1
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Sabnis A, Edwards AM. Lipopolysaccharide as an antibiotic target. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119507. [PMID: 37268022 DOI: 10.1016/j.bbamcr.2023.119507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/18/2023] [Accepted: 05/14/2023] [Indexed: 06/04/2023]
Abstract
Gram-negative bacteria, including Escherichia coli, Pseudomonas aeruginosa and Acinetobacter baumannii are amongst the highest priority drug-resistant pathogens, for which new antibiotics are urgently needed. Whilst antibiotic drug development is inherently challenging, this is particularly true for Gram-negative bacteria due to the presence of the outer membrane, a highly selective permeability barrier that prevents the ingress of several classes of antibiotic. This selectivity is largely due to an outer leaflet composed of the glycolipid lipopolysaccharide (LPS), which is essential for the viability of almost all Gram-negative bacteria. This essentiality, coupled with the conservation of the synthetic pathway across species and recent breakthroughs in our understanding of transport and membrane homeostasis has made LPS an attractive target for novel antibiotic drug development. Several different targets have been explored and small molecules developed that show promising activity in vitro. However, these endeavours have met limited success in clinical testing and the polymyxins, discovered more than 70 years ago, remain the only LPS-targeting drugs to enter the clinic thus far. In this review, we will discuss efforts to develop therapeutic inhibitors of LPS synthesis and transport and the reasons for limited success, and explore new developments in understanding polymyxin mode of action and the identification of new analogues with reduced toxicity and enhanced activity.
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Affiliation(s)
- Akshay Sabnis
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Rd, London SW7 2AZ, UK
| | - Andrew M Edwards
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Rd, London SW7 2AZ, UK.
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2
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Trotta KL, Hayes BM, Schneider JP, Wang J, Todor H, Rockefeller Grimes P, Zhao Z, Hatleberg WL, Silvis MR, Kim R, Koo BM, Basler M, Chou S. Lipopolysaccharide transport regulates bacterial sensitivity to a cell wall-degrading intermicrobial toxin. PLoS Pathog 2023; 19:e1011454. [PMID: 37363922 PMCID: PMC10328246 DOI: 10.1371/journal.ppat.1011454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/07/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023] Open
Abstract
Gram-negative bacteria can antagonize neighboring microbes using a type VI secretion system (T6SS) to deliver toxins that target different essential cellular features. Despite the conserved nature of these targets, T6SS potency can vary across recipient species. To understand the functional basis of intrinsic T6SS susceptibility, we screened for essential Escherichia coli (Eco) genes that affect its survival when antagonized by a cell wall-degrading T6SS toxin from Pseudomonas aeruginosa, Tae1. We revealed genes associated with both the cell wall and a separate layer of the cell envelope, lipopolysaccharide, that modulate Tae1 toxicity in vivo. Disruption of genes in early lipopolysaccharide biosynthesis provided Eco with novel resistance to Tae1, despite significant cell wall degradation. These data suggest that Tae1 toxicity is determined not only by direct substrate damage, but also by indirect cell envelope homeostasis activities. We also found that Tae1-resistant Eco exhibited reduced cell wall synthesis and overall slowed growth, suggesting that reactive cell envelope maintenance pathways could promote, not prevent, self-lysis. Together, our study reveals the complex functional underpinnings of susceptibility to Tae1 and T6SS which regulate the impact of toxin-substrate interactions in vivo.
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Affiliation(s)
- Kristine L. Trotta
- Department of Biochemistry & Biophysics, University of California–San Francisco, San Francisco, California, United States of America
| | - Beth M. Hayes
- Department of Biochemistry & Biophysics, University of California–San Francisco, San Francisco, California, United States of America
| | | | - Jing Wang
- Biozentrum, University of Basel, Basel, Switzerland
| | - Horia Todor
- Department of Cell and Tissue Biology, University of California–San Francisco, San Francisco, California, United States of America
| | - Patrick Rockefeller Grimes
- Department of Biochemistry & Biophysics, University of California–San Francisco, San Francisco, California, United States of America
| | - Ziyi Zhao
- Department of Biochemistry & Biophysics, University of California–San Francisco, San Francisco, California, United States of America
| | | | - Melanie R. Silvis
- Department of Cell and Tissue Biology, University of California–San Francisco, San Francisco, California, United States of America
| | - Rachel Kim
- Department of Biochemistry & Biophysics, University of California–San Francisco, San Francisco, California, United States of America
| | - Byoung Mo Koo
- Department of Cell and Tissue Biology, University of California–San Francisco, San Francisco, California, United States of America
| | - Marek Basler
- Biozentrum, University of Basel, Basel, Switzerland
| | - Seemay Chou
- Department of Biochemistry & Biophysics, University of California–San Francisco, San Francisco, California, United States of America
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3
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Trotta KL, Hayes BM, Schneider JP, Wang J, Todor H, Grimes PR, Zhao Z, Hatleberg WL, Silvis MR, Kim R, Koo BM, Basler M, Chou S. Lipopolysaccharide integrity primes bacterial sensitivity to a cell wall-degrading intermicrobial toxin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.20.524922. [PMID: 36747731 PMCID: PMC9900751 DOI: 10.1101/2023.01.20.524922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Gram-negative bacteria can antagonize neighboring microbes using a type VI secretion system (T6SS) to deliver toxins that target different essential cellular features. Despite the conserved nature of these targets, T6SS potency can vary across recipient species. To understand the molecular basis of intrinsic T6SS susceptibility, we screened for essential Escherichia coli genes that affect its survival when antagonized by a cell wall-degrading T6SS toxin from Pseudomonas aeruginosa , Tae1. We revealed genes associated with both the cell wall and a separate layer of the cell envelope, surface lipopolysaccharide, that modulate Tae1 toxicity in vivo . Disruption of lipopolysaccharide synthesis provided Escherichia coli (Eco) with novel resistance to Tae1, despite significant cell wall degradation. These data suggest that Tae1 toxicity is determined not only by direct substrate damage, but also by indirect cell envelope homeostasis activities. We also found that Tae1-resistant Eco exhibited reduced cell wall synthesis and overall slowed growth, suggesting that reactive cell envelope maintenance pathways could promote, not prevent, self-lysis. Together, our study highlights the consequences of co-regulating essential pathways on recipient fitness during interbacterial competition, and how antibacterial toxins leverage cellular vulnerabilities that are both direct and indirect to their specific targets in vivo .
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Affiliation(s)
- Kristine L Trotta
- Department of Biochemistry & Biophysics, University of California – San Francisco, San Francisco, CA, USA
| | - Beth M Hayes
- Department of Biochemistry & Biophysics, University of California – San Francisco, San Francisco, CA, USA
| | - Johannes P Schneider
- Focal Area Infection Biology, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH - 4056 Basel, Switzerland
| | - Jing Wang
- Focal Area Infection Biology, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH - 4056 Basel, Switzerland
| | - Horia Todor
- Department of Cell and Tissue Biology, University of California – San Francisco, San Francisco, CA, USA
| | - Patrick Rockefeller Grimes
- Department of Biochemistry & Biophysics, University of California – San Francisco, San Francisco, CA, USA
| | - Ziyi Zhao
- Department of Biochemistry & Biophysics, University of California – San Francisco, San Francisco, CA, USA
| | | | - Melanie R Silvis
- Department of Cell and Tissue Biology, University of California – San Francisco, San Francisco, CA, USA
| | - Rachel Kim
- Department of Biochemistry & Biophysics, University of California – San Francisco, San Francisco, CA, USA
| | - Byoung Mo Koo
- Department of Cell and Tissue Biology, University of California – San Francisco, San Francisco, CA, USA
| | - Marek Basler
- Focal Area Infection Biology, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH - 4056 Basel, Switzerland
| | - Seemay Chou
- Department of Biochemistry & Biophysics, University of California – San Francisco, San Francisco, CA, USA
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4
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Galazzo L, Bordignon E. Electron paramagnetic resonance spectroscopy in structural-dynamic studies of large protein complexes. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2023; 134-135:1-19. [PMID: 37321755 DOI: 10.1016/j.pnmrs.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/11/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Macromolecular protein assemblies are of fundamental importance for many processes inside the cell, as they perform complex functions and constitute central hubs where reactions occur. Generally, these assemblies undergo large conformational changes and cycle through different states that ultimately are connected to specific functions further regulated by additional small ligands or proteins. Unveiling the 3D structural details of these assemblies at atomic resolution, identifying the flexible parts of the complexes, and monitoring with high temporal resolution the dynamic interplay between different protein regions under physiological conditions is key to fully understanding their properties and to fostering biomedical applications. In the last decade, we have seen remarkable advances in cryo-electron microscopy (EM) techniques, which deeply transformed our vision of structural biology, especially in the field of macromolecular assemblies. With cryo-EM, detailed 3D models of large macromolecular complexes in different conformational states became readily available at atomic resolution. Concomitantly, nuclear magnetic resonance (NMR) and electron paramagnetic resonance spectroscopy (EPR) have benefited from methodological innovations which also improved the quality of the information that can be achieved. Such enhanced sensitivity widened their applicability to macromolecular complexes in environments close to physiological conditions and opened a path towards in-cell applications. In this review we will focus on the advantages and challenges of EPR techniques with an integrative approach towards a complete understanding of macromolecular structures and functions.
