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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Cui D, Liu L, Sun L, Lin X, Lin L, Zhang C. Genome-wide analysis reveals Hsf1 maintains high transcript abundance of target genes controlled by strong constitutive promoter in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:72. [PMID: 37118827 PMCID: PMC10141939 DOI: 10.1186/s13068-023-02322-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/16/2023] [Indexed: 04/30/2023]
Abstract
BACKGROUND In synthetic biology, the strength of promoter elements is the basis for precise regulation of target gene transcription levels, which in turn increases the yield of the target product. However, the results of many researches proved that excessive transcription levels of target genes actually reduced the yield of the target product. This phenomenon has been found in studies using different microorganisms as chassis cells, thus, it becomes a bottleneck problem to improve the yield of the target product. RESULTS In this study, promoters PGK1p and TDH3p with different strengths were used to regulate the transcription level of alcohol acetyl transferase encoding gene ATF1. The results demonstrated that the strong promoter TDH3p decreased the production of ethyl acetate. The results of Real-time PCR proved that the transcription level of ATF1 decreased rapidly under the control of TDH3p, and the unfolded protein reaction was activated, which may be the reason for the abnormal production caused by the strong promoter. RNA-sequencing analysis showed that the overexpression of differential gene HSP30 increased the transcriptional abundance of ATF1 gene and production of ethyl acetate. Interestingly, deletion of the heat shock protein family (e.g., Hsp26, Hsp78, Hsp82) decreased the production of ethyl acetate, suggesting that the Hsp family was also involved in the regulation of ATF1 gene transcription. Furthermore, the results proved that the Hsf1, an upstream transcription factor of Hsps, had a positive effect on alleviating the unfolded protein response and that overexpression of Hsf1 reprogramed the pattern of ATF1 gene transcript levels. The combined overexpression of Hsf1 and Hsps further increased the production of ethyl acetate. In addition, kinase Rim15 may be involved in this regulatory pathway. Finally, the regulation effect of Hsf1 on recombinant strains constructed by other promoters was verified, which confirmed the universality of the strategy. CONCLUSIONS Our results elucidated the mechanism by which Rim15-Hsf1-Hsps pathway reconstructed the repression of high transcription level stress and increased the production of target products, thereby providing new insights and application strategies for the construction of recombinant strains in synthetic biology.
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Affiliation(s)
- Danyao Cui
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Ling Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Lijing Sun
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Xue Lin
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Liangcai Lin
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
| | - Cuiying Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
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3
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Pan Z, Fan L, Zhong Y, Guo J, Dong X, Xu X, Wang C, Su Y. Quantitative proteomics reveals reduction in central carbon and energy metabolisms contributes to gentamicin resistance in Staphylococcus aureus. J Proteomics 2023; 277:104849. [PMID: 36809838 DOI: 10.1016/j.jprot.2023.104849] [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: 01/15/2023] [Revised: 02/11/2023] [Accepted: 02/12/2023] [Indexed: 02/22/2023]
Abstract
The emergence of antibiotic resistance greatly increases the difficulty of treating bacterial infections. In order to develop effective treatments, the underlying mechanisms of antibiotic resistance must be understood. In this study, Staphylococcus aureus ATCC6538 strain was passaged in medium with and without gentamicin and obtained lab-evolved gentamicin-resistant S. aureus (RGEN) and gentamicin-sensitive S. aureus (SGEN) strains, respectively. Data-Independent Acquisition (DIA)-based proteomics approach was applied to compare the two strains. A total of 1426 proteins were identified, of which 462 were significantly different: 126 were upregulated and 336 were downregulated in RGEN compared to SGEN. Further analysis found that reduced protein biosynthesis was a characteristic feature in RGEN, related to metabolic suppression. The most differentially expressed proteins were involved in metabolic pathways. In RGEN, central carbon metabolism was dysregulated and energy metabolism decreased. After verification, it was found that the levels of NADH, ATP, and reactive oxygen species (ROS) decreased, and superoxide dismutase and catalase activities increased. These findings suggest that inhibition of central carbon and energy metabolic pathways may play an important role in the resistance of S. aureus to gentamicin, and that gentamicin resistance is associated with oxidative stress. Significance: The overuse and misuse of antibiotics have led to bacterial antibiotic resistance, which is a serious threat to human health. Understanding the mechanisms of antibiotic resistance will help better control these antibiotic-resistant pathogens in the future. The present study characterized the differential proteome of gentamicin-resistant Staphylococcus aureus using the most advanced DIA-based proteomics technology. Many of the differential expressed proteins were related to metabolism, specifically, reduced central carbon and energy metabolism. Lower levels of NADH, ROS, and ATP were detected as a consequence of the reduced metabolism. These results reveal that downregulation of protein expression affecting central carbon and energy metabolisms may play an important role in the resistance of S. aureus to gentamicin.
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Affiliation(s)
- Zhiyu Pan
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Lvyuan Fan
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yilin Zhong
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Juan Guo
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xuesa Dong
- Shandong Freshwater Fisheries Research Institute, Jinan 250013, China
| | - Xiao Xu
- Shandong Freshwater Fisheries Research Institute, Jinan 250013, China
| | - Chao Wang
- Shandong Freshwater Fisheries Research Institute, Jinan 250013, China.
| | - Yubin Su
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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4
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Li Y, Chen T, You K, Peng T, Li T. Sequence determinants and solution conditions underlying liquid to solid phase transition. Am J Physiol Cell Physiol 2023; 324:C236-C246. [PMID: 36503242 DOI: 10.1152/ajpcell.00280.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Life consists of numberless functional biomolecules that exist in various states. Besides well-dissolved phases, biomolecules especially proteins and nucleic acids can form liquid droplets through liquid-liquid phase separation (LLPS). Stronger interactions promote a solid-like state of biomolecular condensates, which are also formerly referred to as detergent-insoluble aggregates. Solid-like condensates exist in vivo physiologically and pathologically, and their formation has not been fully understood. Recently, more and more research has proven that liquid to solid phase transition (LST) is an essential way to form solid condensates. In this review, we summarized the regions in the sequence that have different impacts on phase transition and emphasized that the LST is affected by its sequence characteristics. Moreover, increasing evidence unveiled that LST is affected by various solution conditions. We discussed solution conditions like protein concentration, pH, ATP, ions, and small molecules in a solution. Methods have been established to study these solid phase components. Here, we summarized low-throughput experimental techniques and high-throughput omics methods in the study of the LST.
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Affiliation(s)
- Yuxuan Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, China
| | - Taoyu Chen
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, China
| | - Kaiqing You
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Happy Life Technology, Beijing, China
| | - Tao Peng
- Happy Life Technology, Beijing, China
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, China
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5
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Liu X, Zhang P, Zhao Q, Huang AC. Making small molecules in plants: A chassis for synthetic biology-based production of plant natural products. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:417-443. [PMID: 35852486 DOI: 10.1111/jipb.13330] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Plant natural products have been extensively exploited in food, medicine, flavor, cosmetic, renewable fuel, and other industrial sectors. Synthetic biology has recently emerged as a promising means for the cost-effective and sustainable production of natural products. Compared with engineering microbes for the production of plant natural products, the potential of plants as chassis for producing these compounds is underestimated, largely due to challenges encountered in engineering plants. Knowledge in plant engineering is instrumental for enabling the effective and efficient production of valuable phytochemicals in plants, and also paves the way for a more sustainable future agriculture. In this manuscript, we briefly recap the biosynthesis of plant natural products, focusing primarily on industrially important terpenoids, alkaloids, and phenylpropanoids. We further summarize the plant hosts and strategies that have been used to engineer the production of natural products. The challenges and opportunities of using plant synthetic biology to achieve rapid and scalable production of high-value plant natural products are also discussed.
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Affiliation(s)
- Xinyu Liu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, SUSTech-PKU Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Peijun Zhang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, SUSTech-PKU Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Qiao Zhao
- Shenzhen Institutes of Advanced Technology (SIAT), the Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Ancheng C Huang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, SUSTech-PKU Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
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6
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Roa-Velázquez D, Xoconostle-Cázares B, Benítez-Cardoza CG, Ortega-López J, Shoshani L, Morales-Ríos E, Gallardo-Hernández S. Expression, purification, and refolding of the recombinant extracellular domain β 1-subunit of the dog Na +/K +-ATPase of the epithelial cells. Protein Expr Purif 2022; 200:106167. [PMID: 36057422 DOI: 10.1016/j.pep.2022.106167] [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: 07/18/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/25/2022]
Abstract
The β1-subunit of the Na+/K+-ATPase is a cell membrane protein, beyond its classic functions, it is also a cell adhesion molecule. β1-subunits on the lateral membrane of dog kidney epithelial cells trans-interact with β1-subunits from another neighboring cells. The β-β interaction is essential for the formation and stabilization of intercellular junctions. Previous studies on site-directed mutagenesis and in silico revealed that the interaction interface involves residues 198-207 and 221-229. However, it is necessary to report the interaction interface at the structural level experimentally. Here, we describe the successful cloning, overexpression in E. coli, and purification of the extracellular domain of the β1-subunit from inclusion bodies. Experimental characterization by size exclusion chromatography and DLS indicated similar hydrodynamic properties of the protein refolded. Structural analysis by circular dichroism and Raman spectroscopy revealed the secondary structures in the folded protein of type β-sheet, α-helix, random coil, and turn. We also performed β1-β1 interaction assays with the recombinant protein, showing dimers' formation (6xHisβ1-β1). Given our results, the recombinant extracellular domain of the β1-subunit is highly similar to the native protein, therefore the current work in our laboratory aims to characterize at the atomic level the interaction interface between EDβ1.
