1
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Bu F, Dee DR, Liu B. Structural insight into Escherichia coli CsgA amyloid fibril assembly. mBio 2024; 15:e0041924. [PMID: 38501920 PMCID: PMC11005368 DOI: 10.1128/mbio.00419-24] [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: 02/09/2024] [Accepted: 03/04/2024] [Indexed: 03/20/2024] Open
Abstract
The discovery of functional amyloids in bacteria dates back several decades, and our understanding of the Escherichia coli curli biogenesis system has gradually expanded over time. However, due to its high aggregation propensity and intrinsically disordered nature, CsgA, the main structural component of curli fibrils, has eluded comprehensive structural characterization. Recent advancements in cryo-electron microscopy (cryo-EM) offer a promising tool to achieve high-resolution structural insights into E. coli CsgA fibrils. In this study, we outline an approach to addressing the colloidal instability challenges associated with CsgA, achieved through engineering and electrostatic repulsion. Then, we present the cryo-EM structure of CsgA fibrils at 3.62 Å resolution. This structure provides new insights into the cross-β structure of E. coli CsgA. Additionally, our study identifies two distinct spatial arrangements within several CsgA fibrils, a 2-CsgA-fibril pair and a 3-CsgA-fibril bundle, shedding light on the intricate hierarchy of the biofilm extracellular matrix and laying the foundation for precise manipulation of CsgA-derived biomaterials.IMPORTANCEThe visualization of the architecture of Escherichia coli CsgA amyloid fibril has been a longstanding research question, for which a high-resolution structure is still unavailable. CsgA serves as a major subunit of curli, the primary component of the extracellular matrix generated by bacteria. The support provided by this extracellular matrix enables bacterial biofilms to resist antibiotic treatment, significantly impacting human health. CsgA has been identified in members of Enterobacteriaceae, with pathogenic E. coli being the most well-known model system. Our novel insights into the structure of E. coli CsgA protofilaments form the basis for drug design targeting diseases associated with biofilms. Additionally, CsgA is widely researched in biomaterials due to its self-assembly characteristics. The resolved spatial arrangements of CsgA amyloids revealed in our study will further enhance the precision design of functional biomaterials. Therefore, our study uniquely contributes to the understanding of CsgA amyloids for both microbiology and material science.
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Affiliation(s)
- Fan Bu
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Derek R. Dee
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Bin Liu
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
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2
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Buchanan JA, Varghese NR, Johnston CL, Sunde M. Functional Amyloids: Where Supramolecular Amyloid Assembly Controls Biological Activity or Generates New Functionality. J Mol Biol 2023; 435:167919. [PMID: 37330295 DOI: 10.1016/j.jmb.2022.167919] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 06/19/2023]
Abstract
Functional amyloids are a rapidly expanding class of fibrillar protein structures, with a core cross-β scaffold, where novel and advantageous biological function is generated by the assembly of the amyloid. The growing number of amyloid structures determined at high resolution reveal how this supramolecular template both accommodates a wide variety of amino acid sequences and also imposes selectivity on the assembly process. The amyloid fibril can no longer be considered a generic aggregate, even when associated with disease and loss of function. In functional amyloids the polymeric β-sheet rich structure provides multiple different examples of unique control mechanisms and structures that are finely tuned to deliver assembly or disassembly in response to physiological or environmental cues. Here we review the range of mechanisms at play in natural, functional amyloids, where tight control of amyloidogenicity is achieved by environmental triggers of conformational change, proteolytic generation of amyloidogenic fragments, or heteromeric seeding and amyloid fibril stability. In the amyloid fibril form, activity can be regulated by pH, ligand binding and higher order protofilament or fibril architectures that impact the arrangement of associated domains and amyloid stability. The growing understanding of the molecular basis for the control of structure and functionality delivered by natural amyloids in nearly all life forms should inform the development of therapies for amyloid-associated diseases and guide the design of innovative biomaterials.
