phosphatases. Here, we show that PgpB is the sole, among these multiple phosphatases, displaying this dual activity. The inactivation of PgpB does not confer any apparent growth defect, but its inactivation together with another PAP2 alters the cell envelope integrity increasing the susceptibility to small hydrophobic compounds. Evidence is also provided of an interplay between PAP2s and the peptidoglycan polymerase PBP1A. In contrast to PGP hydrolysis, which relies on a His/Asp/His catalytic triad of PgpB, the mechanism of C55-PP hydrolysis appeared as only requiring the His/Asp diad, which led us to hypothesize distinct processes. Moreover, thermal stability analyses highlighted a substantial structural change upon phosphate binding by PgpB, supporting an induced-fit model of action.
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Affiliation(s)
- Xudong Tian
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Rodolphe Auger
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Guillaume Manat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Frédéric Kerff
- Centre d'Ingénierie des Protéines, InBioS, Université de Liège, Liège, Belgium
| | - Dominique Mengin-Lecreulx
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Thierry Touzé
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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18
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Falchi FA, Di Lorenzo F, Pizzoccheri R, Casino G, Paroni M, Forti F, Molinaro A, Briani F. Overexpression of lpxT Gene in Escherichia coli Inhibits Cell Division and Causes Envelope Defects without Changing the Overall Phosphorylation Level of Lipid A. Microorganisms 2020; 8:E826. [PMID: 32486329 PMCID: PMC7356881 DOI: 10.3390/microorganisms8060826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 12/20/2022] Open
Abstract
LpxT is an inner membrane protein that transfers a phosphate group from the essential lipid undecaprenyl pyrophosphate (C-55PP) to the lipid A moiety of lipopolysaccharide, generating a lipid A tris-phosphorylated species. The protein is encoded by the non-essential lpxT gene, which is conserved in distantly related Gram-negative bacteria. In this work, we investigated the phenotypic effect of lpxT ectopic expression from a plasmid in Escherichia coli. We found that lpxT induction inhibited cell division and led to the formation of elongated cells, mostly with absent or altered septa. Moreover, the cells became sensitive to detergents and to hypo-osmotic shock, indicating that they had cell envelope defects. These effects were not due to lipid A hyperphosphorylation or C-55PP sequestering, but most likely to defective lipopolysaccharide transport. Indeed, lpxT overexpression in mutants lacking the L,D-transpeptidase LdtD and LdtE, which protect cells with outer membrane defects from osmotic lysis, caused cell envelope defects. Moreover, we found that pyrophosphorylated lipid A was also produced in a lpxT deletion mutant, indicating that LpxT is not the only protein able to perform such lipid A modification in E. coli.
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Affiliation(s)
- Federica A. Falchi
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy; (F.A.F.); (R.P.); (G.C.); (M.P.); (F.F.)
| | - Flaviana Di Lorenzo
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, 80126 Napoli, Italy; (F.D.L.); (A.M.)
| | - Roberto Pizzoccheri
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy; (F.A.F.); (R.P.); (G.C.); (M.P.); (F.F.)
| | - Gianluca Casino
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy; (F.A.F.); (R.P.); (G.C.); (M.P.); (F.F.)
| | - Moira Paroni
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy; (F.A.F.); (R.P.); (G.C.); (M.P.); (F.F.)
| | - Francesca Forti
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy; (F.A.F.); (R.P.); (G.C.); (M.P.); (F.F.)
| | - Antonio Molinaro
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, 80126 Napoli, Italy; (F.D.L.); (A.M.)
| | - Federica Briani
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy; (F.A.F.); (R.P.); (G.C.); (M.P.); (F.F.)
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19
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Workman SD, Strynadka NCJ. A Slippery Scaffold: Synthesis and Recycling of the Bacterial Cell Wall Carrier Lipid. J Mol Biol 2020; 432:4964-4982. [PMID: 32234311 DOI: 10.1016/j.jmb.2020.03.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 01/20/2023]
Abstract
The biosynthesis of bacterial cell envelope polysaccharides such as peptidoglycan relies on the use of a dedicated carrier lipid both for the assembly of precursors at the cytoplasmic face of the plasma membrane and for the translocation of lipid linked oligosaccharides across the plasma membrane into the periplasmic space. This dedicated carrier lipid, undecaprenyl phosphate, results from the dephosphorylation of undecaprenyl pyrophosphate, which is generated de novo in the cytoplasm by undecaprenyl pyrophosphate synthase and released as a by-product when newly synthesized glycans are incorporated into the existing cell envelope. The de novo synthesis of undecaprenyl pyrophosphate has been thoroughly characterized from a structural and mechanistic standpoint; however, its dephosphorylation to the active carrier lipid form, both in the course of de novo synthesis and recycling, has only been begun to be studied in depth in recent years. This review provides an overview of bacterial carrier lipid synthesis and presents the current state of knowledge regarding bacterial carrier lipid recycling.
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Affiliation(s)
- Sean D Workman
- Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada V6T 1Z3
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada V6T 1Z3.
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20
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Kapach G, Nuri R, Schmidt C, Danin A, Ferrera S, Savidor A, Gerlach RG, Shai Y. Loss of the Periplasmic Chaperone Skp and Mutations in the Efflux Pump AcrAB-TolC Play a Role in Acquired Resistance to Antimicrobial Peptides in Salmonella typhimurium. Front Microbiol 2020; 11:189. [PMID: 32210923 PMCID: PMC7075815 DOI: 10.3389/fmicb.2020.00189] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/27/2020] [Indexed: 01/01/2023] Open
Abstract
Bacterial resistance to antibiotics is a major concern worldwide, leading to an extensive search for alternative drugs. Promising candidates are antimicrobial peptides (AMPs), innate immunity molecules, shown to be highly efficient against multidrug resistant bacteria. Therefore, it is essential to study bacterial resistance mechanisms against them. For that purpose, we used experimental evolution, and isolated a Salmonella enterica serovar typhimurium-resistant line to the AMP 4DK5L7. This AMP displayed promising features including widespread activity against Gram-negative bacteria and protection from proteolytic degradation. However, the resistance that evolved in the isolated strain was particularly high. Whole genome sequencing revealed that five spontaneous mutations had evolved. Of these, three are novel in the context of acquired AMP resistance. Two mutations are related to the AcrAB-TolC multidrug efflux pump. One occurred in AcrB, the substrate-binding domain of the system, and the second in RamR, a transcriptional regulator of the system. Together, the mutations increased the minimal inhibitory concentration (MIC) by twofold toward this AMP. Moreover, the mutation in AcrB induced hypersusceptibility toward ampicillin and colistin. The last mutation occurred in Skp, a periplasmic chaperone that participates in the biogenesis of outer membrane proteins (OMPs). This mutation increased the MIC by twofold to 4DK5L7 and by fourfold to another AMP, seg5D. Proteomic analysis revealed that the mutation abolished Skp expression, reduced OMP abundance, and increased DegP levels. DegP, a protease that was reported to have an additional chaperone activity, escorts OMPs through the periplasm along with Skp, but is also associated with AMP resistance. In conclusion, our data demonstrate that both loss of Skp and manipulation of the AcrAB-TolC system are alternative strategies of AMP acquired resistance in Salmonella typhimurium and might represent a common mechanism in other Gram-negative bacteria.
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Affiliation(s)
- Gal Kapach
- Departmant of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Reut Nuri
- Departmant of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Adi Danin
- Departmant of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shir Ferrera
- Departmant of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Savidor
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Roman G Gerlach
- Project Group 5, Robert Koch Institute, Wernigerode, Germany
| | - Yechiel Shai
- Departmant of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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21
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Simpson BW, Trent MS. Pushing the envelope: LPS modifications and their consequences. Nat Rev Microbiol 2020; 17:403-416. [PMID: 31142822 DOI: 10.1038/s41579-019-0201-x] [Citation(s) in RCA: 236] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The defining feature of the Gram-negative cell envelope is the presence of two cellular membranes, with the specialized glycolipid lipopolysaccharide (LPS) exclusively found on the surface of the outer membrane. The surface layer of LPS contributes to the stringent permeability properties of the outer membrane, which is particularly resistant to permeation of many toxic compounds, including antibiotics. As a common surface antigen, LPS is recognized by host immune cells, which mount defences to clear pathogenic bacteria. To alter properties of the outer membrane or evade the host immune response, Gram-negative bacteria chemically modify LPS in a wide variety of ways. Here, we review key features and physiological consequences of LPS biogenesis and modifications.
