1
|
Ou H, Zhang P, Wang X, Lin M, Li Y, Wang G. Gaining insights into the responses of individual yeast cells to ethanol fermentation using Raman tweezers and chemometrics. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 319:124584. [PMID: 38838600 DOI: 10.1016/j.saa.2024.124584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 05/18/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024]
Abstract
Saccharomyces cerevisiae is the most common microbe used for the industrial production of bioethanol, and it encounters various stresses that inhibit cell growth and metabolism during fermentation. However, little is currently known about the physiological changes that occur in individual yeast cells during ethanol fermentation. Therefore, in this work, Raman spectroscopy and chemometric techniques were employed to monitor the metabolic changes of individual yeast cells at distinct stages during high gravity ethanol fermentation. Raman tweezers was used to acquire the Raman spectra of individual yeast cells. Multivariate curve resolution-alternating least squares (MCR-ALS) and principal component analysis were employed to analyze the Raman spectra dataset. MCR-ALS extracted the spectra of proteins, phospholipids, and triacylglycerols and their relative contents in individual cells. Changes in intracellular biomolecules showed that yeast cells undergo three distinct physiological stages during fermentation. In addition, heterogeneity among yeast cells significantly increased in the late fermentation period, and different yeast cells may respond to ethanol stress via different mechanisms. Our findings suggest that the combination of Raman tweezers and chemometrics approaches allows for characterizing the dynamics of molecular components within individual cells. This approach can serve as a valuable tool in investigating the resistance mechanism and metabolic heterogeneity of yeast cells during ethanol fermentation.
Collapse
Affiliation(s)
- Haisheng Ou
- Institute of Eco-Environmental Research, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi 530007, China; College of Physics Science and Technology, Guangxi Normal University, 15 Yucai Road, Guilin, Guangxi 541004, China
| | - Pengfei Zhang
- School of Precision Instruments and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
| | - Xiaochun Wang
- Institute of Eco-Environmental Research, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi 530007, China
| | - Manman Lin
- School of Electronic and Information Engineering, Zhongyuan University of Technology, Zhengzhou 450007, China
| | - Yuanpeng Li
- College of Physics Science and Technology, Guangxi Normal University, 15 Yucai Road, Guilin, Guangxi 541004, China
| | - Guiwen Wang
- Institute of Eco-Environmental Research, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi 530007, China.
| |
Collapse
|
2
|
Ferreira MADM, da Silveira WB, Nikoloski Z. PARROT: Prediction of enzyme abundances using protein-constrained metabolic models. PLoS Comput Biol 2023; 19:e1011549. [PMID: 37856550 PMCID: PMC10617714 DOI: 10.1371/journal.pcbi.1011549] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/31/2023] [Accepted: 09/29/2023] [Indexed: 10/21/2023] Open
Abstract
Protein allocation determines the activity of cellular pathways and affects growth across all organisms. Therefore, different experimental and machine learning approaches have been developed to quantify and predict protein abundance and how they are allocated to different cellular functions, respectively. Yet, despite advances in protein quantification, it remains challenging to predict condition-specific allocation of enzymes in metabolic networks. Here, using protein-constrained metabolic models, we propose a family of constrained-based approaches, termed PARROT, to predict how much of each enzyme is used based on the principle of minimizing the difference between a reference and an alternative growth condition. To this end, PARROT variants model the minimization of enzyme reallocation using four different (combinations of) distance functions. We demonstrate that the PARROT variant that minimizes the Manhattan distance between the enzyme allocation of a reference and an alternative condition outperforms existing approaches based on the parsimonious distribution of fluxes or enzymes for both Escherichia coli and Saccharomyces cerevisiae. Further, we show that the combined minimization of flux and enzyme allocation adjustment leads to inconsistent predictions. Together, our findings indicate that minimization of protein allocation rather than flux redistribution is a governing principle determining steady-state pathway activity for microorganism grown in alternative growth conditions.