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Affiliation(s)
- Jessica A Buchanan
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Nikhil R Varghese
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Caitlin L Johnston
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Margaret Sunde
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
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3
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Hassan MN, Nabi F, Khan AN, Hussain M, Siddiqui WA, Uversky VN, Khan RH. The amyloid state of proteins: A boon or bane? Int J Biol Macromol 2022; 200:593-617. [PMID: 35074333 DOI: 10.1016/j.ijbiomac.2022.01.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 11/05/2022]
Abstract
Proteins and their aggregation is significant field of research due to their association with various conformational maladies including well-known neurodegenerative diseases like Alzheimer's (AD), Parkinson's (PD), and Huntington's (HD) diseases. Amyloids despite being given negative role for decades are also believed to play a functional role in bacteria to humans. In this review, we discuss both facets of amyloid. We have shed light on AD, which is one of the most common age-related neurodegenerative disease caused by accumulation of Aβ fibrils as extracellular senile plagues. We also discuss PD caused by the aggregation and deposition of α-synuclein in form of Lewy bodies and neurites. Other amyloid-associated diseases such as HD and amyotrophic lateral sclerosis (ALS) are also discussed. We have also reviewed functional amyloids that have various biological roles in both prokaryotes and eukaryotes that includes formation of biofilm and cell attachment in bacteria to hormone storage in humans, We discuss in detail the role of Curli fibrils' in biofilm formation, chaplins in cell attachment to peptide hormones, and Pre-Melansomal Protein (PMEL) roles. The disease-related and functional amyloids are compared with regard to their structural integrity, variation in regulation, and speed of forming aggregates and elucidate how amyloids have turned from foe to friend.
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Affiliation(s)
- Md Nadir Hassan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Faisal Nabi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Asra Nasir Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Murtaza Hussain
- Department of Biochemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Waseem A Siddiqui
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Vladimir N Uversky
- Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, 10 Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy 11 of Sciences", Pushchino, Moscow Region 142290, Russia; Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College 13 of Medicine, University of South Florida, Tampa, FL 33612, United States
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India.
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4
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Ke PC, Zhou R, Serpell LC, Riek R, Knowles TPJ, Lashuel HA, Gazit E, Hamley IW, Davis TP, Fändrich M, Otzen DE, Chapman MR, Dobson CM, Eisenberg DS, Mezzenga R. Half a century of amyloids: past, present and future. Chem Soc Rev 2020; 49:5473-5509. [PMID: 32632432 PMCID: PMC7445747 DOI: 10.1039/c9cs00199a] [Citation(s) in RCA: 304] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Amyloid diseases are global epidemics with profound health, social and economic implications and yet remain without a cure. This dire situation calls for research into the origin and pathological manifestations of amyloidosis to stimulate continued development of new therapeutics. In basic science and engineering, the cross-β architecture has been a constant thread underlying the structural characteristics of pathological and functional amyloids, and realizing that amyloid structures can be both pathological and functional in nature has fuelled innovations in artificial amyloids, whose use today ranges from water purification to 3D printing. At the conclusion of a half century since Eanes and Glenner's seminal study of amyloids in humans, this review commemorates the occasion by documenting the major milestones in amyloid research to date, from the perspectives of structural biology, biophysics, medicine, microbiology, engineering and nanotechnology. We also discuss new challenges and opportunities to drive this interdisciplinary field moving forward.
