1
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Marijan D, Momchilova EA, Burns D, Chandhok S, Zapf R, Wille H, Potoyan DA, Audas TE. Protein thermal sensing regulates physiological amyloid aggregation. Nat Commun 2024; 15:1222. [PMID: 38336721 PMCID: PMC10858206 DOI: 10.1038/s41467-024-45536-0] [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: 05/24/2023] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
To survive, cells must respond to changing environmental conditions. One way that eukaryotic cells react to harsh stimuli is by forming physiological, RNA-seeded subnuclear condensates, termed amyloid bodies (A-bodies). The molecular constituents of A-bodies induced by different stressors vary significantly, suggesting this pathway can tailor the cellular response by selectively aggregating a subset of proteins under a given condition. Here, we identify critical structural elements that regulate heat shock-specific amyloid aggregation. Our data demonstrates that manipulating structural pockets in constituent proteins can either induce or restrict their A-body targeting at elevated temperatures. We propose a model where selective aggregation within A-bodies is mediated by the thermal stability of a protein, with temperature-sensitive structural regions acting as an intrinsic form of post-translational regulation. This system would provide cells with a rapid and stress-specific response mechanism, to tightly control physiological amyloid aggregation or other cellular stress response pathways.
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Affiliation(s)
- Dane Marijan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Evgenia A Momchilova
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Daniel Burns
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Sahil Chandhok
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Richard Zapf
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Holger Wille
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, T6G 2M8, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Davit A Potoyan
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA
| | - Timothy E Audas
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
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2
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Cell-free synthesis of amyloid fibrils with infectious properties and amenable to sub-milligram magic-angle spinning NMR analysis. Commun Biol 2022; 5:1202. [DOI: 10.1038/s42003-022-04175-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022] Open
Abstract
AbstractStructural investigations of amyloid fibrils often rely on heterologous bacterial overexpression of the protein of interest. Due to their inherent hydrophobicity and tendency to aggregate as inclusion bodies, many amyloid proteins are challenging to express in bacterial systems. Cell-free protein expression is a promising alternative to classical bacterial expression to produce hydrophobic proteins and introduce NMR-active isotopes that can improve and speed up the NMR analysis. Here we implement the cell-free synthesis of the functional amyloid prion HET-s(218-289). We present an interesting case where HET-s(218-289) directly assembles into infectious fibril in the cell-free expression mixture without the requirement of denaturation procedures and purification. By introducing tailored 13C and 15N isotopes or CF3 and 13CH2F labels at strategic amino-acid positions, we demonstrate that cell-free synthesized amyloid fibrils are readily amenable to high-resolution magic-angle spinning NMR at sub-milligram quantity.
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3
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Tarasca MV, Naser D, Schaefer A, Soule TG, Meiering EM. Quenched hydrogen-deuterium amide exchange optimization for high-resolution structural analysis of cellular protein aggregates. Anal Biochem 2022; 652:114675. [PMID: 35390328 DOI: 10.1016/j.ab.2022.114675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 12/17/2022]
Abstract
Inclusion bodies (IBs) are large, insoluble aggregates that often form during the overexpression of proteins in bacteria. These aggregates are of broad fundamental and practical significance, for recombinant protein preparation and due to their relevance to aggregation-related medical conditions and their recent emergence as promising functional nanomaterials. Despite their significance, high resolution knowledge of IB structure remains very limited. Such knowledge will advance understanding and control of IB formation and properties in myriad practical applications. Here, we report a detailed quenched hydrogen-deuterium amide exchange (qHDX) method with NMR readout to define the structure of IBs at the level of individual residues throughout the protein. Applying proper control of experimental conditions, such as sample pH, water content, temperature, and intrinsic rate of amide exchange, yields in depth results for these cellular protein aggregates. qHDX results illustrated for Cu, Zn superoxide dismutase 1 (SOD1) and Adnectins show their IBs include native-like structure and some but not all mutations alter IB structure.
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Affiliation(s)
| | - Dalia Naser
- Department of Chemistry, University of Waterloo, Waterloo, Canada
| | - Anna Schaefer
- Department of Chemistry, University of Waterloo, Waterloo, Canada
| | - Tyler Gb Soule
- Department of Chemistry, University of Waterloo, Waterloo, Canada
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4
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Naser D, Tarasca MV, Siebeneichler B, Schaefer A, Deol HK, Soule TGB, Almey J, Kelso S, Mishra GG, Simon H, Meiering EM. High-Resolution NMR H/D Exchange of Human Superoxide Dismutase Inclusion Bodies Reveals Significant Native Features Despite Structural Heterogeneity. Angew Chem Int Ed Engl 2022; 61:e202112645. [PMID: 35316563 DOI: 10.1002/anie.202112645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Indexed: 01/16/2023]
Abstract
Protein aggregation is central to aging, disease and biotechnology. While there has been recent progress in defining structural features of cellular protein aggregates, many aspects remain unclear due to heterogeneity of aggregates presenting obstacles to characterization. Here we report high-resolution analysis of cellular inclusion bodies (IBs) of immature human superoxide dismutase (SOD1) mutants using NMR quenched amide hydrogen/deuterium exchange (qHDX), FTIR and Congo red binding. The extent of aggregation is correlated with mutant global stability and, notably, the free energy of native dimer dissociation, indicating contributions of native-like monomer associations to IB formation. This is further manifested by a common pattern of extensive protection against H/D exchange throughout nine mutant SOD1s despite their diverse characteristics. These results reveal multiple aggregation-prone regions in SOD1 and illuminate how aggregation may occur via an ensemble of pathways.
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Affiliation(s)
- Dalia Naser
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Michael V Tarasca
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Bruna Siebeneichler
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Anna Schaefer
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Harmeen K Deol
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Tyler G B Soule
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.,Current address: Department of Clinical Neurosciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Johnathan Almey
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Susan Kelso
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.,Current address: Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - Gyana G Mishra
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.,Current address: Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Hilary Simon
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
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5
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Guncheva M. Role of ionic liquids on stabilization of therapeutic proteins and model proteins. Protein J 2022; 41:369-380. [PMID: 35661292 DOI: 10.1007/s10930-022-10058-5] [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] [Accepted: 05/24/2022] [Indexed: 11/26/2022]
Abstract
Ionic liquids (ILs) exhibit potential as excipients to stabilize proteins in solutions. This mini-review is not a detailed reference book on ILs, rather a brief overview of the main achievements published in the literature on their effect on protein aggregation, unfolding, structural and thermal stability, and activity. The main focus of the manuscript is three widely studied groups of ionic liquids: imidazolium-, cholinium- and alkylammonium-based and their effect on the model and therapeutic proteins.
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Affiliation(s)
- Maya Guncheva
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. 9, 1113, Sofia, Bulgaria.
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6
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Characterization of the enzymes involved in the diol synthase metabolic pathway in Pseudomonas aeruginosa. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Györkei Á, Daruka L, Balogh D, Őszi E, Magyar Z, Szappanos B, Fekete G, Fuxreiter M, Horváth P, Pál C, Kintses B, Papp B. Proteome-wide landscape of solubility limits in a bacterial cell. Sci Rep 2022; 12:6547. [PMID: 35449391 PMCID: PMC9023497 DOI: 10.1038/s41598-022-10427-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/28/2022] [Indexed: 11/16/2022] Open
Abstract
Proteins are prone to aggregate when expressed above their solubility limits. Aggregation may occur rapidly, potentially as early as proteins emerge from the ribosome, or slowly, following synthesis. However, in vivo data on aggregation rates are scarce. Here, we classified the Escherichia coli proteome into rapidly and slowly aggregating proteins using an in vivo image-based screen coupled with machine learning. We find that the majority (70%) of cytosolic proteins that become insoluble upon overexpression have relatively low rates of aggregation and are unlikely to aggregate co-translationally. Remarkably, such proteins exhibit higher folding rates compared to rapidly aggregating proteins, potentially implying that they aggregate after reaching their folded states. Furthermore, we find that a substantial fraction (~ 35%) of the proteome remain soluble at concentrations much higher than those found naturally, indicating a large margin of safety to tolerate gene expression changes. We show that high disorder content and low surface stickiness are major determinants of high solubility and are favored in abundant bacterial proteins. Overall, our study provides a global view of aggregation rates and hence solubility limits of proteins in a bacterial cell.
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Affiliation(s)
- Ádám Györkei
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary
- Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Lejla Daruka
- Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Dávid Balogh
- Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Erika Őszi
- Biological Research Centre, Institute of Plant Biology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Zoltán Magyar
- Biological Research Centre, Institute of Plant Biology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Balázs Szappanos
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary
- Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Gergely Fekete
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary
- Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Mónika Fuxreiter
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Laboratory of Protein Dynamics, University of Debrecen, Debrecen, Hungary
| | - Péter Horváth
- Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
- Institute for Molecular Medicine Finland-FIMM, Helsinki Institute of Life Science-HiLIFE, University of Helsinki, Helsinki, Finland
| | - Csaba Pál
- Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary.
| | - Bálint Kintses
- Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary.
- HCEMM-BRC Translational Microbiology Research Group, Szeged, Hungary.
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary.
| | - Balázs Papp
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary.
- Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary.
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8
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Naser D, Tarasca MV, Siebeneichler B, Schaefer A, Deol HK, Soule TGB, Almey J, Kelso S, Mishra GG, Simon H, Meiering EM. High‐Resolution NMR H/D Exchange of Human Superoxide Dismutase Inclusion Bodies Reveals Significant Native Features Despite Structural Heterogeneity. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Dalia Naser
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
| | - Michael V. Tarasca
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
| | | | - Anna Schaefer
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
| | - Harmeen K. Deol
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
| | - Tyler G. B. Soule
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
- Current address: Department of Clinical Neurosciences University of Calgary Calgary, AB T2N 1N4 Canada
| | - Johnathan Almey
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
| | - Susan Kelso
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
- Current address: Department of Molecular Genetics University of Toronto Toronto, ON M5S 1A1 Canada
| | - Gyana G. Mishra
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
- Current address: Department of Biology University of Waterloo Waterloo, ON N2L 3G1 Canada
| | - Hilary Simon
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
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9
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Restrepo-Pineda S, Sánchez-Puig N, Pérez NO, García-Hernández E, Valdez-Cruz NA, Trujillo-Roldán MA. The pre-induction temperature affects recombinant HuGM-CSF aggregation in thermoinducible Escherichia coli. Appl Microbiol Biotechnol 2022; 106:2883-2902. [PMID: 35412129 PMCID: PMC9002048 DOI: 10.1007/s00253-022-11908-z] [Citation(s) in RCA: 6] [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: 11/02/2021] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 02/06/2023]
Abstract
The overproduction of recombinant proteins in Escherichia coli leads to insoluble aggregates of proteins called inclusion bodies (IBs). IBs are considered dynamic entities that harbor high percentages of the recombinant protein, which can be found in different conformational states. The production conditions influence the properties of IBs and recombinant protein recovery and solubilization. The E. coli growth in thermoinduced systems is generally carried out at 30 °C and then recombinant protein production at 42 °C. Since the heat shock response in E. coli is triggered above 34 °C, the synthesis of heat shock proteins can modify the yields of the recombinant protein and the structural quality of IBs. The objective of this work was to evaluate the effect of different pre-induction temperatures (30 and 34 °C) on the growth of E. coli W3110 producing the human granulocyte-macrophage colony-stimulating factor (rHuGM-CSF) and on the IBs structure in a λpL/pR-cI857 thermoinducible system. The recombinant E. coli cultures growing at 34 °C showed a ~ 69% increase in the specific growth rate compared to cultures grown at 30 °C. The amount of rHuGM-CSF in IBs was significantly higher in cultures grown at 34 °C. Main folding chaperones (DnaK and GroEL) were associated with IBs and their co-chaperones (DnaJ and GroES) with the soluble protein fraction. Finally, IBs from cultures that grew at 34 °C had a lower content of amyloid-like structure and were more sensitive to proteolytic degradation than IBs obtained from cultures at 30 °C. Our study presents evidence that increasing the pre-induction temperature in a thermoinduced system allows obtaining higher recombinant protein and reducing amyloid contents of the IBs. KEY POINTS: • Pre-induction temperature determines inclusion bodies architecture • In pre-induction (above 34 °C), the heat shock response increases recombinant protein production • Inclusion bodies at higher pre-induction temperature show a lower amyloid content.
