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Cited by 1Lipid Membrane Structure and BehaviorBacterial Genetics and BiotechnologyEscherichia coli research studies

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A computational model for lipid-anchored polysaccharide export by the outer membrane protein GfcD

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Fruet, Cecilia, Martinez-Goikoetxea, Mikel, Merino, Felipe, Lupas, Andrei N.·2024·Biophysical Journal
DOI 10.1016/j.bpj.2024.08.012PMC PMC11494523

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Abstract

Abstract Many bacteria are protected by different types of polysaccharide capsules, structures formed of long repetitive glycan chains that are sometimes free and sometimes anchored to the outer membrane via lipid tails. One type, called group 4 capsule, results from expression of the gfcABCDE-etp-etk operon in Escherichia coli . Of the proteins encoded in this operon, GfcE is thought to provide the export pore for free polysaccharide chains, but none of the proteins has been implicated in the export of chains carrying a lipid anchor. For this function, GfcD has been a focus of attention as the only outer-membrane β-barrel encoded in the operon. AlphaFold predicts two β-barrel domains in GfcD, a canonical N-terminal one of 12 strands and an unusual C-terminal one of 13 strands, which features a large lateral aperture between strands β1 and β13. This immediately suggests a lateral exit gate for hydrophobic molecules into the membrane, analogous to the one proposed for the lipopolysaccharide export pore LptD. Here, we report an unsteered molecular dynamics study of GfcD embedded in the bacterial outer membrane, with the common polysaccharide anchor, lipid A, inserted in the pore of the C-terminal barrel. Our results show that the lateral aperture does not collapse during simulations, that membrane lipids nevertheless do not penetrate the barrel, but that the lipid chains of the lipid A molecule readily exit into the membrane. Statement of Significance Despite the essential role polysaccharide capsules play in the resilience of bacteria to hostile environments, many aspects of their biogenesis are still poorly understood. One aspect concerns the export of capsular polysaccharides carrying a lipid anchor, for which even the proteins mediating the process are unknown. Here we propose that one of the largest families of β-barrel proteins in the bacterial outer membrane is a key agent of this process and show by biophysical simulation that it allows the exit of lipid anchors into the membrane through a lateral opening. More generally, our model illuminates the lateral exit mechanisms proposed for the export of hydrophobic macromolecules into the bacterial outer membrane. Graphical abstract

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Research works printed but not linked: 53

