1
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Maity H, Nguyen HT, Hori N, Thirumalai D. Salt-Dependent Self-Association of Trinucleotide Repeat RNA Sequences. J Phys Chem Lett 2024; 15:3820-3827. [PMID: 38557079 DOI: 10.1021/acs.jpclett.3c03553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Repeat RNA sequences self-associate to form condensates. Simulations of a coarse-grained single-interaction site model for (CAG)n (n = 30 and 31) show that the salt-dependent free energy gap, ΔGS, between the ground (perfect hairpin) and the excited state (slipped hairpin (SH) with one CAG overhang) of the monomer for (n even) is the primary factor that determines the rates and yield of self-assembly. For odd n, the free energy (GS) of the ground state, which is an SH, is used to predict the self-association kinetics. As the monovalent salt concentration, CS, increases, ΔGS and GS increase, which decreases the rates of dimer formation. In contrast, ΔGS for shuffled sequences, with the same length and sequence composition as (CAG)31, is larger, which suppresses their propensities to aggregate. Although demonstrated explicitly for (CAG) polymers, the finding of inverse correlation between the free energy gap and RNA aggregation is general.
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Affiliation(s)
- Hiranmay Maity
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hung T Nguyen
- Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Naoto Hori
- School of Pharmacy, University of Nottingham, Nottingham NG72RD, United Kingdom
| | - D Thirumalai
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
- Department of Physics, University of Texas at Austin, Austin, Texas 78712, United States
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2
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de Souza CJF, da Silva CS, Ramos AV, Garcia-Rojas EE, Pierucci APTR. Yeast cells-xanthan gum coacervation for hydrosoluble bioactive encapsulation. Int J Biol Macromol 2023; 253:127148. [PMID: 37832622 DOI: 10.1016/j.ijbiomac.2023.127148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023]
Abstract
This study assessed the technological feasibility of microencapsulating vitamin C (VC) via coacervation between yeast cells (YC) and xanthan gum (XG). The interaction efficiency between YC and XG was examined across various pHs and ratios, while characterizing the microcapsules in terms of encapsulation efficiency, particle size, and thermal and chemical stability. Additionally, in vitro digestion experiments were conducted to determine the digestion efficiency and bioavailability of the bioactive compound. The optimally produced microcapsules exhibited favorable functional attributes, including low water activity (≤ 0.3) and particle size (≤ 33.52 μm), coupled with a high encapsulation efficiency (∼ 86.12 %). The microcapsules were able to increase the stability of VC at high temperatures and during storage when compared to the control. The in vitro experiment revealed that the microcapsules effectively retained approximately 50 % of the VC in simulated gastric fluid, with up to 80 % released in simulated intestinal fluid. However, due to prior degradation in the simulated gastric fluid, the achieved bioavailability was around 68 %. These results are promising, underscoring the potential of these microcapsules as a viable technology for encapsulating, protect, and releasing water-soluble bioactives in the GI tract.
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Affiliation(s)
- Clitor Júnior Fernandes de Souza
- Program in Food, Nutrition and Health (PPGANS), School of Health Sciences, Federal University of Grande Dourados, Avenue Dourados-Itahum, Km 12, Dourados, MS 79804-970, Brazil; Josué de Castro Nutrition Institute, Federal University of Rio de Janeiro, Health Sciences Center, 373 Carlos Chagas Filho Avenue, Unit J, 21941-902 Rio de Janeiro, Brazil.
| | - Caroline Santos da Silva
- Program in Food, Nutrition and Health (PPGANS), School of Health Sciences, Federal University of Grande Dourados, Avenue Dourados-Itahum, Km 12, Dourados, MS 79804-970, Brazil
| | - Andresa Viana Ramos
- Nanotechnology Engineering Department, Alberto Luiz Coimbra Institute for Graduate Studies and Research in Engineering, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Edwin Elard Garcia-Rojas
- Agroindustrial Engineering and Technology Laboratory (LETA), Fluminense Federal University (UFF), Av. dos Trabalhadores, 420, Volta Redonda, RJ 27255-125, Brazil
| | - Anna Paola Trindade Rocha Pierucci
- Josué de Castro Nutrition Institute, Federal University of Rio de Janeiro, Health Sciences Center, 373 Carlos Chagas Filho Avenue, Unit J, 21941-902 Rio de Janeiro, Brazil
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3
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Antunes M, Kale D, Sychrová H, Sá-Correia I. The Hrk1 kinase is a determinant of acetic acid tolerance in yeast by modulating H + and K + homeostasis. MICROBIAL CELL (GRAZ, AUSTRIA) 2023; 10:261-276. [PMID: 38053573 PMCID: PMC10695635 DOI: 10.15698/mic2023.12.809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/15/2023] [Accepted: 10/26/2023] [Indexed: 12/07/2023]
Abstract
Acetic acid-induced stress is a common challenge in natural environments and industrial bioprocesses, significantly affecting the growth and metabolic performance of Saccharomyces cerevisiae. The adaptive response and tolerance to this stress involves the activation of a complex network of molecular pathways. This study aims to delve deeper into these mechanisms in S. cerevisiae, particularly focusing on the role of the Hrk1 kinase. Hrk1 is a key determinant of acetic acid tolerance, belonging to the NPR/Hal family, whose members are implicated in the modulation of the activity of plasma membrane transporters that orchestrate nutrient uptake and ion homeostasis. The influence of Hrk1 on S. cerevisiae adaptation to acetic acid-induced stress was explored by employing a physiological approach based on previous phosphoproteomics analyses. The results from this study reflect the multifunctional roles of Hrk1 in maintaining proton and potassium homeostasis during different phases of acetic acid-stressed cultivation. Hrk1 is shown to play a role in the activation of plasma membrane H+-ATPase, maintaining pH homeostasis, and in the modulation of plasma membrane potential under acetic acid stressed cultivation. Potassium (K+) supplementation of the growth medium, particularly when provided at limiting concentrations, led to a notable improvement in acetic acid stress tolerance of the hrk1Δ strain. Moreover, abrogation of this kinase expression is shown to confer a physiological advantage to growth under K+ limitation also in the absence of acetic acid stress. The involvement of the alkali metal cation/H+ exchanger Nha1, another proposed molecular target of Hrk1, in improving yeast growth under K+ limitation or acetic acid stress, is proposed.
