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Zhang H, Yang Z, Liu J. Genetic Analysis of the Plasmid-Based Temperature-Lethal Mutant pa1792|lpxH(Ts) in Pseudomonas aeruginosa. Genes (Basel) 2024; 15:784. [PMID: 38927720 PMCID: PMC11202943 DOI: 10.3390/genes15060784] [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: 05/23/2024] [Revised: 06/08/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Many enzymes in the Raetz pathway for lipid A biosynthesis in Escherichia coli are essential. A homologous protein Pa1792|LpxH in Pseudomonas aeruginosa is known to complement the loss of LpxH in E. coli. Genome-wide transposon-insertion sequencing analysis indicates that lpxH is essential in P. aeruginosa. However, genetic analysis of lpxH in P. aeruginosa has not been carried out, partly because the conditional alleles of essential genes are not readily constructed. In this study, we first constructed a plasmid-based temperature-sensitive mutant ΔlpxH/pTS-lpxH or lpxH(Ts) in P. aeruginosa PAO1. Spot-plating assay indicated that lpxH(Ts) was lethal at a restrictive temperature, confirming its essentiality for growth. Microscopic analysis revealed that lpxH(Ts) exhibited an oval-shaped morphology, suggesting that lpxH was required for rod-shape formation. SDS-PAGE and Western blotting analysis showed that lpxH(Ts) failed to synthesize lipid A, consistent with its function in lipid A biosynthesis. Strong expression of lpxH but not the non-homologous isoenzyme lpxI or lpxG impeded growth and caused cell lysis, implying that lpxH-specific cofactors were required for this toxic effect in P. aeruginosa. Together, our results demonstrate that lpxH is essential for lipid A biosynthesis, rod-shaped growth, and viability in P. aeruginosa. We propose that this plasmid-based conditional allele is a useful tool for the genetic study of essential genes in P. aeruginosa.
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Affiliation(s)
| | | | - Jianhua Liu
- Systems Biology, School for Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (H.Z.); (Z.Y.)
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2
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Cronan JE. Unsaturated fatty acid synthesis in bacteria: Mechanisms and regulation of canonical and remarkably noncanonical pathways. Biochimie 2024; 218:137-151. [PMID: 37683993 PMCID: PMC10915108 DOI: 10.1016/j.biochi.2023.09.007] [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: 06/19/2023] [Revised: 08/02/2023] [Accepted: 09/04/2023] [Indexed: 09/10/2023]
Abstract
Unsaturated phospholipid acyl chains are required for membrane function in most bacteria. The double bonds of the cis monoenoic chains arise by two distinct pathways depending on whether oxygen is required. The oxygen-independent pathway (traditionally called the anaerobic pathway) introduces the cis double bond by isomerization of the trans double bond intermediate of the fatty acid elongation cycle. Double bond isomerization occurs at an intermediate chain length (e.g., C10) and the isomerization product is elongated to the C16-C18 chains that become phospholipid monoenoic acyl chains. This pathway was first delineated in Escherichia coli and became the paradigm pathway. However, studies of other bacteria show deviations from this paradigm, the most exceptional being reversal of the fatty acid elongation cycle by a reaction paralleling the initial step in the β-oxidative degradation of fatty acids. In the oxygen-dependent pathway diiron enzymes called desaturases introduce a double bond into a saturated acyl chain by regioselective cis dehydrogenation through activation of molecular oxygen with an active-site diiron cluster. This difficult hydrogen abstraction from a methylene group often occurs at the midpoint of a saturated fatty acyl chain. In bacteria the acyl chain is a phospholipid acyl chain, and the desaturase is membrane bound. Both the oxygen-independent oxygen-dependent pathways are transcriptionally regulated by repressor and activator proteins that respond to small molecule ligands such as acyl-CoAs. However, in Bacillus subtilis the desaturase is synthesized only at low growth temperatures, a process controlled by a signal transduction regulatory pathway dependent on membrane lipid properties.
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Affiliation(s)
- John E Cronan
- Departments of Microbiology and Biochemistry, University of Illinois, Urbana, 61801, USA.
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3
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Gupta R, Singh M, Pathania R. Chemical genetic approaches for the discovery of bacterial cell wall inhibitors. RSC Med Chem 2023; 14:2125-2154. [PMID: 37974958 PMCID: PMC10650376 DOI: 10.1039/d3md00143a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/10/2023] [Indexed: 11/19/2023] Open
Abstract
Antimicrobial resistance (AMR) in bacterial pathogens is a worldwide health issue. The innovation gap in discovering new antibiotics has remained a significant hurdle in combating the AMR problem. Currently, antibiotics target various vital components of the bacterial cell envelope, nucleic acid and protein biosynthesis machinery and metabolic pathways essential for bacterial survival. The critical role of the bacterial cell envelope in cell morphogenesis and integrity makes it an attractive drug target. While a significant number of in-clinic antibiotics target peptidoglycan biosynthesis, several components of the bacterial cell envelope have been overlooked. This review focuses on various antibacterial targets in the bacterial cell wall and the strategies employed to find their novel inhibitors. This review will further elaborate on combining forward and reverse chemical genetic approaches to discover antibacterials that target the bacterial cell envelope.
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Affiliation(s)
- Rinki Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Mangal Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Ranjana Pathania
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
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4
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Maniyeri A, Wieczorek A, Ayyolath A, Sugalska W, Klein G, Raina S. Suppressors of lapC Mutation Identify New Regulators of LpxC, Which Mediates the First Committed Step in Lipopolysaccharide Biosynthesis. Int J Mol Sci 2023; 24:15174. [PMID: 37894855 PMCID: PMC10607373 DOI: 10.3390/ijms242015174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Gram-negative bacteria, such as Escherichia coli, are characterized by an asymmetric outer membrane (OM) with lipopolysaccharide (LPS) located in the outer leaflet and phospholipids facing the inner leaflet. E. coli recruits LPS assembly proteins LapB, LapC and LapD in concert with FtsH protease to ensure a balanced biosynthesis of LPS and phospholipids. We recently reported that bacteria either lacking the periplasmic domain of the essential LapC protein (lapC190) or in the absence of LapD exhibit an elevated degradation of LpxC, which catalyzes the first committed step in LPS biosynthesis. To further understand the functions of LapC and LapD in regulating LPS biosynthesis, we show that the overproduction of the intact LapD suppresses the temperature sensitivity (Ts) of lapC190, but not when either its N-terminal transmembrane anchor or specific conserved amino acids in the C-terminal domain are mutated. Moreover, overexpression of srrA, marA, yceJ and yfgM genes can rescue the Ts phenotype of lapC190 bacteria by restoring LpxC amounts. We further show that MarA-mediated suppression requires the expression of mla genes, whose products participate in the maintenance of OM asymmetry, and the SrrA-mediated suppression requires the presence of cardiolipin synthase A.
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Affiliation(s)
| | | | | | | | - Gracjana Klein
- Laboratory of Bacterial Genetics, Gdansk University of Technology, 80-233 Gdansk, Poland; (A.M.); (A.W.); (A.A.); (W.S.)
| | - Satish Raina
- Laboratory of Bacterial Genetics, Gdansk University of Technology, 80-233 Gdansk, Poland; (A.M.); (A.W.); (A.A.); (W.S.)
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5
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Tian L, Yang Z, Wang J, Liu J. Analysis of the Plasmid-Based ts-Mutant Δ fabA/pTS-fabA Reveals Its Lethality under Aerobic Growth Conditions That Is Suppressed by Mild Overexpression of desA at a Restrictive Temperature in Pseudomonas aeruginosa. Microbiol Spectr 2023; 11:e0133823. [PMID: 37191499 PMCID: PMC10269440 DOI: 10.1128/spectrum.01338-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 04/29/2023] [Indexed: 05/17/2023] Open
Abstract
It is uncertain whether PA1610|fabA is essential or dispensable for growth on LB-agar plates under aerobic conditions in Pseudomonas aeruginosa PAO1. To examine its essentiality, we disrupted fabA in the presence of a native promoter-controlled complementary copy on ts-plasmid. In this analysis, we showed that the plasmid-based ts-mutant ΔfabA/pTS-fabA failed to grow at a restrictive temperature, consistent with the observation by Hoang and Schweizer (T. T. Hoang, H. P. Schweizer, J Bacteriol 179:5326-5332, 1997, https://doi.org/10.1128/jb.179.17.5326-5332.1997), and expanded on this by showing that ΔfabA exhibited curved cell morphology. On the other hand, strong induction of fabA-OE or PA3645|fabZ-OE impeded the growth of cells displaying oval morphology. Suppressor analysis revealed a mutant sup gene that suppressed a growth defect but not cell morphology of ΔfabA. Genome resequencing and transcriptomic profiling of sup identified PA0286|desA, whose promoter carried a single-nucleotide polymorphism (SNP), and transcription was significantly upregulated (level increase of >2-fold, P < 0.05). By integration of the SNP-bearing promoter-controlled desA gene into the chromosome of ΔfabA/pTS-fabA, we showed that the SNP is sufficient for ΔfabA to phenocopy the sup mutant. Furthermore, mild induction of the araC-PBAD-controlled desA gene but not desB rescued ΔfabA. These results validated that mild overexpression of desA fully suppressed the lethality but not the curved cell morphology of ΔfabA. Similarly, Zhu et al. (Zhu K, Choi K-H, Schweizer HP, Rock CO, Zhang Y-M, Mol Microbiol 60:260-273, 2006, https://doi.org/10.1111/j.1365-2958.2006.05088.x) showed that multicopy desA partially alleviated the slow growth phenotype of ΔfabA, the difference in which was that ΔfabA was viable. Taken together, our results demonstrate that fabA is essential for aerobic growth. We propose that the plasmid-based ts-allele is useful for exploring the genetic suppression interaction of essential genes of interest in P. aeruginosa. IMPORTANCE Pseudomonas aeruginosa is an opportunistic pathogen whose multidrug resistance demands new drug development. Fatty acids are essential for viability, and essential genes are ideal drug targets. However, the growth defect of essential gene mutants can be suppressed. Suppressors tend to be accumulated during the construction of essential gene deletion mutants, hampering the genetic analysis. To circumvent this issue, we constructed a deletion allele of fabA in the presence of a native promoter-controlled complementary copy in the ts-plasmid. In this analysis, we showed that ΔfabA/pTS-fabA failed to grow at a restrictive temperature, supporting its essentiality. Suppressor analysis revealed desA, whose promoter carried a SNP and whose transcription was upregulated. We validated that both the SNP-bearing promoter-controlled and regulable PBAD promoter-controlled desA suppressed the lethality of ΔfabA. Together, our results demonstrate that fabA is essential for aerobic growth. We propose that plasmid-based ts-alleles are suitable for genetic analysis of essential genes of interest.
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Affiliation(s)
- Liyan Tian
- Systems Biology, School of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Zhili Yang
- Systems Biology, School of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Jianxin Wang
- Systems Biology, School of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Jianhua Liu
- Systems Biology, School of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, Zhejiang, China
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6
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Raina S. Lipopolysaccharides: Regulated Biosynthesis and Structural Diversity. Int J Mol Sci 2023; 24:7498. [PMID: 37108660 PMCID: PMC10145120 DOI: 10.3390/ijms24087498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The cell envelope of Gram-negative bacteria contains two distinct membranes, an inner (IM) and an outer (OM) membrane, separated by the periplasm, a hydrophilic compartment that includes a thin layer of peptidoglycan [...].
