1
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Pollack D, Nozoe T, Kussell E. Proteolytic stability and aggregation in a key metabolic enzyme of bacteria. Proc Natl Acad Sci U S A 2024; 121:e2301458121. [PMID: 38683989 PMCID: PMC11087809 DOI: 10.1073/pnas.2301458121] [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: 01/31/2023] [Accepted: 03/07/2024] [Indexed: 05/02/2024] Open
Abstract
Proteins that are kinetically stable are thought to be less prone to both aggregation and proteolysis. We demonstrate that the classical lac system of Escherichia coli can be leveraged as a model system to study this relation. β-galactosidase (LacZ) plays a critical role in lactose metabolism and is an extremely stable protein that can persist in growing cells for multiple generations after expression has stopped. By attaching degradation tags to the LacZ protein, we find that LacZ can be transiently degraded during lac operon expression but once expression has stopped functional LacZ is protected from degradation. We reversibly destabilize its tetrameric assembly using α-complementation, and show that unassembled LacZ monomers and dimers can either be degraded or lead to formation of aggregates within cells, while the tetrameric state protects against proteolysis and aggregation. We show that the presence of aggregates is associated with cell death, and that these proteotoxic stress phenotypes can be alleviated by attaching an ssrA tag to LacZ monomers which leads to their degradation. We unify our findings using a biophysical model that enables the interplay of protein assembly, degradation, and aggregation to be studied quantitatively in vivo. This work may yield approaches to reversing and preventing protein-misfolding disease states, while elucidating the functions of proteolytic stability in constant and fluctuating environments.
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Affiliation(s)
- Dan Pollack
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY10003
| | - Takashi Nozoe
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo153-8902, Japan
- Research Center for Complex Systems Biology, The University of Tokyo, Tokyo153-8902, Japan
- Universal Biology Institute, The University of Tokyo, Tokyo113-0033, Japan
| | - Edo Kussell
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY10003
- Department of Physics, New York University, New York, NY10003
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2
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Mortier J, Cambré A, Schack S, Christie G, Aertsen A. Impact of Protein Aggregates on Sporulation and Germination of Bacillus subtilis. Microorganisms 2023; 11:2365. [PMID: 37764209 PMCID: PMC10536567 DOI: 10.3390/microorganisms11092365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
In order to improve our general understanding of protein aggregate (PA) management and impact in bacteria, different model systems and processes need to be investigated. As such, we developed an inducible synthetic PA model system to investigate PA dynamics in the Gram-positive model organism Bacillus subtilis. This confirmed previous observations that PA segregation in this organism seems to follow the Escherichia coli paradigm of nucleoid occlusion governing polar localization and asymmetric segregation during vegetative growth. However, our findings also revealed that PAs can readily persist throughout the entire sporulation process after encapsulation in the forespore during sporulation. Moreover, no deleterious effects of PA presence on sporulation, germination and spore survival against heat or UV stress could be observed. Our findings therefore indicate that the sporulation process is remarkably robust against perturbations by PAs and misfolded proteins.
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Affiliation(s)
- Julien Mortier
- Department of Microbial and Molecular Systems, KU Leuven, B-3000 Leuven, Belgium; (J.M.); (A.C.)
| | - Alexander Cambré
- Department of Microbial and Molecular Systems, KU Leuven, B-3000 Leuven, Belgium; (J.M.); (A.C.)
| | - Sina Schack
- Department of Chemical Engineering & Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK; (S.S.); (G.C.)
| | - Graham Christie
- Department of Chemical Engineering & Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK; (S.S.); (G.C.)
| | - Abram Aertsen
- Department of Microbial and Molecular Systems, KU Leuven, B-3000 Leuven, Belgium; (J.M.); (A.C.)
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3
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Kuczyńska-Wiśnik D, Stojowska-Swędrzyńska K, Laskowska E. Liquid-Liquid Phase Separation and Protective Protein Aggregates in Bacteria. Molecules 2023; 28:6582. [PMID: 37764358 PMCID: PMC10534466 DOI: 10.3390/molecules28186582] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/09/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) and the formation of membraneless organelles (MLOs) contribute to the spatiotemporal organization of various physiological processes in the cell. These phenomena have been studied and characterized mainly in eukaryotic cells. However, increasing evidence indicates that LLPS-driven protein condensation may also occur in prokaryotes. Recent studies indicate that aggregates formed during proteotoxic stresses may also play the role of MLOs and increase the fitness of bacteria under stress. The beneficial effect of aggregates may result from the sequestration and protection of proteins against irreversible inactivation or degradation, activation of the protein quality control system and induction of dormancy. The most common stress that bacteria encounter in the natural environment is water loss. Therefore, in this review, we focus on protein aggregates formed in E. coli upon desiccation-rehydration stress. In silico analyses suggest that various mechanisms and interactions are responsible for their formation, including LLPS, disordered sequences and aggregation-prone regions. These data support findings that intrinsically disordered proteins and LLPS may contribute to desiccation tolerance not only in eukaryotic cells but also in bacteria. LLPS-driven aggregation may be a strategy used by pathogens to survive antibiotic treatment and desiccation stress in the hospital environment.
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Affiliation(s)
| | | | - Ewa Laskowska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (D.K.-W.); (K.S.-S.)
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4
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Motamedi H, Alvandi A, Fathollahi M, Ari MM, Moradi S, Moradi J, Abiri R. In silico designing and immunoinformatics analysis of a novel peptide vaccine against metallo-beta-lactamase (VIM and IMP) variants. PLoS One 2023; 18:e0275237. [PMID: 37471423 PMCID: PMC10358925 DOI: 10.1371/journal.pone.0275237] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/12/2022] [Indexed: 07/22/2023] Open
Abstract
The rapid spread of acquired metallo-beta-lactamases (MBLs) among gram negative pathogens is becoming a global concern. Improper use of broad-spectrum antibiotics can trigger the colonization and spread of resistant strains which lead to increased mortality and significant economic loss. In the present study, diverse immunoinformatic approaches are applied to design a potential epitope-based vaccine against VIM and IMP MBLs. The amino acid sequences of VIM and IMP variants were retrieved from the GenBank database. ABCpred and BCPred online Web servers were used to analyze linear B cell epitopes, while IEDB was used to determine the dominant T cell epitopes. Sequence validation, allergenicity, toxicity and physiochemical analysis were performed using web servers. Seven sequences were identified for linear B cell dominant epitopes and 4 sequences were considered as dominant CD4+ T cell epitopes, and the predicted epitopes were joined by KK and GPGPG linkers. Stabilized multi-epitope protein structure was obtained using molecular dynamics simulation. Molecular docking showed that the designed vaccine exhibited sustainable and strong binding interactions with Toll-like receptor 4 (TLR4). Finally, codon adaptation and in silico cloning studies were performed to design an effective vaccine production strategy. Immune simulation significantly provided high levels of immunoglobulins, T helper cells, T-cytotoxic cells and INF-γ. Even though the introduced vaccine candidate demonstrates a very potent immunogenic potential, but wet-lab validation is required to further assessment of the effectiveness of this proposed vaccine candidate.
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Affiliation(s)
- Hamid Motamedi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amirhoushang Alvandi
- Medical Technology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Matin Fathollahi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Marzie Mahdizade Ari
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Sajad Moradi
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Jale Moradi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ramin Abiri
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Fertility and Infertility Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
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5
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Richter P, Melzer B, Müller FD. Interacting bactofilins impact cell shape of the MreB-less multicellular Rhodomicrobium vannielii. PLoS Genet 2023; 19:e1010788. [PMID: 37256900 DOI: 10.1371/journal.pgen.1010788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 05/16/2023] [Indexed: 06/02/2023] Open
Abstract
Most non-spherical bacteria rely on the actin-like MreB cytoskeleton to control synthesis of a cell-shaping and primarily rod-like cell wall. Diverging from simple rod shape generally requires accessory cytoskeletal elements, which locally interfere with the MreB-guided cell wall synthesis. Conserved and widespread representatives of this accessory cytoskeleton are bactofilins that polymerize into static, non-polar bundles of filaments. Intriguingly, many species of the Actinobacteria and Rhizobiales manage to grow rod-like without MreB by tip extension, yet some of them still possess bactofilin genes, whose function in cell morphogenesis is unknown. An intricate representative of these tip-growing bacteria is Rhodomicrobium vannielii; a member of the hitherto genetically not tractable and poorly studied Hyphomicrobiaceae within the MreB-less Rhizobiales order. R. vannielii displays complex asymmetric cell shapes and differentiation patterns including filamentous hyphae to produce offspring and to build dendritic multicellular arrays. Here, we introduce techniques to genetically access R. vannielii, and we elucidate the role of bactofilins in its sophisticated morphogenesis. By targeted mutagenesis and fluorescence microscopy, protein interaction studies and peptidoglycan incorporation analysis we show that the R. vannielii bactofilins are associated with the hyphal growth zones and that one of them is essential to form proper hyphae. Another paralog is suggested to represent a novel hybrid and co-polymerizing bactofilin. Notably, we present R. vannielii as a powerful new model to understand prokaryotic cell development and control of multipolar cell growth in the absence of the conserved cytoskeletal element, MreB.