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Affiliation(s)
- Daniela Roa-Velázquez
- Programa de Doctorado en Nanociencias y Nanotecnología, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, Ciudad de México, 07360, Mexico.
| | - Beatriz Xoconostle-Cázares
- Departamento de Bioingeniería y Biotecnología, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, Ciudad de México, 07360, Mexico.
| | - Claudia G Benítez-Cardoza
- Laboratorio de Investigación Bioquímica, Escuela Nacional de Medicina y Homeopatía-Instituto Politécnico Nacional, Guillermo Massieu Helguera 239, Ciudad de México, 07320, Mexico.
| | - Jaime Ortega-López
- Departamento de Bioingeniería y Biotecnología, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, Ciudad de México, 07360, Mexico.
| | - Liora Shoshani
- Departamento de Fisiología Biofísica y Neurociencias, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, Ciudad de México, 07360, Mexico.
| | - Edgar Morales-Ríos
- Departamento de Bioquímica, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, Ciudad de México, 07360, Mexico.
| | - Salvador Gallardo-Hernández
- Departamento de Física, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, Ciudad de México, 07360, Mexico.
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7
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Getting Closer to Decrypting the Phase Transitions of Bacterial Biomolecules. Biomolecules 2022; 12:biom12070907. [PMID: 35883463 PMCID: PMC9312465 DOI: 10.3390/biom12070907] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/24/2022] [Accepted: 06/26/2022] [Indexed: 12/31/2022] Open
Abstract
Liquid–liquid phase separation (LLPS) of biomolecules has emerged as a new paradigm in cell biology, and the process is one proposed mechanism for the formation of membraneless organelles (MLOs). Bacterial cells have only recently drawn strong interest in terms of studies on both liquid-to-liquid and liquid-to-solid phase transitions. It seems that these processes drive the formation of prokaryotic cellular condensates that resemble eukaryotic MLOs. In this review, we present an overview of the key microbial biomolecules that undergo LLPS, as well as the formation and organization of biomacromolecular condensates within the intracellular space. We also discuss the current challenges in investigating bacterial biomacromolecular condensates. Additionally, we highlight a summary of recent knowledge about the participation of bacterial biomolecules in a phase transition and provide some new in silico analyses that can be helpful for further investigations.
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8
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Gao Z, Zhang W, Chang R, Zhang S, Yang G, Zhao G. Liquid-Liquid Phase Separation: Unraveling the Enigma of Biomolecular Condensates in Microbial Cells. Front Microbiol 2021; 12:751880. [PMID: 34759902 PMCID: PMC8573418 DOI: 10.3389/fmicb.2021.751880] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/06/2021] [Indexed: 12/12/2022] Open
Abstract
Numerous examples of microbial phase-separated biomolecular condensates have now been identified following advances in fluorescence imaging and single molecule microscopy technologies. The structure, function, and potential applications of these microbial condensates are currently receiving a great deal of attention. By neatly compartmentalizing proteins and their interactors in membrane-less organizations while maintaining free communication between these macromolecules and the external environment, microbial cells are able to achieve enhanced metabolic efficiency. Typically, these condensates also possess the ability to rapidly adapt to internal and external changes. The biological functions of several phase-separated condensates in small bacterial cells show evolutionary convergence with the biological functions of their eukaryotic paralogs. Artificial microbial membrane-less organelles are being constructed with application prospects in biocatalysis, biosynthesis, and biomedicine. In this review, we provide an overview of currently known biomolecular condensates driven by liquid-liquid phase separation (LLPS) in microbial cells, and we elaborate on their biogenesis mechanisms and biological functions. Additionally, we highlight the major challenges and future research prospects in studying microbial LLPS.
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Affiliation(s)
| | | | | | | | - Guiwen Yang
- College of Life Science, Shandong Normal University, Jinan, China
| | - Guoyan Zhao
- College of Life Science, Shandong Normal University, Jinan, China
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9
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Petrovskaya LE, Ziganshin RH, Kryukova EA, Zlobinov AV, Gapizov SS, Shingarova LN, Mironov VA, Lomakina GY, Dolgikh DA, Kirpichnikov MP. Increased Synthesis of a Magnesium Transporter MgtA During Recombinant Autotransporter Expression in Escherichia coli. Appl Biochem Biotechnol 2021; 193:3672-3703. [PMID: 34351586 DOI: 10.1007/s12010-021-03634-5] [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: 05/07/2021] [Accepted: 07/19/2021] [Indexed: 12/01/2022]
Abstract
Overproduction of the membrane proteins in Escherichia coli cells is a common approach to obtain sufficient material for their functional and structural studies. However, the efficiency of this process can be limited by toxic effects which decrease the viability of the host and lead to low yield of the product. During the expression of the esterase autotransporter AT877 from Psychrobacter cryohalolentis K5T, we observed significant growth inhibition of the C41(DE3) cells in comparison with the same cells producing other recombinant proteins. Induction of AT877 synthesis also resulted in the elevated expression of a magnesium transporter MgtA and decreased ATP content of the cells. To characterize the response to overexpression of the autotransporter in bacterial cells, we performed a comparative analysis of their proteomic profile by mass spectrometry. According to the obtained data, E. coli cells which synthesize AT877 experience complex stress condition presumably associated with secretion apparatus overloading and improper localization of the recombinant protein. Several response pathways were shown to be activated by AT877 overproduction including Cpx, PhoP/PhoQ, Psp, and σE The obtained results open new opportunities for optimization of the recombinant membrane protein expression in E. coli for structural studies and biotechnological applications.
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Affiliation(s)
- Lada E Petrovskaya
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia.
| | - Rustam H Ziganshin
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
| | - Elena A Kryukova
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
- Emanuel Institute of Biochemical Physics, Kosygina str., 4, Moscow, 119334, Russia
| | - Alexander V Zlobinov
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
| | - Sultan Sh Gapizov
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
- Emanuel Institute of Biochemical Physics, Kosygina str., 4, Moscow, 119334, Russia
- Department of Biology, M. V. Lomonosov Moscow State University, Leninskie gory, 1, Moscow, 119234, Russia
| | - Lyudmila N Shingarova
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
| | - Vasiliy A Mironov
- Roche Diagnostics Rus LLC, Letnikovskaya str. 2/2, Moscow, 115114, Russia
| | - Galina Yu Lomakina
- Department of Chemistry, M. V. Lomonosov Moscow State University, Leninskie Gory, 1/3, Moscow, 119991, Russia
- Bauman Moscow State Technical University, Baumanskaya 2-ya, 5/1, Moscow, 105005, Russia
| | - Dmitriy A Dolgikh
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
- Emanuel Institute of Biochemical Physics, Kosygina str., 4, Moscow, 119334, Russia
- Department of Biology, M. V. Lomonosov Moscow State University, Leninskie gory, 1, Moscow, 119234, Russia
| | - Mikhail P Kirpichnikov
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
- Department of Biology, M. V. Lomonosov Moscow State University, Leninskie gory, 1, Moscow, 119234, Russia
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10
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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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11
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Pasieka A, Panek D, Szałaj N, Espargaró A, Więckowska A, Malawska B, Sabaté R, Bajda M. Dual Inhibitors of Amyloid-β and Tau Aggregation with Amyloid-β Disaggregating Properties: Extended In Cellulo, In Silico, and Kinetic Studies of Multifunctional Anti-Alzheimer's Agents. ACS Chem Neurosci 2021; 12:2057-2068. [PMID: 34019757 PMCID: PMC8291496 DOI: 10.1021/acschemneuro.1c00235] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
![]()
In Alzheimer’s
disease, neurons slowly degenerate due to
the accumulation of misfolded amyloid β and tau proteins. In
our research, we performed extended studies directed at amyloid β
and tau aggregation inhibition using in cellulo (Escherichia coli model of protein aggregation), in silico, and in vitro kinetic studies.
We tested our library of 1-benzylamino-2-hydroxyalkyl multifunctional
anti-Alzheimer’s agents and identified very potent dual aggregation
inhibitors. Among the tested derivatives, we selected compound 18, which exhibited a unique profile of biological activity.
This compound was the most potent and balanced dual aggregation inhibitor
(Aβ42 inhibition (inh.) 80.0%, tau inh. 68.3% in
10 μM), with previously reported in vitro inhibitory
activity against hBuChE, hBACE1,
and Aβ (hBuChE IC50 = 5.74 μM; hBACE1 IC50 = 41.6 μM; Aβ aggregation
(aggr.) inh. IC50 = 3.09 μM). In docking studies
for both proteins, we tried to explain the different structural requirements
for the inhibition of Aβ vs tau. Moreover, docking and kinetic
studies showed that compound 18 could inhibit the amyloid
aggregation process at several steps and also displayed disaggregating
properties. These results may help to design the next generations
of dual or selective aggregation inhibitors.