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Affiliation(s)
- Satish Raina
- Laboratory of Bacterial Genetics, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland
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7
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Dietl A, Wellach K, Mahadevan P, Mertes N, Winter S, Kutsch T, Walz C, Schlichting I, Fabritz S, Barends TM. Structures of an unusual 3-hydroxyacyl dehydratase (FabZ) from a ladderane-producing organism with an unexpected substrate preference. J Biol Chem 2023; 299:104602. [PMID: 36907440 PMCID: PMC10139942 DOI: 10.1016/j.jbc.2023.104602] [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: 05/23/2022] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
The genomes of anaerobic ammonium-oxidizing (anammox) bacteria contain a gene cluster comprising genes of unusual fatty acid biosynthesis enzymes that were suggested to be involved in the synthesis of the unique "ladderane" lipids produced by these organisms. This cluster encodes an acyl carrier protein (denoted as "amxACP") and a variant of FabZ, an ACP-3-hydroxyacyl dehydratase. In this study, we characterize this enzyme, which we call anammox-specific FabZ ("amxFabZ"), to investigate the unresolved biosynthetic pathway of ladderane lipids. We find that amxFabZ displays distinct sequence differences to "canonical" FabZ, such as a bulky, apolar residue on the inside of the substrate binding tunnel, where the canonical enzyme has a glycine. Additionally, substrate screens suggest that amxFabZ efficiently converts substrates with acyl chain lengths of up to eight carbons, whereas longer substrates are converted much more slowly under the conditions used. We also present crystal structures of amxFabZs, mutational studies and the structure of a complex between amxFabZ and amxACP, which show that the structures alone cannot explain the apparent differences from canonical FabZ. Moreover, we find that while amxFabZ does dehydrate substrates bound to amxACP, it does not convert substrates bound to canonical ACP of the same anammox organism. We discuss the possible functional relevance of these observations in the light of proposals for the mechanism for ladderane biosynthesis.
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Affiliation(s)
- Andreas Dietl
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany.
| | - Kathrin Wellach
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Pavithra Mahadevan
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Nicole Mertes
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - SophieL Winter
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Tobias Kutsch
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Carlo Walz
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Sebastian Fabritz
- Mass Spectrometry Core Facility, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - ThomasR M Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany.
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8
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Hummels KR, Berry SP, Li Z, Taguchi A, Min JK, Walker S, Marks DS, Bernhardt TG. Coordination of bacterial cell wall and outer membrane biosynthesis. Nature 2023; 615:300-304. [PMID: 36859542 PMCID: PMC9995270 DOI: 10.1038/s41586-023-05750-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 01/23/2023] [Indexed: 03/03/2023]
Abstract
Gram-negative bacteria surround their cytoplasmic membrane with a peptidoglycan (PG) cell wall and an outer membrane (OM) with an outer leaflet composed of lipopolysaccharide (LPS)1. This complex envelope presents a formidable barrier to drug entry and is a major determinant of the intrinsic antibiotic resistance of these organisms2. The biogenesis pathways that build the surface are also targets of many of our most effective antibacterial therapies3. Understanding the molecular mechanisms underlying the assembly of the Gram-negative envelope therefore promises to aid the development of new treatments effective against the growing problem of drug-resistant infections. Although the individual pathways for PG and OM synthesis and assembly are well characterized, almost nothing is known about how the biogenesis of these essential surface layers is coordinated. Here we report the discovery of a regulatory interaction between the committed enzymes for the PG and LPS synthesis pathways in the Gram-negative pathogen Pseudomonas aeruginosa. We show that the PG synthesis enzyme MurA interacts directly and specifically with the LPS synthesis enzyme LpxC. Moreover, MurA was shown to stimulate LpxC activity in cells and in a purified system. Our results support a model in which the assembly of the PG and OM layers in many proteobacterial species is coordinated by linking the activities of the committed enzymes in their respective synthesis pathways.
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Affiliation(s)
- Katherine R Hummels
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Samuel P Berry
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Zhaoqi Li
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Atsushi Taguchi
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Japan
| | - Joseph K Min
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Suzanne Walker
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Debora S Marks
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Thomas G Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
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9
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McNaught KJ, Kuatsjah E, Zahn M, Prates ÉT, Shao H, Bentley GJ, Pickford AR, Gruber JN, Hestmark KV, Jacobson DA, Poirier BC, Ling C, San Marchi M, Michener WE, Nicora CD, Sanders JN, Szostkiewicz CJ, Veličković D, Zhou M, Munoz N, Kim YM, Magnuson JK, Burnum-Johnson KE, Houk KN, McGeehan JE, Johnson CW, Beckham GT. Initiation of fatty acid biosynthesis in Pseudomonas putida KT2440. Metab Eng 2023; 76:193-203. [PMID: 36796578 DOI: 10.1016/j.ymben.2023.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023]
Abstract
Deciphering the mechanisms of bacterial fatty acid biosynthesis is crucial for both the engineering of bacterial hosts to produce fatty acid-derived molecules and the development of new antibiotics. However, gaps in our understanding of the initiation of fatty acid biosynthesis remain. Here, we demonstrate that the industrially relevant microbe Pseudomonas putida KT2440 contains three distinct pathways to initiate fatty acid biosynthesis. The first two routes employ conventional β-ketoacyl-ACP synthase III enzymes, FabH1 and FabH2, that accept short- and medium-chain-length acyl-CoAs, respectively. The third route utilizes a malonyl-ACP decarboxylase enzyme, MadB. A combination of exhaustive in vivo alanine-scanning mutagenesis, in vitro biochemical characterization, X-ray crystallography, and computational modeling elucidate the presumptive mechanism of malonyl-ACP decarboxylation via MadB. Given that functional homologs of MadB are widespread throughout domain Bacteria, this ubiquitous alternative fatty acid initiation pathway provides new opportunities to target a range of biotechnology and biomedical applications.
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Affiliation(s)
- Kevin J McNaught
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Eugene Kuatsjah
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Michael Zahn
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Érica T Prates
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Huiling Shao
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA, 90095, USA
| | - Gayle J Bentley
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Andrew R Pickford
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Josephine N Gruber
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Kelley V Hestmark
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Daniel A Jacobson
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Brenton C Poirier
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Chen Ling
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Myrsini San Marchi
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA, 90095, USA
| | - William E Michener
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Jacob N Sanders
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA, 90095, USA
| | - Caralyn J Szostkiewicz
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Dušan Veličković
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Nathalie Munoz
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA; Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Young-Mo Kim
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Jon K Magnuson
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Kristin E Burnum-Johnson
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA; Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA, 90095, USA
| | - John E McGeehan
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Christopher W Johnson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.
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10
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Hou A, Dickschat JS. Labelling studies in the biosynthesis of polyketides and non-ribosomal peptides. Nat Prod Rep 2023; 40:470-499. [PMID: 36484402 DOI: 10.1039/d2np00071g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: 2015 to 2022In this review, we discuss the recent advances in the use of isotopically labelled compounds to investigate the biosynthesis of polyketides, non-ribosomally synthesised peptides, and their hybrids. Also, we highlight the use of isotopes in the elucidation of their structures and investigation of enzyme mechanisms. The biosynthetic pathways of selected examples are presented in detail to reveal the principles of the discussed labelling experiments. The presented examples demonstrate that the application of isotopically labelled compounds is still the state of the art and can provide valuable information for the biosynthesis of natural products.
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Affiliation(s)
- Anwei Hou
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, West 7th Avenue No. 32, 300308 Tianjin, China.,Institute of Microbiology, Jiangxi Academy of Sciences, Changdong Road No. 7777, 330096 Nanchang, China
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.
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11
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Long X, Wang X, Mao D, Wu W, Luo Y. A Novel XRE-Type Regulator Mediates Phage Lytic Development and Multiple Host Metabolic Processes in Pseudomonas aeruginosa. Microbiol Spectr 2022; 10:e0351122. [PMID: 36445133 PMCID: PMC9769523 DOI: 10.1128/spectrum.03511-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/28/2022] [Indexed: 12/02/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen, the leading cause of acute and chronic infections in immunocompromised patients, frequently with high morbidity and mortality rates. The xenobiotic response element (XRE) family proteins are the second most common transcriptional regulators (TRs) in P. aeruginosa. However, only a few XRE-like TRs have been reported to regulate multiple bacterial cellular processes, encompassing virulence, metabolism, antibiotic synthesis or resistance, stress responses, and phage infection, etc. Our understanding of what roles these XRE-like small regulatory proteins play in P. aeruginosa remains limited. Here, we aimed to decipher the role of a putative XRE-type transcriptional regulator (designated LfsT) from a prophage region on the chromosome of a clinical P. aeruginosa isolate, P8W. Southern blot and reverse transcription quantitative PCR (RT-qPCR) assays demonstrated that LfsT controlled host sensitivity to the phage PP9W2 and was essential for efficient phage replication. In addition, electrophoretic mobility shift assays (EMSAs) and transcriptional lacZ fusion analyses indicated that LfsT repressed the lysogenic development and promoted the lytic cycle of phage PP9W2 by binding to the promoter regions of the gp71 gene (encoding a CI-like repressor) and several vital phage genes. Combined with RNA-seq and a series of phenotypic validation tests, our results showed that LfsT bound to the flexible palindromic sites within the promoters upstream of several genes in the bacterial genome, regulating fatty acid (FA) metabolism, spermidine (SPD) transport, as well as the type III secretion system (T3SS). Overall, this study reveals novel regulatory roles of LfsT in P. aeruginosa, improving our understanding of the molecular mechanisms behind bacterium-phage interactions. IMPORTANCE This work elucidates the novel roles of a putative XRE family TR, LfsT, in the intricate regulatory systems of P. aeruginosa. We found that LfsT bound directly to the core promoter regions upstream of the start codons of numerous genes involved in various processes, including phage infection, FA metabolism, SPD transport, and the T3SS, regulating as the repressor or activator. The identified partial palindromic motif NAACN(5,8)GTTN recognized by LfsT suggests extensive effects of LfsT on gene expression by maintaining preferential binding to nucleotide sites under evolutionary pressure. In summary, these findings indicate that LfsT enhances metabolic activity in P. aeruginosa, while it reduces host resistance to the phage. This study helps us better understand the coevolution of bacteria and phages (e.g., survival comes at a cost) and provides clues for designing novel antimicrobials against P. aeruginosa infections.
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Affiliation(s)
- Xiang Long
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, China
| | - Xiaolong Wang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, China
| | - Daqing Mao
- School of Medicine, Nankai University, Tianjin, China
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, China
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
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12
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A New Factor LapD Is Required for the Regulation of LpxC Amounts and Lipopolysaccharide Trafficking. Int J Mol Sci 2022; 23:ijms23179706. [PMID: 36077106 PMCID: PMC9456370 DOI: 10.3390/ijms23179706] [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: 07/29/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Lipopolysaccharide (LPS) constitutes the major component of the outer membrane and is essential for bacteria, such as Escherichia coli. Recent work has revealed the essential roles of LapB and LapC proteins in regulating LPS amounts; although, if any additional partners are involved is unknown. Examination of proteins co-purifying with LapB identified LapD as a new partner. The purification of LapD reveals that it forms a complex with several proteins involved in LPS and phospholipid biosynthesis, including FtsH-LapA/B and Fab enzymes. Loss of LapD causes a reduction in LpxC amounts and vancomycin sensitivity, which can be restored by mutations that stabilize LpxC (mutations in lapB, ftsH and lpxC genes), revealing that LapD acts upstream of LapB-FtsH in regulating LpxC amounts. Interestingly, LapD absence results in the substantial retention of LPS in the inner membranes and synthetic lethality when either the lauroyl or the myristoyl acyl transferase is absent, which can be overcome by single-amino acid suppressor mutations in LPS flippase MsbA, suggesting LPS translocation defects in ΔlapD bacteria. Several genes whose products are involved in cell envelope homeostasis, including clsA, waaC, tig and micA, become essential in LapD’s absence. Furthermore, the overproduction of acyl carrier protein AcpP or transcriptional factors DksA, SrrA can overcome certain defects of the LapD-lacking strain.
