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Herdman M, Isbilir B, von Kügelgen A, Schulze U, Wainman A, Bharat TAM. Cell cycle dependent coordination of surface layer biogenesis in Caulobacter crescentus. Nat Commun 2024; 15:3355. [PMID: 38637514 PMCID: PMC11026435 DOI: 10.1038/s41467-024-47529-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 04/04/2024] [Indexed: 04/20/2024] Open
Abstract
Surface layers (S-layers) are proteinaceous, two-dimensional paracrystalline arrays that constitute a major component of the cell envelope in many prokaryotic species. In this study, we investigated S-layer biogenesis in the bacterial model organism Caulobacter crescentus. Fluorescence microscopy revealed localised incorporation of new S-layer at the poles and mid-cell, consistent with regions of cell growth in the cell cycle. Light microscopy and electron cryotomography investigations of drug-treated bacteria revealed that localised S-layer insertion is retained when cell division is inhibited, but is disrupted upon dysregulation of MreB or lipopolysaccharide. We further uncovered that S-layer biogenesis follows new peptidoglycan synthesis and localises to regions of high cell wall turnover. Finally, correlated cryo-light microscopy and electron cryotomographic analysis of regions of S-layer insertion showed the presence of discontinuities in the hexagonal S-layer lattice, contrasting with other S-layers completed by defined symmetric defects. Our findings present insights into how C. crescentus cells form an ordered S-layer on their surface in coordination with the biogenesis of other cell envelope components.
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Affiliation(s)
- Matthew Herdman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Buse Isbilir
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Andriko von Kügelgen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Ulrike Schulze
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Alan Wainman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Tanmay A M Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
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2
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Zivanov J, Otón J, Ke Z, von Kügelgen A, Pyle E, Qu K, Morado D, Castaño-Díez D, Zanetti G, Bharat TAM, Briggs JAG, Scheres SHW. A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0. eLife 2022; 11:83724. [PMID: 36468689 PMCID: PMC9815803 DOI: 10.7554/elife.83724] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/04/2022] [Indexed: 12/12/2022] Open
Abstract
We present a new approach for macromolecular structure determination from multiple particles in electron cryo-tomography (cryo-ET) data sets. Whereas existing subtomogram averaging approaches are based on 3D data models, we propose to optimise a regularised likelihood target that approximates a function of the 2D experimental images. In addition, analogous to Bayesian polishing and contrast transfer function (CTF) refinement in single-particle analysis, we describe the approaches that exploit the increased signal-to-noise ratio in the averaged structure to optimise tilt-series alignments, beam-induced motions of the particles throughout the tilt-series acquisition, defoci of the individual particles, as well as higher-order optical aberrations of the microscope. Implementation of our approaches in the open-source software package RELION aims to facilitate their general use, particularly for those researchers who are already familiar with its single-particle analysis tools. We illustrate for three applications that our approaches allow structure determination from cryo-ET data to resolutions sufficient for de novo atomic modelling.
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Affiliation(s)
- Jasenko Zivanov
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom,Laboratory of Biomedical Imaging (LIB)LausanneSwitzerland,BioEM lab, Biozentrum, University of BaselBaselSwitzerland
| | - Joaquín Otón
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom,ALBA SynchrotronBarcelonaSpain
| | - Zunlong Ke
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom,Max Planck Institute of BiochemistryMartinsriedGermany
| | - Andriko von Kügelgen
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom,Sir William Dunn School of Pathology, University of OxfordOxfordUnited Kingdom
| | - Euan Pyle
- Institute of Structural and Molecular Biology, Birkbeck CollegeLondonUnited Kingdom
| | - Kun Qu
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Dustin Morado
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom,Max Planck Institute of BiochemistryMartinsriedGermany
| | - Daniel Castaño-Díez
- BioEM lab, Biozentrum, University of BaselBaselSwitzerland,Instituto BiofisikaLeioaSpain
| | - Giulia Zanetti
- Institute of Structural and Molecular Biology, Birkbeck CollegeLondonUnited Kingdom
| | - Tanmay AM Bharat
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom,Sir William Dunn School of Pathology, University of OxfordOxfordUnited Kingdom
| | - John AG Briggs
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom,Max Planck Institute of BiochemistryMartinsriedGermany
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3
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Herdman M, von Kügelgen A, Kureisaite-Ciziene D, Duman R, El Omari K, Garman EF, Kjaer A, Kolokouris D, Löwe J, Wagner A, Stansfeld PJ, Bharat TAM. High-resolution mapping of metal ions reveals principles of surface layer assembly in Caulobacter crescentus cells. Structure 2021; 30:215-228.e5. [PMID: 34800371 PMCID: PMC8828063 DOI: 10.1016/j.str.2021.10.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 08/17/2021] [Accepted: 10/22/2021] [Indexed: 12/02/2022]
Abstract
Surface layers (S-layers) are proteinaceous crystalline coats that constitute the outermost component of most prokaryotic cell envelopes. In this study, we have investigated the role of metal ions in the formation of the Caulobacter crescentus S-layer using high-resolution structural and cell biology techniques, as well as molecular simulations. Utilizing optical microscopy of fluorescently tagged S-layers, we show that calcium ions facilitate S-layer lattice formation and cell-surface binding. We report all-atom molecular dynamics simulations of the S-layer lattice, revealing the importance of bound metal ions. Finally, using electron cryomicroscopy and long-wavelength X-ray diffraction experiments, we mapped the positions of metal ions in the S-layer at near-atomic resolution, supporting our insights from the cellular and simulations data. Our findings contribute to the understanding of how C. crescentus cells form a regularly arranged S-layer on their surface, with implications on fundamental S-layer biology and the synthetic biology of self-assembling biomaterials. Live imaging shows Ca2+-dependent expansion of the C. crescentus S-layer Molecular simulations reveal Ca2+-binding properties of the S-layer Ca2+ ion mapping in three-dimensional crystals using in-vacuum X-ray anomalous diffraction Ca2+ replacement by Ho3+ allows cryo-EM mapping of heavy metals
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Affiliation(s)
- Matthew Herdman
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | | | | | - Ramona Duman
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Kamel El Omari
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Andreas Kjaer
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | | | - Jan Löwe
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Armin Wagner
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Phillip J Stansfeld
- School of Life Sciences and Department of Chemistry, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL, UK.
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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4
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Aharon E, Mookherjee A, Pérez-Montaño F, Mateus da Silva G, Sathyamoorthy R, Burdman S, Jurkevitch E. Secretion systems play a critical role in resistance to predation by Bdellovibrio bacteriovorus. Res Microbiol 2021; 172:103878. [PMID: 34492337 DOI: 10.1016/j.resmic.2021.103878] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 08/02/2021] [Accepted: 08/07/2021] [Indexed: 11/28/2022]
Abstract
Bdellovibrio bacteriovorus, a Gram-negative predatory bacterium belonging to the Bdellovibrio and like organisms (BALOs), predate on Gram-negative bacteria. BALO strains differ in prey range but so far, the genetic basis of resistance against BALO predation is hardly understood. We developed a loss-of-function approach to screen for sensitive mutants in a library of strain M6, a predation-resistant strain of the plant pathogen Acidovorax citrulli. The screen is based on tracking the growth of a B. bacteriovorus strain expressing the fluorescent reporter Tdtomato in mutant pools to reveal predation-sensitive variants. Two independent loci were identified in mutant strains exhibiting significant levels of susceptibility to the predator. Genes in the two loci were analysed using both protein sequence homology and protein structure modeling. Both were secretion-related proteins and thus associated to the bacterial cell wall. Successful complementation of gspK, a gene encoding for a minor pseudopilin protein confirmed the involvement of the type II secretion system in A. citrulli M6 resistance. This proof of concept study shows that our approach can identify key elements of the BALO-prey interaction, and it validates the hypothesis that mutational changes in a single gene can drastically impact prey resistance to BALO predation.
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Affiliation(s)
- Einav Aharon
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Abhirup Mookherjee
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Francisco Pérez-Montaño
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel; Department of Microbiology, University of Seville, Seville, Spain.
| | - Gustavo Mateus da Silva
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Rajesh Sathyamoorthy
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Saul Burdman
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel.
