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Papouskova K, Zimmermannova O, Sychrova H. Distinct regions of its first intracellular loop contribute to the proper localization, transport activity and substrate-affinity adjustment of the main yeast K + importer Trk1. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184369. [PMID: 38969203 DOI: 10.1016/j.bbamem.2024.184369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 06/04/2024] [Accepted: 07/01/2024] [Indexed: 07/07/2024]
Abstract
Trk1 is the main K+ importer of Saccharomyces cerevisiae. Its proper functioning enables yeast cells to grow in environments with micromolar amounts of K+. Although the structure of Trk1 has not been experimentally determined, the transporter is predicted to be composed of four MPM (transmembrane segment - pore loop - transmembrane segment) motifs which are connected by intracellular loops. Of those, in particular the first loop (IL1) is unique in its length; it forms more than half of the entire protein. The deletion of the majority of IL1 does not abolish the transport activity of Trk1. However IL1 is thought to be involved in the modulation of the transporter's functioning. In this work, we prepared a series of internally shortened versions of Trk1 that lacked various parts of IL1, and we studied their properties in S. cerevisiae cells without chromosomal copies of TRK genes. Using this approach, we were able to determine that both N- and C-border regions of IL1 are necessary for the proper localization of Trk1. Moreover, the N-border part of IL1 is also important for the functioning of Trk1, as its absence resulted in a decrease in the transporter's substrate affinity. In addition, in the internal part of IL1, we newly identified a stretch of amino-acid residues that are indispensable for retaining the transporter's maximum velocity, and another region whose deletion affected the ability of Trk1 to adjust its affinity in response to external levels of K+.
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Affiliation(s)
- Klara Papouskova
- Laboratory of Membrane Transport, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague 4, Czech Republic.
| | - Olga Zimmermannova
- Laboratory of Membrane Transport, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague 4, Czech Republic.
| | - Hana Sychrova
- Laboratory of Membrane Transport, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague 4, Czech Republic.
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Antunes M, Sá-Correia I. The role of ion homeostasis in adaptation and tolerance to acetic acid stress in yeasts. FEMS Yeast Res 2024; 24:foae016. [PMID: 38658183 PMCID: PMC11092280 DOI: 10.1093/femsyr/foae016] [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: 03/19/2024] [Revised: 04/16/2024] [Accepted: 04/23/2024] [Indexed: 04/26/2024] Open
Abstract
Maintenance of asymmetric ion concentrations across cellular membranes is crucial for proper yeast cellular function. Disruptions of these ionic gradients can significantly impact membrane electrochemical potential and the balance of other ions, particularly under stressful conditions such as exposure to acetic acid. This weak acid, ubiquitous to both yeast metabolism and industrial processes, is a major inhibitor of yeast cell growth in industrial settings and a key determinant of host colonization by pathogenic yeast. Acetic acid toxicity depends on medium composition, especially on the pH (H+ concentration), but also on other ions' concentrations. Regulation of ion fluxes is essential for effective yeast response and adaptation to acetic acid stress. However, the intricate interplay among ion balancing systems and stress response mechanisms still presents significant knowledge gaps. This review offers a comprehensive overview of the mechanisms governing ion homeostasis, including H+, K+, Zn2+, Fe2+/3+, and acetate, in the context of acetic acid toxicity, adaptation, and tolerance. While focus is given on Saccharomyces cerevisiae due to its extensive physiological characterization, insights are also provided for biotechnologically and clinically relevant yeast species whenever available.