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Affiliation(s)
- Anna Pasieka
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland
| | - Dawid Panek
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland
| | - Natalia Szałaj
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland
| | - Alba Espargaró
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, School of Pharmacy and Food Sciences, University of Barcelona, Av Joan XXIII 27-31, 08028 Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), Av Joan XXIII, S/N, 08028 Barcelona, Spain
| | - Anna Więckowska
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland
| | - Barbara Malawska
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland
| | - Raimon Sabaté
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, School of Pharmacy and Food Sciences, University of Barcelona, Av Joan XXIII 27-31, 08028 Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), Av Joan XXIII, S/N, 08028 Barcelona, Spain
| | - Marek Bajda
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland
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12
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Khodaparast L, Wu G, Khodaparast L, Schmidt BZ, Rousseau F, Schymkowitz J. Bacterial Protein Homeostasis Disruption as a Therapeutic Intervention. Front Mol Biosci 2021; 8:681855. [PMID: 34150852 PMCID: PMC8206779 DOI: 10.3389/fmolb.2021.681855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/04/2021] [Indexed: 12/15/2022] Open
Abstract
Cells have evolved a complex molecular network, collectively called the protein homeostasis (proteostasis) network, to produce and maintain proteins in the appropriate conformation, concentration and subcellular localization. Loss of proteostasis leads to a reduction in cell viability, which occurs to some degree during healthy ageing, but is also the root cause of a group of diverse human pathologies. The accumulation of proteins in aberrant conformations and their aggregation into specific beta-rich assemblies are particularly detrimental to cell viability and challenging to the protein homeostasis network. This is especially true for bacteria; it can be argued that the need to adapt to their changing environments and their high protein turnover rates render bacteria particularly vulnerable to the disruption of protein homeostasis in general, as well as protein misfolding and aggregation. Targeting bacterial proteostasis could therefore be an attractive strategy for the development of novel antibacterial therapeutics. This review highlights advances with an antibacterial strategy that is based on deliberately inducing aggregation of target proteins in bacterial cells aiming to induce a lethal collapse of protein homeostasis. The approach exploits the intrinsic aggregation propensity of regions residing in the hydrophobic core regions of the polypeptide sequence of proteins, which are genetically conserved because of their essential role in protein folding and stability. Moreover, the molecules were designed to target multiple proteins, to slow down the build-up of resistance. Although more research is required, results thus far allow the hope that this strategy may one day contribute to the arsenal to combat multidrug-resistant bacterial infections.
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Affiliation(s)
- Laleh Khodaparast
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Guiqin Wu
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Ladan Khodaparast
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Béla Z Schmidt
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
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13
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Labourel F, Rajon E. Resource uptake and the evolution of moderately efficient enzymes. Mol Biol Evol 2021; 38:3938-3952. [PMID: 33964160 PMCID: PMC8382906 DOI: 10.1093/molbev/msab132] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Enzymes speed up reactions that would otherwise be too slow to sustain the metabolism of selfreplicators. Yet, most enzymes seem only moderately efficient, exhibiting kinetic parameters orders of magnitude lower than their expected physically achievable maxima and spanning over surprisingly large ranges of values. Here, we question how these parameters evolve using a mechanistic model where enzyme efficiency is a key component of individual competition for resources. We show that kinetic parameters are under strong directional selection only up to a point, above which enzymes appear to evolve under near-neutrality, thereby confirming the qualitative observation of other modeling approaches. While the existence of a large fitness plateau could potentially explain the extensive variation in enzyme features reported, we show using a population genetics model that such a widespread distribution is an unlikely outcome of evolution on a common landscape, as mutation–selection–drift balance occupy a narrow area even when very moderate biases towards lower efficiency are considered. Instead, differences in the evolutionary context encountered by each enzyme should be involved, such that each evolves on an individual, unique landscape. Our results point to drift and effective population size playing an important role, along with the kinetics of nutrient transporters, the tolerance to high concentrations of intermediate metabolites, and the reversibility of reactions. Enzyme concentration also shapes selection on kinetic parameters, but we show that the joint evolution of concentration and efficiency does not yield extensive variance in evolutionary outcomes when documented costs to protein expression are applied.
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Affiliation(s)
- Florian Labourel
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, Villeurbanne, F-69622, France
| | - Etienne Rajon
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, Villeurbanne, F-69622, France
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14
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Bollen C, Dewachter L, Michiels J. Protein Aggregation as a Bacterial Strategy to Survive Antibiotic Treatment. Front Mol Biosci 2021; 8:669664. [PMID: 33937340 PMCID: PMC8085434 DOI: 10.3389/fmolb.2021.669664] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 03/29/2021] [Indexed: 11/18/2022] Open
Abstract
While protein aggregation is predominantly associated with loss of function and toxicity, it is also known to increase survival of bacteria under stressful conditions. Indeed, protein aggregation not only helps bacteria to cope with proteotoxic stresses like heat shocks or oxidative stress, but a growing number of studies suggest that it also improves survival during antibiotic treatment by inducing dormancy. A well-known example of dormant cells are persisters, which are transiently refractory to the action of antibiotics. These persister cells can switch back to the susceptible state and resume growth in the absence of antibiotics, and are therefore considered an important cause of recurrence of infections. Mounting evidence now suggests that this antibiotic-tolerant persister state is tightly linked to-or perhaps even driven by-protein aggregation. Moreover, another dormant bacterial phenotype, the viable but non-culturable (VBNC) state, was also shown to be associated with aggregation. These results indicate that persisters and VBNC cells may constitute different stages of the same dormancy program induced by progressive protein aggregation. In this mini review, we discuss the relation between aggregation and bacterial dormancy, focusing on both persisters and VBNC cells. Understanding the link between protein aggregation and dormancy will not only provide insight into the fundamentals of bacterial survival, but could prove highly valuable in our future battle to fight them.
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Affiliation(s)
- Celien Bollen
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB-KU Leuven, Leuven, Belgium
| | - Liselot Dewachter
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB-KU Leuven, Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB-KU Leuven, Leuven, Belgium
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15
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Cell-Free Expression of a Plant Membrane Protein BrPT2 From Boesenbergia Rotunda. Mol Biotechnol 2021; 63:316-326. [PMID: 33565047 DOI: 10.1007/s12033-021-00304-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2021] [Indexed: 10/22/2022]
Abstract
Prenylation of aromatic natural products by membrane-bound prenyltransferases (PTs) is an important biosynthesis step of many bioactive compounds. At present, only a few plant flavonoid-related PT genes have been functionally characterized, mainly due to the difficulties of expressing these membrane proteins. Rapid and effective methods to produce functional plant membrane proteins are thus indispensable. Here, we evaluated expression systems through cell-based and cell-free approaches to express Boesenbergia rotunda BrPT2 encoding a membrane-bound prenyltransferase. We attempted to express BrPT2 in Escherichia coli and tobacco plants but failed to detect this protein using the Western-blot technique, whereas an intact single band of 43 kDa was detected when BrPT2 was expressed using a cell-free protein synthesis system (PURE). Under in vitro enzymatic condition, the synthesized BrPT2 successfully catalyzed pinostrobin chalcone to pinostrobin. Molecular docking analysis showed that pinostrobin chalcone interacts with BrPT2 at two cavities: (1) the main binding site at the central cavity and (2) the allosteric binding site located away from the central cavity. Our findings suggest that cell-free protein synthesis could be an alternative for rapid production of valuable difficult-to-express membrane proteins.
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16
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Efficiency and Robustness of Processes Driven by Nucleoid Exclusion in Escherichia coli. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020. [PMID: 32894477 DOI: 10.1007/978-3-030-46886-6_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
The internal spatial organization of prokaryotic organisms, including Escherichia coli, is essential for the proper functioning of processes such as cell division. One source of this organization in E. coli is the nucleoid, which causes the exclusion of macromolecules - e.g. protein aggregates and the chemotaxis network - from midcell. Similarly, following DNA replication, the nucleoid(s) assist in placing the Z-ring at midcell. These processes need to be efficient in optimal conditions and robust to suboptimal conditions. After reviewing recent findings on these topics, we make use of past data to study the efficiency of the spatial constraining of Z-rings, chemotaxis networks, and protein aggregates, as a function of the nucleoid(s) morphology. Also, we compare the robustness of these processes to nonoptimal temperatures. We show that Z-rings, Tsr clusters, and protein aggregates have temperature-dependent spatial distributions along the major cell axis that are consistent with the nucleoid(s) morphology and the volume-exclusion phenomenon. Surprisingly, the consequences of the changes in nucleoid size with temperature are most visible in the kurtosis of these spatial distributions, in that it has a statistically significant linear correlation with the mean nucleoid length and, in the case of Z-rings, with the distance between nucleoids prior to cell division. Interestingly, we also find a negative, statistically significant linear correlation between the efficiency of these processes at the optimal condition and their robustness to suboptimal conditions, suggesting a trade-off between these traits.
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17
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Wichur T, Więckowska A, Więckowski K, Godyń J, Jończyk J, Valdivieso ÁDR, Panek D, Pasieka A, Sabaté R, Knez D, Gobec S, Malawska B. 1-Benzylpyrrolidine-3-amine-based BuChE inhibitors with anti-aggregating, antioxidant and metal-chelating properties as multifunctional agents against Alzheimer's disease. Eur J Med Chem 2019; 187:111916. [PMID: 31812794 DOI: 10.1016/j.ejmech.2019.111916] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/25/2019] [Accepted: 11/25/2019] [Indexed: 01/07/2023]
Abstract
Complex pathomechanism of Alzheimer's disease (AD) prompts researchers to develop multifunctional molecules in order to find effective therapy against AD. We designed and synthesized novel multifunctional ligands for which we assessed their activities towards butyrylcholinesterase, beta secretase, amyloid beta (Aβ) and tau protein aggregation as well as antioxidant and metal-chelating properties. All compounds showed dual anti-aggregating properties towards Aβ and tau protein in the in cellulo assay in Escherichia coli. Of particular interest are compounds 24b and 25b, which efficiently inhibit aggregation of Aβ and tau protein at 10 μM (24b: 45% for Aβ, 53% for tau; 25b: 49% for Aβ, 54% for tau). They display free radical scavenging capacity and antioxidant activity in ABTS and FRAP assays, respectively, and selectively chelate copper ions. Compounds 24b and 25b are also the most potent inhibitors of BuChE with IC50 of 2.39 μM and 1.94 μM, respectively. Promising in vitro activities of the presented multifunctional ligands as well as their original scaffold are a very interesting starting point for further research towards effective anti-AD treatment.
