Architectures of Lipid Transport Systems for the Bacterial Outer Membrane

How phospholipids are trafficked between the bacterial inner and outer membranes through the hydrophilic space of the periplasm is not known. We report that members of the mammalian cell entry (MCE) protein family form hexameric assemblies with a central channel capable of mediating lipid transport. The E. coli MCE protein, MlaD, forms a ring associated with an ABC transporter complex in the inner membrane. A soluble lipid-binding protein, MlaC, ferries lipids between MlaD and an outer membrane protein complex. In contrast, EM structures of two other E. coli MCE proteins show that YebT forms an elongated tube consisting of seven stacked MCE rings, and PqiB adopts a syringe-like architecture. Both YebT and PqiB create channels of sufficient length to span the periplasmic space. This work reveals diverse architectures of highly conserved protein-based channels implicated in the transport of lipids between the membranes of bacteria and some eukaryotic organelles.

[1]  Dominika Elmlund,et al.  SIMPLE: Software for ab initio reconstruction of heterogeneous single-particles. , 2012, Journal of structural biology.

[2]  H. Nikaido Molecular Basis of Bacterial Outer Membrane Permeability Revisited , 2003, Microbiology and Molecular Biology Reviews.

[3]  Andrea Carpentieri,et al.  Functional Analysis of the Protein Machinery Required for Transport of Lipopolysaccharide to the Outer Membrane of Escherichia coli , 2008, Journal of bacteriology.

[4]  Dominika Elmlund,et al.  PRIME: probabilistic initial 3D model generation for single-particle cryo-electron microscopy. , 2013, Structure.

[5]  K. Orth,et al.  Outer membrane adhesion factor multivalent adhesion molecule 7 initiates host cell binding during infection by Gram-negative pathogens , 2011, Proceedings of the National Academy of Sciences.

[6]  D. G. Gibson,et al.  Enzymatic assembly of DNA molecules up to several hundred kilobases , 2009, Nature Methods.

[7]  R. Knights,et al.  Cloning of an M. tuberculosis DNA fragment associated with entry and survival inside cells. , 1993, Science.

[8]  M. Vaara,et al.  rfaP mutants of Salmonella typhimurium. , 1989, European journal of biochemistry.

[9]  Rebecca L. Roston,et al.  TGD1, -2, and -3 Proteins Involved in Lipid Trafficking Form ATP-binding Cassette (ABC) Transporter with Multiple Substrate-binding Proteins* , 2012, The Journal of Biological Chemistry.

[10]  Vincent B. Chen,et al.  Correspondence e-mail: , 2000 .

[11]  A. Kropinski,et al.  Susceptibility of lipopolysaccharide-defective mutants of Pseudomonas aeruginosa strain PAO to dyes, detergents, and antibiotics , 1978, Antimicrobial Agents and Chemotherapy.

[12]  David N Mastronarde,et al.  Automated electron microscope tomography using robust prediction of specimen movements. , 2005, Journal of structural biology.

[13]  Christopher M. Sassetti,et al.  Mycobacterial persistence requires the utilization of host cholesterol , 2008, Proceedings of the National Academy of Sciences.

[14]  N. Casali,et al.  A phylogenomic analysis of the Actinomycetales mce operons , 2007, BMC Genomics.

[15]  Z. Jia,et al.  Novel structure of the conserved gram-negative lipopolysaccharide transport protein A and mutagenesis analysis. , 2008, Journal of molecular biology.

[16]  Hao Wu,et al.  Molecular Mechanism of V(D)J Recombination from Synaptic RAG1-RAG2 Complex Structures , 2015, Cell.

[17]  M. Wenk,et al.  Defining key roles for auxiliary proteins in an ABC transporter that maintains bacterial outer membrane lipid asymmetry , 2016, eLife.

[18]  B. Lugtenberg,et al.  Molecular architecture and functioning of the outer membrane of Escherichia coli and other gram-negative bacteria. , 1983, Biochimica et biophysica acta.

[19]  Michael J E Sternberg,et al.  The Phyre2 web portal for protein modeling, prediction and analysis , 2015, Nature Protocols.

[20]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[21]  N. Krogan,et al.  Phenotypic Landscape of a Bacterial Cell , 2011, Cell.

[22]  D. Ojcius,et al.  The mammalian cell entry (Mce) protein of pathogenic Leptospira species is responsible for RGD motif‐dependent infection of cells and animals , 2012, Molecular microbiology.

[23]  D. Agard,et al.  Electron counting and beam-induced motion correction enable near atomic resolution single particle cryoEM , 2013, Nature Methods.

[24]  J. Tommassen,et al.  Lipopolysaccharide Transport to the Bacterial Outer Membrane in Spheroplasts* , 2005, Journal of Biological Chemistry.