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13
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Shu S, Mi W. Regulatory mechanisms of lipopolysaccharide synthesis in Escherichia coli. Nat Commun 2022; 13:4576. [PMID: 35931690 PMCID: PMC9356133 DOI: 10.1038/s41467-022-32277-1] [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: 07/25/2022] [Indexed: 11/09/2022] Open
Abstract
Lipopolysaccharide (LPS) is an essential glycolipid and forms a protective permeability barrier for most Gram-negative bacteria. In E. coli, LPS levels are under feedback control, achieved by FtsH-mediated degradation of LpxC, which catalyzes the first committed step in LPS synthesis. FtsH is a membrane-bound AAA+ protease, and its protease activity toward LpxC is regulated by essential membrane proteins LapB and YejM. However, the regulatory mechanisms are elusive. We establish an in vitro assay to analyze the kinetics of LpxC degradation and demonstrate that LapB is an adaptor protein that utilizes its transmembrane helix to interact with FtsH and its cytoplasmic domains to recruit LpxC. Our YejM/LapB complex structure reveals that YejM is an anti-adaptor protein, competing with FtsH for LapB to inhibit LpxC degradation. Structural analysis unravels that LapB and LPS have overlapping binding sites in YejM. Thus, LPS levels control formation of the YejM/LapB complex to determine LpxC protein levels.
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Affiliation(s)
- Sheng Shu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Wei Mi
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA. .,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
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14
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Fujita K, Takata I, Yoshida I, Okumura H, Otake K, Takashima H, Sugiyama H. TP0586532, a non-hydroxamate LpxC inhibitor, has in vitro and in vivo antibacterial activities against Enterobacteriaceae. J Antibiot (Tokyo) 2022; 75:98-107. [PMID: 34837061 DOI: 10.1038/s41429-021-00486-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/15/2021] [Accepted: 10/06/2021] [Indexed: 02/08/2023]
Abstract
The emergence of multi-drug resistant pathogenic bacteria, especially Gram-negative bacteria, is a worldwide health problem. New antibiotics directed at previously unexplored targets are urgently needed to overcome resistance to existing antibiotic classes. UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC) is an attractive target for a new antibacterial agent. Although a number of LpxC inhibitors have been identified, none have been approved as antibacterial agents. These LpxC inhibitors contain a hydroxamate moiety, which is a robust zinc ion chelator. The nonspecific inhibition of metalloenzymes through zinc ion chelation is one of possibilities leading to unwanted side effects. Herein, we report that TP0586532, a non-hydroxamate LpxC inhibitor, has a broad spectrum of antibacterial activity against carbapenem-resistant Enterobacteriaceae. The MIC90 of TP0586532 against clinical isolates of carbapenem-resistant Klebsiella pneumoniae was 4 μg ml-1. TP0586532 also showed an in vivo efficacy against murine systemic, urinary tract and lung infection models caused by meropenem- or ciprofloxacin-resistant strains. The estimated maximum unbound plasma concentration value at the effective dose of TP0586532 in murine infection models was around 13 μg ml-1. TP0586532 is predicted to exhibit a in vivo efficacy without cardiovascular toxicity and showed the potential of non-hydroxamate LpxC inhibitors as antibacterial agents against carbapenem-resistant Enterobacteriaceae.
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15
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Yin Z, Liebhart E, Stegmann E, Brötz-Oesterhelt H, Dickschat JS. An isotopic probe to follow the stereochemical course of dehydratase reactions in polyketide and fatty acid biosynthesis. Org Chem Front 2022. [DOI: 10.1039/d2qo00272h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Four stereoisomeric and isotopically labelled probes that are suitable to easily follow the stereochemical course of dehydratases have been synthesised.
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Affiliation(s)
- Zhiyong Yin
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Elisa Liebhart
- Interfaculty Institute of Microbiology and Infection Medicine, Deptartment of Microbial Bioactive Compounds, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine, Deptartment of Microbial Bioactive Compounds, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- Interfaculty Institute of Microbiology and Infection Medicine, Deptartment of Microbial Bioactive Compounds, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Jeroen S. Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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16
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Checkpoints That Regulate Balanced Biosynthesis of Lipopolysaccharide and Its Essentiality in Escherichia coli. Int J Mol Sci 2021; 23:ijms23010189. [PMID: 35008618 PMCID: PMC8745692 DOI: 10.3390/ijms23010189] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/17/2021] [Accepted: 12/22/2021] [Indexed: 12/17/2022] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria, such as Escherichia coli, is essential for their viability. Lipopolysaccharide (LPS) constitutes the major component of OM, providing the permeability barrier, and a tight balance exists between LPS and phospholipids amounts as both of these essential components use a common metabolic precursor. Hence, checkpoints are in place, right from the regulation of the first committed step in LPS biosynthesis mediated by LpxC through its turnover by FtsH and HslUV proteases in coordination with LPS assembly factors LapB and LapC. After the synthesis of LPS on the inner leaflet of the inner membrane (IM), LPS is flipped by the IM-located essential ATP-dependent transporter to the periplasmic face of IM, where it is picked up by the LPS transport complex spanning all three components of the cell envelope for its delivery to OM. MsbA exerts its intrinsic hydrocarbon ruler function as another checkpoint to transport hexa-acylated LPS as compared to underacylated LPS. Additional checkpoints in LPS assembly are: LapB-assisted coupling of LPS synthesis and translocation; cardiolipin presence when LPS is underacylated; the recruitment of RfaH transcriptional factor ensuring the transcription of LPS core biosynthetic genes; and the regulated incorporation of non-stoichiometric modifications, controlled by the stress-responsive RpoE sigma factor, small RNAs and two-component systems.
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17
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Guest RL, Rutherford ST, Silhavy TJ. Border Control: Regulating LPS Biogenesis. Trends Microbiol 2021; 29:334-345. [PMID: 33036869 PMCID: PMC7969359 DOI: 10.1016/j.tim.2020.09.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/20/2022]
Abstract
The outer membrane (OM) is a defining feature of Gram-negative bacteria that serves as a permeability barrier and provides rigidity to the cell. Critical to OM function is establishing and maintaining an asymmetrical bilayer structure with phospholipids in the inner leaflet and the complex glycolipid lipopolysaccharide (LPS) in the outer leaflet. Cells ensure this asymmetry by regulating the biogenesis of lipid A, the conserved and essential anchor of LPS. Here we review the consequences of disrupting the regulatory components that control lipid A biogenesis, focusing on the rate-limiting step performed by LpxC. Dissection of these processes provides critical insights into bacterial physiology and potential new targets for antibiotics able to overcome rapidly spreading resistance mechanisms.
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Affiliation(s)
- Randi L Guest
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Steven T Rutherford
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Thomas J Silhavy
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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18
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Abstract
Gram-negative bacteria produce an asymmetric outer membrane (OM) that is particularly impermeant to many antibiotics and characterized by lipopolysaccharide (LPS) exclusively at the cell surface. LPS biogenesis remains an ideal target for therapeutic intervention, as disruption could kill bacteria or increase sensitivity to existing antibiotics. While it has been known that LPS synthesis is regulated by proteolytic control of LpxC, the enzyme that catalyzes the first committed step of LPS synthesis, it remains unknown which signals direct this regulation. New details have been revealed during study of a cryptic essential inner membrane protein, YejM. Multiple functions have been proposed over the years for YejM, including a controversial hypothesis that it transports cardiolipin from the inner membrane to the OM. Strong evidence now indicates that YejM senses LPS in the periplasm and directs proteolytic regulation. Here, we discuss the standing literature of YejM and highlight exciting new insights into cell envelope maintenance.
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Affiliation(s)
- Brent W Simpson
- Department of Infectious Diseases, The University of Georgia, College of Veterinary Medicine, Athens, Georgia, USA
| | - Martin V Douglass
- Department of Infectious Diseases, The University of Georgia, College of Veterinary Medicine, Athens, Georgia, USA
| | - M Stephen Trent
- Department of Infectious Diseases, The University of Georgia, College of Veterinary Medicine, Athens, Georgia, USA
- Department of Microbiology, The University of Georgia, College of Veterinary Medicine, Athens, Georgia, USA
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19
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YejM Controls LpxC Levels by Regulating Protease Activity of the FtsH/YciM Complex of Escherichia coli. J Bacteriol 2020; 202:JB.00303-20. [PMID: 32540932 DOI: 10.1128/jb.00303-20] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 06/09/2020] [Indexed: 11/20/2022] Open
Abstract
LpxC is a deacetylase that catalyzes the first committed step of lipid A biosynthesis in Escherichia coli LpxC competes for a common precursor, R-3-hydroxymyristoyl-UDP-GlcNAc, with FabZ, whose dehydratase activity catalyzes the first committed step of phospholipid biosynthesis. To maintain the optimum flow of the common precursor to these two competing pathways, the LpxC level is controlled by FtsH/YciM-mediated proteolysis. It is not known whether this complex or another protein senses the status of lipid A synthesis to control LpxC proteolysis. The work carried out in this study began with a novel mutation, yejM1163, which causes hypersensitivity to large antibiotics such as vancomycin and erythromycin. Isolates resistant to these antibiotics carried suppressor mutations in the ftsH and yciM genes. Western blot analysis showed a dramatically reduced LpxC level in the yejM1163 background, while the presence of ftsH or yciM suppressor mutations restored LpxC levels to different degrees. Based on these observations, it is proposed that YejM is a sensor of lipid A synthesis and controls LpxC levels by modulating the activity of the FtsH/YciM complex. The truncation of the periplasmic domain in the YejM1163 protein causes unregulated proteolysis of LpxC, thus diverting a greater pool of R-3-hydroxymyristoyl-UDP-GlcNAc toward phospholipid synthesis. This imbalance in lipid synthesis perturbs the outer membrane permeability barrier, causing hypersensitivity toward vancomycin and erythromycin. yejM1163 suppressor mutations in ftsH and yciM lower the proteolytic activity toward LpxC, thus restoring lipid homeostasis and the outer membrane permeability barrier.IMPORTANCE Lipid homeostasis is critical for proper envelope functions. The level of LpxC, which catalyzes the first committed step of lipopolysaccharide (LPS) synthesis, is controlled by an essential protease complex comprised of FtsH and YciM. Work carried out here suggests YejM, an essential envelope protein, plays a central role in sensing the state of LPS synthesis and controls LpxC levels by regulating the activity of FtsH/YciM. All four essential proteins are attractive targets of therapeutic development.