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Affiliation(s)
- Pu Chun Ke
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Zhongshan Hospital, Fudan University, 111 Yixueyuan Rd, Xuhui District, Shanghai, China
| | - Ruhong Zhou
- Institute of Quantitative Biology, Zhejiang University, Hangzhou 310058, China; Department of Chemistry, Columbia University, New York, New York, 10027, USA
| | - Louise C. Serpell
- School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK
| | - Roland Riek
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Wolfgang-Pauli-Str. 10, 8093 Zurich, Switzerland
| | - Tuomas P. J. Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Cavendish Laboratory, University of Cambridge, J J Thomson Avenue, CB3 0HE, Cambridge, UK
| | - Hilal A. Lashuel
- Laboratory of Molecular Neurobiology and Neuroproteomics, Brain Mind Institute, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences; Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Ian W. Hamley
- School of Chemistry, Food Biosciences and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Thomas P. Davis
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane Qld 4072, Australia
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
| | - Daniel Erik Otzen
- Department of Molecular Biology, Center for Insoluble Protein Structures (inSPIN), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Matthew R. Chapman
- Department of Molecular, Cellular and Developmental Biology, Centre for Microbial Research, University of Michigan, Ann Arbor, MI 48109-1048, USA
| | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - David S. Eisenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute and Howard Hughes Medical Institute, UCLA, Los Angeles, CA, USA
| | - Raffaele Mezzenga
- Department of Health Science & Technology, ETH Zurich, Schmelzbergstrasse 9, LFO, E23, 8092 Zurich, Switzerland
- Department of Materials, ETH Zurich, Wolfgang Pauli Strasse 10, 8093 Zurich, Switzerland
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5
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Cryo-EM structure of the nonameric CsgG-CsgF complex and its implications for controlling curli biogenesis in Enterobacteriaceae. PLoS Biol 2020; 18:e3000748. [PMID: 32559189 PMCID: PMC7304575 DOI: 10.1371/journal.pbio.3000748] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 05/20/2020] [Indexed: 01/21/2023] Open
Abstract
Curli play critical roles in biofilm formation, host cell adhesion, and colonization of inert surfaces in many Enterobacteriaceae. In Escherichia coli, curli biogenesis requires 7 curli-specific gene (csg) products—CsgA through G—working in concert. Of them, CsgG and CsgF are 2 outer membrane (OM)-localized components that consists of the core apparatus for secretion and assembly of curli structural subunits, CsgB and CsgA. Here, we report the cryogenic electron microscopy (cryo-EM) structure of CsgG in complex with CsgF from E. coli. The structure reveals that CsgF forms a stable complex with CsgG via a 1:1 stoichiometry by lining the upper lumen of the nonameric CsgG channel via its N-terminal 27 residues, forming a funnel-like entity plugged in the CsgG channel and creating a unique secretion channel with 2 constriction regions, consistent with the recently reported structure of the CsgG-CsgF complex. Functional studies indicate that export of CsgF to the cell surface requires the CsgG channel, and CsgF not only functions as an adaptor that bridges CsgB with CsgG but also may play important roles in controlling the rates of translocation and/or polymerization for curli structural subunits. Importantly, we found that a series of CsgF-derived peptides are able to efficiently inhibit curli production to E. coli when administrated exogenously, highlighting a potential strategy to interfere biofilm formation in E. coli strains. Curli are functional amyloids that play critical roles in biofilm formation and adhesion in many Enterobacteriaceae. Two outer membrane proteins, CsgG and CsgF, form the core apparatus for secretion and assembly of the curli structural subunits. The cryo-EM structure of the CsgG-CsgF complex reveals a unique amyloid secretion channel with two tandem constriction regions.
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6
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Sewell L, Stylianou F, Xu Y, Taylor J, Sefer L, Matthews S. NMR insights into the pre-amyloid ensemble and secretion targeting of the curli subunit CsgA. Sci Rep 2020; 10:7896. [PMID: 32398666 PMCID: PMC7217966 DOI: 10.1038/s41598-020-64135-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/08/2020] [Indexed: 01/08/2023] Open
Abstract
The biofilms of Enterobacteriaceae are fortified by assembly of curli amyloid fibres on the cell surface. Curli not only provides structural reinforcement, but also facilitates surface adhesion. To prevent toxic intracellular accumulation of amyloid precipitate, secretion of the major curli subunit, CsgA, is tightly regulated. In this work, we have employed solution state NMR spectroscopy to characterise the structural ensemble of the pre-fibrillar state of CsgA within the bacterial periplasm, and upon recruitment to the curli pore, CsgG, and the secretion chaperone, CsgE. We show that the N-terminal targeting sequence (N) of CsgA binds specifically to CsgG and that its subsequent sequestration induces a marked transition in the conformational ensemble, which is coupled to a preference for CsgE binding. These observations lead us to suggest a sequential model for binding and structural rearrangement of CsgA at the periplasmic face of the secretion machinery.