[25]  T. Silhavy,et al.  An ABC transport system that maintains lipid asymmetry in the Gram-negative outer membrane , 2009, Proceedings of the National Academy of Sciences.

[26]  T. Silhavy,et al.  Identification of a protein complex that assembles lipopolysaccharide in the outer membrane of Escherichia coli. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[27]  David E. Kim,et al.  Large-scale determination of previously unsolved protein structures using evolutionary information , 2015, eLife.

[28]  D. Lim,et al.  Isolation and Characterization of Toluene-Sensitive Mutants from the Toluene-Resistant Bacterium Pseudomonas putida GM73 , 1998, Journal of bacteriology.

[29]  R. Darveau,et al.  Escherichia coli msbB Gene as a Virulence Factor and a Therapeutic Target , 1999, Infection and Immunity.

[30]  J. Froehlich,et al.  A permease‐like protein involved in ER to thylakoid lipid transfer in Arabidopsis , 2003, The EMBO journal.

[31]  L. Dijkhuizen,et al.  The Actinobacterial mce4 Locus Encodes a Steroid Transporter* , 2008, Journal of Biological Chemistry.

[32]  H. Mori,et al.  Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection , 2006, Molecular systems biology.

[33]  Liisa Holm,et al.  Dali server: conservation mapping in 3D , 2010, Nucleic Acids Res..

[34]  D. Kahne,et al.  Cytoplasmic ATP Hydrolysis Powers Transport of Lipopolysaccharide Across the Periplasm in E. coli , 2012, Science.

[35]  Brittany D. Needham,et al.  The Vps/VacJ ABC Transporter Is Required for Intercellular Spread of Shigella flexneri , 2013, Infection and Immunity.

[36]  H. Nikaido,et al.  Outer membrane of Salmonella typhimurium: accessibility of phospholipid head groups to phospholipase c and cyanogen bromide activated dextran in the external medium. , 1976, Biochemistry.

[37]  Rebecca L. Roston,et al.  Arabidopsis chloroplast lipid transport protein TGD2 disrupts membranes and is part of a large complex. , 2011, The Plant journal : for cell and molecular biology.

[38]  Kai Zhang,et al.  Gctf: Real-time CTF determination and correction , 2015, bioRxiv.

[39]  Free mycolic acid accumulation in the cell wall of the mce1 operon mutant strain of Mycobacterium tuberculosis , 2013, Journal of Microbiology.

[40]  T. Silhavy,et al.  Outer membrane lipoprotein biogenesis: Lol is not the end , 2015, Philosophical Transactions of the Royal Society B: Biological Sciences.

[41]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[42]  David Baker,et al.  High-resolution comparative modeling with RosettaCM. , 2013, Structure.

[43]  Z. Chong,et al.  Osmoporin OmpC forms a complex with MlaA to maintain outer membrane lipid asymmetry in Escherichia coli , 2015, Molecular microbiology.

[44]  H. Nikaido,et al.  Outer membrane of Salmonella typhimurium: chemical analysis and freeze-fracture studies with lipopolysaccharide mutants , 1975, Journal of bacteriology.

[45]  Andrew Leis,et al.  Disclosure of the mycobacterial outer membrane: Cryo-electron tomography and vitreous sections reveal the lipid bilayer structure , 2008, Proceedings of the National Academy of Sciences.

[46]  J. Gilsdorf,et al.  Molecular Basis of Increased Serum Resistance among Pulmonary Isolates of Non-typeable Haemophilus influenzae , 2011, PLoS pathogens.

[47]  Ying Cheng,et al.  The European Nucleotide Archive , 2010, Nucleic Acids Res..

[48]  David J. Sherman,et al.  Lipopolysaccharide transport to the cell surface: periplasmic transport and assembly into the outer membrane , 2015, Philosophical Transactions of the Royal Society B: Biological Sciences.

[49]  Randy J. Read,et al.  Improved molecular replacement by density- and energy-guided protein structure optimization , 2011, Nature.

[50]  William R. Jacobs,et al.  Complex lipid determines tissue-specific replication of Mycobacterium tuberculosis in mice , 1999, Nature.

[51]  K. C. Huang,et al.  Disruption of lipid homeostasis in the Gram-negative cell envelope activates a novel cell death pathway , 2016, Proceedings of the National Academy of Sciences.

[52]  J. Willemse,et al.  Mammalian cell entry genes in Streptomyces may provide clues to the evolution of bacterial virulence , 2013, Scientific Reports.

[53]  Robert J Collier,et al.  Atomic structure of anthrax protective antigen pore elucidates toxin translocation , 2015 .

[54]  E. Rubin,et al.  Genome-wide requirements for Mycobacterium tuberculosis adaptation and survival in macrophages. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[55]  Noah Linden,et al.  A de novo peptide hexamer with a mutable channel , 2011, Nature chemical biology.