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Affiliation(s)
- Pia Richter
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
- Faculty of Biology, University of Marburg, Marburg, Germany
| | - Brigitte Melzer
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
- Max Rubner-Institute, Federal Research Institute of Nutrition and Food, Kulmbach, Germany
| | - Frank D Müller
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
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6
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Kachhawaha K, Singh S, Joshi K, Nain P, Singh SK. Bioprocessing of recombinant proteins from Escherichia coli inclusion bodies: insights from structure-function relationship for novel applications. Prep Biochem Biotechnol 2022; 53:728-752. [PMID: 36534636 DOI: 10.1080/10826068.2022.2155835] [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: 12/23/2022]
Abstract
The formation of inclusion bodies (IBs) during expression of recombinant therapeutic proteins using E. coli is a significant hurdle in producing high-quality, safe, and efficacious medicines. The improved understanding of the structure-function relationship of the IBs has resulted in the development of novel biotechnologies that have streamlined the isolation, solubilization, refolding, and purification of the active functional proteins from the bacterial IBs. Together, this overall effort promises to radically improve the scope of experimental biology of therapeutic protein production and expand new prospects in IBs usage. Notably, the IBs are increasingly used for applications in more pristine areas such as drug delivery and material sciences. In this review, we intend to provide a comprehensive picture of the bio-processing of bacterial IBs, including assessing critical gaps that still need to be addressed and potential solutions to overcome them. We expect this review to be a useful resource for those working in the area of protein refolding and therapeutic protein production.
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Affiliation(s)
- Kajal Kachhawaha
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Santanu Singh
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Khyati Joshi
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Priyanka Nain
- Department of Chemical and Bimolecular Engineering, University of Delaware, Newark, DE, USA
| | - Sumit K Singh
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
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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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Matavacas J, von Wachenfeldt C. Update on the Protein Homeostasis Network in Bacillus subtilis. Front Microbiol 2022; 13:865141. [PMID: 35350626 PMCID: PMC8957991 DOI: 10.3389/fmicb.2022.865141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Protein homeostasis is fundamental to cell function and survival. It relies on an interconnected network of processes involving protein synthesis, folding, post-translational modification and degradation as well as regulators of these processes. Here we provide an update on the roles, regulation and subcellular localization of the protein homeostasis machinery in the Gram-positive model organism Bacillus subtilis. We discuss emerging ideas and current research gaps in the field that, if tackled, increase our understanding of how Gram-positive bacteria, including several human pathogens, maintain protein homeostasis and cope with stressful conditions that challenge their survival.
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9
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Xiong Q, Zheng T, Shen X, Li B, Fu J, Zhao X, Wang C, Yu Z. Expanding the functionality of proteins with genetically encoded dibenzo[ b, f][1,4,5]thiadiazepine: a photo-transducer for photo-click decoration. Chem Sci 2022; 13:3571-3581. [PMID: 35432856 PMCID: PMC8943893 DOI: 10.1039/d1sc05710c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 02/28/2022] [Indexed: 12/15/2022] Open
Abstract
Genetic incorporation of novel noncanonical amino acids (ncAAs) that are specialized for the photo-click reaction allows the precisely orthogonal and site-specific functionalization of proteins in living cells under photo-control. However, the development of a r̲ing-strain i̲n situ l̲oadable d̲ipolarophile (RILD) as a genetically encodable reporter for photo-click bioconjugation with spatiotemporal controllability is quite rare. Herein, we report the design and synthesis of a photo-switchable d̲ib̲enzo[b,f][1,4,5]t̲hiad̲iazepine-based a̲lanine (DBTDA) ncAA, together with the directed evolution of a pyrrolysyl-tRNA synthetase/tRNACUA pair (PylRS/tRNACUA), to encode the DBTDA into recombinant proteins as a RILD in living E. coli cells. The fast-responsive photo-isomerization of the DBTDA residue can be utilized as a converter of photon energy into ring-strain energy to oscillate the conformational changes of the parent proteins. Due to the photo-activation of RILD, the photo-switching of the DBTDA residue on sfGFP and OmpC is capable of promoting the photo-click ligation with diarylsydnone (DASyd) derived probes with high efficiency and selectivity. We demonstrate that the genetic code expansion (GCE) with DBTDA benefits the studies on the distribution of decorated OmpC-DBTD on specific E. coli cells under a spatiotemporal resolved photo-stimulation. The GCE for encoding DBTDA enables further functional diversity of artificial proteins in living systems.
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Affiliation(s)
- Qin Xiong
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Tingting Zheng
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Xin Shen
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Baolin Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Jielin Fu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Xiaohu Zhao
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Chunxia Wang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Zhipeng Yu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
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10
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Dudanova I. Biosensors for Studying Neuronal Proteostasis. Front Mol Neurosci 2022; 15:829365. [PMID: 35345600 PMCID: PMC8957107 DOI: 10.3389/fnmol.2022.829365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/31/2022] [Indexed: 01/18/2023] Open
Abstract
Cellular health depends on the integrity and functionality of the proteome. Each cell is equipped with a protein quality control machinery that maintains protein homeostasis (proteostasis) by helping proteins adopt and keep their native structure, and ensuring the degradation of damaged proteins. Postmitotic cells such as neurons are especially vulnerable to disturbances of proteostasis. Defects of protein quality control occur in aging and have been linked to several disorders, including neurodegenerative diseases. However, the exact nature and time course of such disturbances in the context of brain diseases remain poorly understood. Sensors that allow visualization and quantitative analysis of proteostasis capacity in neurons are essential for gaining a better understanding of disease mechanisms and for testing potential therapies. Here, I provide an overview of available biosensors for assessing the functionality of the neuronal proteostasis network, point out the advantages and limitations of different sensors, and outline their potential for biological discoveries and translational applications.
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Affiliation(s)
- Irina Dudanova
- Molecular Neurodegeneration Group, Max Planck Institute of Neurobiology, Martinsried, Germany
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11
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Vasilchenko NG, Prazdnova EV, Lewitin E. Epigenetic Mechanisms of Gene Expression Regulation in Bacteria of the Genus Bacillus. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422010124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Szoke T, Nussbaum-Shochat A, Amster-Choder O. Evolutionarily conserved mechanism for membrane recognition from bacteria to mitochondria. FEBS Lett 2021; 595:2805-2815. [PMID: 34644400 DOI: 10.1002/1873-3468.14203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/13/2021] [Accepted: 09/28/2021] [Indexed: 11/09/2022]
Abstract
The mechanisms controlling membrane recognition by proteins with one hydrophobic stretch at their carboxyl terminus (tail anchor, TA) are poorly defined. The Escherichia coli TAs of ElaB and YqjD, which share sequential and structural similarity with the Saccharomyces cerevisiae TA of Fis1, were shown to localize to mitochondria. We show that YqjD and ElaB are directed by their TAs to bacterial cell poles. Fis1(TA) expressed in E. coli localizes like the endogenous TAs. The yeast and bacterial TAs are inserted in the E. coli inner membrane, and they all show affiliation to phosphatidic acid (PA), found in the membrane of the bacterial cell poles and of the yeast mitochondria. Our results suggest a mechanism for TA membrane recognition conserved from bacteria to mitochondria and raise the possibility that through their interaction with PA, and TAs play a role across prokaryotes and eukaryotes in controlling cell/organelle fate.
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Affiliation(s)
- Tamar Szoke
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Anat Nussbaum-Shochat
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem, Israel
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13
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Steiner UK. Senescence in Bacteria and Its Underlying Mechanisms. Front Cell Dev Biol 2021; 9:668915. [PMID: 34222238 PMCID: PMC8249858 DOI: 10.3389/fcell.2021.668915] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/14/2021] [Indexed: 12/11/2022] Open
Abstract
Bacteria have been thought to flee senescence by dividing into two identical daughter cells, but this notion of immortality has changed over the last two decades. Asymmetry between the resulting daughter cells after binary fission is revealed in physiological function, cell growth, and survival probabilities and is expected from theoretical understanding. Since the discovery of senescence in morphologically identical but physiologically asymmetric dividing bacteria, the mechanisms of bacteria aging have been explored across levels of biological organization. Quantitative investigations are heavily biased toward Escherichia coli and on the role of inclusion bodies—clusters of misfolded proteins. Despite intensive efforts to date, it is not evident if and how inclusion bodies, a phenotype linked to the loss of proteostasis and one of the consequences of a chain of reactions triggered by reactive oxygen species, contribute to senescence in bacteria. Recent findings in bacteria question that inclusion bodies are only deleterious, illustrated by fitness advantages of cells holding inclusion bodies under varying environmental conditions. The contributions of other hallmarks of aging, identified for metazoans, remain elusive. For instance, genomic instability appears to be age independent, epigenetic alterations might be little age specific, and other hallmarks do not play a major role in bacteria systems. What is surprising is that, on the one hand, classical senescence patterns, such as an early exponential increase in mortality followed by late age mortality plateaus, are found, but, on the other hand, identifying mechanisms that link to these patterns is challenging. Senescence patterns are sensitive to environmental conditions and to genetic background, even within species, which suggests diverse evolutionary selective forces on senescence that go beyond generalized expectations of classical evolutionary theories of aging. Given the molecular tool kits available in bacteria, the high control of experimental conditions, the high-throughput data collection using microfluidic systems, and the ease of life cell imaging of fluorescently marked transcription, translation, and proteomic dynamics, in combination with the simple demographics of growth, division, and mortality of bacteria, make the challenges surprising. The diversity of mechanisms and patterns revealed and their environmental dependencies not only present challenges but also open exciting opportunities for the discovery and deeper understanding of aging and its mechanisms, maybe beyond bacteria and aging.
