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Sano K, Kobayashi H, Chuta H, Matsuyoshi N, Kato Y, Ogasawara H. CsgI (YccT) Is a Novel Inhibitor of Curli Fimbriae Formation in Escherichia coli Preventing CsgA Polymerization and Curli Gene Expression. Int J Mol Sci 2023; 24:ijms24054357. [PMID: 36901788 PMCID: PMC10002515 DOI: 10.3390/ijms24054357] [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: 12/31/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Curli fimbriae are amyloids-found in bacteria (Escherichia coli)-that are involved in solid-surface adhesion and bacterial aggregation during biofilm formation. The curli protein CsgA is coded by a csgBAC operon gene, and the transcription factor CsgD is essential to induce its curli protein expression. However, the complete mechanism underlying curli fimbriae formation requires elucidation. Herein, we noted that curli fimbriae formation was inhibited by yccT-i.e., a gene that encodes a periplasmic protein of unknown function regulated by CsgD. Furthermore, curli fimbriae formation was strongly repressed by CsgD overexpression caused by a multicopy plasmid in BW25113-the non-cellulose-producing strain. YccT deficiency prevented these CsgD effects. YccT overexpression led to intracellular YccT accumulation and reduced CsgA expression. These effects were addressed by deleting the N-terminal signal peptide of YccT. Localization, gene expression, and phenotypic analyses revealed that YccT-dependent inhibition of curli fimbriae formation and curli protein expression was mediated by the two-component regulatory system EnvZ/OmpR. Purified YccT inhibited CsgA polymerization; however, no intracytoplasmic interaction between YccT and CsgA was detected. Thus, YccT-renamed CsgI (curli synthesis inhibitor)-is a novel inhibitor of curli fimbriae formation and has a dual role as an OmpR phosphorylation modulator and CsgA polymerization inhibitor.
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Affiliation(s)
- Kotaro Sano
- Research Center for Advanced Science and Technology, Division of Gene Research, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
- Department of Applied Biology, Graduated School of Science and Technology, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
| | - Hiroaki Kobayashi
- Research Center for Advanced Science and Technology, Division of Gene Research, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
- Department of Applied Biology, Graduated School of Science and Technology, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
| | - Hirotaka Chuta
- Research Center for Advanced Science and Technology, Division of Gene Research, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
- Department of Applied Biology, Graduated School of Science and Technology, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
| | - Nozomi Matsuyoshi
- Research Center for Advanced Science and Technology, Division of Gene Research, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
- Department of Applied Biology, Graduated School of Science and Technology, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
| | - Yuki Kato
- Research Center for Advanced Science and Technology, Division of Gene Research, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
- Department of Applied Biology, Graduated School of Science and Technology, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
| | - Hiroshi Ogasawara
- Research Center for Advanced Science and Technology, Division of Gene Research, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
- Academic Assembly School of Humanities and Social Sciences Institute of Humanities, Shinshu University, Matsumoto 390-8621, Japan
- Institute for Fiber Engineering (IFES), Interdisciplinary Cluster for Cutting Edge Research (ICCER), Shinshu University, Tokida 3-15-1, Ueda, Nagano 386-8567, Japan
- Renaissance Center for Applied Microbiology, Shinshu University, Nagano-shi, Nagano 380-8553, Japan
- Correspondence: ; Tel.: +81-268-21-5803
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2
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Zhao D, Peng Z, Fang J, Fang Z, Zhang J. Programmable and low-cost biohybrid membrane for efficient heavy metal removal from water. Sep Purif Technol 2023. [DOI: 10.1016/j.seppur.2022.122751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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3
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Arhar T, Shkedi A, Nadel CM, Gestwicki JE. The interactions of molecular chaperones with client proteins: why are they so weak? J Biol Chem 2021; 297:101282. [PMID: 34624315 PMCID: PMC8567204 DOI: 10.1016/j.jbc.2021.101282] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 12/30/2022] Open
Abstract
The major classes of molecular chaperones have highly variable sequences, sizes, and shapes, yet they all bind to unfolded proteins, limit their aggregation, and assist in their folding. Despite the central importance of this process to protein homeostasis, it has not been clear exactly how chaperones guide this process or whether the diverse families of chaperones use similar mechanisms. For the first time, recent advances in NMR spectroscopy have enabled detailed studies of how unfolded, "client" proteins interact with both ATP-dependent and ATP-independent classes of chaperones. Here, we review examples from four distinct chaperones, Spy, Trigger Factor, DnaK, and HscA-HscB, highlighting the similarities and differences between their mechanisms. One striking similarity is that the chaperones all bind weakly to their clients, such that the chaperone-client interactions are readily outcompeted by stronger, intra- and intermolecular contacts in the folded state. Thus, the relatively weak affinity of these interactions seems to provide directionality to the folding process. However, there are also key differences, especially in the details of how the chaperones release clients and how ATP cycling impacts that process. For example, Spy releases clients in a largely folded state, while clients seem to be unfolded upon release from Trigger Factor or DnaK. Together, these studies are beginning to uncover the similarities and differences in how chaperones use weak interactions to guide protein folding.