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Affiliation(s)
- Tomasz Wichur
- Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688, Kraków, Poland
| | - Anna Więckowska
- Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688, Kraków, Poland
| | - Krzysztof Więckowski
- Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688, Kraków, Poland
| | - Justyna Godyń
- Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688, Kraków, Poland
| | - Jakub Jończyk
- Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688, Kraków, Poland
| | | | - Dawid Panek
- Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688, Kraków, Poland
| | - Anna Pasieka
- Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688, Kraków, Poland
| | - Raimon Sabaté
- Department of Pharmacy and Pharmaceutical Technology and Physical Chemistry, Faculty of Pharmacy and Food Science, University of Barcelona, Av Joan XXIII 27-31, 08028, Barcelona, Spain; Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Av Joan XXIII, S/N, 08028, Barcelona, Spain
| | - Damijan Knez
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Stanislav Gobec
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Barbara Malawska
- Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688, Kraków, Poland.
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18
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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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19
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Goemans CV, Vertommen D, Agrebi R, Collet JF. CnoX Is a Chaperedoxin: A Holdase that Protects Its Substrates from Irreversible Oxidation. Mol Cell 2018; 70:614-627.e7. [PMID: 29754824 DOI: 10.1016/j.molcel.2018.04.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/22/2018] [Accepted: 04/03/2018] [Indexed: 02/01/2023]
Abstract
Bleach (HOCl) is a powerful oxidant that kills bacteria in part by causing protein aggregation. It inactivates ATP-dependent chaperones, rendering cellular proteins mostly dependent on holdases. Here we identified Escherichia coli CnoX (YbbN) as a folding factor that, when activated by bleach via chlorination, functions as an efficient holdase, protecting the substrates of the major folding systems GroEL/ES and DnaK/J/GrpE. Remarkably, CnoX uniquely combines this function with the ability to prevent the irreversible oxidation of its substrates. This dual activity makes CnoX the founding member of a family of proteins, the "chaperedoxins." Because CnoX displays a thioredoxin fold and a tetratricopeptide (TPR) domain, two structural motifs conserved in all organisms, this investigation sets the stage for the discovery of additional chaperedoxins in bacteria and eukaryotes that could cooperate with proteins from both the Hsp60 and Hsp70 families.
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Affiliation(s)
- Camille V Goemans
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Didier Vertommen
- de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Rym Agrebi
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Jean-François Collet
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium.
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20
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Crespo R, Villar-Alvarez E, Taboada P, Rocha FA, Damas AM, Martins PM. Insoluble Off-Pathway Aggregates as Crowding Agents during Amyloid Fibril Formation. J Phys Chem B 2017; 121:2288-2298. [DOI: 10.1021/acs.jpcb.7b01120] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Rosa Crespo
- LEPABE,
Laboratório de Engenharia de Processos, Ambiente, Biotecnologia
e Energia, Departamento de Engenharia Química, Faculdade de Engenharia da Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Eva Villar-Alvarez
- Área
de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Pablo Taboada
- Área
de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Fernando A. Rocha
- LEPABE,
Laboratório de Engenharia de Processos, Ambiente, Biotecnologia
e Energia, Departamento de Engenharia Química, Faculdade de Engenharia da Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Ana M. Damas
- ICBAS
− Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto 4050-313, Portugal
| | - Pedro M. Martins
- LEPABE,
Laboratório de Engenharia de Processos, Ambiente, Biotecnologia
e Energia, Departamento de Engenharia Química, Faculdade de Engenharia da Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ICBAS
− Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto 4050-313, Portugal
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21
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Ishtikhar M, Rahisuddin, Khan MV, Khan RH. Anti-aggregation property of thymoquinone induced by copper-nanoparticles: A biophysical approach. Int J Biol Macromol 2016; 93:1174-1182. [DOI: 10.1016/j.ijbiomac.2016.09.089] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 09/24/2016] [Accepted: 09/26/2016] [Indexed: 12/14/2022]
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22
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Liu X, Zhang W, Zhao Z, Dai X, Yang Y, Bai Z. Protein secretion in Corynebacterium glutamicum. Crit Rev Biotechnol 2016; 37:541-551. [PMID: 27737570 DOI: 10.1080/07388551.2016.1206059] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Corynebacterium glutamicum, a Gram-positive bacterium, has been widely used for the industrial production of amino acids, such as glutamate and lysine, for decades. Due to several characteristics - its ability to secrete properly folded and functional target proteins into culture broth, its low levels of endogenous extracellular proteins and its lack of detectable extracellular hydrolytic enzyme activity - C. glutamicum is also a very favorable host cell for the secretory production of heterologous proteins, important enzymes, and pharmaceutical proteins. The target proteins are secreted into the culture medium, which has attractive advantages over the manufacturing process for inclusion of body expression - the simplified downstream purification process. The secretory process of proteins is complicated and energy consuming. There are two major secretory pathways in C. glutamicum, the Sec pathway and the Tat pathway, both have specific signal peptides that mediate the secretion of the target proteins. In the present review, we critically discuss recent progress in the secretory production of heterologous proteins and examine in depth the mechanisms of the protein translocation process in C. glutamicum. Some successful case studies of actual applications of this secretory expression host are also evaluated. Finally, the existing issues and solutions in using C. glutamicum as a host of secretory proteins are specifically addressed.
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Affiliation(s)
- Xiuxia Liu
- a National Engineering Laboratory for Cereal Fermentation Technology , Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology, Ministry of Education , School of Biotechnology, Jiangnan University , Wuxi , China
| | - Wei Zhang
- a National Engineering Laboratory for Cereal Fermentation Technology , Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology, Ministry of Education , School of Biotechnology, Jiangnan University , Wuxi , China
| | - Zihao Zhao
- a National Engineering Laboratory for Cereal Fermentation Technology , Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology, Ministry of Education , School of Biotechnology, Jiangnan University , Wuxi , China
| | - Xiaofeng Dai
- a National Engineering Laboratory for Cereal Fermentation Technology , Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology, Ministry of Education , School of Biotechnology, Jiangnan University , Wuxi , China
| | - Yankun Yang
- a National Engineering Laboratory for Cereal Fermentation Technology , Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology, Ministry of Education , School of Biotechnology, Jiangnan University , Wuxi , China
| | - Zhonghu Bai
- a National Engineering Laboratory for Cereal Fermentation Technology , Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology, Ministry of Education , School of Biotechnology, Jiangnan University , Wuxi , China
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23
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Yan S, Wu G. Evolutionary evidence on suitability of SecD as a target for development of antibacterial agents against Staphylococcus aureus. Ecol Evol 2016; 6:1393-410. [PMID: 27087922 PMCID: PMC4775529 DOI: 10.1002/ece3.1951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 12/15/2015] [Accepted: 12/16/2015] [Indexed: 11/22/2022] Open
Abstract
Staphylococcus aureus causes many infections and its drug resistance is a worrying challenge for medical care. The SecD subunit of Sec secretion system in methicillin‐resistant S. aureus is an attractive target because SecD dysfunction leads to the death of bacteria and SecD as a target is more efficient than SecA and SecF. Evolution could have made SecD to become insensitive to antibacterial agents although the drugs directly against SecD have yet to develop. So far, no detailed information on SecD evolution has been available, thus 2686 SecD sequences with full taxonomic information from kingdom to species were analyzed. First, the variance of pairwise p‐distance was evaluated for each taxonomic group. Second, the variance was further partitioned into intergroup and intragroup variances for quantification of horizontal and vertical gene transfer. Third, phylogenetic tree was built to trace the evolutionary pathway. The results showed that overall evolution of SecDs appears to have undergone horizontal and vertical gene transfer. Only 0.5% horizontal transfers were found between any two SecDs in S. aureus, 6.8% and 8.8% horizontal transfers were found between any two Staphylococcus SecDs from different and the same species, and only one SecD from S. aureus was located far away from its sister cluster. Thus, statistic and evolutionary analyses demonstrate that the SecDs from staphylococcus species have a small chance of mutating, and provide taxonomic evidence to use the SecD as a potential target for new generation of antibacterial agents against S. aureus.