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Affiliation(s)
- Ulrich Karl Steiner
- Evolutionary Demography Group, Institute of Biology, Freie Universität Berlin, Berlin, Germany
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14
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Mehta R, Rivera DD, Reilley DJ, Tan D, Thomas PW, Hinojosa A, Stewart AC, Cheng Z, Thomas CA, Crowder MW, Alexandrova AN, Fast W, Que EL. Visualizing the Dynamic Metalation State of New Delhi Metallo-β-lactamase-1 in Bacteria Using a Reversible Fluorescent Probe. J Am Chem Soc 2021; 143:8314-8323. [PMID: 34038127 DOI: 10.1021/jacs.1c00290] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
New Delhi metallo-β-lactamase (NDM) grants resistance to a broad spectrum of β-lactam antibiotics, including last-resort carbapenems, and is emerging as a global antibiotic resistance threat. Limited zinc availability adversely impacts the ability of NDM-1 to provide resistance, but a number of clinical variants have emerged that are more resistant to zinc scarcity (e.g., NDM-15). To provide a novel tool to better study metal ion sequestration in host-pathogen interactions, we describe the development of a fluorescent probe that reports on the dynamic metalation state of NDM within Escherichia coli. The thiol-containing probe selectively coordinates the dizinc metal cluster of NDM and results in a 17-fold increase in fluorescence intensity. Reversible binding enables competition and time-dependent studies that reveal fluorescence changes used to detect enzyme localization, substrate and inhibitor engagement, and changes to metalation state through the imaging of live E. coli using confocal microscopy. NDM-1 is shown to be susceptible to demetalation by intracellular and extracellular metal chelators in a live-cell model of zinc dyshomeostasis, whereas the NDM-15 metalation state is shown to be more resistant to zinc flux. The development of this reversible turn-on fluorescent probe for the metalation state of NDM provides a new tool for monitoring the impact of metal ion sequestration by host defense mechanisms and for detecting inhibitor-target engagement during the development of therapeutics to counter this resistance determinant.
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Affiliation(s)
- Radhika Mehta
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street Stop A5300, Austin, Texas 78712, United States
| | - Dann D Rivera
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - David J Reilley
- Department of Chemistry and Biochemistry, University of California-Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
| | - Dominique Tan
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street Stop A5300, Austin, Texas 78712, United States
| | - Pei W Thomas
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Abigail Hinojosa
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street Stop A5300, Austin, Texas 78712, United States
| | - Alesha C Stewart
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Caitlyn A Thomas
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California-Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
| | - Walter Fast
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Emily L Que
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street Stop A5300, Austin, Texas 78712, United States
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15
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Küsters K, Pohl M, Krauss U, Ölçücü G, Albert S, Jaeger KE, Wiechert W, Oldiges M. Construction and comprehensive characterization of an EcLDCc-CatIB set-varying linkers and aggregation inducing tags. Microb Cell Fact 2021; 20:49. [PMID: 33596923 PMCID: PMC7891155 DOI: 10.1186/s12934-021-01539-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/05/2021] [Indexed: 12/03/2022] Open
Abstract
Background
In recent years, the production of inclusion bodies that retained substantial catalytic activity was demonstrated. These catalytically active inclusion bodies (CatIBs) were formed by genetic fusion of an aggregation inducing tag to a gene of interest via short linker polypeptides and overproduction of the resulting gene fusion in Escherichia coli. The resulting CatIBs are known for their high stability, easy and cost efficient production, and recyclability and thus provide an interesting alternative to conventionally immobilized enzymes. Results Here, we present the construction and characterization of a CatIB set of the lysine decarboxylase from Escherichia coli (EcLDCc), constructed via Golden Gate Assembly. A total of ten EcLDCc variants consisting of combinations of two linker and five aggregation inducing tag sequences were generated. A flexible Serine/Glycine (SG)- as well as a rigid Proline/Threonine (PT)-Linker were tested in combination with the artificial peptides (18AWT, L6KD and GFIL8) or the coiled-coil domains (TDoT and 3HAMP) as aggregation inducing tags. The linkers were fused to the C-terminus of the EcLDCc to form a linkage between the enzyme and the aggregation inducing tags. Comprehensive morphology and enzymatic activity analyses were performed for the ten EcLDCc-CatIB variants and a wild type EcLDCc control to identify the CatIB variant with the highest activity for the decarboxylation of l-lysine to 1,5-diaminopentane. Interestingly, all of the CatIB variants possessed at least some activity, whilst most of the combinations with the rigid PT-Linker showed the highest conversion rates. EcLDCc-PT-L6KD was identified as the best of all variants allowing a volumetric productivity of 457 g L− 1 d− 1 and a specific volumetric productivity of 256 g L− 1 d− 1 gCatIB−1. Noteworthy, wild type EcLDCc, without specific aggregation inducing tags, also partially formed CatIBs, which, however showed lower activity compared to most of the newly constructed CatIB variants (volumetric productivity: 219 g L− 1 d− 1, specific volumetric activity: 106 g L− 1 d− 1 gCatIB− 1). Furthermore, we demonstrate that microscopic analysis can serve as a tool to find CatIB producing strains and thus allow for prescreening at an early stage to save time and resources. Conclusions Our results clearly show that the choice of linker and aggregation inducing tag has a strong influence on the morphology and the enzymatic activity of the CatIBs. Strikingly, the linker had the most pronounced influence on these characteristics.
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Affiliation(s)
- Kira Küsters
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Institute of Biotechnology, RWTH Aachen University, 52074, Aachen, Germany
| | - Martina Pohl
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Ulrich Krauss
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Gizem Ölçücü
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Sandor Albert
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Faculty of Biotechnology, University of Applied Sciences Mannheim, 68163, Mannheim, Germany
| | - Karl-Erich Jaeger
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, 52074, Aachen, Germany
| | - Marco Oldiges
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany. .,Institute of Biotechnology, RWTH Aachen University, 52074, Aachen, Germany.
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16
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Howitz N, Su T, Lazazzera BA. Meta-Tyrosine Induces Cytotoxic Misregulation of Metabolism in Escherichia coli. J Mol Biol 2020; 432:166716. [PMID: 33220263 DOI: 10.1016/j.jmb.2020.11.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 12/16/2022]
Abstract
The non-protein amino acid meta-Tyrosine (m-Tyr) is produced in cells under conditions of oxidative stress, and m-Tyr has been shown to be toxic to a broad range of biological systems. However, the mechanism by which m-Tyr damages cells is unclear. In E. coli, the quality control (QC) function of phenyalanyl-tRNA synthetase (PheRS) is required for resistantce to m-Tyr. To determine the mechanism of m-Tyr toxicity, we utilitized a strain of E. coli that expresses a QC-defective PheRS. The global responses of E. coli cells to m-Tyr were assessed by RNA-seq, and >500 genes were differentially expressed after the addition of m-Tyr. The most strongly up-regulated genes are involved in unfolded-protein stress response, and cells exposed to m-Tyr contained large, electron-dense protein aggregates, indicating that m-Tyr destabilized a large fraction of the proteome. Additionally, we observed that amino acid biosynthesis and transport regulons, controlled by ArgR, TrpR, and TyrR, and the stringent-response regulon, controlled by DksA/ppGpp, were differentially expressed. m-Tyr resistant mutants were isolated and found to have altered a promoter to increase expression of the enzymes for Phe production or to have altered transporters, which likely result in less uptake or increased efflux of m-Tyr. These findings indicate that when m-Tyr has passed the QC checkpoint by the PheRS, this toxicity of m-Tyr may result from interfering with amino acid metabolism, destabalizing a large number of proteins, and the formation of protein aggregates.
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Affiliation(s)
- Nathaniel Howitz
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Trent Su
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA; Institute for Quantitative and Computational Biology, University of California, Los Angeles, CA 90095, USA
| | - Beth A Lazazzera
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
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17
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Liu Y, Chen C, Sun LY, Gao H, Zhen JB, Yang KW. meta-Substituted benzenesulfonamide: a potent scaffold for the development of metallo-β-lactamase ImiS inhibitors. RSC Med Chem 2020; 11:259-267. [PMID: 33479632 PMCID: PMC7412727 DOI: 10.1039/c9md00455f] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 11/26/2019] [Indexed: 01/25/2023] Open
Abstract
Metallo-β-lactamase (MβL) ImiS contributes to the emergence of carbapenem resistance. A potent scaffold, meta-substituted benzenesulfonamide, was constructed and assayed against MβLs. The twenty-one obtained molecules specifically inhibited ImiS (IC50 = 0.11-9.3 μM); 2g was found to be the best inhibitor (IC50 = 0.11 μM), and 1g and 2g exhibited partially mixed inhibition with K i of 8.0 and 0.55 μM. The analysis of the structure-activity relationship revealed that the meta-substitutes improved the inhibitory activity of the inhibitors. Isothermal titration calorimetry (ITC) assays showed that 2g reversibly inhibited ImiS. The benzenesulfonamides exhibited synergistic antibacterial effects against E. coli BL21 (DE3) cells with ImiS, resulting in a 2-4-fold reduction in the MIC of imipenem and meropenem. Also, mouse experiments showed that 2g had synergistic efficacy with meropenem and significantly reduced the bacterial load in the spleen and liver after a single intraperitoneal dose. Tracing the ImiS in living E. coli cells by RS at a super-resolution level (3D-SIM) showed that the target was initially associated on the surface of the cells, then there was a high density of uniform localization distributed in the cytosol of cells, and it finally accumulated in the formation of inclusion bodies at the cell poles. Docking studies suggested that the sulfonamide group acted as a zinc-binding group to coordinate with Zn(ii) and the residual amino acid within the CphA active center, tightly anchoring the inhibitor at the active site. This study provides a highly promising scaffold for the development of inhibitors of ImiS, even the B2 subclasses of MβLs.
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Affiliation(s)
- Ya Liu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education , College of Chemistry and Materials Science , Northwest University , Xi'an 710127 , P. R. China .
| | - Cheng Chen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education , College of Chemistry and Materials Science , Northwest University , Xi'an 710127 , P. R. China .
| | - Le-Yun Sun
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education , College of Chemistry and Materials Science , Northwest University , Xi'an 710127 , P. R. China .
| | - Han Gao
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education , College of Chemistry and Materials Science , Northwest University , Xi'an 710127 , P. R. China .
| | - Jian-Bin Zhen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education , College of Chemistry and Materials Science , Northwest University , Xi'an 710127 , P. R. China .
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education , College of Chemistry and Materials Science , Northwest University , Xi'an 710127 , P. R. China .
