Differentiation of gram-negative intermembrane phospholipid transporter function by intrinsic substrate preference

The outer membrane of diderm Gram-negative bacteria acts as a barrier from chemical and physical stress. Anterograde phospholipid transport to the outer membrane has long been an area of intense investigation and, in E. coli K-12, it has recently been shown to be mediated by three related proteins: YhdP, TamB, and YdbH, which appear to provide hydrophobic channels for phospholipid diffusion, with YhdP and TamB playing the major roles. However, YhdP and TamB have different phenotypes suggesting distinct phospholipid transport functions. We investigated these functions using the synthetic cold sensitivity of a strain with ΔyhdP (but not ΔtamB or ΔydbH) and ΔfadR, a transcriptional regulator allowing switching between fatty acid degradation and synthesis and regulating unsaturated fatty acid production. Deletion of tamB, forcing phospholipid transport to YdbH, suppresses the ΔyhdP ΔfadR cold sensitivity suggesting this phenotype is due to TamB dysfunction. Increased levels of cardiolipin and fatty acid saturation are necessary for cold sensitivity and lowering levels of either suppresses this sensitivity. Our data support a model where YhdP primarily transports more saturated phospholipids, TamB primarily transports phospholipids with more than one carbon unsaturation, and cardiolipin obstructs TamB by selectively clogging its channel. Thus, the multiple phospholipid transporters may allow the saturation state of the outer membrane to be regulated independently of the inner membrane by altering the YhdP-TamB activity ratio. Maintaining membrane physical integrity and function under changing conditions may require envelope remodeling including altered phospholipid composition and intermembrane trafficking. Our data provide a potential mechanism for this regulation. Importance Gram-negative bacteria possess an impermeable outer membrane protecting against environmental stress and antibiotics. Outer membrane phospholipid transport remained mysterious until recently when YhdP, TamB, and YdbH were implicated in phospholipid transport between the inner and outer membranes of E. coli. TamB also modulates phospholipid transport in a distantly related diderm Fermicute. Here, we investigate functional differentiation between YhdP and TamB. Our data strongly suggest YhdP’s and TamB’s functions are distinguished by the saturation state of phospholipids with YhdP preferentially transporting more saturated phospholipids and TamB transporting more unsaturated phospholipids. Cardiolipin headgroup specificity may also contribute to TamB inhibition, perhaps due to the bulky nature of cardiolipin inhibiting the passage of other phospholipids. Diversification of function between YhdP and TamB provides a mechanism for regulation of phospholipid composition, and possibly the mechanical strength and permeability of the outer membrane, and so the cell’s intrinsic antibiotic resistance, in changing environmental conditions.

[1]  S. Gribaldo,et al.  Bridges instead of boats? The Mla system of diderm Firmicute Veillonella parvula reveals an ancestral transenvelope core of phospholipid trafficking , 2023, bioRxiv.

[2]  M. Bogdanov Renovating a double fence with or without notifying the next door and across the street neighbors: why the biogenic cytoplasmic membrane of Gram-negative bacteria display asymmetry? , 2023, Emerging topics in life sciences.

[3]  K. C. Huang,et al.  The Effects of Temperature on Cellular Physiology. , 2022, Annual review of biophysics.

[4]  M. Trent,et al.  Absence of YhdP, TamB, and YdbH leads to defects in glycerophospholipid transport and cell morphology in Gram-negative bacteria , 2022, PLoS genetics.

[5]  A. Rai,et al.  ElyC and Cyclic Enterobacterial Common Antigen Regulate Synthesis of Phosphoglyceride-Linked Enterobacterial Common Antigen , 2021, mBio.

[6]  D. Hassabis,et al.  AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models , 2021, Nucleic Acids Res..

[7]  N. Ruiz,et al.  YhdP, TamB, and YdbH Are Redundant but Essential for Growth and Lipid Homeostasis of the Gram-Negative Outer Membrane , 2021, mBio.

[8]  B. Hoogenboom,et al.  Phase separation in the outer membrane of Escherichia coli , 2021, Proceedings of the National Academy of Sciences.

[9]  C. Nguyen-the,et al.  Short-Chain and Unsaturated Fatty Acids Increase Sequentially From the Lag Phase During Cold Growth of Bacillus cereus , 2021, Frontiers in Microbiology.

[10]  Oriol Vinyals,et al.  Highly accurate protein structure prediction with AlphaFold , 2021, Nature.