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Affiliation(s)
- Sara Restrepo-Pineda
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, CP, 04510, México
| | - Nuria Sánchez-Puig
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad Universitaria, Ciudad de México, 04510, México
| | - Néstor O Pérez
- Probiomed S.A. de C.V. Planta Tenancingo, Cruce de Carreteras Acatzingo-Zumpahuacan SN, Tenancingo, CP 52400, Estado de México, México
| | - Enrique García-Hernández
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad Universitaria, Ciudad de México, 04510, México
| | - Norma A Valdez-Cruz
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, CP, 04510, México
| | - Mauricio A Trujillo-Roldán
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, CP, 04510, México.
- Departamento de Biología Molecular y Biotecnología, Unidad de Bioprocesos, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, CP, 04510, México.
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10
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Hrabarova E, Belkova M, Koszagova R, Nahalka J. Pull-Down Into Active Inclusion Bodies and Their Application in the Detection of (Poly)-Phosphates and Metal-Ions. Front Bioeng Biotechnol 2022; 10:833192. [PMID: 35299638 PMCID: PMC8921494 DOI: 10.3389/fbioe.2022.833192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/09/2022] [Indexed: 11/13/2022] Open
Abstract
Inclusion bodies are typically ignored as they are considered unwanted protein waste generated by prokaryotic host cells during recombinant protein production or harmful protein inclusions in human cell biology. However, these protein particles may have applications for in vivo immobilization in industrial biocatalysis or as cell-tolerable protein materials for the pharmaceuticals industry and clinical development. Thus, there is a need to in vivo “pull-down” (insolubilize) soluble enzymes and proteins into inclusion bodies. Accordingly, in this study, sequences from the short-chain polyphosphatase ygiF were used to design pull-down tags capable of detecting (poly)-phosphates and metal ions. These tags were compared with the entire CHAD domain from Escherichia coli ygiF and SACS2 CHAD from Saccharolobus solfataricus. The results demonstrated that highly soluble green fluorescent protein variants could be pulled down into the inclusion bodies and could have modified sensitivity to metals and di-/tri-inorganic phosphates.
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Affiliation(s)
- Eva Hrabarova
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Bratislava, Slovakia
- Institute of Chemistry, Centre of Excellence for White-green Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia
| | - Martina Belkova
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Bratislava, Slovakia
- Institute of Chemistry, Centre of Excellence for White-green Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia
| | - Romana Koszagova
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Bratislava, Slovakia
- Institute of Chemistry, Centre of Excellence for White-green Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia
| | - Jozef Nahalka
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Bratislava, Slovakia
- Institute of Chemistry, Centre of Excellence for White-green Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia
- *Correspondence: Jozef Nahalka,
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11
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Sorokina I, Mushegian AR, Koonin EV. Is Protein Folding a Thermodynamically Unfavorable, Active, Energy-Dependent Process? Int J Mol Sci 2022; 23:521. [PMID: 35008947 PMCID: PMC8745595 DOI: 10.3390/ijms23010521] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 02/04/2023] Open
Abstract
The prevailing current view of protein folding is the thermodynamic hypothesis, under which the native folded conformation of a protein corresponds to the global minimum of Gibbs free energy G. We question this concept and show that the empirical evidence behind the thermodynamic hypothesis of folding is far from strong. Furthermore, physical theory-based approaches to the prediction of protein folds and their folding pathways so far have invariably failed except for some very small proteins, despite decades of intensive theory development and the enormous increase of computer power. The recent spectacular successes in protein structure prediction owe to evolutionary modeling of amino acid sequence substitutions enhanced by deep learning methods, but even these breakthroughs provide no information on the protein folding mechanisms and pathways. We discuss an alternative view of protein folding, under which the native state of most proteins does not occupy the global free energy minimum, but rather, a local minimum on a fluctuating free energy landscape. We further argue that ΔG of folding is likely to be positive for the majority of proteins, which therefore fold into their native conformations only through interactions with the energy-dependent molecular machinery of living cells, in particular, the translation system and chaperones. Accordingly, protein folding should be modeled as it occurs in vivo, that is, as a non-equilibrium, active, energy-dependent process.
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Affiliation(s)
| | - Arcady R. Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, VA 22314, USA;
- Clare Hall College, University of Cambridge, Cambridge CB3 9AL, UK
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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12
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Caballero AB, Gamez P, Sabate R, Espargaró A. Anti-Amyloid Drug Screening Methods Using Bacterial Inclusion Bodies. Methods Mol Biol 2022; 2538:165-188. [PMID: 35951300 DOI: 10.1007/978-1-0716-2529-3_12] [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] [Indexed: 06/15/2023]
Abstract
Amyloid aggregation is linked to a number of human disorders that range from non-neurological illnesses such as type 2 diabetes to neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. The formation of insoluble protein aggregates with amyloid conformation inside bacteria, namely, in bacterial inclusion bodies, offers the possibility to use bacteria as simple models to study amyloid aggregation processes and potential effects of both anti-amyloid drugs and/or pro-aggregative compounds. This chapter describes fast, simple, inexpensive, highly reproducible, and tunable in vitro and in cellulo methods that use bacterial inclusion bodies as preliminary screening tools for anti-amyloid drugs.
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Affiliation(s)
- Ana B Caballero
- NanoBIC, Department of Inorganic and Organic Chemistry, Faculty of Chemistry, University of Barcelona, Barcelona, Catalonia, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Barcelona, Catalonia, Spain
| | - Patrick Gamez
- NanoBIC, Department of Inorganic and Organic Chemistry, Faculty of Chemistry, University of Barcelona, Barcelona, Catalonia, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Barcelona, Catalonia, Spain
- Catalan Institution for Research and Advanced Studies, Passeig Lluís Companys 23, Barcelona, Catalonia, Spain
| | - Raimon Sabate
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Barcelona, Catalonia, Spain
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Catalonia, Spain
| | - Alba Espargaró
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Barcelona, Catalonia, Spain.
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Catalonia, Spain.
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Saikia C, Ben-Nissan G, Reuveny E, Karbat I. Production of recombinant venom peptides as tools for ion channel research. Methods Enzymol 2021; 654:169-201. [PMID: 34120712 DOI: 10.1016/bs.mie.2021.01.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Animal venom is a rich source for peptide toxins that bind and modulate the function of ion channels. Owing to their ability to bind receptor sites on the channel protein with high affinity and specificity, peptide neurotoxins have become an indispensable tool for ion channel research. Recent breakthroughs in structural biology and advances in computer simulations of biomolecules have sparked a new interest in animal toxins as probes of channel protein structure and function. Here, we focus on methods used to produce animal toxins for research purposes using recombinant expression. The specific challenges associated with heterologous production of venom peptides are discussed, and several methods targeting these issues are presented with an emphasis on E. coli based systems. An efficient protocol for the bacterial expression, folding, and purification of recombinant venom peptides is described.
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Affiliation(s)
- Chandamita Saikia
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Eitan Reuveny
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
| | - Izhar Karbat
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
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14
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Chang Z, Deng J, Zhao W, Yang J. Amyloid-like aggregation and fibril core determination of TDP-43 C-terminal domain. Biochem Biophys Res Commun 2020; 532:655-661. [PMID: 32907712 DOI: 10.1016/j.bbrc.2020.08.096] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/15/2022]
Abstract
Cytoplasmic inclusion of TAR DNA-binding protein 43 (TDP-43) is a hallmark of most ALS (amyotrophic lateral sclerosis) and FTLD (Frontotemporal dementia), yet the aggregation of TDP-43 remains unclear. In this study, we proved the existence of amyloid-like structures of C-terminal domain of TDP-43 (TDP-C) in bacterial inclusion bodies (IBs), and obtained a homogenous fibril sample by seeding from the components of aggregated TDP-C in Escherichiacoli IBs. The results from solid-state NMR spectroscopy suggest that the homogenous fibrils were seeded from a tiny amount of aggregated TDP-C compositions in IBs; the structure characteristics of the rigid fibril core are identified of β-rich structures, and show subtle relativity with the hydrophobicity of residues. Our study here provides a further understanding of TDP-43 protein aggregation and fibrillation.
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Affiliation(s)
- Ziwei Chang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, PR China
| | - Jing Deng
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Weijing Zhao
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, PR China
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, PR China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, PR China.
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15
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Garcia AM, Giorgiutti C, El Khoury Y, Bauer V, Spiegelhalter C, Leize-Wagner E, Hellwig P, Potier N, Torbeev V. Aggregation and Amyloidogenicity of the Nuclear Coactivator Binding Domain of CREB-Binding Protein. Chemistry 2020; 26:9889-9899. [PMID: 32364648 DOI: 10.1002/chem.202001847] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 04/30/2020] [Indexed: 12/28/2022]
Abstract
The nuclear coactivator binding domain (NCBD) of transcriptional co-regulator CREB-binding protein (CBP) is an example of conformationally malleable proteins that can bind to structurally unrelated protein targets and adopt distinct folds in the respective protein complexes. Here, we show that the folding landscape of NCBD contains an alternative pathway that results in protein aggregation and self-assembly into amyloid fibers. The initial steps of such protein misfolding are driven by intermolecular interactions of its N-terminal α-helix bringing multiple NCBD molecules into contact. These oligomers then undergo slow but progressive interconversion into β-sheet-containing aggregates. To reveal the concealed aggregation potential of NCBD we used a chemically synthesized mirror-image d-NCBD form. The addition of d-NCBD promoted self-assembly into amyloid precipitates presumably due to formation of thermodynamically more stable racemic β-sheet structures. The unexpected aggregation of NCBD needs to be taken into consideration given the multitude of protein-protein interactions and resulting biological functions mediated by CBP.