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18
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Abstract
Longevity reflects the ability to maintain homeostatic conditions necessary for life as an organism ages. A long-lived organism must contend not only with environmental hazards but also with internal entropy and macromolecular damage that result in the loss of fitness during ageing, a phenomenon known as senescence. Although central to many of the core concepts in biology, ageing and longevity have primarily been investigated in sexually reproducing, multicellular organisms. However, growing evidence suggests that microorganisms undergo senescence, and can also exhibit extreme longevity. In this Review, we integrate theoretical and empirical insights to establish a unified perspective on senescence and longevity. We discuss the evolutionary origins, genetic mechanisms and functional consequences of microbial ageing. In addition to having biomedical implications, insights into microbial ageing shed light on the role of ageing in the origin of life and the upper limits to longevity.
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19
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Proenca AM, Rang CU, Qiu A, Shi C, Chao L. Cell aging preserves cellular immortality in the presence of lethal levels of damage. PLoS Biol 2019; 17:e3000266. [PMID: 31120870 PMCID: PMC6532838 DOI: 10.1371/journal.pbio.3000266] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 04/29/2019] [Indexed: 12/13/2022] Open
Abstract
Cellular aging, a progressive functional decline driven by damage accumulation, often culminates in the mortality of a cell lineage. Certain lineages, however, are able to sustain long-lasting immortality, as prominently exemplified by stem cells. Here, we show that Escherichia coli cell lineages exhibit comparable patterns of mortality and immortality. Through single-cell microscopy and microfluidic techniques, we find that these patterns are explained by the dynamics of damage accumulation and asymmetric partitioning between daughter cells. At low damage accumulation rates, both aging and rejuvenating lineages retain immortality by reaching their respective states of physiological equilibrium. We show that both asymmetry and equilibrium are present in repair mutants lacking certain repair chaperones, suggesting that intact repair capacity is not essential for immortal proliferation. We show that this growth equilibrium, however, is displaced by extrinsic damage in a dosage-dependent response. Moreover, we demonstrate that aging lineages become mortal when damage accumulation rates surpass a threshold, whereas rejuvenating lineages within the same population remain immortal. Thus, the processes of damage accumulation and partitioning through asymmetric cell division are essential in the determination of proliferative mortality and immortality in bacterial populations. This study provides further evidence for the characterization of cellular aging as a general process, affecting prokaryotes and eukaryotes alike and according to similar evolutionary constraints. A study of Escherichia coli shows that bacterial lineages maintain replicative immortality by reaching an equilibrium between aging and rejuvenation; when this equilibrium is disrupted, aging lineages cross their immortality threshold, becoming mortal, while rejuvenating lineages are favored by asymmetry and retain immortality within the same population.
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Affiliation(s)
- Audrey Menegaz Proenca
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
- CAPES Foundation, Ministry of Education of Brazil, Brasilia, Brazil
- * E-mail: (AMP); (LC)
| | - Camilla Ulla Rang
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Andrew Qiu
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Chao Shi
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Lin Chao
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
- * E-mail: (AMP); (LC)
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20
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Ebsulfur as a potent scaffold for inhibition and labelling of New Delhi metallo-β-lactamase-1 in vitro and in vivo. Bioorg Chem 2019; 84:192-201. [DOI: 10.1016/j.bioorg.2018.11.035] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 11/19/2018] [Accepted: 11/20/2018] [Indexed: 11/20/2022]
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21
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Jäger VD, Kloss R, Grünberger A, Seide S, Hahn D, Karmainski T, Piqueray M, Embruch J, Longerich S, Mackfeld U, Jaeger KE, Wiechert W, Pohl M, Krauss U. Tailoring the properties of (catalytically)-active inclusion bodies. Microb Cell Fact 2019; 18:33. [PMID: 30732596 PMCID: PMC6367779 DOI: 10.1186/s12934-019-1081-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 01/30/2019] [Indexed: 01/02/2023] Open
Abstract
Background Immobilization is an appropriate tool to ease the handling and recycling of enzymes in biocatalytic processes and to increase their stability. Most of the established immobilization methods require case-to-case optimization, which is laborious and time-consuming. Often, (chromatographic) enzyme purification is required and stable immobilization usually includes additional cross-linking or adsorption steps. We have previously shown in a few case studies that the molecular biological fusion of an aggregation-inducing tag to a target protein induces the intracellular formation of protein aggregates, so called inclusion bodies (IBs), which to a certain degree retain their (catalytic) function. This enables the combination of protein production and immobilization in one step. Hence, those biologically-produced immobilizates were named catalytically-active inclusion bodies (CatIBs) or, in case of proteins without catalytic activity, functional IBs (FIBs). While this strategy has been proven successful, the efficiency, the potential for optimization and important CatIB/FIB properties like yield, activity and morphology have not been investigated systematically. Results We here evaluated a CatIB/FIB toolbox of different enzymes and proteins. Different optimization strategies, like linker deletion, C- versus N-terminal fusion and the fusion of alternative aggregation-inducing tags were evaluated. The obtained CatIBs/FIBs varied with respect to formation efficiency, yield, composition and residual activity, which could be correlated to differences in their morphology; as revealed by (electron) microscopy. Last but not least, we demonstrate that the CatIB/FIB formation efficiency appears to be correlated to the solvent-accessible hydrophobic surface area of the target protein, providing a structure-based rationale for our strategy and opening up the possibility to predict its efficiency for any given target protein. Conclusion We here provide evidence for the general applicability, predictability and flexibility of the CatIB/FIB immobilization strategy, highlighting the application potential of CatIB-based enzyme immobilizates for synthetic chemistry, biocatalysis and industry. Electronic supplementary material The online version of this article (10.1186/s12934-019-1081-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- V D Jäger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), c/o, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - R Kloss
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), c/o, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - A Grünberger
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Multiscale Bioengineering, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - S Seide
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - D Hahn
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - T Karmainski
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - M Piqueray
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - J Embruch
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - S Longerich
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - U Mackfeld
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - K-E Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany.,IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), c/o, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - W Wiechert
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), c/o, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - M Pohl
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), c/o, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - U Krauss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany. .,Bioeconomy Science Center (BioSC), c/o, Forschungszentrum Jülich, 52425, Jülich, Germany.
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22
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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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23
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Age structure landscapes emerge from the equilibrium between aging and rejuvenation in bacterial populations. Nat Commun 2018; 9:3722. [PMID: 30213942 PMCID: PMC6137065 DOI: 10.1038/s41467-018-06154-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 08/16/2018] [Indexed: 12/22/2022] Open
Abstract
The physiological asymmetry between daughters of a mother bacterium is produced by the inheritance of either old poles, carrying non-genetic damage, or newly synthesized poles. However, as bacteria display long-term growth stability leading to physiological immortality, there is controversy on whether asymmetry corresponds to aging. Here we show that deterministic age structure landscapes emerge from physiologically immortal bacterial lineages. Through single-cell microscopy and microfluidic techniques, we demonstrate that aging and rejuvenating bacterial lineages reach two distinct states of growth equilibria. These equilibria display stabilizing properties, which we quantified according to the compensatory trajectories of continuous lineages throughout generations. Finally, we show that the physiological asymmetry between aging and rejuvenating lineages produces complex age structure landscapes, resulting in a deterministic phenotypic heterogeneity that is neither an artifact of starvation nor a product of extrinsic damage. These findings indicate that physiological immortality and cellular aging can both be manifested in single celled organisms. Some daughter cells inherit the maternal old pole during bacterial division, but does this correspond to aging? Here, Proenca et al. show that constant patterns of aging and rejuvenation connect distinct growth equilibria within bacterial clonal populations, providing evidence for deterministic age structures.
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24
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Park JM, Lee MH, Kang CH, Oh KH, Lee JS, Yoon JH. Enzymatic characterization of a soluble aggregate induced by N-terminal extension to a lipolytic enzyme. J Biotechnol 2018; 281:130-136. [PMID: 29981449 DOI: 10.1016/j.jbiotec.2018.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 05/25/2018] [Accepted: 07/03/2018] [Indexed: 11/26/2022]
Abstract
A self-assembling peptide (27PEP) was isolated from an open reading frame (ORF). The ORF consisted of an unknown functional domain and a catalytic (lipolytic and phospholipolytic) domain (MPlaG) on metagenomic fosmid clone. This extension of 27 amino acids prior to the N-terminus of the catalytic domain (27PEP-MPlaG), starting at Met261, produced an aggregate of high molecular weight (> 700 kDa). Compared with MPlaG, 27PEP-MPlaG showed the same temperature and pH effect for maximum activity but was stable in the presence of inhibitors such as EDTA and PMSF. The 27PEP-MPlaG exhibited lower specific activity than that of MPlaG, but when pre-incubated for 30 min at temperatures between 4 and 100 °C, its activity increased at temperatures greater than 40 °C under alkaline conditions and eventually reached the specific activity level of MPlaG at 60 °C. We experimentally determined that the aggregate caused by 27PEP was dissociated at elevated temperatures resulting in an active catalytic monomer. The 27PEP-indued aggregation may be attractive as application tool for improving or engineering of biocatalysts and biomaterials.
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Affiliation(s)
- Ji-Min Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Mi-Hwa Lee
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea; Korea Research Institute of Bioscience and Biotechnology,125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Chul-Hyung Kang
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea; Green Chemistry and Environmental Biotechnology program, School of Science, University of Science and Technology (UST), Yuseong, Daejeon 305-333, Republic of Korea
| | - Ki-Hoon Oh
- Korea Research Institute of Bioscience and Biotechnology,125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Jung-Sook Lee
- Korea Research Institute of Bioscience and Biotechnology,125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea; Green Chemistry and Environmental Biotechnology program, School of Science, University of Science and Technology (UST), Yuseong, Daejeon 305-333, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea.