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Affiliation(s)
- Laura Galazzo
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Genève 4, Switzerland.
| | - Enrica Bordignon
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Genève 4, Switzerland.
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5
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Bali K, Guffick C, McCoy R, Lu Z, Kaminski CF, Mela I, Owens RM, van Veen HW. Biosensor for Multimodal Characterization of an Essential ABC Transporter for Next-Generation Antibiotic Research. ACS APPLIED MATERIALS & INTERFACES 2023; 15:12766-12776. [PMID: 36866935 PMCID: PMC10020959 DOI: 10.1021/acsami.2c21556] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/15/2023] [Indexed: 05/21/2023]
Abstract
As the threat of antibiotic resistance increases, there is a particular focus on developing antimicrobials against pathogenic bacteria whose multidrug resistance is especially entrenched and concerning. One such target for novel antimicrobials is the ATP-binding cassette (ABC) transporter MsbA that is present in the plasma membrane of Gram-negative pathogenic bacteria where it is fundamental to the survival of these bacteria. Supported lipid bilayers (SLBs) are useful in monitoring membrane protein structure and function since they can be integrated with a variety of optical, biochemical, and electrochemical techniques. Here, we form SLBs containing Escherichia coli MsbA and use atomic force microscopy (AFM) and structured illumination microscopy (SIM) as high-resolution microscopy techniques to study the integrity of the SLBs and incorporated MsbA proteins. We then integrate these SLBs on microelectrode arrays (MEA) based on the conducting polymer poly(3,4-ethylenedioxy-thiophene) poly(styrene sulfonate) (PEDOT:PSS) using electrochemical impedance spectroscopy (EIS) to monitor ion flow through MsbA proteins in response to ATP hydrolysis. These EIS measurements can be correlated with the biochemical detection of MsbA-ATPase activity. To show the potential of this SLB approach, we observe not only the activity of wild-type MsbA but also the activity of two previously characterized mutants along with quinoline-based MsbA inhibitor G907 to show that EIS systems can detect changes in ABC transporter activity. Our work combines a multitude of techniques to thoroughly investigate MsbA in lipid bilayers as well as the effects of potential inhibitors of this protein. We envisage that this platform will facilitate the development of next-generation antimicrobials that inhibit MsbA or other essential membrane transporters in microorganisms.
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Affiliation(s)
- Karan Bali
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, U. K.
| | - Charlotte Guffick
- Department
of Pharmacology, University of Cambridge, CB2 1PD Cambridge, U. K.
| | - Reece McCoy
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, U. K.
| | - Zixuan Lu
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, U. K.
| | - Clemens F. Kaminski
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, U. K.
| | - Ioanna Mela
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, U. K.
| | - Róisín M. Owens
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, U. K.
| | - Hendrik W. van Veen
- Department
of Pharmacology, University of Cambridge, CB2 1PD Cambridge, U. K.
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6
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Guest RL, Silhavy TJ. Cracking outer membrane biogenesis. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119405. [PMID: 36455781 PMCID: PMC9878550 DOI: 10.1016/j.bbamcr.2022.119405] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/25/2022] [Accepted: 11/07/2022] [Indexed: 11/30/2022]
Abstract
The outer membrane is a distinguishing feature of the Gram-negative envelope. It lies on the external face of the peptidoglycan sacculus and forms a robust permeability barrier that protects extracytoplasmic structures from environmental insults. Overcoming the barrier imposed by the outer membrane presents a significant hurdle towards developing novel antibiotics that are effective against Gram-negative bacteria. As the outer membrane is an essential component of the cell, proteins involved in its biogenesis are themselves promising antibiotic targets. Here, we summarize key findings that have built our understanding of the outer membrane. Foundational studies describing the discovery and composition of the outer membrane as well as the pathways involved in its construction are discussed.
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Affiliation(s)
- Randi L Guest
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ, 08544, United States of America
| | - Thomas J Silhavy
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ, 08544, United States of America.
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7
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Galazzo L, Meier G, Januliene D, Parey K, De Vecchis D, Striednig B, Hilbi H, Schäfer LV, Kuprov I, Moeller A, Bordignon E, Seeger MA. The ABC transporter MsbA adopts the wide inward-open conformation in E. coli cells. SCIENCE ADVANCES 2022; 8:eabn6845. [PMID: 36223470 PMCID: PMC9555771 DOI: 10.1126/sciadv.abn6845] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 08/24/2022] [Indexed: 05/28/2023]
Abstract
Membrane proteins are currently investigated after detergent extraction from native cellular membranes and reconstitution into artificial liposomes or nanodiscs, thereby removing them from their physiological environment. However, to truly understand the biophysical properties of membrane proteins in a physiological environment, they must be investigated within living cells. Here, we used a spin-labeled nanobody to interrogate the conformational cycle of the ABC transporter MsbA by double electron-electron resonance. Unexpectedly, the wide inward-open conformation of MsbA, commonly considered a nonphysiological state, was found to be prominently populated in Escherichia coli cells. Molecular dynamics simulations revealed that extensive lateral portal opening is essential to provide access of its large natural substrate core lipid A to the binding cavity. Our work paves the way to investigate the conformational landscape of membrane proteins in cells.
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Affiliation(s)
- Laura Galazzo
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
- Department of Physical Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Gianmarco Meier
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
| | - Dovile Januliene
- Department of Structural Biology, Osnabrück University, 49076 Osnabrück, Germany
| | - Kristian Parey
- Department of Structural Biology, Osnabrück University, 49076 Osnabrück, Germany
| | - Dario De Vecchis
- Center for Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Bianca Striednig
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
| | - Hubert Hilbi
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
| | - Lars V. Schäfer
- Center for Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Ilya Kuprov
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK
| | - Arne Moeller
- Department of Structural Biology, Osnabrück University, 49076 Osnabrück, Germany
| | - Enrica Bordignon
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
- Department of Physical Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Markus A. Seeger
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
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8
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Verma VA, Wang L, Labadie SS, Liang J, Sellers BD, Wang J, Dong L, Wang Q, Zhang S, Xu Z, Zhang Y, Niu Y, Wang X, Wai J, Koehler MFT, Hu H, Alexander MK, Nishiyama M, Miu A, Xu Y, Pang J, Katakam AK, Reichelt M, Austin CD, Ho H, Payandeh J, Koth CM. Discovery of Inhibitors of the Lipopolysaccharide Transporter MsbA: From a Screening Hit to Potent Wild-Type Gram-Negative Activity. J Med Chem 2022; 65:4085-4120. [DOI: 10.1021/acs.jmedchem.1c01909] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vishal A. Verma
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Lan Wang
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Sharada S. Labadie
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jun Liang
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Benjamin D. Sellers
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jian Wang
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Liting Dong
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Qiuyue Wang
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Shuang Zhang
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Zhongya Xu
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Yexia Zhang
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Yanan Niu
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Xinxin Wang
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - John Wai
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | | | - Huiyong Hu
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Mary Kate Alexander
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Mireille Nishiyama
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Anh Miu
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Yiming Xu
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jodie Pang
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Anand K. Katakam
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Michael Reichelt
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Cary D. Austin
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Hoangdung Ho
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jian Payandeh
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Christopher M. Koth
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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9
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Fosfomycin Resistance Evolutionary Pathways of Stenotrophomonas maltophilia in Different Growing Conditions. Int J Mol Sci 2022; 23:ijms23031132. [PMID: 35163052 PMCID: PMC8835530 DOI: 10.3390/ijms23031132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 12/24/2022] Open
Abstract
The rise of multidrug-resistant Gram-negative pathogens and the lack of novel antibiotics to address this problem has led to the rescue of old antibiotics without a relevant use, such as fosfomycin. Stenotrophomonas maltophilia is a Gram-negative, non-fermenter opportunistic pathogen that presents a characteristic low susceptibility to several antibiotics of common use. Previous work has shown that while the so-far described mechanisms of fosfomycin resistance in most bacteria consist of the inactivation of the target or the transporters of this antibiotic, as well as the production of antibiotic-inactivating enzymes, these mechanisms are not selected in S. maltophilia fosfomycin-resistant mutants. In this microorganism, fosfomycin resistance is caused by the inactivation of enzymes belonging to its central carbon metabolism, hence linking metabolism with antibiotic resistance. Consequently, it is relevant to determine how different growing conditions, including urine and synthetic sputum medium that resemble infection, could impact the evolutionary pathways towards fosfomycin resistance in S. maltophilia. Our results show that S. maltophilia is able to acquire high-level fosfomycin resistance under all tested conditions. However, although some of the genetic changes leading to resistance are common, there are specific mutations that are selected under each of the tested conditions. These results indicate that the pathways of S. maltophilia evolution can vary depending on the infection point and provide information for understanding in more detail the routes of fosfomycin resistance evolution in S. maltophilia.
