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Springer E, Heimsch KC, Rahlfs S, Becker K, Przyborski JM. Real-time measurements of ATP dynamics via ATeams in Plasmodium falciparum reveal drug-class-specific response patterns. Antimicrob Agents Chemother 2024; 68:e0169023. [PMID: 38501806 PMCID: PMC11064498 DOI: 10.1128/aac.01690-23] [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: 12/20/2023] [Accepted: 02/26/2024] [Indexed: 03/20/2024] Open
Abstract
Malaria tropica, caused by the parasite Plasmodium falciparum (P. falciparum), remains one of the greatest public health burdens for humankind. Due to its pivotal role in parasite survival, the energy metabolism of P. falciparum is an interesting target for drug design. To this end, analysis of the central metabolite adenosine triphosphate (ATP) is of great interest. So far, only cell-disruptive or intensiometric ATP assays have been available in this system, with various drawbacks for mechanistic interpretation and partly inconsistent results. To address this, we have established fluorescent probes, based on Förster resonance energy transfer (FRET) and known as ATeam, for use in blood-stage parasites. ATeams are capable of measuring MgATP2- levels in a ratiometric manner, thereby facilitating in cellulo measurements of ATP dynamics in real-time using fluorescence microscopy and plate reader detection and overcoming many of the obstacles of established ATP analysis methods. Additionally, we established a superfolder variant of the ratiometric pH sensor pHluorin (sfpHluorin) in P. falciparum to monitor pH homeostasis and control for pH fluctuations, which may affect ATeam measurements. We characterized recombinant ATeam and sfpHluorin protein in vitro and stably integrated the sensors into the genome of the P. falciparum NF54attB cell line. Using these new tools, we found distinct sensor response patterns caused by several different drug classes. Arylamino alcohols increased and redox cyclers decreased ATP; doxycycline caused first-cycle cytosol alkalization; and 4-aminoquinolines caused aberrant proteolysis. Our results open up a completely new perspective on drugs' mode of action, with possible implications for target identification and drug development.
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Affiliation(s)
- Eric Springer
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, Giessen, Germany
| | - Kim C. Heimsch
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, Giessen, Germany
| | - Stefan Rahlfs
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, Giessen, Germany
| | - Katja Becker
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, Giessen, Germany
| | - Jude M. Przyborski
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, Giessen, Germany
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2
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King MR, Ruff KM, Lin AZ, Pant A, Farag M, Lalmansingh JM, Wu T, Fossat MJ, Ouyang W, Lew MD, Lundberg E, Vahey MD, Pappu RV. Macromolecular condensation organizes nucleolar sub-phases to set up a pH gradient. Cell 2024; 187:1889-1906.e24. [PMID: 38503281 DOI: 10.1016/j.cell.2024.02.029] [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: 07/18/2023] [Revised: 01/02/2024] [Accepted: 02/22/2024] [Indexed: 03/21/2024]
Abstract
Nucleoli are multicomponent condensates defined by coexisting sub-phases. We identified distinct intrinsically disordered regions (IDRs), including acidic (D/E) tracts and K-blocks interspersed by E-rich regions, as defining features of nucleolar proteins. We show that the localization preferences of nucleolar proteins are determined by their IDRs and the types of RNA or DNA binding domains they encompass. In vitro reconstitutions and studies in cells showed how condensation, which combines binding and complex coacervation of nucleolar components, contributes to nucleolar organization. D/E tracts of nucleolar proteins contribute to lowering the pH of co-condensates formed with nucleolar RNAs in vitro. In cells, this sets up a pH gradient between nucleoli and the nucleoplasm. By contrast, juxta-nucleolar bodies, which have different macromolecular compositions, featuring protein IDRs with very different charge profiles, have pH values that are equivalent to or higher than the nucleoplasm. Our findings show that distinct compositional specificities generate distinct physicochemical properties for condensates.
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Affiliation(s)
- Matthew R King
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Kiersten M Ruff
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Andrew Z Lin
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Avnika Pant
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Mina Farag
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Jared M Lalmansingh
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Tingting Wu
- Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Department of Electrical and Systems Engineering, James F. McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Martin J Fossat
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Wei Ouyang
- Department of Bioengineering, Schools of Engineering and Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA; Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Matthew D Lew
- Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Department of Electrical and Systems Engineering, James F. McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Emma Lundberg
- Department of Bioengineering, Schools of Engineering and Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA; Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Michael D Vahey
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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3
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Cutler HB, Madsen S, Masson SWC, Cooke KC, Potter M, Burchfield JG, Stöckli J, Nelson ME, Cooney GJ, James DE. Dual Tracer Test to Measure Tissue-Specific Insulin Action in Individual Mice Identifies In Vivo Insulin Resistance Without Fasting Hyperinsulinemia. Diabetes 2024; 73:359-373. [PMID: 37699358 PMCID: PMC10882155 DOI: 10.2337/db23-0035] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023]
Abstract
The ability of metabolically active tissues to increase glucose uptake in response to insulin is critical to whole-body glucose homeostasis. This report describes the Dual Tracer Test, a robust method involving sequential retro-orbital injection of [14C]2-deoxyglucose ([14C]2DG) alone, followed 40 min later by injection of [3H]2DG with a maximal dose of insulin to quantify both basal and insulin-stimulated 2DG uptake in the same mouse. The collection of both basal and insulin-stimulated measures from a single animal is imperative for generating high-quality data since differences in insulin action may be misinterpreted mechanistically if basal glucose uptake is not accounted for. The approach was validated in a classic diet-induced model of insulin resistance and a novel transgenic mouse with reduced GLUT4 expression that, despite ubiquitous peripheral insulin resistance, did not exhibit fasting hyperinsulinemia. This suggests that reduced insulin-stimulated glucose disposal is not a primary contributor to chronic hyperinsulinemia. The Dual Tracer Test offers a technically simple assay that enables the study of insulin action in many tissues simultaneously. By administering two tracers and accounting for both basal and insulin-stimulated glucose transport, this assay halves the required sample size for studies in inbred mice and demonstrates increased statistical power to detect insulin resistance, relative to other established approaches, using a single tracer. The Dual Tracer Test is a valuable addition to the metabolic phenotyping toolbox. ARTICLE HIGHLIGHTS
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Affiliation(s)
- Harry B Cutler
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Søren Madsen
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Stewart W C Masson
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Kristen C Cooke
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Meg Potter
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - James G Burchfield
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Jacqueline Stöckli
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Marin E Nelson
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Gregory J Cooney
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
- Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales, Australia
| | - David E James
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
- Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales, Australia
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Maull V, Pla Mauri J, Conde Pueyo N, Solé R. A synthetic microbial Daisyworld: planetary regulation in the test tube. J R Soc Interface 2024; 21:20230585. [PMID: 38321922 PMCID: PMC10847846 DOI: 10.1098/rsif.2023.0585] [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: 10/07/2023] [Accepted: 01/12/2024] [Indexed: 02/08/2024] Open
Abstract
The idea that the Earth system self-regulates in a habitable state was proposed in the 1970s by James Lovelock, who conjectured that life plays a self-regulatory role on a planetary-level scale. A formal approach to such hypothesis was presented afterwards under a toy model known as the Daisyworld. The model showed how such life-geosphere homeostasis was an emergent property of the system, where two species with different properties adjusted their populations to the changing external environment. So far, this ideal world exists only as a mathematical or computational construct, but it would be desirable to have a real, biological implementation of Lovelock's picture beyond our one biosphere. Inspired by the exploration of synthetic ecosystems using genetic engineering and recent cell factory designs, here we propose a possible implementation for a microbial Daisyworld. This includes: (i) an explicit proposal for an engineered design of a two-strain consortia, using pH as the external, abiotic control parameter and (ii) several theoretical and computational case studies including two, three and multiple species assemblies. The special alternative implementations and their implications in other synthetic biology scenarios, including ecosystem engineering, are outlined.
