1
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Armbruster KM, Jiang J, Sartorio MG, Scott NE, Peterson JM, Sexton JZ, Feldman MF, Koropatkin NM. Identification and Characterization of the Lipoprotein N-acyltransferase in Bacteroides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596883. [PMID: 38853980 PMCID: PMC11160734 DOI: 10.1101/2024.05.31.596883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Members of the Bacteroidota compose a large portion of the human gut microbiota, contributing to overall gut health via the degradation of various polysaccharides. This process is facilitated by lipoproteins, globular proteins anchored to the cell surface by a lipidated N-terminal cysteine. Despite their importance, lipoprotein synthesis by these bacteria is understudied. In E. coli, the α-amino linked lipid of lipoproteins is added by the lipoprotein N-acyltransferase Lnt. Herein, we have identified a protein distinct from Lnt responsible for the same process in Bacteroides, named lipoprotein N-acyltransferase in Bacteroides (Lnb). Deletion of Lnb yields cells that synthesize diacylated lipoproteins, with impacts on cell viability and morphology, growth on polysaccharides, and protein composition of membranes and outer membrane vesicles (OMVs). Our results not only challenge the accepted paradigms of lipoprotein biosynthesis in Gram-negative bacteria, but also support the establishment of a new family of lipoprotein N-acyltransferases.
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Affiliation(s)
- Krista M Armbruster
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Jiawen Jiang
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Mariana G Sartorio
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Nichollas E Scott
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, 3000, Australia
| | - Jenna M Peterson
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Jonathan Z Sexton
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Mario F Feldman
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
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2
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Craven T, Nolan MD, Bailey J, Olatunji S, Bann SJ, Bowen K, Ostrovitsa N, Da Costa TM, Ballantine RD, Weichert D, Levine PM, Stewart LJ, Bhardwaj G, Geoghegan JA, Cochrane SA, Scanlan EM, Caffrey M, Baker D. Computational Design of Cyclic Peptide Inhibitors of a Bacterial Membrane Lipoprotein Peptidase. ACS Chem Biol 2024; 19:1125-1130. [PMID: 38712757 PMCID: PMC11106742 DOI: 10.1021/acschembio.4c00076] [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] [Indexed: 05/08/2024]
Abstract
There remains a critical need for new antibiotics against multi-drug-resistant Gram-negative bacteria, a major global threat that continues to impact mortality rates. Lipoprotein signal peptidase II is an essential enzyme in the lipoprotein biosynthetic pathway of Gram-negative bacteria, making it an attractive target for antibacterial drug discovery. Although natural inhibitors of LspA have been identified, such as the cyclic depsipeptide globomycin, poor stability and production difficulties limit their use in a clinical setting. We harness computational design to generate stable de novo cyclic peptide analogues of globomycin. Only 12 peptides needed to be synthesized and tested to yield potent inhibitors, avoiding costly preparation of large libraries and screening campaigns. The most potent analogues showed comparable or better antimicrobial activity than globomycin in microdilution assays against ESKAPE-E pathogens. This work highlights computational design as a general strategy to combat antibiotic resistance.
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Affiliation(s)
- Timothy
W. Craven
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Mark D. Nolan
- School
of Chemistry, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Jonathan Bailey
- School
of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
- Biological
Inorganic Chemistry Laboratory, The Francis
Crick Institute, London NW1 1AT, U.K.
| | - Samir Olatunji
- School
of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Samantha J. Bann
- School
of
Chemistry and Chemical Engineering, Queen’s
University Belfast, David
Keir Building, Stranmillis Road, Belfast BT9 5AG, U.K.
| | - Katherine Bowen
- School
of Chemistry, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Nikita Ostrovitsa
- School
of Chemistry, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Thaina M. Da Costa
- Department
of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College
Dublin, Dublin D02 VF25, Ireland
| | - Ross D. Ballantine
- School
of
Chemistry and Chemical Engineering, Queen’s
University Belfast, David
Keir Building, Stranmillis Road, Belfast BT9 5AG, U.K.
| | - Dietmar Weichert
- School
of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Paul M. Levine
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Lance J. Stewart
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Gaurav Bhardwaj
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Joan A. Geoghegan
- Department
of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College
Dublin, Dublin D02 VF25, Ireland
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, U.K.
| | - Stephen A. Cochrane
- School
of
Chemistry and Chemical Engineering, Queen’s
University Belfast, David
Keir Building, Stranmillis Road, Belfast BT9 5AG, U.K.
| | - Eoin M. Scanlan
- School
of Chemistry, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Martin Caffrey
- School
of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
| | - David Baker
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Howard
Hughes Medical Institute, University of
Washington, Seattle, Washington 98195, United States
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3
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McClain MS, Boeglin WE, Algood HMS, Brash AR. Fatty acids of Helicobacter pylori lipoproteins CagT and Lpp20. Microbiol Spectr 2024; 12:e0047024. [PMID: 38501821 PMCID: PMC11064636 DOI: 10.1128/spectrum.00470-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 03/04/2024] [Indexed: 03/20/2024] Open
Abstract
Bacterial lipoproteins are post-translationally modified by the addition of acyl chains that anchor the protein to bacterial membranes. This modification includes two ester-linked and one amide-linked acyl chain on lipoproteins from Gram-negative bacteria. Helicobacter pylori lipoproteins have important functions in pathogenesis (including delivering the CagA oncoprotein to mammalian cells) and are recognized by host innate and adaptive immune systems. The number and variety of acyl chains on lipoproteins impact the innate immune response through Toll-like receptor 2. The acyl chains added to lipoproteins are derived from membrane phospholipids. H. pylori membrane phospholipids have previously been shown to consist primarily of C14:0 and C19:0 cyclopropane-containing acyl chains. However, the acyl composition of H. pylori lipoproteins has not been determined. In this study, we characterized the acyl composition of two representative H. pylori lipoproteins, Lpp20 and CagT. Fatty acid methyl esters were prepared from both purified lipoproteins and analyzed by gas chromatography-mass spectrometry. For comparison, we also analyzed H. pylori phospholipids. Consistent with previous studies, we observed that the H. pylori phospholipids contain primarily C14:0 and C19:0 cyclopropane-containing fatty acids. In contrast, both the ester-linked and amide-linked fatty acids found in H. pylori lipoproteins were observed to be almost exclusively C16:0 and C18:0. A discrepancy between the acyl composition of membrane phospholipids and lipoproteins as reported here for H. pylori has been previously reported in other bacteria including Borrelia and Brucella. We discuss possible mechanisms.IMPORTANCEColonization of the stomach by Helicobacter pylori is an important risk factor in the development of gastric cancer, the third leading cause of cancer-related death worldwide. H. pylori persists in the stomach despite an immune response against the bacteria. Recognition of lipoproteins by TLR2 contributes to the innate immune response to H. pylori. However, the role of H. pylori lipoproteins in bacterial persistence is poorly understood. As the host response to lipoproteins depends on the acyl chain content, defining the acyl composition of H. pylori lipoproteins is an important step in characterizing how lipoproteins contribute to persistence.
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Affiliation(s)
- Mark S. McClain
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - William E. Boeglin
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Holly M. Scott Algood
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Center for Immunobiology, Vanderbilt Medical Center, Nashville, Tennessee, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, USA
| | - Alan R. Brash
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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4
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Krawinski P, Smithers L, van Dalsen L, Boland C, Ostrovitsa N, Pérez J, Caffrey M. 7.10 MAG. A Novel Host Monoacylglyceride for In Meso (Lipid Cubic Phase) Crystallization of Membrane Proteins. CRYSTAL GROWTH & DESIGN 2024; 24:2985-3001. [PMID: 38585376 PMCID: PMC10995948 DOI: 10.1021/acs.cgd.4c00087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 04/09/2024]
Abstract
A novel monoacylglycerol, 7.10 MAG, has been produced for use in the in meso (lipid cubic phase) crystallization of membrane proteins and complexes. 7.10 MAG differs from monoolein, the most extensively used lipid for in meso crystallization, in that it is shorter in chain length by one methylene and its cis olefinic bond is two carbons closer to the glycerol headgroup. These changes in structure alter the phase behavior of the hydrated lipid and the microstructure of the corresponding mesophases formed. Temperature-composition phase diagrams for 7.10 MAG have been constructed using small- and wide-angle X-ray scattering over a range of temperatures and hydration levels that span those used for crystallization. The phase diagrams include lamellar crystalline, fluid isotropic, lamellar liquid-crystalline, cubic-Ia3d, and cubic-Pn3m phases, as observed with monoolein. Conspicuous by its absence is the inverted hexagonal phase which is rationalized on the basis of 7.10 MAG's chemical constitution. The cubic phase prepared with the new lipid facilitates the growth of crystals that were used to generate high-resolution structures of intramembrane β-barrel and α-helical proteins. Compatibility of fully hydrated 7.10 MAG with cholesterol and phosphatidylcholine means that these two lipids can be used as additives to optimize crystallogenesis in screening trials with 7.10 MAG as the host lipid.