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Affiliation(s)
- Taylor Arhar
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA
| | - Arielle Shkedi
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA
| | - Cory M Nadel
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA.
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4
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Mayer MP. The Hsp70-Chaperone Machines in Bacteria. Front Mol Biosci 2021; 8:694012. [PMID: 34164436 PMCID: PMC8215388 DOI: 10.3389/fmolb.2021.694012] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/20/2021] [Indexed: 12/02/2022] Open
Abstract
The ATP-dependent Hsp70s are evolutionary conserved molecular chaperones that constitute central hubs of the cellular protein quality surveillance network. None of the other main chaperone families (Tig, GroELS, HtpG, IbpA/B, ClpB) have been assigned with a comparable range of functions. Through a multitude of functions Hsp70s are involved in many cellular control circuits for maintaining protein homeostasis and have been recognized as key factors for cell survival. Three mechanistic properties of Hsp70s are the basis for their high versatility. First, Hsp70s bind to short degenerate sequence motifs within their client proteins. Second, Hsp70 chaperones switch in a nucleotide-controlled manner between a state of low affinity for client proteins and a state of high affinity for clients. Third, Hsp70s are targeted to their clients by a large number of cochaperones of the J-domain protein (JDP) family and the lifetime of the Hsp70-client complex is regulated by nucleotide exchange factors (NEF). In this review I will discuss advances in the understanding of the molecular mechanism of the Hsp70 chaperone machinery focusing mostly on the bacterial Hsp70 DnaK and will compare the two other prokaryotic Hsp70s HscA and HscC with DnaK.
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Affiliation(s)
- Matthias P Mayer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, Heidelberg, Germany
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5
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Bhatwa A, Wang W, Hassan YI, Abraham N, Li XZ, Zhou T. Challenges Associated With the Formation of Recombinant Protein Inclusion Bodies in Escherichia coli and Strategies to Address Them for Industrial Applications. Front Bioeng Biotechnol 2021; 9:630551. [PMID: 33644021 PMCID: PMC7902521 DOI: 10.3389/fbioe.2021.630551] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
Recombinant proteins are becoming increasingly important for industrial applications, where Escherichia coli is the most widely used bacterial host for their production. However, the formation of inclusion bodies is a frequently encountered challenge for producing soluble and functional recombinant proteins. To overcome this hurdle, different strategies have been developed through adjusting growth conditions, engineering host strains of E. coli, altering expression vectors, and modifying the proteins of interest. These approaches will be comprehensively highlighted with some of the new developments in this review. Additionally, the unique features of protein inclusion bodies, the mechanism and influencing factors of their formation, and their potential advantages will also be discussed.
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Affiliation(s)
- Arshpreet Bhatwa
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Weijun Wang
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
| | - Yousef I. Hassan
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
| | - Nadine Abraham
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Xiu-Zhen Li
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
| | - Ting Zhou
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
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6
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Milardi D, Gazit E, Radford SE, Xu Y, Gallardo RU, Caflisch A, Westermark GT, Westermark P, Rosa CL, Ramamoorthy A. Proteostasis of Islet Amyloid Polypeptide: A Molecular Perspective of Risk Factors and Protective Strategies for Type II Diabetes. Chem Rev 2021; 121:1845-1893. [PMID: 33427465 PMCID: PMC10317076 DOI: 10.1021/acs.chemrev.0c00981] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The possible link between hIAPP accumulation and β-cell death in diabetic patients has inspired numerous studies focusing on amyloid structures and aggregation pathways of this hormone. Recent studies have reported on the importance of early oligomeric intermediates, the many roles of their interactions with lipid membrane, pH, insulin, and zinc on the mechanism of aggregation of hIAPP. The challenges posed by the transient nature of amyloid oligomers, their structural heterogeneity, and the complex nature of their interaction with lipid membranes have resulted in the development of a wide range of biophysical and chemical approaches to characterize the aggregation process. While the cellular processes and factors activating hIAPP-mediated cytotoxicity are still not clear, it has recently been suggested that its impaired turnover and cellular processing by proteasome and autophagy may contribute significantly toward toxic hIAPP accumulation and, eventually, β-cell death. Therefore, studies focusing on the restoration of hIAPP proteostasis may represent a promising arena for the design of effective therapies. In this review we discuss the current knowledge of the structures and pathology associated with hIAPP self-assembly and point out the opportunities for therapy that a detailed biochemical, biophysical, and cellular understanding of its aggregation may unveil.