[11]  Ryan K. Dale,et al.  Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping , 2021, eLife.

[12]  J. Cronan The Escherichia coli FadR transcription factor: Too much of a good thing? , 2020, Molecular microbiology.

[13]  Nadezhda T. Doncheva,et al.  The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets , 2020, Nucleic Acids Res..

[14]  Q. Luo,et al.  Structural insights into outer membrane asymmetry maintenance in Gram-negative bacteria by MlaFEDB , 2020, Nature Structural & Molecular Biology.

[15]  D. Kahne,et al.  Assembly and Maintenance of Lipids at the Bacterial Outer Membrane. , 2020, Chemical reviews.

[16]  A. Rai,et al.  Enterobacterial Common Antigen: Synthesis and Function of an Enigmatic Molecule , 2020, mBio.

[17]  N. Wingreen,et al.  The inner membrane protein YhdP modulates the rate of anterograde phospholipid flow in Escherichia coli , 2020, Proceedings of the National Academy of Sciences.

[18]  Z. Guan,et al.  Phospholipid distribution in the cytoplasmic membrane of Gram-negative bacteria is highly asymmetric, dynamic, and cell shape-dependent , 2020, Science Advances.

[19]  T. Otomo,et al.  ATG2A transfers lipids between membranes in vitro , 2019, Autophagy.

[20]  Steven L Salzberg,et al.  Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype , 2019, Nature Biotechnology.

[21]  T. Silhavy,et al.  Envelope stress responses: balancing damage repair and toxicity , 2019, Nature Reviews Microbiology.

[22]  T. Silhavy,et al.  Envelope stress responses: balancing damage repair and toxicity , 2019, Nature Reviews Microbiology.

[23]  T. Walz,et al.  ATG2 transports lipids to promote autophagosome biogenesis , 2019, The Journal of cell biology.

[24]  P. De Camilli,et al.  VPS13A and VPS13C are lipid transport proteins differentially localized at ER contact sites , 2018, The Journal of cell biology.

[25]  T. Silhavy,et al.  Cyclic Enterobacterial Common Antigen Maintains the Outer Membrane Permeability Barrier of Escherichia coli in a Manner Controlled by YhdP , 2018, mBio.

[26]  P. Gameiro,et al.  Revealing cardiolipins influence in the construction of a significant mitochondrial membrane model. , 2018, Biochimica et biophysica acta. Biomembranes.

[27]  J. Theriot,et al.  The outer membrane is an essential load-bearing element in Gram-negative bacteria , 2018, Nature.

[28]  T. Silhavy,et al.  The Escherichia coli Phospholipase PldA Regulates Outer Membrane Homeostasis via Lipid Signaling , 2018, mBio.

[29]  T. Lithgow,et al.  The Structure of a Conserved Domain of TamB Reveals a Hydrophobic β Taco Fold , 2017, Structure.

[30]  T. Silhavy,et al.  Outer Membrane Biogenesis. , 2017, Annual review of microbiology.

[31]  H. Taegtmeyer,et al.  Impact of Membrane Phospholipid Alterations in Escherichia coli on Cellular Function and Bacterial Stress Adaptation , 2017, Journal of bacteriology.

[32]  T. Silhavy,et al.  Redefining the essential trafficking pathway for outer membrane lipoproteins , 2017, Proceedings of the National Academy of Sciences.

[33]  Anthony M. Kennedy,et al.  Distinct membrane properties are differentially influenced by cardiolipin content and acyl chain composition in biomimetic membranes. , 2017, Biochimica et biophysica acta. Biomembranes.

[34]  T. Silhavy,et al.  Novel RpoS-Dependent Mechanisms Strengthen the Envelope Permeability Barrier during Stationary Phase , 2016, Journal of bacteriology.

[35]  B. Fox,et al.  The Power of Asymmetry: Architecture and Assembly of the Gram-Negative Outer Membrane Lipid Bilayer. , 2016, Annual review of microbiology.

[36]  M. Bogdanov,et al.  Effects of elevated growth temperature and heat shock on the lipid composition of the inner and outer membranes of Yersinia pseudotuberculosis. , 2016, Biochimie.

[37]  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.

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

[39]  William Stafford Noble,et al.  The MEME Suite , 2015, Nucleic Acids Res..

[40]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[41]  Kay Nieselt,et al.  Global Transcriptional Start Site Mapping Using Differential RNA Sequencing Reveals Novel Antisense RNAs in Escherichia coli , 2014, Journal of bacteriology.