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Affiliation(s)
- Pawel Krawinski
- Membrane
Structural and Functional Biology Group, School of Medicine and School
of Biochemistry and Immunology, Trinity
College Dublin, Dublin D02 R590, Ireland
| | - Luke Smithers
- Membrane
Structural and Functional Biology Group, School of Medicine and School
of Biochemistry and Immunology, Trinity
College Dublin, Dublin D02 R590, Ireland
| | - Leendert van Dalsen
- Membrane
Structural and Functional Biology Group, School of Medicine and School
of Biochemistry and Immunology, Trinity
College Dublin, Dublin D02 R590, Ireland
- School
of Chemistry, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Coilin Boland
- Membrane
Structural and Functional Biology Group, School of Medicine and School
of Biochemistry and Immunology, Trinity
College Dublin, Dublin D02 R590, Ireland
| | - Nikita Ostrovitsa
- School
of Chemistry, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Javier Pérez
- SWING
Beamline, Synchrotron Soleil, Saint-Aubin 91190, France
| | - Martin Caffrey
- Membrane
Structural and Functional Biology Group, School of Medicine and School
of Biochemistry and Immunology, Trinity
College Dublin, Dublin D02 R590, Ireland
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5
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Miravet-Verde S, Mazzolini R, Segura-Morales C, Broto A, Lluch-Senar M, Serrano L. ProTInSeq: transposon insertion tracking by ultra-deep DNA sequencing to identify translated large and small ORFs. Nat Commun 2024; 15:2091. [PMID: 38453908 PMCID: PMC10920889 DOI: 10.1038/s41467-024-46112-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/14/2024] [Indexed: 03/09/2024] Open
Abstract
Identifying open reading frames (ORFs) being translated is not a trivial task. ProTInSeq is a technique designed to characterize proteomes by sequencing transposon insertions engineered to express a selection marker when they occur in-frame within a protein-coding gene. In the bacterium Mycoplasma pneumoniae, ProTInSeq identifies 83% of its annotated proteins, along with 5 proteins and 153 small ORF-encoded proteins (SEPs; ≤100 aa) that were not previously annotated. Moreover, ProTInSeq can be utilized for detecting translational noise, as well as for relative quantification and transmembrane topology estimation of fitness and non-essential proteins. By integrating various identification approaches, the number of initially annotated SEPs in this bacterium increases from 27 to 329, with a quarter of them predicted to possess antimicrobial potential. Herein, we describe a methodology complementary to Ribo-Seq and mass spectroscopy that can identify SEPs while providing other insights in a proteome with a flexible and cost-effective DNA ultra-deep sequencing approach.
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Affiliation(s)
- Samuel Miravet-Verde
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003, Barcelona, Spain.
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland.
| | | | - Carolina Segura-Morales
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003, Barcelona, Spain
| | - Alicia Broto
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003, Barcelona, Spain
| | - Maria Lluch-Senar
- Pulmobiotics, Dr Aiguader 88, 08003, Barcelona, Spain.
- Institute of Biotechnology and Biomedicine "Vicent Villar Palasi" (IBB), Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- ICREA, Pg. Lluis Companys 23, 08010, Barcelona, Spain.
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6
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Smithers L, Degtjarik O, Weichert D, Huang CY, Boland C, Bowen K, Oluwole A, Lutomski C, Robinson CV, Scanlan EM, Wang M, Olieric V, Shalev-Benami M, Caffrey M. Structure snapshots reveal the mechanism of a bacterial membrane lipoprotein N-acyltransferase. SCIENCE ADVANCES 2023; 9:eadf5799. [PMID: 37390210 PMCID: PMC10313180 DOI: 10.1126/sciadv.adf5799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 05/26/2023] [Indexed: 07/02/2023]
Abstract
Bacterial lipoproteins (BLPs) decorate the surface of membranes in the cell envelope. They function in membrane assembly and stability, as enzymes, and in transport. The final enzyme in the BLP synthesis pathway is the apolipoprotein N-acyltransferase, Lnt, which is proposed to act by a ping-pong mechanism. Here, we use x-ray crystallography and cryo-electron microscopy to chart the structural changes undergone during the progress of the enzyme through the reaction. We identify a single active site that has evolved to bind, individually and sequentially, substrates that satisfy structural and chemical criteria to position reactive parts next to the catalytic triad for reaction. This study validates the ping-pong mechanism, explains the molecular bases for Lnt's substrate promiscuity, and should facilitate the design of antibiotics with minimal off-target effects.
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Affiliation(s)
- Luke Smithers
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Oksana Degtjarik
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Dietmar Weichert
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Chia-Ying Huang
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Coilín Boland
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Katherine Bowen
- School of Chemistry, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Abraham Oluwole
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Corinne Lutomski
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Eoin M. Scanlan
- School of Chemistry, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Moran Shalev-Benami
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Martin Caffrey
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
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7
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Kadeřábková N, Mahmood AJS, Furniss RCD, Mavridou DAI. Making a chink in their armor: Current and next-generation antimicrobial strategies against the bacterial cell envelope. Adv Microb Physiol 2023; 83:221-307. [PMID: 37507160 PMCID: PMC10517717 DOI: 10.1016/bs.ampbs.2023.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Gram-negative bacteria are uniquely equipped to defeat antibiotics. Their outermost layer, the cell envelope, is a natural permeability barrier that contains an array of resistance proteins capable of neutralizing most existing antimicrobials. As a result, its presence creates a major obstacle for the treatment of resistant infections and for the development of new antibiotics. Despite this seemingly impenetrable armor, in-depth understanding of the cell envelope, including structural, functional and systems biology insights, has promoted efforts to target it that can ultimately lead to the generation of new antibacterial therapies. In this article, we broadly overview the biology of the cell envelope and highlight attempts and successes in generating inhibitors that impair its function or biogenesis. We argue that the very structure that has hampered antibiotic discovery for decades has untapped potential for the design of novel next-generation therapeutics against bacterial pathogens.
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Affiliation(s)
- Nikol Kadeřábková
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - Ayesha J S Mahmood
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - R Christopher D Furniss
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Despoina A I Mavridou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States; John Ring LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, TX, United States.
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8
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Atz K, Guba W, Grether U, Schneider G. Machine Learning and Computational Chemistry for the Endocannabinoid System. Methods Mol Biol 2023; 2576:477-493. [PMID: 36152211 DOI: 10.1007/978-1-0716-2728-0_39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Computational methods in medicinal chemistry facilitate drug discovery and design. In particular, machine learning methodologies have recently gained increasing attention. This chapter provides a structured overview of the current state of computational chemistry and its applications for the interrogation of the endocannabinoid system (ECS), highlighting methods in structure-based drug design, virtual screening, ligand-based quantitative structure-activity relationship (QSAR) modeling, and de novo molecular design. We emphasize emerging methods in machine learning and anticipate a forecast of future opportunities of computational medicinal chemistry for the ECS.
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Affiliation(s)
- Kenneth Atz
- ETH Zurich, Department of Chemistry and Applied Biosciences, Zurich, Switzerland
| | - Wolfgang Guba
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Uwe Grether
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland.
| | - Gisbert Schneider
- ETH Zurich, Department of Chemistry and Applied Biosciences, Zurich, Switzerland
- ETH Singapore SEC Ltd, Singapore, Singapore
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9
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Bei W, Luo Q, Shi H, Zhou H, Zhou M, Zhang X, Huang Y. Cryo-EM structures of LolCDE reveal the molecular mechanism of bacterial lipoprotein sorting in Escherichia coli. PLoS Biol 2022; 20:e3001823. [PMID: 36228045 PMCID: PMC9595528 DOI: 10.1371/journal.pbio.3001823] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 10/25/2022] [Accepted: 09/12/2022] [Indexed: 11/06/2022] Open
Abstract
Bacterial lipoproteins perform a diverse array of functions including bacterial envelope biogenesis and microbe–host interactions. Lipoproteins in gram-negative bacteria are sorted to the outer membrane (OM) via the localization of lipoproteins (Lol) export pathway. The ATP-binding cassette (ABC) transporter LolCDE initiates the Lol pathway by selectively extracting and transporting lipoproteins for trafficking. Here, we report cryo-EM structures of LolCDE in apo, lipoprotein-bound, and AMPPNP-bound states at a resolution of 3.5 to 4.2 Å. Structure-based disulfide crosslinking, photo-crosslinking, and functional complementation assay verify the apo-state structure and reveal the molecular details regarding substrate selectivity and substrate entry route. Our studies snapshot 3 functional states of LolCDE in a transport cycle, providing deep insights into the mechanisms that underlie LolCDE-mediated lipoprotein sorting in E. coli. Lipoproteins in Gram-negative bacteria are sorted to the outer membrane via the Lol export pathway. The ABC transporter LolCDE initiates this pathway by selectively extracting and transporting lipoproteins for trafficking; this study provides a structural basis for the LolCDE-mediated bacterial lipoprotein sorting, with implications for novel antibiotic design against Gram-negative bacterial pathogens.
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Affiliation(s)
- Weiwei Bei
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qingshan Luo
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Huigang Shi
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haizhen Zhou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Min Zhou
- Institute of Bio-analytical Chemistry, School of Chemical Engineering, Nanjing University of Science and Technology, No.200 Xiao Ling Wei Street, Nanjing, China
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- * E-mail: (XZ); (YH)
| | - Yihua Huang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- * E-mail: (XZ); (YH)
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10
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Zhou J, Cai Y, Liu Y, An H, Deng K, Ashraf MA, Zou L, Wang J. Breaking down the cell wall: Still an attractive antibacterial strategy. Front Microbiol 2022; 13:952633. [PMID: 36212892 PMCID: PMC9544107 DOI: 10.3389/fmicb.2022.952633] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
Since the advent of penicillin, humans have known about and explored the phenomenon of bacterial inhibition via antibiotics. However, with changes in the global environment and the abuse of antibiotics, resistance mechanisms have been selected in bacteria, presenting huge threats and challenges to the global medical and health system. Thus, the study and development of new antimicrobials is of unprecedented urgency and difficulty. Bacteria surround themselves with a cell wall to maintain cell rigidity and protect against environmental insults. Humans have taken advantage of antibiotics to target the bacterial cell wall, yielding some of the most widely used antibiotics to date. The cell wall is essential for bacterial growth and virulence but is absent from humans, remaining a high-priority target for antibiotic screening throughout the antibiotic era. Here, we review the extensively studied targets, i.e., MurA, MurB, MurC, MurD, MurE, MurF, Alr, Ddl, MurI, MurG, lipid A, and BamA in the cell wall, starting from the very beginning to the latest developments to elucidate antimicrobial screening. Furthermore, recent advances, including MraY and MsbA in peptidoglycan and lipopolysaccharide, and tagO, LtaS, LspA, Lgt, Lnt, Tol-Pal, MntC, and OspA in teichoic acid and lipoprotein, have also been profoundly discussed. The review further highlights that the application of new methods such as macromolecular labeling, compound libraries construction, and structure-based drug design will inspire researchers to screen ideal antibiotics.