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Affiliation(s)
- Danilo Milardi
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via P. Gaifami 18, 95126 Catania, Italy
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Yong Xu
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Rodrigo U Gallardo
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Zürich CH-8057, Switzerland
| | - Gunilla T Westermark
- Department of Medical Cell Biology, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Per Westermark
- Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Carmelo La Rosa
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Ayyalusamy Ramamoorthy
- Biophysics, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 41809-1055, United States
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7
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Hierarchical Model for the Role of J-Domain Proteins in Distinct Cellular Functions. J Mol Biol 2020; 433:166750. [PMID: 33310019 DOI: 10.1016/j.jmb.2020.166750] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 12/04/2020] [Accepted: 12/04/2020] [Indexed: 01/28/2023]
Abstract
In Escherichia coli, the major bacterial Hsp70 system consists of DnaK, three J-domain proteins (JDPs: DnaJ, CbpA, and DjlA), and nucleotide exchange factor GrpE. JDPs determine substrate specificity for the Hsp70 system; however, knowledge on their specific role in bacterial cellular functions is limited. In this study, we demonstrated the role of JDPs in bacterial survival during heat stress and the DnaK-regulated formation of curli-extracellular amyloid fibers involved in biofilm formation. Genetic analysis demonstrate that only DnaJ is essential for survival at high temperature. On the other hand, either DnaJ or CbpA, but not DjlA, is sufficient to activate DnaK in curli production. Additionally, several DnaK mutants with reduced activity are able to complement the loss of curli production in E. coli ΔdnaK, whereas they do not recover the growth defect of the mutant strain at high temperature. Biochemical analyses reveal that DnaJ and CbpA are involved in the expression of the master regulator CsgD through the solubilization of MlrA, a DNA-binding transcriptional activator for the csgD promoter. Furthermore, DnaJ and CbpA also keep CsgA in a translocation-competent state by preventing its aggregation in the cytoplasm. Our findings support a hierarchical model wherein the role of JDPs in the Hsp70 system differs according to individual cellular functions.
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8
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Ruan A, Ren C, Quan S. Conversion of the molecular chaperone Spy into a novel fusion tag to enhance recombinant protein expression. J Biotechnol 2020; 307:131-138. [DOI: 10.1016/j.jbiotec.2019.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 11/05/2019] [Accepted: 11/05/2019] [Indexed: 10/25/2022]
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9
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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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10
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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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11
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Amyloid by Design: Intrinsic Regulation of Microbial Amyloid Assembly. J Mol Biol 2018; 430:3631-3641. [PMID: 30017921 DOI: 10.1016/j.jmb.2018.07.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/01/2018] [Accepted: 07/09/2018] [Indexed: 12/14/2022]
Abstract
The term amyloid has historically been used to describe fibrillar aggregates formed as the result of protein misfolding and that are associated with a range of diseases broadly termed amyloidoses. The discovery of "functional amyloids" expanded the amyloid umbrella to encompass aggregates structurally similar to disease-associated amyloids but that engage in a variety of biologically useful tasks without incurring toxicity. The mechanisms by which functional amyloid systems ensure nontoxic assembly has provided insights into potential therapeutic strategies for treating amyloidoses. Some of the most-studied functional amyloids are ones produced by bacteria. Curli amyloids are extracellular fibers made by enteric bacteria that function to encase and protect bacterial communities during biofilm formation. Here we review recent studies highlighting microbial functional amyloid assembly systems that are tailored to enable the assembly of non-toxic amyloid aggregates.