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Affiliation(s)
- Ana Maria Garcia
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and, icFRC (International Center for Frontier Research in Chemistry), University of Strasbourg, CNRS-UMR 7006, 8 allée Gaspard Monge, 67083, Strasbourg, France
| | - Christophe Giorgiutti
- Laboratory of Mass-Spectrometry of Interactions and Systems, University of Strasbourg, CNRS-UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
| | - Youssef El Khoury
- Laboratory of Bioelectrochemistry and Spectroscopy, University of Strasbourg, CNRS-UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
| | - Valentin Bauer
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and, icFRC (International Center for Frontier Research in Chemistry), University of Strasbourg, CNRS-UMR 7006, 8 allée Gaspard Monge, 67083, Strasbourg, France
| | - Coralie Spiegelhalter
- Imaging Center, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), INSERM-U964, University of Strasbourg, CNRS-UMR 7104, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Emmanuelle Leize-Wagner
- Laboratory of Mass-Spectrometry of Interactions and Systems, University of Strasbourg, CNRS-UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
| | - Petra Hellwig
- Laboratory of Bioelectrochemistry and Spectroscopy, University of Strasbourg, CNRS-UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
- Institute for Advanced Study, USIAS University of Strasbourg, 5 allée du Général Rouvillois, 67083, Strasbourg, France
| | - Noelle Potier
- Laboratory of Mass-Spectrometry of Interactions and Systems, University of Strasbourg, CNRS-UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
| | - Vladimir Torbeev
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and, icFRC (International Center for Frontier Research in Chemistry), University of Strasbourg, CNRS-UMR 7006, 8 allée Gaspard Monge, 67083, Strasbourg, France
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16
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Gil-Garcia M, Navarro S, Ventura S. Coiled-coil inspired functional inclusion bodies. Microb Cell Fact 2020; 19:117. [PMID: 32487230 PMCID: PMC7268670 DOI: 10.1186/s12934-020-01375-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/25/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Recombinant protein expression in bacteria often leads to the formation of intracellular insoluble protein deposits, a major bottleneck for the production of soluble and active products. However, in recent years, these bacterial protein aggregates, commonly known as inclusion bodies (IBs), have been shown to be a source of stable and active protein for biotechnological and biomedical applications. The formation of these functional IBs is usually facilitated by the fusion of aggregation-prone peptides or proteins to the protein of interest, leading to the formation of amyloid-like nanostructures, where the functional protein is embedded. RESULTS In order to offer an alternative to the classical amyloid-like IBs, here we develop functional IBs exploiting the coiled-coil fold. An in silico analysis of coiled-coil and aggregation propensities, net charge, and hydropathicity of different potential tags identified the natural homo-dimeric and anti-parallel coiled-coil ZapB bacterial protein as an optimal candidate to form assemblies in which the native state of the fused protein is preserved. The protein itself forms supramolecular fibrillar networks exhibiting only α-helix secondary structure. This non-amyloid self-assembly propensity allows generating innocuous IBs in which the recombinant protein of interest remains folded and functional, as demonstrated using two different fluorescent proteins. CONCLUSIONS Here, we present a proof of concept for the use of a natural coiled-coil domain as a versatile tool for the production of functional IBs in bacteria. This α-helix-based strategy excludes any potential toxicity drawback that might arise from the amyloid nature of β-sheet-based IBs and renders highly active and homogeneous submicrometric particles.
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Affiliation(s)
- Marcos Gil-Garcia
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Susanna Navarro
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
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17
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Schwaighofer A, Ablasser S, Lux L, Kopp J, Herwig C, Spadiut O, Lendl B, Slouka C. Production of Active Recombinant Hyaluronidase Inclusion Bodies from Apis mellifera in E. coli Bl21(DE3) and characterization by FT-IR Spectroscopy. Int J Mol Sci 2020; 21:E3881. [PMID: 32485932 PMCID: PMC7313074 DOI: 10.3390/ijms21113881] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 12/12/2022] Open
Abstract
The bacterium E. coli is one of the most important hosts for recombinant protein production. The benefits are high growth rates, inexpensive media, and high protein titers. However, complex proteins with high molecular weight and many disulfide bonds are expressed as inclusion bodies (IBs). In the last decade, the overall perception of these IBs being not functional proteins changed, as enzyme activity was found within IBs. Several applications for direct use of IBs are already reported in literature. While fluorescent proteins or protein tags are used for determination of IB activity to date, direct measurements of IB protein activity are scacre. The expression of recombinant hyaluronidase from Apis mellifera in E. coli BL21(DE3) was analyzed using a face centered design of experiment approach. Hyaluronidase is a hard to express protein and imposes a high metabolic burden to the host. Conditions giving a high specific IB titer were found at 25 °C at low specific substrate uptake rates and induction times of 2 to 4 h. The protein activity of hyaluronidase IBs was verified using (Fourier transform) FT-IR spectroscopy. Degradation of the substrate hyaluronan occurred at increased rates with higher IB concentrations. Active recombinant hyaluronidase IBs can be immediately used for direct degradation of hyaluronan without further down streaming steps. FT-IR spectroscopy was introduced as a method for tracking IB activity and showed differences in degradation behavior of hyaluronan dependent on the applied active IB concentration.
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Affiliation(s)
- Andreas Schwaighofer
- FG Environmental Analytics, Process Analytics and Sensors, Institute of Chemical Technology and Analytics, Vienna University of Technology, Getreidemarkt 9/164, 1060 Wien, Austria; (A.S.); (L.L.); (B.L.)
| | - Sarah Ablasser
- FG Bioprocess Technology, ICEBE, Vienna University of Technology, Gumpendorferstrasse 1a, 1060 Vienna, Austria; (S.A.); (J.K.); (C.H.)
| | - Laurin Lux
- FG Environmental Analytics, Process Analytics and Sensors, Institute of Chemical Technology and Analytics, Vienna University of Technology, Getreidemarkt 9/164, 1060 Wien, Austria; (A.S.); (L.L.); (B.L.)
| | - Julian Kopp
- FG Bioprocess Technology, ICEBE, Vienna University of Technology, Gumpendorferstrasse 1a, 1060 Vienna, Austria; (S.A.); (J.K.); (C.H.)
| | - Christoph Herwig
- FG Bioprocess Technology, ICEBE, Vienna University of Technology, Gumpendorferstrasse 1a, 1060 Vienna, Austria; (S.A.); (J.K.); (C.H.)
| | - Oliver Spadiut
- FG Integrated Bioprocess Development, ICEBE, Vienna University of Technology, Gumpendorferstrasse 1a, 1060 Vienna, Austria;
| | - Bernhard Lendl
- FG Environmental Analytics, Process Analytics and Sensors, Institute of Chemical Technology and Analytics, Vienna University of Technology, Getreidemarkt 9/164, 1060 Wien, Austria; (A.S.); (L.L.); (B.L.)
| | - Christoph Slouka
- FG Integrated Bioprocess Development, ICEBE, Vienna University of Technology, Gumpendorferstrasse 1a, 1060 Vienna, Austria;
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18
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Singh A, Upadhyay V, Singh A, Panda AK. Structure-Function Relationship of Inclusion Bodies of a Multimeric Protein. Front Microbiol 2020; 11:876. [PMID: 32457730 PMCID: PMC7225587 DOI: 10.3389/fmicb.2020.00876] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 04/15/2020] [Indexed: 12/17/2022] Open
Abstract
High level expression of recombinant proteins in bacteria often results in their aggregation into inclusion bodies. Formation of inclusion bodies poses a major bottleneck in high-throughput recovery of recombinant protein. These aggregates have amyloid-like nature and can retain biological activity. Here, effect of expression temperature on the quality of Escherichia coli asparaginase II (a tetrameric protein) inclusion bodies was evaluated. Asparaginase was expressed as inclusion bodies at different temperatures. Purified inclusion bodies were checked for biological activities and analyzed for structural properties in order to establish a structure-activity relationship. Presence of activity in inclusion bodies showed the existence of properly folded asparaginase tetramers. Expression temperature affected the properties of asparaginase inclusion bodies. Inclusion bodies expressed at higher temperatures were characterized by higher biological activity and less amyloid content as evident by Thioflavin T binding and Fourier Transform Infrared (FTIR) spectroscopy. Complex kinetics of proteinase K digestion of asparaginase inclusion bodies expressed at higher temperatures indicate higher extent of conformational heterogeneity in these aggregates.
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Affiliation(s)
- Anupam Singh
- Product Development Cell, National Institute of Immunology, New Delhi, India
| | - Vaibhav Upadhyay
- Product Development Cell, National Institute of Immunology, New Delhi, India
| | - Akansha Singh
- Product Development Cell, National Institute of Immunology, New Delhi, India
| | - Amulya K Panda
- Product Development Cell, National Institute of Immunology, New Delhi, India
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19
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Sánchez JM, López‐Laguna H, Álamo P, Serna N, Sánchez‐Chardi A, Nolan V, Cano‐Garrido O, Casanova I, Unzueta U, Vazquez E, Mangues R, Villaverde A. Artificial Inclusion Bodies for Clinical Development. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1902420. [PMID: 32042562 PMCID: PMC7001620 DOI: 10.1002/advs.201902420] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/30/2019] [Indexed: 05/05/2023]
Abstract
Bacterial inclusion bodies (IBs) are mechanically stable protein particles in the microscale, which behave as robust, slow-protein-releasing amyloids. Upon exposure to cultured cells or upon subcutaneous or intratumor injection, these protein materials secrete functional IB polypeptides, functionally mimicking the endocrine release of peptide hormones from secretory amyloid granules. Being appealing as delivery systems for prolonged protein drug release, the development of IBs toward clinical applications is, however, severely constrained by their bacterial origin and by the undefined and protein-to-protein, batch-to-batch variable composition. In this context, the de novo fabrication of artificial IBs (ArtIBs) by simple, cell-free physicochemical methods, using pure components at defined amounts is proposed here. By this, the resulting functional protein microparticles are intriguing, chemically defined biomimetic materials that replicate relevant functionalities of natural IBs, including mammalian cell penetration and local or remote release of functional ArtIB-forming protein. In default of severe regulatory issues, the concept of ArtIBs is proposed as a novel exploitable category of biomaterials for biotechnological and biomedical applications, resulting from simple fabrication and envisaging soft developmental routes to clinics.
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Affiliation(s)
- Julieta M. Sánchez
- Institut de Biotecnologia i de BiomedicinaUniversitat Autònoma de BarcelonaBellaterra08193BarcelonaSpain
- Instituto de Investigaciones Biológicas y Tecnológicas (IIBYT) (CONICET‐Universidad Nacional de Córdoba)ICTA & Cátedra de Química BiológicaDepartamento de QuímicaFCEFyN, UNC. Av. Velez Sarsfield 1611X 5016GCACórdobaArgentina
| | - Hèctor López‐Laguna
- Institut de Biotecnologia i de BiomedicinaUniversitat Autònoma de BarcelonaBellaterra08193BarcelonaSpain
- Departament de Genètica i de MicrobiologiaUniversitat Autònoma de BarcelonaBellaterra08193BarcelonaSpain
- CIBER de BioingenieríaBiomateriales y Nanomedicina (CIBER‐BBN)28029MadridSpain
| | - Patricia Álamo
- CIBER de BioingenieríaBiomateriales y Nanomedicina (CIBER‐BBN)28029MadridSpain
- Biomedical Research Institute Sant Pau (IIB‐Sant Pau) and Josep Carreras Research InstituteHospital de la Santa Creu i Sant Pau08041BarcelonaSpain
| | - Naroa Serna
- Institut de Biotecnologia i de BiomedicinaUniversitat Autònoma de BarcelonaBellaterra08193BarcelonaSpain
- Departament de Genètica i de MicrobiologiaUniversitat Autònoma de BarcelonaBellaterra08193BarcelonaSpain
- CIBER de BioingenieríaBiomateriales y Nanomedicina (CIBER‐BBN)28029MadridSpain
| | | | - Verónica Nolan
- Instituto de Investigaciones Biológicas y Tecnológicas (IIBYT) (CONICET‐Universidad Nacional de Córdoba)ICTA & Cátedra de Química BiológicaDepartamento de QuímicaFCEFyN, UNC. Av. Velez Sarsfield 1611X 5016GCACórdobaArgentina
| | - Olivia Cano‐Garrido
- Institut de Biotecnologia i de BiomedicinaUniversitat Autònoma de BarcelonaBellaterra08193BarcelonaSpain
- Departament de Genètica i de MicrobiologiaUniversitat Autònoma de BarcelonaBellaterra08193BarcelonaSpain
- Present address:
Nanoligent SLEdifici EurekaUniversitat Autònoma de BarcelonaBellaterra08193BarcelonaSpain
| | - Isolda Casanova
- CIBER de BioingenieríaBiomateriales y Nanomedicina (CIBER‐BBN)28029MadridSpain
- Biomedical Research Institute Sant Pau (IIB‐Sant Pau) and Josep Carreras Research InstituteHospital de la Santa Creu i Sant Pau08041BarcelonaSpain
| | - Ugutz Unzueta
- CIBER de BioingenieríaBiomateriales y Nanomedicina (CIBER‐BBN)28029MadridSpain
- Biomedical Research Institute Sant Pau (IIB‐Sant Pau) and Josep Carreras Research InstituteHospital de la Santa Creu i Sant Pau08041BarcelonaSpain
| | - Esther Vazquez
- Institut de Biotecnologia i de BiomedicinaUniversitat Autònoma de BarcelonaBellaterra08193BarcelonaSpain
- Departament de Genètica i de MicrobiologiaUniversitat Autònoma de BarcelonaBellaterra08193BarcelonaSpain
- CIBER de BioingenieríaBiomateriales y Nanomedicina (CIBER‐BBN)28029MadridSpain
| | - Ramon Mangues
- CIBER de BioingenieríaBiomateriales y Nanomedicina (CIBER‐BBN)28029MadridSpain
- Biomedical Research Institute Sant Pau (IIB‐Sant Pau) and Josep Carreras Research InstituteHospital de la Santa Creu i Sant Pau08041BarcelonaSpain
| | - Antonio Villaverde
- Institut de Biotecnologia i de BiomedicinaUniversitat Autònoma de BarcelonaBellaterra08193BarcelonaSpain
- Departament de Genètica i de MicrobiologiaUniversitat Autònoma de BarcelonaBellaterra08193BarcelonaSpain
- CIBER de BioingenieríaBiomateriales y Nanomedicina (CIBER‐BBN)28029MadridSpain
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20
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Łapińska U, Glover G, Capilla-Lasheras P, Young AJ, Pagliara S. Bacterial ageing in the absence of external stressors. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180442. [PMID: 31587633 PMCID: PMC6792439 DOI: 10.1098/rstb.2018.0442] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2019] [Indexed: 12/03/2022] Open
Abstract
Evidence of ageing in the bacterium Escherichia coli was a landmark finding in senescence research, as it suggested that even organisms with morphologically symmetrical fission may have evolved strategies to permit damage accumulation. However, recent work has suggested that ageing is only detectable in this organism in the presence of extrinsic stressors, such as the fluorescent proteins and strong light sources typically used to excite them. Here we combine microfluidics with brightfield microscopy to provide evidence of ageing in E. coli in the absence of these stressors. We report (i) that the doubling time of the lineage of cells that consistently inherits the 'maternal old pole' progressively increases with successive rounds of cell division until it reaches an apparent asymptote, and (ii) that the parental cell divides asymmetrically, with the old pole daughter showing a longer doubling time and slower glucose accumulation than the new pole daughter. Notably, these patterns arise without the progressive accumulation or asymmetric partitioning of observable misfolded-protein aggregates, phenomena previously hypothesized to cause the ageing phenotype. Our findings suggest that ageing is part of the naturally occurring ecologically-relevant phenotype of this bacterium and highlight the importance of alternative mechanisms of damage accumulation in this context. This article is part of a discussion meeting issue 'Single cell ecology'.