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Affiliation(s)
- Lee Sewell
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | | | - Yingqi Xu
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Jonathan Taylor
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Lea Sefer
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Steve Matthews
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
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7
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Yan Z, Yin M, Chen J, Li X. Assembly and substrate recognition of curli biogenesis system. Nat Commun 2020; 11:241. [PMID: 31932609 PMCID: PMC6957492 DOI: 10.1038/s41467-019-14145-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 11/29/2019] [Indexed: 01/22/2023] Open
Abstract
A major component of bacterial biofilms is curli amyloid fibrils secreted by the curli biogenesis system. Understanding the curli biogenesis mechanism is critical for developing therapeutic agents for biofilm-related infections. Here we report a systematic study of the curli biogenesis system, highlighted by structural, biochemical and functional analysis of the secretion channel complexes (CsgF-CsgG) with and without the curli substrate. The dual-pore architecture of the CsgF-CsgG complex was observed and used to develop an approach to inhibit the curli secretion by physically reducing the size of the CsgF pore. We further elucidated the assembly of the CsgFG complex with curli components (CsgA and CsgB) and curli-cell association through CsgF. Importantly, the recognition of the CsgA substrate by CsgG was uncovered. Nine crevices outside of the CsgG channel provide specific and highly-conserved recognition sites for CsgA N-terminus. Together with analysis of CsgE, our study provides comprehensive insights into curli biogenesis. A major component of bacterial biofilms is curli amyloid fibrils secreted by the curli biogenesis system. Here authors use cryo-EM to visualize the secretion channel complexes (CsgF-CsgG) with and without the curli substrate and provide insights into curli biogenesis.
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Affiliation(s)
- Zhaofeng Yan
- Key Laboratory of Protein Sciences (Tsinghua University), Ministry of Education, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
| | - Meng Yin
- Key Laboratory of Protein Sciences (Tsinghua University), Ministry of Education, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Jianan Chen
- Key Laboratory of Protein Sciences (Tsinghua University), Ministry of Education, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
| | - Xueming Li
- Key Laboratory of Protein Sciences (Tsinghua University), Ministry of Education, Beijing, China. .,School of Life Sciences, Tsinghua University, Beijing, China. .,Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China. .,Tsinghua-Peking Joint Center for Life Sciences, Beijing, China.
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8
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Structural Insights into Curli CsgA Cross-β Fibril Architecture Inspire Repurposing of Anti-amyloid Compounds as Anti-biofilm Agents. PLoS Pathog 2019; 15:e1007978. [PMID: 31469892 PMCID: PMC6748439 DOI: 10.1371/journal.ppat.1007978] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 09/17/2019] [Accepted: 07/11/2019] [Indexed: 12/14/2022] Open
Abstract
Curli amyloid fibrils secreted by Enterobacteriaceae mediate host cell adhesion and contribute to biofilm formation, thereby promoting bacterial resistance to environmental stressors. Here, we present crystal structures of amyloid-forming segments from the major curli subunit, CsgA, revealing steric zipper fibrils of tightly mated β-sheets, demonstrating a structural link between curli and human pathological amyloids. D-enantiomeric peptides, originally developed to interfere with Alzheimer's disease-associated amyloid-β, inhibited CsgA fibrillation and reduced biofilm formation in Salmonella typhimurium. Moreover, as previously shown, CsgA fibrils cross-seeded fibrillation of amyloid-β, providing support for the proposed structural resemblance and potential for cross-species amyloid interactions. The presented findings provide structural insights into amyloidogenic regions important for curli formation, suggest a novel strategy for disrupting amyloid-structured biofilms, and hypothesize on the formation of self-propagating prion-like species originating from a microbial source that could influence neurodegenerative diseases.