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Affiliation(s)
- Jingxuan Zhou
- The People’s Hospital of China Three Gorges University, Yichang, Hubei, China
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Yi Cai
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Ying Liu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Haoyue An
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Kaihong Deng
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Muhammad Awais Ashraf
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Lili Zou
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Jun Wang
- The People’s Hospital of China Three Gorges University, Yichang, Hubei, China
- *Correspondence: Jun Wang,
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11
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Smithers L, Olatunji S, Caffrey M. Bacterial Lipoprotein Posttranslational Modifications. New Insights and Opportunities for Antibiotic and Vaccine Development. Front Microbiol 2021; 12:788445. [PMID: 34950121 PMCID: PMC8689077 DOI: 10.3389/fmicb.2021.788445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 11/16/2021] [Indexed: 12/17/2022] Open
Abstract
Lipoproteins are some of the most abundant proteins in bacteria. With a lipid anchor to the cell membrane, they function as enzymes, inhibitors, transporters, structural proteins, and as virulence factors. Lipoproteins activate the innate immune system and have biotechnological applications. The first lipoprotein was described by Braun and Rehn in 1969. Up until recently, however, work on lipoproteins has been sluggish, in part due to the challenges of handling proteins that are anchored to membranes by covalently linked lipids or are membrane integral. Activity in the area has quickened of late. In the past 5 years, high-resolution structures of the membrane enzymes of the canonical lipoprotein synthesis pathway have been determined, new lipoprotein types have been discovered and the enzymes responsible for their synthesis have been characterized biochemically. This has led to a flurry of activity aimed at developing novel antibiotics targeting these enzymes. In addition, surface exposed bacterial lipoproteins have been utilized as candidate vaccine antigens, and their potential to act as self-adjuvanting antigens is increasingly recognized. A summary of the latest developments in lipoproteins and their synthesis, as well as how this information is being exploited for therapeutic purposes is presented here.
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Affiliation(s)
- Luke Smithers
- School of Medicine, Trinity College Dublin, Dublin, Ireland
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Samir Olatunji
- School of Medicine, Trinity College Dublin, Dublin, Ireland
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Martin Caffrey
- School of Medicine, Trinity College Dublin, Dublin, Ireland
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
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12
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Müller H, Terholsen H, Godehard SP, Badenhorst CPS, Bornscheuer UT. Recent Insights and Future Perspectives on Promiscuous Hydrolases/Acyltransferases. ACS Catal 2021. [DOI: 10.1021/acscatal.1c04543] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Henrik Müller
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
- Competence Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, 8820, Wädenswil, Switzerland
| | - Henrik Terholsen
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Simon P. Godehard
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Christoffel P. S. Badenhorst
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
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13
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Giglione C, Meinnel T. Mapping the myristoylome through a complete understanding of protein myristoylation biochemistry. Prog Lipid Res 2021; 85:101139. [PMID: 34793862 DOI: 10.1016/j.plipres.2021.101139] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 12/22/2022]
Abstract
Protein myristoylation is a C14 fatty acid modification found in all living organisms. Myristoylation tags either the N-terminal alpha groups of cysteine or glycine residues through amide bonds or lysine and cysteine side chains directly or indirectly via glycerol thioester and ester linkages. Before transfer to proteins, myristate must be activated into myristoyl coenzyme A in eukaryotes or, in bacteria, to derivatives like phosphatidylethanolamine. Myristate originates through de novo biosynthesis (e.g., plants), from external uptake (e.g., human tissues), or from mixed origins (e.g., unicellular organisms). Myristate usually serves as a molecular anchor, allowing tagged proteins to be targeted to membranes and travel across endomembrane networks in eukaryotes. In this review, we describe and discuss the metabolic origins of protein-bound myristate. We review strategies for in vivo protein labeling that take advantage of click-chemistry with reactive analogs, and we discuss new approaches to the proteome-wide discovery of myristate-containing proteins. The machineries of myristoylation are described, along with how protein targets can be generated directly from translating precursors or from processed proteins. Few myristoylation catalysts are currently described, with only N-myristoyltransferase described to date in eukaryotes. Finally, we describe how viruses and bacteria hijack and exploit myristoylation for their pathogenicity.
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Affiliation(s)
- Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
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14
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Vickery ON, Stansfeld PJ. CG2AT2: an Enhanced Fragment-Based Approach for Serial Multi-scale Molecular Dynamics Simulations. J Chem Theory Comput 2021; 17:6472-6482. [PMID: 34492188 PMCID: PMC8515810 DOI: 10.1021/acs.jctc.1c00295] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Coarse-grained molecular
dynamics provides a means for simulating
the assembly and interactions of macromolecular complexes at a reduced
level of representation, thereby allowing both longer timescale and
larger sized simulations. Here, we describe an enhanced fragment-based
protocol for converting macromolecular complexes from coarse-grained
to atomistic resolution, for further refinement and analysis. While
the focus is upon systems that comprise an integral membrane protein
embedded in a phospholipid bilayer, the technique is also suitable
for membrane-anchored and soluble protein/nucleotide complexes. Overall,
this provides a method for generating an accurate and well-equilibrated
atomic-level description of a macromolecular complex. The approach
is evaluated using a diverse test set of 11 system configurations
of varying size and complexity. Simulations are assessed in terms
of protein stereochemistry, conformational drift, lipid/protein interactions,
and lipid dynamics.
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Affiliation(s)
- Owen N Vickery
- School of Life Sciences & Department of Chemistry, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, U.K
| | - Phillip J Stansfeld
- School of Life Sciences & Department of Chemistry, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, U.K
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15
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Sharaf NG, Shahgholi M, Kim E, Lai JY, VanderVelde DG, Lee AT, Rees DC. Characterization of the ABC methionine transporter from Neisseria meningitidis reveals that lipidated MetQ is required for interaction. eLife 2021; 10:69742. [PMID: 34409939 PMCID: PMC8416018 DOI: 10.7554/elife.69742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 08/18/2021] [Indexed: 01/05/2023] Open
Abstract
NmMetQ is a substrate-binding protein (SBP) from Neisseria meningitidis that has been identified as a surface-exposed candidate antigen for meningococcal vaccines. However, this location for NmMetQ challenges the prevailing view that SBPs in Gram-negative bacteria are localized to the periplasmic space to promote interaction with their cognate ABC transporter embedded in the bacterial inner membrane. To elucidate the roles of NmMetQ, we characterized NmMetQ with and without its cognate ABC transporter (NmMetNI). Here, we show that NmMetQ is a lipoprotein (lipo-NmMetQ) that binds multiple methionine analogs and stimulates the ATPase activity of NmMetNI. Using single-particle electron cryo-microscopy, we determined the structures of NmMetNI in the presence and absence of lipo-NmMetQ. Based on our data, we propose that NmMetQ tethers to membranes via a lipid anchor and has dual function and localization, playing a role in NmMetNI-mediated transport at the inner membrane and moonlighting on the bacterial surface.
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Affiliation(s)
- Naima G Sharaf
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, United States
| | - Mona Shahgholi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - Esther Kim
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - Jeffrey Y Lai
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, United States
| | - David G VanderVelde
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - Allen T Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, United States
| | - Douglas C Rees
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, United States
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16
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McLean JT, Milbeo P, Lynch DM, McSweeney L, Scanlan EM. Radical‐Mediated Acyl Thiol‐Ene Reaction for Rapid Synthesis of Biomolecular Thioester Derivatives. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Joshua T. McLean
- School of Chemistry Trinity College Dublin The University of Dublin College Green Dublin 2 Ireland
| | - Pierre Milbeo
- School of Chemistry Trinity College Dublin The University of Dublin College Green Dublin 2 Ireland
| | - Dylan M. Lynch
- School of Chemistry Trinity College Dublin The University of Dublin College Green Dublin 2 Ireland
| | - Lauren McSweeney
- School of Chemistry Trinity College Dublin The University of Dublin College Green Dublin 2 Ireland
| | - Eoin M. Scanlan
- School of Chemistry Trinity College Dublin The University of Dublin College Green Dublin 2 Ireland
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17
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Olatunji S, Bowen K, Huang CY, Weichert D, Singh W, Tikhonova IG, Scanlan EM, Olieric V, Caffrey M. Structural basis of the membrane intramolecular transacylase reaction responsible for lyso-form lipoprotein synthesis. Nat Commun 2021; 12:4254. [PMID: 34253723 PMCID: PMC8275575 DOI: 10.1038/s41467-021-24475-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/08/2021] [Indexed: 11/08/2022] Open
Abstract
Lipoproteins serve diverse functions in the bacterial cell and some are essential for survival. Some lipoproteins are adjuvants eliciting responses from the innate immune system of the host. The growing list of membrane enzymes responsible for lipoprotein synthesis includes the recently discovered lipoprotein intramolecular transacylase, Lit. Lit creates a lipoprotein that is less immunogenic, possibly enabling the bacteria to gain a foothold in the host by stealth. Here, we report the crystal structure of the Lit enzyme from Bacillus cereus and describe its mechanism of action. Lit consists of four transmembrane helices with an extracellular cap. Conserved residues map to the cap-membrane interface. They include two catalytic histidines that function to effect unimolecular transacylation. The reaction involves acyl transfer from the sn-2 position of the glyceryl moiety to the amino group on the N-terminal cysteine of the substrate via an 8-membered ring intermediate. Transacylation takes place in a confined aromatic residue-rich environment that likely evolved to bring distant moieties on the substrate into proximity and proper orientation for catalysis.
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Affiliation(s)
- Samir Olatunji
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Katherine Bowen
- School of Chemistry, Trinity College Dublin, Dublin, Ireland
| | - Chia-Ying Huang
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Dietmar Weichert
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Warispreet Singh
- School of Pharmacy, Queen's University Belfast, Belfast, United Kingdom
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
- Hub for Biotechnology in Build Environment, Newcastle upon Tyne, United Kingdom
| | - Irina G Tikhonova
- School of Pharmacy, Queen's University Belfast, Belfast, United Kingdom
| | - Eoin M Scanlan
- School of Chemistry, Trinity College Dublin, Dublin, Ireland
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Martin Caffrey
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland.