  1. Rendueles, 2017, Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens, PLoS Pathog., 13, 10.1371/journal.ppat.1006525 · DOI · Paper page
  2. Wang, 2015, Role of Capsular Polysaccharides in Biofilm Formation: An AFM Nanomechanics Study, ACS Appl. Mater. Interfaces, 7, 13007, 10.1021/acsami.5b03041 · DOI
  3. Sathiyamoorthy, 2011, The Crystal Structure of Escherichia coli Group 4 Capsule Protein GfcC Reveals a Domain Organization Resembling That of Wza, Biochemistry, 50, 5465, 10.1021/bi101869h · DOI
  4. Chris, 2009, Structure and Assembly of Escherichia coli Capsules, EcoSal Plus, 3
  5. Whitfield, 2006, Biosynthesis and Assembly of Capsular Polysaccharides in Escherichia coli, Annu. Rev. Biochem., 75, 39, 10.1146/annurev.biochem.75.103004.142545 · DOI
  6. Peleg, 2005, Identification of an Escherichia coli Operon Required for Formation of the O-Antigen Capsule, J. Bacteriol., 187, 5259, 10.1128/JB.187.15.5259-5266.2005 · DOI
  7. Solan, 2021, Gram-negative outer-membrane proteins with multiple β-barrel domains Proceedings of the National Academy of Sciences, Proc. Natl. Acad. Sci. USA, 118, 10.1073/pnas.2104059118 · DOI
  8. Ionescu, 2009, Overproduction of Exopolysaccharides by an Escherichia coli K-12 rpoS Mutant in Response to Osmotic Stress, Appl. Environ. Microbiol., 75, 483, 10.1128/AEM.01616-08 · DOI
  9. Ferrières, 2007, The yjbEFGH locus in Escherichia coli K-12 is an operon encoding proteins involved in exopolysaccharide production, Microbiology, 153, 1070, 10.1099/mic.0.2006/002907-0 · DOI
  10. Croxatto, 2007, Vibrio anguillarum colonization of rainbow trout integument requires a DNA locus involved in exopolysaccharide transport and biosynthesis, Environ. Microbiol., 9, 370, 10.1111/j.1462-2920.2006.01147.x · DOI
  11. Botos, 2017, Insertion of proteins and lipopolysaccharides into the bacterial outer membrane, Phil. Trans. Biol. Sci., 372, 20160224, 10.1098/rstb.2016.0224 · DOI
  12. Bishop, 2014, Lipopolysaccharide rolls out the barrel, Nature, 511, 37, 10.1038/nature13508 · DOI
  13. Li, 2015, Trapped lipopolysaccharide and LptD intermediates reveal lipopolysaccharide translocation steps across the \emphEscherichia coli outer membrane, Sci. Rep., 5
  14. Khan, 2009, Molecular Mechanism for Lateral Lipid Diffusion between the Outer Membrane External Leaflet and a textbeta-Barrel Hydrocarbon Ruler, Biochemistry, 48, 9745, 10.1021/bi9013566 · DOI
  15. Hearn, 2009, Transmembrane passage of hydrophobic compounds through a protein channel wall, Nature, 458, 367, 10.1038/nature07678 · DOI
  16. Van Den Berg, 2004, Crystal Structure of the Long-Chain Fatty Acid Transporter FadL, Science, 304, 1506, 10.1126/science.1097524 · DOI
  17. Dong, 2014, Structural basis for outer membrane lipopolysaccharide insertion, Nature, 511, 52, 10.1038/nature13464 · DOI
  18. Amor, 1997, Molecular and functional analysis of genes required for expression of group IB K antigens in Escherichia coli : characterization of the his- region containing gene clusters for multiple cell-surface polysaccharides, Mol. Microbiol., 26, 145, 10.1046/j.1365-2958.1997.5631930.x · DOI
  19. Nielsen, 1997, Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites, Protein Eng., 10, 1, 10.1093/protein/10.1.1 · DOI
  20. Almagro Armenteros, 2019, SignalP 5.0 improves signal peptide predictions using deep neural networks, Nat. Biotechnol., 37, 420, 10.1038/s41587-019-0036-z · DOI
  21. Jo, 2008, CHARMM-GUI: A web-based graphical user interface for CHARMM, J. Comput. Chem., 29, 1859, 10.1002/jcc.20945 · DOI · Paper page
  22. Lee, 2019, CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans, J. Chem. Theor. Comput., 15, 775, 10.1021/acs.jctc.8b01066 · DOI
  23. Lee, 2020, CHARMM-GUI supports the Amber force fields, J. Chem. Phys., 153
  24. Kern, 2022, CHARMM-GUI multicomponent assembler for modeling and simulation of complex multicomponent systems, Biophys. J., 121, 10.1016/j.bpj.2021.11.2789 · DOI
  25. Piggot, 2011, Electroporation of the E. coli and S. Aureus Membranes: Molecular Dynamics Simulations of Complex Bacterial Membranes, J. Phys. Chem. B, 115, 13381, 10.1021/jp207013v · DOI
  26. Shearer, 2020, Molecular dynamics simulations of bacterial outer membrane lipid extraction: Adequate sampling?, J. Chem. Phys., 153
  27. Shearer, 2018, Communication between the leaflets of asymmetric membranes revealed from coarse-grain molecular dynamics simulations, Sci. Rep., 8, 1805, 10.1038/s41598-018-20227-1 · DOI
  28. Lugtenberg, 1976, Distribution of lipids in cytoplasmic and outer membranes of Escherichia coli K12, Biochim. Biophys. Acta, 441, 38, 10.1016/0005-2760(76)90279-4 · DOI
  29. Berendsen, 1995, GROMACS: A message-passing parallel molecular dynamics implementation, Comput. Phys. Commun., 91, 43, 10.1016/0010-4655(95)00042-E · DOI