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9
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Abstract
In 1989, Normark and coworkers reported on fibrous surface structures called curli on strains of Escherichia coli that were suspected of causing bovine mastitis. Subsequent work by many groups has revealed an elegant and highly regulated curli biogenesis pathway also referred to as the type VIII secretion system. Curli biogenesis is governed by two divergently transcribed operons, csgBAC and csgDEFG. The csgBAC operon encodes the structural subunits of curli, CsgA and CsgB, along with a chaperone-like protein, CsgC. The csgDEFG operon encodes the accessory proteins required for efficient transcription, secretion, and assembly of the curli fiber. CsgA and CsgB are secreted as largely unstructured proteins and transition to β-rich structures that aggregate into regular fibers at the cell surface. Since both of these proteins have been shown to be amyloidogenic in nature, the correct spatiotemporal synthesis of the curli fiber is of paramount importance for proper functioning and viability. Gram-negative bacteria have evolved an elegant machinery for the safe handling, secretion, and extracellular assembly of these amyloidogenic proteins.
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10
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Bacterial functional amyloids: Order from disorder. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:954-960. [PMID: 31195143 DOI: 10.1016/j.bbapap.2019.05.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/24/2019] [Accepted: 05/30/2019] [Indexed: 12/15/2022]
Abstract
The discovery of intrinsic disorderness in proteins and peptide regions has given a new and useful insight into the working of biological systems. Due to enormous plasticity and heterogeneity, intrinsically disordered proteins or regions in proteins can perform myriad of functions. The flexibility in disordered proteins allows them to undergo conformation transition to form homopolymers of proteins called amyloids. Amyloids are highly structured protein aggregates associated with many neurodegenerative diseases. However, amyloids have gained much appreciation in recent years due to their functional roles. A functional amyloid fiber called curli is assembled on the bacterial cell surface as a part of the extracellular matrix during biofilm formation. The extracellular matrix that encases cells in a biofilm protects the cells and provides resistance against many environmental stresses. Several of the Csg (curli specific genes) proteins that are required for curli amyloid assembly are predicted to be intrinsically disordered. Therefore, curli amyloid formation is highly orchestrated so that these intrinsically disordered proteins do not inappropriately aggregate at the wrong time or place. The curli proteins are compartmentalized and there are chaperone-like proteins that prevent inappropriate aggregation and allow the controlled assembly of curli amyloids. Here we review the biogenesis of curli amyloids and the role that intrinsically disordered proteins play in the process.
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11
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Abstract
The biogenesis of periplasmic and outer membrane proteins (OMPs) in Escherichia coli is assisted by a variety of processes that help with their folding and transport to their final destination in the cellular envelope. Chaperones are macromolecules, usually proteins, that facilitate the folding of proteins or prevent their aggregation without becoming part of the protein's final structure. Because chaperones often bind to folding intermediates, they often (but not always) act to slow protein folding. Protein folding catalysts, on the other hand, act to accelerate specific steps in the protein folding pathway, including disulfide bond formation and peptidyl prolyl isomerization. This review is primarily concerned with E. coli and Salmonella periplasmic and cellular envelope chaperones; it also discusses periplasmic proline isomerization.
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12
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Abstract
To interact with the external environments, bacteria often display long proteinaceous appendages on their cell surface, called pili or fimbriae. These non-flagellar thread-like structures are polymers composed of covalently or non-covalently interacting repeated pilin subunits. Distinct pilus classes can be identified on basis of their assembly pathways, including chaperone-usher pili, type V pili, type IV pili, curli and fap fibers, conjugative and type IV secretion pili, as well as sortase-mediated pili. Pili play versatile roles in bacterial physiology, and can be involved in adhesion and host cell invasion, DNA and protein secretion and uptake, biofilm formation, cell motility and more. Recent advances in structure determination of components involved in the various pilus systems has enabled a better molecular understanding of their mechanisms of assembly and function. In this chapter we describe the diversity in structure, biogenesis and function of the different pilus systems found in Gram-positive and Gram-negative bacteria, and review their potential as anti-microbial targets.
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Affiliation(s)
- Magdalena Lukaszczyk
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050, Brussels, Belgium
| | - Brajabandhu Pradhan
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050, Brussels, Belgium
| | - Han Remaut
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050, Brussels, Belgium.