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10
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MsbA: an ABC transporter paradigm. Biochem Soc Trans 2021; 49:2917-2927. [PMID: 34821931 DOI: 10.1042/bst20211030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/27/2021] [Accepted: 11/03/2021] [Indexed: 12/27/2022]
Abstract
ATP-binding cassette (ABC) transporters play an important role in various cellular processes. They display a similar architecture and share a mechanism which couples ATP hydrolysis to substrate transport. However, in the light of current data and recent experimental progress, this protein superfamily appears as multifaceted as their broad substrate range. Among the prokaryotic ABC transporters, MsbA can serve as a paradigm for research in this field. It is located in the inner membrane of Gram-negative bacteria and functions as a floppase for the lipopolysaccharide (LPS) precursor core-LPS, which is involved in the biogenesis of the bacterial outer membrane. While MsbA shows high similarity to eukaryotic ABC transporters, its expression in Gram-negative bacteria makes it conveniently accessible for many experimental approaches from spectroscopy to 3D structure determination. As an essential protein for bacterial membrane integrity, MsbA has also become an attractive target for the development of novel antibiotics. Furthermore, it serves as a model for multidrug efflux pumps. Here we provide an overview of recent findings and their relevance to the field, highlight the potential of methods such as solid-state NMR and EPR spectroscopy and provide a perspective for future work.
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11
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Czolkoss S, Safronov X, Rexroth S, Knoke LR, Aktas M, Narberhaus F. Agrobacterium tumefaciens Type IV and Type VI Secretion Systems Reside in Detergent-Resistant Membranes. Front Microbiol 2021; 12:754486. [PMID: 34899640 PMCID: PMC8656257 DOI: 10.3389/fmicb.2021.754486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/25/2021] [Indexed: 11/17/2022] Open
Abstract
Cell membranes are not homogenous but compartmentalized into lateral microdomains, which are considered as biochemical reaction centers for various physiological processes in eukaryotes and prokaryotes. Due to their special lipid and protein composition, some of these microdomains are resistant to treatment with non-ionic detergents and can be purified as detergent-resistant membranes (DRMs). Here we report the proteome of DRMs from the Gram-negative phytopathogen Agrobacterium tumefaciens. Using label-free liquid chromatography-tandem mass spectrometry, we identified proteins enriched in DRMs isolated under normal and virulence-mimicking growth conditions. Prominent microdomain marker proteins such as the SPFH (stomatin/prohibitin/flotillin/HflKC) proteins HflK, HflC and Atu3772, along with the protease FtsH were highly enriched in DRMs isolated under any given condition. Moreover, proteins involved in cell envelope biogenesis, transport and secretion, as well as motility- and chemotaxis-associated proteins were overrepresented in DRMs. Most strikingly, we found virulence-associated proteins such as the VirA/VirG two-component system, and the membrane-spanning type IV and type VI secretion systems enriched in DRMs. Fluorescence microscopy of the cellular localization of both secretion systems and of marker proteins was in agreement with the results from the proteomics approach. These findings suggest that virulence traits are micro-compartmentalized into functional microdomains in A. tumefaciens.
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Affiliation(s)
- Simon Czolkoss
- Department of Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | - Xenia Safronov
- Department of Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | - Sascha Rexroth
- Department of Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Lisa R Knoke
- Department of Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | - Meriyem Aktas
- Department of Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | - Franz Narberhaus
- Department of Microbial Biology, Ruhr University Bochum, Bochum, Germany
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12
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Septal Class A Penicillin-Binding Protein Activity and ld-Transpeptidases Mediate Selection of Colistin-Resistant Lipooligosaccharide-Deficient Acinetobacter baumannii. mBio 2021; 12:mBio.02185-20. [PMID: 33402533 PMCID: PMC8545086 DOI: 10.1128/mbio.02185-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Despite dogma suggesting that lipopolysaccharide/lipooligosaccharide (LOS) was essential for viability of Gram-negative bacteria, several Acinetobacter baumannii clinical isolates produced LOS− colonies after colistin selection. Inactivation of the conserved class A penicillin-binding protein, PBP1A, was a compensatory mutation that supported isolation of LOS−A. baumannii, but the impact of PBP1A mutation was not characterized. Here, we show that the absence of PBP1A causes septation defects and that these, together with ld-transpeptidase activity, support isolation of LOS−A. baumannii. PBP1A contributes to proper cell division in A. baumannii, and its absence induced cell chaining. Only isolates producing three or more septa supported selection of colistin-resistant LOS−A. baumannii. PBP1A was enriched at the midcell, where the divisome complex facilitates daughter cell formation, and its localization was dependent on glycosyltransferase activity. Transposon mutagenesis showed that genes encoding two putative ld-transpeptidases (LdtJ and LdtK) became essential in the PBP1A mutant. Both LdtJ and LdtK were required for selection of LOS−A. baumannii, but each had distinct enzymatic activities in the cell. Together, these findings demonstrate that defects in PBP1A glycosyltransferase activity and ld-transpeptidase activity remodel the cell envelope to support selection of colistin-resistant LOS−A. baumannii.
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13
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Lundstedt E, Kahne D, Ruiz N. Assembly and Maintenance of Lipids at the Bacterial Outer Membrane. Chem Rev 2020; 121:5098-5123. [PMID: 32955879 DOI: 10.1021/acs.chemrev.0c00587] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The outer membrane of Gram-negative bacteria is essential for their survival in harsh environments and provides intrinsic resistance to many antibiotics. This membrane is remarkable; it is a highly asymmetric lipid bilayer. The inner leaflet of the outer membrane contains phospholipids, whereas the fatty acyl chains attached to lipopolysaccharide (LPS) comprise the hydrophobic portion of the outer leaflet. This lipid asymmetry, and in particular the exclusion of phospholipids from the outer leaflet, is key to creating an almost impenetrable barrier to hydrophobic molecules that can otherwise pass through phospholipid bilayers. It has long been known that these lipids are not made in the outer membrane. It is now believed that conserved multisubunit protein machines extract these lipids after their synthesis is completed at the inner membrane and transport them to the outer membrane. A longstanding question is how the cell builds and maintains this asymmetric lipid bilayer in coordination with the assembly of the other components of the cell envelope. This Review describes the trans-envelope lipid transport systems that have been identified to participate in outer-membrane biogenesis: LPS transport via the Lpt machine, and phospholipid transport via the Mla pathway and several recently proposed transporters.
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Affiliation(s)
- Emily Lundstedt
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Natividad Ruiz
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
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14
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Ford RC, Hellmich UA. What monomeric nucleotide binding domains can teach us about dimeric ABC proteins. FEBS Lett 2020; 594:3857-3875. [PMID: 32880928 DOI: 10.1002/1873-3468.13921] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/06/2020] [Accepted: 08/24/2020] [Indexed: 12/12/2022]
Abstract
The classic conceptualization of ATP binding cassette (ABC) transporter function is an ATP-dependent conformational change coupled to transport of a substrate across a biological membrane via the transmembrane domains (TMDs). The binding of two ATP molecules within the transporter's two nucleotide binding domains (NBDs) induces their dimerization. Despite retaining the ability to bind nucleotides, isolated NBDs frequently fail to dimerize. ABC proteins without a TMD, for example ABCE and ABCF, have NBDs tethered via elaborate linkers, further supporting that NBD dimerization does not readily occur for isolated NBDs. Intriguingly, even in full-length transporters, the NBD-dimerized, outward-facing state is not as frequently observed as might be expected. This leads to questions regarding what drives NBD interaction and the role of the TMDs or linkers. Understanding the NBD-nucleotide interaction and the subsequent NBD dimerization is thus pivotal for understanding ABC transporter activity in general. Here, we hope to provide new insights into ABC protein function by discussing the perplexing issue of (missing) NBD dimerization in isolation and in the context of full-length ABC proteins.