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Affiliation(s)
- Brent W Simpson
- Department of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - M Stephen Trent
- Department of Infectious Diseases, University of Georgia, Athens, GA, USA. .,Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA. .,Department of Microbiology, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, USA.
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22
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Zhu L, Zhou Z, Liu Y, Lin Z, Shuai X, Xu L, Chen H. Comprehensive Understanding of the Plasmid-Mediated Colistin Resistance Gene mcr-1 in Aquatic Environments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:1603-1613. [PMID: 31886662 DOI: 10.1021/acs.est.9b05919] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The emergence of plasmid-mediated colistin resistance gene mcr-1 has attracted global attention and raised serious concerns about its possible cross-environment dissemination. However, the systematic exploration of mcr-1 both by monitoring and genetic dissection in aquatic environments has not been conducted. This study addresses the gap related to the occurrence and distribution of mcr-1 in watersheds, eastern China. The results showed an abundance of mcr-1 gene in four watersheds, and the highest level of mcr-1 reached 1.8 × 109 gene copies per liter of water. Furthermore, the transfer frequencies of the plasmids in isolated Escherichia coli were 2.76 × 10-6-6.11 × 10-4 within genera and minimal inhibitory concentrations of polymyxin resistance were 8-16 mg/L for transconjugants. Mass spectrometry data allowed visualization of the function of mcr-1 expression, rendering bacterial resistance to colistin. The genetic details of six mcr-1-harboring plasmids in E. coli isolates of aquatic origin were obtained by single-molecule real-time sequencing. These plasmids were closely associated with E. coli strains of pig and human origin, supporting the concept of mcr-1 dissemination across natural environments, livestock farms, and humans. In conclusion, this study provides the first glimpse of the profile of mcr-1-harboring plasmids and their genetic environment in aquatic ecosystems.
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Affiliation(s)
- Lin Zhu
- Department of Environmental Engineering, College of Environmental and Resource Sciences , Zhejiang University , Hangzhou 310058 , China
| | - Zhenchao Zhou
- Department of Environmental Engineering, College of Environmental and Resource Sciences , Zhejiang University , Hangzhou 310058 , China
| | - Yang Liu
- Department of Environmental Engineering, College of Environmental and Resource Sciences , Zhejiang University , Hangzhou 310058 , China
| | - Zejun Lin
- Department of Environmental Engineering, College of Environmental and Resource Sciences , Zhejiang University , Hangzhou 310058 , China
| | - Xinyi Shuai
- Department of Environmental Engineering, College of Environmental and Resource Sciences , Zhejiang University , Hangzhou 310058 , China
| | - Lan Xu
- Department of Environmental Engineering, College of Environmental and Resource Sciences , Zhejiang University , Hangzhou 310058 , China
| | - Hong Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences , Zhejiang University , Hangzhou 310058 , China
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23
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Ji Y, An J, Hwang D, Ha DH, Lim SM, Lee C, Zhao J, Song HK, Yang EG, Zhou P, Chung HS. Metabolic engineering of Escherichia coli to produce a monophosphoryl lipid A adjuvant. Metab Eng 2020; 57:193-202. [PMID: 31786244 PMCID: PMC6960009 DOI: 10.1016/j.ymben.2019.11.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/09/2019] [Accepted: 11/26/2019] [Indexed: 12/22/2022]
Abstract
Monophosphoryl lipid A (MPLA) species, including MPL (a trade name of GlaxoSmithKline) and GLA (a trade name of Immune Design, a subsidiary of Merck), are widely used as an adjuvant in vaccines, allergy drugs, and immunotherapy to boost the immune response. Even though MPLA is a derivative of lipopolysaccharide (LPS), a component of the outer membrane of Gram-negative bacteria, bacterial strains producing MPLA have not been found in nature nor engineered. In fact, MPLA generation involves expensive and laborious procedures based on synthetic routes or chemical transformation of precursors isolated from Gram-negative bacteria. Here, we report the engineering of an Escherichia coli strain for in situ production and accumulation of MPLA. Furthermore, we establish a succinct method for purifying MPLA from the engineered E. coli strain. We show that the purified MPLA (named EcML) stimulates the mouse immune system to generate antigen-specific IgG antibodies similarly to commercially available MPLA, but with a dramatically reduced manufacturing time and cost. Our system, employing the first engineered E. coli strain that directly produces the adjuvant EcML, could transform the current standard of industrial MPLA production.
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Affiliation(s)
- Yuhyun Ji
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, Republic of Korea; Department of Life Sciences, Korea University, Seoul, 02841, Republic of Korea
| | - Jinsu An
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul, 02792, Republic of Korea
| | - Dohyeon Hwang
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul, 02792, Republic of Korea
| | - Da Hui Ha
- Eubiologics.CO.,Ltd, V Plant 125, Wonmudong-gil, Dongsan-myeon, Chuncheon-si, Gangwon-do, Republic of Korea
| | - Sang Min Lim
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul, 02792, Republic of Korea; Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Chankyu Lee
- Eubiologics.CO.,Ltd, V Plant 125, Wonmudong-gil, Dongsan-myeon, Chuncheon-si, Gangwon-do, Republic of Korea
| | - Jinshi Zhao
- Department of Biochemistry, Duke University Medical Center, Durham, 27710, USA
| | - Hyun Kyu Song
- Department of Life Sciences, Korea University, Seoul, 02841, Republic of Korea
| | - Eun Gyeong Yang
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Pei Zhou
- Department of Biochemistry, Duke University Medical Center, Durham, 27710, USA
| | - Hak Suk Chung
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul, 02792, Republic of Korea.
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24
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HupA, the main undecaprenyl pyrophosphate and phosphatidylglycerol phosphate phosphatase in Helicobacter pylori is essential for colonization of the stomach. PLoS Pathog 2019; 15:e1007972. [PMID: 31487328 PMCID: PMC6748449 DOI: 10.1371/journal.ppat.1007972] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 09/17/2019] [Accepted: 07/09/2019] [Indexed: 12/24/2022] Open
Abstract
The biogenesis of bacterial cell-envelope polysaccharides requires the translocation, across the plasma membrane, of sugar sub-units that are produced inside the cytoplasm. To this end, the hydrophilic sugars are anchored to a lipid phosphate carrier (undecaprenyl phosphate (C55-P)), yielding membrane intermediates which are translocated to the outer face of the membrane. Finally, the glycan moiety is transferred to a nascent acceptor polymer, releasing the carrier in the “inactive” undecaprenyl pyrophosphate (C55-PP) form. Thus, C55-P is generated through the dephosphorylation of C55-PP, itself arising from either de novo synthesis or recycling. Two types of integral membrane C55-PP phosphatases were described: BacA enzymes and a sub-group of PAP2 enzymes (type 2 phosphatidic acid phosphatases). The human pathogen Helicobacter pylori does not contain BacA homologue but has four membrane PAP2 proteins: LpxE, LpxF, HP0350 and HP0851. Here, we report the physiological role of HP0851, renamed HupA, via multiple and complementary approaches ranging from a detailed biochemical characterization to the assessment of its effect on cell envelope metabolism and microbe-host interactions. HupA displays a dual function as being the main C55-PP pyrophosphatase (UppP) and phosphatidylglycerol phosphate phosphatase (PGPase). Although not essential in vitro, HupA was essential in vivo for stomach colonization. In vitro, the remaining UppP activity was carried out by LpxE in addition to its lipid A 1-phosphate phosphatase activity. Both HupA and LpxE have crucial roles in the biosynthesis of several cell wall polysaccharides and thus constitute potential targets for new therapeutic strategies. Helicobacter pylori colonizes the human’s gastric mucosa and infects around 50% of the world’s population. This pathogen is responsible for chronic gastritis, peptic ulcers and in worst cases leads to gastric cancer. It has been classified as a class I carcinogen by the World Health Organization in 1994. Here, we show that HP0851, renamed HupA, is the major undecaprenyl pyrophosphate (C55-PP) phosphatase (UppP) and the major phosphatidylglycerol phosphate phosphatase (PGPase). This enzyme is also involved in cationic antimicrobial peptide (CAMP) resistance to which H. pylori hupA mutant shows an increased sensitivity (4 fold). This mutant was unable to colonize the stomach in mouse model of infection showing that even if hupA was not essential in vitro, this gene was essential in vivo. Both HupA and LpxE have crucial roles in the biosynthesis of several cell wall polysaccharides and thus constitute potential targets for new therapeutic strategies.
