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Yoon Y, Song S. Structural Insights into the Lipopolysaccharide Transport (Lpt) System as a Novel Antibiotic Target. J Microbiol 2024; 62:261-275. [PMID: 38816673 DOI: 10.1007/s12275-024-00137-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 06/01/2024]
Abstract
Lipopolysaccharide (LPS) is a critical component of the extracellular leaflet within the bacterial outer membrane, forming an effective physical barrier against environmental threats in Gram-negative bacteria. After LPS is synthesized and matured in the bacterial cytoplasm and the inner membrane (IM), LPS is inserted into the outer membrane (OM) through the ATP-driven LPS transport (Lpt) pathway, which is an energy-intensive process. A trans-envelope complex that contains seven Lpt proteins (LptA-LptG) is crucial for extracting LPS from the IM and transporting it across the periplasm to the OM. The last step in LPS transport involves the mediation of the LptDE complex, facilitating the insertion of LPS into the outer leaflet of the OM. As the Lpt system plays an essential role in maintaining the impermeability of the OM via LPS decoration, the interactions between these interconnected subunits, which are meticulously regulated, may be potential targets for the development of new antibiotics to combat multidrug-resistant Gram-negative bacteria. In this review, we aimed to provide an overview of current research concerning the structural interactions within the Lpt system and their implications to clarify the function and regulation of LPS transport in the overall process of OM biogenesis. Additionally, we explored studies on the development of therapeutic inhibitors of LPS transport, the factors that limit success, and future prospects.
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Affiliation(s)
- Yurim Yoon
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Saemee Song
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea.
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Cina NP, Frank DW, Klug CS. Residues within the LptC transmembrane helix are critical for Escherichia coli LptB 2 FG ATPase regulation. Protein Sci 2024; 33:e4879. [PMID: 38131105 PMCID: PMC10804673 DOI: 10.1002/pro.4879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/20/2023] [Accepted: 12/19/2023] [Indexed: 12/23/2023]
Abstract
Lipopolysaccharide (LPS) synthesis in Gram-negative bacteria is completed at the outer leaflet of the inner membrane (IM). Following synthesis, seven LPS transport (Lpt) proteins facilitate the movement of LPS to the outer membrane (OM), an essential process that if disrupted at any stage has lethal effects on bacterial viability. LptB2 FG, the IM component of the Lpt bridge system, is a type VI ABC transporter that provides the driving force for LPS extraction from the IM and subsequent transport across a stable protein bridge to the outer leaflet of the OM. LptC is a periplasmic protein anchored to the IM by a single transmembrane (TM) helix intercalating within the lateral gate formed by LptF TM5 and LptG TM1. LptC facilitates the hand-off of LPS from LptB2 FG to the periplasmic protein LptA and has been shown to regulate the ATPase activity of LptB2 FG. Here, using an engineered chromosomal knockout system in Escherichia coli to assess the effects of LptC mutations in vivo, we identified six partial loss of function LptC mutations in the first unbiased alanine screen of this essential protein. To investigate the functional effects of these mutations, nanoDSF (differential scanning fluorimetry) and site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy in combination with an in vitro ATPase assay show that specific residues in the TM helix of LptC destabilize the LptB2 FGC complex and regulate the ATPase activity of LptB.