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13
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Structure-Function Analysis of the Curli Accessory Protein CsgE Defines Surfaces Essential for Coordinating Amyloid Fiber Formation. mBio 2018; 9:mBio.01349-18. [PMID: 30018113 PMCID: PMC6050966 DOI: 10.1128/mbio.01349-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Curli amyloid fibers are produced as part of the extracellular biofilm matrix and are composed primarily of the major structural subunit CsgA. The CsgE chaperone facilitates the secretion of CsgA through CsgG by forming a cap at the base of the nonameric CsgG outer membrane pore. We elucidated a series of finely tuned nonpolar and charge-charge interactions that facilitate the oligomerization of CsgE and its ability to transport unfolded CsgA to CsgG for translocation. CsgE oligomerization in vitro is temperature dependent and is disrupted by mutations in the W48 and F79 residues. Using nuclear magnetic resonance (NMR), we identified two regions of CsgE involved in the CsgE-CsgA interaction: a head comprising a positively charged patch centered around R47 and a stem comprising a negatively charged patch containing E31 and E85. Negatively charged residues in the intrinsically disordered N- and C-terminal "tails" were not implicated in this interaction. Head and stem residues were mutated and interrogated using in vivo measurements of curli production and in vitro amyloid polymerization assays. The R47 head residue of CsgE is required for stabilization of CsgA- and CsgE-mediated curli fiber formation. Mutation of the E31 and E85 stem residues to positively charged side chains decreased CsgE-mediated curli fiber formation but increased CsgE-mediated stabilization of CsgA. No single-amino-acid substitutions in the head, stem, or tail regions affected the ability of CsgE to cap the CsgG pore as determined by a bile salt sensitivity assay. These mechanistic insights into the directed assembly of functional amyloids in extracellular biofilms elucidate possible targets for biofilm-associated bacterial infections.IMPORTANCE Curli represent a class of functional amyloid fibers produced by Escherichia coli and other Gram-negative bacteria that serve as protein scaffolds in the extracellular biofilm matrix. Despite the lack of sequence conservation among different amyloidogenic proteins, the structural and biophysical properties of functional amyloids such as curli closely resemble those of amyloids associated with several common neurodegenerative diseases. These parallels are underscored by the observation that certain proteins and chemicals can prevent amyloid formation by the major curli subunit CsgA and by alpha-synuclein, the amyloid-forming protein found in Lewy bodies during Parkinson's disease. CsgA subunits are targeted to the CsgG outer membrane pore by CsgE prior to secretion and assembly into fibers. Here, we use biophysical, biochemical, and genetic approaches to elucidate a mechanistic understanding of CsgE function in curli biogenesis.
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14
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Malishev R, Abbasi R, Jelinek R, Chai L. Bacterial Model Membranes Reshape Fibrillation of a Functional Amyloid Protein. Biochemistry 2018; 57:5230-5238. [DOI: 10.1021/acs.biochem.8b00002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ravit Malishev
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Razan Abbasi
- Institute of Chemistry, The Hebrew University of Jerusalem and The Center for Nanoscience and Nanotechnology, Edmond J. Safra Campus, Jerusalem 91904, Israel
| | - Raz Jelinek
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Liraz Chai
- Institute of Chemistry, The Hebrew University of Jerusalem and The Center for Nanoscience and Nanotechnology, Edmond J. Safra Campus, Jerusalem 91904, Israel
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15
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Schubeis T, Spehr J, Viereck J, Köpping L, Nagaraj M, Ahmed M, Ritter C. Structural and functional characterization of the Curli adaptor protein CsgF. FEBS Lett 2018; 592:1020-1029. [DOI: 10.1002/1873-3468.13002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 12/12/2017] [Accepted: 02/03/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Tobias Schubeis
- Laboratory for Macromolecular Interactions; Helmholtz Centre for Infection Research; Braunschweig Germany
| | - Johannes Spehr
- Laboratory for Macromolecular Interactions; Helmholtz Centre for Infection Research; Braunschweig Germany
| | - Janika Viereck
- Laboratory for Macromolecular Interactions; Helmholtz Centre for Infection Research; Braunschweig Germany
| | - Laura Köpping
- Laboratory for Macromolecular Interactions; Helmholtz Centre for Infection Research; Braunschweig Germany
| | - Madhu Nagaraj
- Laboratory for Macromolecular Interactions; Helmholtz Centre for Infection Research; Braunschweig Germany
| | - Mumdooh Ahmed
- Laboratory for Macromolecular Interactions; Helmholtz Centre for Infection Research; Braunschweig Germany
| | - Christiane Ritter
- Laboratory for Macromolecular Interactions; Helmholtz Centre for Infection Research; Braunschweig Germany
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16