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25
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Sperandeo P, Polissi A, De Fabiani E. Fat Matters for Bugs: How Lipids and Lipid Modifications Make the Difference in Bacterial Life. EUR J LIPID SCI TECH 2019. [DOI: 10.1002/ejlt.201900204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Paola Sperandeo
- Dipartimento di Scienze Farmacologiche e BiomolecolariUniversità degli Studi di MilanoVia Balzaretti 920133MilanoItaly
| | - Alessandra Polissi
- Dipartimento di Scienze Farmacologiche e BiomolecolariUniversità degli Studi di MilanoVia Balzaretti 920133MilanoItaly
| | - Emma De Fabiani
- Dipartimento di Scienze Farmacologiche e BiomolecolariUniversità degli Studi di MilanoVia Balzaretti 920133MilanoItaly
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26
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Temperature-dependent regulation of the Escherichia coli lpxT gene. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:786-795. [DOI: 10.1016/j.bbagrm.2019.06.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/28/2019] [Accepted: 06/30/2019] [Indexed: 01/11/2023]
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27
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Abstract
The cell envelope is the first line of defense between a bacterium and the world-at-large. Often, the initial steps that determine the outcome of chemical warfare, bacteriophage infections, and battles with other bacteria or the immune system greatly depend on the structure and composition of the bacterial cell surface. One of the most studied bacterial surface molecules is the glycolipid known as lipopolysaccharide (LPS), which is produced by most Gram-negative bacteria. Much of the initial attention LPS received in the early 1900s was owed to its ability to stimulate the immune system, for which the glycolipid was commonly known as endotoxin. It was later discovered that LPS also creates a permeability barrier at the cell surface and is a main contributor to the innate resistance that Gram-negative bacteria display against many antimicrobials. Not surprisingly, these important properties of LPS have driven a vast and still prolific body of literature for more than a hundred years. LPS research has also led to pioneering studies in bacterial envelope biogenesis and physiology, mostly using Escherichia coli and Salmonella as model systems. In this review, we will focus on the fundamental knowledge we have gained from studies of the complex structure of the LPS molecule and the biochemical pathways for its synthesis, as well as the transport of LPS across the bacterial envelope and its assembly at the cell surface.
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28
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Abstract
Resistance to last-line polymyxins mediated by the plasmid-borne mobile colistin resistance gene (mcr-1) represents a new threat to global human health. Here we present the complete genome sequence of an mcr-1-positive multidrug-resistant Escherichia coli strain (MS8345). We show that MS8345 belongs to serotype O2:K1:H4, has a large 241,164-bp IncHI2 plasmid that carries 15 other antibiotic resistance genes (including the extended-spectrum β-lactamase bla CTX-M-1) and 3 putative multidrug efflux systems, and contains 14 chromosomally encoded antibiotic resistance genes. MS8345 also carries a large ColV-like virulence plasmid that has been associated with E. coli bacteremia. Whole-genome phylogeny revealed that MS8345 clusters within a discrete clade in the sequence type 95 (ST95) lineage, and MS8345 is very closely related to the highly virulent O45:K1:H4 clone associated with neonatal meningitis. Overall, the acquisition of a plasmid carrying resistance to colistin and multiple other antibiotics in this virulent E. coli lineage is concerning and might herald an era where the empirical treatment of ST95 infections becomes increasingly more difficult.IMPORTANCE Escherichia coli ST95 is a globally disseminated clone frequently associated with bloodstream infections and neonatal meningitis. However, the ST95 lineage is defined by low levels of drug resistance amongst clinical isolates, which normally provides for uncomplicated treatment options. Here, we provide the first detailed genomic analysis of an E. coli ST95 isolate that has both high virulence potential and resistance to multiple antibiotics. Using the genome, we predicted its virulence and antibiotic resistance mechanisms, which include resistance to last-line antibiotics mediated by the plasmid-borne mcr-1 gene. Finding an ST95 isolate resistant to nearly all antibiotics that also has a high virulence potential is of major clinical importance and underscores the need to monitor new and emerging trends in antibiotic resistance development in this important global lineage.
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Contribution of Novel Amino Acid Alterations in PmrA or PmrB to Colistin Resistance in mcr-Negative Escherichia coli Clinical Isolates, Including Major Multidrug-Resistant Lineages O25b:H4-ST131- H30Rx and Non-x. Antimicrob Agents Chemother 2018; 62:AAC.00864-18. [PMID: 29914952 DOI: 10.1128/aac.00864-18] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 06/02/2018] [Indexed: 11/20/2022] Open
Abstract
Colistin is a last-line drug for multidrug-resistant Gram-negative bacteria. We previously reported four plasmid-mediated colistin resistance (mcr) gene-negative colistin-resistant Escherichia coli clinical isolates, including the major pathogenic and fluoroquinolone-resistant strains O25b:H4-ST131-H30Rx (isolates SRE34 and SRE44; MIC for colistin = 16 mg/liter), non-x (SME296; MIC = 8 mg/liter), and O18-ST416 (SME222; MIC = 4 mg/liter). In this study, we investigated the colistin resistance mechanism and identified novel amino acid substitutions or deletions in the PmrAB two-component system that activates eptA (encoding a phosphoethanolamine transferase) and arnT (encoding an undecaprenyl phosphate-alpha-4-amino-4-deoxy-l-arabinose arabinosyl transferase) in all colistin-resistant isolates. SRE34 possessed deletion Δ27-45 (LISVFWLWHESTEQIQLFE) in PmrB, SRE44 possessed substitution L105P in PmrA, and both SME222 and SME296 included substitution G206D in PmrB. Matrix-assisted laser desorption ionization-time of flight mass spectrometry revealed that lipid A is modified with phosphoethanolamine in all four isolates. Deletion of pmrAB decreased colistin MICs to 0.5 mg/liter and lowered eptA and arnT expression. Chromosomal replacement of mutated pmrA or pmrB in colistin-susceptible O25b:H4-ST131 strain SME98 (colistin MIC = 0.5 mg/liter) increased the colistin MIC to that of the respective parent colistin-resistant isolate. In addition, SME98 mutants in which pmrAB was replaced with mutated pmrAB showed no significant differences in bacterial growth and competition culture from the parent strain, except for the mutant with L105P in PmrA, whose growth was significantly suppressed in the presence of the parent strain. In conclusion, some O25b:H4-ST131 strains appear to acquire colistin resistance via phosphoethanolamine modification of lipid A through amino acid changes in PmrAB, and the amino acid changes in PmrB do not influence bacterial growth.
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Dik DA, Fisher JF, Mobashery S. Cell-Wall Recycling of the Gram-Negative Bacteria and the Nexus to Antibiotic Resistance. Chem Rev 2018; 118:5952-5984. [PMID: 29847102 PMCID: PMC6855303 DOI: 10.1021/acs.chemrev.8b00277] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The importance of the cell wall to the viability of the bacterium is underscored by the breadth of antibiotic structures that act by blocking key enzymes that are tasked with cell-wall creation, preservation, and regulation. The interplay between cell-wall integrity, and the summoning forth of resistance mechanisms to deactivate cell-wall-targeting antibiotics, involves exquisite orchestration among cell-wall synthesis and remodeling and the detection of and response to the antibiotics through modulation of gene regulation by specific effectors. Given the profound importance of antibiotics to the practice of medicine, the assertion that understanding this interplay is among the most fundamentally important questions in bacterial physiology is credible. The enigmatic regulation of the expression of the AmpC β-lactamase, a clinically significant and highly regulated resistance response of certain Gram-negative bacteria to the β-lactam antibiotics, is the exemplar of this challenge. This review gives a current perspective to this compelling, and still not fully solved, 35-year enigma.