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5
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Engineering High-Yield Biopolymer Secretion Creates an Extracellular Protein Matrix for Living Materials. mSystems 2021; 6:6/2/e00903-20. [PMID: 33758029 PMCID: PMC8546985 DOI: 10.1128/msystems.00903-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The bacterial extracellular matrix forms autonomously, giving rise to complex material properties and multicellular behaviors. Synthetic matrix analogues can replicate these functions but require exogenously added material or have limited programmability. Here, we design a two-strain bacterial system that self-synthesizes and structures a synthetic extracellular matrix of proteins. We engineered Caulobacter crescentus to secrete an extracellular matrix protein composed of an elastin-like polypeptide (ELP) hydrogel fused to supercharged SpyCatcher [SC(-)]. This biopolymer was secreted at levels of 60 mg/liter, an unprecedented level of biomaterial secretion by a native type I secretion apparatus. The ELP domain was swapped with either a cross-linkable variant of ELP or a resilin-like polypeptide, demonstrating this system is flexible. The SC(-)-ELP matrix protein bound specifically and covalently to the cell surface of a C. crescentus strain that displays a high-density array of SpyTag (ST) peptides via its engineered surface layer. Our work develops protein design guidelines for type I secretion in C. crescentus and demonstrates the autonomous secretion and assembly of programmable extracellular protein matrices, offering a path forward toward the formation of cohesive engineered living materials.IMPORTANCE Engineered living materials (ELM) aim to mimic characteristics of natural occurring systems, bringing the benefits of self-healing, synthesis, autonomous assembly, and responsiveness to traditional materials. Previous research has shown the potential of replicating the bacterial extracellular matrix (ECM) to mimic biofilms. However, these efforts require energy-intensive processing or have limited tunability. We propose a bacterially synthesized system that manipulates the protein content of the ECM, allowing for programmable interactions and autonomous material formation. To achieve this, we engineered a two-strain system to secrete a synthetic extracellular protein matrix (sEPM). This work is a step toward understanding the necessary parameters to engineering living cells to autonomously construct ELMs.
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6
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Turk M, Baumeister W. The promise and the challenges of cryo-electron tomography. FEBS Lett 2020; 594:3243-3261. [PMID: 33020915 DOI: 10.1002/1873-3468.13948] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 01/11/2023]
Abstract
Structural biologists have traditionally approached cellular complexity in a reductionist manner in which the cellular molecular components are fractionated and purified before being studied individually. This 'divide and conquer' approach has been highly successful. However, awareness has grown in recent years that biological functions can rarely be attributed to individual macromolecules. Most cellular functions arise from their concerted action, and there is thus a need for methods enabling structural studies performed in situ, ideally in unperturbed cellular environments. Cryo-electron tomography (Cryo-ET) combines the power of 3D molecular-level imaging with the best structural preservation that is physically possible to achieve. Thus, it has a unique potential to reveal the supramolecular architecture or 'molecular sociology' of cells and to discover the unexpected. Here, we review state-of-the-art Cryo-ET workflows, provide examples of biological applications, and discuss what is needed to realize the full potential of Cryo-ET.
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Affiliation(s)
- Martin Turk
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
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7
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Abstract
The bacterial cell envelope is essential for viability, the environmental gatekeeper and first line of defense against external stresses. For most bacteria, the envelope biosynthesis is also the site of action of some of the most important groups of antibiotics. It is a complex, often multicomponent structure, able to withstand the internally generated turgor pressure. Thus, elucidating the architecture and dynamics of the cell envelope is important, to unravel not only the complexities of cell morphology and maintenance of integrity but also how interventions such as antibiotics lead to death. To address these questions requires the capacity to visualize the cell envelope in situ via high-spatial resolution approaches. In recent years, atomic force microscopy (AFM) has brought novel molecular insights into the assembly, dynamics, and functions of bacterial cell envelopes. The ultrafine resolution and physical sensitivity of the technique have revealed a wealth of ultrastructural features that are invisible to traditional optical microscopy techniques or imperceptible in their true physiological state by electron microscopy. Here, we discuss recent progress in our use of AFM imaging for understanding the architecture and dynamics of the bacterial envelope. We survey recent studies that demonstrate the power of the technique to observe isolated membranes and live cells at (sub)nanometer resolution and under physiological conditions and to track in vitro structural dynamics in response to growth or to drugs.
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8
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von Kügelgen A, Tang H, Hardy GG, Kureisaite-Ciziene D, Brun YV, Stansfeld PJ, Robinson CV, Bharat TAM. In Situ Structure of an Intact Lipopolysaccharide-Bound Bacterial Surface Layer. Cell 2020; 180:348-358.e15. [PMID: 31883796 PMCID: PMC6978808 DOI: 10.1016/j.cell.2019.12.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/22/2019] [Accepted: 12/04/2019] [Indexed: 12/15/2022]
Abstract
Most bacterial and all archaeal cells are encapsulated by a paracrystalline, protective, and cell-shape-determining proteinaceous surface layer (S-layer). On Gram-negative bacteria, S-layers are anchored to cells via lipopolysaccharide. Here, we report an electron cryomicroscopy structure of the Caulobacter crescentus S-layer bound to the O-antigen of lipopolysaccharide. Using native mass spectrometry and molecular dynamics simulations, we deduce the length of the O-antigen on cells and show how lipopolysaccharide binding and S-layer assembly is regulated by calcium. Finally, we present a near-atomic resolution in situ structure of the complete S-layer using cellular electron cryotomography, showing S-layer arrangement at the tip of the O-antigen. A complete atomic structure of the S-layer shows the power of cellular tomography for in situ structural biology and sheds light on a very abundant class of self-assembling molecules with important roles in prokaryotic physiology with marked potential for synthetic biology and surface-display applications.
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Affiliation(s)
- Andriko von Kügelgen
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom; Central Oxford Structural Microscopy and Imaging Centre, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Haiping Tang
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3TA, United Kingdom
| | - Gail G Hardy
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | | | - Yves V Brun
- Department of Biology, Indiana University, Bloomington, IN 47405, USA; Département de microbiologie, infectiologie et immunologie, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3TA, United Kingdom
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom; Central Oxford Structural Microscopy and Imaging Centre, South Parks Road, Oxford OX1 3RE, United Kingdom.
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9
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Charrier M, Li D, Mann VR, Yun L, Jani S, Rad B, Cohen BE, Ashby PD, Ryan KR, Ajo-Franklin CM. Engineering the S-Layer of Caulobacter crescentus as a Foundation for Stable, High-Density, 2D Living Materials. ACS Synth Biol 2019; 8:181-190. [PMID: 30577690 DOI: 10.1021/acssynbio.8b00448] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Materials synthesized by organisms, such as bones and wood, combine the ability to self-repair with remarkable mechanical properties. This multifunctionality arises from the presence of living cells within the material and hierarchical assembly of different components across nanometer to micron scales. While creating engineered analogues of these natural materials is of growing interest, our ability to hierarchically order materials using living cells largely relies on engineered 1D protein filaments. Here, we lay the foundation for bottom-up assembly of engineered living material composites in 2D along the cell body using a synthetic biology approach. We engineer the paracrystalline surface-layer (S-layer) of Caulobacter crescentus to display SpyTag peptides that form irreversible isopeptide bonds to SpyCatcher-modified proteins, nanocrystals, and biopolymers on the extracellular surface. Using flow cytometry and confocal microscopy, we show that attachment of these materials to the cell surface is uniform, specific, and covalent, and its density can be controlled on the basis of the insertion location within the S-layer protein, RsaA. Moreover, we leverage the irreversible nature of this attachment to demonstrate via SDS-PAGE that the engineered S-layer can display a high density of materials, reaching 1 attachment site per 288 nm2. Finally, we show that ligation of quantum dots to the cell surface does not impair cell viability, and this composite material remains intact over a period of 2 weeks. Taken together, this work provides a platform for self-organization of soft and hard nanomaterials on a cell surface with precise control over 2D density, composition, and stability of the resulting composite, and is a key step toward building hierarchically ordered engineered living materials with emergent properties.
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10
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Melia CE, Bharat TAM. Locating macromolecules and determining structures inside bacterial cells using electron cryotomography. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2018; 1866:973-981. [PMID: 29908328 PMCID: PMC6052677 DOI: 10.1016/j.bbapap.2018.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/30/2018] [Accepted: 06/11/2018] [Indexed: 01/01/2023]
Abstract
Electron cryotomography (cryo-ET) is an imaging technique uniquely suited to the study of bacterial ultrastructure and cell biology. Recent years have seen a surge in structural and cell biology research on bacteria using cryo-ET. This research has driven major technical developments in the field, with applications emerging to address a wide range of biological questions. In this review, we explore the diversity of cryo-ET approaches used for structural and cellular microbiology, with a focus on in situ localization and structure determination of macromolecules. The first section describes strategies employed to locate target macromolecules within large cellular volumes. Next, we explore methods to study thick specimens by sample thinning. Finally, we review examples of macromolecular structure determination in a cellular context using cryo-ET. The examples outlined serve as powerful demonstrations of how the cellular location, structure, and function of any bacterial macromolecule of interest can be investigated using cryo-ET.