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20
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Outer Membrane Lipid Secretion and the Innate Immune Response to Gram-Negative Bacteria. Infect Immun 2020; 88:IAI.00920-19. [PMID: 32253250 DOI: 10.1128/iai.00920-19] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria is an asymmetric lipid bilayer that consists of inner leaflet phospholipids and outer leaflet lipopolysaccharides (LPS). The asymmetric character and unique biochemistry of LPS molecules contribute to the OM's ability to function as a molecular permeability barrier that protects the bacterium against hazards in the environment. Assembly and regulation of the OM have been extensively studied for understanding mechanisms of antibiotic resistance and bacterial defense against host immunity; however, there is little knowledge on how Gram-negative bacteria release their OMs into their environment to manipulate their hosts. Discoveries in bacterial lipid trafficking, OM lipid homeostasis, and host recognition of microbial patterns have shed new light on how microbes secrete OM vesicles (OMVs) to influence inflammation, cell death, and disease pathogenesis. Pathogens release OMVs that contain phospholipids, like cardiolipins, and components of LPS molecules, like lipid A endotoxins. These multiacylated lipid amphiphiles are molecular patterns that are differentially detected by host receptors like the Toll-like receptor 4/myeloid differentiation factor 2 complex (TLR4/MD-2), mouse caspase-11, and human caspases 4 and 5. We discuss how lipid ligands on OMVs engage these pattern recognition receptors on the membranes and in the cytosol of mammalian cells. We then detail how bacteria regulate OM lipid asymmetry, negative membrane curvature, and the phospholipid-to-LPS ratio to control OMV formation. The goal is to highlight intersections between OM lipid regulation and host immunity and to provide working models for how bacterial lipids influence vesicle formation.
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21
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Ma X, Prathapam R, Wartchow C, Chie-Leon B, Ho CM, De Vicente J, Han W, Li M, Lu Y, Ramurthy S, Shia S, Steffek M, Uehara T. Structural and Biological Basis of Small Molecule Inhibition of Escherichia coli LpxD Acyltransferase Essential for Lipopolysaccharide Biosynthesis. ACS Infect Dis 2020; 6:1480-1489. [PMID: 31402665 DOI: 10.1021/acsinfecdis.9b00127] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
LpxD, acyl-ACP-dependent N-acyltransferase, is the third enzyme of lipid A biosynthesis in Gram-negative bacteria. A recent probe-based screen identified several compounds, including 6359-0284 (compound 1), that inhibit the enzymatic activity of Escherichia coli (E. coli) LpxD. Here, we use these inhibitors to chemically validate LpxD as an attractive antibacterial target. We first found that compound 1 was oxidized in solution to the more stable aromatized tetrahydro-pyrazolo-quinolinone compound 1o. From the Escherichia coli strain deficient in efflux, we isolated a mutant that was less susceptible to compound 1o and had an lpxD missense mutation (Gly268Cys), supporting the cellular on-target activity. Using surface plasma resonance, we showed direct binding to E. coli LpxD for compound 1o and other reported LpxD inhibitors in vitro. Furthermore, we determined eight cocrystal structures of E. coli LpxD/inhibitor complexes. These costructures pinpointed the 4'-phosphopantetheine binding site as the common ligand binding hotspot, where hydrogen bonds to Gly269 and/or Gly287 were important for inhibitor binding. In addition, the LpxD/compound 1o costructure rationalized the reduced activity of compound 1o in the LpxDGly268Cys mutant. Moreover, we obtained the LpxD structure in complex with a previously reported LpxA/LpxD dual targeting peptide inhibitor, RJPXD33, providing structural rationale for the unique dual targeting properties of this peptide. Given that the active site residues of LpxD are conserved in multidrug resistant Enterobacteriaceae, this work paves the way for future LpxD drug discovery efforts combating these Gram-negative pathogens.
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22
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An Essential Membrane Protein Modulates the Proteolysis of LpxC to Control Lipopolysaccharide Synthesis in Escherichia coli. mBio 2020; 11:mBio.00939-20. [PMID: 32430473 PMCID: PMC7240159 DOI: 10.1128/mbio.00939-20] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The outer membrane is a major determinant of the intrinsic antibiotic resistance of Gram-negative bacteria. It is composed of both lipopolysaccharide (LPS) and phospholipid, and the synthesis of these lipid species must be balanced for the membrane to maintain its barrier function in blocking drug entry. In this study, we identified an essential protein of unknown function as a key new factor in modulating LPS synthesis in the model bacterium Escherichia coli. Our results provide novel insight into how this organism and most likely other Gram-negative bacteria maintain membrane homeostasis and their intrinsic resistance to antibiotics. Gram-negative bacteria are surrounded by a complex cell envelope that includes two membranes. The outer membrane prevents many drugs from entering these cells and is thus a major determinant of their intrinsic antibiotic resistance. This barrier function is imparted by the asymmetric architecture of the membrane with lipopolysaccharide (LPS) in the outer leaflet and phospholipids in the inner leaflet. The LPS and phospholipid synthesis pathways share an intermediate. Proper membrane biogenesis therefore requires that the flux through each pathway be balanced. In Escherichia coli, a major control point in establishing this balance is the committed step of LPS synthesis mediated by LpxC. Levels of this enzyme are controlled through its degradation by the inner membrane protease FtsH and its presumed adapter protein LapB (YciM). How turnover of LpxC is controlled has remained unclear for many years. Here, we demonstrate that the essential protein of unknown function YejM (PbgA) participates in this regulatory pathway. Suppressors of YejM essentiality were identified in lpxC and lapB, and LpxC overproduction was shown to be sufficient to allow survival of ΔyejM mutants. Furthermore, the stability of LpxC was shown to be reduced in cells lacking YejM, and genetic and physical interactions between LapB and YejM were detected. Taken together, our results are consistent with a model in which YejM directly modulates LpxC turnover by FtsH-LapB to regulate LPS synthesis and maintain membrane homeostasis.
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23
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Quantitative proteomic analysis reveals the influence of plantaricin BM-1 on metabolic pathways and peptidoglycan synthesis in Escherichia coli K12. PLoS One 2020; 15:e0231975. [PMID: 32324803 PMCID: PMC7179913 DOI: 10.1371/journal.pone.0231975] [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: 12/11/2019] [Accepted: 04/03/2020] [Indexed: 11/19/2022] Open
Abstract
Plantaricin BM-1 is a class IIa bacteriocin with a strong bactericidal effect on gram-positive bacteria. Although plantaricin BM-1 also inhibits the growth of some gram-negative bacteria, including Escherichia coli, the mechanism is not clear. In this study, we used tandem mass tag-based quantitative proteomics analysis to examine the inhibitory mechanism of plantaricin BM-1 against E. coli K12, and evaluated the morphological effects by electron microscopy. The results demonstrated that plantaricin BM-1 inhibits the growth of E. coli K12 by bacteriostatic action, mainly acting on the surface of the cell wall, leading to its collapse. Proteomic analysis identified 976 differentially expressed proteins (>1.2-fold change, p < 0.05) under treatment with plantaricin BM-1, including 490 up-regulated proteins and 486 down-regulated proteins. These proteins were mainly involved in peptidoglycan synthesis and energy metabolism pathways, including amino acid, glyoxylate and dicarboxylate, ABC transporter, and quorum-sensing pathways. Specifically, plantaricin BM-1 treatment significantly improved peptidoglycan synthesis and enhanced the tricarboxylic acid cycle in E. coli K12, and altered the expression of cell membrane proteins. These results provide new insight into the inhibition mechanism of class IIa bacteriocins on gram-negative bacteria, which can lay the foundation for its broader use as an alternative to conventional antibiotics.
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24
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Han W, Ma X, Balibar CJ, Baxter Rath CM, Benton B, Bermingham A, Casey F, Chie-Leon B, Cho MK, Frank AO, Frommlet A, Ho CM, Lee PS, Li M, Lingel A, Ma S, Merritt H, Ornelas E, De Pascale G, Prathapam R, Prosen KR, Rasper D, Ruzin A, Sawyer WS, Shaul J, Shen X, Shia S, Steffek M, Subramanian S, Vo J, Wang F, Wartchow C, Uehara T. Two Distinct Mechanisms of Inhibition of LpxA Acyltransferase Essential for Lipopolysaccharide Biosynthesis. J Am Chem Soc 2020; 142:4445-4455. [DOI: 10.1021/jacs.9b13530] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wooseok Han
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Xiaolei Ma
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Carl J. Balibar
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | | | - Bret Benton
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Alun Bermingham
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Fergal Casey
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Barbara Chie-Leon
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Min-Kyu Cho
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Andreas O. Frank
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Alexandra Frommlet
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Chi-Min Ho
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Patrick S. Lee
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Min Li
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Sylvia Ma
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Hanne Merritt
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Elizabeth Ornelas
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Gianfranco De Pascale
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Ramadevi Prathapam
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Katherine R. Prosen
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Dita Rasper
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Alexey Ruzin
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - William S. Sawyer
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Jacob Shaul
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Xiaoyu Shen
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Steven Shia
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Micah Steffek
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Sharadha Subramanian
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Jason Vo
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Feng Wang
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Charles Wartchow
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Tsuyoshi Uehara
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
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Sankaranarayanan K, Antaris XX, Palanski BA, El Gamal A, Kao CM, Fitch WL, Fischer CR, Khosla C. Tunable Enzymatic Synthesis of the Immunomodulator Lipid IV A To Enable Structure-Activity Analysis. J Am Chem Soc 2019; 141:9474-9478. [PMID: 31184877 PMCID: PMC7206895 DOI: 10.1021/jacs.9b03066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Lipid A family of glycolipids, found in the outer membranes of all Gram-negative bacteria, exhibits considerable structural diversity in both lipid and glycan moieties. The lack of facile methods to prepare analogues of these natural products represents a major roadblock in understanding the relationship between their structure and immunomodulatory activities. Here we present a modular, cell-free multienzymatic platform to access these structure-activity relationships. By individually purifying 19 Escherichia coli proteins and reconstituting them in vitro in the presence of acetyl-CoA, UDP- N-acetylglucosamine, NADPH, and ATP, we have developed a system capable of synthesizing Lipid IVA, the first bioactive intermediate in the Lipid A pathway. Our reconstituted multienzyme system revealed considerable promiscuity for orthologs with distinct substrate specificity, as illustrated by swapping enzymes from distantly related cyanobacterial and Pseudomonas species. Analysis of the agonistic and antagonistic activities of the resulting products against the THP-1 human monocytic cell line revealed hitherto unrecognized trends, while opening the door to harnessing the potent biological activities of these complex glycolipid natural products.