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Affiliation(s)
- Urszula Łapińska
- Biosciences, University of Exeter, Exeter, Devon EX4 4QD, UK
- Living Systems Institute, University of Exeter, Exeter, Devon EX4 4QD, UK
| | - Georgina Glover
- Biosciences, University of Exeter, Exeter, Devon EX4 4QD, UK
- Living Systems Institute, University of Exeter, Exeter, Devon EX4 4QD, UK
| | - Pablo Capilla-Lasheras
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE, UK
| | - Andrew J. Young
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE, UK
| | - Stefano Pagliara
- Biosciences, University of Exeter, Exeter, Devon EX4 4QD, UK
- Living Systems Institute, University of Exeter, Exeter, Devon EX4 4QD, UK
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21
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Kumar A, Bhakuni K, Venkatesu P. Strategic planning of proteins in ionic liquids: future solvents for the enhanced stability of proteins against multiple stresses. Phys Chem Chem Phys 2019; 21:23269-23282. [PMID: 31621726 DOI: 10.1039/c9cp04772g] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ionic liquids (ILs) present a vast number of solvents capable of replacing toxic organic solvents in chemical, biotechnology and biomedical applications. ILs are inexpensive and environmentally friendly as the materials can be recycled conveniently. Chemists use a variety of cation and anion combinations to produce an IL that fits the requirements of the sustainable future through the pursuit of greener chemical processes. As such, the development of various types of ILs has been recognized as the emergence of environmentally friendly solvents to attain enhanced protein stability in vitro. The literature survey reveals that there exist a large number of scholarly articles as well as elegant reviews on protein stability in ILs. Biomolecules have adapted to antagonistic environmental stresses that normally denature proteins, and the mechanism of adaptation that protects the cellular components against denaturation involves the intracellular concentration of co-solvents. In this regard, recent experimental results distinctly demonstrated that ILs are stabilizing proteins against denaturing stresses, and their presence in the cells does not alter protein functional activities. However, a review focusing particularly on the refolding and counteracting effects of the ILs against denatured proteins by multiple stresses is still missing. This perspective unveils the studies that have been conducted to improve protein stabilities with ILs as well as the refolding and counteracting abilities of these ILs against the denatured proteins under the influence of multiple stresses. We believe that ILs can provide significant environmental and economic advantages for biochemical processes in the near future. Essentially, numerous investigations are required to allow us to further explore the stabilizing properties of ILs over proteins.
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Affiliation(s)
- Awanish Kumar
- Department of Chemistry, University of Delhi, Delhi-110 007, India.
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22
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Caballero AB, Espargaró A, Pont C, Busquets MA, Estelrich J, Muñoz-Torrero D, Gamez P, Sabate R. Bacterial Inclusion Bodies for Anti-Amyloid Drug Discovery: Current and Future Screening Methods. Curr Protein Pept Sci 2019; 20:563-576. [PMID: 30924417 DOI: 10.2174/1389203720666190329120007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 03/20/2019] [Accepted: 03/22/2019] [Indexed: 11/22/2022]
Abstract
Amyloid aggregation is linked to an increasing number of human disorders from nonneurological pathologies such as type-2 diabetes to neurodegenerative ones such as Alzheimer or Parkinson's diseases. Thirty-six human proteins have shown the capacity to aggregate into pathological amyloid structures. To date, it is widely accepted that amyloid folding/aggregation is a universal process present in eukaryotic and prokaryotic cells. In the last decade, several studies have unequivocally demonstrated that bacterial inclusion bodies - insoluble protein aggregates usually formed during heterologous protein overexpression in bacteria - are mainly composed of overexpressed proteins in amyloid conformation. This fact shows that amyloid-prone proteins display a similar aggregation propensity in humans and bacteria, opening the possibility to use bacteria as simple models to study amyloid aggregation process and the potential effect of both anti-amyloid drugs and pro-aggregative compounds. Under these considerations, several in vitro and in cellulo methods, which exploit the amyloid properties of bacterial inclusion bodies, have been proposed in the last few years. Since these new methods are fast, simple, inexpensive, highly reproducible, and tunable, they have aroused great interest as preliminary screening tools in the search for anti-amyloid (beta-blocker) drugs for conformational diseases. The aim of this mini-review is to compile recently developed methods aimed at tracking amyloid aggregation in bacteria, discussing their advantages and limitations, and the future potential applications of inclusion bodies in anti-amyloid drug discovery.
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Affiliation(s)
- Ana B Caballero
- Department of Inorganic and Organic Chemistry, Faculty of Chemistry, University of Barcelona, E-08028 Barcelona, Spain.,Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain
| | - Alba Espargaró
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain.,Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
| | - Caterina Pont
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain.,Institute of Biomedicine (IBUB), University of Barcelona, E-08028 Barcelona, Spain
| | - Maria Antònia Busquets
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain.,Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
| | - Joan Estelrich
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain.,Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
| | - Diego Muñoz-Torrero
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain.,Institute of Biomedicine (IBUB), University of Barcelona, E-08028 Barcelona, Spain
| | - Patrick Gamez
- Department of Inorganic and Organic Chemistry, Faculty of Chemistry, University of Barcelona, E-08028 Barcelona, Spain.,Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Raimon Sabate
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain.,Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
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23
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Sukhanova A, Poly S, Bozrova S, Lambert É, Ewald M, Karaulov A, Molinari M, Nabiev I. Nanoparticles With a Specific Size and Surface Charge Promote Disruption of the Secondary Structure and Amyloid-Like Fibrillation of Human Insulin Under Physiological Conditions. Front Chem 2019; 7:480. [PMID: 31417892 PMCID: PMC6683663 DOI: 10.3389/fchem.2019.00480] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 06/24/2019] [Indexed: 01/08/2023] Open
Abstract
Nanoparticles attract much interest as fluorescent labels for diagnostic and therapeutic tools, although their applications are often hindered by size- and shape-dependent cytotoxicity. This cytotoxicity is related not only to the leak of toxic metals from nanoparticles into a biological solution, but also to molecular cytotoxicity effects determined by the formation of a protein corona, appearance of an altered protein conformation leading to exposure of cryptic epitopes and cooperative effects involved in the interaction of proteins and peptides with nanoparticles. In the last case, nanoparticles may serve, depending on their nature, as centers of self-association or fibrillation of proteins and peptides, provoking amyloid-like proteinopathies, or as inhibitors of self-association of proteins, or they can self-assemble on biopolymers as on templates. In this study, human insulin protein was used to analyze nanoparticle-induced proteinopathy in physiological conditions. It is known that human insulin may form amyloid fibers, but only under extreme experimental conditions (very low pH and high temperatures). Here, we have shown that the quantum dots (QDs) may induce amyloid-like fibrillation of human insulin under physiological conditions through a complex process strongly dependent on the size and surface charge of QDs. The insulin molecular structure and fibril morphology have been shown to be modified at different stages of its fibrillation, which has been proved by comparative analysis of the data obtained using circular dichroism, dynamic light scattering, amyloid-specific thioflavin T (ThT) assay, transmission electron microscopy, and high-speed atomic force microscopy. We have found important roles of the QD size and surface charge in the destabilization of the insulin structure and the subsequent fibrillation. Remodeling of the insulin secondary structure accompanied by remarkable increase in the rate of formation of amyloid-like fibrils under physiologically normal conditions was observed when the protein was incubated with QDs of exact specific diameter coated with slightly negative specific polyethylene glycol (PEG) derivatives. Strongly negatively or slightly positively charged PEG-modified QDs of the same specific diameter or QDs of bigger or smaller diameters had no effect on insulin fibrillation. The observed effects pave the way to the control of amyloidosis proteinopathy by varying the nanoparticle size and surface charge.
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Affiliation(s)
- Alyona Sukhanova
- Laboratoire de Recherche en Nanosciences, LRN-EA4682, UFR de Pharmacie, Université de Reims Champagne-Ardenne, Reims, France.,Laboratory of Nano-Bioengineering, Moscow Engineering Physics Institute, National Research Nuclear University MEPhI, Moscow, Russia
| | - Simon Poly
- Department of Membrane Biophysics, Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Svetlana Bozrova
- Laboratory of Nano-Bioengineering, Moscow Engineering Physics Institute, National Research Nuclear University MEPhI, Moscow, Russia
| | - Éléonore Lambert
- Laboratoire de Recherche en Nanosciences, LRN-EA4682, UFR de Pharmacie, Université de Reims Champagne-Ardenne, Reims, France
| | - Maxime Ewald
- Laboratoire de Recherche en Nanosciences, LRN-EA4682, UFR de Pharmacie, Université de Reims Champagne-Ardenne, Reims, France
| | - Alexander Karaulov
- Department of Clinical Immunology and Allergology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Michael Molinari
- Laboratoire de Recherche en Nanosciences, LRN-EA4682, UFR de Pharmacie, Université de Reims Champagne-Ardenne, Reims, France
| | - Igor Nabiev
- Laboratoire de Recherche en Nanosciences, LRN-EA4682, UFR de Pharmacie, Université de Reims Champagne-Ardenne, Reims, France.,Laboratory of Nano-Bioengineering, Moscow Engineering Physics Institute, National Research Nuclear University MEPhI, Moscow, Russia
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24
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Espargaró A, Pont C, Gamez P, Muñoz-Torrero D, Sabate R. Amyloid Pan-inhibitors: One Family of Compounds To Cope with All Conformational Diseases. ACS Chem Neurosci 2019; 10:1311-1317. [PMID: 30380841 DOI: 10.1021/acschemneuro.8b00398] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Amyloids are ubiquitous protein aggregates sharing common internal structural features; they are present in all organisms, from prokaryotes to eukaryotes, where they play physiological or pathological roles. Importantly, amyloids, which are generated by aggregation of a range of distinct proteins, could be a key factor in a number of major human disorders, the so-called conformational diseases. Because all amyloids exhibit similar cross-β motifs, one may envisage that molecules capable of blocking the formation of β-sheet structures could abolish aggregation of all amyloid proteins, albeit with different efficacies. Herein, two different β-sheet blockers were tested against a selection of amyloidogenic proteins, encompassing all the major types of amyloid-based disorders. Analysis of their blocking efficiency, using a simple but contrasted cell-based screening procedure, unequivocally confirms that they indeed behave as aggregation pan-inhibitors. The significant inhibitory effects observed for these compounds against all tested amyloidogenic proteins could spur a broader biological evaluation of other known and new amyloid aggregation inhibitors to further determine the potential use of this class of compounds for the universal treatment of conformational diseases.