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12
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Sugimoto S, Arita-Morioka KI, Terao A, Yamanaka K, Ogura T, Mizunoe Y. Multitasking of Hsp70 chaperone in the biogenesis of bacterial functional amyloids. Commun Biol 2018; 1:52. [PMID: 30271935 PMCID: PMC6123696 DOI: 10.1038/s42003-018-0056-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 04/19/2018] [Indexed: 11/21/2022] Open
Abstract
Biofilms are intricate communities of microorganisms embedded in a self-produced matrix of extracellular polymer, which provides microbes survival advantages in stressful environments and can cause chronic infections in humans. Curli are functional amyloids that assemble on the extracellular surface of enteric bacteria such as Escherichia coli during biofilm development and colonization. The molecular chaperone DnaK, a bacterial Hsp70 homologue, promotes curli biogenesis via unknown mechanism(s). Here we show that DnaK increases the expression of CsgA and CsgB—the major and minor structural components of curli, respectively—via a quantity and quality control of RpoS, a stationary phase-specific alternative sigma factor regulating bacterial transcription, and CsgD, the master transcriptional regulator of curli formation. DnaK also keeps CsgA and CsgB in a translocation-competent state by binding to their signal peptides prone to aggregation. Our findings suggest that DnaK controls the homoeostasis of curli biogenesis at multiple stages to organize the biofilm matrix. Shinya Sugimoto et al. demonstrate how molecular chaperone DnaK regulates biofilm formation through the production of curli, which anchor enteric bacteria to the biofilm. This finding provides mechanistic insights into the development of anti-biofilm agents as antibiotics.
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Affiliation(s)
- Shinya Sugimoto
- Department of Bacteriology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan. .,Jikei Center for Biofilm Science and Technology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan.
| | - Ken-Ichi Arita-Morioka
- Department of Molecular Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-Ku, Kumamoto, 860-0811, Japan.,Advanced Science Research Center, Fukuoka Dental College, 2-15-1 Tamura, Sawara-Ku, Fukuoka, 814-0193, Japan
| | - Akari Terao
- Department of Bacteriology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan
| | - Kunitoshi Yamanaka
- Department of Molecular Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-Ku, Kumamoto, 860-0811, Japan
| | - Teru Ogura
- Department of Molecular Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-Ku, Kumamoto, 860-0811, Japan
| | - Yoshimitsu Mizunoe
- Department of Bacteriology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan.,Jikei Center for Biofilm Science and Technology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan
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13
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Abstract
Many bacteria can assemble functional amyloid fibers on their cell surface. Most bacterial amyloids contribute to biofilm or other community behaviors where cells interact with a surface or with other cells. Bacterial amyloids, like all functional amyloids, share structural and biochemical properties with disease-associated eukaryotic amyloids. The general ability of amyloids to bind specific dyes, like Congo red and Thioflavin T, and their resistance to denaturation have provided useful tools for scoring and quantifying bacterial amyloid formation. Here, we present basic approaches to study bacterial amyloids by focusing on the well-studied curli amyloid fibers expressed by Enterobacteriaceae. These methods exploit the specific tinctorial and biophysical properties of amyloids. The methods described here are straightforward and can be easily applied by any modern molecular biology lab for the study of other bacterial amyloids.
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Affiliation(s)
- Margery L Evans
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Elizabeth Gichana
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Yizhou Zhou
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Matthew R Chapman
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
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14
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Koldewey P, Horowitz S, Bardwell JCA. Chaperone-client interactions: Non-specificity engenders multifunctionality. J Biol Chem 2017; 292:12010-12017. [PMID: 28620048 DOI: 10.1074/jbc.r117.796862] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Here, we provide an overview of the different mechanisms whereby three different chaperones, Spy, Hsp70, and Hsp60, interact with folding proteins, and we discuss how these chaperones may guide the folding process. Available evidence suggests that even a single chaperone can use many mechanisms to aid in protein folding, most likely due to the need for most chaperones to bind clients promiscuously. Chaperone mechanism may be better understood by always considering it in the context of the client's folding pathway and biological function.
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Affiliation(s)
- Philipp Koldewey
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Scott Horowitz
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - James C A Bardwell
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan 48109.