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Affiliation(s)
- Charlotte E Melia
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom; Central Oxford Structural and Molecular Imaging Centre, University of Oxford, Oxford OX1 3RE, United Kingdom.
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11
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Khursigara CM, Koval SF, Moyles DM, Harris RJ. Inroads through the bacterial cell envelope: seeing is believing. Can J Microbiol 2018; 64:601-617. [DOI: 10.1139/cjm-2018-0091] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A singular feature of all prokaryotic cells is the presence of a cell envelope composed of a cytoplasmic membrane and a cell wall. The introduction of bacterial cell fractionation techniques in the 1950s and 1960s along with developments in procedures for electron microscopy opened the window towards an understanding of the chemical composition and architecture of the cell envelope. This review traces the contribution of Terry Beveridge in these endeavours, beginning with his doctoral studies in the 1970s on the structure of paracrystalline surface arrays (S-layers), followed by an exploration of cryogenic methods for preserving bacteria for ultrastructural analyses. His insights are reflected in a current example of the contribution of cryo-electron microscopy to S-layer studies — the structure and assembly of the surface array of Caulobacter crescentus. The review then focuses on Terry’s contributions to imaging the ultrastructure of bacterial cell envelopes and to the development of cryo-electron microscopy techniques, including the use of CEMOVIS (Cryo-electron Microscopy of Vitreous Sections) to “see” the ultrastructure of the Gram-positive cell envelope — his last scientific endeavour.
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Affiliation(s)
- Cezar M. Khursigara
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
- Molecular and Cellular Imaging Facility, Advanced Analysis Centre, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Susan F. Koval
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 5C1, Canada
| | - Dianne M. Moyles
- Molecular and Cellular Imaging Facility, Advanced Analysis Centre, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Robert J. Harris
- Molecular and Cellular Imaging Facility, Advanced Analysis Centre, University of Guelph, Guelph, ON N1G 2W1, Canada
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12
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Herrmann J, Jabbarpour F, Bargar PG, Nomellini JF, Li PN, Lane TJ, Weiss TM, Smit J, Shapiro L, Wakatsuki S. Environmental Calcium Controls Alternate Physical States of the Caulobacter Surface Layer. Biophys J 2017; 112:1841-1851. [PMID: 28494955 PMCID: PMC5425405 DOI: 10.1016/j.bpj.2017.04.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/28/2017] [Accepted: 04/06/2017] [Indexed: 11/23/2022] Open
Abstract
Surface layers (S-layers) are paracrystalline, proteinaceous structures found in most archaea and many bacteria. Often the outermost cell envelope component, S-layers serve diverse functions including aiding pathogenicity and protecting against predators. We report that the S-layer of Caulobacter crescentus exhibits calcium-mediated structural plasticity, switching irreversibly between an amorphous aggregate state and the crystalline state. This finding invalidates the common assumption that S-layers serve only as static wall-like structures. In vitro, the Caulobacter S-layer protein, RsaA, enters the aggregate state at physiological temperatures and low divalent calcium ion concentrations. At higher concentrations, calcium ions stabilize monomeric RsaA, which can then transition to the two-dimensional crystalline state. Caulobacter requires micromolar concentrations of calcium for normal growth and development. Without an S-layer, Caulobacter is even more sensitive to changes in environmental calcium concentration. Therefore, this structurally dynamic S-layer responds to environmental conditions as an ion sensor and protects Caulobacter from calcium deficiency stress, a unique mechanism of bacterial adaptation. These findings provide a biochemical and physiological basis for RsaA's calcium-binding behavior, which extends far beyond calcium's commonly accepted role in aiding S-layer biogenesis or oligomerization and demonstrates a connection to cellular fitness.
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Affiliation(s)
- Jonathan Herrmann
- Department of Structural Biology, Stanford University, Stanford, California; Bioscience Division, SLAC National Accelerator Laboratory, Menlo Park, California.
| | - Fatemeh Jabbarpour
- Department of Structural Biology, Stanford University, Stanford, California
| | | | - John F Nomellini
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Po-Nan Li
- Department of Electrical Engineering, Stanford University, Stanford, California
| | - Thomas J Lane
- Bioscience Division, SLAC National Accelerator Laboratory, Menlo Park, California
| | - Thomas M Weiss
- Bioscience Division, SLAC National Accelerator Laboratory, Menlo Park, California
| | - John Smit
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University, Stanford, California.
| | - Soichi Wakatsuki
- Department of Structural Biology, Stanford University, Stanford, California; Bioscience Division, SLAC National Accelerator Laboratory, Menlo Park, California.
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13
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Bharat TA, Kureisaite-Ciziene D, Hardy GG, Yu EW, Devant JM, Hagen WJ, Brun YV, Briggs JA, Löwe J. Structure of the hexagonal surface layer on Caulobacter crescentus cells. Nat Microbiol 2017; 2:17059. [PMID: 28418382 PMCID: PMC5699643 DOI: 10.1038/nmicrobiol.2017.59] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 03/24/2017] [Indexed: 12/12/2022]
Abstract
Many prokaryotic cells are encapsulated by a surface layer (S-layer) consisting of repeating units of S-layer proteins. S-layer proteins are a diverse class of molecules found in Gram-positive and Gram-negative bacteria and most archaea1-5. S-layers protect cells from the outside, provide mechanical stability and also play roles in pathogenicity. In situ structural information about this highly abundant class of proteins is scarce, so atomic details of how S-layers are arranged on the surface of cells have remained elusive. Here, using purified Caulobacter crescentus' sole S-layer protein RsaA, we obtained a 2.7 Å X-ray structure that shows the hexameric S-layer lattice. We also solved a 7.4 Å structure of the S-layer through electron cryotomography and sub-tomogram averaging of cell stalks. The X-ray structure was docked unambiguously into the electron cryotomography map, resulting in a pseudo-atomic-level description of the in vivo S-layer, which agrees completely with the atomic X-ray lattice model. The cellular S-layer atomic structure shows that the S-layer is porous, with a largest gap dimension of 27 Å, and is stabilized by multiple Ca2+ ions bound near the interfaces. This study spans different spatial scales from atoms to cells by combining X-ray crystallography with electron cryotomography and sub-nanometre-resolution sub-tomogram averaging.
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Affiliation(s)
- Tanmay A.M. Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | | | - Gail G. Hardy
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Ellen W. Yu
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Jessica M. Devant
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Wim J.H. Hagen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany
| | - Yves V. Brun
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - John A.G. Briggs
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany
| | - Jan Löwe
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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Jones MD, Chan ACK, Nomellini JF, Murphy MEP, Smit J. Surface-layer protein from Caulobacter crescentus: expression, purification and X-ray crystallographic analysis. Acta Crystallogr F Struct Biol Commun 2016; 72:677-80. [PMID: 27599857 PMCID: PMC5012206 DOI: 10.1107/s2053230x16011638] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 07/16/2016] [Indexed: 11/10/2022] Open
Abstract
Protein surface layers are self-assembling, paracrystalline lattices on the surface of many prokaryotes. Surface-layer proteins have not benefited from widespread structural analysis owing to their resistance to crystallization. Here, the successful expression of a truncated version of RsaA, the surface-layer protein from Caulobacter crescentus, from a Caulobacter protein-expression system is reported. The purification, crystallization and initial X-ray diffraction analysis of the truncated RsaA, the largest surface-layer protein studied to date and the first from a Gram-negative bacterium, are also reported.