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Affiliation(s)
| | - Xirui X. Antaris
- Department of Chemistry, Stanford, California 94305, United States
| | - Brad A. Palanski
- Department of Chemistry, Stanford, California 94305, United States
| | - Abrahim El Gamal
- Department of Chemistry, Stanford, California 94305, United States
| | - Camilla M. Kao
- Department of Biochemistry, and Stanford, California 94305, United States
| | - William L. Fitch
- Department of Medicine, and Stanford, California 94305, United States
| | - Curt R. Fischer
- Department of Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
| | - Chaitan Khosla
- Department of Chemical Engineering, Stanford, California 94305, United States
- Department of Chemistry, Stanford, California 94305, United States
- Department of Biochemistry, and Stanford, California 94305, United States
- Department of Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
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26
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Babele PK, Kumar J, Chaturvedi V. Proteomic De-Regulation in Cyanobacteria in Response to Abiotic Stresses. Front Microbiol 2019; 10:1315. [PMID: 31263458 PMCID: PMC6584798 DOI: 10.3389/fmicb.2019.01315] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 05/27/2019] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria are oxygenic photoautotrophs, exhibiting a cosmopolitan distribution in almost all possible environments and are significantly responsible for half of the global net primary productivity. They are well adapted to the diverse environments including harsh conditions by evolving a range of fascinating repertoires of unique biomolecules and secondary metabolites to support their growth and survival. These phototrophs are proved as excellent models for unraveling the mysteries of basic biochemical and physiological processes taking place in higher plants. Several known species of cyanobacteria have tremendous biotechnological applications in diverse fields such as biofuels, biopolymers, secondary metabolites and much more. Due to their potential biotechnological and commercial applications in various fields, there is an imperative need to engineer robust cyanobacteria in such a way that they can tolerate and acclimatize to ever-changing environmental conditions. Adaptations to stress are mainly governed by a precise gene regulation pathways resulting in the expression of novel protein/enzymes and metabolites. Despite the demand, till date few proteins/enzymes have been identified which play a potential role in improving tolerance against abiotic stresses. Therefore, it is utmost important to study environmental stress responses related to post-genomic investigations, including proteomic changes employing advanced proteomics, synthetic and structural biology workflows. In this respect, the study of stress proteomics offers exclusive advantages to scientists working on these aspects. Advancements on these fields could be helpful in dissecting, characterization and manipulation of physiological and metabolic systems of cyanobacteria to understand the stress induced proteomic responses. Till date, it remains ambiguous how cyanobacteria perceive changes in the ambient environment that lead to the stress-induced proteins thus metabolic deregulation. This review briefly describes the current major findings in the fields of proteome research on the cyanobacteria under various abiotic stresses. These findings may improve and advance the information on the role of different class of proteins associated with the mechanism(s) of stress mitigation in cyanobacteria under harsh environmental conditions.
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Affiliation(s)
- Piyoosh Kumar Babele
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Jay Kumar
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Venkatesh Chaturvedi
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
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Flores-Kim J, Dobihal GS, Fenton A, Rudner DZ, Bernhardt TG. A switch in surface polymer biogenesis triggers growth-phase-dependent and antibiotic-induced bacteriolysis. eLife 2019; 8:44912. [PMID: 30964003 PMCID: PMC6456293 DOI: 10.7554/elife.44912] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 03/11/2019] [Indexed: 01/21/2023] Open
Abstract
Penicillin and related antibiotics disrupt cell wall synthesis to induce bacteriolysis. Lysis in response to these drugs requires the activity of cell wall hydrolases called autolysins, but how penicillins misactivate these deadly enzymes has long remained unclear. Here, we show that alterations in surface polymers called teichoic acids (TAs) play a key role in penicillin-induced lysis of the Gram-positive pathogen Streptococcus pneumoniae (Sp). We find that during exponential growth, Sp cells primarily produce lipid-anchored TAs called lipoteichoic acids (LTAs) that bind and sequester the major autolysin LytA. However, penicillin-treatment or prolonged stationary phase growth triggers the degradation of a key LTA synthase, causing a switch to the production of wall-anchored TAs (WTAs). This change allows LytA to associate with and degrade its cell wall substrate, thus promoting osmotic lysis. Similar changes in surface polymer assembly may underlie the mechanism of antibiotic- and/or growth phase-induced lysis for other important Gram-positive pathogens.
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Affiliation(s)
- Josué Flores-Kim
- Department of Microbiology, Harvard Medical School, Boston, United States
| | | | - Andrew Fenton
- Department of Microbiology, Harvard Medical School, Boston, United States.,The Florey Institute, Molecular Biology Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - David Z Rudner
- Department of Microbiology, Harvard Medical School, Boston, United States
| | - Thomas G Bernhardt
- Department of Microbiology, Harvard Medical School, Boston, United States.,Howard Hughes Medical Institute, Boston, United States
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28
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Structural and dynamical rationale for fatty acid unsaturation in Escherichia coli. Proc Natl Acad Sci U S A 2019; 116:6775-6783. [PMID: 30872475 DOI: 10.1073/pnas.1818686116] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Fatty acid biosynthesis in α- and γ-proteobacteria requires two functionally distinct dehydratases, FabA and FabZ. Here, mechanistic cross-linking facilitates the structural characterization of a stable hexameric complex of six Escherichia coli FabZ dehydratase subunits with six AcpP acyl carrier proteins. The crystal structure sheds light on the divergent substrate selectivity of FabA and FabZ by revealing distinct architectures of the binding pocket. Molecular dynamics simulations demonstrate differential biasing of substrate orientations and conformations within the active sites of FabA and FabZ such that FabZ is preorganized to catalyze only dehydration, while FabA is primed for both dehydration and isomerization.
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29
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Thomanek N, Arends J, Lindemann C, Barkovits K, Meyer HE, Marcus K, Narberhaus F. Intricate Crosstalk Between Lipopolysaccharide, Phospholipid and Fatty Acid Metabolism in Escherichia coli Modulates Proteolysis of LpxC. Front Microbiol 2019; 9:3285. [PMID: 30692974 PMCID: PMC6339880 DOI: 10.3389/fmicb.2018.03285] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 12/17/2018] [Indexed: 12/26/2022] Open
Abstract
Lipopolysaccharides (LPS) in the outer membrane of Gram-negative bacteria provide the first line of defense against antibiotics and other harmful compounds. LPS biosynthesis critically depends on LpxC catalyzing the first committed enzyme in this process. In Escherichia coli, the cellular concentration of LpxC is adjusted in a growth rate-dependent manner by the FtsH protease making sure that LPS biosynthesis is coordinated with the cellular demand. As a result, LpxC is stable in fast-growing cells and prone to degradation in slow-growing cells. One of the factors involved in this process is the alarmone guanosine tetraphosphate (ppGpp) but previous studies suggested the involvement of yet unknown factors in LpxC degradation. We established a quantitative proteomics approach aiming at the identification of proteins that are associated with LpxC and/or FtsH at high or low growth rates. The identification of known LpxC and FtsH interactors validated our approach. A number of proteins involved in fatty acid biosynthesis and degradation, including the central regulator FadR, were found in the LpxC and/or FtsH interactomes. Another protein associated with LpxC and FtsH was WaaH, a LPS-modifying enzyme. When overproduced, several members of the LpxC/FtsH interactomes were able to modulate LpxC proteolysis. Our results go beyond the previously established link between LPS and phospholipid biosynthesis and uncover a far-reaching network that controls LPS production by involving multiple enzymes in fatty acid metabolism, phospholipid biosynthesis and LPS modification.
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Affiliation(s)
- Nikolas Thomanek
- Medical Proteome Center, Ruhr University Bochum, Bochum, Germany
| | - Jan Arends
- Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | | | | | - Helmut E Meyer
- Medical Proteome Center, Ruhr University Bochum, Bochum, Germany.,Biomedical Research, Leibniz-Institut für Analytische Wissenschaften - ISAS - e. V., Dortmund, Germany
| | - Katrin Marcus
- Medical Proteome Center, Ruhr University Bochum, Bochum, Germany
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Interplay of Klebsiella pneumoniae fabZ and lpxC Mutations Leads to LpxC Inhibitor-Dependent Growth Resulting from Loss of Membrane Homeostasis. mSphere 2018; 3:3/5/e00508-18. [PMID: 30381354 PMCID: PMC6211225 DOI: 10.1128/msphere.00508-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Emergence of antibiotic resistance has prompted efforts to identify and optimize novel inhibitors of antibacterial targets such as LpxC. This enzyme catalyzes the first committed step of lipid A synthesis, which is necessary to generate lipopolysaccharide and ultimately the Gram-negative protective outer membrane. Investigation of this pathway and its interrelationship with inner membrane (phospholipid) biosynthesis or other pathways is therefore highly important to the fundamental understanding of Gram-negative bacteria and by extension to antibiotic discovery. Here we exploited the availability of a novel LpxC inhibitor to engender the generation of K. pneumoniae resistant mutants whose growth depends on chemical inhibition of LpxC. Inhibitor dependency resulted from the interaction of different resistance mutations and was based on loss of normal cellular mechanisms required to establish membrane homeostasis. This study provides new insights into the importance of this process in K. pneumoniae and how it may be linked to novel biosynthetic pathway inhibitors. Tight coordination of inner and outer membrane biosynthesis is very important in Gram-negative bacteria. Biosynthesis of the lipid A moiety of lipopolysaccharide, which comprises the outer leaflet of the outer membrane has garnered interest for Gram-negative antibacterial discovery. In particular, several potent inhibitors of LpxC (the first committed step of the lipid A pathway) are described. Here we show that serial passaging of Klebsiella pneumoniae in increasing levels of an LpxC inhibitor yielded mutants that grew only in the presence of the inhibitor. These strains had mutations in fabZ and lpxC occurring together (encoding either FabZR121L/LpxCV37G or FabZF51L/LpxCV37G). K. pneumoniae mutants having only LpxCV37G or LpxCV37A or various FabZ mutations alone were less susceptible to the LpxC inhibitor and did not require LpxC inhibition for growth. Western blotting revealed that LpxCV37G accumulated to high levels, and electron microscopy of cells harboring FabZR121L/LpxCV37G indicated an extreme accumulation of membrane in the periplasm when cells were subcultured without LpxC inhibitor. Significant accumulation of detergent-like lipid A pathway intermediates that occur downstream of LpxC (e.g., lipid X and disaccharide monophosphate [DSMP]) was also seen. Taken together, our results suggest that redirection of lipid A pathway substrate by less active FabZ variants, combined with increased activity from LpxCV37G was overdriving the lipid A pathway, necessitating LpxC chemical inhibition, since native cellular maintenance of membrane homeostasis was no longer functioning. IMPORTANCE Emergence of antibiotic resistance has prompted efforts to identify and optimize novel inhibitors of antibacterial targets such as LpxC. This enzyme catalyzes the first committed step of lipid A synthesis, which is necessary to generate lipopolysaccharide and ultimately the Gram-negative protective outer membrane. Investigation of this pathway and its interrelationship with inner membrane (phospholipid) biosynthesis or other pathways is therefore highly important to the fundamental understanding of Gram-negative bacteria and by extension to antibiotic discovery. Here we exploited the availability of a novel LpxC inhibitor to engender the generation of K. pneumoniae resistant mutants whose growth depends on chemical inhibition of LpxC. Inhibitor dependency resulted from the interaction of different resistance mutations and was based on loss of normal cellular mechanisms required to establish membrane homeostasis. This study provides new insights into the importance of this process in K. pneumoniae and how it may be linked to novel biosynthetic pathway inhibitors.
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31
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Richie DL, Wang L, Chan H, De Pascale G, Six DA, Wei JR, Dean CR. A pathway-directed positive growth restoration assay to facilitate the discovery of lipid A and fatty acid biosynthesis inhibitors in Acinetobacter baumannii. PLoS One 2018; 13:e0193851. [PMID: 29505586 PMCID: PMC5837183 DOI: 10.1371/journal.pone.0193851] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 02/19/2018] [Indexed: 11/19/2022] Open
Abstract
Acinetobacter baumannii ATCC 19606 can grow without lipooligosaccharide (LOS). Lack of LOS can result from disruption of the early lipid A biosynthetic pathway genes lpxA, lpxC or lpxD. Although LOS itself is not essential for growth of A. baumannii ATCC 19606, it was previously shown that depletion of the lipid A biosynthetic enzyme LpxK in cells inhibited growth due to the toxic accumulation of lipid A pathway intermediates. Growth of LpxK-depleted cells was restored by chemical inhibition of LOS biosynthesis using CHIR-090 (LpxC) and fatty acid biosynthesis using cerulenin (FabB/F) and pyridopyrimidine (acetyl-CoA-carboxylase). Here, we expand on this by showing that inhibition of enoyl-acyl carrier protein reductase (FabI), responsible for converting trans-2-enoyl-ACP into acyl-ACP during the fatty acid elongation cycle also restored growth during LpxK depletion. Inhibition of fatty acid biosynthesis during LpxK depletion rescued growth at 37°C, but not at 30°C, whereas rescue by LpxC inhibition was temperature independent. We exploited these observations to demonstrate proof of concept for a targeted medium-throughput growth restoration screening assay to identify small molecule inhibitors of LOS and fatty acid biosynthesis. The differential temperature dependence of fatty acid and LpxC inhibition provides a simple means by which to separate growth stimulating compounds by pathway. Targeted cell-based screening platforms such as this are important for faster identification of compounds inhibiting pathways of interest in antibacterial discovery for clinically relevant Gram-negative pathogens.