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15
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Lee YS, Lee J, Ryu KS, Lee Y, Jung TG, Jang JH, Sim DW, Kim EH, Seo MD, Lee KW, Won HS. Semi-Empirical Structure Determination of Escherichia coli Hsp33 and Identification of Dynamic Regulatory Elements for the Activation Process. J Mol Biol 2015; 427:3850-61. [DOI: 10.1016/j.jmb.2015.09.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 09/21/2015] [Accepted: 09/30/2015] [Indexed: 11/27/2022]
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16
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Taylor JD, Matthews SJ. New insight into the molecular control of bacterial functional amyloids. Front Cell Infect Microbiol 2015; 5:33. [PMID: 25905048 PMCID: PMC4389571 DOI: 10.3389/fcimb.2015.00033] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 03/19/2015] [Indexed: 11/16/2022] Open
Abstract
Amyloid protein structure has been discovered in a variety of functional or pathogenic contexts. What distinguishes the former from the latter is that functional amyloid systems possess dedicated molecular control systems that determine the timing, location, and structure of the fibers. Failure to guide this process can result in cytotoxicity, as observed in several pathologies like Alzheimer's and Parkinson's Disease. Many gram-negative bacteria produce an extracellular amyloid fiber known as curli via a multi-component secretion system. During this process, aggregation-prone, semi-folded curli subunits have to cross the periplasm and outer-membrane and self-assemble into surface-attached fibers. Two recent breakthroughs have provided molecular details regarding periplasmic chaperoning and subunit secretion. This review offers a combined perspective on these first mechanistic insights into the curli system.
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Affiliation(s)
- Jonathan D Taylor
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College of Science, Technology and Medicine London, UK
| | - Steve J Matthews
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College of Science, Technology and Medicine London, UK
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17
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Evans ML, Chorell E, Taylor JD, Åden J, Götheson A, Li F, Koch M, Sefer L, Matthews SJ, Wittung-Stafshede P, Almqvist F, Chapman MR. The bacterial curli system possesses a potent and selective inhibitor of amyloid formation. Mol Cell 2015; 57:445-55. [PMID: 25620560 PMCID: PMC4320674 DOI: 10.1016/j.molcel.2014.12.025] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 10/28/2014] [Accepted: 12/16/2014] [Indexed: 12/22/2022]
Abstract
Curli are extracellular functional amyloids that are assembled by enteric bacteria during biofilm formation and host colonization. An efficient secretion system and chaperone network ensures that the major curli fiber subunit, CsgA, does not form intracellular amyloid aggregates. We discovered that the periplasmic protein CsgC was a highly effective inhibitor of CsgA amyloid formation. In the absence of CsgC, CsgA formed toxic intracellular aggregates. In vitro, CsgC inhibited CsgA amyloid formation at substoichiometric concentrations and maintained CsgA in a non-β-sheet-rich conformation. Interestingly, CsgC inhibited amyloid assembly of human α-synuclein, but not Aβ42, in vitro. We identified a common D-Q-Φ-X0,1-G-K-N-ζ-E motif in CsgC client proteins that is not found in Aβ42. CsgC is therefore both an efficient and selective amyloid inhibitor. Dedicated functional amyloid inhibitors may be a key feature that distinguishes functional amyloids from disease-associated amyloids.
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Affiliation(s)
- Margery L Evans
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA
| | - Erik Chorell
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Jonathan D Taylor
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - Jörgen Åden
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Anna Götheson
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Fei Li
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA
| | - Marion Koch
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - Lea Sefer
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - Steve J Matthews
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | | | - Fredrik Almqvist
- Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden; Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Matthew R Chapman
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA; Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden.
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18
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Syed AK, Boles BR. Fold modulating function: bacterial toxins to functional amyloids. Front Microbiol 2014; 5:401. [PMID: 25136340 PMCID: PMC4118032 DOI: 10.3389/fmicb.2014.00401] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 07/16/2014] [Indexed: 12/11/2022] Open
Abstract
Many bacteria produce cytolytic toxins that target host cells or other competing microbes. It is well known that environmental factors control toxin expression, however, recent work suggests that some bacteria manipulate the fold of these protein toxins to control their function. The β-sheet rich amyloid fold is a highly stable ordered aggregate that many toxins form in response to specific environmental conditions. When in the amyloid state, toxins become inert, losing the cytolytic activity they display in the soluble form. Emerging evidence suggest that some amyloids function as toxin storage systems until they are again needed, while other bacteria utilize amyloids as a structural matrix component of biofilms. This amyloid matrix component facilitates resistance to biofilm disruptive challenges. The bacterial amyloids discussed in this review reveal an elegant system where changes in protein fold and solubility dictate the function of proteins in response to the environment.