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The Production of Curli Amyloid Fibers Is Deeply Integrated into the Biology of Escherichia coli. Biomolecules 2017; 7:biom7040075. [PMID: 29088115 PMCID: PMC5745457 DOI: 10.3390/biom7040075] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 10/13/2017] [Accepted: 10/23/2017] [Indexed: 12/29/2022] Open
Abstract
Curli amyloid fibers are the major protein component of the extracellular matrix produced by Enterobacteriaceae during biofilm formation. Curli are required for proper biofilm development and environmental persistence by Escherichia coli. Here, we present a complete and vetted genetic analysis of functional amyloid fiber biogenesis. The Keio collection of single gene deletions was screened on Congo red indicator plates to identify E. coli mutants that had defective amyloid production. We discovered that more than three hundred gene products modulated curli production. These genes were involved in fundamental cellular processes such as regulation, environmental sensing, respiration, metabolism, cell envelope biogenesis, transport, and protein turnover. The alternative sigma factors, σS and σE, had opposing roles in curli production. Mutations that induced the σE or Cpx stress response systems had reduced curli production, while mutant strains with increased σS levels had increased curli production. Mutations in metabolic pathways, including gluconeogenesis and the biosynthesis of lipopolysaccharide (LPS), produced less curli. Regulation of the master biofilm regulator, CsgD, was diverse, and the screen revealed several proteins and small RNAs (sRNA) that regulate csgD messenger RNA (mRNA) levels. Using previously published studies, we found minimal overlap between the genes affecting curli biogenesis and genes known to impact swimming or swarming motility, underlying the distinction between motile and sessile lifestyles. Collectively, the diversity and number of elements required suggest curli production is part of a highly regulated and complex developmental pathway in E. coli.
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17
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Rouse SL, Hawthorne WJ, Berry JL, Chorev DS, Ionescu SA, Lambert S, Stylianou F, Ewert W, Mackie U, Morgan RML, Otzen D, Herbst FA, Nielsen PH, Dueholm M, Bayley H, Robinson CV, Hare S, Matthews S. A new class of hybrid secretion system is employed in Pseudomonas amyloid biogenesis. Nat Commun 2017; 8:263. [PMID: 28811582 PMCID: PMC5557850 DOI: 10.1038/s41467-017-00361-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 06/23/2017] [Indexed: 11/25/2022] Open
Abstract
Gram-negative bacteria possess specialised biogenesis machineries that facilitate the export of amyloid subunits for construction of a biofilm matrix. The secretion of bacterial functional amyloid requires a bespoke outer-membrane protein channel through which unfolded amyloid substrates are translocated. Here, we combine X-ray crystallography, native mass spectrometry, single-channel electrical recording, molecular simulations and circular dichroism measurements to provide high-resolution structural insight into the functional amyloid transporter from Pseudomonas, FapF. FapF forms a trimer of gated β-barrel channels in which opening is regulated by a helical plug connected to an extended coil-coiled platform spanning the bacterial periplasm. Although FapF represents a unique type of secretion system, it shares mechanistic features with a diverse range of peptide translocation systems. Our findings highlight alternative strategies for handling and export of amyloid protein sequences. Gram-negative bacteria assemble biofilms from amyloid fibres, which translocate across the outer membrane as unfolded amyloid precursors through a secretion system. Here, the authors characterise the structural details of the amyloid transporter FapF in Pseudomonas.
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Affiliation(s)
- Sarah L Rouse
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - William J Hawthorne
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Jamie-Lee Berry
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Dror S Chorev
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Sandra A Ionescu
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Sebastian Lambert
- Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Fisentzos Stylianou
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Wiebke Ewert
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Uma Mackie
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK.,Walthamstow School for Girls, London, E17 9RZ, UK
| | - R Marc L Morgan
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Daniel Otzen
- Interdisciplinary Nanoscience Center (iNANO), Centre for Insoluble Protein Structures (inSPIN), Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Florian-Alexander Herbst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per H Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Hagan Bayley
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Carol V Robinson
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Stephen Hare
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Stephen Matthews
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK.