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Affiliation(s)
- Michael D. Jones
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Anson C. K. Chan
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - John F. Nomellini
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Michael E. P. Murphy
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - John Smit
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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15
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Park DM, Reed DW, Yung MC, Eslamimanesh A, Lencka MM, Anderko A, Fujita Y, Riman RE, Navrotsky A, Jiao Y. Bioadsorption of Rare Earth Elements through Cell Surface Display of Lanthanide Binding Tags. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:2735-42. [PMID: 26836847 PMCID: PMC5381720 DOI: 10.1021/acs.est.5b06129] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
With the increasing demand for rare earth elements (REEs) in many emerging clean energy technologies, there is an urgent need for the development of new approaches for efficient REE extraction and recovery. As a step toward this goal, we genetically engineered the aerobic bacterium Caulobacter crescentus for REE adsorption through high-density cell surface display of lanthanide binding tags (LBTs) on its S-layer. The LBT-displayed strains exhibited enhanced adsorption of REEs compared to cells lacking LBT, high specificity for REEs, and an adsorption preference for REEs with small atomic radii. Adsorbed Tb(3+) could be effectively recovered using citrate, consistent with thermodynamic speciation calculations that predicted strong complexation of Tb(3+) by citrate. No reduction in Tb(3+) adsorption capacity was observed following citrate elution, enabling consecutive adsorption/desorption cycles. The LBT-displayed strain was effective for extracting REEs from the acid leachate of core samples collected at a prospective rare earth mine. Our collective results demonstrate a rapid, efficient, and reversible process for REE adsorption with potential industrial application for REE enrichment and separation.
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Affiliation(s)
- Dan M. Park
- Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California 92550, United States
| | - David W. Reed
- Idaho National Laboratory, Idaho Falls, Idaho 83415, United States
| | - Mimi C. Yung
- Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California 92550, United States
| | - Ali Eslamimanesh
- OLI Systems, Inc., 240 Cedar Knolls Road, Suite 301, Cedar Knolls, New Jersey 07927, United States
| | - Malgorzata M. Lencka
- OLI Systems, Inc., 240 Cedar Knolls Road, Suite 301, Cedar Knolls, New Jersey 07927, United States
| | - Andrzej Anderko
- OLI Systems, Inc., 240 Cedar Knolls Road, Suite 301, Cedar Knolls, New Jersey 07927, United States
| | - Yoshiko Fujita
- Idaho National Laboratory, Idaho Falls, Idaho 83415, United States
| | - Richard E. Riman
- Department of Materials Science and Engineering, Rutgers, The State University of New Jersey, 607 Taylor Road, Piscataway, New Jersey 08855, United States
| | - Alexandra Navrotsky
- Peter A. Rock Thermochemistry Laboratory and NEAT ORU, University of California Davis, Davis, California 95616, United States
| | - Yongqin Jiao
- Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California 92550, United States
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16
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Mijouin L, Hillion M, Ramdani Y, Jaouen T, Duclairoir-Poc C, Follet-Gueye ML, Lati E, Yvergnaux F, Driouich A, Lefeuvre L, Farmer C, Misery L, Feuilloley MGJ. Effects of a skin neuropeptide (substance p) on cutaneous microflora. PLoS One 2013; 8:e78773. [PMID: 24250813 PMCID: PMC3826737 DOI: 10.1371/journal.pone.0078773] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 09/16/2013] [Indexed: 01/01/2023] Open
Abstract
Background Skin is the largest human neuroendocrine organ and hosts the second most numerous microbial population but the interaction of skin neuropeptides with the microflora has never been investigated. We studied the effect of Substance P (SP), a peptide released by nerve endings in the skin on bacterial virulence. Methodology/Principal Findings Bacillus cereus, a member of the skin transient microflora, was used as a model. Exposure to SP strongly stimulated the cytotoxicity of B. cereus (+553±3% with SP 10−6 M) and this effect was rapid (<5 min). Infection of keratinocytes with SP treated B. cereus led to a rise in caspase1 and morphological alterations of the actin cytoskeleton. Secretome analysis revealed that SP stimulated the release of collagenase and superoxide dismutase. Moreover, we also noted a shift in the surface polarity of the bacteria linked to a peel-off of the S-layer and the release of S-layer proteins. Meanwhile, the biofilm formation activity of B. cereus was increased. The Thermo unstable ribosomal Elongation factor (Ef-Tu) was identified as the SP binding site in B. cereus. Other Gram positive skin bacteria, namely Staphylococcus aureus and Staphylococcus epidermidis also reacted to SP by an increase of virulence. Thermal water from Uriage-les-Bains and an artificial polysaccharide (Teflose®) were capable to antagonize the effect of SP on bacterial virulence. Conclusions/Significance SP is released in sweat during stress and is known to be involved in the pathogenesis of numerous skin diseases through neurogenic inflammation. Our study suggests that a direct effect of SP on the skin microbiote should be another mechanism.
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Affiliation(s)
- Lily Mijouin
- Laboratory of Microbiology Signals and Microenvironnement LMSM, EA 4312, Normandie Université, Université Rouen, Evreux, France
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17
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Hughes HV, Lisher JP, Hardy GG, Kysela DT, Arnold RJ, Giedroc DP, Brun YV. Co-ordinate synthesis and protein localization in a bacterial organelle by the action of a penicillin-binding-protein. Mol Microbiol 2013; 90:1162-77. [PMID: 24118129 DOI: 10.1111/mmi.12422] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2013] [Indexed: 11/29/2022]
Abstract
Organelles with specialized form and function occur in diverse bacteria. Within the Alphaproteobacteria, several species extrude thin cellular appendages known as stalks, which function in nutrient uptake, buoyancy and reproduction. Consistent with their specialization, stalks maintain a unique molecular composition compared with the cell body, but how this is achieved remains to be fully elucidated. Here we dissect the mechanism of localization of StpX, a stalk-specific protein in Caulobacter crescentus. Using a forward genetics approach, we identify a penicillin-binding-protein, PbpC, which is required for the localization of StpX in the stalk. We show that PbpC acts at the stalked cell pole to anchor StpX to rigid components of the outer membrane of the elongating stalk, concurrent with stalk synthesis. Stalk-localized StpX in turn functions in cellular responses to copper and zinc, suggesting that the stalk may contribute to metal homeostasis in Caulobacter. Together, these results identify a novel role for a penicillin-binding-protein in compartmentalizing a bacterial organelle it itself helps create, raising the possibility that cell wall-synthetic enzymes may broadly serve not only to synthesize the diverse shapes of bacteria, but also to functionalize them at the molecular level.
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Affiliation(s)
- H Velocity Hughes
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
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18
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Shin SH, Comolli LR, Tscheliessnig R, Wang C, Nam KT, Hexemer A, Siegerist CE, De Yoreo JJ, Bertozzi CR. Self-assembly of "S-bilayers", a step toward expanding the dimensionality of S-layer assemblies. ACS NANO 2013; 7:4946-4953. [PMID: 23705800 DOI: 10.1021/nn400263j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Protein-based assemblies with ordered nanometer-scale features in three dimensions are of interest as functional nanomaterials but are difficult to generate. Here we report that a truncated S-layer protein assembles into stable bilayers, which we characterized using cryogenic-electron microscopy, tomography, and X-ray spectroscopy. We find that emergence of this supermolecular architecture is the outcome of hierarchical processes; the proteins condense in solution to form 2-D crystals, which then stack parallel to one another to create isotropic bilayered assemblies. Within this bilayered structure, registry between lattices in two layers was disclosed, whereas the intrinsic symmetry in each layer was altered. Comparison of these data to images of wild-type SbpA layers on intact cells gave insight into the interactions responsible for bilayer formation. These results establish a platform for engineering S-layer assemblies with 3-D architecture.
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Affiliation(s)
- Seong-Ho Shin
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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19
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Kanonenberg K, Schwarz CKW, Schmitt L. Type I secretion systems - a story of appendices. Res Microbiol 2013; 164:596-604. [PMID: 23541474 DOI: 10.1016/j.resmic.2013.03.011] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 03/13/2013] [Indexed: 12/28/2022]
Abstract
Secretion is an essential task for prokaryotic organisms to interact with their surrounding environment. In particular, the production of extracellular proteins and peptides is important for many aspects of an organism's survival and adaptation to its ecological niche. In Gram-negative bacteria, six different protein secretion systems have been identified so far, named Type I to Type VI; differing greatly in their composition and mechanism of action (Economou et al., 2006). The two membranes present in Gram-negative bacteria are negotiated either by one-step transport mechanisms (Type I and Type III), where the unfolded substrate is translocated directly into the extracellular space, without any periplasmic intermediates, or by two-step mechanisms (Type II and Type V), where the substrate is first transported into the periplasm to allow folding before a second transport step across the outer membrane occurs. Here we focus on Type I secretion systems and summarise our current knowledge of these one-step transport machineries with emphasis on the N-terminal extensions found in many Type I-specific ABC transporters. ABC transporters containing an N-terminal C39 peptidase domain cut off a leader peptide present in the substrate prior to secretion. The function of the second type of appendix, the C39 peptidase-like domain (CLD), is not yet completely understood. Recent results have shown that it is nonetheless essential for secretion and interacts specifically with the substrate of the transporter. The third group present does not contain any appendix. In light of this difference we compare the function of the appendix and the differences that might exist among the three families of T1SS.