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Affiliation(s)
- Victor Maull
- Institució Catalana de Recerca i Estudis Avançats, Psg Lluis Companys, Barcelona, Spain
- Complex Systems Lab, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Jordi Pla Mauri
- Institució Catalana de Recerca i Estudis Avançats, Psg Lluis Companys, Barcelona, Spain
- Complex Systems Lab, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Nuria Conde Pueyo
- Complex Systems Lab, Universitat Pompeu Fabra, Barcelona 08003, Spain
- EMBL Barcelona, European Molecular Biology Laboratory (EMBL), Barcelona 08003, Spain
| | - Ricard Solé
- Institució Catalana de Recerca i Estudis Avançats, Psg Lluis Companys, Barcelona, Spain
- Complex Systems Lab, Universitat Pompeu Fabra, Barcelona 08003, Spain
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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5
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Li SA, Meng XY, Zhang YJ, Chen CL, Jiao YX, Zhu YQ, Liu PP, Sun W. Progress in pH-Sensitive sensors: essential tools for organelle pH detection, spotlighting mitochondrion and diverse applications. Front Pharmacol 2024; 14:1339518. [PMID: 38269286 PMCID: PMC10806205 DOI: 10.3389/fphar.2023.1339518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 12/20/2023] [Indexed: 01/26/2024] Open
Abstract
pH-sensitive fluorescent proteins have revolutionized the field of cellular imaging and physiology, offering insight into the dynamic pH changes that underlie fundamental cellular processes. This comprehensive review explores the diverse applications and recent advances in the use of pH-sensitive fluorescent proteins. These remarkable tools enable researchers to visualize and monitor pH variations within subcellular compartments, especially mitochondria, shedding light on organelle-specific pH regulation. They play pivotal roles in visualizing exocytosis and endocytosis events in synaptic transmission, monitoring cell death and apoptosis, and understanding drug effects and disease progression. Recent advancements have led to improved photostability, pH specificity, and subcellular targeting, enhancing their utility. Techniques for multiplexed imaging, three-dimensional visualization, and super-resolution microscopy are expanding the horizon of pH-sensitive protein applications. The future holds promise for their integration into optogenetics and drug discovery. With their ever-evolving capabilities, pH-sensitive fluorescent proteins remain indispensable tools for unravelling cellular dynamics and driving breakthroughs in biological research. This review serves as a comprehensive resource for researchers seeking to harness the potential of pH-sensitive fluorescent proteins.
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Affiliation(s)
- Shu-Ang Li
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiao-Yan Meng
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Ying-Jie Zhang
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Cai-Li Chen
- Department of Immunology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Yu-Xue Jiao
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yong-Qing Zhu
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Pei-Pei Liu
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wei Sun
- Department of Burn and Repair Reconstruction, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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6
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Torello Pianale L, Caputo F, Olsson L. Four ways of implementing robustness quantification in strain characterisation. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:195. [PMID: 38115067 PMCID: PMC10729505 DOI: 10.1186/s13068-023-02445-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]
Abstract
BACKGROUND In industrial bioprocesses, microorganisms are generally selected based on performance, whereas robustness, i.e., the ability of a system to maintain a stable performance, has been overlooked due to the challenges in its quantification and implementation into routine experimental procedures. This work presents four ways of implementing robustness quantification during strain characterisation. One Saccharomyces cerevisiae laboratory strain (CEN.PK113-7D) and two industrial strains (Ethanol Red and PE2) grown in seven different lignocellulosic hydrolysates were assessed for growth-related functions (specific growth rate, product yields, etc.) and eight intracellular parameters (using fluorescent biosensors). RESULTS Using flasks and high-throughput experimental setups, robustness was quantified in relation to: (i) stability of growth functions in response to the seven hydrolysates; (ii) stability of growth functions across different strains to establish the impact of perturbations on yeast metabolism; (iii) stability of intracellular parameters over time; (iv) stability of intracellular parameters within a cell population to indirectly quantify population heterogeneity. Ethanol Red was the best-performing strain under all tested conditions, achieving the highest growth function robustness. PE2 displayed the highest population heterogeneity. Moreover, the intracellular environment varied in response to non-woody or woody lignocellulosic hydrolysates, manifesting increased oxidative stress and unfolded protein response, respectively. CONCLUSIONS Robustness quantification is a powerful tool for strain characterisation as it offers novel information on physiological and biochemical parameters. Owing to the flexibility of the robustness quantification method, its implementation was successfully validated at single-cell as well as high-throughput levels, showcasing its versatility and potential for several applications.
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Affiliation(s)
- Luca Torello Pianale
- Industrial Biotechnology Division, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Fabio Caputo
- Industrial Biotechnology Division, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Lisbeth Olsson
- Industrial Biotechnology Division, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden.
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Ghosh S, Lai JY. Recent advances in the design of intracellular pH sensing nanoprobes based on organic and inorganic materials. ENVIRONMENTAL RESEARCH 2023; 237:117089. [PMID: 37683789 DOI: 10.1016/j.envres.2023.117089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/16/2023] [Accepted: 09/05/2023] [Indexed: 09/10/2023]
Abstract
In the biological system, the intracellular pH (pHi) plays an important role in regulating diverse physiological activities, including enzymatic action, ion transport, cell proliferation, metabolism, and programmed cell death. The monitoring of pH inside living cells is also crucial for studying cellular events such as phagocytosis, endocytosis, and receptor-ligand internalization. Furthermore, some organelles, viz., endosomes and lysosomes, have intracompartmental pH, which is critical for maintaining the stability of protein structure and function. The dysfunction and abnormal pH regulation can result in terminal diseases such as cancer, Alzheimer, and so forth. Therefore, the accuracy of intracellular pH measurement is always the top priority and demands cutting-edge research and analysis. Such techniques, such as Raman spectroscopy and fluorescence imaging, preferably use nanotechnology due to their remarkable advantages, such as a non-invasive approach and providing accuracy, repeatability, and reproducibility. In the past decades, there have been numerous attempts to design and construct non-invasive organic and inorganic materials-based nanoprobes for pHi sensing. For Raman-based techniques, metal nanostructures such as Au/Ag/Cu nanoparticles are utilized to enhance the signal intensity. As for the fluorescence-based studies, the organic-based small molecules, such as dyes, show higher sensitivity toward pH. However, they possess several drawbacks, including high photobleaching rate, and autofluorescence background signals. To this end, there are alternative nanomaterials proposed, including semiconductor quantum dots (QDs), carbon QDs, upconversion nanoparticles, and so forth. Moreover, the fluorescence technique allows for ratiometric measurement of pHi, which as a result, offers a reliable calibration curve. This timely review will critically examine the current progression in the existing nanoprobes. In addition, based on our knowledge and available research findings, we provide a brief future outlook that may advance the state-of-the-art methodologies for pHi sensing.
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Affiliation(s)
- Sandip Ghosh
- Department of Biomedical Engineering, Chang Gung University, Taoyuan, 33302, Taiwan
| | - Jui-Yang Lai
- Department of Biomedical Engineering, Chang Gung University, Taoyuan, 33302, Taiwan; Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou, Taoyuan, 33305, Taiwan; Department of Materials Engineering, Ming Chi University of Technology, New Taipei City, 24301, Taiwan; Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, 33303, Taiwan.