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Affiliation(s)
- Miguel Antunes
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Deepika Kale
- Laboratory of Membrane Transport, Institute of Physiology, Czech Academy of Sciences, Videnska 1083, 142 00 Prague 4, Czech Republic
| | - Hana Sychrová
- Laboratory of Membrane Transport, Institute of Physiology, Czech Academy of Sciences, Videnska 1083, 142 00 Prague 4, Czech Republic
| | - Isabel Sá-Correia
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
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4
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Popova LG, Khramov DE, Nedelyaeva OI, Volkov VS. Yeast Heterologous Expression Systems for the Study of Plant Membrane Proteins. Int J Mol Sci 2023; 24:10768. [PMID: 37445944 DOI: 10.3390/ijms241310768] [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: 04/28/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Researchers are often interested in proteins that are present in cells in small ratios compared to the total amount of proteins. These proteins include transcription factors, hormones and specific membrane proteins. However, sufficient amounts of well-purified protein preparations are required for functional and structural studies of these proteins, including the creation of artificial proteoliposomes and the growth of protein 2D and 3D crystals. This aim can be achieved by the expression of the target protein in a heterologous system. This review describes the applications of yeast heterologous expression systems in studies of plant membrane proteins. An initial brief description introduces the widely used heterologous expression systems of the baker's yeast Saccharomyces cerevisiae and the methylotrophic yeast Pichia pastoris. S. cerevisiae is further considered a convenient model system for functional studies of heterologously expressed proteins, while P. pastoris has the advantage of using these yeast cells as factories for producing large quantities of proteins of interest. The application of both expression systems is described for functional and structural studies of membrane proteins from plants, namely, K+- and Na+-transporters, various ATPases and anion transporters, and other transport proteins.
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Affiliation(s)
- Larissa G Popova
- K.A. Timiryazev Institute of Plant Physiology RAS, 127276 Moscow, Russia
| | - Dmitrii E Khramov
- K.A. Timiryazev Institute of Plant Physiology RAS, 127276 Moscow, Russia
| | - Olga I Nedelyaeva
- K.A. Timiryazev Institute of Plant Physiology RAS, 127276 Moscow, Russia
| | - Vadim S Volkov
- K.A. Timiryazev Institute of Plant Physiology RAS, 127276 Moscow, Russia
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5
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Guo Y, Wang H, Wei X, Wang Z, Wang H, Chen J, Li J, Liu J. Utilization of high-K+-cane molasses for enhanced S-Adenosylmethionine production by manipulation of a K+ transport channel in Saccharomyces cerevisiae. Biochem Eng J 2023. [DOI: 10.1016/j.bej.2023.108846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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6
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Scanning electrochemical microscope as a tool for the electroporation of living yeast cells. Biosens Bioelectron 2022; 205:114096. [PMID: 35219018 DOI: 10.1016/j.bios.2022.114096] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 12/31/2022]
Abstract
In this study, a scanning electrochemical microscope (SECM) was for the first time adapted to perform the electroporation process of living yeast cells. We have demonstrated that relatively low voltage pulses of 1-2 V vs. Ag/AglCl,Cl-sat applied to gold-based ultramicroelectrode (Au-UME) are performing reversible electroporation of yeast cells immobilized on fluorine-doped tin oxide (FTO)/glass surface. SECM and electrochemical impedance spectroscopy (EIS) were used for the determination of quantitative electrochemical characteristics before and after the electroporation. The electrochemical impedance spectroscopy (EIS) illustrated significant electrochemical changes of electroporated yeast cells, while SECM feedback mode surface vertical scan current-distance curves showed that the diameter of the area affected by the electrical pulse is about 25 times larger than the diameter of the Au-UME used for the electroporation process. The results presented in this research open up a possibility to develop a targeted electroporation system which will affect only the selected area of tissue or some other cell-covered surface. Such model is promising for the selective treatment of selected cells in tissues and/or other sensitive biological systems while selecting the location and size of electroporated areas.
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7
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Wu Y, Pegoraro AF, Weitz DA, Janmey P, Sun SX. The correlation between cell and nucleus size is explained by an eukaryotic cell growth model. PLoS Comput Biol 2022; 18:e1009400. [PMID: 35180215 PMCID: PMC8893647 DOI: 10.1371/journal.pcbi.1009400] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 03/03/2022] [Accepted: 01/12/2022] [Indexed: 12/19/2022] Open
Abstract
In eukaryotes, the cell volume is observed to be strongly correlated with the nuclear volume. The slope of this correlation depends on the cell type, growth condition, and the physical environment of the cell. We develop a computational model of cell growth and proteome increase, incorporating the kinetics of amino acid import, protein/ribosome synthesis and degradation, and active transport of proteins between the cytoplasm and the nucleoplasm. We also include a simple model of ribosome biogenesis and assembly. Results show that the cell volume is tightly correlated with the nuclear volume, and the cytoplasm-nucleoplasm transport rates strongly influence the cell growth rate as well as the cell/nucleus volume ratio (C/N ratio). Ribosome assembly and the ratio of ribosomal proteins to mature ribosomes also influence the cell volume and the cell growth rate. We find that in order to regulate the cell growth rate and the cell/nucleus volume ratio, the cell must optimally control groups of kinetic and transport parameters together, which could explain the quantitative roles of canonical growth pathways. Finally, although not explicitly demonstrated in this work, we point out that it is possible to construct a detailed proteome distribution using our model and RNAseq data, provided that a quantitative cell division mechanism is known.
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Affiliation(s)
- Yufei Wu
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | | | - David A. Weitz
- Department of Physics, Harvard University, Boston, Massachusetts, United States of America
| | - Paul Janmey
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Sean X. Sun
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, United States of America
- Center for Cell Dynamics, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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8
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Codjoe JM, Miller K, Haswell ES. Plant cell mechanobiology: Greater than the sum of its parts. THE PLANT CELL 2022; 34:129-145. [PMID: 34524447 PMCID: PMC8773992 DOI: 10.1093/plcell/koab230] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/09/2021] [Indexed: 05/04/2023]
Abstract
The ability to sense and respond to physical forces is critical for the proper function of cells, tissues, and organisms across the evolutionary tree. Plants sense gravity, osmotic conditions, pathogen invasion, wind, and the presence of barriers in the soil, and dynamically integrate internal and external stimuli during every stage of growth and development. While the field of plant mechanobiology is growing, much is still poorly understood-including the interplay between mechanical and biochemical information at the single-cell level. In this review, we provide an overview of the mechanical properties of three main components of the plant cell and the mechanoperceptive pathways that link them, with an emphasis on areas of complexity and interaction. We discuss the concept of mechanical homeostasis, or "mechanostasis," and examine the ways in which cellular structures and pathways serve to maintain it. We argue that viewing mechanics and mechanotransduction as emergent properties of the plant cell can be a useful conceptual framework for synthesizing current knowledge and driving future research.