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Affiliation(s)
- Alba Espargaró
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain
| | - Caterina Pont
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
| | - Patrick Gamez
- Department of Organic and Inorganic Chemistry, Faculty of Chemistry, University of Barcelona, E-08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), E-08010 Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain
| | - Diego Muñoz-Torrero
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
- Institute of Biomedicine (IBUB), University of Barcelona, E-08028 Barcelona, Spain
| | - Raimon Sabate
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain
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25
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de Marco A, Ferrer-Miralles N, Garcia-Fruitós E, Mitraki A, Peternel S, Rinas U, Trujillo-Roldán MA, Valdez-Cruz NA, Vázquez E, Villaverde A. Bacterial inclusion bodies are industrially exploitable amyloids. FEMS Microbiol Rev 2019; 43:53-72. [PMID: 30357330 DOI: 10.1093/femsre/fuy038] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/23/2018] [Indexed: 12/13/2022] Open
Abstract
Understanding the structure, functionalities and biology of functional amyloids is an issue of emerging interest. Inclusion bodies, namely protein clusters formed in recombinant bacteria during protein production processes, have emerged as unanticipated, highly tunable models for the scrutiny of the physiology and architecture of functional amyloids. Based on an amyloidal skeleton combined with varying amounts of native or native-like protein forms, bacterial inclusion bodies exhibit an unusual arrangement that confers mechanical stability, biological activity and conditional protein release, being thus exploitable as versatile biomaterials. The applicability of inclusion bodies in biotechnology as enriched sources of protein and reusable catalysts, and in biomedicine as biocompatible topographies, nanopills or mimetics of endocrine secretory granules has been largely validated. Beyond these uses, the dissection of how recombinant bacteria manage the aggregation of functional protein species into structures of highly variable complexity offers insights about unsuspected connections between protein quality (conformational status compatible with functionality) and cell physiology.
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Affiliation(s)
- Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Vipavska Cesta 13, 5000 Nova Gorica, Slovenia
| | - Neus Ferrer-Miralles
- Institut de Biotecnologia i de Biomedicina (IBB), Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,Departament de Genètica i de Microbiologia, Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Carrer de la Vall Moronta s/n, 08193 Cerdanyola del Vallès, Spain
| | - Elena Garcia-Fruitós
- Department of Ruminant Production, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, 08140 Caldes de Montbui, Barcelona, Spain
| | - Anna Mitraki
- Department of Materials Science and Technology, University of Crete, Vassilika Vouton, 70013 Heraklion, Crete, Greece.,Institute of Electronic Structure and Laser (IESL), Foundation for Research and Technology Hellas (FORTH), N. Plastira 100, Vassilika Vouton, 70013 Heraklion, Crete, Greece
| | | | - Ursula Rinas
- Leibniz University of Hannover, Technical Chemistry and Life Science, 30167 Hannover, Germany.,Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Mauricio A Trujillo-Roldán
- Programa de Investigación de Producción de Biomoléculas, Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510 Ciudad de México, México
| | - Norma A Valdez-Cruz
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510 Ciudad de México, México
| | - Esther Vázquez
- Institut de Biotecnologia i de Biomedicina (IBB), Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,Departament de Genètica i de Microbiologia, Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Carrer de la Vall Moronta s/n, 08193 Cerdanyola del Vallès, Spain
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina (IBB), Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,Departament de Genètica i de Microbiologia, Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Carrer de la Vall Moronta s/n, 08193 Cerdanyola del Vallès, Spain
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26
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Chura-Chambi RM, da Silva CMR, Pereira LR, Bartolini P, Ferreira LCDS, Morganti L. Protein refolding based on high hydrostatic pressure and alkaline pH: Application on a recombinant dengue virus NS1 protein. PLoS One 2019; 14:e0211162. [PMID: 30682103 PMCID: PMC6347194 DOI: 10.1371/journal.pone.0211162] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 01/08/2019] [Indexed: 12/13/2022] Open
Abstract
In this study we evaluated the association of high hydrostatic pressure (HHP) and alkaline pH as a minimally denaturing condition for the solubilization of inclusion bodies (IBs) generated by recombinant proteins expressed by Escherichia coli strains. The method was successfully applied to a recombinant form of the dengue virus (DENV) non-structural protein 1 (NS1). The minimal pH for IBs solubilization at 1 bar was 12 while a pH of 10 was sufficient for solubilization at HHP: 2.4 kbar for 90 min and 0.4 kbar for 14 h 30 min. An optimal refolding condition was achieved by compression of IBs at HHP and pH 10.5 in the presence of arginine, oxidized and reduced glutathiones, providing much higher yields (up to 8-fold) than association of HHP and GdnHCl via an established protocol. The refolded NS1, 109 ± 9.5 mg/L bacterial culture was recovered mainly as monomer and dimer, corresponding up to 90% of the total protein and remaining immunologically active. The proposed conditions represent an alternative for the refolding of immunologically active recombinant proteins expressed as IBs.
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Affiliation(s)
- Rosa Maria Chura-Chambi
- Centro de Biotecnologia, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP, São Paulo, São Paulo, Brazil
| | - Cleide Mara Rosa da Silva
- Centro de Biotecnologia, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP, São Paulo, São Paulo, Brazil
| | - Lennon Ramos Pereira
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Paolo Bartolini
- Centro de Biotecnologia, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP, São Paulo, São Paulo, Brazil
| | - Luis Carlos de Souza Ferreira
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Ligia Morganti
- Centro de Biotecnologia, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP, São Paulo, São Paulo, Brazil
- * E-mail:
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27
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28
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Flores SS, Nolan V, Perillo MA, Sánchez JM. Superactive β-galactosidase inclusion bodies. Colloids Surf B Biointerfaces 2018; 173:769-775. [PMID: 30384274 DOI: 10.1016/j.colsurfb.2018.10.049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/23/2018] [Accepted: 10/17/2018] [Indexed: 12/14/2022]
Abstract
Bacterial inclusion bodies (IBs) were historically considered one of the major obstacles in protein production through recombinant DNA techniques and conceived as amorphous deposits formed by passive and rather unspecific structures of unfolded proteins aggregates. Subsequent studies demonstrated that IBs contained an important quantity of active protein. In this work, we proved that recombinant β-galactosidase inclusion bodies (IBβ-Gal) are functional aggregates. Moreover, they exhibit particular features distinct to the soluble version of the enzyme. The particulate enzyme was highly active against lactose in physiological and in acid pH and also retained its activity upon a pre-incubation at high temperature. IBβ-Gal washing or dilution induced the spontaneous release of active enzymes from the supramolecular aggregates. Along this process, we observed a continuous change in the values of several kinetic parameters, including specific activity and Michaelis-Menten constant, measured in the IBβ-Gal suspensions. Simultaneously, IBβ-Gal turned into a more heterogeneous population where smaller particles appeared. The released protein exhibited secondary structure features more similar to those of the soluble species than to the aggregated enzyme. Concluding, IBβ-Gal represents a reservoir and packed source of highly active and stable enzyme.
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Affiliation(s)
- Sandra S Flores
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Córdoba, Argentina; CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIBYT), Córdoba, Argentina
| | - Verónica Nolan
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Córdoba, Argentina; CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIBYT), Córdoba, Argentina
| | - María A Perillo
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Córdoba, Argentina; CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIBYT), Córdoba, Argentina
| | - Julieta M Sánchez
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Córdoba, Argentina; CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIBYT), Córdoba, Argentina.
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29
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Abstract
Protein misfolding and aggregation into amyloid conformations have been described to underlie the onset of several human neurodegenerative diseases. Although a large number of biophysical approaches are available to study amyloids in vitro, we still need robust methods to address their self-assembly in living cells. In this context, simple cellular models, like bacteria and yeast, expressing recombinant amyloidogenic proteins are emerging as convenient systems for studying the formation of protein inclusions, their toxicity, propagation, and interactions. We describe here a simple and fast flow cytometry method able to detect intracellular inclusions, as well as to analyze the distribution of the amyloidogenic protein of interest in intact cells. Using specific fluorescent amyloid-dyes, such as thioflavin-S and ProteoStat, or the fusion of fluorescent molecules, such as GFP, the technique can be applied in the quantification of intracellular amyloid content, for the screening of antiamyloidogenic compounds, and to test epigenetic or environmental conditions able to modulate amyloid deposition in vivo.
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30
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Nakka PP, Li K, Forciniti D. Effect of Differences in the Primary Structure of the A-Chain on the Aggregation of Insulin Fragments. ACS OMEGA 2018; 3:9636-9647. [PMID: 31459094 PMCID: PMC6645046 DOI: 10.1021/acsomega.8b00500] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 08/08/2018] [Indexed: 06/10/2023]
Abstract
Bovine and human insulin have similar primary structures. In this article, the region of the insulin A-chain of bovine and human insulin where the amino acid composition is different was studied. Bovine insulin fragment (BIF) and human insulin fragment (HIF) were synthesized in solid-phase peptide synthesis. The effects of pH, temperature, urea, ionic strength, and stirring on the formation of fibrils were studied using a fractional factorial resolution III experimental design. Fibrillation was monitored by fluorescence and infrared spectroscopy and optical microscopy. Both fragments formed fibrils at pH 1.6 and a temperature of 60 °C. The lag time and apparent aggregation growth rate constant were determined using a two-parameter kinetic model. It was found that the bovine insulin fragment has a shorter lag time than the human insulin one, whereas the exponential phase rate was faster for HIF than for BIF. An increase in β-sheets content with time was observed in both fragments. The increase in β-sheets was preceded by an initial decrease in α-helices followed by an intermediate increase during the transition from the lag phase to elongation phase. Temperature and ionic strength are among the most important experimental factors during the lag phase, whereas ionic strength is replaced by pH during the elongation phase for both the fragments. Congo red binding confirmed the presence of ringlike oligomer structures rich in antiparallel β-sheets, which tend to form fibrils rich in parallel β-sheets.