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Grimes B, Jacob W, Liberman AR, Kim N, Zhao X, Masison DC, Greene LE. The Properties and Domain Requirements for Phase Separation of the Sup35 Prion Protein In Vivo. Biomolecules 2023; 13:1370. [PMID: 37759770 PMCID: PMC10526957 DOI: 10.3390/biom13091370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
The Sup35 prion protein of budding yeast has been reported to undergo phase separation to form liquid droplets both at low pH in vitro and when energy depletion decreases the intracellular pH in vivo. It also has been shown using purified proteins that this phase separation is driven by the prion domain of Sup35 and does not re-quire its C-terminal domain. In contrast, we now find that a Sup35 fragment consisting of only the N-terminal prion domain and the M-domain does not phase separate in vivo; this phase separation of Sup35 requires the C-terminal domain, which binds Sup45 to form the translation termination complex. The phase-separated Sup35 not only colocalizes with Sup45 but also with Pub1, a stress granule marker protein. In addition, like stress granules, phase separation of Sup35 appears to require mRNA since cycloheximide treatment, which inhibits mRNA release from ribosomes, prevents phase separation of Sup35. Finally, unlike Sup35 in vitro, Sup35 condensates do not disassemble in vivo when the intracellular pH is increased. These results suggest that, in energy-depleted cells, Sup35 forms supramolecular assemblies that differ from the Sup35 liquid droplets that form in vitro.
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Affiliation(s)
- Bryan Grimes
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Walter Jacob
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amanda R. Liberman
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nathan Kim
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaohong Zhao
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C. Masison
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lois E. Greene
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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9
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Torello Pianale L, Olsson L. ScEnSor Kit for Saccharomyces cerevisiae Engineering and Biosensor-Driven Investigation of the Intracellular Environment. ACS Synth Biol 2023; 12:2493-2497. [PMID: 37552581 PMCID: PMC10443032 DOI: 10.1021/acssynbio.3c00124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Indexed: 08/10/2023]
Abstract
In this study, the three-step build-transform-assess toolbox for real-time monitoring of the yeast intracellular environment has been expanded and upgraded to the two-module ScEnSor (S. cerevisiae Engineering + Biosensor) Kit. The Biosensor Module includes eight fluorescent reporters for the intracellular environment; three of them (unfolded protein response, pyruvate metabolism, and ethanol consumption) were newly implemented to complement the original five. The Genome-Integration Module comprises a set of backbone plasmids for the assembly of 1-6 transcriptional units (each consisting of promoter, coding sequence, and terminator) for efficient marker-free single-locus genome integration (in HO and/or X2 loci). Altogether, the ScEnSor Kit enables rapid and easy construction of strains with new transcriptional units as well as high-throughput investigation of the yeast intracellular environment.
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Affiliation(s)
- Luca Torello Pianale
- Industrial
Biotechnology Division, Department of Life Sciences, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Lisbeth Olsson
- Industrial
Biotechnology Division, Department of Life Sciences, Chalmers University of Technology, 412 96, Gothenburg, Sweden
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10
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Garces Daza F, Haitz F, Born A, Boles E. An optimized reverse β-oxidation pathway to produce selected medium-chain fatty acids in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:71. [PMID: 37101299 PMCID: PMC10134560 DOI: 10.1186/s13068-023-02317-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/06/2023] [Indexed: 04/28/2023]
Abstract
BACKGROUND Medium-chain fatty acids are molecules with applications in different industries and with growing demand. However, the current methods for their extraction are not environmentally sustainable. The reverse β-oxidation pathway is an energy-efficient pathway that produces medium-chain fatty acids in microorganisms, and its use in Saccharomyces cerevisiae, a broadly used industrial microorganism, is desired. However, the application of this pathway in this organism has so far either led to low titers or to the predominant production of short-chain fatty acids. RESULTS We genetically engineered Saccharomyces cerevisiae to produce the medium-chain fatty acids hexanoic and octanoic acid using novel variants of the reverse β-oxidation pathway. We first knocked out glycerolphosphate dehydrogenase GPD2 in an alcohol dehydrogenases knock-out strain (△adh1-5) to increase the NADH availability for the pathway, which significantly increased the production of butyric acid (78 mg/L) and hexanoic acid (2 mg/L) when the pathway was expressed from a plasmid with BktB as thiolase. Then, we tested different enzymes for the subsequent pathway reactions: the 3-hydroxyacyl-CoA dehydrogenase PaaH1 increased hexanoic acid production to 33 mg/L, and the expression of enoyl-CoA hydratases Crt2 or Ech was critical to producing octanoic acid, reaching titers of 40 mg/L in both cases. In all cases, Ter from Treponema denticola was the preferred trans-enoyl-CoA reductase. The titers of hexanoic acid and octanoic acid were further increased to almost 75 mg/L and 60 mg/L, respectively, when the pathway expression cassette was integrated into the genome and the fermentation was performed in a highly buffered YPD medium. We also co-expressed a butyryl-CoA pathway variant to increase the butyryl-CoA pool and support the chain extension. However, this mainly increased the titers of butyric acid and only slightly increased that of hexanoic acid. Finally, we also tested the deletion of two potential medium-chain acyl-CoA depleting reactions catalyzed by the thioesterase Tes1 and the medium-chain fatty acyl CoA synthase Faa2. However, their deletion did not affect the production titers. CONCLUSIONS By engineering the NADH metabolism and testing different reverse β-oxidation pathway variants, we extended the product spectrum and obtained the highest titers of octanoic acid and hexanoic acid reported in S. cerevisiae. Product toxicity and enzyme specificity must be addressed for the industrial application of the pathway in this organism.
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Affiliation(s)
- Fernando Garces Daza
- Faculty of Biological Sciences, Institute of Molecular Bioscience, Goethe-Universität Frankfurt Am Main, Max-von-Laue-Str.9, 60438, Frankfurt am Main, Germany
| | - Fabian Haitz
- Faculty of Biological Sciences, Institute of Molecular Bioscience, Goethe-Universität Frankfurt Am Main, Max-von-Laue-Str.9, 60438, Frankfurt am Main, Germany
| | - Alice Born
- Faculty of Biological Sciences, Institute of Molecular Bioscience, Goethe-Universität Frankfurt Am Main, Max-von-Laue-Str.9, 60438, Frankfurt am Main, Germany
| | - Eckhard Boles
- Faculty of Biological Sciences, Institute of Molecular Bioscience, Goethe-Universität Frankfurt Am Main, Max-von-Laue-Str.9, 60438, Frankfurt am Main, Germany.
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11
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Deschamps A, Thines L, Colinet AS, Stribny J, Morsomme P. The yeast Gdt1 protein mediates the exchange of H + for Ca 2+ and Mn 2+ influencing the Golgi pH. J Biol Chem 2023; 299:104628. [PMID: 36963491 PMCID: PMC10148156 DOI: 10.1016/j.jbc.2023.104628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/24/2023] [Accepted: 03/16/2023] [Indexed: 03/26/2023] Open
Abstract
The GDT1 family is broadly spread and highly conserved among living organisms. GDT1 members have functions in key processes like glycosylation in humans and yeasts, and photosynthesis in plants. These functions are mediated by their ability to transport ions. While transport of Ca2+ or Mn2+ is well established for several GDT1 members, their transport mechanism is poorly understood. Here, we demonstrate that H+ ions are transported in exchange for Ca2+ and Mn2+ cations by the Golgi-localized yeast Gdt1 protein. We performed direct transport measurement across a biological membrane by expressing Gdt1p in Lactococcus lactis bacterial cells and by recording either the extracellular pH or the intracellular pH during the application of Ca2+, Mn2+ or H+ gradients. Besides, in vivo cytosolic and Golgi pH measurements were performed in Saccharomyces cerevisiae with genetically encoded pH probes targeted to those subcellular compartments. These data point out that the flow of H+ ions carried by Gdt1p could be reversed according to the physiological conditions. Together, our experiments unravel the influence of the relative concentration gradients for Gdt1p-mediated H+ transport and pave the way to decipher the regulatory mechanisms driving the activity of GDT1 orthologs in various biological contexts.