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Affiliation(s)
- Robert C Ford
- Faculty of Biology Medicine and Health, The University of Manchester, UK
| | - Ute A Hellmich
- Department of Chemistry, Johannes Gutenberg-University, Mainz, Germany.,Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University, Frankfurt, Germany
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15
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Kolich LR, Chang YT, Coudray N, Giacometti SI, MacRae MR, Isom GL, Teran EM, Bhabha G, Ekiert DC. Structure of MlaFB uncovers novel mechanisms of ABC transporter regulation. eLife 2020; 9:e60030. [PMID: 32602838 PMCID: PMC7367683 DOI: 10.7554/elife.60030] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 06/24/2020] [Indexed: 12/12/2022] Open
Abstract
ABC transporters facilitate the movement of diverse molecules across cellular membranes, but how their activity is regulated post-translationally is not well understood. Here we report the crystal structure of MlaFB from E. coli, the cytoplasmic portion of the larger MlaFEDB ABC transporter complex, which drives phospholipid trafficking across the bacterial envelope to maintain outer membrane integrity. MlaB, a STAS domain protein, binds the ABC nucleotide binding domain, MlaF, and is required for its stability. Our structure also implicates a unique C-terminal tail of MlaF in self-dimerization. Both the C-terminal tail of MlaF and the interaction with MlaB are required for the proper assembly of the MlaFEDB complex and its function in cells. This work leads to a new model for how an important bacterial lipid transporter may be regulated by small proteins, and raises the possibility that similar regulatory mechanisms may exist more broadly across the ABC transporter family.
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Affiliation(s)
- Ljuvica R Kolich
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Ya-Ting Chang
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Nicolas Coudray
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
- Applied Bioinformatics Laboratory, New York University School of MedicineNew YorkUnited States
| | - Sabrina I Giacometti
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Mark R MacRae
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Georgia L Isom
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Evelyn M Teran
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Gira Bhabha
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Damian C Ekiert
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
- Department of Microbiology, New York University School of MedicineNew YorkUnited States
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16
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Multiple ways to kill bacteria via inhibiting novel cell wall or membrane targets. Future Med Chem 2020; 12:1253-1279. [PMID: 32538147 DOI: 10.4155/fmc-2020-0046] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The rise of antibiotic-resistant infections has been well documented and the need for novel antibiotics cannot be overemphasized. US FDA approved antibiotics target only a small fraction of bacterial cell wall or membrane components, well-validated antimicrobial targets. In this review, we highlight small molecules that inhibit relatively unexplored cell wall and membrane targets. Some of these targets include teichoic acids-related proteins (DltA, LtaS, TarG and TarO), lipid II, Mur family enzymes, components of LPS assembly (MsbA, LptA, LptB and LptD), penicillin-binding protein 2a in methicillin-resistant Staphylococcus aureus, outer membrane protein transport (such as LepB and BamA) and lipoprotein transport components (LspA, LolC, LolD and LolE). Inhibitors of SecA, cell division protein, FtsZ and compounds that kill persister cells via membrane targeting are also covered.
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17
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Moura ECCM, Baeta T, Romanelli A, Laguri C, Martorana AM, Erba E, Simorre JP, Sperandeo P, Polissi A. Thanatin Impairs Lipopolysaccharide Transport Complex Assembly by Targeting LptC-LptA Interaction and Decreasing LptA Stability. Front Microbiol 2020; 11:909. [PMID: 32477309 PMCID: PMC7237710 DOI: 10.3389/fmicb.2020.00909] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/17/2020] [Indexed: 11/13/2022] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria is a highly selective permeability barrier due to its asymmetric structure with lipopolysaccharide (LPS) in the outer leaflet. In Escherichia coli, LPS is transported to the cell surface by the LPS transport (Lpt) system composed of seven essential proteins forming a transenvelope bridge. Transport is powered by the ABC transporter LptB2FGC, which extracts LPS from the inner membrane (IM) and transfers it, through LptC protein, to the periplasmic protein LptA. Then, LptA delivers LPS to the OM LptDE translocon for final assembly at the cell surface. The Lpt protein machinery operates as a single device, since depletion of any component leads to the accumulation of a modified LPS decorated with repeating units of colanic acid at the IM outer leaflet. Moreover, correct machine assembly is essential for LPS transit and disruption of the Lpt complex results in LptA degradation. Due to its vital role in cell physiology, the Lpt system represents a good target for antimicrobial drugs. Thanatin is a naturally occurring antimicrobial peptide reported to cause defects in membrane assembly and demonstrated in vitro to bind to the N-terminal β-strand of LptA. Since this region is involved in both LptA dimerization and interaction with LptC, we wanted to elucidate the mechanism of inhibition of thanatin and discriminate whether its antibacterial effect is exerted by the disruption of the interaction of LptA with itself or with LptC. For this purpose, we here implemented the Bacterial Adenylate Cyclase Two-Hybrid (BACTH) system to probe in vivo the Lpt interactome in the periplasm. With this system, we found that thanatin targets both LptC–LptA and LptA–LptA interactions, with a greater inhibitory effect on the former. We confirmed in vitro the disruption of LptC–LptA interaction using two different biophysical techniques. Finally, we observed that in cells treated with thanatin, LptA undergoes degradation and LPS decorated with colanic acid accumulates. These data further support inhibition or disruption of Lpt complex assembly as the main killing mechanism of thanatin against Gram-negative bacteria.
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Affiliation(s)
- Elisabete C C M Moura
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Tiago Baeta
- Université Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Alessandra Romanelli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milan, Italy
| | - Cedric Laguri
- Université Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Alessandra M Martorana
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Emanuela Erba
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milan, Italy
| | | | - Paola Sperandeo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Alessandra Polissi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
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18
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Structural Kinetics of MsbA Investigated by Stopped-Flow Time-Resolved Small-Angle X-Ray Scattering. Structure 2019; 28:348-354.e3. [PMID: 31899087 DOI: 10.1016/j.str.2019.12.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/06/2019] [Accepted: 12/02/2019] [Indexed: 12/19/2022]
Abstract
Recent structures of full-length ATP-binding cassette (ABC) transporter MsbA in different states indicate large conformational changes during the reaction cycle that involve transient dimerization of its nucleotide-binding domains (NBDs). However, a detailed molecular understanding of the structural changes and associated kinetics of MsbA upon ATP binding and hydrolysis is still missing. Here, we employed time-resolved small-angle X-ray scattering, initiated by stopped-flow mixing, to investigate the kinetics and accompanying structural changes of NBD dimerization (upon ATP binding) and subsequent dissociation (upon ATP hydrolysis) in the context of isolated NBDs as well as full-length MsbA in lipid nanodiscs. Our data allowed us to structurally characterize the major states involved in the process and determine time constants for NBD dimerization and dissociation. In the full-length protein, these structural transitions occur on much faster time scales, indicating close-proximity effects and structural coupling of the transmembrane domains with the NBDs.
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19
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Sperandeo P, Polissi A, De Fabiani E. Fat Matters for Bugs: How Lipids and Lipid Modifications Make the Difference in Bacterial Life. EUR J LIPID SCI TECH 2019. [DOI: 10.1002/ejlt.201900204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Paola Sperandeo
- Dipartimento di Scienze Farmacologiche e BiomolecolariUniversità degli Studi di MilanoVia Balzaretti 920133MilanoItaly
| | - Alessandra Polissi
- Dipartimento di Scienze Farmacologiche e BiomolecolariUniversità degli Studi di MilanoVia Balzaretti 920133MilanoItaly
| | - Emma De Fabiani
- Dipartimento di Scienze Farmacologiche e BiomolecolariUniversità degli Studi di MilanoVia Balzaretti 920133MilanoItaly
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20
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The Lpt ABC transporter for lipopolysaccharide export to the cell surface. Res Microbiol 2019; 170:366-373. [PMID: 31376484 DOI: 10.1016/j.resmic.2019.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/11/2019] [Accepted: 07/13/2019] [Indexed: 10/26/2022]
Abstract
The surface of the outer membrane of Gram-negative bacteria is covered by a tightly packed layer of lipopolysaccharide molecules which provide a barrier against many toxic compounds and antibiotics. Lipopolysaccharide, synthesized in the cytoplasm, is assembled in the periplasmic leaflet of the inner membrane where the intermembrane Lpt system mediates its transport to the cell surface. The first step of lipopolysaccharide transport is its extraction from the outer leaflet of inner membrane powered by the atypical LptB2FGC ABC transporter. Here we review latest advances leading to understanding at molecular level how lipopolysaccharide is transported irreversibly to the outer membrane.
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21
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Poole RK, Cozens AG, Shepherd M. The CydDC family of transporters. Res Microbiol 2019; 170:407-416. [PMID: 31279084 DOI: 10.1016/j.resmic.2019.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/12/2019] [Accepted: 06/25/2019] [Indexed: 12/23/2022]
Abstract
The CydDC family of ABC transporters export the low molecular weight thiols glutathione and cysteine to the periplasm of a variety of bacterial species. The CydDC complex has previously been shown to be important for disulfide folding, motility, respiration, and tolerance to nitric oxide and antibiotics. In addition, CydDC is thus far unique amongst ABC transporters in that it binds a haem cofactor that appears to modulate ATPase activity. CydDC has a diverse impact upon bacterial metabolism, growth, and virulence, and is of interest to those working on membrane transport mechanisms, redox biology, aerobic respiration, and stress sensing/tolerance during infection.
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Affiliation(s)
- Robert K Poole
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
| | - Adam G Cozens
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Mark Shepherd
- School of Biosciences, University of Kent, Canterbury, United Kingdom.