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Affiliation(s)
- Paul P. Nakka
- Kielhorn Research Laboratory, Chemical
and Biochemical Engineering Department, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | - Ke Li
- Kielhorn Research Laboratory, Chemical
and Biochemical Engineering Department, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | - Daniel Forciniti
- Kielhorn Research Laboratory, Chemical
and Biochemical Engineering Department, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
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31
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Kaur G, Kapoor S, Thakur KG. Bacillus subtilis HelD, an RNA Polymerase Interacting Helicase, Forms Amyloid-Like Fibrils. Front Microbiol 2018; 9:1934. [PMID: 30186259 PMCID: PMC6111841 DOI: 10.3389/fmicb.2018.01934] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 07/30/2018] [Indexed: 12/26/2022] Open
Abstract
HelD, an RNA polymerase binding protein from Bacillus subtilis, stimulates transcription and helps in timely adaptation of cells under diverse environmental conditions. At present, no structural information is available for HelD. In the current study, we performed size exclusion chromatography coupled to small angle X-ray scattering (SEC-SAXS) which suggests that HelD is predominantly monomeric and globular in solution. Using combination of size exclusion chromatography and analytical ultracentrifugation, we also show that HelD has a tendency to form higher order oligomers in solution. CD experiments suggest that HelD has both α-helical (∼35%) and β sheet (∼26%) secondary structural elements. Thermal melting experiments suggest that even at 90°C, there is only about 30% loss in secondary structural contents with Tm of 44°C. However, with the increase in temperature, there was a gain in the β-sheet content and significant irreversible loss of α-helical content. Using a combination of X-ray fiber diffraction analysis, and dye based assays including Thioflavin-T based fluorescence and Congo red binding assays, we discovered that HelD forms amyloid-like fibrils at physiologically relevant conditions in vitro. Using confocal imaging, we further show that HelD forms amyloid inclusions in Escherichia coli. Bioinformatics-based sequence analysis performed using three independent web-based servers suggests that HelD has more than 20 hot-spots spread across the sequence that may aid the formation of amyloid-like fibrils. This discovery adds one more member to the growing list of amyloid or amyloid-like fibril forming cytosolic proteins in bacteria. Future studies aimed at resolving the function of amyloid-like fibrils or amyloid inclusions may help better understand their role, if any, in the bacterial physiology.
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Affiliation(s)
- Gundeep Kaur
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Srajan Kapoor
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Krishan G Thakur
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
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32
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Kell DB, Pretorius E. No effects without causes: the Iron Dysregulation and Dormant Microbes hypothesis for chronic, inflammatory diseases. Biol Rev Camb Philos Soc 2018; 93:1518-1557. [PMID: 29575574 PMCID: PMC6055827 DOI: 10.1111/brv.12407] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 02/12/2018] [Accepted: 02/15/2018] [Indexed: 12/11/2022]
Abstract
Since the successful conquest of many acute, communicable (infectious) diseases through the use of vaccines and antibiotics, the currently most prevalent diseases are chronic and progressive in nature, and are all accompanied by inflammation. These diseases include neurodegenerative (e.g. Alzheimer's, Parkinson's), vascular (e.g. atherosclerosis, pre-eclampsia, type 2 diabetes) and autoimmune (e.g. rheumatoid arthritis and multiple sclerosis) diseases that may appear to have little in common. In fact they all share significant features, in particular chronic inflammation and its attendant inflammatory cytokines. Such effects do not happen without underlying and initially 'external' causes, and it is of interest to seek these causes. Taking a systems approach, we argue that these causes include (i) stress-induced iron dysregulation, and (ii) its ability to awaken dormant, non-replicating microbes with which the host has become infected. Other external causes may be dietary. Such microbes are capable of shedding small, but functionally significant amounts of highly inflammagenic molecules such as lipopolysaccharide and lipoteichoic acid. Sequelae include significant coagulopathies, not least the recently discovered amyloidogenic clotting of blood, leading to cell death and the release of further inflammagens. The extensive evidence discussed here implies, as was found with ulcers, that almost all chronic, infectious diseases do in fact harbour a microbial component. What differs is simply the microbes and the anatomical location from and at which they exert damage. This analysis offers novel avenues for diagnosis and treatment.
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Affiliation(s)
- Douglas B. Kell
- School of ChemistryThe University of Manchester, 131 Princess StreetManchesterLancsM1 7DNU.K.
- The Manchester Institute of BiotechnologyThe University of Manchester, 131 Princess StreetManchesterLancsM1 7DNU.K.
- Department of Physiological SciencesStellenbosch University, Stellenbosch Private Bag X1Matieland7602South Africa
| | - Etheresia Pretorius
- Department of Physiological SciencesStellenbosch University, Stellenbosch Private Bag X1Matieland7602South Africa
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33
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Takekiyo T, Yoshimura Y. Suppression and dissolution of amyloid aggregates using ionic liquids. Biophys Rev 2018; 10:853-860. [PMID: 29696571 DOI: 10.1007/s12551-018-0421-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 04/08/2018] [Indexed: 12/22/2022] Open
Abstract
Amyloid aggregates are composed of protein fibrils with a dominant β-sheet structure, are water-insoluble, and are involved in the pathogenesis of many neurodegenerative diseases. Development of pharmaceuticals to treat these diseases and the design of recovery agents for amyloid-type inclusion bodies require the successful suppression and dissolution of such aggregates. Since ionic liquids (ILs) are composed of both a cation and anion and are known to suppress protein aggregation and to dissolve water-insoluble compounds such as cellulose; they may also have potential use as suppression/dissolution agents for amyloid aggregates. In the following review, we present the suppression and dissolution effects of ILs on amyloid aggregates so far reported. The protein-IL affinity (the ability of ILs to interact with amyloid proteins) was found to be the biochemical basis for ILs' suppression of amyloid formation, and the hydrogen-bonding basicity of ILs might be the basis for their ability to dissolve amyloid aggregates. These findings present the potential of ILs to serve as novel pharmaceuticals to treat neurodegenerative diseases and as recovery agents for various amyloid aggregates.
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Affiliation(s)
- Takahiro Takekiyo
- Department of Applied Chemistry, National Defense Academy, 1-10-20, Hashirimizu, Yokosuka, Kanagawa, 239-8686, Japan.
| | - Yukihiro Yoshimura
- Department of Applied Chemistry, National Defense Academy, 1-10-20, Hashirimizu, Yokosuka, Kanagawa, 239-8686, Japan
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34
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Khodaparast L, Khodaparast L, Gallardo R, Louros NN, Michiels E, Ramakrishnan R, Ramakers M, Claes F, Young L, Shahrooei M, Wilkinson H, Desager M, Mengistu Tadesse W, Nilsson KPR, Hammarström P, Aertsen A, Carpentier S, Van Eldere J, Rousseau F, Schymkowitz J. Aggregating sequences that occur in many proteins constitute weak spots of bacterial proteostasis. Nat Commun 2018; 9:866. [PMID: 29491361 PMCID: PMC5830399 DOI: 10.1038/s41467-018-03131-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 01/17/2018] [Indexed: 01/18/2023] Open
Abstract
Aggregation is a sequence-specific process, nucleated by short aggregation-prone regions (APRs) that can be exploited to induce aggregation of proteins containing the same APR. Here, we find that most APRs are unique within a proteome, but that a small minority of APRs occur in many proteins. When aggregation is nucleated in bacteria by such frequently occurring APRs, it leads to massive and lethal inclusion body formation containing a large number of proteins. Buildup of bacterial resistance against these peptides is slow. In addition, the approach is effective against drug-resistant clinical isolates of Escherichiacoli and Acinetobacterbaumannii, reducing bacterial load in a murine bladder infection model. Our results indicate that redundant APRs are weak points of bacterial protein homeostasis and that targeting these may be an attractive antibacterial strategy. Aggregation is sequence-specific and nucleated by short aggregating protein segments (APR). Here authors use a multidisciplinary approach to show that in E.coli some frequently occurring APRs lead to protein aggregation and ultimately bacterial cell death, which could serve as antibacterial strategy.
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Affiliation(s)
- Ladan Khodaparast
- Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology and Immunology, KULeuven, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, Herestraat 49, 3000, Leuven, Belgium
| | - Laleh Khodaparast
- Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology and Immunology, KULeuven, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, Herestraat 49, 3000, Leuven, Belgium
| | - Rodrigo Gallardo
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, Herestraat 49, 3000, Leuven, Belgium
| | - Nikolaos N Louros
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, Herestraat 49, 3000, Leuven, Belgium
| | - Emiel Michiels
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, Herestraat 49, 3000, Leuven, Belgium
| | - Reshmi Ramakrishnan
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, Herestraat 49, 3000, Leuven, Belgium
| | - Meine Ramakers
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, Herestraat 49, 3000, Leuven, Belgium
| | - Filip Claes
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, Herestraat 49, 3000, Leuven, Belgium
| | - Lydia Young
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Mohammad Shahrooei
- Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology and Immunology, KULeuven, Herestraat 49, 3000, Leuven, Belgium
| | - Hannah Wilkinson
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, Herestraat 49, 3000, Leuven, Belgium
| | - Matyas Desager
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, Herestraat 49, 3000, Leuven, Belgium
| | - Wubishet Mengistu Tadesse
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems (M²S), KULeuven, Kasteelpark Arenberg 22, 3001, Leuven, Belgium
| | - K Peter R Nilsson
- Department of Physics, Chemistry and Biology, Linköping University, SE-581 83, Linköping, Sweden
| | - Per Hammarström
- Department of Physics, Chemistry and Biology, Linköping University, SE-581 83, Linköping, Sweden
| | - Abram Aertsen
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems (M²S), KULeuven, Kasteelpark Arenberg 22, 3001, Leuven, Belgium
| | - Sebastien Carpentier
- Systems Biology based Mass Spectrometry Laboratory (SyBioMa), KULeuven, Herestraat 49, 3000, Leuven, Belgium
| | - Johan Van Eldere
- Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology and Immunology, KULeuven, Herestraat 49, 3000, Leuven, Belgium.
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium. .,Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, Herestraat 49, 3000, Leuven, Belgium.
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium. .,Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, Herestraat 49, 3000, Leuven, Belgium.
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35
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Abstract
Mammalian prion proteins (PrPs) that cause transmissible spongiform encephalopathies are misfolded conformations of the host cellular PrP. The misfolded form, the scrapie PrP (PrP(Sc)), can aggregate into amyloid fibrils that progressively accumulate in the brain, evolving to a pathological phenotype. A particular characteristic of PrP(Sc) is to be found as different strains, related to the diversity of conformational states it can adopt. Prion strains are responsible for the multiple phenotypes observed in prion diseases, presenting different incubation times and diverse deposition profiles in the brain. PrP biochemical properties are also strain-dependent, such as different digestion pattern after proteolysis and different stability. Although they have long been studied, strain formation is still a major unsolved issue in prion biology. The recreation of strain-specific conformational features is of fundamental importance to study this unique pathogenic phenomenon. In our recent paper, we described that murine PrP, when expressed in bacteria, forms amyloid inclusion bodies that possess different strain-like characteristics, depending on the PrP construct. Here, we present an extra-view of these data and propose that bacteria might become a successful model to generate preparative amounts of prion strain-specific assemblies for high-resolution structural analysis as well as for addressing the determinants of infectivity and transmissibility.
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Affiliation(s)
- Bruno Macedo
- a Institut de Biotecnologia i de Biomedicina and Departament de Bioquimica i Biologia Molecular , Universitat Autonoma de Barcelona , Bellaterra ( Barcelona ), Spain ;,b Faculdade de Farmacia , Universidade Federal do Rio de Janeiro, Rio de Janeiro , Brazil
| | - Yraima Cordeiro
- b Faculdade de Farmacia , Universidade Federal do Rio de Janeiro, Rio de Janeiro , Brazil
| | - Salvador Ventura
- a Institut de Biotecnologia i de Biomedicina and Departament de Bioquimica i Biologia Molecular , Universitat Autonoma de Barcelona , Bellaterra ( Barcelona ), Spain
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36
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Hayward S, Milner-White EJ. Geometrical principles of homomeric β-barrels and β-helices: Application to modeling amyloid protofilaments. Proteins 2017. [PMID: 28646497 DOI: 10.1002/prot.25341] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Examples of homomeric β-helices and β-barrels have recently emerged. Here we generalize the theory for the shear number in β-barrels to encompass β-helices and homomeric structures. We introduce the concept of the "β-strip," the set of parallel or antiparallel neighboring strands, from which the whole helix can be generated giving it n-fold rotational symmetry. In this context, the shear number is interpreted as the sum around the helix of the fixed register shift between neighboring identical β-strips. Using this approach, we have derived relationships between helical width, pitch, angle between strand direction and helical axis, mass per length, register shift, and number of strands. The validity and unifying power of the method is demonstrated with known structures including α-hemolysin, T4 phage spike, cylindrin, and the HET-s(218-289) prion. From reported dimensions measured by X-ray fiber diffraction on amyloid fibrils, the relationships can be used to predict the register shift and the number of strands within amyloid protofilaments. This was used to construct models of transthyretin and Alzheimer β(40) amyloid protofilaments that comprise a single strip of in-register β-strands folded into a "β-strip helix." Results suggest both stabilization of an individual β-strip helix and growth by addition of further β-strip helices can involve the same pair of sequence segments associating with β-sheet hydrogen bonding at the same register shift. This process would be aided by a repeat sequence. Hence, understanding how the register shift (as the distance between repeat sequences) relates to helical dimensions will be useful for nanotube design.