Collapse
Affiliation(s)
| | | | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| |
Collapse
|
3
|
Deciphering the mechanism of anhydrobiosis in the entomopathogenic nematode Heterorhabditis indica through comparative transcriptomics. PLoS One 2022; 17:e0275342. [PMID: 36301967 PMCID: PMC9612587 DOI: 10.1371/journal.pone.0275342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 09/14/2022] [Indexed: 11/07/2022] Open
Abstract
The entomopathogenic nematode, Heterorhabditis indica, is a popular biocontrol agent of high commercial significance. It possesses tremendous genetic architecture to survive desiccation stress by undergoing anhydrobiosis to increase its lifespan-an attribute exploited in the formulation technology. The comparative transcriptome of unstressed and anhydrobiotic H. indica revealed several previously concealed metabolic events crucial for adapting towards the moisture stress. During the induction of anhydrobiosis in the infective juveniles (IJ), 1584 transcripts were upregulated and 340 downregulated. As a strategy towards anhydrobiotic survival, the IJ showed activation of several genes critical to antioxidant defense, detoxification pathways, signal transduction, unfolded protein response and molecular chaperones and ubiquitin-proteasome system. Differential expression of several genes involved in gluconeogenesis - β-oxidation of fatty acids, glyoxylate pathway; glyceroneogenesis; fatty acid biosynthesis; amino-acid metabolism - shikimate pathway, sachharopine pathway, kyneurine pathway, lysine biosynthesis; one-carbon metabolism-polyamine pathway, transsulfuration pathway, folate cycle, methionine cycle, nucleotide biosynthesis; mevalonate pathway; and glyceraldehyde-3-phosphate dehydrogenase were also observed. We report the role of shikimate pathway, sachharopine pathway and glyceroneogenesis in anhydrobiotes, and seven classes of repeat proteins, specifically in H. indica for the first time. These results provide insights into anhydrobiotic survival strategies which can be utilized to strengthen the development of novel formulations with enhanced and sustained shelf-life.
Collapse
|
4
|
de Moura Ferreira MA, da Silveira FA, da Silveira WB. Ethanol stress responses in Kluyveromyces marxianus: current knowledge and perspectives. Appl Microbiol Biotechnol 2022; 106:1341-1353. [DOI: 10.1007/s00253-022-11799-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 11/02/2022]
|
5
|
Navarro-Tapia E, Pérez-Torrado R. Indirect Methods To Measure Unfolded Proteins In Living Cells Using Fluorescent Proteins. Methods Mol Biol 2022; 2378:31-44. [PMID: 34985692 DOI: 10.1007/978-1-0716-1732-8_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In the study of the unfolded protein response pathway, it is essential to determine the amount of unfolded proteins that the cell is accumulating. Besides being essential it is one of the most challenging technique because of the difficulty to detect unfolded proteins without producing protein denaturation with the method itself. Thus, indirect methods became very useful as the use of fluorescent proteins. In this chapter, we present some of the most used methods to indirectly measure protein folding in living cells using fluorescent proteins.
Collapse
|
6
|
Flores-Cotera LB, Chávez-Cabrera C, Martínez-Cárdenas A, Sánchez S, García-Flores OU. Deciphering the mechanism by which the yeast Phaffia rhodozyma responds adaptively to environmental, nutritional, and genetic cues. J Ind Microbiol Biotechnol 2021; 48:kuab048. [PMID: 34302341 PMCID: PMC8788774 DOI: 10.1093/jimb/kuab048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/16/2021] [Indexed: 11/13/2022]
Abstract
Phaffia rhodozyma is a basidiomycetous yeast that synthesizes astaxanthin (ASX), which is a powerful and highly valuable antioxidant carotenoid pigment. P. rhodozyma cells accrue ASX and gain an intense red-pink coloration when faced with stressful conditions such as nutrient limitations (e.g., nitrogen or copper), the presence of toxic substances (e.g., antimycin A), or are affected by mutations in the genes that are involved in nitrogen metabolism or respiration. Since cellular accrual of ASX occurs under a wide variety of conditions, this yeast represents a valuable model for studying the growth conditions that entail oxidative stress for yeast cells. Recently, we proposed that ASX synthesis can be largely induced by conditions that lead to reduction-oxidation (redox) imbalances, particularly the state of the NADH/NAD+ couple together with an oxidative environment. In this work, we review the multiple known conditions that elicit ASX synthesis expanding on the data that we formerly examined. When considered alongside the Mitchell's chemiosmotic hypothesis, the study served to rationalize the induction of ASX synthesis and other adaptive cellular processes under a much broader set of conditions. Our aim was to propose an underlying mechanism that explains how a broad range of divergent conditions converge to induce ASX synthesis in P. rhodozyma. The mechanism that links the induction of ASX synthesis with the occurrence of NADH/NAD+ imbalances may help in understanding how other organisms detect any of a broad array of stimuli or gene mutations, and then adaptively respond to activate numerous compensatory cellular processes.