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Affiliation(s)
- Adnan K Syed
- Department of Molecular Cellular and Developmental Biology, University of Michigan Ann Arbor, MI, USA
| | - Blaise R Boles
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa Iowa City, IA, USA
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19
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Evans ML, Chapman MR. Curli biogenesis: order out of disorder. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1843:1551-8. [PMID: 24080089 PMCID: PMC4243835 DOI: 10.1016/j.bbamcr.2013.09.010] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 09/18/2013] [Accepted: 09/19/2013] [Indexed: 10/26/2022]
Abstract
Many bacteria assemble extracellular amyloid fibers on their cell surface. Secretion of proteins across membranes and the assembly of complex macromolecular structures must be highly coordinated to avoid the accumulation of potentially toxic intracellular protein aggregates. Extracellular amyloid fiber assembly poses an even greater threat to cellular health due to the highly aggregative nature of amyloids and the inherent toxicity of amyloid assembly intermediates. Therefore, temporal and spatial control of amyloid protein secretion is paramount. The biogenesis and assembly of the extracellular bacterial amyloid curli is an ideal system for studying how bacteria cope with the many challenges of controlled and ordered amyloid assembly. Here, we review the recent progress in the curli field that has made curli biogenesis one of the best-understood functional amyloid assembly pathways. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Margery L Evans
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 North University, Ann Arbor, MI 48109, USA
| | - Matthew R Chapman
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 North University, Ann Arbor, MI 48109, USA.
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20
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Niforou K, Cheimonidou C, Trougakos IP. Molecular chaperones and proteostasis regulation during redox imbalance. Redox Biol 2014; 2:323-32. [PMID: 24563850 PMCID: PMC3926111 DOI: 10.1016/j.redox.2014.01.017] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 01/11/2014] [Accepted: 01/18/2014] [Indexed: 02/05/2023] Open
Abstract
Free radicals originate from both exogenous environmental sources and as by-products of the respiratory chain and cellular oxygen metabolism. Sustained accumulation of free radicals, beyond a physiological level, induces oxidative stress that is harmful for the cellular homeodynamics as it promotes the oxidative damage and stochastic modification of all cellular biomolecules including proteins. In relation to proteome stability and maintenance, the increased concentration of oxidants disrupts the functionality of cellular protein machines resulting eventually in proteotoxic stress and the deregulation of the proteostasis (homeostasis of the proteome) network (PN). PN curates the proteome in the various cellular compartments and the extracellular milieu by modulating protein synthesis and protein machines assembly, protein recycling and stress responses, as well as refolding or degradation of damaged proteins. Molecular chaperones are key players of the PN since they facilitate folding of nascent polypeptides, as well as holding, folding, and/or degradation of unfolded, misfolded, or non-native proteins. Therefore, the expression and the activity of the molecular chaperones are tightly regulated at both the transcriptional and post-translational level at organismal states of increased oxidative and, consequently, proteotoxic stress, including ageing and various age-related diseases (e.g. degenerative diseases and cancer). In the current review we present a synopsis of the various classes of intra- and extracellular chaperones, the effects of oxidants on cellular homeodynamics and diseases and the redox regulation of chaperones. Free radicals originate from various sources and at physiological concentrations are essential for the modulation of cell signalling pathways. Abnormally high levels of free radicals induce oxidative stress and damage all cellular biomolecules, including proteins. Molecular chaperones facilitate folding of nascent polypeptides, as well as holding, folding, and/or degradation of damaged proteins. The expression and the activity of chaperones during oxidative stress are regulated at both the transcriptional and post-translational level.