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25
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Collet C, Thomassin JL, Francetic O, Genevaux P, Tran Van Nhieu G. Protein polarization driven by nucleoid exclusion of DnaK(HSP70)-substrate complexes. Nat Commun 2018; 9:2027. [PMID: 29795186 PMCID: PMC5966378 DOI: 10.1038/s41467-018-04414-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 04/23/2018] [Indexed: 11/18/2022] Open
Abstract
Many bacterial proteins require specific subcellular localization for function. How Escherichia coli proteins localize at one pole, however, is still not understood. Here, we show that the DnaK (HSP70) chaperone controls unipolar localization of the Shigella IpaC type III secretion substrate. While preventing the formation of lethal IpaC aggregates, DnaK promoted the incorporation of IpaC into large and dynamic complexes (LDCs) restricted at the bacterial pole through nucleoid occlusion. Unlike stable polymers and aggregates, LDCs show dynamic behavior indicating that nucleoid occlusion also applies to complexes formed through transient interactions. Fluorescence recovery after photobleaching analysis shows DnaK-IpaC exchanges between opposite poles and DnaKJE-mediated incorporation of immature substrates in LDCs. These findings reveal a key role for LDCs as reservoirs of functional DnaK-substrates that can be rapidly mobilized for secretion triggered upon bacterial contact with host cells. Many bacterial proteins exhibit spatially defined localization important for function. Here the authors show that the polar localization of Shigella IpaC type III secretion substrate is mediated by its interaction with the DnaK chaperone and occlusion by the bacterial nucleoid.
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Affiliation(s)
- Clémence Collet
- Equipe Communication Intercellulaire et Infections Microbiennes. Centre de Recherche Interdisciplinaire en Biologie (CIRB). Collège de France, 11, Place Marcelin Berthelot, 75005, Paris, France.,Institut National de la Santé et de la Recherche Médicale (Inserm) U1050, Paris, Cedex 15, France.,Centre National de la Recherche Scientifique (CNRS) UMR7241, 75016, Paris, France.,MEMOLIFE Laboratory of excellence and Paris Science Lettre, Paris, Cedex 15, France
| | - Jenny-Lee Thomassin
- Equipe Communication Intercellulaire et Infections Microbiennes. Centre de Recherche Interdisciplinaire en Biologie (CIRB). Collège de France, 11, Place Marcelin Berthelot, 75005, Paris, France.,Institut National de la Santé et de la Recherche Médicale (Inserm) U1050, Paris, Cedex 15, France.,Centre National de la Recherche Scientifique (CNRS) UMR7241, 75016, Paris, France.,MEMOLIFE Laboratory of excellence and Paris Science Lettre, Paris, Cedex 15, France
| | - Olivera Francetic
- Biochemistry of Macromolecular Interactions Unit, Institut Pasteur, Department of Structural Biology and Chemistry, CNRS UMR3528, 28 rue du Dr Roux, 75724, Paris, Cedex 15, France
| | - Pierre Genevaux
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 118 route de Narbonne, 31062, Toulouse, Cedex 9, France
| | - Guy Tran Van Nhieu
- Equipe Communication Intercellulaire et Infections Microbiennes. Centre de Recherche Interdisciplinaire en Biologie (CIRB). Collège de France, 11, Place Marcelin Berthelot, 75005, Paris, France. .,Institut National de la Santé et de la Recherche Médicale (Inserm) U1050, Paris, Cedex 15, France. .,Centre National de la Recherche Scientifique (CNRS) UMR7241, 75016, Paris, France. .,MEMOLIFE Laboratory of excellence and Paris Science Lettre, Paris, Cedex 15, France.
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26
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Catalytically active inclusion bodies of L-lysine decarboxylase from E. coli for 1,5-diaminopentane production. Sci Rep 2018; 8:5856. [PMID: 29643457 PMCID: PMC5895699 DOI: 10.1038/s41598-018-24070-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 03/26/2018] [Indexed: 01/27/2023] Open
Abstract
Sustainable and eco-efficient alternatives for the production of platform chemicals, fuels and chemical building blocks require the development of stable, reusable and recyclable biocatalysts. Here we present a novel concept for the biocatalytic production of 1,5-diaminopentane (DAP, trivial name: cadaverine) using catalytically active inclusion bodies (CatIBs) of the constitutive L-lysine decarboxylase from E. coli (EcLDCc-CatIBs) to process L-lysine-containing culture supernatants from Corynebacterium glutamicum. EcLDCc-CatIBs can easily be produced in E. coli followed by a simple purification protocol yielding up to 43% dry CatIBs per dry cell weight. The stability and recyclability of EcLDCc-CatIBs was demonstrated in (repetitive) batch experiments starting from L-lysine concentrations of 0.1 M and 1 M. EcLDC-CatIBs exhibited great stability under reaction conditions with an estimated half-life of about 54 h. High conversions to DAP of 87-100% were obtained in 30-60 ml batch reactions using approx. 180-300 mg EcLDCc-CatIBs, respectively. This resulted in DAP titres of up to 88.4 g l-1 and space-time yields of up to 660 gDAP l-1 d-1 per gram dry EcLDCc-CatIBs. The new process for DAP production can therefore compete with the currently best fermentative process as described in the literature.
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27
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Zhang W, Lu J, Zhang S, Liu L, Pang X, Lv J. Development an effective system to expression recombinant protein in E. coli via comparison and optimization of signal peptides: Expression of Pseudomonas fluorescens BJ-10 thermostable lipase as case study. Microb Cell Fact 2018; 17:50. [PMID: 29592803 PMCID: PMC5872382 DOI: 10.1186/s12934-018-0894-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 03/17/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Thermostable lipases from microbial sources have been substantially overexpressed in E. coli, however, these enzymes are often produced with low-level enzymatic activity and mainly in the form of inclusion bodies. Several studies have reported that the secretory production of recombinant proteins fused their N-terminus to a signal peptide has been employed to resolve the problem. In general, the feasibility of this approach largely depends on the secretory pathway of signal peptide and the type of target protein to be secreted. This study was performed to compare and optimize signal peptides for efficient secretion of thermostable lipase lipBJ10 from Pseudomonas fluorescens BJ-10. Meanwhile, a comparative study between this method and cytoplasmic secretion was implemented in secreting soluble and active lipases. RESULTS Fusion expression using six signal peptides, i.e., PelB and five native E. coli signal peptides, as fusion partners produced more soluble and functional recombinant lipBJ10 than non-fusion expression. Recombinant lipBJ10, fused to these six diverse signal peptides, was secreted into the periplasm in E. coli. The total lipase activity in all cases of fusion expression was higher than those in non-fusion expression. The relative activity peaked when lipBJ10 was fused to DsbA, yielding a value 73.3 times greater than that of the non-fusion protein. When DsbA was used as the fusion partner, the highest activity (265.41 U/ml) was achieved with the least formation of inclusion bodies; the other four E. coli signal peptides, to some extent, led to low activity and insoluble inclusion bodies. Therefore, DsbA is the optimal signal peptide partner to fuse with lipBJ10 to efficiently produce soluble and functional protein. CONCLUSION We found that fusing to these signal peptides, especially that of DsbA, can significantly decrease the formation of inclusion bodies and enhance the function and solubility of lipBJ10 compared to non-fusion lipBJ10. Our results reported here can provide a reference for the high-level expression of other lipases with respect to a possible industrial application.
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Affiliation(s)
- Weiqing Zhang
- Institute of Agro-food Science and Technology, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Jing Lu
- Institute of Agro-food Science and Technology, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Shuwen Zhang
- Institute of Agro-food Science and Technology, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Lu Liu
- Institute of Agro-food Science and Technology, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Xiaoyang Pang
- Institute of Agro-food Science and Technology, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Jiaping Lv
- Institute of Agro-food Science and Technology, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
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28
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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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29
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Kloss R, Karmainski T, Jäger VD, Hahn D, Grünberger A, Baumgart M, Krauss U, Jaeger KE, Wiechert W, Pohl M. Tailor-made catalytically active inclusion bodies for different applications in biocatalysis. Catal Sci Technol 2018. [DOI: 10.1039/c8cy01891j] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
CatIB properties can be tailored to the requirements of different reaction systems using two different coiled-coil domains as fusion tags.
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30
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Chen C, Xiang Y, Yang KW, Zhang Y, Wang WM, Su JP, Ge Y, Liu Y. A protein structure-guided covalent scaffold selectively targets the B1 and B2 subclass metallo-β-lactamases. Chem Commun (Camb) 2018; 54:4802-4805. [DOI: 10.1039/c8cc01067f] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We report the discovery of ebselen-based dual covalent inhibitors of metallo-β-lactamases.