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Affiliation(s)
- Kerstin Kanonenberg
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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20
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The bacterial surface layer provides protection against antimicrobial peptides. Appl Environ Microbiol 2012; 78:5452-6. [PMID: 22635987 DOI: 10.1128/aem.01493-12] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This report describes a previously unrecognized role for bacterial surface layers as barriers that confer protection against antimicrobial peptides. As antimicrobial peptides exist in natural environments, S-layers may provide a bacterial survival mechanism that has been selected for through evolution.
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21
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Gandham L, Nomellini JF, Smit J. Evaluating secretion and surface attachment of SapA, an S-layer-associated metalloprotease of Caulobacter crescentus. Arch Microbiol 2012; 194:865-77. [DOI: 10.1007/s00203-012-0819-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 03/23/2012] [Accepted: 04/23/2012] [Indexed: 11/30/2022]
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22
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Linhartová I, Bumba L, Mašín J, Basler M, Osička R, Kamanová J, Procházková K, Adkins I, Hejnová-Holubová J, Sadílková L, Morová J, Sebo P. RTX proteins: a highly diverse family secreted by a common mechanism. FEMS Microbiol Rev 2011; 34:1076-112. [PMID: 20528947 PMCID: PMC3034196 DOI: 10.1111/j.1574-6976.2010.00231.x] [Citation(s) in RCA: 355] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Repeats-in-toxin (RTX) exoproteins of Gram-negative bacteria form a steadily growing family of proteins with diverse biological functions. Their common feature is the unique mode of export across the bacterial envelope via the type I secretion system and the characteristic, typically nonapeptide, glycine- and aspartate-rich repeats binding Ca2+ ions. In this review, we summarize the current state of knowledge on the organization of rtx loci and on the biological and biochemical activities of therein encoded proteins. Applying several types of bioinformatic screens on the steadily growing set of sequenced bacterial genomes, over 1000 RTX family members were detected, with the biological functions of most of them remaining to be characterized. Activities of the so far characterized RTX family members are then discussed and classified according to functional categories, ranging from the historically first characterized pore-forming RTX leukotoxins, through the large multifunctional enzymatic toxins, bacteriocins, nodulation proteins, surface layer proteins, up to secreted hydrolytic enzymes exhibiting metalloprotease or lipase activities of industrial interest.
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Affiliation(s)
- Irena Linhartová
- Institute of Microbiology AS CR v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
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23
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Sleytr UB, Schuster B, Egelseer EM, Pum D, Horejs CM, Tscheliessnig R, Ilk N. Nanobiotechnology with S-layer proteins as building blocks. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 103:277-352. [PMID: 21999999 DOI: 10.1016/b978-0-12-415906-8.00003-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
One of the key challenges in nanobiotechnology is the utilization of self- assembly systems, wherein molecules spontaneously associate into reproducible aggregates and supramolecular structures. In this contribution, we describe the basic principles of crystalline bacterial surface layers (S-layers) and their use as patterning elements. The broad application potential of S-layers in nanobiotechnology is based on the specific intrinsic features of the monomolecular arrays composed of identical protein or glycoprotein subunits. Most important, physicochemical properties and functional groups on the protein lattice are arranged in well-defined positions and orientations. Many applications of S-layers depend on the capability of isolated subunits to recrystallize into monomolecular arrays in suspension or on suitable surfaces (e.g., polymers, metals, silicon wafers) or interfaces (e.g., lipid films, liposomes, emulsomes). S-layers also represent a unique structural basis and patterning element for generating more complex supramolecular structures involving all major classes of biological molecules (e.g., proteins, lipids, glycans, nucleic acids, or combinations of these). Thus, S-layers fulfill key requirements as building blocks for the production of new supramolecular materials and nanoscale devices as required in molecular nanotechnology, nanobiotechnology, biomimetics, and synthetic biology.
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Affiliation(s)
- Uwe B Sleytr
- Department of NanoBiotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
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24
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The Structure of Bacterial S-Layer Proteins. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 103:73-130. [DOI: 10.1016/b978-0-12-415906-8.00004-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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25
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Analysis of the intact surface layer of Caulobacter crescentus by cryo-electron tomography. J Bacteriol 2010; 192:5855-65. [PMID: 20833802 DOI: 10.1128/jb.00747-10] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The surface layers (S layers) of those bacteria and archaea that elaborate these crystalline structures have been studied for 40 years. However, most structural analysis has been based on electron microscopy of negatively stained S-layer fragments separated from cells, which can introduce staining artifacts and allow rearrangement of structures prone to self-assemble. We present a quantitative analysis of the structure and organization of the S layer on intact growing cells of the Gram-negative bacterium Caulobacter crescentus using cryo-electron tomography (CET) and statistical image processing. Instead of the expected long-range order, we observed different regions with hexagonally organized subunits exhibiting short-range order and a broad distribution of periodicities. Also, areas of stacked double layers were found, and these increased in extent when the S-layer protein (RsaA) expression level was elevated by addition of multiple rsaA copies. Finally, we combined high-resolution amino acid residue-specific Nanogold labeling and subtomogram averaging of CET volumes to improve our understanding of the correlation between the linear protein sequence and the structure at the 2-nm level of resolution that is presently available. The results support the view that the U-shaped RsaA monomer predicted from negative-stain tomography proceeds from the N terminus at one vertex, corresponding to the axis of 3-fold symmetry, to the C terminus at the opposite vertex, which forms the prominent 6-fold symmetry axis. Such information will help future efforts to analyze subunit interactions and guide selection of internal sites for display of heterologous protein segments.
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26
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Amat F, Comolli L, Moussavi F, Downing KH, Horowitz M. Subtomogram alignment by adaptive Fourier coefficient thresholding. J Struct Biol 2010; 171:332-44. [PMID: 20621702 PMCID: PMC4189811 DOI: 10.1016/j.jsb.2010.05.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Revised: 05/25/2010] [Accepted: 05/26/2010] [Indexed: 10/19/2022]
Abstract
In the past few years, three-dimensional (3D) subtomogram alignment has become an important tool in cryo-electron tomography (CET). This technique allows one to produce higher resolution images of structures which can not be reconstructed using single-particle methods. Building on previous work, we present a new dissimilarity measure between subtomograms that works well for the noisy images that often occur in CET images. A technique that is more robust to noise provides the ability to analyze macromolecules in thicker samples such as whole cells or lower the defocus in thinner samples to push the first zero of the Contrast Transfer Function (CTF). Our method, Threshold Constrained Cross-Correlation (TCCC), uses statistics of the noise to automatically select only a small percentage of the Fourier coefficients to compute the cross-correlation, which has two main advantages: first, it reduces the influence of the noise by looking at only those peaks dominated by signal; and second, it avoids the missing wedge normalization problem since we consider the same number of coefficients for all possible pairs of subtomograms. We present results with synthetic and real data to compare our approach with other existing methods under different SNR and missing wedge conditions, and show that TCCC improves alignment results for datasets with SNR<0.1. We have made our source code freely available for the community.