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Affiliation(s)
- Antoine Deschamps
- UCLouvain, Louvain Institute of Biomolecular Science and Technology (LIBST), Group of Molecular Physiology, Croix du Sud 4-5, B-1348 Louvain-la-Neuve, Belgium
| | - Louise Thines
- UCLouvain, Louvain Institute of Biomolecular Science and Technology (LIBST), Group of Molecular Physiology, Croix du Sud 4-5, B-1348 Louvain-la-Neuve, Belgium
| | - Anne-Sophie Colinet
- UCLouvain, Louvain Institute of Biomolecular Science and Technology (LIBST), Group of Molecular Physiology, Croix du Sud 4-5, B-1348 Louvain-la-Neuve, Belgium
| | - Jiri Stribny
- UCLouvain, Louvain Institute of Biomolecular Science and Technology (LIBST), Group of Molecular Physiology, Croix du Sud 4-5, B-1348 Louvain-la-Neuve, Belgium
| | - Pierre Morsomme
- UCLouvain, Louvain Institute of Biomolecular Science and Technology (LIBST), Group of Molecular Physiology, Croix du Sud 4-5, B-1348 Louvain-la-Neuve, Belgium.
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12
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Zhao J, Zhou P, Zhang L, Liu W, Liu W, Zhang Y, Li Y, Shi Z, Gao J. N-region of Cry1Ia: A novel fusion tag for Escherichia coli and Pichia pastoris. J Biotechnol 2023; 366:54-64. [PMID: 36822476 DOI: 10.1016/j.jbiotec.2023.02.006] [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: 11/29/2022] [Revised: 02/20/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023]
Abstract
Secretory signal peptides (SPs) can increase enhanced green fluorescent protein (eGFP) expression in cytosol. In this study, SPs Iasp (Cry1Ia), Vasp (Vip3A), and their local sequences were used as fusion tags to compare their effects on eGFP expression in Escherichia coli MC4100 and Pichia pastoris GS115. In E coli, the solubility was almost opposite between the proteins encoded by Vegfp and Iegfp. This may be because the overall hydrophobicity of the SPs differed. When the hydrophobic H-region and C-region were removed, the negative effects on eGFP solubility of the N-regions of both SPs (IaN and VN) were significantly reduced without compromise on the expression level. IaN promotes eGFP protein yield 7.1-fold more than Iasp, and using this peptide in tandem (Ia3N) further enhanced fluorescent fusion protein solubility with an efficacy similar to that of a polycationic tag. Furthermore, the GS-IaNeGFP strain produced the highest fluorescent signal intensity when these fusion proteins were expressed in P. pastoris, and the expression was higher than in other strains, including eGFP. In conclusion, we revealed the potential of the N-region of Iasp as a fusion tag in both prokaryotic and eukaryotic cells and further demonstrated the value of the N-regions of abundant SPs.
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Affiliation(s)
- Juanli Zhao
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Pu Zhou
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Luyao Zhang
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Wenhui Liu
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Wei Liu
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Yuqi Zhang
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Yi Li
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Zongyong Shi
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China.
| | - Jianhua Gao
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China.
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13
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Yukawa T, Bamba T, Matsuda M, Yoshida T, Inokuma K, Kim J, Won Lee J, Jin YS, Kondo A, Hasunuma T. Enhanced production of 3,4-dihydroxybutyrate from xylose by engineered yeast via xylonate re-assimilation under alkaline condition. Biotechnol Bioeng 2023; 120:511-523. [PMID: 36321324 DOI: 10.1002/bit.28278] [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: 06/14/2022] [Revised: 09/27/2022] [Accepted: 10/28/2022] [Indexed: 11/07/2022]
Abstract
To realize lignocellulose-based bioeconomy, efficient conversion of xylose into valuable chemicals by microbes is necessary. Xylose oxidative pathways that oxidize xylose into xylonate can be more advantageous than conventional xylose assimilation pathways because of fewer reaction steps without loss of carbon and ATP. Moreover, commodity chemicals like 3,4-dihydroxybutyrate and 3-hydroxybutyrolactone can be produced from the intermediates of xylose oxidative pathway. However, successful implementations of xylose oxidative pathway in yeast have been hindered because of the secretion and accumulation of xylonate which is a key intermediate of the pathway, leading to low yield of target product. Here, high-yield production of 3,4-dihydroxybutyrate from xylose by engineered yeast was achieved through genetic and environmental perturbations. Specifically, 3,4-dihydroxybutyrate biosynthetic pathway was established in yeast through deletion of ADH6 and overexpression of yneI. Also, inspired by the mismatch of pH between host strain and key enzyme of XylD, alkaline fermentations (pH ≥ 7.0) were performed to minimize xylonate accumulation. Under the alkaline conditions, xylonate was re-assimilated by engineered yeast and combined product yields of 3,4-dihydroxybutyrate and 3-hydroxybutyrolactone resulted in 0.791 mol/mol-xylose, which is highest compared with previous study. These results shed light on the utility of the xylose oxidative pathway in yeast.
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Affiliation(s)
- Takahiro Yukawa
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Takahiro Bamba
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Mami Matsuda
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan.,Engineering Biology Research Center, Kobe University, Kobe, Japan
| | - Takanobu Yoshida
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Kentaro Inokuma
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Jungyeon Kim
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jae Won Lee
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan.,Engineering Biology Research Center, Kobe University, Kobe, Japan.,RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan.,Engineering Biology Research Center, Kobe University, Kobe, Japan.,RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
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14
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Gelova SP, Chan K. Mutagenesis induced by protonation of single-stranded DNA is linked to glycolytic sugar metabolism. Mutat Res 2023; 826:111814. [PMID: 36634476 DOI: 10.1016/j.mrfmmm.2023.111814] [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: 10/09/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023]
Abstract
Mutagenesis can be thought of as random, in the sense that the occurrence of each mutational event cannot be predicted with precision in space or time. However, when sufficiently large numbers of mutations are analyzed, recurrent patterns of base changes called mutational signatures can be identified. To date, some 60 single base substitution or SBS signatures have been derived from analysis of cancer genomics data. We recently reported that the ubiquitous signature SBS5 matches the pattern of single nucleotide polymorphisms (SNPs) in humans and has analogs in many species. Using a temperature-sensitive single-stranded DNA (ssDNA) mutation reporter system, we also showed that a similar mutational pattern in yeast is dependent on error-prone translesion DNA synthesis (TLS) and glycolytic sugar metabolism. Here, we further investigated mechanisms that are responsible for this form of mutagenesis in yeast. We first confirmed that excess sugar metabolism leads to increased mutation rate, which was detectable by fluctuation assay. Since glycolysis is known to produce excess protons, we then investigated the effects of experimental manipulations on pH and mutagenesis. We hypothesized that yeast metabolizing 8% glucose would produce more excess protons than cells metabolizing 2% glucose. Consistent with this, cells metabolizing 8% glucose had lower intracellular and extracellular pH values. Similarly, deletion of vma3 (encoding a vacuolar H+-ATPase subunit) increased mutagenesis. We also found that treating cells with edelfosine (which renders membranes more permeable, including to protons) or culturing in low pH media increased mutagenesis. Analysis of the mutational pattern attributable to 20 µM edelfosine treatment revealed similarity to the SBS5-like TLS- and glycolysis-dependant mutational patterns previously observed in ssDNA. Altogether, our results agree with multiple biochemical studies showing that protonation of nitrogenous bases can alter base pairing so as to stabilize some mispairs, and shed new light on a common form of intrinsic mutagenesis.