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18
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Mychack A, Janakiraman A. Defects in The First Step of Lipoprotein Maturation Underlie The Synthetic Lethality of Escherichia coli Lacking The Inner Membrane Proteins YciB And DcrB. J Bacteriol 2021; 203:JB.00640-20. [PMID: 33431434 PMCID: PMC8095458 DOI: 10.1128/jb.00640-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 12/14/2020] [Indexed: 11/20/2022] Open
Abstract
Nearly a quarter of the Escherichia coli genome encodes for inner membrane proteins of which approximately a third have unassigned or poorly understood function. We had previously demonstrated that the synergy between the functional roles of the inner membrane-spanning YciB and the inner membrane lipoprotein DcrB, is essential in maintaining cell envelope integrity. In yciB dcrB cells, the abundant outer membrane lipoprotein, Lpp, mislocalizes to the inner membrane where it forms toxic linkages to peptidoglycan. Here, we report that the aberrant localization of Lpp in this double mutant is due to inefficient lipid modification at the first step in lipoprotein maturation. Both Cpx and Rcs signaling systems are upregulated in response to the envelope stress. The phosphatidylglycerol-pre-prolipoprotein diacylglyceryl transferase, Lgt, catalyzes the initial step in lipoprotein maturation. Our results suggest that the attenuation in Lgt-mediated transacylation in the double mutant is not a consequence of lowered phosphatidylglycerol levels. Instead, we posit that altered membrane fluidity, perhaps due to changes in lipid homeostasis, may lead to the impairment in Lgt function. Consistent with this idea, a dcrB null is not viable when grown at low temperatures, conditions which impact membrane fluidity. Like the yciB dcrB double mutant, dcrB null-mediated toxicity can be overcome in distinct ways - by increased expression of Lgt, deletion of lpp, or removal of Lpp-peptidoglycan linkages. The last of these events leads to elevated membrane vesiculation and lipid loss, which may, in turn, impact membrane homeostasis in the double mutant.Importance A distinguishing feature of Gram-negative bacteria is their double-membraned cell envelope which presents a formidable barrier against environmental stress. In E. coli, more than a quarter of the cellular proteins reside at the inner membrane but about a third of these proteins are functionally unassigned or their function is incompletely understood. Here, we show that the synthetic lethality underlying the inactivation of two inner membrane proteins, a small integral membrane protein YciB, and a lipoprotein, DcrB, results from the attenuation of the first step of lipoprotein maturation at the inner membrane. We propose that these two inner membrane proteins YciB and DcrB play a role in membrane homeostasis in E. coli and related bacteria.
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Affiliation(s)
- Aaron Mychack
- Department of Biology, 160 Convent Ave. MR 526, The City College of CUNY, New York, NY, 100031, USA
- Program in Biology, The Graduate Center, CUNY, Fifth Avenue, New York, NY, 10016, USA
| | - Anuradha Janakiraman
- Department of Biology, 160 Convent Ave. MR 526, The City College of CUNY, New York, NY, 100031, USA
- Program in Biology, The Graduate Center, CUNY, Fifth Avenue, New York, NY, 10016, USA
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19
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El Rayes J, Rodríguez-Alonso R, Collet JF. Lipoproteins in Gram-negative bacteria: new insights into their biogenesis, subcellular targeting and functional roles. Curr Opin Microbiol 2021; 61:25-34. [PMID: 33667939 DOI: 10.1016/j.mib.2021.02.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 02/06/2023]
Abstract
Bacterial lipoproteins are globular proteins anchored to a membrane by a lipid moiety. By discovering new functions carried out by lipoproteins, recent research has highlighted the crucial roles played by these proteins in the cell envelope of Gram-negative bacteria. Here, after discussing the wide range of activities carried out by lipoproteins in the model bacterium Escherichia coli, we review new insights into the essential mechanisms involved in lipoprotein maturation, sorting and targeting to their final destination. A special attention will also be given to the recent identification of lipoproteins on the surface of E. coli and of other bacteria. The renewed interest in lipoproteins is driven by the need to identify novel targets for antibiotic development.
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Affiliation(s)
- Jessica El Rayes
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Raquel Rodríguez-Alonso
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Jean-François Collet
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium.
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20
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Legood S, Boneca IG, Buddelmeijer N. Mode of action of lipoprotein modification enzymes-Novel antibacterial targets. Mol Microbiol 2021; 115:356-365. [PMID: 32979868 PMCID: PMC8048626 DOI: 10.1111/mmi.14610] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/10/2020] [Indexed: 01/04/2023]
Abstract
Lipoproteins are characterized by a fatty acid moiety at their amino-terminus through which they are anchored into membranes. They fulfill a variety of essential functions in bacterial cells, such as cell wall maintenance, virulence, efflux of toxic elements including antibiotics, and uptake of nutrients. The posttranslational modification process of lipoproteins involves the sequential action of integral membrane enzymes and phospholipids as acyl donors. In recent years, the structures of the lipoprotein modification enzymes have been solved by X-ray crystallography leading to a greater insight into their function and the molecular mechanism of the reactions. The catalytic domains of the enzymes are exposed to the periplasm or external milieu and are readily accessible to small molecules. Since the lipoprotein modification pathway is essential in proteobacteria, it is a potential target for the development of novel antibiotics. In this review, we discuss recent literature on the structural characterization of the enzymes, and the in vitro activity assays compatible with high-throughput screening for inhibitors, with perspectives on the development of new antimicrobial agents.
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Affiliation(s)
- Simon Legood
- Institut PasteurUnité Biologie et Génétique de la Paroi BactérienneParisFrance
- CNRS, UMR 2001 « Microbiologie intégrative et Moléculaire »ParisFrance
- INSERM Groupe AvenirParisFrance
- Université de ParisSorbonne Paris CitéParisFrance
| | - Ivo G. Boneca
- Institut PasteurUnité Biologie et Génétique de la Paroi BactérienneParisFrance
- CNRS, UMR 2001 « Microbiologie intégrative et Moléculaire »ParisFrance
- INSERM Groupe AvenirParisFrance
| | - Nienke Buddelmeijer
- Institut PasteurUnité Biologie et Génétique de la Paroi BactérienneParisFrance
- CNRS, UMR 2001 « Microbiologie intégrative et Moléculaire »ParisFrance
- INSERM Groupe AvenirParisFrance
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21
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Icke C, Hodges FJ, Pullela K, McKeand SA, Bryant JA, Cunningham AF, Cole JA, Henderson IR. Glycine acylation and trafficking of a new class of bacterial lipoprotein by a composite secretion system. eLife 2021; 10:63762. [PMID: 33625358 PMCID: PMC7943197 DOI: 10.7554/elife.63762] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/23/2021] [Indexed: 01/21/2023] Open
Abstract
Protein acylation is critical for many cellular functions across all domains of life. In bacteria, lipoproteins have important roles in virulence and are targets for the development of antimicrobials and vaccines. Bacterial lipoproteins are secreted from the cytosol via the Sec pathway and acylated on an N-terminal cysteine residue through the action of three enzymes. In Gram-negative bacteria, the Lol pathway transports lipoproteins to the outer membrane. Here, we demonstrate that the Aat secretion system is a composite system sharing similarity with elements of a type I secretion systems and the Lol pathway. During secretion, the AatD subunit acylates the substrate CexE on a highly conserved N-terminal glycine residue. Mutations disrupting glycine acylation interfere with membrane incorporation and trafficking. Our data reveal CexE as the first member of a new class of glycine-acylated lipoprotein, while Aat represents a new secretion system that displays the substrate lipoprotein on the cell surface.
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Affiliation(s)
- Christopher Icke
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Freya J Hodges
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Karthik Pullela
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | | | | | - Adam F Cunningham
- Institute of Microbiology and Infection, Birmingham, United Kingdom.,Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Jeff A Cole
- Institute of Microbiology and Infection, Birmingham, United Kingdom
| | - Ian R Henderson
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
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22
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Heywood A, Lamont IL. Cell envelope proteases and peptidases of Pseudomonas aeruginosa: multiple roles, multiple mechanisms. FEMS Microbiol Rev 2020; 44:857-873. [PMID: 32804218 DOI: 10.1093/femsre/fuaa036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 08/05/2020] [Indexed: 12/15/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium that is commonly isolated from damp environments. It is also a major opportunistic pathogen, causing a wide range of problematic infections. The cell envelope of P. aeruginosa, comprising the cytoplasmic membrane, periplasmic space, peptidoglycan layer and outer membrane, is critical to the bacteria's ability to adapt and thrive in a wide range of environments. Over 40 proteases and peptidases are located in the P. aeruginosa cell envelope. These enzymes play many crucial roles. They are required for protein secretion out of the cytoplasm to the periplasm, outer membrane, cell surface or the environment; for protein quality control and removal of misfolded proteins; for controlling gene expression, allowing adaptation to environmental changes; for modification and remodelling of peptidoglycan; and for metabolism of small molecules. The key roles of cell envelope proteases in ensuring normal cell functioning have prompted the development of inhibitors targeting some of these enzymes as potential new anti-Pseudomonas therapies. In this review, we summarise the current state of knowledge across the breadth of P. aeruginosa cell envelope proteases and peptidases, with an emphasis on recent findings, and highlight likely future directions in their study.