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Affiliation(s)
- Steven Hayward
- D'Arcy Thompson Centre for Computational Biology, School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - E James Milner-White
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
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37
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Elia F, Cantini F, Chiti F, Dobson CM, Bemporad F. Direct Conversion of an Enzyme from Native-like to Amyloid-like Aggregates within Inclusion Bodies. Biophys J 2017; 112:2540-2551. [PMID: 28636911 PMCID: PMC5479110 DOI: 10.1016/j.bpj.2017.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 05/02/2017] [Accepted: 05/08/2017] [Indexed: 01/29/2023] Open
Abstract
The acylphosphatase from Sulfolobus solfataricus (Sso AcP) is a globular protein able to aggregate in vitro from a native-like conformational ensemble without the need for a transition across the major unfolding energy barrier. This process leads to the formation of assemblies in which the protein retains its native-like structure, which subsequently convert into amyloid-like aggregates. Here, we investigate the mechanism by which Sso AcP aggregates in vivo to form bacterial inclusion bodies after expression in E. coli. Shortly after the initiation of expression, Sso AcP is incorporated into inclusion bodies as a native-like protein, still exhibiting small but significant enzymatic activity. Additional experiments revealed that this overall process of aggregation is enhanced by the presence of the unfolded N-terminal region of the sequence and by destabilization of the globular segment of the protein. At later times, the Sso AcP molecules in the inclusion bodies lose their native-like properties and convert into β-sheet-rich amyloid-like structures, as indicated by their ability to bind thioflavin T and Congo red. These results show that the aggregation behavior of this protein is similar in vivo to that observed in vitro, and that, at least for a predominant part of the protein population, the transition from a native to an amyloid-like structure occurs within the aggregate state.
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Affiliation(s)
- Francesco Elia
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio," University of Florence, Firenze, Italy
| | - Francesca Cantini
- Centro Risonanze Magnetiche (CERM) and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio," University of Florence, Firenze, Italy
| | | | - Francesco Bemporad
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio," University of Florence, Firenze, Italy.
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38
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Rinas U, Garcia-Fruitós E, Corchero JL, Vázquez E, Seras-Franzoso J, Villaverde A. Bacterial Inclusion Bodies: Discovering Their Better Half. Trends Biochem Sci 2017; 42:726-737. [PMID: 28254353 DOI: 10.1016/j.tibs.2017.01.005] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 01/23/2017] [Accepted: 01/26/2017] [Indexed: 01/07/2023]
Abstract
Bacterial inclusion bodies (IBs) are functional, non-toxic amyloids occurring in recombinant bacteria showing analogies with secretory granules of the mammalian endocrine system. The scientific interest in these mesoscale protein aggregates has been historically masked by their status as a hurdle in recombinant protein production. However, progressive understanding of how the cell handles the quality of recombinant polypeptides and the main features of their intriguing molecular organization has stimulated the interest in inclusion bodies and spurred their use in diverse technological fields. The engineering and tailoring of IBs as functional protein particles for materials science and biomedicine is a good example of how formerly undesired bacterial byproducts can be rediscovered as promising functional materials for a broad spectrum of applications.
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Affiliation(s)
- Ursula Rinas
- Leibniz University of Hannover, Technical Chemistry and Life Science, Hannover, Germany; Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Elena Garcia-Fruitós
- Department of Ruminant Production, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, 08140 Caldes de Montbui, Barcelona, Spain
| | - José Luis Corchero
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Bellaterra, 08193 Cerdanyola del Vallès, Spain; Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Cerdanyola del Vallès, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Cerdanyola del Vallès, Spain
| | - Esther Vázquez
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Bellaterra, 08193 Cerdanyola del Vallès, Spain; Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Cerdanyola del Vallès, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Cerdanyola del Vallès, Spain
| | - Joaquin Seras-Franzoso
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Bellaterra, 08193 Cerdanyola del Vallès, Spain; Molecular Biology and Biochemistry Research Center for Nanomedicine (Cibbim-Nanomedicine), Hospital Vall d'Hebron, Passeig de la Vall d'Hebron, 119-129, 08035 Barcelona, Spain
| | - Antonio Villaverde
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Bellaterra, 08193 Cerdanyola del Vallès, Spain; Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Cerdanyola del Vallès, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Cerdanyola del Vallès, Spain.
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39
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Berini F, Presti I, Beltrametti F, Pedroli M, Vårum KM, Pollegioni L, Sjöling S, Marinelli F. Production and characterization of a novel antifungal chitinase identified by functional screening of a suppressive-soil metagenome. Microb Cell Fact 2017; 16:16. [PMID: 28137256 PMCID: PMC5282697 DOI: 10.1186/s12934-017-0634-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 01/20/2017] [Indexed: 01/20/2023] Open
Abstract
Background Through functional screening of a fosmid library, generated from a phytopathogen-suppressive soil metagenome, the novel antifungal chitinase—named Chi18H8 and belonging to family 18 glycosyl hydrolases—was previously discovered. The initial extremely low yield of Chi18H8 recombinant production and purification from Escherichia coli cells (21 μg/g cell) limited its characterization, thus preventing further investigation on its biotechnological potential. Results We report on how we succeeded in producing hundreds of milligrams of pure and biologically active Chi18H8 by developing and scaling up to a high-yielding, 30 L bioreactor process, based on a novel method of mild solubilization of E. coli inclusion bodies in lactic acid aqueous solution, coupled with a single step purification by hydrophobic interaction chromatography. Chi18H8 was characterized as a Ca2+-dependent mesophilic chitobiosidase, active on chitin substrates at acidic pHs and possessing interesting features, such as solvent tolerance, long-term stability in acidic environment and antifungal activity against the phytopathogens Fusarium graminearum and Rhizoctonia solani. Additionally, Chi18H8 was found to operate according to a non-processive endomode of action on a water-soluble chitin-like substrate. Conclusions Expression screening of a metagenomic library may allow access to the functional diversity of uncultivable microbiota and to the discovery of novel enzymes useful for biotechnological applications. A persisting bottleneck, however, is the lack of methods for large scale production of metagenome-sourced enzymes from genes of unknown origin in the commonly used microbial hosts. To our knowledge, this is the first report on a novel metagenome-sourced enzyme produced in hundreds-of-milligram amount by recovering the protein in the biologically active form from recombinant E. coli inclusion bodies. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0634-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Francesca Berini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy. .,"The Protein Factory Research Center", Politecnico di Milano and University of Insubria, Varese, Italy.
| | - Ilaria Presti
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.,"The Protein Factory Research Center", Politecnico di Milano and University of Insubria, Varese, Italy.,Chemo Biosynthesis, Corana, Pavia, Italy
| | | | | | - Kjell M Vårum
- NOBIPOL, Department of Biotechnology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.,"The Protein Factory Research Center", Politecnico di Milano and University of Insubria, Varese, Italy
| | - Sara Sjöling
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Huddinge, Sweden
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.,"The Protein Factory Research Center", Politecnico di Milano and University of Insubria, Varese, Italy
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40
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Proteins behaving badly. Substoichiometric molecular control and amplification of the initiation and nature of amyloid fibril formation: lessons from and for blood clotting. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 123:16-41. [DOI: 10.1016/j.pbiomolbio.2016.08.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 08/14/2016] [Accepted: 08/19/2016] [Indexed: 02/08/2023]
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41
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Marchese D, de Groot NS, Lorenzo Gotor N, Livi CM, Tartaglia GG. Advances in the characterization of RNA-binding proteins. WILEY INTERDISCIPLINARY REVIEWS. RNA 2016; 7:793-810. [PMID: 27503141 PMCID: PMC5113702 DOI: 10.1002/wrna.1378] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 06/14/2016] [Accepted: 06/23/2016] [Indexed: 12/14/2022]
Abstract
From transcription, to transport, storage, and translation, RNA depends on association with different RNA-binding proteins (RBPs). Methods based on next-generation sequencing and protein mass-spectrometry have started to unveil genome-wide interactions of RBPs but many aspects still remain out of sight. How many of the binding sites identified in high-throughput screenings are functional? A number of computational methods have been developed to analyze experimental data and to obtain insights into the specificity of protein-RNA interactions. How can theoretical models be exploited to identify RBPs? In addition to oligomeric complexes, protein and RNA molecules can associate into granular assemblies whose physical properties are still poorly understood. What protein features promote granule formation and what effects do these assemblies have on cell function? Here, we describe the newest in silico, in vitro, and in vivo advances in the field of protein-RNA interactions. We also present the challenges that experimental and computational approaches will have to face in future studies. WIREs RNA 2016, 7:793-810. doi: 10.1002/wrna.1378 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Domenica Marchese
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Natalia Sanchez de Groot
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Nieves Lorenzo Gotor
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Carmen Maria Livi
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- IFOM Foundation, FIRC Institute of Molecular Oncology Foundation, Milan, Italy
| | - Gian G Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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42
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González MC, Romero JM, Ingaramo MC, Muñoz Sosa CJ, Curtino JA, Carrizo ME. Enhancement by GOSPEL protein of GAPDH aggregation induced by nitric oxide donor and its inhibition by NAD(.). FEBS Lett 2016; 590:2210-20. [PMID: 27282776 DOI: 10.1002/1873-3468.12242] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 05/31/2016] [Accepted: 06/06/2016] [Indexed: 11/12/2022]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase's (GAPDH's) competitor of Siah Protein Enhances Life (GOSPEL) is the protein that competes with Siah1 for binding to GAPDH under NO-induced stress conditions preventing Siah1-bound GAPDH nuclear translocation and subsequent apoptosis. Under these conditions, GAPDH may also form amyloid-like aggregates proposed to be involved in cell death. Here, we report the in vitro enhancement by GOSPEL of NO-induced GAPDH aggregation resulting in the formation GOSPEL-GAPDH co-aggregates with some amyloid-like properties. Our findings suggest a new function for GOSPEL, contrasting with its helpful role against the apoptotic nuclear translocation of GAPDH. NAD(+) inhibited both GAPDH aggregation and co-aggregation with GOSPEL, a hitherto undescribed effect of the coenzyme against the consequences of oxidative stress.