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Affiliation(s)
- Jennette M Codjoe
- Department of Biology and Center for Engineering Mechanobiology, Washington University in St Louis, St Louis, Missouri, 63130, USA
| | - Kari Miller
- Department of Biology and Center for Engineering Mechanobiology, Washington University in St Louis, St Louis, Missouri, 63130, USA
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9
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The Influence of Biomolecule Composition on Colloidal Beer Structure. Biomolecules 2021; 12:biom12010024. [PMID: 35053172 PMCID: PMC8774254 DOI: 10.3390/biom12010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 11/16/2022] Open
Abstract
Recent studies have revealed an interest in the composition of beer biomolecules as a colloidal system and their influence on the formation of beer taste. The purpose of this research was to establish biochemical interactions between the biomolecules of plant-based raw materials of beer in order to understand the overall structure of beer as a complex system of bound biomolecules. Generally accepted methods of analytical research in the field of brewing, biochemistry and proteomics were used to solve the research objectives. The studies allowed us to establish the relationship between the grain and plant-based raw materials used, as well as the processing technologies and biomolecular profiles of beer. The qualitative profile of the distribution of protein compounds as a framework for the formation of a colloidal system and the role of carbohydrate dextrins and phenol compounds are given. This article provides information about the presence of biogenic compounds in the structure of beer that positively affect the functioning of the body. A critical assessment of the influence of some parameters on the completeness of beer taste by biomolecules is given. Conclusion: the conducted analytical studies allowed us to confirm the hypothesis about the nitrogen structure of beer and the relationship of other biomolecules with protein substances, and to identify the main factors affecting the distribution of biomolecules by fractions.
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10
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Köpnick AL, Jansen A, Geistlinger K, Epalle NH, Beitz E. Basigin drives intracellular accumulation of l-lactate by harvesting protons and substrate anions. PLoS One 2021; 16:e0249110. [PMID: 33770122 PMCID: PMC7996999 DOI: 10.1371/journal.pone.0249110] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/11/2021] [Indexed: 12/22/2022] Open
Abstract
Transmembrane transport of l-lactate by members of the monocarboxylate transporter family, MCT, is vital in human physiology and a malignancy factor in cancer. Interaction with an accessory protein, typically basigin, is required to deliver the MCT to the plasma membrane. It is unknown whether basigin additionally exerts direct effects on the transmembrane l-lactate transport of MCT1. Here, we show that the presence of basigin leads to an intracellular accumulation of l-lactate 4.5-fold above the substrate/proton concentrations provided by the external buffer. Using basigin truncations we localized the effect to arise from the extracellular Ig-I domain. Identification of surface patches of condensed opposite electrostatic potential, and experimental analysis of charge-affecting Ig-I mutants indicated a bivalent harvesting antenna functionality for both, protons and substrate anions. From these data, and determinations of the cytosolic pH with a fluorescent probe, we conclude that the basigin Ig-I domain drives lactate uptake by locally increasing the proton and substrate concentration at the extracellular MCT entry site. The biophysical properties are physiologically relevant as cell growth on lactate media was strongly promoted in the presence of the Ig-I domain. Lack of the domain due to shedding, or misfolding due to breakage of a stabilizing disulfide bridge reversed the effect. Tumor progression according to classical or reverse Warburg effects depends on the transmembrane l-lactate distribution, and this study shows that the basigin Ig-I domain is a pivotal determinant.
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Affiliation(s)
- Anna-Lena Köpnick
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Annika Jansen
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Katharina Geistlinger
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Nathan Hugo Epalle
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Eric Beitz
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Kiel, Germany
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11
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Shah AA, Liu B, Tang Z, Wang W, Yang W, Hu Q, Liu Y, Zhang N, Liu K. Hydrogen sulfide treatment at the late growth stage of Saccharomyces cerevisiae extends chronological lifespan. Aging (Albany NY) 2021; 13:9859-9873. [PMID: 33744847 PMCID: PMC8064171 DOI: 10.18632/aging.202738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/16/2021] [Indexed: 11/25/2022]
Abstract
Previous studies demonstrated that lifelong treatment with a slow H2S releasing donor extends yeast chronological lifespan (CLS), but it is not clear when the action of H2S benefits to CLS during yeast growth. Here, we show that short H2S treatments by using NaHS as a fast H2S releasing donor at 96 hours after inoculation extended yeast CLS while NaHS treatments earlier than 72 hours after inoculation failed to do so. To reveal the mechanism, we analyzed the transcriptome of yeast cells with or without the early and late NaHS treatments. We found that both treatments had similar effects on pathways related to CLS regulation. Follow-up qPCR and ROS analyses suggest that altered expression of some antioxidant genes by the early NaHS treatments were not stable enough to benefit CLS. Moreover, transcriptome data also indicated that some genes were regulated differently by the early and late H2S treatment. Specifically, we found that the expression of YPK2, a human SGK2 homolog and also a key regulator of the yeast cell wall synthesis, was significantly altered by the late NaHS treatment but not altered by the early NaHS treatment. Finally, the key role of YPK2 in CLS regulation by H2S is revealed by CLS data showing that the late NaHS treatment did not enhance the CLS of a ypk2 knockout mutant. This study sheds light on the molecular mechanism of CLS extension induced by H2S, and for the first time addresses the importance of H2S treatment timing for lifespan extension.
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Affiliation(s)
- Arman Ali Shah
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Binghua Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Zhihuai Tang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Wang Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Wenjie Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Quanjun Hu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Yan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Nianhui Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Ke Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
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12
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Roden C, Gladfelter AS. RNA contributions to the form and function of biomolecular condensates. Nat Rev Mol Cell Biol 2021; 22:183-195. [PMID: 32632317 PMCID: PMC7785677 DOI: 10.1038/s41580-020-0264-6] [Citation(s) in RCA: 329] [Impact Index Per Article: 109.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2020] [Indexed: 01/08/2023]
Abstract
Biomolecular condensation partitions cellular contents and has important roles in stress responses, maintaining homeostasis, development and disease. Many nuclear and cytoplasmic condensates are rich in RNA and RNA-binding proteins (RBPs), which undergo liquid-liquid phase separation (LLPS). Whereas the role of RBPs in condensates has been well studied, less attention has been paid to the contribution of RNA to LLPS. In this Review, we discuss the role of RNA in biomolecular condensation and highlight considerations for designing condensate reconstitution experiments. We focus on RNA properties such as composition, length, structure, modifications and expression level. These properties can modulate the biophysical features of native condensates, including their size, shape, viscosity, liquidity, surface tension and composition. We also discuss the role of RNA-protein condensates in development, disease and homeostasis, emphasizing how their properties and function can be determined by RNA. Finally, we discuss the multifaceted cellular functions of biomolecular condensates, including cell compartmentalization through RNA transport and localization, supporting catalytic processes, storage and inheritance of specific molecules, and buffering noise and responding to stress.
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Affiliation(s)
- Christine Roden
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- The Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Amy S Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- The Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
- Whitman Center, Marine Biology Laboratory, Woods Hole, MA, USA.