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Affiliation(s)
- Astra Heywood
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
| | - Iain L Lamont
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
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23
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Membrane protein crystallography in the era of modern structural biology. Biochem Soc Trans 2020; 48:2505-2524. [DOI: 10.1042/bst20200066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023]
Abstract
The aim of structural biology has been always the study of biological macromolecules structures and their mechanistic behaviour at molecular level. To achieve its goal, multiple biophysical methods and approaches have become part of the structural biology toolbox. Considered as one of the pillars of structural biology, X-ray crystallography has been the most successful method for solving three-dimensional protein structures at atomic level to date. It is however limited by the success in obtaining well-ordered protein crystals that diffract at high resolution. This is especially true for challenging targets such as membrane proteins (MPs). Understanding structure-function relationships of MPs at the biochemical level is vital for medicine and drug discovery as they play critical roles in many cellular processes. Though difficult, structure determination of MPs by X-ray crystallography has significantly improved in the last two decades, mainly due to many relevant technological and methodological developments. Today, numerous MP crystal structures have been solved, revealing many of their mechanisms of action. Yet the field of structural biology has also been through significant technological breakthroughs in recent years, particularly in the fields of single particle electron microscopy (cryo-EM) and X-ray free electron lasers (XFELs). Here we summarise the most important advancements in the field of MP crystallography and the significance of these developments in the present era of modern structural biology.
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24
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Belmont-Monroy L, Saitz-Rojas W, Soria-Bustos J, Mickey AS, Sherman NE, Orsburn BC, Ruiz-Perez F, Santiago AE. Characterization of a novel AraC/XylS-regulated family of N-acyltransferases in pathogens of the order Enterobacterales. PLoS Pathog 2020; 16:e1008776. [PMID: 32845938 PMCID: PMC7478709 DOI: 10.1371/journal.ppat.1008776] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 09/08/2020] [Accepted: 07/04/2020] [Indexed: 11/18/2022] Open
Abstract
Enteroaggregative Escherichia coli (EAEC) is a diarrheagenic pathotype associated with traveler’s diarrhea, foodborne outbreaks and sporadic diarrhea in industrialized and developing countries. Regulation of virulence in EAEC is mediated by AggR and its negative regulator Aar. Together, they control the expression of at least 210 genes. On the other hand, we observed that about one third of Aar-regulated genes are related to metabolism and transport. In this study we show the AggR/Aar duo controls the metabolism of lipids. Accordingly, we show that AatD, encoded in the AggR-regulated aat operon (aatPABCD) is an N-acyltransferase structurally similar to the essential Apolipoprotein N-acyltransferase Lnt and is required for the acylation of Aap (anti-aggregation protein). Deletion of aatD impairs post-translational modification of Aap and causes its accumulation in the bacterial periplasm. trans-complementation of 042aatD mutant with the AatD homolog of ETEC or with the N-acyltransferase Lnt reestablished translocation of Aap. Site-directed mutagenesis of the E207 residue in the putative acyltransferase catalytic triad disrupted the activity of AatD and caused accumulation of Aap in the periplasm due to reduced translocation of Aap at the bacterial surface. Furthermore, Mass spectroscopy revealed that Aap is acylated in a putative lipobox at the N-terminal of the mature protein, implying that Aap is a lipoprotein. Lastly, deletion of aatD impairs bacterial colonization of the streptomycin-treated mouse model. Our findings unveiled a novel N-acyltransferase family associated with bacterial virulence, and that is tightly regulated by AraC/XylS regulators in the order Enterobacterales. Although the regulatory scheme of AggR is well understood, the biological relevance of half of AggR-regulated proteins remains unknown. In this study we provide experimental evidence that the AggR-regulated AatD is a novel N-acyltransferase restricted to pathogens of the order Enterobacterales, including EAEC, ETEC, Yersinia sp., and C. rodentium. AatD is structurally similar to Lnt. However, unlike Lnt which is essential for cellular functions, AatD is a dedicated N-acyltransferase required for post-translational modification of virulence factors. Aap was identified as a lipoprotein acylated by AatD. Lipid modification in Aap provides an important post-translational mechanism to regulate the trafficking, stability and subcellular localization of Aap. In the absence of AatD, Aap is retained in the periplasmic space and cannot be translocated to the bacterial surface, presumably, restricting the biological function of the protein. Our data suggest that AggR and Aar virulence regulators, not only regulate the expression of Aap virulence factor at the transcriptional level, but also regulate translocation of Aap to the bacterial surface, which is required for full virulence of EAEC, unveiling an important mechanism of virulence regulation.
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Affiliation(s)
- Laura Belmont-Monroy
- Department of Pediatrics, University of Virginia School of Medicine and University of Virginia Children’s Hospital, Charlottesville, Virginia, United States of America
- Department of Public Health, UNAM School of Medicine and Federico Gomez Children’s Hospital, Mexico City, Mexico
| | - Waleska Saitz-Rojas
- Department of Pediatrics, University of Virginia School of Medicine and University of Virginia Children’s Hospital, Charlottesville, Virginia, United States of America
| | - Jorge Soria-Bustos
- Department of Pediatrics, University of Virginia School of Medicine and University of Virginia Children’s Hospital, Charlottesville, Virginia, United States of America
| | - Abigail S. Mickey
- Department of Pediatrics, University of Virginia School of Medicine and University of Virginia Children’s Hospital, Charlottesville, Virginia, United States of America
| | - Nicholas E. Sherman
- W. M. Keck Biomedical Mass Spectrometry Lab. University of Virginia, Charlottesville, Virginia, United States of America
| | - Benjamin C. Orsburn
- W. M. Keck Biomedical Mass Spectrometry Lab. University of Virginia, Charlottesville, Virginia, United States of America
| | - Fernando Ruiz-Perez
- Department of Pediatrics, University of Virginia School of Medicine and University of Virginia Children’s Hospital, Charlottesville, Virginia, United States of America
| | - Araceli E. Santiago
- Department of Pediatrics, University of Virginia School of Medicine and University of Virginia Children’s Hospital, Charlottesville, Virginia, United States of America
- * E-mail: .
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Lipoprotein N-Acylation in Staphylococcus aureus Is Catalyzed by a Two-Component Acyl Transferase System. mBio 2020; 11:mBio.01619-20. [PMID: 32723923 PMCID: PMC7387801 DOI: 10.1128/mbio.01619-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Although it has long been known that S. aureus forms triacylated Lpps, a lack of homologs to known N-acylation genes found in Gram-negative bacteria has until now precluded identification of the genes responsible for this Lpp modification. Here, we demonstrate N-terminal Lpp acylation and chemotype conversion to the tri-acylated state is directed by a unique acyl transferase system encoded by two noncontiguous staphylococci genes (lnsAB). Since triacylated Lpps stimulate TLR2 more weakly than their diacylated counterparts, Lpp N-acylation is an important TLR2 immunoevasion factor for determining tolerance or nontolerance in niches such as in the skin microbiota. The discovery of the LnsAB system expands the known diversity of Lpp biosynthesis pathways and acyl transfer biochemistry in bacteria, advances our understanding of Lpp structural heterogeneity, and helps differentiate commensal and noncommensal microbiota. Bacterial lipoproteins (Lpps) are a class of membrane-associated proteins universally distributed among all bacteria. A characteristic N-terminal cysteine residue that is variably acylated anchors C-terminal globular domains to the extracellular surface, where they serve numerous roles, including in the capture and transport of essential nutrients. Lpps are also ligands for the Toll-like receptor 2 (TLR2) family, a key component of the innate immune system tasked with bacterial recognition. While Lpp function is conserved in all prokaryotes, structural heterogeneity in the N-terminal acylation state is widespread among Firmicutes and can differ between otherwise closely related species. In this study, we identify a novel two-gene system that directs the synthesis of N-acylated Lpps in the commensal and opportunistic pathogen subset of staphylococci. The two genes, which we have named the lipoprotein N-acylation transferase system (Lns), bear no resemblance to previously characterized N-terminal Lpp tailoring enzymes. LnsA (SAOUHSC_00822) is an NlpC/P60 superfamily enzyme, whereas LnsB (SAOHSC_02761) has remote homology to the CAAX protease and bacteriocin-processing enzyme (CPBP) family. Both LnsA and LnsB are together necessary and alone sufficient for N-acylation in Staphylococcus aureus and convert the Lpp chemotype from diacyl to triacyl when heterologously expressed in Listeria monocytogenes. Acquisition of lnsAB decreases TLR2-mediated detection of S. aureus by nearly 10-fold and shifts the activated TLR2 complex from TLR2/6 to TLR2/1. LnsAB thus has a dual role in attenuating TLR2 signaling in addition to a broader role in bacterial cell envelope physiology.
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Stix R, Lee CJ, Faraldo-Gómez JD, Banerjee A. Structure and Mechanism of DHHC Protein Acyltransferases. J Mol Biol 2020; 432:4983-4998. [PMID: 32522557 DOI: 10.1016/j.jmb.2020.05.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 01/01/2023]
Abstract
S-acylation, whereby a fatty acid chain is covalently linked to a cysteine residue by a thioester linkage, is the most prevalent kind of lipid modification of proteins. Thousands of proteins are targets of this post-translational modification, which is catalyzed by a family of eukaryotic integral membrane enzymes known as DHHC protein acyltransferases (DHHC-PATs). Our knowledge of the repertoire of S-acylated proteins has been rapidly expanding owing to development of the chemoproteomic techniques. There has also been an increasing number of reports in the literature documenting the importance of S-acylation in human physiology and disease. Recently, the first atomic structures of two different DHHC-PATs were determined using X-ray crystallography. This review will focus on the insights gained into the molecular mechanism of DHHC-PATs from these structures and highlight representative data from the biochemical literature that they help explain.