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Affiliation(s)
- David A. Dik
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jed F. Fisher
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame, Indiana 46556, United States
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31
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Kawakami N, Fujisaki S. Undecaprenyl phosphate metabolism in Gram-negative and Gram-positive bacteria. Biosci Biotechnol Biochem 2018; 82:940-946. [DOI: 10.1080/09168451.2017.1401915] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Undecaprenyl phosphate (UP) is essential for the biosynthesis of bacterial extracellular polysaccharides. UP is produced by the dephosphorylation of undecaprenyl diphosphate (UPP) via de novo synthetic and recycling pathways. Gram-positive bacteria contain remarkable amounts of undecaprenol (UOH), which is phosphorylated to UP, although UOH has not been found in Gram-negative bacteria. Here, current knowledge about UPP phosphatase and UOH kinase is reviewed. Dephosphorylation of UPP is catalyzed by a BacA homologue and a type-2 phosphatidic acid phosphatase (PAP2) homologue. The presence of one of these UPP phosphatases is essential for bacterial growth. The catalytic center of both types of enzyme is located outside the cytoplasmic membrane. In Gram-positive bacteria, an enzyme homologous to DgkA, which is the diacylglycerol kinase of Escherichia coli, catalyzes UOH phosphorylation. The possible role of UOH and the significance of systematic construction of Staphylococcus aureus mutants to determine UP metabolism are discussed.
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Affiliation(s)
- Naoki Kawakami
- Faculty of Science, Department of Biomolecular Science, Toho University, Funabashi, Japan
| | - Shingo Fujisaki
- Faculty of Science, Department of Biomolecular Science, Toho University, Funabashi, Japan
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32
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Hernández-Rocamora VM, Otten CF, Radkov A, Simorre JP, Breukink E, VanNieuwenhze M, Vollmer W. Coupling of polymerase and carrier lipid phosphatase prevents product inhibition in peptidoglycan synthesis. ACTA ACUST UNITED AC 2018; 2:1-13. [PMID: 30046664 PMCID: PMC6053597 DOI: 10.1016/j.tcsw.2018.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 04/13/2018] [Accepted: 04/13/2018] [Indexed: 11/30/2022]
Abstract
Peptidoglycan (PG) is an essential component of the bacterial cell wall that maintains the shape and integrity of the cell. The PG precursor lipid II is assembled at the inner leaflet of the cytoplasmic membrane, translocated to the periplasmic side, and polymerized to glycan chains by membrane anchored PG synthases, such as the class A Penicillin-binding proteins (PBPs). Polymerization of PG releases the diphosphate form of the carrier lipid, undecaprenyl pyrophosphate (C55-PP), which is converted to the monophosphate form by membrane-embedded pyrophosphatases, generating C55-P for a new round of PG precursor synthesis. Here we report that deletion of the C55-PP pyrophosphatase gene pgpB in E. coli increases the susceptibility to cefsulodin, a β-lactam specific for PBP1A, indicating that the cellular function of PBP1B is impaired in the absence of PgpB. Purified PBP1B interacted with PgpB and another C55-PP pyrophosphatase, BacA and both, PgpB and BacA stimulated the glycosyltransferase activity of PBP1B. C55-PP was found to be a potent inhibitor of PBP1B. Our data suggest that the stimulation of PBP1B by PgpB is due to the faster removal and processing of C55-PP, and that PBP1B interacts with C55-PP phosphatases during PG synthesis to couple PG polymerization with the recycling of the carrier lipid and prevent product inhibition by C55-PP.
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Affiliation(s)
- Víctor M Hernández-Rocamora
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
| | - Christian F Otten
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
| | - Atanas Radkov
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN 47405-7102, USA
| | - Jean-Pierre Simorre
- Institut de Biologie Structurale, Université Grenoble Alpes, Grenoble, France
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, University of Utrecht, Padualaan 8, 3584 Utrecht, The Netherlands
| | - Michael VanNieuwenhze
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN 47405-7102, USA
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
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Hong X, Chen HD, Groisman EA. Gene expression kinetics governs stimulus-specific decoration of the Salmonella outer membrane. Sci Signal 2018; 11:11/529/eaar7921. [PMID: 29739882 DOI: 10.1126/scisignal.aar7921] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Lipid A is the innermost component of the lipopolysaccharide (LPS) molecules that occupy the outer leaflet of the outer membrane in Gram-negative bacteria. Lipid A is recognized by the host immune system and targeted by cationic antimicrobial compounds. In Salmonella enterica serovar Typhimurium, the phosphates of lipid A are chemically modified by enzymes encoded by targets of the transcriptional regulator PmrA. These modifications increase resistance to the cationic peptide antibiotic polymyxin B by reducing the negative charge of the LPS. We report the mechanism by which Salmonella produces different lipid A profiles when PmrA is activated by low Mg2+ versus a mildly acidic pH. Low Mg2+ favored modification of the lipid A phosphates with 4-amino-4-deoxy-l-aminoarabinose (l-Ara4N) by activating the regulatory protein PhoP, which initially increased the LPS negative charge by promoting transcription of lpxT, encoding an enzyme that adds an additional phosphate group to lipid A. Later, PhoP activated PmrA posttranslationally, resulting in expression of PmrA-activated genes, including those encoding the LpxT inhibitor PmrR and enzymes responsible for the incorporation of l-Ara4N. By contrast, a mildly acidic pH favored modification of the lipid A phosphates with a mixture of l-Ara4N and phosphoethanolamine (pEtN) by simultaneously inducing the PhoP-activated lpxT and PmrA-activated pmrR genes. Although l-Ara4N reduces the LPS negative charge more than does pEtN, modification of lipid A phosphates solely with l-Ara4N required a prior transient increase in lipid A negative charge. Our findings demonstrate how bacteria tailor their cell surface to different stresses, such as those faced inside phagocytes.
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Affiliation(s)
- Xinyu Hong
- Department of Cell Biology, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA.,Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA.,Yale Microbial Sciences Institute, P.O. Box 27389, West Haven, CT 06516, USA.,Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06536, USA
| | - H Deborah Chen
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
| | - Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA. .,Yale Microbial Sciences Institute, P.O. Box 27389, West Haven, CT 06516, USA
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Angioni S, Millia L, Mustarelli P, Doria E, Temporiti M, Mannucci B, Corana F, Quartarone E. Photosynthetic microbial fuel cell with polybenzimidazole membrane: synergy between bacteria and algae for wastewater removal and biorefinery. Heliyon 2018; 4:e00560. [PMID: 29862335 PMCID: PMC5968083 DOI: 10.1016/j.heliyon.2018.e00560] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/09/2018] [Accepted: 02/26/2018] [Indexed: 11/18/2022] Open
Abstract
Here, we demonstrate a very efficient simultaneous approach of bioenergy generation from wastewater and added-value compounds production by using a photosynthetic microalgae microbial fuel cells (PMFC), based on polybenzimidazole (PBI) composite membrane as separator. The use of PBI was proved to be very promising, even more convenient than Nafion™ in terms of energy performances as well as cost and sustainability. This polymer is also easily autoclavable, so allowing a re-use of the separator with a consequent beneficial cost effect. Two PMFCs were investigated: 1) Pt electrocatalysed and 2) Pt-free. They were operated as microbial carbon capture (MCC) device under continuous illumination, by using a domestic wastewater as anolyte and Scenedesmus acutus strain in the catholyte. The Pt-based cell allowed to generate higher volumetric power density (∼400 mW m−3) after more than 100 operating days. This resulted in an improved wastewater treatment efficiency, determined in terms of normalised energy recovery (NER > 0.19 kWh kgCOD−1 in case of Pt). The CO2 fixation of the PMFC-grown microalgae leaded to a high accumulation of added-value products, namely pigments and fatty acids. A significant quantity of lutein was observed as well as a relevant amount of other valuable carotenoids, as violaxanthin, astaxanthin and cantaxanthin. The lipids were even excellently accumulated (49%dw). Their profile was mainly composed by fatty acids in the range C16-18, which are particularly indicated for the biofuel production. These results demonstrate the feasibility and the implemented sustainability of such PMFCs as a great potential technology for the wastewater treatment and the simultaneous production of valuable products.