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Key Words
- AGEs, Advanced Glycation End Products
- ALS, Autophagy Lysosome System
- AP-1, Activator Protein-1
- CLU, apolipoprotein J/Clusterin
- Chaperones
- Diseases
- EPMs, Enzymatic Protein Modifications
- ER, Endoplasmic Reticulum
- ERAD, ER-Associated protein Degradation
- Free radicals
- GPx7, Glutathione Peroxidase 7
- GRP78, Glucose Regulated Protein of 78 kDa
- HSF1, Heat Shock transcription Factor-1
- HSP, Heat Shock Protein
- Hb, Haemoglobin
- Keap1, Kelch-like ECH-associated protein 1
- NADH, Nicotinamide Adenine Dinucleotide
- NEPMs, Non-Enzymatic Protein Modifications
- NOS, Nitric Oxide Synthase
- NOx, NAD(P)H Oxidase
- Nrf2, NF-E2-related factor 2
- Oxidative stress
- PDI, Protein Disulfide Isomerase
- PDR, Proteome Damage Responses
- PN, Proteostasis Network
- Proteome
- RNS, Reactive Nitrogen Species
- ROS, Reactive Oxygen Species
- Redox signalling
- UPR, Unfolded Protein Response
- UPS, Ubiquitin Proteasome System
- α(2)M, α(2)-Macroglobulin
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Affiliation(s)
- Katerina Niforou
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 15784, Greece
| | - Christina Cheimonidou
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 15784, Greece
| | - Ioannis P Trougakos
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 15784, Greece
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21
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Guerrero-Muñoz MJ, Castillo-Carranza DL, Kayed R. Therapeutic approaches against common structural features of toxic oligomers shared by multiple amyloidogenic proteins. Biochem Pharmacol 2014; 88:468-78. [PMID: 24406245 DOI: 10.1016/j.bcp.2013.12.023] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 12/18/2013] [Accepted: 12/19/2013] [Indexed: 02/03/2023]
Abstract
Impaired proteostasis is one of the main features of all amyloid diseases, which are associated with the formation of insoluble aggregates from amyloidogenic proteins. The aggregation process can be caused by overproduction or poor clearance of these proteins. However, numerous reports suggest that amyloid oligomers are the most toxic species, rather than insoluble fibrillar material, in Alzheimer's, Parkinson's, and Prion diseases, among others. Although the exact protein that aggregates varies between amyloid disorders, they all share common structural features that can be used as therapeutic targets. In this review, we focus on therapeutic approaches against shared features of toxic oligomeric structures and future directions.
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Affiliation(s)
- Marcos J Guerrero-Muñoz
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, USA; Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Diana L Castillo-Carranza
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, USA; Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, USA; Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, USA.
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22
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Andersson EK, Bengtsson C, Evans ML, Chorell E, Sellstedt M, Lindgren AE, Hufnagel DA, Bhattacharya M, Tessier PM, Wittung-Stafshede P, Almqvist F, Chapman MR. Modulation of curli assembly and pellicle biofilm formation by chemical and protein chaperones. CHEMISTRY & BIOLOGY 2013; 20:1245-54. [PMID: 24035282 PMCID: PMC4243843 DOI: 10.1016/j.chembiol.2013.07.017] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 07/19/2013] [Accepted: 07/30/2013] [Indexed: 12/22/2022]
Abstract
Enteric bacteria assemble functional amyloid fibers, curli, on their surfaces that share structural and biochemical properties with disease-associated amyloids. Here, we test rationally designed 2-pyridone compounds for their ability to alter amyloid formation of the major curli subunit CsgA. We identified several compounds that discourage CsgA amyloid formation and several compounds that accelerate CsgA amyloid formation. The ability of inhibitor compounds to stop growing CsgA fibers was compared to the same property of the CsgA chaperone, CsgE. CsgE blocked CsgA amyloid assembly and arrested polymerization when added to actively polymerizing fibers. Additionally, CsgE and the 2-pyridone inhibitors prevented biofilm formation by Escherichia coli at the air-liquid interface of a static culture. We demonstrate that curli amyloid assembly and curli-dependent biofilm formation can be modulated not only by protein chaperones, but also by "chemical chaperones."
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Affiliation(s)
- Emma K. Andersson
- Umeå Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Christoffer Bengtsson
- Umeå Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Margery L. Evans
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA
| | - Erik Chorell
- Umeå Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Magnus Sellstedt
- Umeå Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | | | - David A. Hufnagel
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA
| | - Moumita Bhattacharya
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Peter M. Tessier
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | | | - Fredrik Almqvist
- Umeå Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Matthew R. Chapman
- Umeå Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA
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23
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Hutt DM, Balch WE. Expanding proteostasis by membrane trafficking networks. Cold Spring Harb Perspect Biol 2013; 5:cshperspect.a013383. [PMID: 23426524 DOI: 10.1101/cshperspect.a013383] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The folding biology common to all three kingdoms of life (Archaea, Bacteria, and Eukarya) is proteostasis. The proteostasis network (PN) functions as a "cloud" to generate, protect, and degrade the proteome. Whereas microbes (Bacteria, Archaea) have a single compartment, Eukarya have numerous subcellular compartments. We examine evidence that Eukarya compartments use coat, tether, and fusion (CTF) membrane trafficking components to form an evolutionarily advanced arm of the PN that we refer to as the "trafficking PN" (TPN). We suggest that the TPN builds compartments by generating a mosaic of integrated cargo-specific trafficking signatures (TRaCKS). TRaCKS control the temporal and spatial features of protein-folding biology based on the Anfinsen principle that the local environment plays a critical role in managing protein structure. TPN-generated endomembrane compartments apply a "quinary" level of structural control to modify the secondary, tertiary, and quaternary structures defined by the primary polypeptide-chain sequence. The development of Anfinsen compartments provides a unifying foundation for understanding the purpose of endomembrane biology and its capacity to drive extant Eukarya function and diversity.