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Affiliation(s)
- Fernando Amat
- Department of Electrical Engineering, Stanford University, Stanford, CA USA
| | - Luis Comolli
- Life Sciences Division, Lawrence Berkeley National Labs, Berkeley, CA USA
| | - Farshid Moussavi
- Department of Electrical Engineering, Stanford University, Stanford, CA USA
| | - Kenneth H. Downing
- Life Sciences Division, Lawrence Berkeley National Labs, Berkeley, CA USA
| | - Mark Horowitz
- Department of Electrical Engineering, Stanford University, Stanford, CA USA
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27
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Patel J, Zhang Q, McKay RML, Vincent R, Xu Z. Genetic Engineering of Caulobacter crescentus for Removal of Cadmium from Water. Appl Biochem Biotechnol 2009; 160:232-43. [DOI: 10.1007/s12010-009-8540-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2008] [Accepted: 01/20/2009] [Indexed: 11/28/2022]
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28
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29
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Tsai Y, Sawaya MR, Cannon GC, Cai F, Williams EB, Heinhorst S, Kerfeld CA, Yeates TO. Structural analysis of CsoS1A and the protein shell of the Halothiobacillus neapolitanus carboxysome. PLoS Biol 2007; 5:e144. [PMID: 17518518 PMCID: PMC1872035 DOI: 10.1371/journal.pbio.0050144] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2006] [Accepted: 03/21/2007] [Indexed: 01/07/2023] Open
Abstract
The carboxysome is a bacterial organelle that functions to enhance the efficiency of CO2 fixation by encapsulating the enzymes ribulose bisphosphate carboxylase/oxygenase (RuBisCO) and carbonic anhydrase. The outer shell of the carboxysome is reminiscent of a viral capsid, being constructed from many copies of a few small proteins. Here we describe the structure of the shell protein CsoS1A from the chemoautotrophic bacterium Halothiobacillus neapolitanus. The CsoS1A protein forms hexameric units that pack tightly together to form a molecular layer, which is perforated by narrow pores. Sulfate ions, soaked into crystals of CsoS1A, are observed in the pores of the molecular layer, supporting the idea that the pores could be the conduit for negatively charged metabolites such as bicarbonate, which must cross the shell. The problem of diffusion across a semiporous protein shell is discussed, with the conclusion that the shell is sufficiently porous to allow adequate transport of small molecules. The molecular layer formed by CsoS1A is similar to the recently observed layers formed by cyanobacterial carboxysome shell proteins. This similarity supports the argument that the layers observed represent the natural structure of the facets of the carboxysome shell. Insights into carboxysome function are provided by comparisons of the carboxysome shell to viral capsids, and a comparison of its pores to the pores of transmembrane protein channels.
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Affiliation(s)
- Yingssu Tsai
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Michael R Sawaya
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
- University of California Los Angeles–United States Department of Energy Institute for Genomics and Proteomics, Los Angeles, California, United States of America
| | - Gordon C Cannon
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi, United States of America
| | - Fei Cai
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi, United States of America
| | - Eric B Williams
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi, United States of America
| | - Sabine Heinhorst
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi, United States of America
| | - Cheryl A Kerfeld
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
- University of California Los Angeles–United States Department of Energy Institute for Genomics and Proteomics, Los Angeles, California, United States of America
- Life Sciences Core, University of California Los Angeles, Los Angeles, California, United States of America
| | - Todd O Yeates
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
- University of California Los Angeles–United States Department of Energy Institute for Genomics and Proteomics, Los Angeles, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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30
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Nomellini JF, Duncan G, Dorocicz IR, Smit J. S-layer-mediated display of the immunoglobulin G-binding domain of streptococcal protein G on the surface of Caulobacter crescentus: development of an immunoactive reagent. Appl Environ Microbiol 2007; 73:3245-53. [PMID: 17384306 PMCID: PMC1907123 DOI: 10.1128/aem.02900-06] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2006] [Accepted: 03/16/2007] [Indexed: 11/20/2022] Open
Abstract
The immunoglobulin G (IgG)-binding streptococcal protein G is often used for immunoprecipitation or immunoadsorption-based assays, as it exhibits binding to a broader spectrum of host species IgG and IgG subclasses than the alternative, Staphylococcus aureus protein A. Caulobacter crescentus produces a hexagonally arranged paracrystalline protein surface layer (S-layer) composed of a single secreted protein, RsaA, that is notably tolerant of heterologous peptide insertions while maintaining the surface-attached crystalline character. Here, a protein G IgG-binding domain, GB1, was expressed as an insertion into full-length RsaA on the cell surface to produce densely packed immunoreactive particles. GB1 insertions at five separate sites were expressed, and all bound rabbit and goat IgG, but expression levels were reduced compared to those of wild-type RsaA and poor binding to mouse IgG was noted. To remedy this, we used the 20-amino-acid Muc1 peptide derived from human mucins as a spacer, since insertions of multiple tandem repeats were well tolerated for RsaA secretion and assembly. This strategy worked remarkably well, and recombinant RsaA proteins, containing up to three GB1 domains, surrounded by Muc1 peptides, not only were secreted and assembled but did so at wild-type levels. The ability to bind IgG (including mouse IgG) increased as GB1 units were added, and those with three GB1 domains bound twice as much rabbit IgG per cell as S. aureus cells (Pansorbin). The ability of recombinant protein G-Caulobacter cells to function as immunoactive reagents was assessed in an immunoprecipitation assay using a FLAG-tagged protein and anti-FLAG mouse monoclonal antibody; their performance was comparable to that of protein G-Sepharose beads. This work demonstrates the potential for using cells expressing recombinant RsaA/GB1 in immunoassays, especially considering that protein G-Caulobacter cells are more cost-effective than protein G beads and exhibit a broader species and IgG isotype binding range than protein A.
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Affiliation(s)
- John F Nomellini
- Department of Microbiology and Immunology, 2509-2350 Health Sciences Mall, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
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Ford MJ, Nomellini JF, Smit J. S-layer anchoring and localization of an S-layer-associated protease in Caulobacter crescentus. J Bacteriol 2007; 189:2226-37. [PMID: 17209028 PMCID: PMC1899406 DOI: 10.1128/jb.01690-06] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The S-layer of the gram-negative bacterium Caulobacter crescentus is composed of a single protein, RsaA, that is secreted and assembled into a hexagonal crystalline array that covers the organism. Despite the widespread occurrence of comparable bacterial S-layers, little is known about S-layer attachment to cell surfaces, especially for gram-negative organisms. Having preliminary indications that the N terminus of RsaA anchors the monomer to the cell surface, we developed an assay to distinguish direct surface attachment from subunit-subunit interactions where small RsaA fragments are incubated with S-layer-negative cells to assess the ability of the fragments to reattach. In doing so, we found that the RsaA anchoring region lies in the first approximately 225 amino acids and that this RsaA anchoring region requires a smooth lipopolysaccharide species found in the outer membrane. By making mutations at six semirandom sites, we learned that relatively minor perturbations within the first approximately 225 amino acids of RsaA caused loss of anchoring. In other studies, we confirmed that only this N-terminal region has a direct role in S-layer anchoring. As a by-product of the anchoring studies, we discovered that Sap, the C. crescentus S-layer-associated protease, recognized a cleavage site in the truncated RsaA fragments that is not detected by Sap in full-length RsaA. This, in turn, led to the discovery that Sap was an extracellular membrane-bound protease, rather than intracellular, as previously proposed. Moreover, Sap was secreted to the cell surface primarily by the S-layer type I secretion apparatus.
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Affiliation(s)
- Matthew J Ford
- Department of Microbiology and Immunology, University of British Columbia, 2509-2350 Health Sciences Mall, Vancouver, BC, Canada V6T 1Z3
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Massias B, Dumetz F, Urdaci MC, Le Hénaff M. Identification of P18, a surface protein produced by the fish pathogen Flavobacterium psychrophilum. J Appl Microbiol 2005; 97:574-80. [PMID: 15281938 DOI: 10.1111/j.1365-2672.2004.02338.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS This study was focused on the identification of associated outer membrane proteins which may play a role in the specific interactions between Flavobacterium psychrophilum (the aetiological agent of cold-water disease and rainbow trout fry syndrome in salmonid fish worldwide) and the fish tissues. METHODS AND RESULTS The surface protein interactions with the outer membrane being mainly ionic, different methods were used for the detachment of proteins from the cell surface of Fl. psychrophilum involving detergent-free buffers or solutions known to perturb the ionic interactions. Such treatments led to the isolation of a surface protein, named P18 in accordance with its relative molecular mass. The expression of P18 was not related to the growth conditions (liquid or solid medium, temperature and aeration) or the strains of Fl. psychrophilum tested here. CONCLUSIONS Preliminary characterization indicated that P18 is a surface antigen which is not sugar-modified and might be a subunit of a surface layer (i.e. S-layer), one of the most common surface structures on bacteria. SIGNIFICANCE AND IMPACT OF THE STUDY Data reported here should be used as the basis for further works involving the purification and characterization of P18 to identify the specific roles of such a surface protein, especially the interaction between this protein and the host surface.