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Affiliation(s)
- Daryl L. Richie
- Novartis Institutes for BioMedical Research, Emeryville, CA, United States of America
| | - Lisha Wang
- Novartis Institutes for BioMedical Research, Emeryville, CA, United States of America
| | - Helen Chan
- Novartis Institutes for BioMedical Research, Emeryville, CA, United States of America
| | - Gianfranco De Pascale
- Novartis Institutes for BioMedical Research, Emeryville, CA, United States of America
| | - David A. Six
- Novartis Institutes for BioMedical Research, Emeryville, CA, United States of America
| | - Jun-Rong Wei
- Novartis Institutes for BioMedical Research, Emeryville, CA, United States of America
| | - Charles R. Dean
- Novartis Institutes for BioMedical Research, Emeryville, CA, United States of America
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32
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Liu Z, Wang Z, Gu H, You J, Hu M, Zhang Y, Zhu Z, Wang Y, Liu S, Chen L, Liu X, Tian Y, Zhou S, Jiang L, Liu L, Wan J. Identification and Phenotypic Characterization of ZEBRA LEAF16 Encoding a β-Hydroxyacyl-ACP Dehydratase in Rice. FRONTIERS IN PLANT SCIENCE 2018; 9:782. [PMID: 29946330 PMCID: PMC6005893 DOI: 10.3389/fpls.2018.00782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 05/23/2018] [Indexed: 05/06/2023]
Abstract
The chloroplast is a self-independent organelle and contains its own transcription and translation systems. The establishment of genetic systems is vital for normal plant growth and development. We isolated a rice zebra leaf 16 (zl16) mutant derived from rice cultivar 9311. The zl16 mutant showed chlorotic abnormalities in the transverse sectors of the young leaves of seedlings. The use of transmission electron microscopy (TEM) demonstrated that dramatic defects occurred in variegated zl16 leaves during the early development of a chloroplast. Map-based cloning revealed that ZL16 encodes a β-hydroxyacyl-ACP dehydratase (HAD) involved in de novo fatty acid synthesis. Compared with the wild type, a missense mutation (Arg164Trp) in the zl16 mutant was identified, which significantly reduced enzymatic activity and altered the three-dimensional modeling structure of the putative protein. ZL16 was ubiquitously expressed in various plant organs, with a pronounced level in the young leaf. A subcellular localization experiment indicated that ZL16 was targeted in the chloroplast. Furthermore, we analyzed the expression of some nuclear genes involved in chloroplast development, and found they were altered in the zl16 mutant. RNA-Seq analysis indicated that some genes related to cell membrane constituents were downregulated in the mutant. An in vivo metabolic assay revealed that the total fatty acid content in the mutant was significantly decreased relative to the wild type. Our results indicate that HAD is essential for the development of chloroplasts by regulating the synthesis of fatty acids in rice.
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Affiliation(s)
- Ziwen Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Zhiyuan Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Han Gu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Jia You
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Manman Hu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Yujun Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Ze Zhu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Yihua Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Shijia Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Liangming Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Xi Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Yunlu Tian
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Shirong Zhou
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Linglong Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Linglong Liu,
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Kumar V, Sharma A, Pratap S, Kumar P. Characterization of isoflavonoids as inhibitors of β-hydroxyacyl-acyl carrier protein dehydratase (FabZ) from Moraxella catarrhalis: Kinetics, spectroscopic, thermodynamics and in silico studies. Biochim Biophys Acta Gen Subj 2017; 1862:726-744. [PMID: 29092780 DOI: 10.1016/j.bbagen.2017.10.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/14/2017] [Accepted: 10/26/2017] [Indexed: 01/02/2023]
Abstract
BACKGROUD β-hydroxyacyl-acyl carrier protein dehydratase (FabZ) is an essential component of type II fatty acid biosynthesis (FAS II) pathway in bacteria. It performs dehydration of β-hydroxyacyl-ACP to trans-2-acyl-ACP in the elongation cycle of the FAS II pathway. FabZ is ubiquitously expressed and has uniform distribution, which makes FabZ an excellent target for developing novel drugs against pathogenic bacteria. METHODS We focused on the biochemical and biophysical characterization of FabZ from drug-resistant pathogen Moraxella catarrhalis (McFabZ). More importantly, we have identified and characterized new inhibitors against McFabZ using biochemical, biophysical and in silico based studies. RESULTS We have identified three isoflavones (daidzein, biochanin A and genistein) as novel inhibitors against McFabZ. Mode of inhibition of these compounds is competitive with IC50 values lie in the range of 6.85μΜ to 27.7μΜ. Conformational changes observed in secondary and tertiary structure marked by a decrease in the helical and the sheet content in McFabZ structure upon inhibitors binding. In addition, thermodynamic data suggest that biochanin A has a strong binding affinity for McFabZ as compare to daidzein and genistein. Molecular docking studies have revealed that these inhibitors are interacting with the active site of McFabZ and making contacts with catalytic and substrate binding tunnel residues. CONCLUSION AND GENERAL SIGNIFICANCE Three new inhibitors against McFabZ have been identified and characterized. These biochemical and biophysical findings lead to the identification of chemical scaffolds, which can lead to broad-spectrum antimicrobial drugs targeted against FabZ, and modification to existing FabZ inhibitors to improve affinity and potency.
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Affiliation(s)
- Vijay Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, 247667, India
| | - Anchal Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, 247667, India
| | - Shivendra Pratap
- Department of Biotechnology, Indian Institute of Technology Roorkee, 247667, India
| | - Pravindra Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, 247667, India.
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Ushijima Y, Ohniwa RL, Morikawa K. Identification of nucleoid associated proteins (NAPs) under oxidative stress in Staphylococcus aureus. BMC Microbiol 2017; 17:207. [PMID: 28969590 PMCID: PMC5625760 DOI: 10.1186/s12866-017-1114-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/13/2017] [Indexed: 01/25/2023] Open
Abstract
Background Bacterial nucleoid consists of genome DNA, RNA, and hundreds of nucleoid-associated proteins (NAPs). Escherichia coli nucleoid is compacted towards the stationary phase, replacing most log-phase NAPs with the major stationary-phase nucleoid protein, Dps. In contrast, Staphylococcus aureus nucleoid sustains the fiber structures throughout the growth. Instead, the Dps homologue, MrgA, expresses under oxidative stress conditions to clump the nucleoid, but the composition of the clumped nucleoid was elusive. Results The staphylococcal nucleoid under oxidative stress was isolated by sucrose gradient centrifugation, and the proteins were analyzed by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). We identified 299 proteins in the nucleoid under oxidative stress, including 113 csNAPs (contaminant-subtracted NAPs). Comparison with the previously identified csNAPs in log- and stationary phase indicated that one fifth of the csNAPs under oxidative stress were the constitutive nucleoid components; importantly, several factors including HU, SarA, FabZ, and ribosomes were sustained under oxidative stress. Some factors (e.g. SA1663 and SA0092/SA0093) with unknown functions were included in the csNAPs list specifically under oxidative stress condition. Conclusion Nucleoid constitutively holds Hu, SarA, FabG, and ribosomal proteins even under the oxidative stress, reflecting the active functions of the clumped nucleoid, unlikely to the dormant E. coli nucleoid compacted in the stationary phase or starvation. Electronic supplementary material The online version of this article (10.1186/s12866-017-1114-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuri Ushijima
- Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan. .,Present address: Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
| | - Ryosuke L Ohniwa
- Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan. .,Center for Biotechnology, National Taiwan University, Taipei 10617, Taiwan, Republic of China.
| | - Kazuya Morikawa
- Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
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Efficient production of free fatty acids from ionic liquid-based acid- or enzyme-catalyzed bamboo hydrolysate. ACTA ACUST UNITED AC 2017; 44:419-430. [DOI: 10.1007/s10295-016-1888-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 12/14/2016] [Indexed: 10/20/2022]
Abstract
Abstract
Two engineered Escherichia coli strains, DQ101 (MG1655 fadD−)/pDQTES and DQ101 (MG1655 fadD−)/pDQTESZ were constructed to investigate the free fatty acid production using ionic liquid-based acid- or enzyme-catalyzed bamboo hydrolysate as carbon source in this study. The plasmid, pDQTES, carrying an acyl-ACP thioesterase ‘TesA of E. coli in pTrc99A was constructed firstly, and then (3R)-hydroxyacyl-ACP dehydratase was ligated after the TesA to give the plasmid pDQTESZ. These two strains exhibited efficient fatty acid production when glucose was used as the sole carbon source, with a final concentration of 2.45 and 3.32 g/L, respectively. The free fatty acid production of the two strains on xylose is not as efficient as that on glucose, which was 2.32 and 2.96 g/L, respectively. For mixed sugars, DQ101 (MG1655 fadD−)-based strains utilized glucose and pentose sequentially under the carbon catabolite repression (CCR) regulation. The highest total FFAs concentration from the mixed sugar culture reached 2.81 g/L by DQ101 (MG1655 fadD−)/pDQTESZ. Furthermore, when ionic liquid-based enzyme-catalyzed bamboo hydrolysate was used as the carbon source, the strain DQ101 (MG1655 fadD−)/pDQTESZ could produce 1.23 g/L FFAs with a yield of 0.13 g/g, and while it just produced 0.65 g/L free fatty acid with the ionic liquid-based acid-catalyzed bamboo hydrolysate as the feedstock. The results suggested that enzymatic catalyzed bamboo hydrolysate with ionic liquid pretreatment could serve as an efficient feedstock for free fatty acid production.
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Identification of a Desaturase Involved in Mycolic Acid Biosynthesis in Mycobacterium smegmatis. PLoS One 2016; 11:e0164253. [PMID: 27741286 PMCID: PMC5065219 DOI: 10.1371/journal.pone.0164253] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 09/07/2016] [Indexed: 11/19/2022] Open
Abstract
Mycolic acids are unique long chain fatty acids found in the cell walls of mycobacteria including the tubercle bacillus, Mycobacterium tuberculosis. The introduction of double bonds in mycolic acids remains poorly understood, however, genes encoding two potential aerobic desaturases have been proposed to be involved in this process. Here we show that one of these genes, desA1, is essential for growth of the saprophytic Mycobacterium smegmatis. Depletion of desA1 in a M. smegmatis conditional mutant led to reduction of mycolic acid biosynthesis and loss of viability. The DesA1-depleted cells exhibited two other phenotypes: using 14[C]-labelling, we detected the accumulation of minor mycolic acid-related species that migrated faster in a silver TLC plate. Spiral Time of Flight Mass Spectroscopic analysis suggested the presence of species with sizes corresponding to what were likely monoenoic derivatives of α-mycolic acids. Additionally, conditional depletion led to the presence of free fatty acyl species of lengths ~C26-C48 in the lysing cells. Cell viability could be rescued in the conditional mutant by Mycobacterium tuberculosis desA1, highlighting the potential of desA1 as a new drug target in pathogenic mycobacteria.