Collapse
Affiliation(s)
- Luis B Flores-Cotera
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México city 07360, México
| | - Cipriano Chávez-Cabrera
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México city 07360, México
| | - Anahi Martínez-Cárdenas
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México city 07360, México
| | - Sergio Sánchez
- Department of Molecular Biology and Biotechnology, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México city 04510, México
| | - Oscar Ulises García-Flores
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México city 07360, México
| |
Collapse
|
7
|
Sunyer-Figueres M, Mas A, Beltran G, Torija MJ. Protective Effects of Melatonin on Saccharomyces cerevisiae under Ethanol Stress. Antioxidants (Basel) 2021; 10:antiox10111735. [PMID: 34829606 PMCID: PMC8615028 DOI: 10.3390/antiox10111735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/21/2021] [Accepted: 10/28/2021] [Indexed: 01/15/2023] Open
Abstract
During alcoholic fermentation, Saccharomyces cerevisiae is subjected to several stresses, among which ethanol is of capital importance. Melatonin, a bioactive molecule synthesized by yeast during alcoholic fermentation, has an antioxidant role and is proposed to contribute to counteracting fermentation-associated stresses. The aim of this study was to unravel the protective effect of melatonin on yeast cells subjected to ethanol stress. For that purpose, the effect of ethanol concentrations (6 to 12%) on a wine strain and a lab strain of S. cerevisiae was evaluated, monitoring the viability, growth capacity, mortality, and several indicators of oxidative stress over time, such as reactive oxygen species (ROS) accumulation, lipid peroxidation, and the activity of catalase and superoxide dismutase enzymes. In general, ethanol exposure reduced the cell growth of S. cerevisiae and increased mortality, ROS accumulation, lipid peroxidation and antioxidant enzyme activity. Melatonin supplementation softened the effect of ethanol, enhancing cell growth and decreasing oxidative damage by lowering ROS accumulation, lipid peroxidation, and antioxidant enzyme activities. However, the effects of melatonin were dependent on strain, melatonin concentration, and growth phase. The results of this study indicate that melatonin has a protective role against mild ethanol stress, mainly by reducing the oxidative stress triggered by this alcohol.
Collapse
|
8
|
Peng K, Kroukamp H, Pretorius IS, Paulsen IT. Yeast Synthetic Minimal Biosensors for Evaluating Protein Production. ACS Synth Biol 2021; 10:1640-1650. [PMID: 34126009 DOI: 10.1021/acssynbio.0c00633] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The unfolded protein response (UPR) is a highly conserved cellular response in eukaryotic cells to counteract endoplasmic reticulum (ER) stress, typically triggered by unfolded protein accumulation. In addition to its relevance to human diseases like cancer, the induction of the UPR has a significant impact on the recombinant protein production in eukaryotic cell factories, including the industrial workhorseSaccharomyces cerevisiae. Being able to accurately detect and measure this ER stress response in single cells, enables the rapid optimization of protein production conditions and high-throughput strain selection strategies. Current methodologies to monitor the UPR in S. cerevisiae are often temporally and spatially removed from the cultivation stage or lack updated systematic evaluation. To this end, we constructed and systematically evaluated a series of high-throughput UPR sensors by different designs, incorporating either yeast native UPR promoters or novel synthetic minimal UPR promoters. The native promoters of DER1 and ERO1 were identified to have suitable UPR biosensor properties and served as an expression level guide for orthogonal sensor benchmarking. Our best synthetic minimal sensor is only 98 bp in length, has minimal homology to other native yeast sequences and displayed superior sensor characteristics. The synthetic minimal UPR sensor was able to accurately distinguish between cells expressing different heterologous proteins and between the different secretion levels of the same protein. This work demonstrated the potential of synthetic UPR biosensors as high-throughput tools to predict the protein production capacity of strains, interrogate protein properties hampering their secretion, and guide rational engineering strategies for optimal heterologous protein production.