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22
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Padayatti PS, Lee SC, Stanfield RL, Wen PC, Tajkhorshid E, Wilson IA, Zhang Q. Structural Insights into the Lipid A Transport Pathway in MsbA. Structure 2019; 27:1114-1123.e3. [PMID: 31130486 PMCID: PMC6610721 DOI: 10.1016/j.str.2019.04.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 03/12/2019] [Accepted: 04/10/2019] [Indexed: 11/27/2022]
Abstract
MsbA is an essential ATP-binding cassette transporter in Gram-negative bacteria that transports lipid A and lipopolysaccharide from the cytoplasmic leaflet to the periplasmic leaflet of the inner membrane. Here we report the X-ray structure of MsbA from Salmonella typhimurium at 2.8-Å resolution in an inward-facing conformation after cocrystallization with lipid A and using a stabilizing facial amphiphile. The structure displays a large amplitude opening in the transmembrane portal, which is likely required for lipid A to pass from its site of synthesis into the protein-enclosed transport pathway. Putative lipid A density is observed further inside the transmembrane cavity, consistent with a trap and flip model. Additional electron density attributed to lipid A is observed near an outer surface cleft at the periplasmic ends of the transmembrane helices. These findings provide new structural insights into the lipid A transport pathway through comparative analysis with existing MsbA structures.
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Affiliation(s)
- Pius S Padayatti
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sung Chang Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Robyn L Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Po-Chao Wen
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Qinghai Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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23
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Abstract
In Gram-negative bacteria, the outer membrane protects the cell against many toxic molecules, and the peptidoglycan layer provides protection against osmotic challenges, allowing bacterial cells to survive in changing environments. Maintaining cell envelope integrity is therefore a question of life or death for a bacterial cell. Here we show that Escherichia coli cells activate the LD-transpeptidase LdtD to introduce 3-3 cross-links in the peptidoglycan layer when the integrity of the outer membrane is compromised, and this response is required to avoid cell lysis. This peptidoglycan remodeling program is a strategy to increase the overall robustness of the bacterial cell envelope in response to defects in the outer membrane. Gram-negative bacteria have a tripartite cell envelope with the cytoplasmic membrane (CM), a stress-bearing peptidoglycan (PG) layer, and the asymmetric outer membrane (OM) containing lipopolysaccharide (LPS) in the outer leaflet. Cells must tightly coordinate the growth of their complex envelope to maintain cellular integrity and OM permeability barrier function. The biogenesis of PG and LPS relies on specialized macromolecular complexes that span the entire envelope. In this work, we show that Escherichia coli cells are capable of avoiding lysis when the transport of LPS to the OM is compromised, by utilizing LD-transpeptidases (LDTs) to generate 3-3 cross-links in the PG. This PG remodeling program relies mainly on the activities of the stress response LDT, LdtD, together with the major PG synthase PBP1B, its cognate activator LpoB, and the carboxypeptidase PBP6a. Our data support a model according to which these proteins cooperate to strengthen the PG in response to defective OM synthesis.
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24
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Abstract
Lipopolysaccharide synthesis and transport pathways are attractive targets for the development of new antimicrobial therapeutics. The ABC (ATP Binding Cassette) transporter MsbA has been recently described as employing a 'trap and flip' mechanism of lipopolysaccharide transport. This represents a novel mechanism amongst known lipid ABC transporters.
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Affiliation(s)
- Bradley J Voss
- Department of Infectious Diseases, Center for Vaccines and Immunology, University of Georgia, College of Veterinary Medicine, Athens, GA 30602, USA
| | - M Stephen Trent
- Department of Infectious Diseases, Center for Vaccines and Immunology, University of Georgia, College of Veterinary Medicine, Athens, GA 30602, USA.
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25
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Abstract
Gram-negative bacteria have an outer membrane that is positioned at the frontline of the cell's interaction with the environment and that serves as a barrier against noxious molecules including many antibiotics. This protective function mainly relies on lipopolysaccharide, a complex glycolipid located in the outer leaflet of the outer membrane. In this chapter we will first summarize lipopolysaccharide structure, functions and biosynthetic pathway and then we will discuss how it is transported and assembled to the cell surface. This is a remarkably complex process, as amphipathic lipopolysaccharide molecules must traverse three different cellular compartments to reach their final destination.
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26
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Bergsveinson J, Kajala I, Goerzen S, Ziola B. Detection of a Hop-Tolerance Gene horA Insertion Variant in Lactic Acid Bacteria That Results in a Truncated HorA Lacking the Walker B Motif Necessary for Transport Function. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-2017-4682-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Jordyn Bergsveinson
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Room 41 Royal University Hospital, 103 Hospital Drive, Saskatoon, SK, S7N 0W8, Canada
| | - Ilkka Kajala
- VTT Technical Research Centre of Finland Ltd., PL 1000, 02044 VTT, Espoo, Finland
| | - Scott Goerzen
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Room 41 Royal University Hospital, 103 Hospital Drive, Saskatoon, SK, S7N 0W8, Canada
| | - Barry Ziola
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Room 41 Royal University Hospital, 103 Hospital Drive, Saskatoon, SK, S7N 0W8, Canada
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27
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Heidari Tajabadi F, Medrano-Soto A, Ahmadzadeh M, Salehi Jouzani G, Saier MH. Comparative Analyses of Transport Proteins Encoded within the Genomes of Bdellovibrio bacteriovorus HD100 and Bdellovibrio exovorus JSS. J Mol Microbiol Biotechnol 2017; 27:332-349. [PMID: 29212086 DOI: 10.1159/000484563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/17/2017] [Indexed: 12/21/2022] Open
Abstract
Bdellovibrio, δ-proteobacteria, including B. bacteriovorus (Bba) and B. exovorus (Bex), are obligate predators of other Gram-negative bacteria. While Bba grows in the periplasm of the prey cell, Bex grows externally. We have analyzed and compared the transport proteins of these 2 organisms based on the current contents of the Transporter Classification Database (TCDB; www.tcdb.org). Bba has 103 transporters more than Bex, 50% more secondary carriers, and 3 times as many MFS carriers. Bba has far more metabolite transporters than Bex as expected from its larger genome, but there are 2 times more carbohydrate uptake and drug efflux systems, and 3 times more lipid transporters. Bba also has polyamine and carboxylate transporters lacking in Bex. Bba has more than twice as many members of the Mot-Exb family of energizers, but both may have energizers for gliding motility. They use entirely different types of systems for iron acquisition. Both contain unexpectedly large numbers of pseudogenes and incomplete systems, suggesting that they are undergoing genome size reduction. Interestingly, all 5 outer-membrane receptors in Bba are lacking in Bex. The 2 organisms have similar numbers and types of peptide and amino acid uptake systems as well as protein and carbohydrate secretion systems. The differences observed correlate with and may account, in part, for the different lifestyles of these 2 bacterial predators.
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28
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Sperandeo P, Martorana AM, Polissi A. The lipopolysaccharide transport (Lpt) machinery: A nonconventional transporter for lipopolysaccharide assembly at the outer membrane of Gram-negative bacteria. J Biol Chem 2017; 292:17981-17990. [PMID: 28878019 DOI: 10.1074/jbc.r117.802512] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The outer membrane (OM) of Gram-negative is a unique lipid bilayer containing LPS in its outer leaflet. Because of the presence of amphipathic LPS molecules, the OM behaves as an effective permeability barrier that makes Gram-negative bacteria inherently resistant to many antibiotics. This review focuses on LPS biogenesis and discusses recent advances that have contributed to our understanding of how this complex molecule is transported across the cellular envelope and is assembled at the OM outer leaflet. Clearly, this knowledge represents an important platform for the development of novel therapeutic options to manage Gram-negative infections.
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Affiliation(s)
- Paola Sperandeo
- From the Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, 20133 Milan and
| | - Alessandra M Martorana
- the Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, 20126 Milan, Italy
| | - Alessandra Polissi
- From the Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, 20133 Milan and
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29
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Probing native metal ion association sites through quenching of fluorophores in the nucleotide-binding domains of the ABC transporter MsbA. Biochem J 2017; 474:1993-2007. [PMID: 28432259 DOI: 10.1042/bcj20161051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 03/24/2017] [Accepted: 04/21/2017] [Indexed: 11/17/2022]
Abstract
ATP-binding cassette (ABC) transporters are ubiquitously present in prokaryotic and eukaryotic cells. Binding of ATP to the nucleotide-binding domains (NBDs) elicits major conformational changes of the transporters resulting in the transport of the substrate across the membrane. The availability of a crystal structure of the NBDs enabled us to elucidate the local structure and small-scale dynamics in the NBDs. Here, we labeled the ABC transporter MsbA, a homodimeric flippase from Escherichia coli, with a fluorescent probe, Alexa532, within the NBDs. ATP application elicited collisional quenching, whereas no quenching was observed after the addition of ATP analogs or ATP hydrolysis inhibitors. The Alexa532-conjugated MsbA variants exhibited transition metal ion Förster resonance energy transfer (tmFRET) after the addition of Ni2+, and ATP decreased this Ni2+-mediated FRET of the NBDs. Structure modeling developed from crystallographic data and examination of tmFRET measurements of MsbA variants in the absence of ATP revealed the presence of metal ion-associated pockets (MiAPs) in the NBDs. Three histidines were predicted to participate in chelating Ni2+ in the two possible MiAPs. Performing histidine-substitution experiments with the NBDs showed that the dissociation constant for Ni2+ of MiAP2 was smaller than that of MiAP1. The structural allocation of the MiAPs was further supported by showing that the addition of Cu2+ resulted in higher quenching than Ni2+ Taken together, the present study showed that the NBDs contain two native binding sites for metal ions and ATP addition affects the Ni2+-binding activity of the MiAPs.