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13
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Volkov V, Schwenke H. A Quest for Mechanisms of Plant Root Exudation Brings New Results and Models, 300 Years after Hales. PLANTS 2020; 10:plants10010038. [PMID: 33375713 PMCID: PMC7823307 DOI: 10.3390/plants10010038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 12/27/2022]
Abstract
The review summarizes some of our current knowledge on the phenomenon of exudation from the cut surface of detached roots with emphasis on results that were mostly established over the last fifty years. The phenomenon is quantitatively documented in the 18th century (by Hales in 1727). By the 19th century, theories mainly ascribed exudation to the secretion of living root cells. The 20th century favored the osmometer model of root exudation. Nevertheless, growing insights into the mechanisms of water transport and new or rediscovered observations stimulated the quest for a more adequate exudation model. The historical overview shows how understanding of exudation changed with time following experimental opportunities and novel ideas from different areas of knowledge. Later theories included cytoskeleton-dependent micro-pulsations of turgor in root cells to explain the observed water exudation. Recent progress in experimental biomedicine led to detailed study of channels and transporters for ion transport via cellular membranes and to the discovery of aquaporins. These universal molecular entities have been incorporated to the more complex models of water transport via plant roots. A new set of ideas and explanations was based on cellular osmoregulation by mechanosensitive ion channels. Thermodynamic calculations predicted the possibility of water transport against osmotic forces based on co-transport of water with ions via cation-chloride cotransporters. Recent observations of rhizodermis exudation, exudation of roots without an external aqueous medium, segments cut from roots, pulses of exudation, a phase shifting of water uptake and exudation, and of effects of physiologically active compounds (like ion channel blockers, metabolic agents, and cytoskeletal agents) will likely refine our understanding of the phenomenon. So far, it seems that more than one mechanism is responsible for root pressure and root exudation, processes which are important for refilling of embolized xylem vessels. However, recent advances in ion and water transport research at the molecular level suggest potential future directions to understanding of root exudation and new models awaiting experimental testing.
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Affiliation(s)
- Vadim Volkov
- Department of Plant Sciences, College of Agricultural and Environmental Sciences, University of California, Davis, CA 95616, USA
- K.A. Timiriazev Institute of Plant Physiology RAS, 35 Botanicheskaya St., Moscow 127276, Russia
- Correspondence: (V.V.); (H.S.)
| | - Heiner Schwenke
- Max Planck Institute for the History of Science, Boltzmannstraße 22, 14195 Berlin, Germany
- Correspondence: (V.V.); (H.S.)
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14
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O' Neill JS, Hoyle NP, Robertson JB, Edgar RS, Beale AD, Peak-Chew SY, Day J, Costa ASH, Frezza C, Causton HC. Eukaryotic cell biology is temporally coordinated to support the energetic demands of protein homeostasis. Nat Commun 2020; 11:4706. [PMID: 32943618 PMCID: PMC7499178 DOI: 10.1038/s41467-020-18330-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 08/13/2020] [Indexed: 12/17/2022] Open
Abstract
Yeast physiology is temporally regulated, this becomes apparent under nutrient-limited conditions and results in respiratory oscillations (YROs). YROs share features with circadian rhythms and interact with, but are independent of, the cell division cycle. Here, we show that YROs minimise energy expenditure by restricting protein synthesis until sufficient resources are stored, while maintaining osmotic homeostasis and protein quality control. Although nutrient supply is constant, cells sequester and store metabolic resources via increased transport, autophagy and biomolecular condensation. Replete stores trigger increased H+ export which stimulates TORC1 and liberates proteasomes, ribosomes, chaperones and metabolic enzymes from non-membrane bound compartments. This facilitates translational bursting, liquidation of storage carbohydrates, increased ATP turnover, and the export of osmolytes. We propose that dynamic regulation of ion transport and metabolic plasticity are required to maintain osmotic and protein homeostasis during remodelling of eukaryotic proteomes, and that bioenergetic constraints selected for temporal organisation that promotes oscillatory behaviour.
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Affiliation(s)
- John S O' Neill
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
| | | | | | - Rachel S Edgar
- Molecular Virology, Department of Medicine, Imperial College, London, W2 1NY, UK
| | - Andrew D Beale
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | | | - Jason Day
- Department of Earth Sciences, University of Cambridge, Cambridge, CB2 3EQ, UK
| | - Ana S H Costa
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, UK.,Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Christian Frezza
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Helen C Causton
- Columbia University Medical Center, New York, NY, 10032, USA.
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15
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Limapichat W, Pornthanakasem W, Satitthammachart C, Chitnumsub P, Leartsakulpanich U. Real-time detection of changes in yeast plasma membrane potential using genetically encoded voltage indicator proteins. FEMS Yeast Res 2020; 20:5874255. [PMID: 32691845 DOI: 10.1093/femsyr/foaa041] [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: 12/19/2019] [Accepted: 07/18/2020] [Indexed: 11/12/2022] Open
Abstract
In yeast, adaptation to varying conditions often requires proper regulation of the plasma membrane potential. To determine yeast membrane potential change, optical methods involving potentiometric dyes have been supplemental to the direct electrode-based method. However, the hydrophobic nature of the dyes and their slow distribution across the membrane still limits their utilization. Genetically encoded voltage indicator (GEVI) proteins employed in neuroscience offer a tantalizing alternative for monitoring yeast membrane potential change. In this work, several widely used GEVI proteins were assessed in Saccharomyces cerevisiae for their expression and function as a voltage reporter. Among them, only ArcLight and Accelerated Sensor of Action Potential (ASAP) proteins could be expressed and transported to the plasma membrane. While the voltage-sensing capability was demonstrated for both ArcLight and ASAP, ArcLight fluorescence was sensitive to the intracellular pH change concurrently with the voltage change. Therefore, we established that ASAP is the more suitable GEVI protein for reporting yeast membrane potential change. This voltage-sensing reporter for yeast based on ASAP offers a new effective strategy for real-time optical detection of yeast membrane potential change, which potentially facilitates many areas of yeast research including optimizing growth conditions for industrial use and investigating yeast ion transport system.