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Affiliation(s)
- Nicholas P. Cina
- Department of BiophysicsMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Dara W. Frank
- Department of Microbiology & ImmunologyMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Candice S. Klug
- Department of BiophysicsMedical College of WisconsinMilwaukeeWisconsinUSA
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Pahil KS, Gilman MSA, Baidin V, Clairfeuille T, Mattei P, Bieniossek C, Dey F, Muri D, Baettig R, Lobritz M, Bradley K, Kruse AC, Kahne D. A new antibiotic traps lipopolysaccharide in its intermembrane transporter. Nature 2024; 625:572-577. [PMID: 38172635 PMCID: PMC10794137 DOI: 10.1038/s41586-023-06799-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 10/30/2023] [Indexed: 01/05/2024]
Abstract
Gram-negative bacteria are extraordinarily difficult to kill because their cytoplasmic membrane is surrounded by an outer membrane that blocks the entry of most antibiotics. The impenetrable nature of the outer membrane is due to the presence of a large, amphipathic glycolipid called lipopolysaccharide (LPS) in its outer leaflet1. Assembly of the outer membrane requires transport of LPS across a protein bridge that spans from the cytoplasmic membrane to the cell surface. Maintaining outer membrane integrity is essential for bacterial cell viability, and its disruption can increase susceptibility to other antibiotics2-6. Thus, inhibitors of the seven lipopolysaccharide transport (Lpt) proteins that form this transenvelope transporter have long been sought. A new class of antibiotics that targets the LPS transport machine in Acinetobacter was recently identified. Here, using structural, biochemical and genetic approaches, we show that these antibiotics trap a substrate-bound conformation of the LPS transporter that stalls this machine. The inhibitors accomplish this by recognizing a composite binding site made up of both the Lpt transporter and its LPS substrate. Collectively, our findings identify an unusual mechanism of lipid transport inhibition, reveal a druggable conformation of the Lpt transporter and provide the foundation for extending this class of antibiotics to other Gram-negative pathogens.
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Affiliation(s)
- Karanbir S Pahil
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Morgan S A Gilman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Vadim Baidin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Thomas Clairfeuille
- Departments of Immunology, Infectious Disease and Ophthalmology (I2O), Medicinal Chemistry and Lead Discovery, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Patrizio Mattei
- Departments of Immunology, Infectious Disease and Ophthalmology (I2O), Medicinal Chemistry and Lead Discovery, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Christoph Bieniossek
- Departments of Immunology, Infectious Disease and Ophthalmology (I2O), Medicinal Chemistry and Lead Discovery, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Fabian Dey
- Departments of Immunology, Infectious Disease and Ophthalmology (I2O), Medicinal Chemistry and Lead Discovery, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Dieter Muri
- Departments of Immunology, Infectious Disease and Ophthalmology (I2O), Medicinal Chemistry and Lead Discovery, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Remo Baettig
- Departments of Immunology, Infectious Disease and Ophthalmology (I2O), Medicinal Chemistry and Lead Discovery, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Michael Lobritz
- Departments of Immunology, Infectious Disease and Ophthalmology (I2O), Medicinal Chemistry and Lead Discovery, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Kenneth Bradley
- Departments of Immunology, Infectious Disease and Ophthalmology (I2O), Medicinal Chemistry and Lead Discovery, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
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He H, Pramanik AS, Swanson SK, Johnson DK, Florens L, Zückert WR. A Borrelia burgdorferi LptD homolog is required for flipping of surface lipoproteins through the spirochetal outer membrane. Mol Microbiol 2023; 119:752-767. [PMID: 37170643 PMCID: PMC10330739 DOI: 10.1111/mmi.15072] [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: 12/21/2022] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/13/2023]
Abstract
Borrelia spirochetes are unique among diderm bacteria in their lack of lipopolysaccharide (LPS) in the outer membrane (OM) and their abundance of surface-exposed lipoproteins with major roles in transmission, virulence, and pathogenesis. Despite their importance, little is known about how surface lipoproteins are translocated through the periplasm and the OM. Here, we characterized Borrelia burgdorferi BB0838, a distant homolog of the OM LPS assembly protein LptD. Using a CRISPR interference approach, we showed that BB0838 is required for cell growth and envelope stability. Upon BB0838 knockdown, surface lipoprotein OspA was retained in the inner leaflet of the OM, as determined by its inaccessibility to in situ proteolysis but its presence in OM vesicles. The topology of the OM porin/adhesin P66 remained unaffected. Quantitative mass spectrometry of the B. burgdorferi membrane-associated proteome confirmed the selective periplasmic retention of surface lipoproteins under BB0838 knockdown conditions. Additional analysis identified a single in situ protease-accessible BB0838 peptide that mapped to a predicted β-barrel surface loop. Alphafold Multimer modeled a B. burgdorferi LptB2 FGCAD complex spanning the periplasm. Together, this suggests that BB0838/LptDBb facilitates the essential terminal step in spirochetal surface lipoprotein secretion, using an orthologous OM component of a pathway that secretes LPS in proteobacteria.