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Affiliation(s)
- Cheng Chen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education
- Innovation Laboratory of Chemical Biology
- College of Chemistry and Materials Science
- Northwest University
- Xi’an 710127
| | - Yang Xiang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education
- Innovation Laboratory of Chemical Biology
- College of Chemistry and Materials Science
- Northwest University
- Xi’an 710127
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education
- Innovation Laboratory of Chemical Biology
- College of Chemistry and Materials Science
- Northwest University
- Xi’an 710127
| | - Yuejuan Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education
- Innovation Laboratory of Chemical Biology
- College of Chemistry and Materials Science
- Northwest University
- Xi’an 710127
| | - Wen-Ming Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education
- Innovation Laboratory of Chemical Biology
- College of Chemistry and Materials Science
- Northwest University
- Xi’an 710127
| | - Jian-Peng Su
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education
- Innovation Laboratory of Chemical Biology
- College of Chemistry and Materials Science
- Northwest University
- Xi’an 710127
| | - Ying Ge
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education
- Innovation Laboratory of Chemical Biology
- College of Chemistry and Materials Science
- Northwest University
- Xi’an 710127
| | - Ya Liu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education
- Innovation Laboratory of Chemical Biology
- College of Chemistry and Materials Science
- Northwest University
- Xi’an 710127
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31
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Mamou G, Fiyaksel O, Sinai L, Ben-Yehuda S. Deficiency in Lipoteichoic Acid Synthesis Causes a Failure in Executing the Colony Developmental Program in Bacillus subtilis. Front Microbiol 2017; 8:1991. [PMID: 29114240 PMCID: PMC5660684 DOI: 10.3389/fmicb.2017.01991] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 09/27/2017] [Indexed: 01/18/2023] Open
Abstract
Colonies are an abundant form of bacterial multicellularity; however, relatively little is known about the initial stages of their construction. We have previously described that colony development of the soil bacterium Bacillus subtilis is a highly ordered process, typically initiating with the formation of extending cell chains arranged in a Y shape structure. Furthermore, we demonstrated that Y arm extension is a key for defining the size of the future colony. Here we conducted a genetic screen surveying for mutants deficient in these early developmental stages, and revealed LtaS, the major lipoteichoic acid (LTA) synthase, to be crucial for execution of these events. We found that the ltaS mutant fails to produce proper Y shape structures, forming extremely elongated chains of cells with no evidence of chain breakage, necessary for Y shape formation. Furthermore, we show that frequent cell death at the tips of the cell chains is a major cause in limiting arm extension. Collectively, these perturbations lead to the production of a small sized colony by the mutant. Thus, deficiency in LTA synthesis causes a mechanical failure in executing the colony developmental program.
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Affiliation(s)
- Gideon Mamou
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical School, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Osher Fiyaksel
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical School, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lior Sinai
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical School, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sigal Ben-Yehuda
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical School, Hebrew University of Jerusalem, Jerusalem, Israel
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32
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Kerkour A, Marquevielle J, Ivashchenko S, Yatsunyk LA, Mergny JL, Salgado GF. High-resolution three-dimensional NMR structure of the KRAS proto-oncogene promoter reveals key features of a G-quadruplex involved in transcriptional regulation. J Biol Chem 2017; 292:8082-8091. [PMID: 28330874 DOI: 10.1074/jbc.m117.781906] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/15/2017] [Indexed: 12/13/2022] Open
Abstract
Non-canonical base pairing within guanine-rich DNA and RNA sequences can produce G-quartets, whose stacking leads to the formation of a G-quadruplex (G4). G4s can coexist with canonical duplex DNA in the human genome and have been suggested to suppress gene transcription, and much attention has therefore focused on studying G4s in promotor regions of disease-related genes. For example, the human KRAS proto-oncogene contains a nuclease-hypersensitive element located upstream of the major transcription start site. The KRAS nuclease-hypersensitive element (NHE) region contains a G-rich element (22RT; 5'-AGGGCGGTGTGGGAATAGGGAA-3') and encompasses a Myc-associated zinc finger-binding site that regulates KRAS transcription. The NEH region therefore has been proposed as a target for new drugs that control KRAS transcription, which requires detailed knowledge of the NHE structure. In this study, we report a high-resolution NMR structure of the G-rich element within the KRAS NHE. We found that the G-rich element forms a parallel structure with three G-quartets connected by a four-nucleotide loop and two short one-nucleotide double-chain reversal loops. In addition, a thymine bulge is found between G8 and G9. The loops of different lengths and the presence of a bulge between the G-quartets are structural elements that potentially can be targeted by small chemical ligands that would further stabilize the structure and interfere or block transcriptional regulators such as Myc-associated zinc finger from accessing their binding sites on the KRAS promoter. In conclusion, our work suggests a possible new route for the development of anticancer agents that could suppress KRAS expression.
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Affiliation(s)
- Abdelaziz Kerkour
- From the Université Bordeaux, INSERM, CNRS, ARNA laboratory, European Institute of Chemistry and Biology, U1212, UMR 5320, 2 Rue Robert Escarpit, 33000 Pessac, France and
| | - Julien Marquevielle
- From the Université Bordeaux, INSERM, CNRS, ARNA laboratory, European Institute of Chemistry and Biology, U1212, UMR 5320, 2 Rue Robert Escarpit, 33000 Pessac, France and
| | - Stefaniia Ivashchenko
- From the Université Bordeaux, INSERM, CNRS, ARNA laboratory, European Institute of Chemistry and Biology, U1212, UMR 5320, 2 Rue Robert Escarpit, 33000 Pessac, France and
| | - Liliya A Yatsunyk
- From the Université Bordeaux, INSERM, CNRS, ARNA laboratory, European Institute of Chemistry and Biology, U1212, UMR 5320, 2 Rue Robert Escarpit, 33000 Pessac, France and.,Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081
| | - Jean-Louis Mergny
- From the Université Bordeaux, INSERM, CNRS, ARNA laboratory, European Institute of Chemistry and Biology, U1212, UMR 5320, 2 Rue Robert Escarpit, 33000 Pessac, France and
| | - Gilmar F Salgado
- From the Université Bordeaux, INSERM, CNRS, ARNA laboratory, European Institute of Chemistry and Biology, U1212, UMR 5320, 2 Rue Robert Escarpit, 33000 Pessac, France and
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33
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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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Caulobacter PopZ forms an intrinsically disordered hub in organizing bacterial cell poles. Proc Natl Acad Sci U S A 2016; 113:12490-12495. [PMID: 27791060 DOI: 10.1073/pnas.1602380113] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite their relative simplicity, bacteria have complex anatomy at the subcellular level. At the cell poles of Caulobacter crescentus, a 177-amino acid (aa) protein called PopZ self-assembles into 3D polymeric superstructures. Remarkably, we find that this assemblage interacts directly with at least eight different proteins, which are involved in cell cycle regulation and chromosome segregation. The binding determinants within PopZ include 24 aa at the N terminus, a 32-aa region near the C-terminal homo-oligomeric assembly domain, and portions of an intervening linker region. Together, the N-terminal 133 aa of PopZ are sufficient for interacting with all binding partners, even in the absence of homo-oligomeric assembly. Structural analysis of this region revealed that it is intrinsically disordered, similar to p53 and other hub proteins that organize complex signaling networks in eukaryotic cells. Through live-cell photobleaching, we find rapid binding kinetics between PopZ and its partners, suggesting many pole-localized proteins become concentrated at cell poles through rapid cycles of binding and unbinding within the PopZ scaffold. We conclude that some bacteria, similar to their eukaryotic counterparts, use intrinsically disordered hub proteins for network assembly and subcellular organization.
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35
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Rehm FBH, Chen S, Rehm BHA. Enzyme Engineering for In Situ Immobilization. Molecules 2016; 21:E1370. [PMID: 27754434 PMCID: PMC6273058 DOI: 10.3390/molecules21101370] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 10/05/2016] [Accepted: 10/05/2016] [Indexed: 11/19/2022] Open
Abstract
Enzymes are used as biocatalysts in a vast range of industrial applications. Immobilization of enzymes to solid supports or their self-assembly into insoluble particles enhances their applicability by strongly improving properties such as stability in changing environments, re-usability and applicability in continuous biocatalytic processes. The possibility of co-immobilizing various functionally related enzymes involved in multistep synthesis, conversion or degradation reactions enables the design of multifunctional biocatalyst with enhanced performance compared to their soluble counterparts. This review provides a brief overview of up-to-date in vitro immobilization strategies while focusing on recent advances in enzyme engineering towards in situ self-assembly into insoluble particles. In situ self-assembly approaches include the bioengineering of bacteria to abundantly form enzymatically active inclusion bodies such as enzyme inclusions or enzyme-coated polyhydroxyalkanoate granules. These one-step production strategies for immobilized enzymes avoid prefabrication of the carrier as well as chemical cross-linking or attachment to a support material while the controlled oriented display strongly enhances the fraction of accessible catalytic sites and hence functional enzymes.
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Affiliation(s)
- Fabian B H Rehm
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand.
| | - Shuxiong Chen
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand.
| | - Bernd H A Rehm
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand.
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36
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González LJ, Bahr G, Nakashige TG, Nolan EM, Bonomo RA, Vila AJ. Membrane anchoring stabilizes and favors secretion of New Delhi metallo-β-lactamase. Nat Chem Biol 2016; 12:516-22. [PMID: 27182662 PMCID: PMC4912412 DOI: 10.1038/nchembio.2083] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 03/14/2016] [Indexed: 01/22/2023]
Abstract
Carbapenems, 'last-resort' β-lactam antibiotics, are inactivated by zinc-dependent metallo-β-lactamases (MBLs). The host innate immune response withholds nutrient metal ions from microbial pathogens by releasing metal-chelating proteins such as calprotectin. We show that metal sequestration is detrimental for the accumulation of MBLs in the bacterial periplasm, because those enzymes are readily degraded in their nonmetallated form. However, the New Delhi metallo-β-lactamase (NDM-1) can persist under conditions of metal depletion. NDM-1 is a lipidated protein that anchors to the outer membrane of Gram-negative bacteria. Membrane anchoring contributes to the unusual stability of NDM-1 and favors secretion of this enzyme in outer-membrane vesicles (OMVs). OMVs containing NDM-1 can protect nearby populations of bacteria from otherwise lethal antibiotic levels, and OMVs from clinical pathogens expressing NDM-1 can carry this MBL and the blaNDM gene. We show that protein export into OMVs can be targeted, providing possibilities of new antibacterial therapeutic strategies.