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Affiliation(s)
- Walrati Limapichat
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Wichai Pornthanakasem
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Chatchaya Satitthammachart
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Ubolsree Leartsakulpanich
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
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16
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Hou J, Daniels PN, Burke MD. Small Molecule Channels Harness Membrane Potential to Concentrate Potassium in trk1Δtrk2Δ Yeast. ACS Chem Biol 2020; 15:1575-1580. [PMID: 32427463 DOI: 10.1021/acschembio.0c00180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many protein ion channels harness membrane potential to move ions in opposition to their chemical gradient. Deficiencies of such proteins cause several human diseases, including cystic fibrosis, Bartter Syndrome, and proximal renal tubular acidosis. Using yeast as a eukaryotic model system, we asked whether, in the context of a protein ion channel deficiency in vivo, small molecule channels could similarly harness membrane potential to concentrate ions. Trk potassium transporters use membrane potential to move potassium from a relatively low concentration outside cells (∼15 mM) to one of >10× higher inside (150-500 mM); trk1Δtrk2Δ are unable to concentrate potassium or grow in standard media. Here we show that potassium-permeable, but not potassium-selective, small-molecule ion channels formed by amphotericin B can harness membrane potential to concentrate potassium and thereby restore trk1Δtrk2Δ growth. This finding expands the list of potential human channelopathies that might be addressed by a molecular prosthetics approach.
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Affiliation(s)
- Jennifer Hou
- Department of Biochemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Ave., Urbana, Illinois 61801, United States
| | - Page N. Daniels
- Department of Biochemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Ave., Urbana, Illinois 61801, United States
| | - Martin D. Burke
- Department of Biochemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Ave., Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Ave., Urbana, Illinois 61801, United States
- Carle Illinois College of Medicine, 807 South Wright Street, Champaign, Illinois 61820, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 West Gregory Dr., Urbana, Illinois 61801, United States
- Arnold and Mabel Beckman Institute, University of Illinois at Urbana−Champaign, 405 North Mathews Ave., Urbana, Illinois 61801, United States
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17
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Jones SM, Heppner DE, Vu K, Kosman DJ, Solomon EI. Rapid Decay of the Native Intermediate in the Metallooxidase Fet3p Enables Controlled Fe II Oxidation for Efficient Metabolism. J Am Chem Soc 2020; 142:10087-10101. [PMID: 32379440 DOI: 10.1021/jacs.0c02384] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The multicopper oxidases (MCOs) couple four 1e- oxidations of substrate to the 4e- reduction of O2 to H2O. These divide into two groups: those that oxidize organic substrates with high turnover frequencies (TOFs) up to 560 s-1 and those that oxidize metal ions with low TOFs, ∼1 s-1 or less. The catalytic mechanism of the organic oxidases has been elucidated, and the high TOF is achieved through rapid intramolecular electron transfer (IET) to the native intermediate (NI), which only slowly decays to the resting form. Here, we uncover the factors that govern the low TOF in Fet3p, a prototypical metallooxidase, in the context of the MCO mechanism. We determine that the NI decays rapidly under optimal turnover conditions, and the mechanism thereby becomes rate-limited by slow IET to the resting enzyme. Development of a catalytic model leads to the important conclusions that proton delivery to the NI controls the mechanism and enables the slow turnover in Fet3p that is functionally significant in Fe metabolism enabling efficient ferroxidase activity while avoiding ROS generation.
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Affiliation(s)
- Stephen M Jones
- Department of Chemistry, Stanford University, 333 Campus Drive Stanford, California 94305, United States
| | - David E Heppner
- Department of Chemistry, Stanford University, 333 Campus Drive Stanford, California 94305, United States
| | - Kenny Vu
- Department of Biochemistry, The University at Buffalo, 140 Farber Hall, 3435 Main Street, Buffalo, New York 14214, United States
| | - Daniel J Kosman
- Department of Biochemistry, The University at Buffalo, 140 Farber Hall, 3435 Main Street, Buffalo, New York 14214, United States
| | - Edward I Solomon
- Department of Chemistry, Stanford University, 333 Campus Drive Stanford, California 94305, United States
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18
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Mohajeri Amiri M, Fazeli MR, Babaee T, Amini M, Hayati Roodbari N, Mousavi SB, Samadi N. Production of Vitamin D 3 Enriched Biomass of Saccharomyces Cerevisiae as A Potential Food Supplement: Evaluation and Optimization of Culture Conditions Using Plackett-Burman and Response Surface Methodological Approaches. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2019; 18:974-987. [PMID: 31531078 PMCID: PMC6706739 DOI: 10.22037/ijpr.2019.1100660] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Vitamin D deficiency causes osteoporosis, osteopenia, fractures, rickets, and more recently is linked with some chronic illnesses such as cancer. Because of the safety and probiotic properties of the yeast Saccharomyces cerevisiae, we hypothesized that yeast cells enriched with cholecalciferol (vitamin D3) could represent a solution for prevention or treatment of vitamin D deficiency. In this study S. cerevisiae was used as a vitamin D3 accumulator for the first time and the optimal conditions for enrichment of S. cerevisiae were determined. The Plackett-Burman screening studies were used for selection of the most important factors affecting cholecalciferol entrapment. Response surface methodology was employed for optimization of cholecalciferol accumulation in S. cerevisiae cells by using Box-Behnken design. A modified quadratic polynomial model fit the data appropriately. The optimal points of variables to maximize the response were cholecalciferol initial concentration of 358021.16 IU/mL, tryptone concentration of 1.82 g/L, sucrose concentration of 7.13 % (w/v), and shaking speed of 140.46 rpm. The maximum amount of cholecalciferol in dry cell weight of S. cerevisiae was 4428.11 IU/g. The cholecalciferol entrapment in yeast biomass increased about two-folds in optimized condition which indicates efficiency of optimization.
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Affiliation(s)
- Morteza Mohajeri Amiri
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohammad Reza Fazeli
- Department of Drug and Food Control, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Tahereh Babaee
- Department of Drug and Food Control, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohsen Amini
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Nasim Hayati Roodbari
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Seyed Babak Mousavi
- Biotechnology Group, Chemical Engineering Department, Tarbiat Modares University, Tehran, Iran
| | - Nasrin Samadi
- Department of Drug and Food Control, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.,Pharmaceutical Quality Assurance Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
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19
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Żywicka A, Wenelska K, Junka A, Czajkowska J, Fijałkowski K. An efficient method of Yarrowia lipolytica immobilization using oil- and emulsion-modified bacterial cellulose carriers. ELECTRON J BIOTECHN 2019. [DOI: 10.1016/j.ejbt.2019.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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20
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Immobilization pattern of morphologically different microorganisms on bacterial cellulose membranes. World J Microbiol Biotechnol 2019; 35:11. [PMID: 30604023 DOI: 10.1007/s11274-018-2584-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 12/18/2018] [Indexed: 10/27/2022]
Abstract
The aim of this study was to assess the immobilization pattern of microorganisms characterized by varying cell shapes and sizes (rod-shaped bacteria Lactobacillus delbruecki, spherical-shaped yeast Saccharomyces cerevisiae and hyphae forms of Yarrowia lipolytica) on bacterial cellulose of various material properties. The 'adsorption-incubation' method was used for the purposes of immobilization. The immobilization pattern included adsorption efficiency, ability of the immobilized cells to multiply within the carrier expressed as incubation efficiency and the degree of release of the immobilized cells from the carrier. The efficiency of adsorption and incubation was affected by the morphology of the immobilized cells and increased together with cellulose surface area. For smaller bacterial cells a higher level of loading was obtained on the same surface as compared to larger yeast cells. During incubation, the number of immobilized bacterial and yeast cells increased significantly in comparison to the number of cells adsorbed on the carrier during the adsorption step. Despite the morphological differences between the S. cerevisiae and Y. lipolytica cells, there were no statistically significant differences in the efficiency of adsorption and incubation. It was also revealed that the release ratio values obtained for L. delbruecki and S. cerevisiae increased along with cellulose surface area. Interestingly, Y. lipolytica cells in the pseudohyphae and hyphae forms penetrated deeply into the three-dimensional network of BC nanofibrils which prevented subsequent cell release. It was confirmed that carrier selection must be individually matched to the type of immobilized cells based especially on its porosity-related parameters.