[42]  Barry L. Wanner,et al.  Unprecedented High-Resolution View of Bacterial Operon Architecture Revealed by RNA Sequencing , 2014, mBio.

[43]  J. Klein-Seetharaman,et al.  X-ray structure, thermodynamics, elastic properties and MD simulations of cardiolipin/dimyristoylphosphatidylcholine mixed membranes. , 2014, Chemistry and physics of lipids.

[44]  G. Kritikos,et al.  A Genome-Wide Screen for Bacterial Envelope Biogenesis Mutants Identifies a Novel Factor Involved in Cell Wall Precursor Metabolism , 2014, PLoS genetics.

[45]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[46]  C. Raetz,et al.  Discovery of a cardiolipin synthase utilizing phosphatidylethanolamine and phosphatidylglycerol as substrates , 2012, Proceedings of the National Academy of Sciences.

[47]  Manoj Rajaure,et al.  The Spanin Complex Is Essential for Lambda Lysis , 2012, Journal of bacteriology.

[48]  Chris Morley,et al.  Open Babel: An open chemical toolbox , 2011, J. Cheminformatics.

[49]  J. Cronan,et al.  Complex binding of the FabR repressor of bacterial unsaturated fatty acid biosynthesis to its cognate promoters , 2011, Molecular microbiology.

[50]  T. Silhavy,et al.  The bacterial cell envelope. , 2010, Cold Spring Harbor perspectives in biology.

[51]  David S. Goodsell,et al.  AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility , 2009, J. Comput. Chem..

[52]  Davis J. McCarthy,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[53]  J. Cronan,et al.  Escherichia coli Unsaturated Fatty Acid Synthesis , 2009, The Journal of Biological Chemistry.

[54]  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.

[55]  C. Rock,et al.  Biosynthesis of Membrane Lipids , 2008, EcoSal Plus.

[56]  R. Bishop Structural biology of membrane-intrinsic beta-barrel enzymes: sentinels of the bacterial outer membrane. , 2008, Biochimica et biophysica acta.

[57]  T. Raivio,et al.  Activation of the Cpx Envelope Stress Response Down-Regulates Expression of Several Locus of Enterocyte Effacement-Encoded Genes in Enteropathogenic Escherichia coli , 2008, Infection and Immunity.

[58]  G. Pabst,et al.  Calorimetric, x-ray diffraction, and spectroscopic studies of the thermotropic phase behavior and organization of tetramyristoyl cardiolipin membranes. , 2007, Biophysical journal.

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

[60]  R. Murphy,et al.  Quantitation of cardiolipin molecular species in spontaneously hypertensive heart failure rats using electrospray ionization mass spectrometry Published, JLR Papers in Press, March 16, 2005. DOI 10.1194/jlr.M500031-JLR200 , 2005, Journal of Lipid Research.

[61]  T. Silhavy,et al.  Chemical Conditionality A GeneticStrategy to Probe Organelle Assembly , 2005, Cell.

[62]  T. Kiuchi,et al.  Activation of the Rcs Signal Transduction System Is Responsible for the Thermosensitive Growth Defect of an Escherichia coli Mutant Lacking Phosphatidylglycerol and Cardiolipin , 2004, Journal of bacteriology.

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

[64]  Julio Collado-Vides,et al.  Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals. , 2003, Journal of molecular biology.

[65]  Kouji Matsumoto,et al.  Envelope Disorder of Escherichia coli Cells Lacking Phosphatidylglycerol , 2002, Journal of bacteriology.

[66]  B. Wanner,et al.  One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[67]  D. Guo,et al.  A second Escherichia coli protein with CL synthase activity. , 2000, Biochimica et biophysica acta.

[68]  Kouji Matsumoto,et al.  Viability of an Escherichia coli pgsANull Mutant Lacking Detectable Phosphatidylglycerol and Cardiolipin , 2000, Journal of bacteriology.

[69]  R. Heath,et al.  Roles of the FabA and FabZ β-Hydroxyacyl-Acyl Carrier Protein Dehydratases in Escherichia coli Fatty Acid Biosynthesis* , 1996, The Journal of Biological Chemistry.

[70]  H. Kaback,et al.  A Phospholipid Acts as a Chaperone in Assembly of a Membrane Transport Protein (*) , 1996, The Journal of Biological Chemistry.

[71]  J. Cronan,et al.  A new mechanism of transcriptional regulation: Release of an activator triggered by small molecule binding , 1992, Cell.