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Gronow S, Brade H. Invited review: Lipopolysaccharide biosynthesis: which steps do bacteria need to survive? ACTA ACUST UNITED AC 2016. [DOI: 10.1177/09680519010070010301] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A detailed knowledge of LPS biosynthesis is of the utmost importance in understanding the function of the outer membrane of Gram-negative bacteria. The regulation of LPS biosynthesis affects many more compartments of the bacterial cell than the outer membrane and thus contributes to the understanding of the physiology of Gram-negative bacteria in general, on the basis of which only mechanisms of virulence and antibiotic resistance can be studied to find new targets for antibacterial treatment. The study of LPS biosynthesis is also an excellent example to demonstrate the limitations of `genomics' and `proteomics', since secondary gene products can be studied only by the combined tools of molecular genetics, enzymology and analytical structural biochemistry. Thus, the door to the field of `glycomics' is opened.
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Affiliation(s)
- Sabine Gronow
- Division of Medical and Biochemical Microbiology, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany,
| | - Helmut Brade
- Division of Medical and Biochemical Microbiology, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany
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Yu G, Wang X, Dou Y, Wang S, Tian M, Qi J, Li T, Ding C, Wu Y, Yu S. Riemerella anatipestifer M949_1360 Gene Functions on the Lipopolysaccharide Biosynthesis and Bacterial Virulence. PLoS One 2016; 11:e0160708. [PMID: 27500736 PMCID: PMC4976936 DOI: 10.1371/journal.pone.0160708] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 07/22/2016] [Indexed: 12/29/2022] Open
Abstract
Riemerella anatipestifer causes septicemic and exudative diseases in poultry, resulting in major economic losses to the duck industry. Lipopolysaccharide (LPS), as an important virulence factor in Gram-negative bacteria, can be recognized by the immune system and plays a crucial role in many interactions between bacteria and animal hosts. In this study, we screened out one LPS defective mutant strain RAΔ604 from a random transposon mutant library of R. anatipestifer serotype 1 strain CH3, which did not react with the anti-CH3 LPS monoclonal antibody 1C1 in an indirect enzyme-linked immunosorbent assay. Southern blot analysis confirmed that the genome of RAΔ604 contained a single Tn4351 insert. Then, we found that the M949_1360 gene was inactivated by insertion of the transposon. Using silver staining and western blot analyses, we found that the LPS pattern of RAΔ604 was defective, as compared with that of the wild-type (WT) strain CH3. The mutant strain RAΔ604 showed no significant influence on bacterial growth, while bacterial counting and Live/dead BacLight Bacterial Viability staining revealed that bacterial viability was decreased, as compared with the WT strain CH3. In addition, the abilities of the mutant strain RAΔ604 to adhere and invade Vero cells were significantly decreased. Animal studies revealed that the virulence of the mutant strain RAΔ604 was decreased by more than 200-fold in a duck infection model, as compared with the WT strain CH3. Furthermore, immunization with live bacteria of the mutant strain RAΔ604 protected 87.5% ducks from challenge with R. anatipestifer serotype 1 strain WJ4, indicating that the mutant strain RAΔ604 could be used as a potential vaccine candidate in the future.
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Affiliation(s)
- Guijing Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
- Yangzhou University, Yangzhou, People’s Republic of China
| | - Xiaolan Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Yafeng Dou
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Shaohui Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Mingxing Tian
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Jingjing Qi
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Tao Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Chan Ding
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Yantao Wu
- Yangzhou University, Yangzhou, People’s Republic of China
| | - Shengqing Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
- * E-mail:
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González-Thuillier I, Venegas-Calerón M, Sánchez R, Garcés R, von Wettstein-Knowles P, Martínez-Force E. Sunflower (Helianthus annuus) fatty acid synthase complex: β-hydroxyacyl-[acyl carrier protein] dehydratase genes. PLANTA 2016; 243:397-410. [PMID: 26433735 DOI: 10.1007/s00425-015-2410-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 09/14/2015] [Indexed: 05/19/2023]
Abstract
Two sunflower hydroxyacyl-[acyl carrier protein] dehydratases evolved into two different isoenzymes showing distinctive expression levels and kinetics' efficiencies. β-Hydroxyacyl-[acyl carrier protein (ACP)]-dehydratase (HAD) is a component of the type II fatty acid synthase complex involved in 'de novo' fatty acid biosynthesis in plants. This complex, formed by four intraplastidial proteins, is responsible for the sequential condensation of two-carbon units, leading to 16- and 18-C acyl-ACP. HAD dehydrates 3-hydroxyacyl-ACP generating trans-2-enoyl-ACP. With the aim of a further understanding of fatty acid biosynthesis in sunflower (Helianthus annuus) seeds, two β-hydroxyacyl-[ACP] dehydratase genes have been cloned from developing seeds, HaHAD1 (GenBank HM044767) and HaHAD2 (GenBank GU595454). Genomic DNA gel blot analyses suggest that both are single copy genes. Differences in their expression patterns across plant tissues were detected. Higher levels of HaHAD2 in the initial stages of seed development inferred its key role in seed storage fatty acid synthesis. That HaHAD1 expression levels remained constant across most tissues suggest a housekeeping function. Heterologous expression of these genes in E. coli confirmed both proteins were functional and able to interact with the bacterial complex 'in vivo'. The large increase of saturated fatty acids in cells expressing HaHAD1 and HaHAD2 supports the idea that these HAD genes are closely related to the E. coli FabZ gene. The proposed three-dimensional models of HaHAD1 and HaHAD2 revealed differences at the entrance to the catalytic tunnel attributable to Phe166/Val1159, respectively. HaHAD1 F166V was generated to study the function of this residue. The 'in vitro' enzymatic characterization of the three HAD proteins demonstrated all were active, with the mutant having intermediate K m and V max values to the wild-type proteins.
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Affiliation(s)
- Irene González-Thuillier
- Instituto de la Grasa (CSIC), Edificio 46, Campus Universitario Pablo de Olavide, Carretera de Utrera Km 1., 41013, Seville, Spain
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, AL5 2JQ, Herts, UK
| | - Mónica Venegas-Calerón
- Instituto de la Grasa (CSIC), Edificio 46, Campus Universitario Pablo de Olavide, Carretera de Utrera Km 1., 41013, Seville, Spain.
| | - Rosario Sánchez
- Instituto de la Grasa (CSIC), Edificio 46, Campus Universitario Pablo de Olavide, Carretera de Utrera Km 1., 41013, Seville, Spain
| | - Rafael Garcés
- Instituto de la Grasa (CSIC), Edificio 46, Campus Universitario Pablo de Olavide, Carretera de Utrera Km 1., 41013, Seville, Spain
| | | | - Enrique Martínez-Force
- Instituto de la Grasa (CSIC), Edificio 46, Campus Universitario Pablo de Olavide, Carretera de Utrera Km 1., 41013, Seville, Spain
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40
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Regulated Control of the Assembly and Diversity of LPS by Noncoding sRNAs. BIOMED RESEARCH INTERNATIONAL 2015; 2015:153561. [PMID: 26618164 PMCID: PMC4651636 DOI: 10.1155/2015/153561] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/07/2015] [Accepted: 10/13/2015] [Indexed: 01/31/2023]
Abstract
The outer membrane (OM) of Gram-negative bacteria is asymmetric due to the presence of lipopolysaccharide (LPS) facing the outer leaflet of the OM and phospholipids facing the periplasmic side. LPS is essential for bacterial viability, since it provides a permeability barrier and is a major virulence determinant in pathogenic bacteria. In Escherichia coli, several steps of LPS biosynthesis and assembly are regulated by the RpoE sigma factor and stress responsive two-component systems as well as dedicated small RNAs. LPS composition is highly heterogeneous and dynamically altered upon stress and other challenges in the environment because of the transcriptional activation of RpoE regulon members and posttranslational control by RpoE-regulated Hfq-dependent RybB and MicA sRNAs. The PhoP/Q two-component system further regulates Kdo2-lipid A modification via MgrR sRNA. Some of these structural alterations are critical for antibiotic resistance, OM integrity, virulence, survival in host, and adaptation to specific environmental niches. The heterogeneity arises following the incorporation of nonstoichiometric modifications in the lipid A part and alterations in the composition of inner and outer core of LPS. The biosynthesis of LPS and phospholipids is tightly coupled. This requires the availability of metabolic precursors, whose accumulation is controlled by sRNAs like SlrA, GlmZ, and GlmY.
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Abstract
The pathways in Escherichia coli and (largely by analogy) S. enterica remain the paradigm of bacterial lipid synthetic pathways, although recently considerable diversity among bacteria in the specific areas of lipid synthesis has been demonstrated. The structural biology of the fatty acid synthetic proteins is essentially complete. However, the membrane-bound enzymes of phospholipid synthesis remain recalcitrant to structural analyses. Recent advances in genetic technology have allowed the essentialgenes of lipid synthesis to be tested with rigor, and as expected most genes are essential under standard growth conditions. Conditionally lethal mutants are available in numerous genes, which facilitates physiological analyses. The array of genetic constructs facilitates analysis of the functions of genes from other organisms. Advances in mass spectroscopy have allowed very accurate and detailed analyses of lipid compositions as well as detection of the interactions of lipid biosynthetic proteins with one another and with proteins outside the lipid pathway. The combination of these advances has resulted in use of E. coli and S. enterica for discovery of new antimicrobials targeted to lipid synthesis and in deciphering the molecular actions of known antimicrobials. Finally,roles for bacterial fatty acids other than as membrane lipid structural components have been uncovered. For example, fatty acid synthesis plays major roles in the synthesis of the essential enzyme cofactors, biotin and lipoic acid. Although other roles for bacterial fatty acids, such as synthesis of acyl-homoserine quorum-sensing molecules, are not native to E. coli introduction of the relevant gene(s) synthesis of these foreign molecules readily proceeds and the sophisticated tools available can used to decipher the mechanisms of synthesis of these molecules.
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Emiola A, George J, Andrews SS. A Complete Pathway Model for Lipid A Biosynthesis in Escherichia coli. PLoS One 2015; 10:e0121216. [PMID: 25919634 PMCID: PMC4412817 DOI: 10.1371/journal.pone.0121216] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Accepted: 02/12/2015] [Indexed: 11/19/2022] Open
Abstract
Lipid A is a highly conserved component of lipopolysaccharide (LPS), itself a major component of the outer membrane of Gram-negative bacteria. Lipid A is essential to cells and elicits a strong immune response from humans and other animals. We developed a quantitative model of the nine enzyme-catalyzed steps of Escherichia coli lipid A biosynthesis, drawing parameters from the experimental literature. This model accounts for biosynthesis regulation, which occurs through regulated degradation of the LpxC and WaaA (also called KdtA) enzymes. The LpxC degradation signal appears to arise from the lipid A disaccharide concentration, which we deduced from prior results, model results, and new LpxK overexpression results. The model agrees reasonably well with many experimental findings, including the lipid A production rate, the behaviors of mutants with defective LpxA enzymes, correlations between LpxC half-lives and cell generation times, and the effects of LpxK overexpression on LpxC concentrations. Its predictions also differ from some experimental results, which suggest modifications to the current understanding of the lipid A pathway, such as the possibility that LpxD can replace LpxA and that there may be metabolic channeling between LpxH and LpxB. The model shows that WaaA regulation may serve to regulate the lipid A production rate when the 3-deoxy-D-manno-oct-2-ulosonic acid (KDO) concentration is low and/or to control the number of KDO residues that get attached to lipid A. Computation of flux control coefficients showed that LpxC is the rate-limiting enzyme if pathway regulation is ignored, but that LpxK is the rate-limiting enzyme if pathway regulation is present, as it is in real cells. Control also shifts to other enzymes if the pathway substrate concentrations are not in excess. Based on these results, we suggest that LpxK may be a much better drug target than LpxC, which has been pursued most often.