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Affiliation(s)
- Robyn Stix
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chul-Jin Lee
- Unit on Structural and Chemical Biology of Membrane Proteins, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anirban Banerjee
- Unit on Structural and Chemical Biology of Membrane Proteins, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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27
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Armbruster KM, Komazin G, Meredith TC. Bacterial lyso-form lipoproteins are synthesized via an intramolecular acyl chain migration. J Biol Chem 2020; 295:10195-10211. [PMID: 32471867 DOI: 10.1074/jbc.ra120.014000] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/22/2020] [Indexed: 01/08/2023] Open
Abstract
All bacterial lipoproteins share a variably acylated N-terminal cysteine residue. Gram-negative bacterial lipoproteins are triacylated with a thioether-linked diacylglycerol moiety and an N-acyl chain. The latter is transferred from a membrane phospholipid donor to the α-amino terminus by the enzyme lipoprotein N-acyltransferase (Lnt), using an active-site cysteine thioester covalent intermediate. Many Gram-positive Firmicutes also have N-acylated lipoproteins, but the enzymes catalyzing N-acylation remain uncharacterized. The integral membrane protein Lit (lipoprotein intramolecular transacylase) from the opportunistic nosocomial pathogen Enterococcus faecalis synthesizes a specific lysoform lipoprotein (N-acyl S-monoacylglycerol) chemotype by an unknown mechanism that helps this bacterium evade immune recognition by the Toll-like receptor 2 family complex. Here, we used a deuterium-labeled lipoprotein substrate with reconstituted Lit to investigate intramolecular acyl chain transfer. We observed that Lit transfers the sn-2 ester-linked lipid from the diacylglycerol moiety to the α-amino terminus without forming a covalent thioester intermediate. Utilizing Mut-Seq to analyze an alanine scan library of Lit alleles, we identified two stretches of functionally important amino acid residues containing two conserved histidines. Topology maps based on reporter fusion assays and cysteine accessibility placed both histidines in the extracellular half of the cytoplasmic membrane. We propose a general acid base-promoted catalytic mechanism, invoking direct nucleophilic attack by the substrate α-amino group on the sn-2 ester to form a cyclic tetrahedral intermediate that then collapses to produce lyso-lipoprotein. Lit is a unique example of an intramolecular transacylase differentiated from that catalyzed by Lnt, and provides insight into the heterogeneity of bacterial lipoprotein biosynthetic systems.
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Affiliation(s)
- Krista M Armbruster
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Gloria Komazin
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Timothy C Meredith
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA .,The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park Pennsylvania, USA
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28
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McClain MS, Voss BJ, Cover TL. Lipoprotein Processing and Sorting in Helicobacter pylori. mBio 2020; 11:e00911-20. [PMID: 32430470 PMCID: PMC7240156 DOI: 10.1128/mbio.00911-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 04/20/2020] [Indexed: 12/14/2022] Open
Abstract
Our current understanding of lipoprotein synthesis and localization in Gram-negative bacteria is based primarily on studies of Escherichia coli Newly synthesized E. coli prolipoproteins undergo posttranslational modifications catalyzed by three essential enzymes (Lgt, LspA, and Lnt). The mature lipoproteins are then sorted to the inner or outer membrane via the Lol system (LolABCDE). Recent studies suggested that this paradigm may not be universally applicable among different classes of proteobacteria. In this study, we conducted a systematic analysis of lipoprotein processing and sorting in Helicobacter pylori, a member of the Epsilonproteobacteria that colonizes the human stomach. We show that H. pylorilgt, lspA, and lnt homologs can complement conditionally lethal E. coli mutant strains in which expression of these genes is conditionally regulated. Mutagenesis studies and analyses of conditionally lethal H. pylori mutant strains indicate that lgt and lspA are essential for H. pylori growth but lnt is dispensable. H. pylorilolA and the single lolC (or lolE) homolog are also essential genes. We then explored the role of lipoproteins in H. pylori Cag type IV secretion system (Cag T4SS) activity. Comparative analysis of the putative VirB7 homolog CagT in wild-type and lnt mutant H. pylori strains indicates that CagT undergoes amino-terminal modifications consistent with lipidation, and we show that CagT lipidation is essential for CagT stability and Cag T4SS function. This work demonstrates that lipoprotein synthesis and localization in H. pylori diverge from the canonical pathways and that lipidation of a T4SS component is necessary for H. pylori Cag T4SS activity.IMPORTANCE Bacterial lipoproteins have diverse roles in multiple aspects of bacterial physiology, antimicrobial resistance, and pathogenesis. Dedicated pathways direct the posttranslational lipidation and localization of lipoproteins, but there is considerable variation in these pathways among the proteobacteria. In this study, we characterized the proteins responsible for lipoprotein synthesis and localization in Helicobacter pylori, a member of the Epsilonproteobacteria that contributes to stomach cancer pathogenesis. We also provide evidence suggesting that lipidation of CagT, a component of the H. pylori Cag T4SS, is required for delivery of the H. pylori CagA oncoprotein into human gastric cells. Overall, these results constitute the first systematic analysis of H. pylori lipoprotein production and localization pathways and reveal how these processes in H. pylori differ from corresponding pathways in model proteobacteria.
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Affiliation(s)
- Mark S McClain
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Bradley J Voss
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Timothy L Cover
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, USA
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29
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Xia J, Feng B, Wen G, Xue W, Ma G, Zhang H, Wu S. Bacterial Lipoprotein Biosynthetic Pathway as a Potential Target for Structure-based Design of Antibacterial Agents. Curr Med Chem 2020; 27:1132-1150. [PMID: 30360704 DOI: 10.2174/0929867325666181008143411] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/31/2018] [Accepted: 08/15/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND Antibiotic resistance is currently a serious problem for global public health. To this end, discovery of new antibacterial drugs that interact with novel targets is important. The biosynthesis of lipoproteins is vital to bacterial survival and its inhibitors have shown efficacy against a range of bacteria, thus bacterial lipoprotein biosynthetic pathway is a potential target. METHODS At first, the literature that covered the basic concept of bacterial lipoprotein biosynthetic pathway as well as biochemical characterization of three key enzymes was reviewed. Then, the recently resolved crystal structures of the three enzymes were retrieved from Protein Data Bank (PDB) and the essential residues in the active sites were analyzed. Lastly, all the available specific inhibitors targeting this pathway and their Structure-activity Relationship (SAR) were discussed. RESULTS We briefly introduce the bacterial lipoprotein biosynthetic pathway and describe the structures and functions of three key enzymes in detail. In addition, we present much knowledge on ligand recognition that may facilitate structure-based drug design. Moreover, we focus on the SAR of LspA inhibitors and discuss their potency and drug-likeness. CONCLUSION This review presents a clear background of lipoprotein biosynthetic pathway and provides practical clues for structure-based drug design. In particular, the most up-to-date knowledge on the SAR of lead compounds targeting this pathway would be a good reference for discovery of a novel class of antibacterial agents.
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Affiliation(s)
- Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Bo Feng
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Gang Wen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Wenjie Xue
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Guixing Ma
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment and SUSTech-HKU joint laboratories for matrix biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hongmin Zhang
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment and SUSTech-HKU joint laboratories for matrix biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Song Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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30
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Rao S, Bates GT, Matthews CR, Newport TD, Vickery ON, Stansfeld PJ. Characterizing Membrane Association and Periplasmic Transfer of Bacterial Lipoproteins through Molecular Dynamics Simulations. Structure 2020; 28:475-487.e3. [PMID: 32053772 PMCID: PMC7139219 DOI: 10.1016/j.str.2020.01.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 11/22/2019] [Accepted: 01/24/2020] [Indexed: 01/09/2023]
Abstract
Escherichia coli lipoprotein precursors at the inner membrane undergo three maturation stages before transport by the Lol system to the outer membrane. Here, we develop a pipeline to simulate the membrane association of bacterial lipoproteins in their four maturation states. This has enabled us to model and simulate 81 of the predicted 114 E. coli lipoproteins and reveal their interactions with the host lipid membrane. As part of this set we characterize the membrane contacts of LolB, the lipoprotein involved in periplasmic translocation. We also consider the means and bioenergetics for lipoprotein localization. Our calculations uncover a preference for LolB over LolA and therefore indicate how a lipoprotein may be favorably transferred from the inner to outer membrane. Finally, we reveal that LolC has a role in membrane destabilization, thereby promoting lipoprotein transfer to LolA.
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Affiliation(s)
- Shanlin Rao
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - George T Bates
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Callum R Matthews
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Thomas D Newport
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Owen N Vickery
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK; School of Life Sciences & Department of Chemistry, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK; School of Life Sciences & Department of Chemistry, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK.
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31
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Identification of Haemophilus parasuis genes uniquely expressed during infection using in vivo-induced antigen technology. Vet Microbiol 2020; 243:108650. [PMID: 32273024 DOI: 10.1016/j.vetmic.2020.108650] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 03/04/2020] [Accepted: 03/17/2020] [Indexed: 01/12/2023]
Abstract
Haemophilus parasuis is the etiological agent of Glässer's disease which is characterized by fibrinous polyserositis, arthritis and meningitis. The pathogenesis of this bacterium remains largely unknown. Genes expressed in vivo may play an important role in the pathogenicity of H. parasuis. The development of in vivo-induced antigen technology (IVIAT) has provided a valuable tool for the identification of in vivo-induced genes during bacterial infection. In this study, IVIAT was applied to identify in vivo-induced antigens of H. parasuis. Pooled swine H. parasuis-positive sera, adsorbed against in vitro-grown cultures of H. parasuis SH0165 and Escherichia coli BL21 (DE3), were used to screen the inducible expression library of genomic proteins from whole genome sequenced H. parsuis SH0165. Finally, 24 unique genes expressed in vivo were successfully identified after secondary and tertiary screening with IVIAT. These genes were implicated in cell surface proteins, metabolism, stress response, regulation, transportation and other processes. Quantitative real-time PCR showed that the mRNA levels of 24 genes were all upregulated in vivo relative to in vitro, with 13 genes were detected significantly upregulated in H. parasuis infected pigs. Several potential virulence-associated genes were found to be uniquely expressed in vivo, including espP, lnt, hutZ, mreC, vtaA, pilB, tex, sunT and aidA. The results indicated that the proteins identified using IVIAT may play important roles in the pathogenesis of H. parasuis infection in vivo.