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Affiliation(s)
- Suzana P Gelova
- University of Ottawa Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada; Agriculture and Agri-Food Canada, 2585 County Road 20, Harrow, Ontario N0R 1G0, Canada
| | - Kin Chan
- University of Ottawa Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada.
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15
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Žunar B, Ito T, Mosrin C, Sugahara Y, Bénédetti H, Guégan R, Vallée B. Confocal imaging of biomarkers at a single-cell resolution: quantifying 'living' in 3D-printable engineered living material based on Pluronic F-127 and yeast Saccharomyces cerevisiae. Biomater Res 2022; 26:85. [PMID: 36539854 PMCID: PMC9769040 DOI: 10.1186/s40824-022-00337-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Engineered living materials (ELMs) combine living cells with non-living scaffolds to obtain life-like characteristics, such as biosensing, growth, and self-repair. Some ELMs can be 3D-printed and are called bioinks, and their scaffolds are mostly hydrogel-based. One such scaffold is polymer Pluronic F127, a liquid at 4 °C but a biocompatible hydrogel at room temperature. In such thermally-reversible hydrogel, the microorganism-hydrogel interactions remain uncharacterized, making truly durable 3D-bioprinted ELMs elusive. METHODS We demonstrate the methodology to assess cell-scaffold interactions by characterizing intact alive yeast cells in cross-linked F127-based hydrogels, using genetically encoded ratiometric biosensors to measure intracellular ATP and cytosolic pH at a single-cell level through confocal imaging. RESULTS When embedded in hydrogel, cells were ATP-rich, in exponential or stationary phase, and assembled into microcolonies, which sometimes merged into larger superstructures. The hydrogels supported (micro)aerobic conditions and induced a nutrient gradient that limited microcolony size. External compounds could diffuse at least 2.7 mm into the hydrogels, although for optimal yeast growth bioprinted structures should be thinner than 0.6 mm. Moreover, the hydrogels could carry whole-cell copper biosensors, shielding them from contaminations and providing them with nutrients. CONCLUSIONS F127-based hydrogels are promising scaffolds for 3D-bioprinted ELMs, supporting a heterogeneous cell population primarily shaped by nutrient availability.
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Affiliation(s)
- Bojan Žunar
- grid.4444.00000 0001 2112 9282Centre de Biophysique Moléculaire (CBM), CNRS, UPR 4301, University of Orléans and INSERM, 45071 Orléans, Cedex 2 France ,grid.4808.40000 0001 0657 4636Department of Chemistry and Biochemistry, Laboratory for Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000, Zagreb, Croatia
| | - Taiga Ito
- grid.5290.e0000 0004 1936 9975Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Tokyo, 169-8555 Japan
| | - Christine Mosrin
- grid.4444.00000 0001 2112 9282Centre de Biophysique Moléculaire (CBM), CNRS, UPR 4301, University of Orléans and INSERM, 45071 Orléans, Cedex 2 France
| | - Yoshiyuki Sugahara
- grid.5290.e0000 0004 1936 9975Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Tokyo, 169-8555 Japan
| | - Hélène Bénédetti
- grid.4444.00000 0001 2112 9282Centre de Biophysique Moléculaire (CBM), CNRS, UPR 4301, University of Orléans and INSERM, 45071 Orléans, Cedex 2 France
| | - Régis Guégan
- grid.5290.e0000 0004 1936 9975Global Center for Advanced Science and Engineering, Faculty of Science and Engineering, Waseda University, Tokyo, 169-8555 Japan ,grid.112485.b0000 0001 0217 6921Institut des Sciences de la Terre d’Orléans (ISTO), UMR 7327, CNRS-Université d’Orléans, 1A Rue de la Férollerie, 45071 Orléans, Cedex 2 France
| | - Béatrice Vallée
- grid.4444.00000 0001 2112 9282Centre de Biophysique Moléculaire (CBM), CNRS, UPR 4301, University of Orléans and INSERM, 45071 Orléans, Cedex 2 France
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16
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Hirschi S, Ward TR, Meier WP, Müller DJ, Fotiadis D. Synthetic Biology: Bottom-Up Assembly of Molecular Systems. Chem Rev 2022; 122:16294-16328. [PMID: 36179355 DOI: 10.1021/acs.chemrev.2c00339] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bottom-up assembly of biological and chemical components opens exciting opportunities to engineer artificial vesicular systems for applications with previously unmet requirements. The modular combination of scaffolds and functional building blocks enables the engineering of complex systems with biomimetic or new-to-nature functionalities. Inspired by the compartmentalized organization of cells and organelles, lipid or polymer vesicles are widely used as model membrane systems to investigate the translocation of solutes and the transduction of signals by membrane proteins. The bottom-up assembly and functionalization of such artificial compartments enables full control over their composition and can thus provide specifically optimized environments for synthetic biological processes. This review aims to inspire future endeavors by providing a diverse toolbox of molecular modules, engineering methodologies, and different approaches to assemble artificial vesicular systems. Important technical and practical aspects are addressed and selected applications are presented, highlighting particular achievements and limitations of the bottom-up approach. Complementing the cutting-edge technological achievements, fundamental aspects are also discussed to cater to the inherently diverse background of the target audience, which results from the interdisciplinary nature of synthetic biology. The engineering of proteins as functional modules and the use of lipids and block copolymers as scaffold modules for the assembly of functionalized vesicular systems are explored in detail. Particular emphasis is placed on ensuring the controlled assembly of these components into increasingly complex vesicular systems. Finally, all descriptions are presented in the greater context of engineering valuable synthetic biological systems for applications in biocatalysis, biosensing, bioremediation, or targeted drug delivery.
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Affiliation(s)
- Stephan Hirschi
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Thomas R Ward
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Wolfgang P Meier
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
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17
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Shariati K, Zhang Y, Giubbolini S, Parra R, Liang S, Edwards A, Hejtmancik JF, Ratto GM, Arosio D, Ku G. A Superfolder Green Fluorescent Protein-Based Biosensor Allows Monitoring of Chloride in the Endoplasmic Reticulum. ACS Sens 2022; 7:2218-2224. [PMID: 35951356 PMCID: PMC9425558 DOI: 10.1021/acssensors.2c00626] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Though the concentration of chloride has been measured in the cytoplasm and in secretory granules of live cells, it cannot be measured within the endoplasmic reticulum (ER) due to poor fluorescence of existing biosensors. We developed a fluorescent biosensor composed of a chloride-sensitive superfolder GFP and long Stokes-shifted mKate2 for simultaneous chloride and pH measurements that retained fluorescence in the ER lumen. Using this sensor, we showed that the chloride concentration in the ER is significantly lower than that in the cytosol. This improved biosensor enables dynamic measurement of chloride in the ER and may be useful in other environments where protein folding is challenging.