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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, 1049-001, Lisbon, Portugal
| | - 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, 1049-001, Lisbon, Portugal
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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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Papoušková K, Gómez M, Kodedová M, Ramos J, Zimmermannová O, Sychrová H. Heterologous expression reveals unique properties of Trk K + importers from nonconventional biotechnologically relevant yeast species together with their potential to support Saccharomyces cerevisiae growth. Yeast 2023; 40:68-83. [PMID: 36539385 DOI: 10.1002/yea.3834] [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: 10/31/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
In the model yeast Saccharomyces cerevisiae, Trk1 is the main K+ importer. It is involved in many important physiological processes, such as the maintenance of ion homeostasis, cell volume, intracellular pH, and plasma-membrane potential. The ScTrk1 protein can be of great interest to industry, as it was shown that changes in its activity influence ethanol production and tolerance in S. cerevisiae and also cell performance in the presence of organic acids or high ammonium under low K+ conditions. Nonconventional yeast species are attracting attention due to their unique properties and as a potential source of genes that encode proteins with unusual characteristics. In this work, we aimed to study and compare Trk proteins from Debaryomyces hansenii, Hortaea werneckii, Kluyveromyces marxianus, and Yarrowia lipolytica, four biotechnologically relevant yeasts that tolerate various extreme environments. Heterologous expression in S. cerevisiae cells lacking the endogenous Trk importers revealed differences in the studied Trk proteins' abilities to support the growth of cells under various cultivation conditions such as low K+ or the presence of toxic cations, to reduce plasma-membrane potential or to take up Rb+ . Examination of the potential of Trks to support the stress resistance of S. cerevisiae wild-type strains showed that Y. lipolytica Trk1 is a promising tool for improving cell tolerance to both low K+ and high salt and that the overproduction of S. cerevisiae's own Trk1 was the most efficient at improving the growth of cells in the presence of highly toxic Li+ ions.
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Affiliation(s)
- Klára Papoušková
- Laboratory of Membrane Transport, Institute of Physiology of the Czech Academy of Sciences, Prague 4, Czech Republic
| | - Marcos Gómez
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, Córdoba, Spain
| | - Marie Kodedová
- Laboratory of Membrane Transport, Institute of Physiology of the Czech Academy of Sciences, Prague 4, Czech Republic
| | - José Ramos
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, Córdoba, Spain
| | - Olga Zimmermannová
- Laboratory of Membrane Transport, Institute of Physiology of the Czech Academy of Sciences, Prague 4, Czech Republic
| | - Hana Sychrová
- Laboratory of Membrane Transport, Institute of Physiology of the Czech Academy of Sciences, Prague 4, Czech Republic
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Masaryk J, Kale D, Pohl P, Ruiz-Castilla FJ, Zimmermannová O, Obšilová V, Ramos J, Sychrová H. The second intracellular loop of the yeast Trk1 potassium transporter is involved in regulation of activity, and interaction with 14-3-3 proteins. Comput Struct Biotechnol J 2023; 21:2705-2716. [PMID: 37168872 PMCID: PMC10165143 DOI: 10.1016/j.csbj.2023.04.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/19/2023] [Accepted: 04/19/2023] [Indexed: 05/13/2023] Open
Abstract
Potassium is an essential intracellular ion, and a sufficient intracellular concentration of it is crucial for many processes; therefore it is fundamental for cells to precisely regulate K+ uptake and efflux through the plasma membrane. The uniporter Trk1 is a key player in K+ acquisition in yeasts. The TRK1 gene is expressed at a low and stable level; thus the activity of the transporter needs to be regulated at a posttranslational level. S. cerevisiae Trk1 changes its activity and affinity for potassium ion quickly and according to both internal and external concentrations of K+, as well as the membrane potential. The molecular basis of these changes has not been elucidated, though phosphorylation is thought to play an important role. In this study, we examined the role of the second, short, and highly conserved intracellular hydrophilic loop of Trk1 (IL2), and identified two phosphorylable residues (Ser882 and Thr900) as very important for 1) the structure of the loop and consequently for the targeting of Trk1 to the plasma membrane, and 2) the upregulation of the transporter's activity reaching maximal affinity under low external K+ conditions. Moreover, we identified three residues (Thr155, Ser414, and Thr900) within the Trk1 protein as strong candidates for interaction with 14-3-3 regulatory proteins, and showed, in an in vitro experiment, that phosphorylated Thr900 of the IL2 indeed binds to both isoforms of yeast 14-3-3 proteins, Bmh1 and Bmh2.