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32
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Structure and Functional Characterization of Membrane Integral Proteins in the Lipid Cubic Phase. J Mol Biol 2020; 432:5104-5123. [PMID: 32113953 DOI: 10.1016/j.jmb.2020.02.024] [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] [Received: 01/04/2020] [Revised: 02/14/2020] [Accepted: 02/19/2020] [Indexed: 12/19/2022]
Abstract
The lipid cubic phase (LCP) has been used extensively as a medium for crystallizing membrane proteins. It is an attractive environment in which to perform such studies because it incorporates a lipid bilayer. It is therefore considered a useful and a faithful biomembrane mimetic. Here, we bring together evidence that supports this view. Biophysical characterizations are described demonstrating that the cubic phase is a porous medium into and out of which water-soluble molecules can diffuse for binding to and reaction with reconstituted proteins. The proteins themselves are shown to be functionally reconstituted into and to have full mobility in the bilayered membrane, a prerequisite for LCP crystallogenesis. Spectroscopic methods have been used to characterize the conformation and disposition of proteins in the mesophase. Procedures for performing activity assays on enzymes directly in the cubic phase have been reported. Specific examples described here include a kinase and two transferases, where quantitative kinetics and mechanism-defining measurements were performed directly or via a coupled assay system. Finally, ligand-binding assays are described, where binding to proteins in the mesophase membrane was monitored directly by eye and indirectly by fluorescence quenching, enabling binding constant determinations for targets with affinity values in the micromolar and nanomolar range. These results make a convincing case that the lipid bilayer of the cubic mesophase is an excellent membrane mimetic and a suitable medium in which to perform not only crystallogenesis but also biochemical and biophysical characterizations of membrane proteins.
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33
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Conformational changes in Apolipoprotein N-acyltransferase (Lnt). Sci Rep 2020; 10:639. [PMID: 31959792 PMCID: PMC6971011 DOI: 10.1038/s41598-020-57419-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 12/31/2019] [Indexed: 11/10/2022] Open
Abstract
Lipoproteins are important components of the cell envelope and are responsible for many essential cellular functions. They are produced by the post-translational covalent attachment of lipids that occurs via a sequential 3-step process controlled by three integral membrane enzymes. The last step of this process, unique to Gram-negative bacteria, is the N-acylation of the terminal cysteine by Apolipoprotein N-acyltransferase (Lnt) to form the final mature lipoprotein. Here we report 2 crystal forms of Lnt from Escherichia coli. In one form we observe a highly dynamic arm that is able to restrict access to the active site as well as a covalent modification to the active site cysteine consistent with the thioester acyl-intermediate. In the second form, the enzyme crystallized in an open conformation exposing the active site to the environment. In total we observe 3 unique Lnt molecules that when taken together suggest the movement of essential loops and residues are triggered by substrate binding that could control the interaction between Lnt and the incoming substrate apolipoprotein. The results provide a dynamic context for residues shown to be central for Lnt function and provide further insights into its mechanism.
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34
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Stix R, Song J, Banerjee A, Faraldo-Gómez JD. DHHC20 Palmitoyl-Transferase Reshapes the Membrane to Foster Catalysis. Biophys J 2019; 118:980-988. [PMID: 31858978 DOI: 10.1016/j.bpj.2019.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/22/2019] [Accepted: 11/08/2019] [Indexed: 12/20/2022] Open
Abstract
Cysteine palmitoylation, a form of S-acylation, is a key posttranslational modification in cellular signaling. This type of reversible lipidation occurs in both plasma and organellar membranes, and is catalyzed by a family of integral membrane proteins known as DHHC acyltransferases. The first step in the S-acylation process is the recognition of free acyl coenzyme A (acyl-CoA) from the lipid bilayer. The DHHC enzyme then becomes autoacylated at a site defined by a conserved Asp-His-His-Cys motif. This reaction entails ionization of the catalytic Cys. Intriguingly, in known DHHC structures, this catalytic Cys appears to be exposed to the hydrophobic interior of the lipid membrane, which would be highly unfavorable for a negatively charged nucleophile, thus hindering autoacylation. Here, we use biochemical and computational methods to reconcile these seemingly contradictory facts. First, we experimentally demonstrate that human DHHC20 is active when reconstituted in POPC nanodiscs. Microsecond-long all-atom molecular dynamics simulations are then calculated for human DHHC20 and for different acyl-CoA forms, also in a POPC membrane. Strikingly, we observe that human DHHC20 induces a drastic deformation in the membrane, particularly on the cytoplasmic side, where autoacylation occurs. As a result, the catalytic Cys becomes hydrated and optimally positioned to encounter the cleavage site in acyl-CoA. In summary, we hypothesize that DHHC enzymes locally reshape the membrane to foster a morphology that is specifically adapted for acyl-CoA recognition and autoacylation.
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Affiliation(s)
- Robyn Stix
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland; Unit on Structural and Chemical Biology of Membrane Proteins, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - James Song
- Unit on Structural and Chemical Biology of Membrane Proteins, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Anirban Banerjee
- Unit on Structural and Chemical Biology of Membrane Proteins, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland.
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland.
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35
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A sensitive fluorescence-based assay to monitor enzymatic activity of the essential integral membrane protein Apolipoprotein N-acyltransferase (Lnt). Sci Rep 2019; 9:15978. [PMID: 31685855 PMCID: PMC6828757 DOI: 10.1038/s41598-019-52106-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 10/08/2019] [Indexed: 12/20/2022] Open
Abstract
Lipoprotein modification is an essential process in Gram-negative bacteria. The action of three integral membrane proteins that catalyze the transfer of fatty acids derived from membrane phospholipids or cleave the signal peptide of the lipoprotein substrate result in the formation of mature triacylated proteins. Inactivation of the enzymes leads to mis-localization of immature lipoproteins and consequently cell death. Biochemical studies and the development of in vitro assays are challenging due to the fact that the enzymes and substrates are all membrane-embedded proteins difficult to overproduce and purify. Here we describe a sensitive fluorescence-based assay to monitor bacterial apolipoprotein N-acyltransferase activity.
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36
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Singh W, Bilal M, McClory J, Dourado D, Quinn D, Moody TS, Sutcliffe I, Huang M. Mechanism of Phosphatidylglycerol Activation Catalyzed by Prolipoprotein Diacylglyceryl Transferase. J Phys Chem B 2019; 123:7092-7102. [DOI: 10.1021/acs.jpcb.9b04227] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Warispreet Singh
- School of Chemistry & Chemical Engineering, Queen’s University Belfast, Belfast BT9 5AG, Northern Ireland, United Kingdom
- Department of Biocatalysis and Isotope Chemistry, Almac Sciences, Almac House, 20 Seagoe Industrial Estate, Craigavon BT63 5QD, Northern Ireland, United Kingdom
| | - Munir Bilal
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, United Kingdom
| | - James McClory
- School of Chemistry & Chemical Engineering, Queen’s University Belfast, Belfast BT9 5AG, Northern Ireland, United Kingdom
| | - Daniel Dourado
- School of Chemistry & Chemical Engineering, Queen’s University Belfast, Belfast BT9 5AG, Northern Ireland, United Kingdom
- Department of Biocatalysis and Isotope Chemistry, Almac Sciences, Almac House, 20 Seagoe Industrial Estate, Craigavon BT63 5QD, Northern Ireland, United Kingdom
| | - Derek Quinn
- Department of Biocatalysis and Isotope Chemistry, Almac Sciences, Almac House, 20 Seagoe Industrial Estate, Craigavon BT63 5QD, Northern Ireland, United Kingdom
| | - Thomas S. Moody
- Department of Biocatalysis and Isotope Chemistry, Almac Sciences, Almac House, 20 Seagoe Industrial Estate, Craigavon BT63 5QD, Northern Ireland, United Kingdom
- Arran Chemical Company Limited, Unit 1 Monksland Industrial Estate, Athlone, Co., Roscommon, N37 DN24, Ireland
| | - Iain Sutcliffe
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, United Kingdom
| | - Meilan Huang
- School of Chemistry & Chemical Engineering, Queen’s University Belfast, Belfast BT9 5AG, Northern Ireland, United Kingdom
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Abstract
Lipoproteins are produced by both Gram-positive and Gram-negative bacteria. Once secreted, lipoproteins are quickly acylated, anchoring them into the plasma membrane. Recent work has shown that Gram-positive bacteria are able to generate considerable diversity in the acylation of their lipoproteins, though the mechanisms involved are only just beginning to emerge. In Gram-negative organisms, most lipoproteins are subsequently trafficked to the outer membrane (OM). Lipoprotein trafficking is an essential pathway in these bacteria. At least one OM lipoprotein component is required by each of the essential machines that assemble the OM (such as the Bam and Lpt machines) and build the peptidoglycan cell wall (Lpo-penicillin-binding protein complexes). The Lol pathway has been the paradigm for OM lipoprotein trafficking: a complex of LolCDE extracts lipoproteins from the plasma membrane, LolA shuttles them through the periplasmic space, and LolB anchors them into the OM. The peptide signals responsible for OM-targeting via LolCDE have long been known for Escherichia coli. Remarkably, production of novel lipoprotein acyl forms in E. coli has reinforced the idea that lipid signals also contribute to OM targeting via LolCDE. Moreover, recent work has shown that lipoprotein trafficking can occur in E. coli without either LolA or LolB. Therefore, current evidence suggests that at least one additional, LolAB-independent route for OM lipoprotein trafficking exists. This chapter reviews the posttranslocation modifications of all lipoproteins, with a focus on the trafficking of lipoproteins to the OM of Gram-negative bacteria.
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El Arnaout T, Soulimane T. Targeting Lipoprotein Biogenesis: Considerations towards Antimicrobials. Trends Biochem Sci 2019; 44:701-715. [PMID: 31036406 DOI: 10.1016/j.tibs.2019.03.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 03/14/2019] [Accepted: 03/25/2019] [Indexed: 12/25/2022]
Abstract
Decades have passed without approval of a new antibiotic class. Several companies have recently halted related discovery efforts because of multiple obstacles. One promising route under research is to target the lipoprotein maturation pathway in light of major recent findings and the virulence roles of lipoproteins. To support the future design of selective drugs, considerations and priority-setting are established for the main lipoprotein processing enzymes (Lgt, LspA, and Lnt) based on microbiology, biochemistry, structural biology, chemical design, and pharmacology. Although not all bacterial species will be similarly impacted by drug candidates, several advantages make LspA a top target to pursue in the development of novel antibiotics effective against bacteria that are resistant to existing drugs.