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Affiliation(s)
- Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) and Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) and Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Toshiki G. Nakashige
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Elizabeth M. Nolan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH; Departments of Medicine, Pharmacology, Microbiology and Molecular Biology, and Biochemistry; Case Western Reserve University, Cleveland, OH, USA
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) and Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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37
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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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38
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Bednarska NG, van Eldere J, Gallardo R, Ganesan A, Ramakers M, Vogel I, Baatsen P, Staes A, Goethals M, Hammarström P, Nilsson KPR, Gevaert K, Schymkowitz J, Rousseau F. Protein aggregation as an antibiotic design strategy. Mol Microbiol 2015; 99:849-65. [PMID: 26559925 DOI: 10.1111/mmi.13269] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2015] [Indexed: 12/12/2022]
Abstract
Taking advantage of the xenobiotic nature of bacterial infections, we tested whether the cytotoxicity of protein aggregation can be targeted to bacterial pathogens without affecting their mammalian hosts. In particular, we examined if peptides encoding aggregation-prone sequence segments of bacterial proteins can display antimicrobial activity by initiating toxic protein aggregation in bacteria, but not in mammalian cells. Unbiased in vitro screening of aggregating peptide sequences from bacterial genomes lead to the identification of several peptides that are strongly bactericidal against methicillin-resistant Staphylococcus aureus. Upon parenteral administration in vivo, the peptides cured mice from bacterial sepsis without apparent toxic side effects as judged from histological and hematological evaluation. We found that the peptides enter and accumulate in the bacterial cytosol where they cause aggregation of bacterial polypeptides. Although the precise chain of events that leads to cell death remains to be elucidated, the ability to tap into aggregation-prone sequences of bacterial proteomes to elicit antimicrobial activity represents a rich and unexplored chemical space to be mined in search of novel therapeutic strategies to fight infectious diseases.
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Affiliation(s)
- Natalia G Bednarska
- Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology and Immunology, KULeuven, Leuven, Belgium.,Switch Laboratory, VIB, Leuven, Belgium
| | - Johan van Eldere
- Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology and Immunology, KULeuven, Leuven, Belgium
| | - Rodrigo Gallardo
- Switch Laboratory, VIB, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Ashok Ganesan
- Switch Laboratory, VIB, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Meine Ramakers
- Switch Laboratory, VIB, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Isabel Vogel
- Laboratory of Immunology, Department of Microbiology and Immunology, KULeuven, Leuven, Belgium
| | - Pieter Baatsen
- Department of Molecular and Developmental Genetics (VIB11 and KULeuven), Electron Microscopy Network (EMoNe), Gasthuisberg, Leuven, Belgium
| | - An Staes
- Department of Medical Protein Research, VIB, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Marc Goethals
- Department of Medical Protein Research, VIB, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Per Hammarström
- Department of Chemistry, Linköping University, Linköping, Sweden
| | | | - Kris Gevaert
- Department of Medical Protein Research, VIB, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
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39
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Sin O, Nollen EAA. Regulation of protein homeostasis in neurodegenerative diseases: the role of coding and non-coding genes. Cell Mol Life Sci 2015; 72:4027-47. [PMID: 26190021 PMCID: PMC4605983 DOI: 10.1007/s00018-015-1985-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 06/10/2015] [Accepted: 07/02/2015] [Indexed: 12/20/2022]
Abstract
Protein homeostasis is fundamental for cell function and survival, because proteins are involved in all aspects of cellular function, ranging from cell metabolism and cell division to the cell's response to environmental challenges. Protein homeostasis is tightly regulated by the synthesis, folding, trafficking and clearance of proteins, all of which act in an orchestrated manner to ensure proteome stability. The protein quality control system is enhanced by stress response pathways, which take action whenever the proteome is challenged by environmental or physiological stress. Aging, however, damages the proteome, and such proteome damage is thought to be associated with aging-related diseases. In this review, we discuss the different cellular processes that define the protein quality control system and focus on their role in protein conformational diseases. We highlight the power of using small organisms to model neurodegenerative diseases and how these models can be exploited to discover genetic modulators of protein aggregation and toxicity. We also link findings from small model organisms to the situation in higher organisms and describe how some of the genetic modifiers discovered in organisms such as worms are functionally conserved throughout evolution. Finally, we demonstrate that the non-coding genome also plays a role in maintaining protein homeostasis. In all, this review highlights the importance of protein and RNA homeostasis in neurodegenerative diseases.
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Affiliation(s)
- Olga Sin
- European Research Institute for the Biology of Aging, University of Groningen, University Medical Centre Groningen, 9700 AD, Groningen, The Netherlands
- Graduate Program in Areas of Basic and Applied Biology, Abel Salazar Biomedical Sciences Institute, University of Porto, 4099-003, Porto, Portugal
| | - Ellen A A Nollen
- European Research Institute for the Biology of Aging, University of Groningen, University Medical Centre Groningen, 9700 AD, Groningen, The Netherlands.
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40
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Doyle MT, Grabowicz M, Morona R. A small conserved motif supports polarity augmentation of Shigella flexneri IcsA. MICROBIOLOGY-SGM 2015; 161:2087-97. [PMID: 26315462 DOI: 10.1099/mic.0.000165] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The rod-shaped enteric intracellular pathogen Shigella flexneri and other Shigella species are the causative agents of bacillary dysentery. S. flexneri are able to spread within the epithelial lining of the gut, resulting in lesion formation, cramps and bloody stools. The outer membrane protein IcsA is essential for this spreading process. IcsA is the initiator of an actin-based form of motility whereby it allows the formation of a filamentous actin 'tail' at the bacterial pole. Importantly, IcsA is specifically positioned at the bacterial pole such that this process occurs asymmetrically. The mechanism of IcsA polarity is not completely understood, but it appears to be a multifactorial process involving factors intrinsic to IcsA and other regulating factors. In this study, we further investigated IcsA polarization by its intramolecular N-terminal and central polar-targeting (PT) regions (nPT and cPT regions, respectively). The results obtained support a role in polar localization for the cPT region and contend the role of the nPT region. We identified single IcsA residues that have measurable impacts on IcsA polarity augmentation, resulting in decreased S. flexneri sprading efficiency. Intriguingly, regions and residues involved in PT clustered around a highly conserved motif which may provide a functional scaffold for polarity-augmenting residues. How these results fit with the current model of IcsA polarity determination is discussed.
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Affiliation(s)
- Matthew Thomas Doyle
- 1Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Marcin Grabowicz
- 2Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014, USA
| | - Renato Morona
- 1Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
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41
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From protein damage to cell aging to population fitness in E. coli: Insights from a multi-level agent-based model. Ecol Modell 2015. [DOI: 10.1016/j.ecolmodel.2015.01.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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42
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Khachatoorian C, Ramirez RA, Hernandez F, Serna R, Kwok EY. Overexpressed Arabidopsis Annexin4 accumulates in inclusion body-like structures. Acta Histochem 2015; 117:279-87. [PMID: 25818562 PMCID: PMC4409563 DOI: 10.1016/j.acthis.2015.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/06/2015] [Accepted: 03/06/2015] [Indexed: 12/31/2022]
Abstract
Large protein complexes form in the cytosol of prokaryotes and eukaryotes as assemblies of functional enzymes or aggregates of misfolded proteins. Their roles in the cell range from critical components of metabolism to disease-causing agents. We have observed a novel structure in the cells of transgenic Arabidopsis thaliana that appears to be a form of inclusion body. These long, spindle-shaped structures form when Arabidopsis are transformed to express high levels of the protein Annexin4 fused to a fluorescent protein. These structures, previously named darts, are visible in all cells of the plant throughout development. Darts take on a variety of morphologies including rings and figure-eights. These structures are not associated with the endomembrane system and are not membrane bounded. Darts appear to be insoluble aggregates of protein analogous to bacterial inclusion bodies and eukaryotic aggresomes. Similar structures have not been observed in untransformed plants, suggesting darts are artifacts of transgenic overexpression.
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Affiliation(s)
- Careen Khachatoorian
- Department of Biology, California State University Northridge, 18111 Nordhoff St., Northridge, CA 91330-8303, USA
| | - Rigoberto A Ramirez
- Department of Biology, California State University Northridge, 18111 Nordhoff St., Northridge, CA 91330-8303, USA
| | - Fernando Hernandez
- Department of Biology, California State University Northridge, 18111 Nordhoff St., Northridge, CA 91330-8303, USA
| | - Raphael Serna
- Department of Biology, California State University Northridge, 18111 Nordhoff St., Northridge, CA 91330-8303, USA
| | - Ernest Y Kwok
- Department of Biology, California State University Northridge, 18111 Nordhoff St., Northridge, CA 91330-8303, USA.
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43
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Doyle MT, Grabowicz M, May KL, Morona R. Lipopolysaccharide surface structure does not influence IcsA polarity. FEMS Microbiol Lett 2015; 362:fnv042. [DOI: 10.1093/femsle/fnv042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2015] [Indexed: 12/26/2022] Open
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44
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Stannek L, Gunka K, Care RA, Gerth U, Commichau FM. Factors that mediate and prevent degradation of the inactive and unstable GudB protein in Bacillus subtilis. Front Microbiol 2015; 5:758. [PMID: 25610436 PMCID: PMC4285742 DOI: 10.3389/fmicb.2014.00758] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 12/12/2014] [Indexed: 11/13/2022] Open
Abstract
The Gram-positive model bacterium Bacillus subtilis contains two glutamate dehydro genase-encoding genes, rocG and gudB. While the rocG gene encodes the functional GDH, the gudB gene is cryptic (gudB(CR) ) in the laboratory strain 168 due to a perfect 18 bp-long direct repeat that renders the GudB enzyme inactive and unstable. Although constitutively expressed the GudB(CR) protein can hardly be detected in B. subtilis as it is rapidly degraded within stationary growth phase. Its high instability qualifies GudB(CR) as a model substrate for studying protein turnover in B. subtilis. Recently, we have developed a visual screen to monitor the GudB(CR) stability in the cell using a GFP-GudB(CR) fusion. Using fluorescent microscopy we found that the GFP protein is simultaneously degraded together with GudB(CR). This allows us to analyze the stability of GudB(CR) in living cells. By combining the visual screen with a transposon mutagenesis approach we looked for mutants that show an increased fluorescence signal compared to the wild type indicating a stabilized GFP-GudB(CR) fusion. We observed, that disruption of the arginine kinase encoding gene mcsB upon transposon insertion leads to increased amounts of the GFP-GudB(CR) fusion in this mutant. Deletion of the cognate arginine phosphatase YwlE in contrast results in reduced levels of the GFP-GudB(CR) fusion. Recently, it was shown that the kinase McsB is involved in phosphorylation of GudB(CR) on arginine residues. Here we show that selected arginine-lysine point mutations of GudB(CR) exhibit no influence on degradation. The activity of McsB and YwlE, however, are crucial for the activation and inhibition, respectively, of a proteolytic machinery that efficiently degrades the unstable GudB(CR) protein in B. subtilis.