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Fathy Mohamed Y, Hamad M, Ortega XP, Valvano MA. The LpxL acyltransferase is required for normal growth and penta-acylation of lipid A in Burkholderia cenocepacia. Mol Microbiol 2017; 104:144-162. [PMID: 28085228 DOI: 10.1111/mmi.13618] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2017] [Indexed: 12/27/2022]
Abstract
Lipid A anchors the lipopolysaccharide (LPS) to the outer membrane and is usually composed of a hexa-acylated diglucosamine backbone. Burkholderia cenocepacia, an opportunistic pathogen, produces a mixture of tetra- and penta-acylated lipid A. "Late" acyltransferases add secondary acyl chains to lipid A after the incorporation of four primary acyl chains to the diglucosamine backbone. Here, we report that B. cenocepacia has only one late acyltransferase, LpxL (BCAL0508), which adds a myristoyl chain to the 2' position of lipid A resulting in penta-acylated lipid A. We also identified PagL (BCAL0788), which acts as an outer membrane lipase by removing the primary β-hydroxymyristate (3-OH-C14:0) chain at the 3 position, leading to tetra-acylated lipid A. Unlike PagL, LpxL depletion caused reduced cell growth and defects in cell morphology, both of which were suppressed by overexpressing the LPS flippase MsbA (BCAL2408), suggesting that lipid A molecules lacking the fifth acyl chain contributed by LpxL are not good substrates for the flippase. We also show that intracellular B. cenocepacia within macrophages produced more penta-acylated lipid A, suggesting lipid A penta-acylation in B. cenocepacia is required not only for bacterial growth and morphology but also for adaptation to intracellular lifestyle.
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Affiliation(s)
- Yasmine Fathy Mohamed
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, BT9 7BL, UK.,Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Mohamad Hamad
- Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Ximena P Ortega
- Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Miguel A Valvano
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, BT9 7BL, UK.,Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada, N6A 5C1
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Sperandeo P, Martorana AM, Polissi A. Lipopolysaccharide biogenesis and transport at the outer membrane of Gram-negative bacteria. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:1451-1460. [PMID: 27760389 DOI: 10.1016/j.bbalip.2016.10.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/11/2016] [Accepted: 10/13/2016] [Indexed: 01/10/2023]
Abstract
The outer membrane (OM) of Gram-negative bacteria is an asymmetric lipid bilayer containing a unique glycolipid, lipopolysaccharide (LPS) in its outer leaflet. LPS molecules confer to the OM peculiar permeability barrier properties enabling Gram-negative bacteria to exclude many toxic compounds, including clinically useful antibiotics, and to survive harsh environments. Transport of LPS poses several problems to the cells due to the amphipatic nature of this molecule. In this review we summarize the current knowledge on the LPS transport machinery, discuss the challenges associated with this process and present the solutions that bacterial cells have evolved to address the problem of LPS transport and assembly at the cell surface. Finally, we discuss how knowledge on LPS biogenesis can be translated for the development of novel antimicrobial therapies. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.
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Affiliation(s)
- Paola Sperandeo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy.
| | - Alessandra M Martorana
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Alessandra Polissi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy.
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32
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Neumann J, Rose-Sperling D, Hellmich UA. Diverse relations between ABC transporters and lipids: An overview. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:605-618. [PMID: 27693344 DOI: 10.1016/j.bbamem.2016.09.023] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/24/2016] [Accepted: 09/26/2016] [Indexed: 12/19/2022]
Abstract
It was first discovered in 1992 that P-glycoprotein (Pgp, ABCB1), an ATP binding cassette (ABC) transporter, can transport phospholipids such as phosphatidylcholine, -ethanolamine and -serine as well as glucosylceramide and glycosphingolipids. Subsequently, many other ABC transporters were identified to act as lipid transporters. For substrate transport by ABC transporters, typically a classic, alternating access model with an ATP-dependent conformational switch between a high and a low affinity substrate binding site is evoked. Transport of small hydrophilic substrates can easily be imagined this way, as the molecule can in principle enter and exit the transporter in the same orientation. Lipids on the other hand need to undergo a 180° degree turn as they translocate from one membrane leaflet to the other. Lipids and lipidated molecules are highly diverse, so there may be various ways how to achieve their flipping and flopping. Nonetheless, an increase in biophysical, biochemical and structural data is beginning to shed some light on specific aspects of lipid transport by ABC transporters. In addition, there is now abundant evidence that lipids affect ABC transporter conformation, dynamics as well as transport and ATPase activity in general. In this review, we will discuss different ways in which lipids and ABC transporters interact and how lipid translocation may be achieved with a focus on the techniques used to investigate these processes. This article is part of a Special Issue entitled: Lipid order/lipid defects and lipid-control of protein activity edited by Dirk Schneider.
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Affiliation(s)
- Jennifer Neumann
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany
| | - Dania Rose-Sperling
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany
| | - Ute A Hellmich
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany.
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Gronow S, Brade H. Invited review: Lipopolysaccharide biosynthesis: which steps do bacteria need to survive? ACTA ACUST UNITED AC 2016. [DOI: 10.1177/09680519010070010301] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A detailed knowledge of LPS biosynthesis is of the utmost importance in understanding the function of the outer membrane of Gram-negative bacteria. The regulation of LPS biosynthesis affects many more compartments of the bacterial cell than the outer membrane and thus contributes to the understanding of the physiology of Gram-negative bacteria in general, on the basis of which only mechanisms of virulence and antibiotic resistance can be studied to find new targets for antibacterial treatment. The study of LPS biosynthesis is also an excellent example to demonstrate the limitations of `genomics' and `proteomics', since secondary gene products can be studied only by the combined tools of molecular genetics, enzymology and analytical structural biochemistry. Thus, the door to the field of `glycomics' is opened.
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Affiliation(s)
- Sabine Gronow
- Division of Medical and Biochemical Microbiology, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany,
| | - Helmut Brade
- Division of Medical and Biochemical Microbiology, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany
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The CydDC ABC transporter of Escherichia coli: new roles for a reductant efflux pump. Biochem Soc Trans 2016; 43:908-12. [PMID: 26517902 DOI: 10.1042/bst20150098] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The CydDC complex of Escherichia coli is a heterodimeric ATP-binding cassette (ABC) transporter that exports cysteine and glutathione to the periplasm. These reductants are thought to modulate periplasmic redox poise, impacting upon the disulfide folding of periplasmic and secreted proteins involved in bacterial virulence. Diminished CydDC activity abolishes the assembly of functional bd-type respiratory oxidases and perturbs haem ligation during the assembly of c-type cytochromes. The focus herein is upon a newly-discovered interaction of the CydDC complex with a haem cofactor; haem has recently been shown to modulate CydDC activity and structural modelling reveals a potential haem-binding site on the periplasmic surface of the complex. These findings have important implications for future investigations into the potential roles for the CydDC-bound haem in redox sensing and tolerance to nitric oxide (NO).
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Simpson BW, May JM, Sherman DJ, Kahne D, Ruiz N. Lipopolysaccharide transport to the cell surface: biosynthesis and extraction from the inner membrane. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2015.0029. [PMID: 26370941 DOI: 10.1098/rstb.2015.0029] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The cell surface of most Gram-negative bacteria is covered with lipopolysaccharide (LPS). The network of charges and sugars provided by the dense packing of LPS molecules in the outer leaflet of the outer membrane interferes with the entry of hydrophobic compounds into the cell, including many antibiotics. In addition, LPS can be recognized by the immune system and plays a crucial role in many interactions between bacteria and their animal hosts. LPS is synthesized in the inner membrane of Gram-negative bacteria, so it must be transported across their cell envelope to assemble at the cell surface. Over the past two decades, much of the research on LPS biogenesis has focused on the discovery and understanding of Lpt, a multi-protein complex that spans the cell envelope and functions to transport LPS from the inner membrane to the outer membrane. This paper focuses on the early steps of the transport of LPS by the Lpt machinery: the extraction of LPS from the inner membrane. The accompanying paper (May JM, Sherman DJ, Simpson BW, Ruiz N, Kahne D. 2015 Phil. Trans. R. Soc. B 370, 20150027. (doi:10.1098/rstb.2015.0027)) describes the subsequent steps as LPS travels through the periplasm and the outer membrane to its final destination at the cell surface.