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Affiliation(s)
- María C González
- Departamento de Química Biológica, Facultad de Ciencias Químicas, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Universidad Nacional de Córdoba-Consejo Nacional de Investigaciones Científicas y Técnicas (UNC-CONICET), Universidad Nacional de Córdoba, Argentina
| | - Jorge M Romero
- Departamento de Química Biológica, Facultad de Ciencias Químicas, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Universidad Nacional de Córdoba-Consejo Nacional de Investigaciones Científicas y Técnicas (UNC-CONICET), Universidad Nacional de Córdoba, Argentina
| | - María C Ingaramo
- Departamento de Química Biológica, Facultad de Ciencias Químicas, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Universidad Nacional de Córdoba-Consejo Nacional de Investigaciones Científicas y Técnicas (UNC-CONICET), Universidad Nacional de Córdoba, Argentina
| | - Christian J Muñoz Sosa
- Departamento de Química Biológica, Facultad de Ciencias Químicas, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Universidad Nacional de Córdoba-Consejo Nacional de Investigaciones Científicas y Técnicas (UNC-CONICET), Universidad Nacional de Córdoba, Argentina
| | - Juan A Curtino
- Departamento de Química Biológica, Facultad de Ciencias Químicas, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Universidad Nacional de Córdoba-Consejo Nacional de Investigaciones Científicas y Técnicas (UNC-CONICET), Universidad Nacional de Córdoba, Argentina
| | - María E Carrizo
- Departamento de Química Biológica, Facultad de Ciencias Químicas, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Universidad Nacional de Córdoba-Consejo Nacional de Investigaciones Científicas y Técnicas (UNC-CONICET), Universidad Nacional de Córdoba, Argentina
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43
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Ultra rapid in vivo screening for anti-Alzheimer anti-amyloid drugs. Sci Rep 2016; 6:23349. [PMID: 27000658 PMCID: PMC4802339 DOI: 10.1038/srep23349] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/02/2016] [Indexed: 12/20/2022] Open
Abstract
More than 46 million people worldwide suffer from Alzheimer’s disease. A
large number of potential treatments have been proposed; among these, the inhibition
of the aggregation of amyloid β-peptide (Aβ), considered one
of the main culprits in Alzheimer’s disease. Limitations in monitoring
the aggregation of Aβ in cells and tissues restrict the screening of
anti-amyloid drugs to in vitro studies in most cases. We have developed a
simple but powerful method to track Aβ aggregation in vivo in
real-time, using bacteria as in vivo amyloid reservoir. We use the specific
amyloid dye Thioflavin-S (Th-S) to stain bacterial inclusion bodies (IBs), in this
case mainly formed of Aβ in amyloid conformation. Th-S binding to
amyloids leads to an increment of fluorescence that can be monitored. The
quantification of the Th-S fluorescence along the time allows tracking
Aβ aggregation and the effect of potential anti-aggregating agents.
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44
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Ensemble Modeling and Intracellular Aggregation of an Engineered Immunoglobulin-Like Domain. J Mol Biol 2016; 428:1365-1374. [DOI: 10.1016/j.jmb.2016.02.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 01/28/2016] [Accepted: 02/12/2016] [Indexed: 11/21/2022]
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45
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Villar-Piqué A, Espargaró A, Ventura S, Sabate R. In vivo amyloid aggregation kinetics tracked by time-lapse confocal microscopy in real-time. Biotechnol J 2016; 11:172-7. [PMID: 26580000 DOI: 10.1002/biot.201500252] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 07/29/2015] [Accepted: 10/15/2015] [Indexed: 11/05/2022]
Abstract
Amyloid polymerization underlies an increasing number of human diseases. Despite this process having been studied extensively in vitro, aggregation is a difficult process to track in vivo due to methodological limitations and the slow kinetics of aggregation reactions in cells and tissues. Herein we exploit the amyloid properties of the inclusions bodies (IBs) formed by amyloidogenic proteins in bacteria to address the kinetics of in vivo amyloid aggregation. To this aim we used time-lapse confocal microscopy and a fusion of the amyloid-beta peptide (A β42) with a fluorescent reporter. This strategy allowed us to follow the intracellular kinetics of amyloid-like aggregation in real-time and to discriminate between variants exhibiting different in vivo aggregation propensity. Overall, the approach opens the possibility to assess the impact of point mutations as well as potential anti-aggregation drugs in the process of amyloid formation in living cells.
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Affiliation(s)
- Anna Villar-Piqué
- Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain.,Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellatera, Spain
| | - Alba Espargaró
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain.,Institut de Nanociència i Nanotecnologia (IN²UB), Spain
| | - Salvador Ventura
- Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain. .,Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellatera, Spain.
| | - Raimon Sabate
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain. .,Institut de Nanociència i Nanotecnologia (IN²UB), Spain.
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Espargaró A, Busquets MA, Estelrich J, Sabate R. Amyloids in solid-state nuclear magnetic resonance: potential causes of the usually low resolution. Int J Nanomedicine 2015; 10:6975-83. [PMID: 26635473 PMCID: PMC4646584 DOI: 10.2147/ijn.s89385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Amyloids are non-crystalline and insoluble, which imply that the classical structural biology tools, ie, X-ray crystallography and solution nuclear magnetic resonance (NMR), are not suitable for their analysis. In the last years, solid-state NMR (ssNMR) has emerged as an alternative tool to decrypt the structural signatures of amyloid fibrils, providing major contributions to our understanding of molecular structures of amyloids such as β-amyloid peptide associated with Alzheimer’s disease or fungal prions, among others. Despite this, the wide majority of amyloid fibrils display low resolution by ssNMR. Usually, this low resolution has been attributed to a high disorder or polymorphism of the fibrils, suggesting the existence of diverse elementary β-sheet structures. Here, we propose that a single β-sheet structure could be responsible for the broadening of the line widths in the ssNMR spectra. Although the fibrils and fibers consist of a single elementary structure, the angle of twist of each individual fibril in the mature fiber depends on the number of individual fibrils as well as the fibril arrangement in the final mature fiber. Thus, a wide range of angles of twist could be observed in the same amyloid sample. These twist variations involve changes in amino acid alignments that could be enough to limit the ssNMR resolution.
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Affiliation(s)
- Alba Espargaró
- Department of Physical Chemistry, School of Pharmacy, Institute of Nanoscience and Nanotechnology (IN UB), University of Barcelona, Barcelona, Spain
| | - Maria Antònia Busquets
- Department of Physical Chemistry, School of Pharmacy, Institute of Nanoscience and Nanotechnology (IN UB), University of Barcelona, Barcelona, Spain
| | - Joan Estelrich
- Department of Physical Chemistry, School of Pharmacy, Institute of Nanoscience and Nanotechnology (IN UB), University of Barcelona, Barcelona, Spain
| | - Raimon Sabate
- Department of Physical Chemistry, School of Pharmacy, Institute of Nanoscience and Nanotechnology (IN UB), University of Barcelona, Barcelona, Spain
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Mammalian prion protein (PrP) forms conformationally different amyloid intracellular aggregates in bacteria. Microb Cell Fact 2015; 14:174. [PMID: 26536866 PMCID: PMC4634817 DOI: 10.1186/s12934-015-0361-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 10/17/2015] [Indexed: 01/21/2023] Open
Abstract
Background An increasing number of proteins are being shown to assemble into amyloid structures that lead to pathological states. Among them, mammalian prions outstand due to their ability to transmit the pathogenic conformation, becoming thus infectious. The structural conversion of the cellular prion protein (PrPC), into its misfolded pathogenic form (PrPSc) is the central event of prion-driven pathologies. The study of the structural properties of intracellular amyloid aggregates in general and of prion-like ones in particular is a challenging task. In this context, the evidence that the inclusion bodies formed by amyloid proteins in bacteria display amyloid-like structural and functional properties make them a privileged system to model intracellular amyloid aggregation. Results Here we provide the first demonstration that recombinant murine PrP and its C-terminal domain (90–231) attain amyloid conformations inside bacteria. Moreover, the inclusions formed by these two PrP proteins display conformational diversity, since they differ in fibril morphology, binding affinity to amyloid dyes, stability, resistance to proteinase K digestion and neurotoxicity. Conclusions Overall, our results suggest that modelling PrP amyloid formation in microbial cell factories might open an avenue for a better understanding of the structural features modulating the pathogenic impact of this intriguing protein. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0361-y) contains supplementary material, which is available to authorized users.
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Eukaryotic aggresomes: from a model of conformational diseases to an emerging type of immobilized biocatalyzers. Appl Microbiol Biotechnol 2015; 100:559-69. [DOI: 10.1007/s00253-015-7107-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 10/14/2015] [Accepted: 10/15/2015] [Indexed: 12/28/2022]
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Navarro S, Carija A, Muñoz-Torrero D, Ventura S. A fast and specific method to screen for intracellular amyloid inhibitors using bacterial model systems. Eur J Med Chem 2015; 121:785-792. [PMID: 26608003 DOI: 10.1016/j.ejmech.2015.10.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 10/23/2015] [Accepted: 10/26/2015] [Indexed: 11/25/2022]
Abstract
The aggregation of a large variety of amyloidogenic proteins is linked to the onset of devastating human disorders. Therefore, there is an urgent need for effective molecules able to modulate the aggregative properties of these polypeptides in their natural environment, in order to prevent, delay or halt the progression of such diseases. On the one hand, the complexity and cost of animal models make them inefficient at early stages of drug discovery, where large chemical libraries are usually screened. On the other hand, in vitro aggregation assays in aqueous solutions hardly reproduce (patho)physiological conditions. In this context, because the formation of insoluble aggregates in bacteria shares mechanistic and functional properties with amyloid self-assembly in higher organisms, they have emerged as a promising system to model aggregation in the cell. Here we show that bacteria provide a powerful and cost-effective system to screen for amyloid inhibitors using fluorescence spectroscopy and flow cytometry, thanks to the ability of the novel red fluorescent ProteoStat dye to detect specifically intracellular amyloid-like aggregates. We validated the approach using the Alzheimer's linked Aβ40 and Aβ42 peptides and tacrine- and huprine-based aggregation inhibitors. Overall, the present method bears the potential to replace classical in vitro anti-aggregation assays.
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Affiliation(s)
- Susanna Navarro
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
| | - Anita Carija
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Diego Muñoz-Torrero
- Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Facultat de Farmàcia, and Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028, Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
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Navarro S, Marinelli P, Diaz-Caballero M, Ventura S. The prion-like RNA-processing protein HNRPDL forms inherently toxic amyloid-like inclusion bodies in bacteria. Microb Cell Fact 2015; 14:102. [PMID: 26160665 PMCID: PMC4498515 DOI: 10.1186/s12934-015-0284-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 06/16/2015] [Indexed: 01/09/2023] Open
Abstract
Background The formation of protein inclusions is connected to the onset of many human diseases. Human RNA binding proteins containing intrinsically disordered regions with an amino acid composition resembling those of yeast prion domains, like TDP-43 or FUS, are being found to aggregate in different neurodegenerative disorders. The structure of the intracellular inclusions formed by these proteins is still unclear and whether these deposits have an amyloid nature or not is a matter of debate. Recently, the aggregation of TDP-43 has been modelled in bacteria, showing that TDP-43 inclusion bodies (IBs) are amorphous but intrinsically neurotoxic. This observation raises the question of whether it is indeed the lack of an ordered structure in these human prion-like protein aggregates the underlying cause of their toxicity in different pathological states. Results Here we characterize the IBs formed by the human prion-like RNA-processing protein HNRPDL. HNRPDL is linked to the development of limb-girdle muscular dystrophy 1G and shares domain architecture with TDP-43. We show that HNRPDL IBs display characteristic amyloid hallmarks, since these aggregates bind to amyloid dyes in vitro and inside the cell, they are enriched in intermolecular β-sheet conformation and contain inner amyloid-like fibrillar structure. In addition, despite their ordered structure, HNRPDL IBs are highly neurotoxic. Conclusions Our results suggest that at least some of the disorders caused by the aggregation of human prion-like proteins would rely on the formation of classical amyloid assemblies rather than being caused by amorphous aggregates. They also illustrate the power of microbial cell factories to model amyloid aggregation. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0284-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Susanna Navarro
- Institut de Biotecnologia i Biomedicina, Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.
| | - Patrizia Marinelli
- Institut de Biotecnologia i Biomedicina, Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.
| | - Marta Diaz-Caballero
- Institut de Biotecnologia i Biomedicina, Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina, Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.
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