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Affiliation(s)
- B Massias
- Laboratoire de Microbiologie et de Biochimie Appliquées, Ecole Nationale d'Ingénieurs des Travaux Agricoles de Bordeaux, Gradignan, France
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Toporowski MC, Nomellini JF, Awram P, Smit J. Two outer membrane proteins are required for maximal type I secretion of the Caulobacter crescentus S-layer protein. J Bacteriol 2004; 186:8000-9. [PMID: 15547272 PMCID: PMC529074 DOI: 10.1128/jb.186.23.8000-8009.2004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Transport of RsaA, the crystalline S-layer subunit protein of Caulobacter crescentus, is mediated by a type I secretion mechanism. Two proteins have been identified that play the role of the outer membrane protein (OMP) component in the RsaA secretion machinery. The genes rsaF(a) and rsaF(b) were identified by similarity to the Escherichia coli hemolysin secretion OMP TolC by using the C. crescentus genome sequence. The rsaF(a) gene is located several kilobases downstream of the other transporter genes, while rsaF(b) is completely unlinked. An rsaF(a) knockout had approximately 56% secretion compared to wild-type levels, while the rsaF(b) knockout reduced secretion levels to approximately 79%. When expression of both proteins was eliminated, there was no RsaA secretion, but a residual level of approximately 9% remained inside the cell, suggesting posttranslational autoregulation. Complementation with either of the individual rsaF genes by use of a multicopy vector, which resulted in 8- to 10-fold overexpression of the proteins, did not restore RsaA secretion to wild-type levels, indicating that both rsaF genes were required for full-level secretion. However, overexpression of rsaF(a) (with normal rsaF(b) levels) in concert with overexpression of rsaA resulted in a 28% increase in RsaA secretion, indicating a potential for significantly increasing expression levels of an already highly expressing type I secretion system. This is the only known example of type I secretion requiring two OMPs to assemble a fully functional system.
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Affiliation(s)
- Michael C Toporowski
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
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Affiliation(s)
- William C Nierman
- Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
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Umelo-Njaka E, Bingle WH, Borchani F, Le KD, Awram P, Blake T, Nomellini JF, Smit J. Caulobacter crescentus synthesizes an S-layer-editing metalloprotease possessing a domain sharing sequence similarity with its paracrystalline S-layer protein. J Bacteriol 2002; 184:2709-18. [PMID: 11976300 PMCID: PMC135016 DOI: 10.1128/jb.184.10.2709-2718.2002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Strains of Caulobacter crescentus elaborate an S-layer, a two-dimensional protein latticework which covers the cell surface. The S-layer protein (RsaA) is secreted by a type I mechanism (relying on a C-terminal signal) and is unusual among type I secreted proteins because high levels of protein are produced continuously. In efforts to adapt the S-layer for display of foreign peptides and proteins, we noted a proteolytic activity that affected S-layer monomers with foreign inserts. The cleavage was precise, resulting in fragments with an unambiguous N-terminal sequence. We developed an assay to screen for loss of this activity (i.e., presentation of foreign peptides without degradation), using transposon and traditional mutagenesis. A metalloprotease gene designated sap (S-layer-associated protease) was identified which could complement the protease-negative mutants. The N-terminal half of Sap possessed significant similarity to other type I secreted proteases (e.g., alkaline protease of Pseudomonas aeruginosa), including the characteristic RTX repeat sequences, but the C-terminal half which normally includes the type I secretion signal exhibited no such similarity. Instead, there was a region of significant similarity to the N-terminal region of RsaA. We hypothesize that Sap evolved by combining the catalytic portion of a type I secreted protease with an S-layer-like protein, perhaps to associate with nascent S-layer monomers to "scan" for modifications.
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Affiliation(s)
- Elizabeth Umelo-Njaka
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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36
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Bingle WH, Nomellini JF, Smit J. Secretion of the Caulobacter crescentus S-layer protein: further localization of the C-terminal secretion signal and its use for secretion of recombinant proteins. J Bacteriol 2000; 182:3298-301. [PMID: 10809716 PMCID: PMC94523 DOI: 10.1128/jb.182.11.3298-3301.2000] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The secretion signal of the Caulobacter crescentus S-layer protein (RsaA) was localized to the C-terminal 82 amino acids of the molecule. Protein yield studies showed that 336 or 242 C-terminal residues of RsaA mediated secretion of >50 mg of a cellulase passenger protein per liter to the culture fluids.
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Affiliation(s)
- W H Bingle
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
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37
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Awram P, Smit J. The Caulobacter crescentus paracrystalline S-layer protein is secreted by an ABC transporter (type I) secretion apparatus. J Bacteriol 1998; 180:3062-9. [PMID: 9620954 PMCID: PMC107805 DOI: 10.1128/jb.180.12.3062-3069.1998] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Caulobacter crescentus is a gram-negative bacterium that produces a two-dimensional crystalline array on its surface composed of a single 98-kDa protein, RsaA. Secretion of RsaA to the cell surface relies on an uncleaved C-terminal secretion signal. In this report, we identify two genes encoding components of the RsaA secretion apparatus. These components are part of a type I secretion system involving an ABC transporter protein. These genes, lying immediately 3' of rsaA, were found by screening a Tn5 transposon library for the loss of RsaA transport and characterizing the transposon-interrupted genes. The two proteins presumably encoded by these genes were found to have significant sequence similarity to ABC transporter and membrane fusion proteins of other type I secretion systems. The greatest sequence similarity was found to the alkaline protease (AprA) transport system of Pseudomonas aeruginosa and the metalloprotease (PrtB) transport system of Erwinia chrysanthemi. The prtB and aprA genes were introduced into C. crescentus, and their products were secreted by the RsaA transport system. Further, defects in the S-layer protein transport system led to the loss of this heterologous secretion. This is the first report of an S-layer protein secreted by a type I secretion apparatus. Unlike other type I secretion systems, the RsaA transport system secretes large amounts of its substrate protein (it is estimated that RsaA accounts for 10 to 12% of the total cell protein). Such levels are expected for bacterial S-layer proteins but are higher than for any other known type I secretion system.
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Affiliation(s)
- P Awram
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
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38
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Kawai E, Akatsuka H, Idei A, Shibatani T, Omori K. Serratia marcescens S-layer protein is secreted extracellularly via an ATP-binding cassette exporter, the Lip system. Mol Microbiol 1998; 27:941-52. [PMID: 9535084 DOI: 10.1046/j.1365-2958.1998.00739.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Serratia marcescens Lip exporter belonging to the ATP-binding cassette (ABC) exporter is known to be involved in signal peptide-independent extracellular secretion of a lipase and a metalloprotease. Although the genes of secretory proteins and their ABC exporters are usually all reported to be linked in several gram-negative bacteria, neither the lipase nor the protease gene is located close to the Lip exporter genes, lipBCD. A gene (slaA) located upstream of the lipBCD genes was cloned, revealing that it encodes a polypeptide of 100 kDa and is partially similar to the Caulobacter crescentus paracrystalline cell surface layer (S-layer) protein. The Lip exporter-deficient mutants of S. marcescens failed to secrete the SlaA protein. Electron micrography demonstrated the cell surface layer of S. marcescens. The S-layer protein was secreted to the cultured media in Escherichia coli cells carrying the Lip exporter. Three ABC exporters, Prt, Has and Hly systems, could not allow the S-layer secretion, indicating that the S. marcescens S-layer protein is strictly recognized by the Lip system. This is the first report concerning secretion of an S-layer protein via its own secretion system.