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Affiliation(s)
- Brent W Simpson
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - Janine M May
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - David J Sherman
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA Department of Molecular and Cellular Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Natividad Ruiz
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
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Abstract
Gram-negative bacteria have a double-membrane cellular envelope that enables them to colonize harsh environments and prevents the entry of many clinically available antibiotics. A main component of most outer membranes is lipopolysaccharide (LPS), a glycolipid containing several fatty acyl chains and up to hundreds of sugars that is synthesized in the cytoplasm. In the past two decades, the proteins that are responsible for transporting LPS across the cellular envelope and assembling it at the cell surface in Escherichia coli have been identified, but it remains unclear how they function. In this Review, we discuss recent advances in this area and present a model that explains how energy from the cytoplasm is used to power LPS transport across the cellular envelope to the cell surface.
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Zhang C, Chen X, Stephanopoulos G, Too HP. Efflux transporter engineering markedly improves amorphadiene production inEscherichia coli. Biotechnol Bioeng 2016; 113:1755-63. [DOI: 10.1002/bit.25943] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/21/2015] [Accepted: 01/18/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Congqiang Zhang
- Chemical and Pharmaceutical Engineering; Singapore-MIT Alliance; 4 Engineering Drive 3 Singapore Singapore
- Biotransformation Innovation Platform (BioTrans); Agency for Science, Technology and Research (A*STAR); Singapore Singapore
| | - Xixian Chen
- Chemical and Pharmaceutical Engineering; Singapore-MIT Alliance; 4 Engineering Drive 3 Singapore Singapore
- Biotransformation Innovation Platform (BioTrans); Agency for Science, Technology and Research (A*STAR); Singapore Singapore
| | - Gregory Stephanopoulos
- Chemical and Pharmaceutical Engineering; Singapore-MIT Alliance; 4 Engineering Drive 3 Singapore Singapore
- Department of Chemical Engineering; Massachusetts Institute of Technology; Cambridge Massachusetts
| | - Heng-Phon Too
- Chemical and Pharmaceutical Engineering; Singapore-MIT Alliance; 4 Engineering Drive 3 Singapore Singapore
- Biotransformation Innovation Platform (BioTrans); Agency for Science, Technology and Research (A*STAR); Singapore Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine; National University of Singapore, 8 Medical Drive; Blk MD7, Level 4 Singapore 117597 Singapore
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Abstract
The major class of integral proteins found in the outer membrane (OM) of E. coli and Salmonella adopt a β-barrel conformation (OMPs). OMPs are synthesized in the cytoplasm with a typical signal sequence at the amino terminus, which directs them to the secretion machinery (SecYEG) located in the inner membrane for translocation to the periplasm. Chaperones such as SurA, or DegP and Skp, escort these proteins across the aqueous periplasm protecting them from aggregation. The chaperones then deliver OMPs to a highly conserved outer membrane assembly site termed the Bam complex. In E. coli, the Bam complex is composed of an essential OMP, BamA, and four associated OM lipoproteins, BamBCDE, one of which, BamD, is also essential. Here we provide an overview of what we know about the process of OMP assembly and outline the various hypotheses that have been proposed to explain how proteins might be integrated into the asymmetric OM lipid bilayer in an environment that lacks obvious energy sources. In addition, we describe the envelope stress responses that ensure the fidelity of OM biogenesis and how factors, such as phage and certain toxins, have coopted this essential machine to gain entry into the cell.
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Matsuhashi A, Tahara H, Ito Y, Uchiyama J, Ogawa S, Ohta H. Slr2019, lipid A transporter homolog, is essential for acidic tolerance in Synechocystis sp. PCC6803. PHOTOSYNTHESIS RESEARCH 2015; 125:267-277. [PMID: 25822232 DOI: 10.1007/s11120-015-0129-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 03/23/2015] [Indexed: 06/04/2023]
Abstract
Living organisms must defend themselves against various environmental stresses. Extracellular polysaccharide-producing cells exhibit enhanced tolerance toward adverse environmental stress. In Synechocystis sp. PCC6803 (Synechocystis), lipopolysaccharide (LPS) may play a role in this protection. To examine the relationship between stress tolerance of Synechocystis and LPS, we focused on Slr2019 because Slr2019 is homologous to MsbA in Escherichia coli, which is related to LPS synthesis. First, to obtain a defective mutant of LPS, we constructed the slr2019 insertion mutant (slr2019) strain. Sodium deoxycholate-polyacrylamide gel electrophoresis indicated that slr2019 strain did not synthesize normal LPS. Second, to clarify the participation of LPS in acid tolerance, wild type (WT) and slr2019 strain were grown under acid stress; slr2019 strain growth was significantly weaker than WT growth. Third, to examine influences on stress tolerance, slr2019 strain was grown under various stresses. Under salinity and temperature stress, slr2019 strain grew significantly slower than WT. To confirm cell morphology, cell shape and envelope of slr2019 strain were observed by transmission electron microscopy; slr2019 cells contained more electron-transparent bodies than WT cells. Finally, to confirm whether electron-transparent bodies are poly-3-hydroxybutyrate (PHB), slr2019 strain was stained with Nile Blue A, a PHB detector, and observed by fluorescence microscopy. The PHB granule content ratio of WT and slr2019 strain grown at BG-11 pH 8.0 was each 7.18 and 8.41 %. At pH 6.0, the PHB granule content ratio of WT and slr2019 strain was 2.99 and 2.60 %. However, the PHB granule content ratio of WT and slr2019 strain grown at BG-11N-reduced was 10.82 and 0.56 %. Because slr2019 strain significantly decreased PHB under BG-11N-reduced compared with WT, LPS synthesis may be related to PHB under particular conditions. These results indicated that Slr2019 is necessary for Synechocystis survival in various stresses.
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Affiliation(s)
- Ayumi Matsuhashi
- Graduate School of Mathematics and Science Education, Tokyo University of Science, Shinjuku-ku, Tokyo, 162-8601, Japan,
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40
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Xie XL, Li CH, Yang YX, Jin L, Tan JJ, Zhang XY, Su JG, Wang CX. Allosteric transitions of ATP-binding cassette transporter MsbA studied by the adaptive anisotropic network model. Proteins 2015; 83:1643-53. [DOI: 10.1002/prot.24850] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 06/02/2015] [Accepted: 06/24/2015] [Indexed: 01/04/2023]
Affiliation(s)
- Xiao Lu Xie
- College of Life Science and Bioengineering, Beijing University of Technology; Beijing 100124 China
| | - Chun Hua Li
- College of Life Science and Bioengineering, Beijing University of Technology; Beijing 100124 China
| | - Yong Xiao Yang
- College of Life Science and Bioengineering, Beijing University of Technology; Beijing 100124 China
| | - Lu Jin
- College of Life Science and Bioengineering, Beijing University of Technology; Beijing 100124 China
| | - Jian Jun Tan
- College of Life Science and Bioengineering, Beijing University of Technology; Beijing 100124 China
| | - Xiao Yi Zhang
- College of Life Science and Bioengineering, Beijing University of Technology; Beijing 100124 China
| | - Ji Guo Su
- College of Science, Yanshan University; Qinhuangdao 066004 China
| | - Cun Xin Wang
- College of Life Science and Bioengineering, Beijing University of Technology; Beijing 100124 China
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41
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Putker F, Bos MP, Tommassen J. Transport of lipopolysaccharide to the Gram-negative bacterial cell surface. FEMS Microbiol Rev 2015; 39:985-1002. [DOI: 10.1093/femsre/fuv026] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2015] [Indexed: 12/15/2022] Open
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Holyoake LV, Poole RK, Shepherd M. The CydDC Family of Transporters and Their Roles in Oxidase Assembly and Homeostasis. Adv Microb Physiol 2015. [PMID: 26210105 DOI: 10.1016/bs.ampbs.2015.04.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The CydDC complex of Escherichia coli is a heterodimeric ATP-binding cassette type transporter (ABC transporter) that exports the thiol-containing redox-active molecules cysteine and glutathione. These reductants are thought to aid redox homeostasis of the periplasm, permitting correct disulphide folding of periplasmic and secreted proteins. Loss of CydDC results in the periplasm becoming more oxidising and abolishes the assembly of functional bd-type respiratory oxidases that couple the oxidation of ubiquinol to the reduction of oxygen to water. In addition, CydDC-mediated redox control is important for haem ligation during cytochrome c assembly. Given the diverse roles for CydDC in redox homeostasis, respiratory metabolism and the maturation of virulence factors, this ABC transporter is an intriguing system for researchers interested in both the physiology of redox perturbations and the role of low-molecular-weight thiols during infection.