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21
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Flowers TJ, Glenn EP, Volkov V. Could vesicular transport of Na+ and Cl- be a feature of salt tolerance in halophytes? ANNALS OF BOTANY 2019; 123:1-18. [PMID: 30247507 PMCID: PMC6344095 DOI: 10.1093/aob/mcy164] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 08/10/2018] [Indexed: 05/18/2023]
Abstract
Background Halophytes tolerate external salt concentrations of 200 mm and more, accumulating salt concentrations of 500 mm and more in their shoots; some, recretohalophytes, excrete salt through glands on their leaves. Ions are accumulated in central vacuoles, but the pathway taken by these ions from the outside of the roots to the vacuoles inside the cells is poorly understood. Do the ions cross membranes through ion channels and transporters or move in vesicles, or both? Vesicular transport from the plasma membrane to the vacuole would explain how halophytes avoid the toxicity of high salt concentrations on metabolism. There is also a role for vesicles in the export of ions via salt glands. Scope and Methods We have collected data on the fluxes of sodium and chloride ions in halophytes, based on the weight of the transporting organs and on the membrane area across which the flux occurs; the latter range from 17 nmol m-2 s-1 to 4.2 μmol m-2 s-1 and values up to 1 μmol m-2 s-1 need to be consistent with whatever transport system is in operation. We have summarized the sizes and rates of turnover of vesicles in plants, where clathrin-independent vesicles are 100 nm or more in diameter and can merge with the plasma membrane at rates of 100 s-1. We gathered evidence for vesicular transport of ions in halophytes and evaluated whether vesicular transport could account for the observable fluxes. Conclusions There is strong evidence in favour of vesicular transport in plants and circumstantial evidence in favour of the movement of ions in vesicles. Estimated rates of vesicle turnover could account for ion transport at the lower reported fluxes (around 20 nmol m-2 s-1), but the higher fluxes may require vesicles of the order of 1 μm or more in diameter. The very high fluxes reported in some salt glands might be an artefact of the way they were measured.
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Affiliation(s)
- Timothy J Flowers
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA, Australia
| | - Edward P Glenn
- Environmental Research Laboratory of the University of Arizona, 1601 East, Airport Drive, Tucson, AZ, USA
| | - Vadim Volkov
- Faculty of Life Sciences and Computing, London Metropolitan University, London N7, UK
- Department of Plant Sciences, College of Agricultural and Environmental Sciences, University of California, Davis, CA, USA
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22
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23
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Lavaisse LM, Hollmann A, Nazareno MA, Disalvo EA. Zeta potential changes of Saccharomyces cerevisiae during fermentative and respiratory cycles. Colloids Surf B Biointerfaces 2018; 174:63-69. [PMID: 30439639 DOI: 10.1016/j.colsurfb.2018.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 01/31/2023]
Abstract
Saccharomyces cerevisiae is a type of yeast, widely used in diverse biotechnological food-beverage processes. Although the performance of an industrial fermentation process depends largely on the number of cells, it is necessary to consider the physiological state of the cultures. In this context, the aim of this study was to determine in a yeast culture how factors such as growth conditions affect surface properties at the different growth stages. Our results show that, S. cerevisiae spp. exhibits different zeta potential mean values along the exponential, post-diauxic and stationary growth phases. In addition, there were differences depending on whether they are in aerobic or anaerobic conditions. When the effect of pH on the media was studied, a different dependence of zeta potential at each stage reveals that in the living cells the surface potential depends on the interaction between secreted acids and the constituents of the surfaces, according to the growth conditions. In order to have a view at the cellular level, the zeta potential on individual cells by optical microscopy has been determined at different stages of culture in aerobic and anaerobic conditions. This single-cell method allows for the identification and following of the development of different cell subpopulations during each growth stage. Furthermore, the behavior of the dead cells provided evidence to relate the large negatively charged population with cell wall damage. Overall, the results obtained in the present work represent an important milestone for a novel application of zeta potential technique on yeast.
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Affiliation(s)
- Lucía M Lavaisse
- Laboratory of Applied Biophysics, CIBAAL - National University of Santiago del Estero and CONICET, 4206, RN 9 Km 1125, Santiago del Estero, Argentina; Laboratory of Antioxidants and Oxidative Process, Institute of Chemical Sciences, Faculty of Agronomy and Agroindustries, National University of Santiago del Estero and CONICET, 4206, RN 9 Km 1125, Santiago del Estero, Argentina
| | - Axel Hollmann
- Laboratory of Bioactive Compounds, CIBAAL - National University of Santiago del Estero and CONICET, 4206, RN 9 Km 1125, Santiago del Estero, Argentina; Laboratory of Molecular Microbiology, Institute of Basic and Applied Microbiology, National University of Quilmes, B1876BXD Bernal, Argentina.
| | - Mónica A Nazareno
- Laboratory of Antioxidants and Oxidative Process, Institute of Chemical Sciences, Faculty of Agronomy and Agroindustries, National University of Santiago del Estero and CONICET, 4206, RN 9 Km 1125, Santiago del Estero, Argentina
| | - Edgardo A Disalvo
- Laboratory of Applied Biophysics, CIBAAL - National University of Santiago del Estero and CONICET, 4206, RN 9 Km 1125, Santiago del Estero, Argentina
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24
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Busto JV, Elting A, Haase D, Spira F, Kuhlman J, Schäfer-Herte M, Wedlich-Söldner R. Lateral plasma membrane compartmentalization links protein function and turnover. EMBO J 2018; 37:embj.201899473. [PMID: 29976762 DOI: 10.15252/embj.201899473] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 06/08/2018] [Accepted: 06/08/2018] [Indexed: 11/09/2022] Open
Abstract
Biological membranes organize their proteins and lipids into nano- and microscale patterns. In the yeast plasma membrane (PM), constituents segregate into a large number of distinct domains. However, whether and how this intricate patchwork contributes to biological functions at the PM is still poorly understood. Here, we reveal an elaborate interplay between PM compartmentalization, physiological function, and endocytic turnover. Using the methionine permease Mup1 as model system, we demonstrate that this transporter segregates into PM clusters. Clustering requires sphingolipids, the tetraspanner protein Nce102, and signaling through TORC2. Importantly, we show that during substrate transport, a simple conformational change in Mup1 mediates rapid relocation into a unique disperse network at the PM Clustered Mup1 is protected from turnover, whereas relocated Mup1 actively recruits the endocytic machinery thereby initiating its own turnover. Our findings suggest that lateral compartmentalization provides an important regulatory link between function and turnover of PM proteins.