[56]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[57]  George M. Sheldrick,et al.  Experimental phasing with SHELXC/D/E: combining chain tracing with density modification , 2010, Acta crystallographica. Section D, Biological crystallography.

[58]  Peter J. Stuckey,et al.  Automatic generation of protein structure cartoons with Pro-origami , 2011, Bioinform..

[59]  Sjors H.W. Scheres,et al.  RELION: Implementation of a Bayesian approach to cryo-EM structure determination , 2012, Journal of structural biology.

[60]  T. Silhavy,et al.  Identification of two inner-membrane proteins required for the transport of lipopolysaccharide to the outer membrane of Escherichia coli , 2008, Proceedings of the National Academy of Sciences.

[61]  Randy J. Read,et al.  Dauter Iterative model building , structure refinement and density modification with the PHENIX AutoBuild wizard , 2007 .

[62]  Martin H. Koldijk,et al.  A Highly Conserved Neutralizing Epitope on Group 2 Influenza A Viruses , 2011, Science.

[63]  A. Biegert,et al.  HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment , 2011, Nature Methods.

[64]  A. Cataldi,et al.  Mutation in mce operons attenuates Mycobacterium tuberculosis virulence. , 2005, Microbes and infection.

[65]  Shaoxia Chen,et al.  Prevention of overfitting in cryo-EM structure determination , 2012, Nature Methods.

[66]  T. Silhavy,et al.  Transport of lipopolysaccharide across the cell envelope: the long road of discovery , 2009, Nature Reviews Microbiology.

[67]  P. Zwart,et al.  Towards automated crystallographic structure refinement with phenix.refine , 2012, Acta crystallographica. Section D, Biological crystallography.

[68]  Wah Chiu,et al.  Structure of the AcrAB-TolC multidrug efflux pump , 2014, Nature.

[69]  David A. Agard,et al.  Anisotropic Correction of Beam-induced Motion for Improved Single-particle Electron Cryo-microscopy , 2016, bioRxiv.

[70]  María Martín,et al.  Activities at the Universal Protein Resource (UniProt) , 2013, Nucleic Acids Res..

[71]  P. Andrew Karplus,et al.  Linking Crystallographic Model and Data Quality , 2012, Science.

[72]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[73]  Riccardo Villa,et al.  Characterization of lptA and lptB, Two Essential Genes Implicated in Lipopolysaccharide Transport to the Outer Membrane of Escherichia coli , 2006, Journal of bacteriology.

[74]  Jue Chen,et al.  Snapshots of the maltose transporter during ATP hydrolysis , 2011, Proceedings of the National Academy of Sciences.

[75]  Jonathan C. Cohen,et al.  Crystal structure of the human sterol transporter ABCG5/ABCG8 , 2016, Nature.

[76]  K. Awai,et al.  A phosphatidic acid-binding protein of the chloroplast inner envelope membrane involved in lipid trafficking. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[77]  M. Jackson,et al.  Impact of the deletion of the six mce operons in Mycobacterium smegmatis. , 2012, Microbes and infection.

[78]  J. McFadden,et al.  Mycobacterium tuberculosis strains disrupted in mce3 and mce4 operons are attenuated in mice. , 2008, Journal of medical microbiology.

[79]  J. Dubochet,et al.  Cryo-Transmission Electron Microscopy of Frozen-Hydrated Sections of Escherichia coli and Pseudomonas aeruginosa , 2003, Journal of bacteriology.

[80]  P. Mühlradt,et al.  Asymmetrical distribution and artifactual reorientation of lipopolysaccharide in the outer membrane bilayer of Salmonella typhimurium. , 1975, European journal of biochemistry.

[81]  D. Baker,et al.  Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information , 2014, eLife.

[82]  S. Fortune,et al.  Characterization of mycobacterial virulence genes through genetic interaction mapping. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[83]  Sjors H.W. Scheres,et al.  A Bayesian View on Cryo-EM Structure Determination , 2012, 2012 9th IEEE International Symposium on Biomedical Imaging (ISBI).

[84]  C. Raetz,et al.  Phosphate Groups of Lipid A Are Essential for Salmonella enterica Serovar Typhimurium Virulence and Affect Innate and Adaptive Immunity , 2012, Infection and Immunity.

[85]  C. Benning,et al.  Lipid Trafficking between the Endoplasmic Reticulum and the Plastid in Arabidopsis Requires the Extraplastidic TGD4 Protein[W] , 2008, The Plant Cell Online.

[86]  J. Klena,et al.  Genetics of lipopolysaccharide biosynthesis in enteric bacteria. , 1993, Microbiological reviews.

[87]  Richard B. Sessions,et al.  Computational design of water-soluble α-helical barrels , 2014, Science.

[88]  Ziqiang Guan,et al.  Attenuated virulence of a Francisella mutant lacking the lipid A 4′-phosphatase , 2007, Proceedings of the National Academy of Sciences.