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Affiliation(s)
- S. Angioni
- Dept. of Chemistry and INSTM, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - L. Millia
- Dept. of Chemistry and INSTM, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - P. Mustarelli
- Dept. of Chemistry and INSTM, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - E. Doria
- Dept. of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - M.E. Temporiti
- Dept. of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - B. Mannucci
- Centro Grandi Strumenty, University of Pavia, Via Bassi 21, 27100 Pavia, Italy
| | - F. Corana
- Centro Grandi Strumenty, University of Pavia, Via Bassi 21, 27100 Pavia, Italy
| | - E. Quartarone
- Dept. of Chemistry and INSTM, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
- Corresponding author.
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Herrera CM, Henderson JC, Crofts AA, Trent MS. Novel coordination of lipopolysaccharide modifications in Vibrio cholerae promotes CAMP resistance. Mol Microbiol 2017; 106:582-596. [PMID: 28906060 DOI: 10.1111/mmi.13835] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2017] [Indexed: 01/02/2023]
Abstract
In the environment and during infection, the human intestinal pathogen Vibrio cholerae must overcome noxious compounds that damage the bacterial outer membrane. The El Tor and classical biotypes of O1 V. cholerae show striking differences in their resistance to membrane disrupting cationic antimicrobial peptides (CAMPs), such as polymyxins. The classical biotype is susceptible to CAMPs, but current pandemic El Tor biotype isolates gain CAMP resistance by altering the net charge of their cell surface through glycine modification of lipid A. Here we report a second lipid A modification mechanism that only functions in the V. cholerae El Tor biotype. We identify a functional EptA ortholog responsible for the transfer of the amino-residue phosphoethanolamine (pEtN) to the lipid A of V. cholerae El Tor that is not functional in the classical biotype. We previously reported that mildly acidic growth conditions (pH 5.8) downregulate expression of genes encoding the glycine modification machinery. In this report, growth at pH 5.8 increases expression of eptA with concomitant pEtN modification suggesting coordinated regulation of these LPS modification systems. Similarly, efficient pEtN lipid A substitution is seen in the absence of lipid A glycinylation. We further demonstrate EptA orthologs from non-cholerae Vibrio species are functional.
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Affiliation(s)
- Carmen M Herrera
- Department of Infectious Diseases, Center for Vaccines and Immunology, University of Georgia, College of Veterinary Medicine, Athens, GA 30602, USA
| | - Jeremy C Henderson
- Department of Infectious Diseases, Center for Vaccines and Immunology, University of Georgia, College of Veterinary Medicine, Athens, GA 30602, USA
| | - Alexander A Crofts
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, TX 78712, USA
| | - M Stephen Trent
- Department of Infectious Diseases, Center for Vaccines and Immunology, University of Georgia, College of Veterinary Medicine, Athens, GA 30602, USA
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Xiao X, Sankaranarayanan K, Khosla C. Biosynthesis and structure-activity relationships of the lipid a family of glycolipids. Curr Opin Chem Biol 2017; 40:127-137. [PMID: 28942130 DOI: 10.1016/j.cbpa.2017.07.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 07/14/2017] [Accepted: 07/20/2017] [Indexed: 10/18/2022]
Abstract
Lipopolysaccharide (LPS), a glycolipid found in the outer membrane of Gram-negative bacteria, is a potent elicitor of innate immune responses in mammals. A typical LPS molecule is composed of three different structural domains: a polysaccharide called the O-antigen, a core oligosaccharide, and Lipid A. Lipid A is the amphipathic glycolipid moiety of LPS. It stimulates the immune system by tightly binding to Toll-like receptor 4. More recently, Lipid A has also been shown to activate intracellular caspase-4 and caspase-5. An impressive diversity is observed in Lipid A structures from different Gram-negative bacteria, and it is well established that subtle changes in chemical structure can result in dramatically different immune activities. For example, Lipid A from Escherichia coli is highly toxic to humans, whereas a biosynthetic precursor called Lipid IVA blocks this toxic activity, and monophosphoryl Lipid A from Salmonella minnesota is a vaccine adjuvant. Thus, an understanding of structure-activity relationships in this glycolipid family could be used to design useful immunomodulatory agents. Here we review the biosynthesis, modification, and structure-activity relationships of Lipid A.
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Affiliation(s)
- Xirui Xiao
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States
| | | | - Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, United States; Stanford ChEM-H, Stanford University, Stanford, CA 94305, United States.
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37
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Ghachi ME, Howe N, Auger R, Lambion A, Guiseppi A, Delbrassine F, Manat G, Roure S, Peslier S, Sauvage E, Vogeley L, Rengifo-Gonzalez JC, Charlier P, Mengin-Lecreulx D, Foglino M, Touzé T, Caffrey M, Kerff F. Crystal structure and biochemical characterization of the transmembrane PAP2 type phosphatidylglycerol phosphate phosphatase from Bacillus subtilis. Cell Mol Life Sci 2017; 74:2319-2332. [PMID: 28168443 PMCID: PMC11107685 DOI: 10.1007/s00018-017-2464-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/14/2016] [Accepted: 01/11/2017] [Indexed: 10/20/2022]
Abstract
Type 2 phosphatidic acid phosphatases (PAP2s) can be either soluble or integral membrane enzymes. In bacteria, integral membrane PAP2s play major roles in the metabolisms of glycerophospholipids, undecaprenyl-phosphate (C55-P) lipid carrier and lipopolysaccharides. By in vivo functional experiments and biochemical characterization we show that the membrane PAP2 coded by the Bacillus subtilis yodM gene is the principal phosphatidylglycerol phosphate (PGP) phosphatase of B. subtilis. We also confirm that this enzyme, renamed bsPgpB, has a weaker activity on C55-PP. Moreover, we solved the crystal structure of bsPgpB at 2.25 Å resolution, with tungstate (a phosphate analog) in the active site. The structure reveals two lipid chains in the active site vicinity, allowing for PGP substrate modeling and molecular dynamic simulation. Site-directed mutagenesis confirmed the residues important for substrate specificity, providing a basis for predicting the lipids preferentially dephosphorylated by membrane PAP2s.
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Affiliation(s)
- Meriem El Ghachi
- Centre d'Ingénierie des Protéines, InBioS, Université de Liège, allée du 6 Août 19, Bât B5a, 4000, Liège, Belgium
| | - Nicole Howe
- Membrane Structural and Functional Biology Group, Schools of Medicine and Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Rodolphe Auger
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Alexandre Lambion
- Centre d'Ingénierie des Protéines, InBioS, Université de Liège, allée du 6 Août 19, Bât B5a, 4000, Liège, Belgium
| | - Annick Guiseppi
- Laboratoire de Chimie Bactérienne UMR 7283, Aix-Marseille Université, Marseille, France
| | - François Delbrassine
- Centre d'Ingénierie des Protéines, InBioS, Université de Liège, allée du 6 Août 19, Bât B5a, 4000, Liège, Belgium
| | - Guillaume Manat
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Sophie Roure
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Sabine Peslier
- Laboratoire de Chimie Bactérienne UMR 7283, Aix-Marseille Université, Marseille, France
| | - Eric Sauvage
- Centre d'Ingénierie des Protéines, InBioS, Université de Liège, allée du 6 Août 19, Bât B5a, 4000, Liège, Belgium
| | - Lutz Vogeley
- Membrane Structural and Functional Biology Group, Schools of Medicine and Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Juan-Carlos Rengifo-Gonzalez
- Centre d'Ingénierie des Protéines, InBioS, Université de Liège, allée du 6 Août 19, Bât B5a, 4000, Liège, Belgium
| | - Paulette Charlier
- Centre d'Ingénierie des Protéines, InBioS, Université de Liège, allée du 6 Août 19, Bât B5a, 4000, Liège, Belgium
| | - Dominique Mengin-Lecreulx
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Maryline Foglino
- Laboratoire de Chimie Bactérienne UMR 7283, Aix-Marseille Université, Marseille, France
| | - Thierry Touzé
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
| | - Martin Caffrey
- Membrane Structural and Functional Biology Group, Schools of Medicine and Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland.
| | - Frédéric Kerff
- Centre d'Ingénierie des Protéines, InBioS, Université de Liège, allée du 6 Août 19, Bât B5a, 4000, Liège, Belgium.