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18
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Structural insights into functional amyloid inhibition in Gram -ve bacteria. Biochem Soc Trans 2017; 44:1643-1649. [PMID: 27913673 PMCID: PMC5135000 DOI: 10.1042/bst20160245] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/20/2016] [Accepted: 09/22/2016] [Indexed: 11/17/2022]
Abstract
Amyloids are proteinaceous aggregates known for their role in debilitating degenerative diseases involving protein dysfunction. Many forms of functional amyloid are also produced in nature and often these systems require careful control of their assembly to avoid the potentially toxic effects. The best-characterised functional amyloid system is the bacterial curli system. Three natural inhibitors of bacterial curli amyloid have been identified and recently characterised structurally. Here, we compare common structural features of CsgC, CsgE and CsgH and discuss the potential implications for general inhibition of amyloid.
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19
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Abstract
Curli are functional amyloids produced by proteobacteria like Escherichia coli as part of the extracellular matrix that holds cells together into biofilms. The molecular events that occur during curli nucleation and fiber extension remain largely unknown. Combining observations from curli amyloidogenesis in bulk solutions with real-time in situ nanoscopic imaging at the single-fiber level, we show that curli display polar growth, and we detect two kinetic regimes of fiber elongation. Single fibers exhibit stop-and-go dynamics characterized by bursts of steady-state growth alternated with periods of stagnation. At high subunit concentrations, fibers show constant, unperturbed burst growth. Curli follow a one-step nucleation process in which monomers contemporaneously fold and oligomerize into minimal fiber units that have growth characteristics identical to those of the mature fibrils. Kinetic data and interaction studies of curli fibrillation in the presence of the natural inhibitor CsgC show that the inhibitor binds curli fibers and predominantly acts at the level of fiber elongation.
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20
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Rouse SL, Hawthorne WJ, Lambert S, Morgan ML, Hare SA, Matthews S. Purification, crystallization and characterization of the Pseudomonas outer membrane protein FapF, a functional amyloid transporter. Acta Crystallogr F Struct Biol Commun 2016; 72:892-896. [PMID: 27917837 PMCID: PMC5137466 DOI: 10.1107/s2053230x16017921] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/08/2016] [Indexed: 11/12/2023] Open
Abstract
Bacteria often produce extracellular amyloid fibres via a multi-component secretion system. Aggregation-prone, unstructured subunits cross the periplasm and are secreted through the outer membrane, after which they self-assemble. Here, significant progress is presented towards solving the high-resolution crystal structure of the novel amyloid transporter FapF from Pseudomonas, which facilitates the secretion of the amyloid-forming polypeptide FapC across the bacterial outer membrane. This represents the first step towards obtaining structural insight into the products of the Pseudomonas fap operon. Initial attempts at crystallizing full-length and N-terminally truncated constructs by refolding techniques were not successful; however, after preparing FapF106-430 from the membrane fraction, reproducible crystals were obtained using the sitting-drop method of vapour diffusion. Diffraction data have been processed to 2.5 Å resolution. These crystals belonged to the monoclinic space group C121, with unit-cell parameters a = 143.4, b = 124.6, c = 80.4 Å, α = γ = 90, β = 96.32° and three monomers in the asymmetric unit. It was found that the switch to complete detergent exchange into C8E4 was crucial for forming well diffracting crystals, and it is suggested that this combined with limited proteolysis is a potentially useful protocol for membrane β-barrel protein crystallography. The three-dimensional structure of FapF will provide invaluable information on the mechanistic differences of biogenesis between the curli and Fap functional amyloid systems.
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Affiliation(s)
- Sarah L. Rouse
- Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, England
| | - Wlliam J. Hawthorne
- Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, England
| | - Sebastian Lambert
- Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Marc L. Morgan
- Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, England
| | - Stephen A. Hare
- Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, England
| | - Stephen Matthews
- Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, England
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