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Affiliation(s)
- Jon V Busto
- Institute of Cell Dynamics and Imaging, Cells-In-Motion Cluster of Excellence (EXC1003 - CiM), University of Münster, Münster, Germany.,Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry, University of the Basque Country, Leioa, Spain
| | - Annegret Elting
- Institute of Cell Dynamics and Imaging, Cells-In-Motion Cluster of Excellence (EXC1003 - CiM), University of Münster, Münster, Germany
| | - Daniel Haase
- Institute of Cell Dynamics and Imaging, Cells-In-Motion Cluster of Excellence (EXC1003 - CiM), University of Münster, Münster, Germany
| | - Felix Spira
- Institute of Cell Dynamics and Imaging, Cells-In-Motion Cluster of Excellence (EXC1003 - CiM), University of Münster, Münster, Germany
| | - Julian Kuhlman
- Institute of Cell Dynamics and Imaging, Cells-In-Motion Cluster of Excellence (EXC1003 - CiM), University of Münster, Münster, Germany
| | - Marco Schäfer-Herte
- Institute of Cell Dynamics and Imaging, Cells-In-Motion Cluster of Excellence (EXC1003 - CiM), University of Münster, Münster, Germany
| | - Roland Wedlich-Söldner
- Institute of Cell Dynamics and Imaging, Cells-In-Motion Cluster of Excellence (EXC1003 - CiM), University of Münster, Münster, Germany
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25
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Mackie TD, Brodsky JL. Investigating Potassium Channels in Budding Yeast: A Genetic Sandbox. Genetics 2018; 209:637-650. [PMID: 29967058 PMCID: PMC6028241 DOI: 10.1534/genetics.118.301026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 05/15/2018] [Indexed: 12/26/2022] Open
Abstract
Like all species, the model eukaryote Saccharomyces cerevisiae, or Bakers' yeast, concentrates potassium in the cytosol as an electrogenic osmolyte and enzyme cofactor. Yeast are capable of robust growth on a wide variety of potassium concentrations, ranging from 10 µM to 2.5 M, due to the presence of a high-affinity potassium uptake system and a battery of cation exchange transporters. Genetic perturbation of either of these systems retards yeast growth on low or high potassium, respectively. However, these potassium-sensitized yeast are a powerful genetic tool, which has been leveraged for diverse studies. Notably, the potassium-sensitive cells can be transformed with plasmids encoding potassium channels from bacteria, plants, or mammals, and subsequent changes in growth rate have been found to correlate with the activity of the introduced potassium channel. Discoveries arising from the use of this assay over the past three decades have increased our understanding of the structure-function relationships of various potassium channels, the mechanisms underlying the regulation of potassium channel function and trafficking, and the chemical basis of potassium channel modulation. In this article, we provide an overview of the major genetic tools used to study potassium channels in S. cerevisiae, a survey of seminal studies utilizing these tools, and a prospective for the future use of this elegant genetic approach.
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Affiliation(s)
- Timothy D Mackie
- Department of Biological Sciences, University of Pittsburgh, Pennsylvania 15260
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pennsylvania 15260
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26
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Guerrero-Galán C, Garcia K, Houdinet G, Zimmermann SD. HcTOK1 participates in the maintenance of K + homeostasis in the ectomycorrhizal fungus Hebeloma cylindrosporum, which is essential for the symbiotic K + nutrition of Pinus pinaster. PLANT SIGNALING & BEHAVIOR 2018; 13:e1480845. [PMID: 29939816 PMCID: PMC6110361 DOI: 10.1080/15592324.2018.1480845] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/16/2018] [Indexed: 05/23/2023]
Abstract
Most land plants rely on root symbioses to complement or improve their mineral nutrition. Recent researches have put forward that mycorrhizal fungi efficiently absorb and transfer potassium (K+) from the soil to host plant roots, but the molecular mechanisms involved are not completely elucidated yet. We have recently revealed that K+ is likely released from the fungal Hartig net to the plant by TOK channels in the ectomycorrhizal model Hebeloma cylindrosporum - Pinus pinaster. H. cylindrosporum harbours three TOK members. Herein, we report that one of them, HcTOK1, has similar features than the yeast ScTOK1. Moreover, we propose a role for this channel in the transport of K+ from the medium to ectomycorrhizal roots under K+ starvation.
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Affiliation(s)
- C. Guerrero-Galán
- BPMP, Univ Montpellier, CNRS, INRA, Montpellier SupAgro, Montpellier, France
| | - K. Garcia
- Biology and Microbiology Department, South Dakota State University, Brookings, South Dakota USA
| | - G. Houdinet
- BPMP, Univ Montpellier, CNRS, INRA, Montpellier SupAgro, Montpellier, France
| | - S. D. Zimmermann
- BPMP, Univ Montpellier, CNRS, INRA, Montpellier SupAgro, Montpellier, France
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27
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Zahumenský J, Jančíková I, Drietomská A, Švenkrtová A, Hlaváček O, Hendrych T, Plášek J, Sigler K, Gášková D. Yeast Tok1p channel is a major contributor to membrane potential maintenance under chemical stress. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1974-1985. [PMID: 28669766 DOI: 10.1016/j.bbamem.2017.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 06/02/2017] [Accepted: 06/27/2017] [Indexed: 11/17/2022]
Abstract
Tok1p is a highly specific yeast plasma membrane potassium channel with strong outward directionality. Its opening is induced by membrane depolarization. Although the biophysical properties of Tok1p are well-described, its potentially important physiological role is currently largely unexplored. To address this issue, we examined the Tok1p activity following chemically-induced depolarization by measuring changes of plasma membrane potential (ΔΨ) using the diS-C3(3) fluorescence assay in a Tok1p-expressing and a Tok1p-deficient strain. We report that Tok1p channel activity in response to chemical stress does not depend solely on the extent of depolarization, as might have been expected, but may also be negatively influenced by accompanying effects of the used compound. The stressors may interact with the plasma membrane or the channel itself, or cause cytosolic acidification. All of these effects may negatively influence the Tok1p channel opening. While ODDC-induced depolarization exhibits the cleanest Tok1p activation, restoring an astonishing 75% of lost ΔΨ, higher BAC concentrations reduce Tok1p activity, probably because of direct interactions with the channel and/or its lipid microenvironment. This is not only the first study of the physiological role of Tok1p in ΔΨ maintenance under chemical stress, but also the first estimate of the extent of depolarization the channel is able to counterbalance.