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Affiliation(s)
- Shaomin Yan
- Guangxi Bioscience and Biotechnology Research Center Guangxi Academy of Sciences 98 Daling Road Nanning Guangxi 530007 China
| | - Guang Wu
- Guangxi Bioscience and Biotechnology Research Center Guangxi Academy of Sciences 98 Daling Road Nanning Guangxi 530007 China
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24
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Moreno-Forero SK, Rojas E, Beggah S, van der Meer JR. Comparison of differential gene expression to water stress among bacteria with relevant pollutant-degradation properties. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:91-102. [PMID: 26616826 DOI: 10.1111/1758-2229.12356] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 11/15/2015] [Accepted: 11/15/2015] [Indexed: 06/05/2023]
Abstract
Resistance to semi-dry environments has been considered a crucial trait for superior growth and survival of strains used for bioaugmentation in contaminated soils. In order to compare water stress programmes, we analyse differential gene expression among three phylogenetically different strains capable of aromatic compound degradation: Arthrobacter chlorophenolicus A6, Sphingomonas wittichii RW1 and Pseudomonas veronii 1YdBTEX2. Standardized laboratory-induced water stress was imposed by shock exposure of liquid cultures to water potential decrease, induced either by addition of solutes (NaCl, solute stress) or by addition of polyethylene glycol (matric stress), both at absolute similar stress magnitudes and at those causing approximately similar decrease of growth rates. Genome-wide differential gene expression was recorded by micro-array hybridizations. Growth of P. veronii 1YdBTEX2 was the most sensitive to water potential decrease, followed by S. wittichii RW1 and A. chlorophenolicus A6. The number of genes differentially expressed under decreasing water potential was lowest for A. chlorophenolicus A6, increasing with increasing magnitude of the stress, followed by S. wittichii RW1 and P. veronii 1YdBTEX2. Gene inspection and gene ontology analysis under stress conditions causing similar growth rate reduction indicated that common reactions among the three strains included diminished expression of flagellar motility and increased expression of compatible solutes (which were strain-specific). Furthermore, a set of common genes with ill-defined function was found between all strains, including ABC transporters and aldehyde dehydrogenases, which may constitute a core conserved response to water stress. The data further suggest that stronger reduction of growth rate of P. veronii 1YdBTEX2 under water stress may be an indirect result of the response demanding heavy NADPH investment, rather than the presence or absence of a suitable stress defence mechanism per se.
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Affiliation(s)
- Silvia K Moreno-Forero
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
| | - Edward Rojas
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
| | - Siham Beggah
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
| | - Jan R van der Meer
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
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Chen A, Sun Y, Zhang W, Peng F, Zhan C, Liu M, Yang Y, Bai Z. Downsizing a pullulanase to a small molecule with improved soluble expression and secretion efficiency in Escherichia coli. Microb Cell Fact 2016; 15:9. [PMID: 26762529 PMCID: PMC4712565 DOI: 10.1186/s12934-015-0403-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/22/2015] [Indexed: 01/30/2023] Open
Abstract
Background Significant challenges, including low expression and extracellular secretion of soluble protein, are encountered in expressing and purifying Bacillus acidopullulyticus pullulanase (BaPul) in Escherichia coli. Methods An N-terminal domain truncation was adopted to facilitate BaPul variant expression and/or secretion. Results BaPul possesses a complex modular architecture that consists of CBM41-X45a-X25-X45b-CBM48-GH13. The activities of M1 (ΔCBM41) and M5 (ΔCBM41ΔX25) variants were 2.9- and 2.4-fold that of wild-type (WT) enzyme, respectively. The enhanced expression of soluble protein is the main reason for these improved activities. PelB-M1 and PelB-M5 were transported to the periplasmic space, where PelB is part of the PelB-pET28a(+) construct, and PelB-M3 (ΔX25) and PelB-WT variants were largely retained in the cytoplasm. After fermentation, about 56.6 and 93.4 % of the total activity of PelB-M1 and PelB-M5 were transferred to the periplasm, respectively, followed by cell lysis and leakage of the partial enzyme into the extracellular medium. The optimal temperature and pH for purified preparations of M1, M3, and M5 were similar to those of the WT enzyme. In a starch saccharification reaction, the dextrose equivalents of M1, M3, and M5 proteins were 94.7, 94.5, and 93.1 %, respectively, which were also essentially identical to that of WT (93.6 %). Conclusion The deletion of CBM41 and/or X25 domain did not affect the enzyme application, and the truncated variants were more highly expressed and secreted in E. coli. Thus, the truncated variants may be more suitable for industrial applications.
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Affiliation(s)
- Ana Chen
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China. .,School of Biochemical Engineering, Anhui Polytechnic University, Wuhu, 241000, China. .,The Key Laboratory of Industrial Biotechnology and The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Yang Sun
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China. .,The Key Laboratory of Industrial Biotechnology and The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Wei Zhang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China. .,The Key Laboratory of Industrial Biotechnology and The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Feng Peng
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China. .,The Key Laboratory of Industrial Biotechnology and The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Chunjun Zhan
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China. .,The Key Laboratory of Industrial Biotechnology and The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Meng Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China. .,The Key Laboratory of Industrial Biotechnology and The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Yankun Yang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China. .,The Key Laboratory of Industrial Biotechnology and The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Zhonghu Bai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China. .,The Key Laboratory of Industrial Biotechnology and The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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Robustness of the Process of Nucleoid Exclusion of Protein Aggregates in Escherichia coli. J Bacteriol 2016; 198:898-906. [PMID: 26728194 DOI: 10.1128/jb.00848-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/22/2015] [Indexed: 02/06/2023] Open
Abstract
UNLABELLED Escherichia coli segregates protein aggregates to the poles by nucleoid exclusion. Combined with cell divisions, this generates heterogeneous aggregate distributions in subsequent cell generations. We studied the robustness of this process with differing medium richness and antibiotics stress, which affect nucleoid size, using multimodal, time-lapse microscopy of live cells expressing both a fluorescently tagged chaperone (IbpA), which identifies in vivo the location of aggregates, and HupA-mCherry, a fluorescent variant of a nucleoid-associated protein. We find that the relative sizes of the nucleoid's major and minor axes change widely, in a positively correlated fashion, with medium richness and antibiotic stress. The aggregate's distribution along the major cell axis also changes between conditions and in agreement with the nucleoid exclusion phenomenon. Consequently, the fraction of aggregates at the midcell region prior to cell division differs between conditions, which will affect the degree of asymmetries in the partitioning of aggregates between cells of future generations. Finally, from the location of the peak of anisotropy in the aggregate displacement distribution, the nucleoid relative size, and the spatiotemporal aggregate distribution, we find that the exclusion of detectable aggregates from midcell is most pronounced in cells with mid-sized nucleoids, which are most common under optimal conditions. We conclude that the aggregate management mechanisms of E. coli are significantly robust but are not immune to stresses due to the tangible effect that these have on nucleoid size. IMPORTANCE Escherichia coli segregates protein aggregates to the poles by nucleoid exclusion. From live single-cell microscopy studies of the robustness of this process to various stresses known to affect nucleoid size, we find that nucleoid size and aggregate preferential locations change concordantly between conditions. Also, the degree of influence of the nucleoid on aggregate positioning differs between conditions, causing aggregate numbers at midcell to differ in cell division events, which will affect the degree of asymmetries in the partitioning of aggregates between cells of future generations. Finally, we find that aggregate segregation to the cell poles is most pronounced in cells with mid-sized nucleoids. We conclude that the energy-free process of the midcell exclusion of aggregates partially loses effectiveness under stressful conditions.
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Oliveira SMD, Neeli-Venkata R, Goncalves NSM, Santinha JA, Martins L, Tran H, Mäkelä J, Gupta A, Barandas M, Häkkinen A, Lloyd-Price J, Fonseca JM, Ribeiro AS. Increased cytoplasm viscosity hampers aggregate polar segregation inEscherichia coli. Mol Microbiol 2015; 99:686-99. [DOI: 10.1111/mmi.13257] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2015] [Indexed: 12/11/2022]
Affiliation(s)
- Samuel M. D. Oliveira
- Laboratory of Biosystem Dynamics; Department of Signal Processing; Tampere University of Technology; 33101 Tampere Finland
| | - Ramakanth Neeli-Venkata
- Laboratory of Biosystem Dynamics; Department of Signal Processing; Tampere University of Technology; 33101 Tampere Finland
| | - Nadia S. M. Goncalves
- Laboratory of Biosystem Dynamics; Department of Signal Processing; Tampere University of Technology; 33101 Tampere Finland
| | - João A. Santinha
- UNINOVA; Instituto de Desenvolvimento de Novas Tecnologias; Campus FCT-UNL; 2829-516 Caparica Portugal
| | - Leonardo Martins
- UNINOVA; Instituto de Desenvolvimento de Novas Tecnologias; Campus FCT-UNL; 2829-516 Caparica Portugal
| | - Huy Tran
- Laboratory of Biosystem Dynamics; Department of Signal Processing; Tampere University of Technology; 33101 Tampere Finland
| | - Jarno Mäkelä
- Laboratory of Biosystem Dynamics; Department of Signal Processing; Tampere University of Technology; 33101 Tampere Finland
| | - Abhishekh Gupta
- Laboratory of Biosystem Dynamics; Department of Signal Processing; Tampere University of Technology; 33101 Tampere Finland
| | - Marilia Barandas
- UNINOVA; Instituto de Desenvolvimento de Novas Tecnologias; Campus FCT-UNL; 2829-516 Caparica Portugal
| | - Antti Häkkinen
- Laboratory of Biosystem Dynamics; Department of Signal Processing; Tampere University of Technology; 33101 Tampere Finland
| | - Jason Lloyd-Price
- Laboratory of Biosystem Dynamics; Department of Signal Processing; Tampere University of Technology; 33101 Tampere Finland
| | - José M. Fonseca
- UNINOVA; Instituto de Desenvolvimento de Novas Tecnologias; Campus FCT-UNL; 2829-516 Caparica Portugal
| | - Andre S. Ribeiro
- Laboratory of Biosystem Dynamics; Department of Signal Processing; Tampere University of Technology; 33101 Tampere Finland
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Mammalian prion protein (PrP) forms conformationally different amyloid intracellular aggregates in bacteria. Microb Cell Fact 2015; 14:174. [PMID: 26536866 PMCID: PMC4634817 DOI: 10.1186/s12934-015-0361-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 10/17/2015] [Indexed: 01/21/2023] Open
Abstract
Background An increasing number of proteins are being shown to assemble into amyloid structures that lead to pathological states. Among them, mammalian prions outstand due to their ability to transmit the pathogenic conformation, becoming thus infectious. The structural conversion of the cellular prion protein (PrPC), into its misfolded pathogenic form (PrPSc) is the central event of prion-driven pathologies. The study of the structural properties of intracellular amyloid aggregates in general and of prion-like ones in particular is a challenging task. In this context, the evidence that the inclusion bodies formed by amyloid proteins in bacteria display amyloid-like structural and functional properties make them a privileged system to model intracellular amyloid aggregation. Results Here we provide the first demonstration that recombinant murine PrP and its C-terminal domain (90–231) attain amyloid conformations inside bacteria. Moreover, the inclusions formed by these two PrP proteins display conformational diversity, since they differ in fibril morphology, binding affinity to amyloid dyes, stability, resistance to proteinase K digestion and neurotoxicity. Conclusions Overall, our results suggest that modelling PrP amyloid formation in microbial cell factories might open an avenue for a better understanding of the structural features modulating the pathogenic impact of this intriguing protein. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0361-y) contains supplementary material, which is available to authorized users.