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38
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Latino L, Caroff M, Pourcel C. Fine structure analysis of lipopolysaccharides in bacteriophage-resistant Pseudomonas aeruginosa PAO1 mutants. Microbiology (Reading) 2017; 163:848-855. [DOI: 10.1099/mic.0.000476] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Libera Latino
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Martine Caroff
- LPS-BioSciences, Bât 409, I2BC, Université Paris-Sud, 91405 Orsay, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Christine Pourcel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
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Appropriate Regulation of the σ E-Dependent Envelope Stress Response Is Necessary To Maintain Cell Envelope Integrity and Stationary-Phase Survival in Escherichia coli. J Bacteriol 2017; 199:JB.00089-17. [PMID: 28373273 DOI: 10.1128/jb.00089-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/27/2017] [Indexed: 12/18/2022] Open
Abstract
The alternative sigma factor σE is a key component of the Escherichia coli response to cell envelope stress and is required for viability even in the absence of stress. The activity of σE increases during entry into stationary phase, suggesting an important role for σE when nutrients are limiting. Elevated σE activity has been proposed to activate a pathway leading to the lysis of nonculturable cells that accumulate during early stationary phase. To better understand σE-directed cell lysis and the role of σE in stationary phase, we investigated the effects of elevated σE activity in cultures grown for 10 days. We demonstrate that high σE activity is lethal for all cells in stationary phase, not only those that are nonculturable. Spontaneous mutants with reduced σE activity, due primarily to point mutations in the region of σE that binds the -35 promoter motif, arise and take over cultures within 5 to 6 days after entry into stationary phase. High σE activity leads to large reductions in the levels of outer membrane porins and increased membrane permeability, indicating membrane defects. These defects can be counteracted and stationary-phase lethality delayed significantly by stabilizing membranes with Mg2+ and buffering the growth medium or by deleting the σE-dependent small RNAs (sRNAs) MicA, RybB, and MicL, which inhibit the expression of porins and Lpp. Expression of these sRNAs also reverses the loss of viability following depletion of σE activity. Our results demonstrate that appropriate regulation of σE activity, ensuring that it is neither too high nor too low, is critical for envelope integrity and cell viability.IMPORTANCE The Gram-negative cell envelope and cytoplasm differ significantly, and separate responses have evolved to combat stress in each compartment. An array of cell envelope stress responses exist, each of which is focused on different parts of the envelope. The σE response is conserved in many enterobacteria and is tuned to monitor pathways for the maturation and delivery of outer membrane porins, lipoproteins, and lipopolysaccharide to the outer membrane. The activity of σE is tightly regulated to match the production of σE regulon members to the needs of the cell. In E. coli, loss of σE results in lethality. Here we demonstrate that excessive σE activity is also lethal and results in decreased membrane integrity, the very phenotype the system is designed to prevent.
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40
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Kato A, Higashino N, Utsumi R. Fe 3+-dependent epistasis between the CpxR-activated loci and the PmrA-activated LPS modification loci in Salmonella enterica. J GEN APPL MICROBIOL 2017; 62:286-296. [PMID: 27829584 DOI: 10.2323/jgam.2016.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Bacteria utilize varying combinations of two-component regulatory systems, many of which respond and adapt closely to stress conditions, thus expanding their niche steadily. While mechanisms of recognition and avoidance of the specific Fe3+ signal by the PmrA/PmrB system is well understood, those of the CpxR/CpxA system are more complex because they can be induced by various stress conditions, which, in turn, expresses a variety of phenotypes. Here, we highlight another aspect of the CpxR/CpxA system; mutations in degP and yqjA genes, which are under the control of the system, exhibit an iron sensitive phenotype in the mutant background defective in the PmrA-dependent gene products that alter the pyrophosphate status of the lipid A moiety of lipopolysaccharide in Salmonella enterica. Therefore, after the PmrA/PmrB-mediated Fe3+-dependent control of the pyrophosphate status on the cell surface, the CpxR/CpxA system is one of the second layers of envelope stress response that allows adaptation to high Fe3+ conditions in this bacterium.
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Affiliation(s)
- Akinori Kato
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University
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41
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Depletion of Undecaprenyl Pyrophosphate Phosphatases Disrupts Cell Envelope Biogenesis in Bacillus subtilis. J Bacteriol 2016; 198:2925-2935. [PMID: 27528508 DOI: 10.1128/jb.00507-16] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/02/2016] [Indexed: 11/20/2022] Open
Abstract
The integrity of the bacterial cell envelope is essential to sustain life by countering the high turgor pressure of the cell and providing a barrier against chemical insults. In Bacillus subtilis, synthesis of both peptidoglycan and wall teichoic acids requires a common C55 lipid carrier, undecaprenyl-pyrophosphate (UPP), to ferry precursors across the cytoplasmic membrane. The synthesis and recycling of UPP requires a phosphatase to generate the monophosphate form Und-P, which is the substrate for peptidoglycan and wall teichoic acid synthases. Using an optimized clustered regularly interspaced short palindromic repeat (CRISPR) system with catalytically inactive ("dead") CRISPR-associated protein 9 (dCas9)-based transcriptional repression system (CRISPR interference [CRISPRi]), we demonstrate that B. subtilis requires either of two UPP phosphatases, UppP or BcrC, for viability. We show that a third predicted lipid phosphatase (YodM), with homology to diacylglycerol pyrophosphatases, can also support growth when overexpressed. Depletion of UPP phosphatase activity leads to morphological defects consistent with a failure of cell envelope synthesis and strongly activates the σM-dependent cell envelope stress response, including bcrC, which encodes one of the two UPP phosphatases. These results highlight the utility of an optimized CRISPRi system for the investigation of synthetic lethal gene pairs, clarify the nature of the B. subtilis UPP-Pase enzymes, and provide further evidence linking the σM regulon to cell envelope homeostasis pathways. IMPORTANCE The emergence of antibiotic resistance among bacterial pathogens is of critical concern and motivates efforts to develop new therapeutics and increase the utility of those already in use. The lipid II cycle is one of the most frequently targeted processes for antibiotics and has been intensively studied. Despite these efforts, some steps have remained poorly defined, partly due to genetic redundancy. CRISPRi provides a powerful tool to investigate the functions of essential genes and sets of genes. Here, we used an optimized CRISPRi system to demonstrate functional redundancy of two UPP phosphatases that are required for the conversion of the initially synthesized UPP lipid carrier to Und-P, the substrate for the synthesis of the initial lipid-linked precursors in peptidoglycan and wall teichoic acid synthesis.