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Affiliation(s)
- Toufic El Arnaout
- Kappa Crystals Ltd, Dublin, Ireland; School of Food Science and Environmental Health, Technological University (TU) Dublin City Campus, TU, Dublin, Dublin, Ireland.
| | - Tewfik Soulimane
- Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland; Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland
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Abstract
The Lpp lipoprotein of Escherichia coli is the first identified protein with a covalently linked lipid. It is chemically bound by its C-terminus to murein (peptidoglycan) and inserts by the lipid at the N-terminus into the outer membrane. As the most abundant protein in E. coli (106 molecules per cell) it plays an important role for the integrity of the cell envelope. Lpp represents the type protein of a large variety of lipoproteins found in Gram-negative and Gram-positive bacteria and in archaea that have in common the lipid structure for anchoring the proteins to membranes but otherwise strongly vary in sequence, structure, and function. Predicted lipoproteins in known prokaryotic genomes comprise 2.7% of all proteins. Lipoproteins are modified by a unique phospholipid pathway and transferred from the cytoplasmic membrane into the outer membrane by a special system. They are involved in protein incorporation into the outer membrane, protein secretion across the cytoplasmic membrane, periplasm and outer membrane, signal transduction, conjugation, cell wall metabolism, antibiotic resistance, biofilm formation, and adhesion to host tissues. They are only found in bacteria and function as signal molecules for the innate immune system of vertebrates, where they cause inflammation and elicit innate and adaptive immune response through Toll-like receptors. This review discusses various aspects of Lpp and other lipoproteins of Gram-negative and Gram-positive bacteria and archaea.
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Affiliation(s)
- Volkmar Braun
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max Planck Ring 5, 72076, Tübingen, Germany.
| | - Klaus Hantke
- IMIT, University of Tuebingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
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40
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Pohlschroder M, Pfeiffer F, Schulze S, Abdul Halim MF. Archaeal cell surface biogenesis. FEMS Microbiol Rev 2018; 42:694-717. [PMID: 29912330 PMCID: PMC6098224 DOI: 10.1093/femsre/fuy027] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/12/2018] [Indexed: 12/13/2022] Open
Abstract
Cell surfaces are critical for diverse functions across all domains of life, from cell-cell communication and nutrient uptake to cell stability and surface attachment. While certain aspects of the mechanisms supporting the biosynthesis of the archaeal cell surface are unique, likely due to important differences in cell surface compositions between domains, others are shared with bacteria or eukaryotes or both. Based on recent studies completed on a phylogenetically diverse array of archaea, from a wide variety of habitats, here we discuss advances in the characterization of mechanisms underpinning archaeal cell surface biogenesis. These include those facilitating co- and post-translational protein targeting to the cell surface, transport into and across the archaeal lipid membrane, and protein anchoring strategies. We also discuss, in some detail, the assembly of specific cell surface structures, such as the archaeal S-layer and the type IV pili. We will highlight the importance of post-translational protein modifications, such as lipid attachment and glycosylation, in the biosynthesis as well as the regulation of the functions of these cell surface structures and present the differences and similarities in the biogenesis of type IV pili across prokaryotic domains.
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Affiliation(s)
| | - Friedhelm Pfeiffer
- Computational Biology Group, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Stefan Schulze
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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41
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Boland C, Olatunji S, Bailey J, Howe N, Weichert D, Fetics SK, Yu X, Merino-Gracia J, Delsaut C, Caffrey M. Membrane (and Soluble) Protein Stability and Binding Measurements in the Lipid Cubic Phase Using Label-Free Differential Scanning Fluorimetry. Anal Chem 2018; 90:12152-12160. [DOI: 10.1021/acs.analchem.8b03176] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Coilín Boland
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Samir Olatunji
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Jonathan Bailey
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Nicole Howe
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Dietmar Weichert
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Susan Kathleen Fetics
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Xiaoxiao Yu
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Javier Merino-Gracia
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Clement Delsaut
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Martin Caffrey
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
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42
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Cheng W, Doyle DA, El Arnaout T. The N-acyltransferase Lnt: Structure-function insights from recent simultaneous studies. Int J Biol Macromol 2018; 117:870-877. [PMID: 29859843 DOI: 10.1016/j.ijbiomac.2018.05.229] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 05/29/2018] [Accepted: 05/30/2018] [Indexed: 02/05/2023]
Abstract
Bacterial lipoproteins have been researched for decades due to their roles in a large number of biological functions. There were no structures of their main three membrane processing enzymes, until 2016 for Lgt and LspA, and then 2017 for Lnt with not one but three simultaneous, independent publications. We have analyzed the recent findings for this apolipoprotein N-acyltransferase Lnt, with comparisons between the novel structures, and with soluble nitrilases, to determine the significance of unique features in terms of substrate's recognition and binding mechanism influenced by exclusive residues, two transmembrane helices, and a flexible loop.
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Affiliation(s)
- Wei Cheng
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, China
| | - Declan A Doyle
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Toufic El Arnaout
- School of Food Science and Environmental Health, Dublin Institute of Technology, Marlborough St, Dublin 1, Ireland.
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43
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Biophysical characterization and stabilization of detergent-solubilized lipoprotein N-acyl transferase from P. aeruginosa and E. coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1384-1393. [PMID: 29573991 DOI: 10.1016/j.bbamem.2018.03.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/18/2018] [Accepted: 03/20/2018] [Indexed: 11/23/2022]
Abstract
Lipoproteins are important for bacterial growth and virulence and interest in them as targets for antibiotic development is growing. Lipoprotein N-acyl transferase (Lnt) catalyzes the final step in the lipoprotein posttranslational processing pathway. The mature lipoprotein can remain in the inner membrane or be trafficked to the outer membrane in the case of diderm prokaryotes. With a view to obtaining high-resolution crystal structures of membrane integral Lnt for use in drug discovery a program was undertaken to generate milligram quantities of stable, homogenous and functional protein. This involved screening across bacterial species for suitable orthologues and optimization at the level of protein expression, solubilization and stability. Combining biophysical and functional characterization, orthologous Lnt from Escherichia coli and the opportunistic human pathogen Pseudomonas aeruginosa was identified as suitable for the proposed structure determination campaign that ultimately yielded crystal structures. The rational approaches taken that eventually provided structure-quality protein are presented in this report.
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44
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Translocation of lipoproteins to the surface of gram negative bacteria. Curr Opin Struct Biol 2018; 51:73-79. [PMID: 29579694 DOI: 10.1016/j.sbi.2018.03.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 03/06/2018] [Accepted: 03/07/2018] [Indexed: 11/21/2022]
Abstract
The surface of many Gram-negative bacteria contains lipidated protein molecules referred to as surface lipoproteins or SLPs. SLPs play critical roles in host immune evasion, nutrient acquisition and regulation of bacterial stress response, and have been extensively studied as vaccine antigens. The aim of this review is to summarize the recent studies that have investigated the biosynthetic and translocation pathways used by different bacterial species to deliver SLPs to the surface. We will specifically focus on Slam, a novel outer membrane protein first discovered in pathogenic Neisseria sp., that is involved in translocation of SLPs across the outer membrane.
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45
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Affiliation(s)
- Marcin Grabowicz
- Department of Microbiology and Immunology; Emory University School of Medicine; Atlanta GA 30322 USA
- Division of Infectious Disease; Department of Medicine; Emory University School of Medicine; Atlanta GA 30322 USA
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46
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Li Z, Tang Y, Wu Y, Zhao S, Bao J, Luo Y, Li D. Structural insights into the committed step of bacterial phospholipid biosynthesis. Nat Commun 2017; 8:1691. [PMID: 29167463 PMCID: PMC5700162 DOI: 10.1038/s41467-017-01821-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/18/2017] [Indexed: 11/09/2022] Open
Abstract
The membrane-integral glycerol 3-phosphate (G3P) acyltransferase PlsY catalyses the committed and essential step in bacterial phospholipid biosynthesis by acylation of G3P, forming lysophosphatidic acid. It contains no known acyltransferase motifs, lacks eukaryotic homologs, and uses the unusual acyl-phosphate as acyl donor, as opposed to acyl-CoA or acyl-carrier protein for other acyltransferases. Previous studies have identified several PlsY inhibitors as potential antimicrobials. Here we determine the crystal structure of PlsY at 1.48 Å resolution, revealing a seven-transmembrane helix fold. Four additional substrate- and product-bound structures uncover the atomic details of its relatively inflexible active site. Structure and mutagenesis suggest a different acylation mechanism of ‘substrate-assisted catalysis’ that, unlike other acyltransferases, does not require a proteinaceous catalytic base to complete. The structure data and a high-throughput enzymatic assay developed in this work should prove useful for virtual and experimental screening of inhibitors against this vital bacterial enzyme. The first step in bacterial phospholipid biosynthesis is the acylation of glycerol 3-phosphate to form lysophosphatidic acid. Here, the authors present the high resolution crystal structure of the glycerol 3-phosphate acyltransferase PlsY, a membrane protein and give insights into its catalytical mechanism.
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Affiliation(s)
- Zhenjian Li
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China
| | - Yannan Tang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China.,University of Chinese Academy of Sciences, Shanghai, 201210, China
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, 333 Middle Huaxia Road, Shanghai, 201210, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, 333 Middle Huaxia Road, Shanghai, 201210, China.,School of Life Science and Technology, ShanghaiTech University, 333 Middle Huaxia Road, Shanghai, 201210, China
| | - Juan Bao
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China
| | - Yitian Luo
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China.,University of Chinese Academy of Sciences, Shanghai, 201210, China.,School of Life Science and Technology, ShanghaiTech University, 333 Middle Huaxia Road, Shanghai, 201210, China
| | - Dianfan Li
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China.
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