  30. Van Der Spoel, 2005, GROMACS: Fast, flexible, and free, J. Comput. Chem., 26, 1701, 10.1002/jcc.20291 · DOI
  31. Hess, 2008, GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation, J. Chem. Theor. Comput., 4, 435, 10.1021/ct700301q · DOI
  32. Best, 2012, Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles, J. Chem. Theor. Comput., 8, 3257, 10.1021/ct300400x · DOI
  33. Klauda, 2010, Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types, J. Phys. Chem. B, 114, 7830, 10.1021/jp101759q · DOI
  34. Huang, 2017, CHARMM36m: an improved force field for folded and intrinsically disordered proteins, Nat. Methods, 14, 71, 10.1038/nmeth.4067 · DOI
  35. Hess, 1997, LINCS: A linear constraint solver for molecular simulations, J. Comput. Chem., 18, 1463, 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H · DOI
  36. Darden, 1993, Particle mesh Ewald: An N ·log( N ) method for Ewald sums in large systems, J. Chem. Phys., 98, 10089, 10.1063/1.464397 · DOI
  37. Bussi, 2007, Canonical sampling through velocity rescaling, J. Chem. Phys., 126
  38. Parrinello, 1981, Polymorphic transitions in single crystals: A new molecular dynamics method, J. Appl. Phys., 52, 7182, 10.1063/1.328693 · DOI
  39. Nosé, 1983, Constant pressure molecular dynamics for molecular systems, Mol. Phys., 50, 1055, 10.1080/00268978300102851 · DOI
  40. Humphrey, 1996, VMD: Visual molecular dynamics, J. Mol. Graph., 14, 33, 10.1016/0263-7855(96)00018-5 · DOI · Paper page
  41. Gowers, 2016, MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations, 98, 10.25080/Majora-629e541a-00e · DOI
  42. Michaud-Agrawal, 2011, MDAnalysis: A toolkit for the analysis of molecular dynamics simulations, J. Comput. Chem., 32, 2319, 10.1002/jcc.21787 · DOI
  43. Tomasello, 2020, The Protein Imager: a full-featured online molecular viewer interface with server-side HQ-rendering capabilities, Bioinformatics, 36, 2909, 10.1093/bioinformatics/btaa009 · DOI
  44. Zimmermann, 2018, A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core, J. Mol. Biol., 430, 2237, 10.1016/j.jmb.2017.12.007 · DOI · Paper page
  45. Gabler, 2020, Protein Sequence Analysis Using the MPI Bioinformatics Toolkit, Curr. Protoc. Bioinformatics, 72
  46. Wu, 2014, E. coli Outer Membrane and Interactions with OmpLA, Biophys. J., 106, 2493, 10.1016/j.bpj.2014.04.024 · DOI
  47. Baaden, 2003, A Molecular Dynamics Investigation of Mono and Dimeric States of the Outer Membrane Enzyme OMPLA, J. Mol. Biol., 331, 177, 10.1016/S0022-2836(03)00718-6 · DOI
  48. Piggot, 2013, Conformational dynamics and membrane interactions of the E. coli outer membrane protein FecA: A molecular dynamics simulation study, Biochim. Biophys. Acta, 1828, 284, 10.1016/j.bbamem.2012.08.021 · DOI
  49. Straatsma, 2009, Characterization of the outer membrane protein OprF of Pseudomonas aeruginosa in a lipopolysaccharide membrane by computer simulation, Proteins, 74, 475, 10.1002/prot.22165 · DOI
  50. Im, 2002, Ions and Counterions in a Biological Channel: A Molecular Dynamics Simulation of OmpF Porin from Escherichia coli in an Explicit Membrane with 1M KCl Aqueous Salt Solution, J. Mol. Biol., 319, 1177, 10.1016/S0022-2836(02)00380-7 · DOI
  51. Rui, 2011, Molecular Dynamics Studies of Ion Permeation in VDAC, Biophys. J., 100, 602, 10.1016/j.bpj.2010.12.3711 · DOI
  52. Rost, 1997, Protein structures sustain evolutionary drift, Folding Des., 2, S19, 10.1016/S1359-0278(97)00059-X · DOI
  53. Qiao, 2014, Structural basis for lipopolysaccharide insertion in the bacterial outer membrane, Nature, 511, 108, 10.1038/nature13484 · DOI

Metadata

Authors
Fruet, C., Martinez-Goikoetxea, M., Merino, F., & Lupas, A. N.
Affiliations
Max Planck Institute for Biology (DE)
Corresponding author
Lupas, Andrei N.
ORCID
Venue
Biophysical Journal
Publisher
Elsevier BV
Published
2024-10
Volume
123
Issue
20
Pages
3491-3499
ISSN
0006-3495 (ISSN-L)
DOI
10.1016/j.bpj.2024.08.012
PMC
PMC11494523
OpenAlex
W4401689750
Cited by
1
References
1
Citations by year
2026: 1
FWCI
0.14
Type
journal article
Language
en
Open access
Licence
Locations
  • Biophysical Journal (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
Max Planck Society
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Lipid Membrane Structure and Behavior
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Immunology and Microbiology › Microbiology › Escherichia coli research studies
Keywords
Escherichia coli, lipid A, polysaccharide capsule
MeSH terms
Bacterial Outer Membrane Proteins, Biological Transport, Escherichia coli, Polysaccharides, Escherichia coli Proteins, Molecular Dynamics Simulation

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