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Affiliation(s)
- E Kawai
- Lead Generation Research Laboratory, Tanabe Seiyaku Co., Ltd, Osaka, Japan
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Nomellini JF, Kupcu S, Sleytr UB, Smit J. Factors controlling in vitro recrystallization of the Caulobacter crescentus paracrystalline S-layer. J Bacteriol 1997; 179:6349-54. [PMID: 9335282 PMCID: PMC179549 DOI: 10.1128/jb.179.20.6349-6354.1997] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The S-layer of Caulobacter is a two-dimensional paracrystalline array on the cell surface composed of a single protein, RsaA. We have established conditions for preparation of stable, soluble protein and then efficient in vitro recrystallization of the purified protein. Efficient recrystallization and long range order could not be obtained with pure protein only, though it was apparent that calcium was required for crystallization. Recrystallization was obtained when lipid vesicles were provided, but only when the vesicles contained the specific species of Caulobacter smooth lipopolysaccharide (SLPS) that previous studies implicated as a requirement for attaching the S-layer to the cell surface. The specific type of phospholipids did not appear critical; phospholipids rather different from those present in Caulobacter membranes or archaebacterial tetraether lipids worked equally well. The source of LPS was critical; rough and smooth variants of Salmonella typhimurium LPS as well as the rough form of Caulobacter LPS were ineffective. The requirement for calcium ions for recrystallization was further evaluated; strontium ions could substitute for calcium, and to a lesser extent, cobalt, barium, manganese and magnesium ions also stimulated crystallization. On the other hand, nickel and cadmium provided only weak crystallization stimulation, and zinc, copper, iron, aluminum ions, and the monovalent potassium, sodium, and lithium ions were ineffective. The recrystallization could also be reproduced with Langmuir-Blodgett lipid monolayers at an air-water interface. As with the vesicle experiments, this was only successful when SLPS was incorporated into the lipid mix. The best method for RsaA preparation, leading to apparently monomeric protein that was stable for many months, was an extraction with a low pH aqueous solution. We also achieved recrystallization, albeit at lower efficiency, using RsaA protein solubilized by 8 M urea, a method which allows retrieval of protein from inclusions, when expressed as heterologous protein in Escherichia coli or when retrieved as shed, precipitated protein from certain mutant caulobacters. In summary, the clarification of recrystallization methods has confirmed the requirement of SLPS as a surface attachment component and suggests that its presence in a membrane-like structure greatly stimulates the extent and quality of S-layer formation. The in vitro approach allowed the demonstration that specific ions are capable of participating in crystallization and now provides an assay for the crystallization potential of modified S-layer proteins, whether they were produced in or can be secreted by caulobacters.
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Affiliation(s)
- J F Nomellini
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
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40
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Beveridge TJ, Pouwels PH, Sára M, Kotiranta A, Lounatmaa K, Kari K, Kerosuo E, Haapasalo M, Egelseer EM, Schocher I, Sleytr UB, Morelli L, Callegari ML, Nomellini JF, Bingle WH, Smit J, Leibovitz E, Lemaire M, Miras I, Salamitou S, Béguin P, Ohayon H, Gounon P, Matuschek M, Koval SF. Functions of S-layers. FEMS Microbiol Rev 1997; 20:99-149. [PMID: 9276929 DOI: 10.1111/j.1574-6976.1997.tb00305.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Although S-layers are being increasingly identified on Bacteria and Archaea, it is enigmatic that in most cases S-layer function continues to elude us. In a few instances, S-layers have been shown to be virulence factors on pathogens (e.g. Campylobacter fetus ssp. fetus and Aeromonas salmonicida), protective against Bdellovibrio, a depository for surface-exposed enzymes (e.g. Bacillus stearothermophilus), shape-determining agents (e.g. Thermoproteus tenax) and nucleation factors for fine-grain mineral development (e.g. Synechococcus GL 24). Yet, for the vast majority of S-layered bacteria, the natural function of these crystalline arrays continues to be evasive. The following review up-dates the functional basis of S-layers and describes such diverse topics as the effect of S-layers on the Gram stain, bacteriophage adsorption in lactobacilli, phagocytosis by human polymorphonuclear leukocytes, the adhesion of a high-molecular-mass amylase, outer membrane porosity, and the secretion of extracellular enzymes of Thermoanaerobacterium. In addition, the functional aspect of calcium on the Caulobacter S-layer is explained.
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Affiliation(s)
- T J Beveridge
- Department of Microbiology, College of Biological Science, University of Guelph, Canada.
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Bingle WH, Nomellini JF, Smit J. Linker mutagenesis of the Caulobacter crescentus S-layer protein: toward a definition of an N-terminal anchoring region and a C-terminal secretion signal and the potential for heterologous protein secretion. J Bacteriol 1997; 179:601-11. [PMID: 9006010 PMCID: PMC178737 DOI: 10.1128/jb.179.3.601-611.1997] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Linker insertion mutagenesis was used to modify the paracrystalline surface layer (S-layer) protein (RsaA) of the gram-negative bacterium Caulobacter crescentus. Eleven unique BamHI linker insertions in the cloned rsaA gene were identified; at the protein level, these linker insertions introduced 4 to 6 amino acids at positions ranging from the extreme N terminus to the extreme C terminus of the 1,026-amino-acid RsaA protein. All linker-peptide insertions in the RsaA N terminus caused the secreted protein to be shed into the growth medium, suggesting that the RsaA N terminus is involved in cell surface anchoring. One linker-peptide insertion in the RsaA C terminus (amino acid 784) had no effect on S-layer biogenesis, while another (amino acid 907) disrupted secretion of the protein, suggesting that RsaA possesses a secretion signal lying C terminal to amino acid 784, near or including amino acid 907. Unlike extreme N- or C-terminal linker-peptide insertions, those more centrally located in the RsaA primary sequence had no apparent effect on S-layer biogenesis. By using a newly introduced linker-encoded restriction site, a 3' fragment of the rsaA gene encoding the last 242 C-terminal amino acids of the S-layer protein was expressed in C. crescentus from heterologous Escherichia coli lacZ transcription and translation initiation information. This C-terminal portion of RsaA was secreted into the growth medium, confirming the presence of a C-terminal secretion signal. The use of the RsaA C terminus for the secretion of heterologous proteins in C. crescentus was explored by fusing 109 amino acids of an envelope glycoprotein from infectious hematopoietic necrosis virus, a pathogen of salmonid fish, to the last 242 amino acids of the RsaA C terminus. The resulting hybrid protein was successfully secreted into the growth medium and accounted for 10% of total protein in a stationary-phase culture. Based on these results and features of the RsaA primary sequence, we propose that the C. crescentus S-layer protein is secreted by a type I secretion system, relying on a stable C-terminal secretion signal in a manner analogous to E. coli alpha-hemolysin, the first example of an S-layer protein secreted by such a pathway.
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Affiliation(s)
- W H Bingle
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, Canada
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Sára M, Sleytr UB. Crystalline bacterial cell surface layers (S-layers): from cell structure to biomimetics. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1996; 65:83-111. [PMID: 9029942 DOI: 10.1016/s0079-6107(96)00007-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- M Sára
- Center for Ultrastructure Research, Universität für Bodenkultur, Vienna, Austria
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Walker SG, Karunaratne DN, Ravenscroft N, Smit J. Characterization of mutants of Caulobacter crescentus defective in surface attachment of the paracrystalline surface layer. J Bacteriol 1994; 176:6312-23. [PMID: 7929003 PMCID: PMC196973 DOI: 10.1128/jb.176.20.6312-6323.1994] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Strains of Caulobacter crescentus express a paracrystalline surface layer (S-layer) consisting of the protein RsaA. Mutants of C. crescentus NA1000 and CB2, isolated for their ability to grow in the absence of calcium ions, uniformly no longer had the S-layer attached to the cell surface. However, RsaA was still produced, and when colonies grown on calcium-sufficient medium were examined, large two-dimensional arrays of S-layer were found intermixed with the cells. Such arrays were not found in calcium-deficient medium even when high levels of magnesium ions were provided. The arrays could be disrupted with divalent ion chelators and more readily with the calcium-selective ethylene glycol-bis (beta-aminoethyl ether)N,N,N',N'-tetraacetic acid (EGTA). Thus, the outer membrane surface was not needed as a template for self-assembly, but calcium likely was. The cell surface and S-layer gene of assembly-defective mutants of NA1000 were examined to determine the basis of the S-layer surface attachment defect. Mutants had no detectable alteration in the rough lipopolysaccharide (LPS) or a characterized capsular polysaccharide, but another polysaccharide molecule was greatly reduced or absent in all calcium-independent mutants. The molecule was shown to be a smooth LPS with a core sugar and fatty acid complement identical to those of the rough LPS and an O polysaccharide of homogeneous length, tentatively considered to be composed of 4,6-dideoxy-4-amino hexose, 3,6-dideoxy-3-amino hexose, and glycerol in equal proportions. This molecule (termed SLPS) was detectable by surface labeling with a specific antiserum only when the S-layer was not present. The rsaA genes from three calcium-independent mutants were cloned and expressed in an S-layer-negative, SLPS-positive strain. A normal S-layer was produced, ruling out defects in rsaA in these cases. It is proposed that SLPS is required for S-layer surface attachment, possibly via calcium bridging. The data support the possibility that calcium binding is required to prevent an otherwise lethal effect of SLPS. If true, mutations that eliminate the O polysaccharide of SLPS eliminate the lethal effects of calcium-deprived SLPS, at the expense of S-layer attachment.
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Affiliation(s)
- S G Walker
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
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