[72]  J. Cronan,et al.  Escherichia coli transcription factor that both activates fatty acid synthesis and represses fatty acid degradation. , 1991, Journal of molecular biology.

[73]  A. Grossman,et al.  A collection of strains containing genetically linked alternating antibiotic resistance elements for genetic mapping of Escherichia coli. , 1989, Microbiological reviews.

[74]  A. Ohta,et al.  Disruption of the Escherichia coli cls gene responsible for cardiolipin synthesis , 1988, Journal of bacteriology.

[75]  C. Rock,et al.  Pathways for the incorporation of exogenous fatty acids into phosphatidylethanolamine in Escherichia coli. , 1985, The Journal of biological chemistry.

[76]  H. Nikaido,et al.  Molecular basis of bacterial outer membrane permeability. , 1985, Microbiological reviews.

[77]  M. Vaara,et al.  Molecular basis of bacterial outer membrane permeability , 1985 .

[78]  L. Enquist,et al.  Experiments With Gene Fusions , 1984 .

[79]  J. Cronan,et al.  Role for fadR in unsaturated fatty acid biosynthesis in Escherichia coli , 1983, Journal of bacteriology.

[80]  J. Cronan,et al.  Thermal regulation of membrane fluidity in Escherichia coli. Effects of overproduction of beta-ketoacyl-acyl carrier protein synthase I. , 1983, The Journal of biological chemistry.

[81]  E. P. Kennedy,et al.  Membrane assembly: movement of phosphatidylserine between the cytoplasmic and outer membranes of Escherichia coli , 1982, Journal of bacteriology.

[82]  J. Cronan,et al.  Beta-ketoacyl-acyl carrier protein synthase II of Escherichia coli. Evidence for function in the thermal regulation of fatty acid synthesis. , 1980, The Journal of biological chemistry.

[83]  C. Raetz,et al.  Cardiolipin Accumulation in the Inner and Outer Membranes of Escherichia coli Mutants Defective in Phosphatidylserine Synthetase , 1979, Journal of bacteriology.

[84]  M. Kito,et al.  Distribution of phospholipid molecular species in outer and cytoplasmic membrane of Escherichia coli. , 1979, Journal of biochemistry.

[85]  G. Pluschke,et al.  Function of phospholipids in Escherichia coli. Characterization of a mutant deficient in cardiolipin synthesis. , 1978, The Journal of biological chemistry.

[86]  M. Osborn,et al.  Translocation of phospholipids between the outer and inner membranes of Salmonella typhimurium. , 1977, The Journal of biological chemistry.

[87]  R. Peters,et al.  Distribution of lipids in cytoplasmic and outer membranes of Escherichia coli K12. , 1976, Biochimica et biophysica acta.

[88]  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.

[89]  E. Gelmann,et al.  An estimate of the minimum amount of unsaturated fatty acid required for growth of Escherichia coli. , 1973, The Journal of biological chemistry.

[90]  J E Gander,et al.  Mechanism of assembly of the outer membrane of Salmonella typhimurium. Isolation and characterization of cytoplasmic and outer membrane. , 1972, The Journal of biological chemistry.

[91]  W. Lennarz,et al.  Distribution of Lipids in the Wall and Cytoplasmic Membrane Subfractions of the Cell Envelope of Escherichia coli , 1972, Journal of bacteriology.

[92]  John L. Ingraham,et al.  EFFECT OF TEMPERATURE ON THE COMPOSITION OF FATTY ACIDS IN ESCHERICHIA COLI , 1962, Journal of bacteriology.

[93]  T. Osawa,et al.  Atg2 mediates direct lipid transfer between membranes for autophagosome formation , 2019, Nature Structural & Molecular Biology.

[94]  Jeffrey E. Barrick,et al.  Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. , 2014, Methods in molecular biology.

[95]  T. Raivio,et al.  Using reporter genes and the Escherichia coli ASKA overexpression library in screens for regulators of the Gram negative envelope stress response. , 2013, Methods in molecular biology.

[96]  Peter D. Karp,et al.  The EcoCyc Database , 2002, Nucleic Acids Res..

[97]  C. Whitfield,et al.  Lipopolysaccharide endotoxins. , 2002, Annual review of biochemistry.

[98]  Charles Elkan,et al.  Fitting a Mixture Model By Expectation Maximization To Discover Motifs In Biopolymer , 1994, ISMB.