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Affiliation(s)
- Akintunde Emiola
- School of Health, Sports and Bioscience, University of East London, London, United Kingdom
- * E-mail:
| | - John George
- School of Health, Sports and Bioscience, University of East London, London, United Kingdom
| | - Steven S. Andrews
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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43
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Finzel K, Lee DJ, Burkart MD. Using modern tools to probe the structure-function relationship of fatty acid synthases. Chembiochem 2015; 16:528-547. [PMID: 25676190 PMCID: PMC4545599 DOI: 10.1002/cbic.201402578] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Indexed: 12/25/2022]
Abstract
Fatty acid biosynthesis is essential to life and represents one of the most conserved pathways in nature, preserving the same handful of chemical reactions across all species. Recent interest in the molecular details of the de novo fatty acid synthase (FAS) has been heightened by demand for renewable fuels and the emergence of multidrug-resistant bacterial strains. Central to FAS is the acyl carrier protein (ACP), a protein chaperone that shuttles the growing acyl chain between catalytic enzymes within the FAS. Human efforts to alter fatty acid biosynthesis for oil production, chemical feedstock, or antimicrobial purposes has been met with limited success, due in part to a lack of detailed molecular information behind the ACP-partner protein interactions inherent to the pathway. This review will focus on recently developed tools for the modification of ACP and analysis of protein-protein interactions, such as mechanism-based crosslinking, and the studies exploiting them. Discussion specific to each enzymatic domain will focus first on mechanism and known inhibitors, followed by available structures and known interactions with ACP. Although significant unknowns remain, new understandings of the intricacies of FAS point to future advances in manipulating this complex molecular factory.
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Affiliation(s)
- Kara Finzel
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358 (USA)
| | - D. John Lee
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358 (USA)
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358 (USA)
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44
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Torto-Alalibo T, Purwantini E, Lomax J, Setubal JC, Mukhopadhyay B, Tyler BM. Genetic resources for advanced biofuel production described with the Gene Ontology. Front Microbiol 2014; 5:528. [PMID: 25346727 PMCID: PMC4193338 DOI: 10.3389/fmicb.2014.00528] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 09/22/2014] [Indexed: 12/12/2022] Open
Abstract
Dramatic increases in research in the area of microbial biofuel production coupled with high-throughput data generation on bioenergy-related microbes has led to a deluge of information in the scientific literature and in databases. Consolidating this information and making it easily accessible requires a unified vocabulary. The Gene Ontology (GO) fulfills that requirement, as it is a well-developed structured vocabulary that describes the activities and locations of gene products in a consistent manner across all kingdoms of life. The Microbial ENergy processes Gene Ontology () project is extending the GO to include new terms to describe microbial processes of interest to bioenergy production. Our effort has added over 600 bioenergy related terms to the Gene Ontology. These terms will aid in the comprehensive annotation of gene products from diverse energy-related microbial genomes. An area of microbial energy research that has received a lot of attention is microbial production of advanced biofuels. These include alcohols such as butanol, isopropanol, isobutanol, and fuels derived from fatty acids, isoprenoids, and polyhydroxyalkanoates. These fuels are superior to first generation biofuels (ethanol and biodiesel esterified from vegetable oil or animal fat), can be generated from non-food feedstock sources, can be used as supplements or substitutes for gasoline, diesel and jet fuels, and can be stored and distributed using existing infrastructure. Here we review the roles of genes associated with synthesis of advanced biofuels, and at the same time introduce the use of the GO to describe the functions of these genes in a standardized way.
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Affiliation(s)
- Trudy Torto-Alalibo
- Department of Biochemistry, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
| | - Endang Purwantini
- Department of Biochemistry, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
| | - Jane Lomax
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome CampusCambridge, UK
| | - João C. Setubal
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
- Departamento de Bioquímica, Instituto de Química, Universidade de São PauloSão Paulo, Brazil
| | - Biswarup Mukhopadhyay
- Department of Biochemistry, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
- Department of Biological Sciences, Oregon State UniversityCorvallis, OR, USA
| | - Brett M. Tyler
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
- Center for Genome Research and Biocomputing, Oregon State UniversityCorvallis, OR, USA
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45
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Metabolic engineering of Escherichia coli for efficient free fatty acid production from glycerol. Metab Eng 2014; 25:82-91. [PMID: 25014174 DOI: 10.1016/j.ymben.2014.06.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 06/23/2014] [Accepted: 06/26/2014] [Indexed: 01/15/2023]
Abstract
Crude glycerol, generated as waste by-product in biodiesel production process, has been considered as an important carbon source for converting to value-added bioproducts recently. Free fatty acids (FFAs) can be used as precursors for the production of biofuels or biochemicals. Microbial biosynthesis of FFAs can be achieved by introducing an acyl-acyl carrier protein thioesterase into Escherichia coli. In this study, the effect of metabolic manipulation of FFAs synthesis cycle, host genetic background and cofactor engineering on FFAs production using glycerol as feed stocks was investigated. The highest concentration of FFAs produced by the engineered stain reached 4.82g/L with the yield of 29.55% (g FFAs/g glycerol), about 83% of the maximum theoretical pathway value by the type II fatty acid synthesis pathway. In addition, crude glycerol from biodiesel plant was also used as feedstock in this study. The FFA production was 3.53g/L with a yield of 24.13%. The yield dropped slightly when crude glycerol was used as a carbon source instead of pure glycerol, while it still can reach about 68% of the maximum theoretical pathway yield.
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46
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Characterization of Amaranthus cruentus L. seed proteins by 2-DE and LC/MS–MS: Identification and cloning of a novel late embryogenesis-abundant protein. J Cereal Sci 2014. [DOI: 10.1016/j.jcs.2014.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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47
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Dissecting Escherichia coli outer membrane biogenesis using differential proteomics. PLoS One 2014; 9:e100941. [PMID: 24967819 PMCID: PMC4072712 DOI: 10.1371/journal.pone.0100941] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 05/30/2014] [Indexed: 11/19/2022] Open
Abstract
The cell envelope of Gram-negative bacteria is a complex multi-layered structure comprising an inner cytoplasmic membrane and an additional asymmetric lipid bilayer, the outer membrane, which functions as a selective permeability barrier and is essential for viability. Lipopolysaccharide, an essential glycolipid located in the outer leaflet of the outer membrane, greatly contributes to the peculiar properties exhibited by the outer membrane. This complex molecule is transported to the cell surface by a molecular machine composed of seven essential proteins LptABCDEFG that form a transenvelope complex and function as a single device. While advances in understanding the mechanisms that govern the biogenesis of the cell envelope have been recently made, only few studies are available on how bacterial cells respond to severe envelope biogenesis defects on a global scale. Here we report the use of differential proteomics based on Multidimensional Protein Identification Technology (MudPIT) to investigate how Escherichia coli cells respond to a block of lipopolysaccharide transport to the outer membrane. We analysed the envelope proteome of a lptC conditional mutant grown under permissive and non permissive conditions and identified 123 proteins whose level is modulated upon LptC depletion. Most such proteins belong to pathways implicated in cell envelope biogenesis, peptidoglycan remodelling, cell division and protein folding. Overall these data contribute to our understanding on how E. coli cells respond to LPS transport defects to restore outer membrane functionality.
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48
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Wang X, Quinn PJ, Yan A. Kdo2 -lipid A: structural diversity and impact on immunopharmacology. Biol Rev Camb Philos Soc 2014; 90:408-27. [PMID: 24838025 PMCID: PMC4402001 DOI: 10.1111/brv.12114] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Revised: 04/10/2014] [Accepted: 04/17/2014] [Indexed: 12/11/2022]
Abstract
3-deoxy-d-manno-octulosonic acid-lipid A (Kdo2-lipid A) is the essential component of lipopolysaccharide in most Gram-negative bacteria and the minimal structural component to sustain bacterial viability. It serves as the active component of lipopolysaccharide to stimulate potent host immune responses through the complex of Toll-like-receptor 4 (TLR4) and myeloid differentiation protein 2. The entire biosynthetic pathway of Escherichia coli Kdo2-lipid A has been elucidated and the nine enzymes of the pathway are shared by most Gram-negative bacteria, indicating conserved Kdo2-lipid A structure across different species. Yet many bacteria can modify the structure of their Kdo2-lipid A which serves as a strategy to modulate bacterial virulence and adapt to different growth environments as well as to avoid recognition by the mammalian innate immune systems. Key enzymes and receptors involved in Kdo2-lipid A biosynthesis, structural modification and its interaction with the TLR4 pathway represent a clear opportunity for immunopharmacological exploitation. These include the development of novel antibiotics targeting key biosynthetic enzymes and utilization of structurally modified Kdo2-lipid A or correspondingly engineered live bacteria as vaccines and adjuvants. Kdo2-lipid A/TLR4 antagonists can also be applied in anti-inflammatory interventions. This review summarizes recent knowledge on both the fundamental processes of Kdo2-lipid A biosynthesis, structural modification and immune stimulation, and applied research on pharmacological exploitations of these processes for therapeutic development.
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Affiliation(s)
- Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, China
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49
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Polissi A, Sperandeo P. The lipopolysaccharide export pathway in Escherichia coli: structure, organization and regulated assembly of the Lpt machinery. Mar Drugs 2014; 12:1023-42. [PMID: 24549203 PMCID: PMC3944529 DOI: 10.3390/md12021023] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 01/22/2014] [Accepted: 01/28/2014] [Indexed: 01/12/2023] Open
Abstract
The bacterial outer membrane (OM) is a peculiar biological structure with a unique composition that contributes significantly to the fitness of Gram-negative bacteria in hostile environments. OM components are all synthesized in the cytosol and must, then, be transported efficiently across three compartments to the cell surface. Lipopolysaccharide (LPS) is a unique glycolipid that paves the outer leaflet of the OM. Transport of this complex molecule poses several problems to the cells due to its amphipatic nature. In this review, the multiprotein machinery devoted to LPS transport to the OM is discussed together with the challenges associated with this process and the solutions that cells have evolved to address the problem of LPS biogenesis.
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Affiliation(s)
- Alessandra Polissi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
| | - Paola Sperandeo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
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50
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Mahalakshmi S, Sunayana MR, SaiSree L, Reddy M. yciMis an essential gene required for regulation of lipopolysaccharide synthesis inEscherichia coli. Mol Microbiol 2013; 91:145-57. [DOI: 10.1111/mmi.12452] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2013] [Indexed: 11/26/2022]
Affiliation(s)
- S. Mahalakshmi
- CSIR-Centre for Cellular and Molecular Biology; Hyderabad India 500007
| | - M. R. Sunayana
- CSIR-Centre for Cellular and Molecular Biology; Hyderabad India 500007
| | - L. SaiSree
- CSIR-Centre for Cellular and Molecular Biology; Hyderabad India 500007
| | - Manjula Reddy
- CSIR-Centre for Cellular and Molecular Biology; Hyderabad India 500007
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