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42
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Trimble MJ, Mlynárčik P, Kolář M, Hancock REW. Polymyxin: Alternative Mechanisms of Action and Resistance. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a025288. [PMID: 27503996 DOI: 10.1101/cshperspect.a025288] [Citation(s) in RCA: 243] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Antibiotic resistance among pathogenic bacteria is an ever-increasing issue worldwide. Unfortunately, very little has been achieved in the pharmaceutical industry to combat this problem. This has led researchers and the medical field to revisit past drugs that were deemed too toxic for clinical use. In particular, the cyclic cationic peptides polymyxin B and colistin, which are specific for Gram-negative bacteria, have been used as "last resort" antimicrobials. Before the 1980s, these drugs were known for their renal and neural toxicities; however, new clinical practices and possibly improved manufacturing have made them safer to use. Previously suggested to primarily attack the membranes of Gram-negative bacteria and to not easily select for resistant mutants, recent research exploring resistance and mechanisms of action has provided new perspectives. This review focuses primarily on the proposed alternative mechanisms of action, known resistance mechanisms, and how these support the alternative mechanisms of action.
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Affiliation(s)
- Michael J Trimble
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Patrik Mlynárčik
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacký University, 771 47 Olomouc, Czech Republic
| | - Milan Kolář
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacký University, 771 47 Olomouc, Czech Republic
| | - Robert E W Hancock
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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43
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Joo HS, Fu CI, Otto M. Bacterial strategies of resistance to antimicrobial peptides. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150292. [PMID: 27160595 PMCID: PMC4874390 DOI: 10.1098/rstb.2015.0292] [Citation(s) in RCA: 205] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2016] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial peptides (AMPs) are a key component of the host's innate immune system, targeting invasive and colonizing bacteria. For successful survival and colonization of the host, bacteria have a series of mechanisms to interfere with AMP activity, and AMP resistance is intimately connected with the virulence potential of bacterial pathogens. In particular, because AMPs are considered as potential novel antimicrobial drugs, it is vital to understand bacterial AMP resistance mechanisms. This review gives a comparative overview of Gram-positive and Gram-negative bacterial strategies of resistance to various AMPs, such as repulsion or sequestration by bacterial surface structures, alteration of membrane charge or fluidity, degradation and removal by efflux pumps.This article is part of the themed issue 'Evolutionary ecology of arthropod antimicrobial peptides'.
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Affiliation(s)
- Hwang-Soo Joo
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases (NIAID), US National Institutes of Health (NIH), 50 South Drive, Bethesda, MD 20892, USA
| | - Chih-Iung Fu
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases (NIAID), US National Institutes of Health (NIH), 50 South Drive, Bethesda, MD 20892, USA
| | - Michael Otto
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases (NIAID), US National Institutes of Health (NIH), 50 South Drive, Bethesda, MD 20892, USA
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44
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Joo HS, Fu CI, Otto M. Bacterial strategies of resistance to antimicrobial peptides. Philos Trans R Soc Lond B Biol Sci 2016. [PMID: 27160595 DOI: 10.1098/rstb.2015.0292.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Antimicrobial peptides (AMPs) are a key component of the host's innate immune system, targeting invasive and colonizing bacteria. For successful survival and colonization of the host, bacteria have a series of mechanisms to interfere with AMP activity, and AMP resistance is intimately connected with the virulence potential of bacterial pathogens. In particular, because AMPs are considered as potential novel antimicrobial drugs, it is vital to understand bacterial AMP resistance mechanisms. This review gives a comparative overview of Gram-positive and Gram-negative bacterial strategies of resistance to various AMPs, such as repulsion or sequestration by bacterial surface structures, alteration of membrane charge or fluidity, degradation and removal by efflux pumps.This article is part of the themed issue 'Evolutionary ecology of arthropod antimicrobial peptides'.
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Affiliation(s)
- Hwang-Soo Joo
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases (NIAID), US National Institutes of Health (NIH), 50 South Drive, Bethesda, MD 20892, USA
| | - Chih-Iung Fu
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases (NIAID), US National Institutes of Health (NIH), 50 South Drive, Bethesda, MD 20892, USA
| | - Michael Otto
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases (NIAID), US National Institutes of Health (NIH), 50 South Drive, Bethesda, MD 20892, USA
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45
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Dwivedi R, Nothaft H, Reiz B, Whittal RM, Szymanski CM. Generation of free oligosaccharides from bacterial protein N-linked glycosylation systems. Biopolymers 2016; 99:772-83. [PMID: 23749285 DOI: 10.1002/bip.22296] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 05/28/2013] [Indexed: 11/10/2022]
Abstract
All Campylobacter species are capable of N-glycosylating their proteins and releasing the same oligosaccharides into the periplasm as free oligosaccharides (fOS). Previously, analysis of fOS production in Campylobacter required fOS derivatization or large culture volumes and several chromatography steps prior to fOS analysis. In this study, label-free fOS extraction and purification methods were developed and coupled with quantitative analysis techniques. Our method follows three simple steps: (1) fOS extraction from the periplasmic space, (2) fOS purification using silica gel chromatography followed by porous graphitized carbon purification and (3) fOS analysis and accurate quantitation using a combination of thin-layer chromatography, mass spectrometry, NMR, and high performance anion exchange chromatography with pulsed amperometric detection. We applied our techniques to analyze fOS from C. jejuni, C. lari, C. rectus, and C. fetus fetus that produce different fOS structures. We accurately quantified fOS in Campylobacter species that ranged from 7.80 (±0.84) to 49.82 (±0.46) nmoles per gram of wet cell pellet and determined that the C. jejuni fOS comprises 2.5% of the dry cell weight. In addition, a novel di-phosphorylated fOS species was identified in C. lari. This method provides a sensitive and quantitative method to investigate the genesis, biology and breakdown of fOS in the bacterial N-glycosylation systems.
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Affiliation(s)
- Ritika Dwivedi
- Alberta Glycomics Center and Department of Biological Sciences, University of Alberta, Canada
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46
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Affiliation(s)
- Fengzhi Li
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071 China.,College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Siwei Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Xiaofen Liu
- College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Xue Yang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071 China
| | - Peng Wang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071 China
| | - Yuequan Shen
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071 China.,College of Life Sciences, Nankai University, Tianjin, 300071 China.,Synergetic Innovation Center of Chemical Science and Engineering, Tianjin, 300071 China
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47
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Manat G, El Ghachi M, Auger R, Baouche K, Olatunji S, Kerff F, Touzé T, Mengin-Lecreulx D, Bouhss A. Membrane Topology and Biochemical Characterization of the Escherichia coli BacA Undecaprenyl-Pyrophosphate Phosphatase. PLoS One 2015; 10:e0142870. [PMID: 26560897 PMCID: PMC4641660 DOI: 10.1371/journal.pone.0142870] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 10/27/2015] [Indexed: 11/18/2022] Open
Abstract
Several integral membrane proteins exhibiting undecaprenyl-pyrophosphate (C55-PP) phosphatase activity were previously identified in Escherichia coli that belonged to two distinct protein families: the BacA protein, which accounts for 75% of the C55-PP phosphatase activity detected in E. coli cell membranes, and three members of the PAP2 phosphatidic acid phosphatase family, namely PgpB, YbjG and LpxT. This dephosphorylation step is required to provide the C55-P carrier lipid which plays a central role in the biosynthesis of various cell wall polymers. We here report detailed investigations of the biochemical properties and membrane topology of the BacA protein. Optimal activity conditions were determined and a narrow-range substrate specificity with a clear preference for C55-PP was observed for this enzyme. Alignments of BacA protein sequences revealed two particularly well-conserved regions and several invariant residues whose role in enzyme activity was questioned by using a site-directed mutagenesis approach and complementary in vitro and in vivo activity assays. Three essential residues Glu21, Ser27, and Arg174 were identified, allowing us to propose a catalytic mechanism for this enzyme. The membrane topology of the BacA protein determined here experimentally did not validate previous program-based predicted models. It comprises seven transmembrane segments and contains in particular two large periplasmic loops carrying the highly-conserved active site residues. Our data thus provide evidence that all the different E. coli C55-PP phosphatases identified to date (BacA and PAP2) catalyze the dephosphorylation of C55-PP molecules on the same (outer) side of the plasma membrane.