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Affiliation(s)
- Lorena Stannek
- Department of General Microbiology, Georg-August-University Göttingen Göttingen, Germany
| | - Katrin Gunka
- Department of General Microbiology, Georg-August-University Göttingen Göttingen, Germany
| | - Rachel A Care
- Department of General Microbiology, Georg-August-University Göttingen Göttingen, Germany
| | - Ulf Gerth
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald Greifswald, Germany
| | - Fabian M Commichau
- Department of General Microbiology, Georg-August-University Göttingen Göttingen, Germany
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45
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de Lorenzo V, Sekowska A, Danchin A. Chemical reactivity drives spatiotemporal organisation of bacterial metabolism. FEMS Microbiol Rev 2014; 39:96-119. [PMID: 25227915 DOI: 10.1111/1574-6976.12089] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In this review, we examine how bacterial metabolism is shaped by chemical constraints acting on the material and dynamic layout of enzymatic networks and beyond. These are moulded not only for optimisation of given metabolic objectives (e.g. synthesis of a particular amino acid or nucleotide) but also for curbing the detrimental reactivity of chemical intermediates. Besides substrate channelling, toxicity is avoided by barriers to free diffusion (i.e. compartments) that separate otherwise incompatible reactions, along with ways for distinguishing damaging vs. harmless molecules. On the other hand, enzymes age and their operating lifetime must be tuned to upstream and downstream reactions. This time dependence of metabolic pathways creates time-linked information, learning and memory. These features suggest that the physical structure of existing biosystems, from operon assemblies to multicellular development may ultimately stem from the need to restrain chemical damage and limit the waste inherent to basic metabolic functions. This provides a new twist of our comprehension of fundamental biological processes in live systems as well as practical take-home lessons for the forward DNA-based engineering of novel biological objects.
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Affiliation(s)
- Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología CSIC, Cantoblanco-Madrid, Spain
| | - Agnieszka Sekowska
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Antoine Danchin
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière, Paris, France
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46
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Chen A, Li Y, Liu X, Long Q, Yang Y, Bai Z. Soluble expression of pullulanase from Bacillus acidopullulyticus in Escherichia coli by tightly controlling basal expression. ACTA ACUST UNITED AC 2014; 41:1803-10. [DOI: 10.1007/s10295-014-1523-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 09/27/2014] [Indexed: 11/27/2022]
Abstract
Abstract
Bacillus acidopullulyticus pullulanase (BaPul13A) is a widely used debranching enzyme in the starch industry. A few details have been reported on the heterologous expression of BaPul13A in Escherichia coli (E. coli). This study compares different E. coli expression systems to improve the soluble expression level of BaPul13A. When pET22b(+)/pET28a(+) was used as the expression vector, the soluble expression of BaPul13A can be achieved by tightly controlling basal expression, whereas pET-20b(+)/pGEX4T2 leads to insoluble inclusion bodies. An efficient process control strategy aimed at minimizing the formation of inclusion bodies and enhancing the production of pullulanase was developed by a step decrease of the temperature in a 5-L fermentor. The highest total enzyme activity of BaPul13A reached 1,156.32 U/mL. This work reveals that the T7 promoter with lac operator and lacI gene collectively contribute to the soluble expression of BaPul13A, whereas either a T7 promoter alone or combined with the lac operator and lacI gene results in poor solubility. Basal expression in the initial growth phase of the host significantly affects the solubility of BaPul13A in E. coli.
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Affiliation(s)
- Ana Chen
- grid.258151.a 0000000107081323 National Engineering Laboratory for Cereal Fermentation Technology Jiangnan University 214122 Wuxi China
- grid.258151.a 0000000107081323 The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University 214122 Wuxi China
- grid.461986.4 0000000417607968 School of Biochemical Engineering Anhui Polytechnic University 241000 Wuhu China
| | - Yamei Li
- grid.258151.a 0000000107081323 National Engineering Laboratory for Cereal Fermentation Technology Jiangnan University 214122 Wuxi China
- grid.258151.a 0000000107081323 The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University 214122 Wuxi China
| | - Xiuxia Liu
- grid.258151.a 0000000107081323 National Engineering Laboratory for Cereal Fermentation Technology Jiangnan University 214122 Wuxi China
| | - Quan Long
- grid.258151.a 0000000107081323 National Engineering Laboratory for Cereal Fermentation Technology Jiangnan University 214122 Wuxi China
| | - Yankun Yang
- grid.258151.a 0000000107081323 National Engineering Laboratory for Cereal Fermentation Technology Jiangnan University 214122 Wuxi China
| | - Zhonghu Bai
- grid.258151.a 0000000107081323 National Engineering Laboratory for Cereal Fermentation Technology Jiangnan University 214122 Wuxi China
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Gao X, Yang S, Zhao C, Ren Y, Wei D. Artificial Multienzyme Supramolecular Device: Highly Ordered Self-Assembly of Oligomeric Enzymes In Vitro and In Vivo. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Gao X, Yang S, Zhao C, Ren Y, Wei D. Artificial Multienzyme Supramolecular Device: Highly Ordered Self-Assembly of Oligomeric Enzymes In Vitro and In Vivo. Angew Chem Int Ed Engl 2014; 53:14027-30. [DOI: 10.1002/anie.201405016] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 06/19/2014] [Indexed: 12/13/2022]
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Zblewska K, Krajewska J, Zolkiewski M, Kędzierska-Mieszkowska S. Role of the disaggregase ClpB in processing of proteins aggregated as inclusion bodies. Arch Biochem Biophys 2014; 555-556:23-7. [PMID: 24943258 DOI: 10.1016/j.abb.2014.05.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Accepted: 05/08/2014] [Indexed: 11/28/2022]
Abstract
Overproduction of heterologous proteins in bacterial systems often results in the formation of insoluble inclusion bodies (IBs), which is a major impediment in biochemical research and biotechnology. In principle, the activity of molecular chaperones could be employed to gain control over the IB formation and to improve the recombinant protein yields, but the potential of each of the major bacterial chaperones (DnaK/J, GroEL/ES, and ClpB) to process IBs has not been fully established yet. We investigated the formation of inclusion bodies (IBs) of two aggregation-prone proteins, VP1LAC and VP1GFP, overproduced in Escherichiacoli in the presence and absence of the chaperone ClpB. We found that both ClpB isoforms, ClpB95 and ClpB80 accumulated in E. coli cells during the production of IBs. The amount of IB proteins increased in the absence of ClpB. ClpB supported the resolubilization and reactivation of the aggregated VP1LAC and VP1GFP in E. coli cells. The IB disaggregation was optimal in the presence of both ClpB95 and ClpB80. Our results indicate an essential role of ClpB in controlling protein aggregation and inclusion body formation in bacteria.
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Affiliation(s)
- Kamila Zblewska
- Department of Biochemistry, University of Gdansk, 80-308 Gdansk, Poland
| | - Joanna Krajewska
- Department of Biochemistry, University of Gdansk, 80-308 Gdansk, Poland
| | - Michal Zolkiewski
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
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Jin M, Chen Y, Xu C, Zhang X. The effect of inhibition of host MreB on the infection of thermophilic phage GVE2 in high temperature environment. Sci Rep 2014; 4:4823. [PMID: 24769758 PMCID: PMC4001104 DOI: 10.1038/srep04823] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 04/03/2014] [Indexed: 11/09/2022] Open
Abstract
In eukaryotes, the manipulation of the host actin cytoskeleton is a necessary strategy for viral pathogens to invade host cells. Increasing evidence indicates that the actin homolog MreB of bacteria plays key roles in cell shape formation, cell polarity, cell wall biosynthesis, and chromosome segregation. However, the role of bacterial MreB in the bacteriophage infection is not extensively investigated. To address this issue, in this study, the MreB of thermophilic Geobacillus sp. E263 from a deep-sea hydrothermal field was characterized by inhibiting the MreB polymerization and subsequently evaluating the bacteriophage GVE2 infection. The results showed that the host MreB played important roles in the bacteriophage infection at high temperature. After the host cells were treated with small molecule drug A22 or MP265, the specific inhibitors of MreB polymerization, the adsorption of GVE2 and the replication of GVE2 genome were significantly repressed. The confocal microscopy data revealed that MreB facilitated the GVE2 infection by inducing the polar distribution of virions during the phage infection. Our study contributed novel information to understand the molecular events of the host in response to bacteriophage challenge and extended our knowledge about the host-virus interaction in deep-sea vent ecosystems.
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Affiliation(s)
- Min Jin
- 1] Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and College of Life Sciences, Zhejiang University, Hangzhou 310058, The People's Republic of China [2]
| | - Yanjiang Chen
- 1] Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and College of Life Sciences, Zhejiang University, Hangzhou 310058, The People's Republic of China [2]
| | - Chenxi Xu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and College of Life Sciences, Zhejiang University, Hangzhou 310058, The People's Republic of China
| | - Xiaobo Zhang
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and College of Life Sciences, Zhejiang University, Hangzhou 310058, The People's Republic of China
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