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Structural basis for allosteric cross-talk between the asymmetric nucleotide binding sites of a heterodimeric ABC exporter. Proc Natl Acad Sci U S A 2014; 111:11025-30. [PMID: 25030449 DOI: 10.1073/pnas.1400485111] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
ATP binding cassette (ABC) transporters mediate vital transport processes in every living cell. ATP hydrolysis, which fuels transport, displays positive cooperativity in numerous ABC transporters. In particular, heterodimeric ABC exporters exhibit pronounced allosteric coupling between a catalytically impaired degenerate site, where nucleotides bind tightly, and a consensus site, at which ATP is hydrolyzed in every transport cycle. Whereas the functional phenomenon of cooperativity is well described, its structural basis remains poorly understood. Here, we present the apo structure of the heterodimeric ABC exporter TM287/288 and compare it to the previously solved structure with adenosine 5'-(β,γ-imido)triphosphate (AMP-PNP) bound at the degenerate site. In contrast to other ABC exporter structures, the nucleotide binding domains (NBDs) of TM287/288 remain in molecular contact even in the absence of nucleotides, and the arrangement of the transmembrane domains (TMDs) is not influenced by AMP-PNP binding, a notion confirmed by double electron-electron resonance (DEER) measurements. Nucleotide binding at the degenerate site results in structural rearrangements, which are transmitted to the consensus site via two D-loops located at the NBD interface. These loops owe their name from a highly conserved aspartate and are directly connected to the catalytically important Walker B motif. The D-loop at the degenerate site ties the NBDs together even in the absence of nucleotides and substitution of its aspartate by alanine is well-tolerated. By contrast, the D-loop of the consensus site is flexible and the aspartate to alanine mutation and conformational restriction by cross-linking strongly reduces ATP hydrolysis and substrate transport.
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Dissecting Escherichia coli outer membrane biogenesis using differential proteomics. PLoS One 2014; 9:e100941. [PMID: 24967819 PMCID: PMC4072712 DOI: 10.1371/journal.pone.0100941] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 05/30/2014] [Indexed: 11/19/2022] Open
Abstract
The cell envelope of Gram-negative bacteria is a complex multi-layered structure comprising an inner cytoplasmic membrane and an additional asymmetric lipid bilayer, the outer membrane, which functions as a selective permeability barrier and is essential for viability. Lipopolysaccharide, an essential glycolipid located in the outer leaflet of the outer membrane, greatly contributes to the peculiar properties exhibited by the outer membrane. This complex molecule is transported to the cell surface by a molecular machine composed of seven essential proteins LptABCDEFG that form a transenvelope complex and function as a single device. While advances in understanding the mechanisms that govern the biogenesis of the cell envelope have been recently made, only few studies are available on how bacterial cells respond to severe envelope biogenesis defects on a global scale. Here we report the use of differential proteomics based on Multidimensional Protein Identification Technology (MudPIT) to investigate how Escherichia coli cells respond to a block of lipopolysaccharide transport to the outer membrane. We analysed the envelope proteome of a lptC conditional mutant grown under permissive and non permissive conditions and identified 123 proteins whose level is modulated upon LptC depletion. Most such proteins belong to pathways implicated in cell envelope biogenesis, peptidoglycan remodelling, cell division and protein folding. Overall these data contribute to our understanding on how E. coli cells respond to LPS transport defects to restore outer membrane functionality.
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45
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ABC Transporters Involved in the Biogenesis of the Outer Membrane in Gram-Negative Bacteria. Biosci Biotechnol Biochem 2014; 75:1044-54. [DOI: 10.1271/bbb.110115] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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46
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Abstract
Lipopolysaccharide molecules represent a unique family of glycolipids based on a highly conserved lipid moiety known as lipid A. These molecules are produced by most gram-negative bacteria, in which they play important roles in the integrity of the outer-membrane permeability barrier and participate extensively in host-pathogen interplay. Few bacteria contain lipopolysaccharide molecules composed only of lipid A. In most forms, lipid A is glycosylated by addition of the core oligosaccharide that, in some bacteria, provides an attachment site for a long-chain O-antigenic polysaccharide. The complexity of lipopolysaccharide structures is reflected in the processes used for their biosynthesis and export. Rapid growth and cell division depend on the bacterial cell's capacity to synthesize and export lipopolysaccharide efficiently and in large amounts. We review recent advances in those processes, emphasizing the reactions that are essential for viability.
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Affiliation(s)
- Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada;
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47
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Polissi A, Sperandeo P. The lipopolysaccharide export pathway in Escherichia coli: structure, organization and regulated assembly of the Lpt machinery. Mar Drugs 2014; 12:1023-42. [PMID: 24549203 PMCID: PMC3944529 DOI: 10.3390/md12021023] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 01/22/2014] [Accepted: 01/28/2014] [Indexed: 01/12/2023] Open
Abstract
The bacterial outer membrane (OM) is a peculiar biological structure with a unique composition that contributes significantly to the fitness of Gram-negative bacteria in hostile environments. OM components are all synthesized in the cytosol and must, then, be transported efficiently across three compartments to the cell surface. Lipopolysaccharide (LPS) is a unique glycolipid that paves the outer leaflet of the OM. Transport of this complex molecule poses several problems to the cells due to its amphipatic nature. In this review, the multiprotein machinery devoted to LPS transport to the OM is discussed together with the challenges associated with this process and the solutions that cells have evolved to address the problem of LPS biogenesis.
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Affiliation(s)
- Alessandra Polissi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
| | - Paola Sperandeo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
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48
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Sestito SE, Sperandeo P, Santambrogio C, Ciaramelli C, Calabrese V, Rovati GE, Zambelloni L, Grandori R, Polissi A, Peri F. Functional Characterization ofE. coliLptC: Interaction with LPS and a Synthetic Ligand. Chembiochem 2014; 15:734-42. [DOI: 10.1002/cbic.201300805] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Indexed: 01/05/2023]
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Ght protein of Neisseria meningitidis is involved in the regulation of lipopolysaccharide biosynthesis. J Bacteriol 2013; 196:780-9. [PMID: 24296673 DOI: 10.1128/jb.00943-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Lipopolysaccharide (LPS) is a major component of the outer membrane of Gram-negative bacteria and is responsible for the barrier function of this membrane. A ght mutant of Neisseria meningitidis that showed increased sensitivity to hydrophobic toxic compounds, suggesting a breach in this permeability barrier, was previously described. Here, we assessed whether this phenotype was possibly caused by a defect in LPS transport or synthesis. The total amount of LPS appeared to be drastically reduced in a ght mutant, but the residual LPS was still detected at the cell surface, suggesting that LPS transport was not impaired. The ght mutant was rapidly overgrown by pseudorevertants that produced normal levels of LPS. Genetic analysis of these pseudorevertants revealed that the lpxC gene, which encodes a key enzyme in LPS synthesis, was fused to the promoter of the upstream-located pilE gene, resulting in severe lpxC overexpression. Analysis of phoA and lacZ gene fusions indicated that Ght is an inner membrane protein with an N-terminal membrane anchor and its bulk located in the cytoplasm, where it could potentially interact with LpxC. Cell fractionation experiments indeed indicated that Ght tethers LpxC to the membrane. We suggest that Ght regulates LPS biosynthesis by affecting the activity of LpxC. Possibly, this mechanism acts in the previously observed feedback inhibition of LPS synthesis that occurs when LPS transport is hampered.
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Inokuchi H, Ito R, Sekiguchi T, Sekiguchi M. Search for proteins required for accurate gene expression under oxidative stress: roles of guanylate kinase and RNA polymerase. J Biol Chem 2013; 288:32952-62. [PMID: 24097971 DOI: 10.1074/jbc.m113.507772] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In aerobically growing cells, in which reactive oxygen species are produced, the guanine base is oxidized to 8-oxo-7,8-dihydroguanine, which can pair with adenine as well as cytosine. This mispairing causes alterations in gene expression, and cells possess mechanisms to prevent such outcomes. In Escherichia coli, 8-oxo-7,8-dihydroguanine-related phenotypic suppression of lacZ amber is enhanced by mutations in genes related to the prevention of abnormal protein synthesis under oxidative stress. A genome-wide search for the genes responsible, followed by DNA sequence determination, revealed that specific amino acid changes in guanylate kinase and in the β and β' subunits of RNA polymerase cause elevated levels of phenotypic suppression, specifically under aerobic conditions. The involvement of the DnaB, DnaN, and MsbA proteins, which are involved in DNA replication and in preserving the membrane structure, was also noted. Interactions of these proteins with each other and also with other molecules may be important for preventing errors in gene expression.
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Affiliation(s)
- Hachiro Inokuchi
- From the Frontier Research Center and Department of Biochemistry, Fukuoka Dental College, Fukuoka 814-0193 and
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