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Affiliation(s)
- Darren M Hutt
- Department of Cell Biology and Department of Chemical Physiology, The Skaggs Institute for Chemical Biology and the Dorris Institute for Neurological Diseases, The Scripps Research Institute, La Jolla, California 92037, USA
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24
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Priya S, Sharma SK, Goloubinoff P. Molecular chaperones as enzymes that catalytically unfold misfolded polypeptides. FEBS Lett 2013; 587:1981-7. [PMID: 23684649 DOI: 10.1016/j.febslet.2013.05.014] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 05/06/2013] [Indexed: 10/26/2022]
Abstract
Stress-denatured or de novo synthesized and translocated unfolded polypeptides can spontaneously reach their native state without assistance of other proteins. Yet, the pathway to native folding is complex, stress-sensitive and prone to errors. Toxic misfolded and aggregated conformers may accumulate in cells and lead to degenerative diseases. Members of the canonical conserved families of molecular chaperones, Hsp100s, Hsp70/110/40s, Hsp60/CCTs, the small Hsps and probably also Hsp90s, can recognize and bind with high affinity, abnormally exposed hydrophobic surfaces on misfolded and aggregated polypeptides. Binding to Hsp100, Hsp70, Hsp110, Hsp40, Hsp60, CCTs and Trigger factor may cause partial unfolding of the misfolded polypeptide substrates, and ATP hydrolysis can induce further unfolding and release from the chaperone, leading to spontaneous refolding into native proteins with low-affinity for the chaperones. Hence, specific chaperones act as catalytic polypeptide unfolding isomerases, rerouting cytotoxic misfolded and aggregated polypeptides back onto their physiological native refolding pathway, thus averting the onset of protein conformational diseases.
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Affiliation(s)
- Smriti Priya
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
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25
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Abstract
Curli are proteinaceous fibrous structures produced on the surface of many gram-negative bacteria. As a major constituent of the extracellular matrix, curli mediate interactions between the bacteria and its environment, and as such, curli play a critical role in biofilm formation. Curli fibers share biophysical properties with a growing number of remarkably stable and ordered protein aggregates called amyloid. Here we describe experimental methods to study the biogenesis and assembly of curli by exploiting their amyloid properties. We also present methods to analyze curli-mediated biofilm formation. These approaches are straightforward and can easily be adapted to study other bacterially produced amyloids.
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26
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DePas WH, Chapman MR. Microbial manipulation of the amyloid fold. Res Microbiol 2012; 163:592-606. [PMID: 23108148 PMCID: PMC3532741 DOI: 10.1016/j.resmic.2012.10.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 10/09/2012] [Indexed: 12/19/2022]
Abstract
Microbial biofilms are encased in a protein, DNA, and polysaccharide matrix that protects the community, promotes interactions with the environment, and helps cells adhere together. The protein component of these matrices is often a remarkably stable, β-sheet-rich polymer called amyloid. Amyloids form ordered, self-templating fibers that are highly aggregative, making them a valuable biofilm component. Some eukaryotic proteins inappropriately adopt the amyloid fold, and these misfolded protein aggregates disrupt normal cellular proteostasis, which can cause significant cytotoxicity. Indeed, until recently amyloids were considered solely the result of protein misfolding. However, research over the past decade has revealed how various organisms have capitalized on the amyloid fold by developing sophisticated biogenesis pathways that coordinate gene expression, protein folding, and secretion so that amyloid-related toxicities are minimized. How microbes manipulate amyloids, by augmenting their advantageous properties and by reducing their undesirable properties, will be the subject of this review.
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Affiliation(s)
- William H. DePas
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-0620, USA
| | - Matthew R. Chapman
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan LSA, 830 North University Ave., Ann Arbor, MI, 48109, USA
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