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Affiliation(s)
- Guillaume Manat
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198, CEA, CNRS, Université Paris Sud, Bâtiment 430, F-91400, Orsay, France
| | - Meriem El Ghachi
- Centre d'Ingénierie des Protéines, Université de Liège, Institut de Physique B5a et Institut de Chimie B6a, Sart-Tilman, B-4000, Liège, Belgium
| | - Rodolphe Auger
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198, CEA, CNRS, Université Paris Sud, Bâtiment 430, F-91400, Orsay, France
| | - Karima Baouche
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198, CEA, CNRS, Université Paris Sud, Bâtiment 430, F-91400, Orsay, France
| | - Samir Olatunji
- Centre d'Ingénierie des Protéines, Université de Liège, Institut de Physique B5a et Institut de Chimie B6a, Sart-Tilman, B-4000, Liège, Belgium
| | - Frédéric Kerff
- Centre d'Ingénierie des Protéines, Université de Liège, Institut de Physique B5a et Institut de Chimie B6a, Sart-Tilman, B-4000, Liège, Belgium
| | - Thierry Touzé
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198, CEA, CNRS, Université Paris Sud, Bâtiment 430, F-91400, Orsay, France
| | - Dominique Mengin-Lecreulx
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198, CEA, CNRS, Université Paris Sud, Bâtiment 430, F-91400, Orsay, France
| | - Ahmed Bouhss
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198, CEA, CNRS, Université Paris Sud, Bâtiment 430, F-91400, Orsay, France
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Teo ACK, Roper DI. Core Steps of Membrane-Bound Peptidoglycan Biosynthesis: Recent Advances, Insight and Opportunities. Antibiotics (Basel) 2015; 4:495-520. [PMID: 27025638 PMCID: PMC4790310 DOI: 10.3390/antibiotics4040495] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/03/2015] [Accepted: 10/26/2015] [Indexed: 11/16/2022] Open
Abstract
We are entering an era where the efficacy of current antibiotics is declining, due to the development and widespread dispersion of antibiotic resistance mechanisms. These factors highlight the need for novel antimicrobial discovery. A large number of antimicrobial natural products elicit their effect by directly targeting discrete areas of peptidoglycan metabolism. Many such natural products bind directly to the essential cell wall precursor Lipid II and its metabolites, i.e., preventing the utlisation of vital substrates by direct binding rather than inhibiting the metabolising enzymes themselves. Concurrently, there has been an increase in the knowledge surrounding the proteins essential to the metabolism of Lipid II at and across the cytoplasmic membrane. In this review, we draw these elements together and look to future antimicrobial opportunities in this area.
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Affiliation(s)
- Alvin C K Teo
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
| | - David I Roper
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
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Mamat U, Wilke K, Bramhill D, Schromm AB, Lindner B, Kohl TA, Corchero JL, Villaverde A, Schaffer L, Head SR, Souvignier C, Meredith TC, Woodard RW. Detoxifying Escherichia coli for endotoxin-free production of recombinant proteins. Microb Cell Fact 2015; 14:57. [PMID: 25890161 PMCID: PMC4404585 DOI: 10.1186/s12934-015-0241-5] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 04/07/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lipopolysaccharide (LPS), also referred to as endotoxin, is the major constituent of the outer leaflet of the outer membrane of virtually all Gram-negative bacteria. The lipid A moiety, which anchors the LPS molecule to the outer membrane, acts as a potent agonist for Toll-like receptor 4/myeloid differentiation factor 2-mediated pro-inflammatory activity in mammals and, thus, represents the endotoxic principle of LPS. Recombinant proteins, commonly manufactured in Escherichia coli, are generally contaminated with endotoxin. Removal of bacterial endotoxin from recombinant therapeutic proteins is a challenging and expensive process that has been necessary to ensure the safety of the final product. RESULTS As an alternative strategy for common endotoxin removal methods, we have developed a series of E. coli strains that are able to grow and express recombinant proteins with the endotoxin precursor lipid IVA as the only LPS-related molecule in their outer membranes. Lipid IVA does not trigger an endotoxic response in humans typical of bacterial LPS chemotypes. Hence the engineered cells themselves, and the purified proteins expressed within these cells display extremely low endotoxin levels. CONCLUSIONS This paper describes the preparation and characterization of endotoxin-free E. coli strains, and demonstrates the direct production of recombinant proteins with negligible endotoxin contamination.
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Affiliation(s)
- Uwe Mamat
- Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 1-40, D-23845, Borstel, Germany.
| | - Kathleen Wilke
- Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 1-40, D-23845, Borstel, Germany.
| | - David Bramhill
- Research Corporation Technologies, Inc, 5210 East Williams Circle, Suite 240, Tucson, AZ, 85711-4410, USA. .,Present address: Bramhill Biological Consulting, LLC, 8240 East Moonstone Drive, Tucson, AZ, 85750, USA.
| | - Andra Beate Schromm
- Division of Immunobiophysics, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 1-40, D-23845, Borstel, Germany.
| | - Buko Lindner
- Division of Bioanalytical Chemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 1-40, D-23845, Borstel, Germany.
| | - Thomas Andreas Kohl
- Division of Molecular Mycobacteriology, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 1-40, D-23845, Borstel, Germany.
| | - José Luis Corchero
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Bellaterra, 08193, Cerdanyola del Vallès, Spain. .,Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Cerdanyola del Vallès, Spain. .,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193, Cerdanyola del Vallès, Spain.
| | - Antonio Villaverde
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Bellaterra, 08193, Cerdanyola del Vallès, Spain. .,Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Cerdanyola del Vallès, Spain. .,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193, Cerdanyola del Vallès, Spain.
| | - Lana Schaffer
- NGS and Microarray Core Facility, The Scripps Research Institute, 10550 North, Pines Road, La Jolla, Torrey, CA, 92037, USA.
| | - Steven Robert Head
- NGS and Microarray Core Facility, The Scripps Research Institute, 10550 North, Pines Road, La Jolla, Torrey, CA, 92037, USA.
| | - Chad Souvignier
- Research Corporation Technologies, Inc, 5210 East Williams Circle, Suite 240, Tucson, AZ, 85711-4410, USA.
| | - Timothy Charles Meredith
- Department of Biochemistry and Molecular Biology, 206 South Frear, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Ronald Wesley Woodard
- Department of Medicinal Chemistry, University of Michigan, 428 Church Street, Ann Arbor, MI, 48109-1065, USA.
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50
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PmrD is required for modifications to escherichia coli endotoxin that promote antimicrobial resistance. Antimicrob Agents Chemother 2015; 59:2051-61. [PMID: 25605366 DOI: 10.1128/aac.05052-14] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In Salmonella enterica, PmrD is a connector protein that links the two-component systems PhoP-PhoQ and PmrA-PmrB. While Escherichia coli encodes a PmrD homolog, it is thought to be incapable of connecting PhoPQ and PmrAB in this organism due to functional divergence from the S. enterica protein. However, our laboratory previously observed that low concentrations of Mg(2+), a PhoPQ-activating signal, leads to the induction of PmrAB-dependent lipid A modifications in wild-type E. coli (C. M. Herrera, J. V. Hankins, and M. S. Trent, Mol Microbiol 76:1444-1460, 2010, http://dx.doi.org/10.1111/j.1365-2958.2010.07150.x). These modifications include phosphoethanolamine (pEtN) and 4-amino-4-deoxy-l-arabinose (l-Ara4N), which promote bacterial resistance to cationic antimicrobial peptides (CAMPs) when affixed to lipid A. Here, we demonstrate that pmrD is required for modification of the lipid A domain of E. coli lipopolysaccharide (LPS) under low-Mg(2+) growth conditions. Further, RNA sequencing shows that E. coli pmrD influences the expression of pmrA and its downstream targets, including genes coding for the modification enzymes that transfer pEtN and l-Ara4N to the lipid A molecule. In line with these findings, a pmrD mutant is dramatically impaired in survival compared with the wild-type strain when exposed to the CAMP polymyxin B. Notably, we also reveal the presence of an unknown factor or system capable of activating pmrD to promote lipid A modification in the absence of the PhoPQ system. These results illuminate a more complex network of protein interactions surrounding activation of PhoPQ and PmrAB in E. coli than previously understood.
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