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Affiliation(s)
- Jakub Masaryk
- Institute of Physiology of the Czech Academy of Sciences, Laboratory of Membrane Transport, 14200 Prague 4, Czech Republic
| | - Deepika Kale
- Institute of Physiology of the Czech Academy of Sciences, Laboratory of Membrane Transport, 14200 Prague 4, Czech Republic
| | - Pavel Pohl
- Institute of Physiology of the Czech Academy of Sciences, Laboratory of Structural Biology of Signaling Proteins, Division BIOCEV, 25250 Vestec, Czech Republic
| | - Francisco J. Ruiz-Castilla
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, 140 71 Córdoba, Spain
| | - Olga Zimmermannová
- Institute of Physiology of the Czech Academy of Sciences, Laboratory of Membrane Transport, 14200 Prague 4, Czech Republic
| | - Veronika Obšilová
- Institute of Physiology of the Czech Academy of Sciences, Laboratory of Structural Biology of Signaling Proteins, Division BIOCEV, 25250 Vestec, Czech Republic
| | - José Ramos
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, 140 71 Córdoba, Spain
| | - Hana Sychrová
- Institute of Physiology of the Czech Academy of Sciences, Laboratory of Membrane Transport, 14200 Prague 4, Czech Republic
- Corresponding author.
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Kulik N, Kale D, Spurna K, Shamayeva K, Hauser F, Milic S, Janout H, Zayats V, Jacak J, Ludwig J. Dimerisation of the Yeast K + Translocation Protein Trk1 Depends on the K + Concentration. Int J Mol Sci 2022; 24:ijms24010398. [PMID: 36613841 PMCID: PMC9820094 DOI: 10.3390/ijms24010398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/16/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
In baker's yeast (Saccharomyces cerevisiae), Trk1, a member of the superfamily of K-transporters (SKT), is the main K+ uptake system under conditions when its concentration in the environment is low. Structurally, Trk1 is made up of four domains, each similar and homologous to a K-channel α subunit. Because most K-channels are proteins containing four channel-building α subunits, Trk1 could be functional as a monomer. However, related SKT proteins TrkH and KtrB were crystallised as dimers, and for Trk1, a tetrameric arrangement has been proposed based on molecular modelling. Here, based on Bimolecular Fluorescence Complementation experiments and single-molecule fluorescence microscopy combined with molecular modelling; we provide evidence that Trk1 can exist in the yeast plasma membrane as a monomer as well as a dimer. The association of monomers to dimers is regulated by the K+ concentration.
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Affiliation(s)
- Natalia Kulik
- Institute of Microbiology of the Czech Academy of Sciences, Zamek 136, 3733 Nove Hrady, Czech Republic
| | - Deepika Kale
- Institute of Microbiology of the Czech Academy of Sciences, Zamek 136, 3733 Nove Hrady, Czech Republic
| | - Karin Spurna
- Institute of Microbiology of the Czech Academy of Sciences, Zamek 136, 3733 Nove Hrady, Czech Republic
| | - Katsiaryna Shamayeva
- Institute of Microbiology of the Czech Academy of Sciences, Zamek 136, 3733 Nove Hrady, Czech Republic
| | - Fabian Hauser
- School of Medical Engineering and Applied Social Sciences, University of Applied Sciences Upper Austria, Garnisonstr, 21, 4020 Linz, Austria
| | - Sandra Milic
- School of Medical Engineering and Applied Social Sciences, University of Applied Sciences Upper Austria, Garnisonstr, 21, 4020 Linz, Austria
| | - Hannah Janout
- Bioinformatics, University of Applied Sciences Upper Austria, 4232 Hagenberg, Austria
- Institute of Symbolic AI, Johannes Kepler University, 4040 Linz, Austria
| | - Vasilina Zayats
- Institute of Microbiology of the Czech Academy of Sciences, Zamek 136, 3733 Nove Hrady, Czech Republic
| | - Jaroslaw Jacak
- School of Medical Engineering and Applied Social Sciences, University of Applied Sciences Upper Austria, Garnisonstr, 21, 4020 Linz, Austria
| | - Jost Ludwig
- Institute of Microbiology of the Czech Academy of Sciences, Zamek 136, 3733 Nove Hrady, Czech Republic
- Correspondence:
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Cai H, Zhang H, Guo DH, Wang Y, Gu J. Genomic Data Mining Reveals Abundant Uncharacterized Transporters in Coccidioides immitis and Coccidioides posadasii. J Fungi (Basel) 2022; 8:jof8101064. [PMID: 36294626 PMCID: PMC9604845 DOI: 10.3390/jof8101064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/01/2022] [Accepted: 10/08/2022] [Indexed: 11/16/2022] Open
Abstract
Coccidioides immitis and Coccidioides posadasii are causative agents of coccidioidomycosis, commonly known as Valley Fever. The increasing Valley Fever cases in the past decades, the expansion of endemic regions, and the rising azole drug-resistant strains have underscored an urgent need for a better understanding of Coccidioides biology and new antifungal strategies. Transporters play essential roles in pathogen survival, growth, infection, and adaptation, and are considered as potential drug targets. However, the composition and roles of transport machinery in Coccidioides remain largely unknown. In this study, genomic data mining revealed an abundant, uncharacterized repertoire of transporters in Coccidioides genomes. The catalog included 1288 and 1235 transporter homologs in C. immitis and C. posadasii, respectively. They were further annotated to class, subclass, family, subfamily and range of substrates based on the Transport Classification (TC) system. They may play diverse roles in nutrient uptake, metabolite secretion, ion homeostasis, drug efflux, or signaling. This study represents an initial effort for a systems-level characterization of the transport machinery in these understudied fungal pathogens.
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Affiliation(s)
- Hong Cai
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Daniel H. Guo
- Strake Jesuit College Preparatory, Houston, TX 77036, USA
| | - Yufeng Wang
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA
- Correspondence: (Y.W.); (J.G.)
| | - Jianying Gu
- Department of Biology, College of Staten Island, City University of New York, Staten Island, New York, NY 10314, USA
- Correspondence: (Y.W.); (J.G.)
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Mota MN, Múgica P, Sá-Correia I. Exploring Yeast Diversity to Produce Lipid-Based Biofuels from Agro-Forestry and Industrial Organic Residues. J Fungi (Basel) 2022; 8:jof8070687. [PMID: 35887443 PMCID: PMC9315891 DOI: 10.3390/jof8070687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 12/04/2022] Open
Abstract
Exploration of yeast diversity for the sustainable production of biofuels, in particular biodiesel, is gaining momentum in recent years. However, sustainable, and economically viable bioprocesses require yeast strains exhibiting: (i) high tolerance to multiple bioprocess-related stresses, including the various chemical inhibitors present in hydrolysates from lignocellulosic biomass and residues; (ii) the ability to efficiently consume all the major carbon sources present; (iii) the capacity to produce lipids with adequate composition in high yields. More than 160 non-conventional (non-Saccharomyces) yeast species are described as oleaginous, but only a smaller group are relatively well characterised, including Lipomyces starkeyi, Yarrowia lipolytica, Rhodotorula toruloides, Rhodotorula glutinis, Cutaneotrichosporonoleaginosus and Cutaneotrichosporon cutaneum. This article provides an overview of lipid production by oleaginous yeasts focusing on yeast diversity, metabolism, and other microbiological issues related to the toxicity and tolerance to multiple challenging stresses limiting bioprocess performance. This is essential knowledge to better understand and guide the rational improvement of yeast performance either by genetic manipulation or by exploring yeast physiology and optimal process conditions. Examples gathered from the literature showing the potential of different oleaginous yeasts/process conditions to produce oils for biodiesel from agro-forestry and industrial organic residues are provided.
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Affiliation(s)
- Marta N. Mota
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
| | - Paula Múgica
- BIOREF—Collaborative Laboratory for Biorefineries, Rua da Amieira, Apartado 1089, São Mamede de Infesta, 4465-901 Matosinhos, Portugal
| | - Isabel Sá-Correia
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- Correspondence:
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