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Affiliation(s)
- Kaavian Shariati
- Diabetes
Center, University of California San Francisco, San Francisco, California 94143, United States
| | - Yaohuan Zhang
- Diabetes
Center, University of California San Francisco, San Francisco, California 94143, United States,Metabolic
Biology Graduate Program, Department of Nutritional Science and Toxicity, University of California Berkeley, Berkeley, California 94720, United States
| | - Simone Giubbolini
- National
Enterprise for NanoScience and NanoTechnology (NEST), Istituto Nanoscienze, Consiglio Nazionale delle Ricerche (CNR) and Scuola
Normale Superiore Pisa, Pisa 56127, Italy
| | - Riccardo Parra
- National
Enterprise for NanoScience and NanoTechnology (NEST), Istituto Nanoscienze, Consiglio Nazionale delle Ricerche (CNR) and Scuola
Normale Superiore Pisa, Pisa 56127, Italy
| | - Steven Liang
- Diabetes
Center, University of California San Francisco, San Francisco, California 94143, United States
| | - Austin Edwards
- Biological
Imaging Development CoLab, University of
California San Francisco, San Francisco, California 94143, United States
| | - J. Fielding Hejtmancik
- Ophthalmic
Genetics and Visual Function Branch, National
Eye Institute, Bethesda, Maryland 20892-1860, United States
| | - Gian Michele Ratto
- National
Enterprise for NanoScience and NanoTechnology (NEST), Istituto Nanoscienze, Consiglio Nazionale delle Ricerche (CNR) and Scuola
Normale Superiore Pisa, Pisa 56127, Italy
| | - Daniele Arosio
- CNR, Institute
of Biophysics, Via alla
Cascata 56/C, Trento 38123, Italy,CIBIO, University
of Trento, Via delle
Regole 101, Trento 38123, Italy
| | - Gregory Ku
- Diabetes
Center and Department of Medicine, Division of Endocrinology, University of California San Francisco, 513 Parnassus Avenue, Box 0534, San Francisco, California94143, United States,
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18
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Harbauer AB, Schneider A, Wohlleber D. Analysis of Mitochondria by Single-Organelle Resolution. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2022; 15:1-16. [PMID: 35303775 DOI: 10.1146/annurev-anchem-061020-111722] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cellular organelles are highly specialized compartments with distinct functions. With the increasing resolution of detection methods, it is becoming clearer that same organelles may have different functions or properties not only within different cell populations of a tissue but also within the same cell. Dysfunction or altered function affects the organelle itself and may also lead to malignancies or undesirable cell death. To understand cellular function or dysfunction, it is therefore necessary to analyze cellular components at the single-organelle level. Here, we review the recent advances in analyzing cellular function at single-organelle resolution using high-parameter flow cytometry or multicolor confocal microscopy. We focus on the analysis of mitochondria, as they are organelles at the crossroads of various cellular signaling pathways and functions. However, most of the applied methods/technologies are transferable to any other organelle, such as the endoplasmic reticulum, lysosomes, or peroxisomes.
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Affiliation(s)
- Angelika B Harbauer
- Max Planck Institute of Neurobiology, Martinsried, Germany;
- Institute of Neuronal Cell Biology, TUM School of Medicine, Technical University of Munich, Munich, Germany
- Munich Cluster for Systems Neurology, Munich, Germany
| | - Annika Schneider
- Institute of Molecular Immunology and Experimental Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany; ,
| | - Dirk Wohlleber
- Institute of Molecular Immunology and Experimental Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany; ,
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19
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Torello Pianale L, Rugbjerg P, Olsson L. Real-Time Monitoring of the Yeast Intracellular State During Bioprocesses With a Toolbox of Biosensors. Front Microbiol 2022; 12:802169. [PMID: 35069506 PMCID: PMC8776715 DOI: 10.3389/fmicb.2021.802169] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/16/2021] [Indexed: 12/19/2022] Open
Abstract
Industrial fermentation processes strive for high robustness to ensure optimal and consistent performance. Medium components, fermentation products, and physical perturbations may cause stress and lower performance. Cellular stress elicits a range of responses, whose extracellular manifestations have been extensively studied; whereas intracellular aspects remain poorly known due to lack of tools for real-time monitoring. Genetically encoded biosensors have emerged as promising tools and have been used to improve microbial productivity and tolerance toward industrially relevant stresses. Here, fluorescent biosensors able to sense the yeast intracellular environment (pH, ATP levels, oxidative stress, glycolytic flux, and ribosome production) were implemented into a versatile and easy-to-use toolbox. Marker-free and efficient genome integration at a conserved site on chromosome X of Saccharomyces cerevisiae strains and a commercial Saccharomyces boulardii strain was developed. Moreover, multiple biosensors were used to simultaneously monitor different intracellular parameters in a single cell. Even when combined together, the biosensors did not significantly affect key physiological parameters, such as specific growth rate and product yields. Activation and response of each biosensor and their interconnection were assessed using an advanced micro-cultivation system. Finally, the toolbox was used to screen cell behavior in a synthetic lignocellulosic hydrolysate that mimicked harsh industrial substrates, revealing differences in the oxidative stress response between laboratory (CEN.PK113-7D) and industrial (Ethanol Red) S. cerevisiae strains. In summary, the toolbox will allow both the exploration of yeast diversity and physiological responses in natural and complex industrial conditions, as well as the possibility to monitor production processes.
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Affiliation(s)
- Luca Torello Pianale
- Industrial Biotechnology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Peter Rugbjerg
- Industrial Biotechnology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Enduro Genetics ApS, Copenhagen, Denmark
| | - Lisbeth Olsson
- Industrial Biotechnology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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20
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Islam MS, Gaston JP, Baker MAB. Fluorescence Approaches for Characterizing Ion Channels in Synthetic Bilayers. MEMBRANES 2021; 11:857. [PMID: 34832086 PMCID: PMC8619978 DOI: 10.3390/membranes11110857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 12/12/2022]
Abstract
Ion channels are membrane proteins that play important roles in a wide range of fundamental cellular processes. Studying membrane proteins at a molecular level becomes challenging in complex cellular environments. Instead, many studies focus on the isolation and reconstitution of the membrane proteins into model lipid membranes. Such simpler, in vitro, systems offer the advantage of control over the membrane and protein composition and the lipid environment. Rhodopsin and rhodopsin-like ion channels are widely studied due to their light-interacting properties and are a natural candidate for investigation with fluorescence methods. Here we review techniques for synthesizing liposomes and for reconstituting membrane proteins into lipid bilayers. We then summarize fluorescence assays which can be used to verify the functionality of reconstituted membrane proteins in synthetic liposomes.
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Affiliation(s)
- Md. Sirajul Islam
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia; (M.S.I.); (J.P.G.)
| | - James P. Gaston
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia; (M.S.I.); (J.P.G.)
| | - Matthew A. B. Baker
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia; (M.S.I.); (J.P.G.)