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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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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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Navarro S, Marinelli P, Diaz-Caballero M, Ventura S. The prion-like RNA-processing protein HNRPDL forms inherently toxic amyloid-like inclusion bodies in bacteria. Microb Cell Fact 2015; 14:102. [PMID: 26160665 PMCID: PMC4498515 DOI: 10.1186/s12934-015-0284-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 06/16/2015] [Indexed: 01/09/2023] Open
Abstract
Background The formation of protein inclusions is connected to the onset of many human diseases. Human RNA binding proteins containing intrinsically disordered regions with an amino acid composition resembling those of yeast prion domains, like TDP-43 or FUS, are being found to aggregate in different neurodegenerative disorders. The structure of the intracellular inclusions formed by these proteins is still unclear and whether these deposits have an amyloid nature or not is a matter of debate. Recently, the aggregation of TDP-43 has been modelled in bacteria, showing that TDP-43 inclusion bodies (IBs) are amorphous but intrinsically neurotoxic. This observation raises the question of whether it is indeed the lack of an ordered structure in these human prion-like protein aggregates the underlying cause of their toxicity in different pathological states. Results Here we characterize the IBs formed by the human prion-like RNA-processing protein HNRPDL. HNRPDL is linked to the development of limb-girdle muscular dystrophy 1G and shares domain architecture with TDP-43. We show that HNRPDL IBs display characteristic amyloid hallmarks, since these aggregates bind to amyloid dyes in vitro and inside the cell, they are enriched in intermolecular β-sheet conformation and contain inner amyloid-like fibrillar structure. In addition, despite their ordered structure, HNRPDL IBs are highly neurotoxic. Conclusions Our results suggest that at least some of the disorders caused by the aggregation of human prion-like proteins would rely on the formation of classical amyloid assemblies rather than being caused by amorphous aggregates. They also illustrate the power of microbial cell factories to model amyloid aggregation. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0284-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Susanna Navarro
- Institut de Biotecnologia i Biomedicina, Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.
| | - Patrizia Marinelli
- Institut de Biotecnologia i Biomedicina, Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.
| | - Marta Diaz-Caballero
- Institut de Biotecnologia i Biomedicina, Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina, Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.
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Chaperone-assisted protein aggregate reactivation: Different solutions for the same problem. Arch Biochem Biophys 2015; 580:121-34. [PMID: 26159839 DOI: 10.1016/j.abb.2015.07.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 07/02/2015] [Accepted: 07/04/2015] [Indexed: 12/15/2022]
Abstract
The oligomeric AAA+ chaperones Hsp104 in yeast and ClpB in bacteria are responsible for the reactivation of aggregated proteins, an activity essential for cell survival during severe stress. The protein disaggregase activity of these members of the Hsp100 family is linked to the activity of chaperones from the Hsp70 and Hsp40 families. The precise mechanism by which these proteins untangle protein aggregates remains unclear. Strikingly, Hsp100 proteins are not present in metazoans. This does not mean that animal cells do not have a disaggregase activity, but that this activity is performed by the Hsp70 system and a representative of the Hsp110 family instead of a Hsp100 protein. This review describes the actual view of Hsp100-mediated aggregate reactivation, including the ATP-induced conformational changes associated with their disaggregase activity, the dynamics of the oligomeric assembly that is regulated by its ATPase cycle and the DnaK system, and the tight allosteric coupling between the ATPase domains within the hexameric ring complexes. The lack of homologs of these disaggregases in metazoans has suggested that they might be used as potential targets to develop antimicrobials. The current knowledge of the human disaggregase machinery and the role of Hsp110 are also discussed.
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Liu X, Yang Y, Zhang W, Sun Y, Peng F, Jeffrey L, Harvey L, McNeil B, Bai Z. Expression of recombinant protein using Corynebacterium Glutamicum: progress, challenges and applications. Crit Rev Biotechnol 2015; 36:652-64. [PMID: 25714007 DOI: 10.3109/07388551.2015.1004519] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Corynebacterium glutamicum (C. glutamicum) is a highly promising alternative prokaryotic host for recombinant protein expression, as it possesses several significant advantages over Escherichia coli (E. coli), the currently leading bacterial protein expression system. During the past decades, several experimental techniques and vector components for genetic manipulation of C. glutamicum have been developed and validated, including strong promoters for tightly regulating target gene expression, various types of plasmid vectors, protein secretion systems and methods of genetically modifying the host strain genome to improve protein production potential. This review critically discusses current progress in establishing C. glutamicum as a host for recombinant protein expression, and examines, in depth, some successful case studies of actual application of this expression system. The established "expression tool box" for developing novel constructs based on C. glutamicum as a host are also evaluated. Finally, the existing issues and solutions in process development with C. glutamicum as a host are specifically addressed.
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Affiliation(s)
- Xiuxia Liu
- a National Engineering Laboratory of Cereal Fermentation Technology , School of Biotechnology, JiangNan University , Wuxi , China and
| | - Yankun Yang
- a National Engineering Laboratory of Cereal Fermentation Technology , School of Biotechnology, JiangNan University , Wuxi , China and
| | - Wei Zhang
- a National Engineering Laboratory of Cereal Fermentation Technology , School of Biotechnology, JiangNan University , Wuxi , China and
| | - Yang Sun
- a National Engineering Laboratory of Cereal Fermentation Technology , School of Biotechnology, JiangNan University , Wuxi , China and
| | - Feng Peng
- a National Engineering Laboratory of Cereal Fermentation Technology , School of Biotechnology, JiangNan University , Wuxi , China and
| | - Laura Jeffrey
- b Institute of Pharmacy & Biomedical Sciences, Strathclyde University , Glasgow , UK
| | - Linda Harvey
- b Institute of Pharmacy & Biomedical Sciences, Strathclyde University , Glasgow , UK
| | - Brian McNeil
- b Institute of Pharmacy & Biomedical Sciences, Strathclyde University , Glasgow , UK
| | - Zhonghu Bai
- a National Engineering Laboratory of Cereal Fermentation Technology , School of Biotechnology, JiangNan University , Wuxi , China and
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Villar-Pique A, Navarro S, Ventura S. Characterization of amyloid-like properties in bacterial intracellular aggregates. Methods Mol Biol 2015; 1258:99-122. [PMID: 25447861 DOI: 10.1007/978-1-4939-2205-5_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Protein aggregation into amyloid conformations is associated with more than 50 different human disorders. Recent studies demonstrate that the expression in bacteria of amyloid proteins results in the formation of intracellular aggregates structurally related to those underlying human diseases. The ease with which prokaryotic organisms can be genetically and biochemically manipulated makes them useful systems for studying how and why protein aggregates inside the cell, providing a tractable environment to rationally model in vivo amyloid formation. In this chapter we present an overview of the methods used to characterize the kinetic, structural, and functional properties of amyloid-like bacterial intracellular aggregates and how they can be employed to screen for lead compounds that might modulate amyloid deposition.
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Affiliation(s)
- Anna Villar-Pique
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Cerdanyola del Vallés, 08193, Barcelona, Spain
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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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Choi SL, Lee SJ, Yeom SJ, Kim HJ, Rhee YH, Jung HC, Lee SG. Controlled localization of functionally active proteins to inclusion bodies using leucine zippers. PLoS One 2014; 9:e97093. [PMID: 24897378 PMCID: PMC4045587 DOI: 10.1371/journal.pone.0097093] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Accepted: 04/14/2014] [Indexed: 11/23/2022] Open
Abstract
Inclusion bodies (IBs) are typically non-functional particles of aggregated proteins. However, some proteins in fusion with amyloid-like peptides, viral coat proteins, and cellulose binding domains (CBDs) generate IB particles retaining the original functions in cells. Here, we attempted to generate CBD IBs displaying functional leucine zipper proteins (LZs) as bait for localizing cytosolic proteins in E. coli. When a red fluorescent protein was tested as a target protein, microscopic observations showed that the IBs red-fluoresced strongly. When different LZ pairs with KDs of 8–1,000 µM were tested as the bait and prey, the localization of the red fluorescence appeared to change following the affinities between the LZs, as observed by fluorescence imaging and flow cytometry. This result proposed that LZ-tagged CBD IBs can be applied as an in vivo matrix to entrap cytosolic proteins in E. coli while maintaining their original activities. In addition, easy detection of localization to IBs provides a unique platform for the engineering and analyses of protein-protein interactions in E. coli.