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Affiliation(s)
- Jakub Zahumenský
- Charles University, Faculty of Mathematics and Physics, Institute of Physics, Prague 121 16, Czech Republic
| | - Iva Jančíková
- Charles University, Faculty of Mathematics and Physics, Institute of Physics, Prague 121 16, Czech Republic
| | - Andrea Drietomská
- Charles University, Faculty of Mathematics and Physics, Institute of Physics, Prague 121 16, Czech Republic
| | - Andrea Švenkrtová
- Institute of Microbiology, CR Academy of Sciences, Prague 142 20, Czech Republic; Institute of Chemical Technology, Faculty of Food and Biochemical Technology, Prague 166 28, Czech Republic
| | - Otakar Hlaváček
- Institute of Microbiology, CR Academy of Sciences, Prague 142 20, Czech Republic
| | - Tomáš Hendrych
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague 128 44, Czech Republic
| | - Jaromír Plášek
- Charles University, Faculty of Mathematics and Physics, Institute of Physics, Prague 121 16, Czech Republic
| | - Karel Sigler
- Institute of Microbiology, CR Academy of Sciences, Prague 142 20, Czech Republic
| | - Dana Gášková
- Charles University, Faculty of Mathematics and Physics, Institute of Physics, Prague 121 16, Czech Republic.
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28
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Mohajeri Amiri M, Fazeli MR, Amini M, Hayati Roodbari N, Samadi N. Optimization of Culture Conditions for Enrichment of Saccharomyces cerevisiae with Dl-α-Tocopherol by Response Surface Methodology. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2017; 16:1546-1554. [PMID: 29552063 PMCID: PMC5843316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Designing enriched probiotic supplements may have some advantages including protection of probiotic microorganism from oxidative destruction, improving enzyme activity of the gastrointestinal tract, and probably increasing half-life of micronutrient. In this study Saccharomyces cerevisiae enriched with dl-α-tocopherol was produced as an accumulator and transporter of a lipid soluble vitamin for the first time. By using one variable at the time screening studies, three independent variables were selected. Optimization of the level of dl-α-tocopherol entrapment in S. cerevisiae cells was performed by using Box-Behnken design via design expert software. A modified quadratic polynomial model appropriately fit the data. The convex shape of three-dimensional plots reveal that we could calculate the optimal point of the response in the range of parameters. The optimum points of independent parameters to maximize the response were dl-α-tocopherol initial concentration of 7625.82 µg/mL, sucrose concentration of 6.86 % w/v, and shaking speed of 137.70 rpm. Under these conditions, the maximum level of dl-α-tocopherol in dry cell weight of S. cerevisiae was 5.74 µg/g. The resemblance between the R-squared and adjusted R-squared and acceptable value of C.V% revealed acceptability and accuracy of the model.
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Affiliation(s)
- Morteza Mohajeri Amiri
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran.
| | - Mohammad Reza Fazeli
- Department of Drug and Food Control, Faculty of Pharmacy and Pharmaceutical Quality Assurance Research Center, Tehran University of Medical Sciences, Tehran, Iran.
| | - Mohsen Amini
- Department of Medicinal Chemistry, Faculty of Pharmacy and Drug Design and Development Research Center, Tehran University of Medical Sciences, Tehran, Iran.
| | - Nasim Hayati Roodbari
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran.
| | - Nasrin Samadi
- Department of Drug and Food Control, Faculty of Pharmacy and Pharmaceutical Quality Assurance Research Center, Tehran University of Medical Sciences, Tehran, Iran. ,Corresponding author: E-mail:
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Cho T, Ishii-Kato A, Fukata Y, Nakayama Y, Iida K, Fukata M, Iida H. Coupling of a voltage-gated Ca 2+ channel homologue with a plasma membrane H + -ATPase in yeast. Genes Cells 2016; 22:94-104. [PMID: 27935186 DOI: 10.1111/gtc.12458] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/08/2016] [Indexed: 01/04/2023]
Abstract
Yeast has a homologue of mammalian voltage-gated Ca2+ channels (VGCCs), enabling the efficient uptake of Ca2+ . It comprises two indispensable subunits, Cch1 and Mid1, equivalent to the mammalian pore-forming α1 and auxiliary α2 /δ subunits, respectively. Unlike the physiological roles of Cch1/Mid1 channels, the regulatory mechanisms of the yeast VGCC homologue remain unclear. Therefore, we screened candidate proteins that interact with Mid1 by an unbiased proteomic approach and identified a plasma membrane H+ -ATPase, Pma1, as a candidate. Mid1 coimmunoprecipitated with Pma1, and Mid1-EGFP colocalized with Pma1-mCherry at the plasma membrane. The physiological relevance of their interaction was determined using the temperature-sensitive mutant, pma1-10. At the nonpermissive temperature, the membrane potential was less negative and Ca2+ uptake was lower in pma1-10 than in wild-type cells. Increased extracellular H+ increased the rate of Ca2+ uptake. Therefore, H+ extrusion by Pma1 may be important for Ca2+ influx through Cch1/Mid1. These results suggest that Pma1 interacts physically with Cch1/Mid1 Ca2+ channels to enhance their activity via its H+ -pumping activity.
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Affiliation(s)
- Toshihiko Cho
- Department of Biology, Tokyo Gakugei University, 4-1-1 Nukui kita-machi, Koganei-shi, Tokyo, 184-8501, Japan
| | - Aya Ishii-Kato
- Department of Biology, Tokyo Gakugei University, 4-1-1 Nukui kita-machi, Koganei-shi, Tokyo, 184-8501, Japan
| | - Yuko Fukata
- Division of Membrane Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, 444-8787, Japan.,Department of Physiological Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, 444-8787, Japan
| | - Yoshitaka Nakayama
- Department of Biology, Tokyo Gakugei University, 4-1-1 Nukui kita-machi, Koganei-shi, Tokyo, 184-8501, Japan
| | - Kazuko Iida
- Laboratory of Biomembrane, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya, Tokyo, 156-8506, Japan
| | - Masaki Fukata
- Division of Membrane Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, 444-8787, Japan.,Department of Physiological Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, 444-8787, Japan
| | - Hidetoshi Iida
- Department of Biology, Tokyo Gakugei University, 4-1-1 Nukui kita-machi, Koganei-shi, Tokyo, 184-8501, Japan
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