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia
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21
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Nam Y, Goo E, Kang Y, Hwang I. Membrane Depolarization and Apoptosis-Like Cell Death in an Alkaline Environment in the Rice Pathogen Burkholderia glumae. Front Microbiol 2021; 12:755596. [PMID: 34712216 PMCID: PMC8546246 DOI: 10.3389/fmicb.2021.755596] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/15/2021] [Indexed: 11/13/2022] Open
Abstract
The rice pathogen Burkholderia glumae uses amino acids as a principal carbon source and thus produces ammonia in amino acid-rich culture medium such as Luria-Bertani (LB) broth. To counteract ammonia-mediated environmental alkaline toxicity, the bacterium produces a public good, oxalate, in a quorum sensing (QS)-dependent manner. QS mutants of B. glumae experience alkaline toxicity and may undergo cell death at the stationary phase when grown in LB medium. Here, we show that the cell-death processes of QS mutants due to alkaline environmental conditions are similar to the apoptosis-like cell death reported in other bacteria. Staining QS mutants with bis-(1,3-dibutylbarbituric acid)-trimethine oxonol revealed membrane depolarization. CellROX™ staining showed excessive generation of reactive oxygen species (ROS) in QS mutants. The expression of genes encoding HNH endonuclease (BGLU_1G15690), oligoribonuclease (BGLU_1G09120), ribonuclease E (BGLU_1G09400), and Hu-beta (BGLU_1G13530) was significantly elevated in QS mutants compared to that in wild-type BGR1, consistent with the degradation of cellular materials as observed under transmission electron microscopy (TEM). A homeostatic neutral pH was not attainable by QS mutants grown in LB broth or by wild-type BGR1 grown in an artificially amended alkaline environment. At an artificially adjusted alkaline pH, wild-type BGR1 underwent apoptosis-like cell death similar to that observed in QS mutants. These results show that environmental alkaline stress interferes with homeostatic neutral cellular pH, induces membrane depolarization, and causes apoptosis-like cell death in B. glumae.
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Affiliation(s)
- Yewon Nam
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Eunhye Goo
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Yongsung Kang
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Ingyu Hwang
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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22
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Methods of measuring presynaptic function with fluorescence probes. Appl Microsc 2021; 51:2. [PMID: 33730244 PMCID: PMC7969681 DOI: 10.1186/s42649-021-00051-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/09/2021] [Indexed: 01/02/2023] Open
Abstract
Synaptic vesicles, which are endogenous to neurotransmitters, are involved in exocytosis by active potentials and release neurotransmitters. Synaptic vesicles used in neurotransmitter release are reused via endocytosis to maintain a pool of synaptic vesicles. Synaptic vesicles show different types of exo- and endocytosis depending on animal species, type of nerve cell, and electrical activity. To accurately understand the dynamics of synaptic vesicles, direct observation of synaptic vesicles is required; however, it was difficult to observe synaptic vesicles of size 40-50 nm in living neurons. The exo-and endocytosis of synaptic vesicles was confirmed by labeling the vesicles with a fluorescent agent and measuring the changes in fluorescence intensity. To date, various methods of labeling synaptic vesicles have been proposed, and each method has its own characteristics, strength, and drawbacks. In this study, we introduce methods that can measure presynaptic activity and describe the characteristics of each technique.
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23
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Schmidl S, Iancu CV, Reifenrath M, Choe JY, Oreb M. A label-free real-time method for measuring glucose uptake kinetics in yeast. FEMS Yeast Res 2020; 21:6041724. [PMID: 33338229 DOI: 10.1093/femsyr/foaa069] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/16/2020] [Indexed: 01/19/2023] Open
Abstract
Glucose uptake assays commonly rely on the isotope-labeled sugar, which is associated with radioactive waste and exposure of the experimenter to radiation. Here, we show that the rapid decrease of the cytosolic pH after a glucose pulse to starved Saccharomyces cerevisiae cells is dependent on the rate of sugar uptake and can be used to determine the kinetic parameters of sugar transporters. The pH-sensitive green fluorescent protein variant pHluorin is employed as a genetically encoded biosensor to measure the rate of acidification as a proxy of transport velocity in real time. The measurements are performed in the hexose transporter-deficient (hxt0) strain EBY.VW4000 that has been previously used to characterize a plethora of sugar transporters from various organisms. Therefore, this method provides an isotope-free, fluorometric approach for kinetic characterization of hexose transporters in a well-established yeast expression system.
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Affiliation(s)
- Sina Schmidl
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Cristina V Iancu
- Department of Chemistry, East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC27834, USA
| | - Mara Reifenrath
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Jun-Yong Choe
- Department of Chemistry, East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC27834, USA
| | - Mislav Oreb
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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24
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Reifenrath M, Oreb M, Boles E, Tripp J. Artificial ER-Derived Vesicles as Synthetic Organelles for in Vivo Compartmentalization of Biochemical Pathways. ACS Synth Biol 2020; 9:2909-2916. [PMID: 33074655 DOI: 10.1021/acssynbio.0c00241] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Compartmentalization in membrane-surrounded organelles has the potential to overcome obstacles associated with the engineering of metabolic pathways, such as unwanted side reactions, accumulation of toxic intermediates, drain of intermediates out of the cell, and long diffusion distances. Strategies utilizing natural organelles suffer from the presence of endogenous pathways. In our approach, we make use of endoplasmic reticulum-derived vesicles loaded with enzymes of a metabolic pathway ("metabolic vesicles"). They are generated by fusion of synthetic peptides containing the N-terminal proline-rich and self-assembling region of the maize storage protein gamma-Zein ("Zera") to the pathway enzymes. We have applied a strategy to integrate three enzymes of a cis,cis-muconic acid production pathway into those vesicles in yeast. Using fluorescence microscopy and cell fractionation techniques, we have proven the formation of metabolic vesicles and the incorporation of enzymes. Activities of the enzymes and functionality of the compartmentalized pathway were demonstrated in fermentation experiments.
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Affiliation(s)
- Mara Reifenrath
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Mislav Oreb
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Eckhard Boles
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Joanna Tripp
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
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25
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Cancer and pH Dynamics: Transcriptional Regulation, Proteostasis, and the Need for New Molecular Tools. Cancers (Basel) 2020; 12:cancers12102760. [PMID: 32992762 PMCID: PMC7601256 DOI: 10.3390/cancers12102760] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/11/2022] Open
Abstract
An emerging hallmark of cancer cells is dysregulated pH dynamics. Recent work has suggested that dysregulated intracellular pH (pHi) dynamics enable diverse cancer cellular behaviors at the population level, including cell proliferation, cell migration and metastasis, evasion of apoptosis, and metabolic adaptation. However, the molecular mechanisms driving pH-dependent cancer-associated cell behaviors are largely unknown. In this review article, we explore recent literature suggesting pHi dynamics may play a causative role in regulating or reinforcing tumorigenic transcriptional and proteostatic changes at the molecular level, and discuss outcomes on tumorigenesis and tumor heterogeneity. Most of the data we discuss are population-level analyses; lack of single-cell data is driven by a lack of tools to experimentally change pHi with spatiotemporal control. Data is also sparse on how pHi dynamics play out in complex in vivo microenvironments. To address this need, at the end of this review, we cover recent advances for live-cell pHi measurement at single-cell resolution. We also discuss the essential role for tool development in revealing mechanisms by which pHi dynamics drive tumor initiation, progression, and metastasis.
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26
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Valbuena FM, Fitzgerald I, Strack RL, Andruska N, Smith L, Glick BS. A photostable monomeric superfolder green fluorescent protein. Traffic 2020; 21:534-544. [PMID: 32415747 DOI: 10.1111/tra.12737] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 05/09/2020] [Accepted: 05/10/2020] [Indexed: 11/30/2022]
Abstract
The green fluorescent protein (GFP) from Aequorea victoria has been engineered extensively in the past to generate variants suitable for protein tagging. Early efforts produced the enhanced variant EGFP and its monomeric derivative mEGFP, which have useful photophysical properties, as well as superfolder GFP, which folds efficiently under adverse conditions. We previously generated msGFP, a monomeric superfolder derivative of EGFP. Unfortunately, compared to EGFP, msGFP and other superfolder GFP variants show faster photobleaching. We now describe msGFP2, which retains monomeric superfolder properties while being as photostable as EGFP. msGFP2 contains modified N- and C-terminal peptides that are expected to reduce nonspecific interactions. Compared to EGFP and mEGFP, msGFP2 is less prone to disturbing the functions of certain partner proteins. For general-purpose protein tagging, msGFP2 may be the best available derivative of A. victoria GFP.