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Affiliation(s)
- Su-Lim Choi
- Biochemicals and Synthetic Biology Research Center, KRIBB, Yuseong-gu, Daejeon, Korea
- Department of Bioscience and Biotechnology, Chungnam National University, Yuseong-gu, Daejeon, Korea
| | - Sang Jun Lee
- Infection and Immunity Biology Research Center, KRIBB, Yuseong-gu, Daejeon, Korea
- Korea University of Science and Technology, Yuseong-gu, Daejeon, Korea
| | - Soo-Jin Yeom
- Biochemicals and Synthetic Biology Research Center, KRIBB, Yuseong-gu, Daejeon, Korea
| | - Hyun Ju Kim
- Infection and Immunity Biology Research Center, KRIBB, Yuseong-gu, Daejeon, Korea
- Korea University of Science and Technology, Yuseong-gu, Daejeon, Korea
| | - Young Ha Rhee
- Department of Bioscience and Biotechnology, Chungnam National University, Yuseong-gu, Daejeon, Korea
| | - Heung-Chae Jung
- Biochemicals and Synthetic Biology Research Center, KRIBB, Yuseong-gu, Daejeon, Korea
| | - Seung-Goo Lee
- Biochemicals and Synthetic Biology Research Center, KRIBB, Yuseong-gu, Daejeon, Korea
- Korea University of Science and Technology, Yuseong-gu, Daejeon, Korea
- * E-mail:
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Prediction of soluble heterologous protein expression levels inEscherichia colifrom sequence-based features and its potential in biopharmaceutical process development. ACTA ACUST UNITED AC 2014. [DOI: 10.4155/pbp.14.23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Navarro S, Villar-Piqué A, Ventura S. Selection against toxic aggregation-prone protein sequences in bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:866-74. [DOI: 10.1016/j.bbamcr.2014.01.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 01/16/2014] [Accepted: 01/21/2014] [Indexed: 01/23/2023]
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Ramón A, Señorale-Pose M, Marín M. Inclusion bodies: not that bad…. Front Microbiol 2014; 5:56. [PMID: 24592259 PMCID: PMC3924032 DOI: 10.3389/fmicb.2014.00056] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 01/28/2014] [Indexed: 12/03/2022] Open
Abstract
The formation of inclusion bodies (IBs) constitute a frequent event during the production of heterologous proteins in bacterial hosts. Although the mechanisms leading to their formation are not completely understood, empirical data have been exploited trying to predict the aggregation propensity of specific proteins while a great number of strategies have been developed to avoid the generation of IBs. However, in many cases, the formation of such aggregates can be considered an advantage for basic research as for protein production. In this review, we focus on this positive side of IBs formation in bacteria. We present a compilation on recent advances on the understanding of IBs formation and their utilization as a model to understand protein aggregation and to explore strategies to control this process. We include recent information about their composition and structure, their use as an attractive approach to produce low cost proteins and other promising applications in Biomedicine.
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Affiliation(s)
- Ana Ramón
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República Montevideo, Uruguay
| | - Mario Señorale-Pose
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República Montevideo, Uruguay
| | - Mónica Marín
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República Montevideo, Uruguay
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40
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Baig F, Fernando LP, Salazar MA, Powell RR, Bruce TF, Harcum SW. Dynamic transcriptional response of Escherichia coli to inclusion body formation. Biotechnol Bioeng 2014; 111:980-99. [PMID: 24338599 DOI: 10.1002/bit.25169] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 11/09/2013] [Accepted: 12/02/2013] [Indexed: 01/27/2023]
Abstract
Escherichia coli is used intensively for recombinant protein production, but one key challenge with recombinant E. coli is the tendency of recombinant proteins to misfold and aggregate into insoluble inclusion bodies (IBs). IBs contain high concentrations of inactive recombinant protein that require recovery steps to salvage a functional recombinant protein. Currently, no universally effective method exists to prevent IB formation in recombinant E. coli. In this study, DNA microarrays were used to compare the E. coli gene expression response dynamics to soluble and insoluble recombinant protein production. As expected and previously reported, the classical heat-shock genes had increased expression due to IB formation, including protein folding chaperones and proteases. Gene expression levels for protein synthesis-related and energy-synthesis pathways were also increased. Many transmembrane transporter and corresponding catabolic pathways genes had decreased expression for substrates not present in the culture medium. Additionally, putative genes represented over one-third of the genes identified to have significant expression changes due to IB formation, indicating many important cellular responses to IB formation still need to be characterized. Interestingly, cells grown in 3% ethanol had significantly reduced gene expression responses due to IB formation. Taken together, these results indicate that IB formation is complex, stimulates the heat-shock response, increases protein and energy synthesis needs, and streamlines transport and catabolic processes, while ethanol diminished all of these responses.
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Affiliation(s)
- Faraz Baig
- Department of Bioengineering, Clemson University, 301 Rhodes Research Center, Clemson, South Carolina, 29634
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41
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Gatti-Lafranconi P, Dijkman WP, Devenish SRA, Hollfelder F. A single mutation in the core domain of the lac repressor reduces leakiness. Microb Cell Fact 2013; 12:67. [PMID: 23834731 PMCID: PMC3722110 DOI: 10.1186/1475-2859-12-67] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 06/29/2013] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The lac operon provides cells with the ability to switch from glucose to lactose metabolism precisely when necessary. This metabolic switch is mediated by the lac repressor (LacI), which in the absence of lactose binds to the operator DNA sequence to inhibit transcription. Allosteric rearrangements triggered by binding of the lactose isomer allolactose to the core domain of the repressor impede DNA binding and lift repression. In Nature, the ability to detect and respond to environmental conditions comes at the cost of the encoded enzymes being constitutively expressed at low levels. The readily-switched regulation provided by LacI has resulted in its widespread use for protein overexpression, and its applications in molecular biology represent early examples of synthetic biology. However, the leakiness of LacI that is essential for the natural function of the lac operon leads to an increased energetic burden, and potentially toxicity, in heterologous protein production. RESULTS Analysis of the features that confer promiscuity to the inducer-binding site of LacI identified tryptophan 220 as a target for saturation mutagenesis. We found that phenylalanine (similarly to tryptophan) affords a functional repressor that is still responsive to IPTG. Characterisation of the W220F mutant, LacIWF, by measuring the time dependence of GFP production at different IPTG concentrations and at various incubation temperatures showed a 10-fold reduction in leakiness and no decrease in GFP production. Cells harbouring a cytotoxic protein under regulatory control of LacIWF showed no decrease in viability in the early phases of cell growth. Changes in responsiveness to IPTG observed in vivo are supported by the thermal shift assay behaviour of purified LacIWF with IPTG and operator DNA. CONCLUSIONS In LacI, long-range communications are responsible for the transmission of the signal from the inducer binding site to the DNA binding domain and our results are consistent with the involvement of position 220 in modulating these. The mutation of this single tryptophan residue to phenylalanine generated an enhanced repressor with a 10-fold decrease in leakiness. By minimising the energetic burden and cytotoxicity caused by leakiness, LacIWF constitutes a useful switch for protein overproduction and synthetic biology.
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Affiliation(s)
| | - Willem P Dijkman
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Sean RA Devenish
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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Plasmodium falciparum heat shock protein 110 stabilizes the asparagine repeat-rich parasite proteome during malarial fevers. Nat Commun 2013; 3:1310. [PMID: 23250440 PMCID: PMC3639100 DOI: 10.1038/ncomms2306] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 11/15/2012] [Indexed: 11/08/2022] Open
Abstract
One-fourth of Plasmodium falciparum proteins have asparagine repeats that increase the propensity for aggregation, especially at elevated temperatures that occur routinely in malaria-infected patients. Here we report that a Plasmodium Asn repeat-containing protein (PFI1155w) formed aggregates in mammalian cells at febrile temperatures, as did a yeast Asn/Gln-rich protein (Sup35). Co-expression of the cytoplasmic P. falciparum heat shock protein 110 (PfHsp110c) prevented aggregation. Human or yeast orthologs were much less effective. All-Asn and all-Gln versions of Sup35 were protected from aggregation by PfHsp110c, suggesting that this chaperone is not limited to handling runs of asparagine. PfHsp110c gene-knockout parasites were not viable and conditional knockdown parasites died slowly in the absence of protein-stabilizing ligand. When exposed to brief heat shock, these knockdowns were unable to prevent aggregation of PFI1155w or Sup35 and died rapidly. We conclude that PfHsp110c protects the parasite from harmful effects of its asparagine repeat-rich proteome during febrile episodes.