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Affiliation(s)
- Huan He
- University of Kansas School of Medicine, Department of Microbiology, Molecular Genetics and Immunology, Kansas City, Kansas, USA
| | - Ankita S. Pramanik
- University of Kansas School of Medicine, Department of Microbiology, Molecular Genetics and Immunology, Kansas City, Kansas, USA
| | | | - David K. Johnson
- University of Kansas, Computational Chemical Biology Core, Lawrence, Kansas, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Wolfram R. Zückert
- University of Kansas School of Medicine, Department of Microbiology, Molecular Genetics and Immunology, Kansas City, Kansas, USA
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Bilsing FL, Anlauf MT, Hachani E, Khosa S, Schmitt L. ABC Transporters in Bacterial Nanomachineries. Int J Mol Sci 2023; 24:ijms24076227. [PMID: 37047196 PMCID: PMC10094684 DOI: 10.3390/ijms24076227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/18/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Members of the superfamily of ABC transporters are found in all domains of life. Most of these primary active transporters act as isolated entities and export or import their substrates in an ATP-dependent manner across biological membranes. However, some ABC transporters are also part of larger protein complexes, so-called nanomachineries that catalyze the vectorial transport of their substrates. Here, we will focus on four bacterial examples of such nanomachineries: the Mac system providing drug resistance, the Lpt system catalyzing vectorial LPS transport, the Mla system responsible for phospholipid transport, and the Lol system, which is required for lipoprotein transport to the outer membrane of Gram-negative bacteria. For all four systems, we tried to summarize the existing data and provide a structure-function analysis highlighting the mechanistical aspect of the coupling of ATP hydrolysis to substrate translocation.
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Suppressor Mutations in LptF Bypass Essentiality of LptC by Forming a Six-Protein Transenvelope Bridge That Efficiently Transports Lipopolysaccharide. mBio 2023; 14:e0220222. [PMID: 36541759 PMCID: PMC9972910 DOI: 10.1128/mbio.02202-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Lipopolysaccharide (LPS) is an essential component of the outer membrane (OM) of many Gram-negative bacteria, providing a barrier against the entry of toxic molecules. In Escherichia coli, LPS is exported to the cell surface by seven essential proteins (LptA-G) that form a transenvelope complex. At the inner membrane, the ATP-binding cassette (ABC) transporter LptB2FG associates with LptC to power LPS extraction from the membrane and transfer to the periplasmic LptA protein, which is in complex with the OM translocon LptDE. LptC interacts both with LptB2FG and LptADE to mediate the formation of the transenvelope bridge and regulates the ATPase activity of LptB2FG. A genetic screen has previously identified suppressor mutants at a residue (R212) of LptF that are viable in the absence of LptC. Here, we present in vivo evidence that the LptF R212G mutant assembles a six-protein transenvelope complex in which LptA mediates interactions with LptF and LptD in the absence of LptC. Furthermore, we present in vitro evidence that the mutant LptB2FG complexes restore the regulation of ATP hydrolysis as it occurs in the LptB2FGC complex to achieve wild-type efficient coupling of ATP hydrolysis and LPS movement. We also show the suppressor mutations restore the wild-type levels of LPS transport both in vivo and in vitro, but remarkably, without restoring the affinity of the inner membrane complex for LptA. Based on the sensitivity of lptF suppressor mutants to selected stress conditions relative to wild-type cells, we show that there are additional regulatory functions of LptF and LptC that had not been identified. IMPORTANCE The presence of an external LPS layer in the outer membrane makes Gram-negative bacteria intrinsically resistant to many antibiotics. Millions of LPS molecules are transported to the cell surface per generation by the Lpt molecular machine made, in E. coli, by seven essential proteins. LptC is the unconventional regulatory subunit of the LptB2FGC ABC transporter, involved in coordinating energy production and LPS transport. Surprisingly, despite being essential for bacterial growth, LptC can be deleted, provided that a specific residue in the periplasmic domain of LptF is mutated and LptA is overexpressed. Here, we apply biochemical techniques to investigate the suppression mechanism. The data produced in this work disclose an unknown regulatory function of LptF in the transporter that not only expands the knowledge about the Lpt complex but can also be targeted by novel LPS biogenesis inhibitors.
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