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Affiliation(s)
- Fernando M Valbuena
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois, USA
| | - Ivy Fitzgerald
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, Illinois, USA
| | - Rita L Strack
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois, USA
| | - Neal Andruska
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois, USA
| | - Luke Smith
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois, USA
| | - Benjamin S Glick
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois, USA
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27
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Kilaru S, Schuster M, Cannon S, Steinberg G. Optimised red- and green-fluorescent proteins for live cell imaging in the industrial enzyme-producing fungus Trichoderma reesei. Fungal Genet Biol 2020; 138:103366. [PMID: 32173466 DOI: 10.1016/j.fgb.2020.103366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 11/30/2022]
Abstract
The filamentous fungus Trichoderma reesei is a major source of cellulolytic enzymes in biofuel production. Despite its economic relevance, our understanding of its secretory pathways is fragmentary. A major challenge is to visualise the dynamic behaviour of secretory vesicles in living cells. To this end, we establish a location juxtaposing the succinate dehydrogenase locus as a "soft-landing" site for controlled expression of 4 green-fluorescent and 5 red-fluorescent protein-encoding genes (GFPs, RFPs). Quantitative and comparative analysis of their fluorescent signals in living cells demonstrates that codon-optimised monomeric superfolder GFP (TrmsGFP) and codon-optimised mCherry (TrmCherry) combine highest signal intensity with significantly improved signal-to-noise ratios. Finally, we show that integration of plasmid near the sdi1 locus does not affect secretion of cellulase activity in RUT-C30. The molecular and live cell imaging tools generated in this study will help our understanding the secretory pathway in the industrial fungus T. reesei.
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Affiliation(s)
- Sreedhar Kilaru
- Biosciences, University of Exeter, Stocker Road, EX4 4QD Exeter, United Kingdom
| | - Martin Schuster
- Biosciences, University of Exeter, Stocker Road, EX4 4QD Exeter, United Kingdom
| | - Stuart Cannon
- Biosciences, University of Exeter, Stocker Road, EX4 4QD Exeter, United Kingdom
| | - Gero Steinberg
- Biosciences, University of Exeter, Stocker Road, EX4 4QD Exeter, United Kingdom.
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28
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A new pH sensor localized in the Golgi apparatus of Saccharomyces cerevisiae reveals unexpected roles of Vph1p and Stv1p isoforms. Sci Rep 2020; 10:1881. [PMID: 32024908 PMCID: PMC7002768 DOI: 10.1038/s41598-020-58795-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 01/21/2020] [Indexed: 12/22/2022] Open
Abstract
The gradual acidification of the secretory pathway is conserved and extremely important for eukaryotic cells, but until now there was no pH sensor available to monitor the pH of the early Golgi apparatus in Saccharomyces cerevisiae. Therefore, we developed a pHluorin-based sensor for in vivo measurements in the lumen of the Golgi. By using this new tool we show that the cis- and medial-Golgi pH is equal to 6.6–6.7 in wild type cells during exponential phase. As expected, V-ATPase inactivation results in a near neutral Golgi pH. We also uncover that surprisingly Vph1p isoform of the V-ATPase is prevalent to Stv1p for Golgi acidification. Additionally, we observe that during changes of the cytosolic pH, the Golgi pH is kept relatively stable, mainly thanks to the V-ATPase. Eventually, this new probe will allow to better understand the mechanisms involved in the acidification and the pH control within the secretory pathway.
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29
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Pedelacq JD, Cabantous S. Development and Applications of Superfolder and Split Fluorescent Protein Detection Systems in Biology. Int J Mol Sci 2019; 20:ijms20143479. [PMID: 31311175 PMCID: PMC6678664 DOI: 10.3390/ijms20143479] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 01/08/2023] Open
Abstract
Molecular engineering of the green fluorescent protein (GFP) into a robust and stable variant named Superfolder GFP (sfGFP) has revolutionized the field of biosensor development and the use of fluorescent markers in diverse area of biology. sfGFP-based self-associating bipartite split-FP systems have been widely exploited to monitor soluble expression in vitro, localization, and trafficking of proteins in cellulo. A more recent class of split-FP variants, named « tripartite » split-FP, that rely on the self-assembly of three GFP fragments, is particularly well suited for the detection of protein–protein interactions. In this review, we describe the different steps and evolutions that have led to the diversification of superfolder and split-FP reporter systems, and we report an update of their applications in various areas of biology, from structural biology to cell biology.
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Affiliation(s)
- Jean-Denis Pedelacq
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31077 Toulouse, France.
| | - Stéphanie Cabantous
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Inserm, Université Paul Sabatier-Toulouse III, CNRS, 31037 Toulouse, France.
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30
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Arce‐Rodríguez A, Volke DC, Bense S, Häussler S, Nikel PI. Non-invasive, ratiometric determination of intracellular pH in Pseudomonas species using a novel genetically encoded indicator. Microb Biotechnol 2019; 12:799-813. [PMID: 31162835 PMCID: PMC6559197 DOI: 10.1111/1751-7915.13439] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 11/30/2022] Open
Abstract
The ability of Pseudomonas species to thrive in all major natural environments (i.e. terrestrial, freshwater and marine) is based on its exceptional capability to adapt to physicochemical changes. Thus, environmental bacteria have to tightly control the maintenance of numerous physiological traits across different conditions. The intracellular pH (pHi ) homoeostasis is a particularly important feature, since the pHi influences a large portion of the biochemical processes in the cell. Despite its importance, relatively few reliable, easy-to-implement tools have been designed for quantifying in vivo pHi changes in Gram-negative bacteria with minimal manipulations. Here we describe a convenient, non-invasive protocol for the quantification of the pHi in bacteria, which is based on the ratiometric fluorescent indicator protein PHP (pH indicator for Pseudomonas). The DNA sequence encoding PHP was thoroughly adapted to guarantee optimal transcription and translation of the indicator in Pseudomonas species. Our PHP-based quantification method demonstrated that pHi is tightly regulated over a narrow range of pH values not only in Pseudomonas, but also in other Gram-negative bacterial species such as Escherichia coli. The maintenance of the cytoplasmic pH homoeostasis in vivo could also be observed upon internal (e.g. redirection of glucose consumption pathways in P. putida) and external (e.g. antibiotic exposure in P. aeruginosa) perturbations, and the PHP indicator was also used to follow dynamic changes in the pHi upon external pH shifts. In summary, our work describes a reliable method for measuring pHi in Pseudomonas, allowing for the detailed investigation of bacterial pHi homoeostasis and its regulation.
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Affiliation(s)
- Alejandro Arce‐Rodríguez
- Department of Molecular BacteriologyHelmholtz Centre for Infection Research38124BraunschweigGermany
| | - Daniel C. Volke
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark2800Kongens LyngbyDenmark
| | - Sarina Bense
- Department of Molecular BacteriologyHelmholtz Centre for Infection Research38124BraunschweigGermany
| | - Susanne Häussler
- Department of Molecular BacteriologyHelmholtz Centre for Infection Research38124BraunschweigGermany
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark2800Kongens LyngbyDenmark
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