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Singh GP, Dash D. Electrostatic mis-interactions cause overexpression toxicity of proteins in E. coli. PLoS One 2013; 8:e64893. [PMID: 23734225 PMCID: PMC3667126 DOI: 10.1371/journal.pone.0064893] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Accepted: 04/19/2013] [Indexed: 01/28/2023] Open
Abstract
A majority of E. coli proteins when overexpressed inhibit its growth, but the reasons behind overexpression toxicity of proteins remain unknown. Understanding the mechanism of overexpression toxicity is important from evolutionary, biotechnological and possibly clinical perspectives. Here we study sequence and functional features of cytosolic proteins of E. coli associated with overexpression toxicity to understand its mechanism. We find that number of positively charged residues is significantly higher in proteins showing overexpression toxicity. Very long proteins also show high overexpression toxicity. Among the functional classes, transcription factors and regulatory proteins are enriched in toxic proteins, while catalytic proteins are depleted. Overexpression toxicity could be predicted with reasonable accuracy using these few properties. The importance of charged residues in overexpression toxicity indicates that nonspecific electrostatic interactions resulting from protein overexpression cause toxicity of these proteins and suggests ways to improve the expression level of native and foreign proteins in E. coli for basic research and biotechnology. These results might also be applicable to other bacterial species.
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Affiliation(s)
- Gajinder Pal Singh
- G. N. Ramachandran Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology (Council of Scientific and Industrial Research), Delhi, India.
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Patterson EI, Swarbrick CMD, Roman N, Forwood JK, Raidal SR. Differential expression of two isolates of beak and feather disease virus capsid protein in Escherichia coli. J Virol Methods 2013; 189:118-24. [PMID: 23403150 DOI: 10.1016/j.jviromet.2013.01.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 01/07/2013] [Accepted: 01/28/2013] [Indexed: 10/27/2022]
Abstract
Expression of recombinant beak and feather disease virus (BFDV) capsid-associated protein (Cap) has relied on inefficient techniques that typically produce low yields or use specialized expression systems, which greatly increase the cost and expertise required for mass production. An Escherichia coli system was used to express recombinant BFDV Cap derived from two isolates of BFDV, from a Long-billed Corella (Cacatua tenuirostris) and an Orange-bellied parrot (OBP; Neophema chrysogaster). Purification by affinity and size exclusion chromatography was optimized through an iterative process involving screening and modification of buffer constituents and pH. A buffer containing glycerol, β-mercaptoethanol, Triton X-100, and a high concentration of NaCl at pH 8 was used to increase solubility of the protein. The final concentration of the corella-isolated BFDV protein was fifteen- to twenty-fold greater than that produced in previous publications using E. coli expression systems. Immunoassays were used to confirm the specific antigenicity of recombinant Cap, verifying its validity for use in continued experimentation as a potential vaccine, a reagent in diagnostic assays, and as a concentrated sample for biological discoveries.
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Affiliation(s)
- Edward I Patterson
- Charles Sturt University, School of Animal and Veterinary Sciences, Boorooma St., Wagga Wagga, New South Wales 2678, Australia
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Brígido C, Oliveira S. Most acid-tolerant chickpea mesorhizobia show induction of major chaperone genes upon acid shock. MICROBIAL ECOLOGY 2013; 65:145-153. [PMID: 22890730 DOI: 10.1007/s00248-012-0098-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 07/16/2012] [Indexed: 06/01/2023]
Abstract
Our goals were to evaluate the tolerance of mesorhizobia to acid and alkaline conditions as well as to investigate whether acid tolerance is related to the species or the origin site of the isolates. In addition, to investigate the molecular basis of acid tolerance, the expression of chaperone genes groEL and dnaKJ was analyzed using acid-tolerant and sensitive mesorhizobia. Tolerance to pH 5 and 9 was evaluated in liquid medium for 98 Portuguese chickpea mesorhizobia belonging to four species clusters. All isolates showed high sensitivity to pH 9. In contrast, mesorhizobia revealed high diversity in terms of tolerance to acid stress: 35 % of the isolates were acid sensitive and 45 % were highly tolerant to pH 5 or moderately acidophilic. An association between mesorhizobia tolerance to acid conditions and the origin soil pH was found. Furthermore, significant differences between species clusters regarding tolerance to acidity were obtained. Ten isolates were used to investigate the expression levels of the chaperone genes by northern hybridization. Interestingly, most acid-tolerant isolates displayed induction of the dnaK and groESL genes upon acid shock while the sensitive ones showed repression. This study suggests that acid tolerance in mesorhizobia is related to the pH of the origin soil and to the species cluster of the isolates. Additionally, the transcriptional analysis suggests a relationship between induction of major chaperone genes and higher tolerance to acid pH in mesorhizobia. This is the first report on transcriptional analysis of the major chaperones genes in mesorhizobia under acidity, contributing to a better understanding of the molecular mechanisms of rhizobia acidity tolerance.
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Affiliation(s)
- Clarisse Brígido
- Laboratório de Microbiologia do Solo, ICAAM (Instituto de Ciências Agrárias e Ambientais Mediterrânicas), Universidade de Évora, Apartado 94, 7002-554, Évora, Portugal
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Zheng X, Tian J, Wu N, Fan Y. Probing the molecular determinant of the lipase-specific foldase Lif26 for the interaction with its cognate Lip26. Int J Biol Macromol 2012; 53:54-61. [PMID: 23153763 DOI: 10.1016/j.ijbiomac.2012.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 11/06/2012] [Indexed: 11/27/2022]
Abstract
As a steric chaperone, the lipase-specific foldase Lif26 from Acinetobacter sp. XMZ-26 is required for correct folding of the lipase Lip26 in in vivo co-expression and in vitro refolding systems. Lif26 interacts with Lip26 as determined by yeast two hybrid assays in vivo and GST pull-down experiments in vitro. To study the molecular determinants of the interaction between Lif26 and Lip26, a homology model-based screening of residues, molecular dynamics (MD) simulation-based calculation of interaction energies, and site-directed mutagenesis to alter individual screened residues were applied. One conserved amino acid in the C-terminal mini-domain of Lif26, Arg332, was involved in the interaction with Lip26. Arg332 could not be replaced by any other residue, based on saturated site-directed mutagenesis, and it formed a conserved and stable salt bridge with Glu112 of Lip26, which may contribute to binding specificity. The residues surrounding Arg332, such as Trp288 in α9, likely stabilized Arg332 in the proper conformation for the interaction with Lip26.
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Affiliation(s)
- Xiaomei Zheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.
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Lapidus LJ. Understanding protein aggregation from the view of monomer dynamics. MOLECULAR BIOSYSTEMS 2012; 9:29-35. [PMID: 23104145 DOI: 10.1039/c2mb25334h] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Much work in recent years has been devoted to understanding the complex process of protein aggregation. This review looks at the earliest stages of aggregation, long before the formation of fibrils that are the hallmark of many aggregation-based diseases, and proposes that the first steps are controlled by the reconfiguration dynamics of the monomer. When reconfiguration is much faster or much slower than bimolecular diffusion, then aggregation is slow, but when they are similar, aggregation is fast. The experimental evidence for this model is reviewed and the prospects for small molecule aggregation inhibitors to prevent disease are discussed.
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Affiliation(s)
- Lisa J Lapidus
- Department of Physics and Astronomy and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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48
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Rouvière PE, Li J, Brill DJ, Reiss LD, Schwartz TR, Butterick LA, Fahnestock SR, Gruber T. Bionanotechnology application of polypeptides in a hair color product: Self-assembly enables expression, processing, and functionality. Biotechnol J 2012; 8:247-56. [DOI: 10.1002/biot.201200008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 06/05/2012] [Accepted: 07/05/2012] [Indexed: 11/09/2022]
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49
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Villar-Pique A, de Groot NS, Sabaté R, Acebrón SP, Celaya G, Fernàndez-Busquets X, Muga A, Ventura S. The Effect of Amyloidogenic Peptides on Bacterial Aging Correlates with Their Intrinsic Aggregation Propensity. J Mol Biol 2012; 421:270-81. [DOI: 10.1016/j.jmb.2011.12.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 12/06/2011] [Accepted: 12/07/2011] [Indexed: 01/03/2023]
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50
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Espargaró A, Villar-Piqué A, Sabaté R, Ventura S. Yeast prions form infectious amyloid inclusion bodies in bacteria. Microb Cell Fact 2012; 11:89. [PMID: 22731490 PMCID: PMC3520751 DOI: 10.1186/1475-2859-11-89] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Accepted: 05/27/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Prions were first identified as infectious proteins associated with fatal brain diseases in mammals. However, fungal prions behave as epigenetic regulators that can alter a range of cellular processes. These proteins propagate as self-perpetuating amyloid aggregates being an example of structural inheritance. The best-characterized examples are the Sup35 and Ure2 yeast proteins, corresponding to [PSI+] and [URE3] phenotypes, respectively. RESULTS Here we show that both the prion domain of Sup35 (Sup35-NM) and the Ure2 protein (Ure2p) form inclusion bodies (IBs) displaying amyloid-like properties when expressed in bacteria. These intracellular aggregates template the conformational change and promote the aggregation of homologous, but not heterologous, soluble prionogenic molecules. Moreover, in the case of Sup35-NM, purified IBs are able to induce different [PSI+] phenotypes in yeast, indicating that at least a fraction of the protein embedded in these deposits adopts an infectious prion fold. CONCLUSIONS An important feature of prion inheritance is the existence of strains, which are phenotypic variants encoded by different conformations of the same polypeptide. We show here that the proportion of infected yeast cells displaying strong and weak [PSI+] phenotypes depends on the conditions under which the prionogenic aggregates are formed in E. coli, suggesting that bacterial systems might become useful tools to generate prion strain diversity.
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Affiliation(s)
- Alba Espargaró
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
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