Collapse
Affiliation(s)
- Kai Peng
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Heinrich Kroukamp
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | | | - Ian T. Paulsen
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| |
Collapse
|
9
|
Phuong HT, Ishiwata-Kimata Y, Nishi Y, Oguchi N, Takagi H, Kimata Y. Aeration mitigates endoplasmic reticulum stress in Saccharomyces cerevisiae even without mitochondrial respiration. MICROBIAL CELL 2021; 8:77-86. [PMID: 33816593 PMCID: PMC8010904 DOI: 10.15698/mic2021.04.746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Saccharomyces cerevisiae is a facultative anaerobic organism that grows well under both aerobic and hypoxic conditions in media containing abundant fermentable nutrients such as glucose. In order to deeply understand the physiological dependence of S. cerevisiae on aeration, we checked endoplasmic reticulum (ER)-stress status by monitoring the splicing of HAC1 mRNA, which is promoted by the ER stress-sensor protein, Ire1. HAC1-mRNA splicing that was caused by conventional ER-stressing agents, including low concentrations of dithiothreitol (DTT), was more potent in hypoxic cultures than in aerated cultures. Moreover, growth retardation was observed by adding low-dose DTT into hypoxic cultures of ire1Δ cells. Unexpectedly, aeration mitigated ER stress and DTT-induced impairment of ER oxidative protein folding even when mitochondrial respiration was halted by the ρo mutation. An ER-located protein Ero1 is known to directly consume molecular oxygen to initiate the ER protein oxidation cascade, which promotes oxidative protein folding of ER client proteins. Our further study using ero1-mutant strains suggested that, in addition to mitochondrial respiration, this Ero1-medaited reaction contributes to mitigation of ER stress by molecular oxygen. Taken together, here we demonstrate a scenario in which aeration acts beneficially on S. cerevisiae cells even under fermentative conditions.
Collapse
Affiliation(s)
- Huong Thi Phuong
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Yuki Ishiwata-Kimata
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Yuki Nishi
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Norie Oguchi
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Hiroshi Takagi
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Yukio Kimata
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| |
Collapse
|
10
|
Pérez-Torrado R, Cubillos FA. Editorial: New Advances in Genetic Studies to Understand Yeast Adaptation to Extreme and Fermentative Environments. Front Genet 2021; 12:663641. [PMID: 33777115 PMCID: PMC7991380 DOI: 10.3389/fgene.2021.663641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Roberto Pérez-Torrado
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de los Alimentos-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Francisco A Cubillos
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.,Agencia Nacional de Investigación y Desarrollo (ANID)-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBIO), Santiago, Chile
| |
Collapse
|
11
|
Kostyuk AI, Panova AS, Kokova AD, Kotova DA, Maltsev DI, Podgorny OV, Belousov VV, Bilan DS. In Vivo Imaging with Genetically Encoded Redox Biosensors. Int J Mol Sci 2020; 21:E8164. [PMID: 33142884 PMCID: PMC7662651 DOI: 10.3390/ijms21218164] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
Redox reactions are of high fundamental and practical interest since they are involved in both normal physiology and the pathogenesis of various diseases. However, this area of research has always been a relatively problematic field in the context of analytical approaches, mostly because of the unstable nature of the compounds that are measured. Genetically encoded sensors allow for the registration of highly reactive molecules in real-time mode and, therefore, they began a new era in redox biology. Their strongest points manifest most brightly in in vivo experiments and pave the way for the non-invasive investigation of biochemical pathways that proceed in organisms from different systematic groups. In the first part of the review, we briefly describe the redox sensors that were used in vivo as well as summarize the model systems to which they were applied. Next, we thoroughly discuss the biological results obtained in these studies in regard to animals, plants, as well as unicellular eukaryotes and prokaryotes. We hope that this work reflects the amazing power of this technology and can serve as a useful guide for biologists and chemists who work in the field of redox processes.
Collapse
Affiliation(s)
- Alexander I. Kostyuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Anastasiya S. Panova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Aleksandra D. Kokova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Daria A. Kotova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Dmitry I. Maltsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Federal Center for Cerebrovascular Pathology and Stroke, 117997 Moscow, Russia
| | - Oleg V. Podgorny
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Vsevolod V. Belousov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Federal Center for Cerebrovascular Pathology and Stroke, 117997 Moscow, Russia
- Institute for Cardiovascular Physiology, Georg August University Göttingen, D-37073 Göttingen, Germany
| | - Dmitry S. Bilan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| |
Collapse
|
12
|
Telini BDP, Menoncin M, Bonatto D. Does Inter-Organellar Proteostasis Impact Yeast Quality and Performance During Beer Fermentation? Front Genet 2020; 11:2. [PMID: 32076433 PMCID: PMC7006503 DOI: 10.3389/fgene.2020.00002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/06/2020] [Indexed: 02/02/2023] Open
Abstract
During beer production, yeast generate ethanol that is exported to the extracellular environment where it accumulates. Depending on the initial carbohydrate concentration in the wort, the amount of yeast biomass inoculated, the fermentation temperature, and the yeast attenuation capacity, a high concentration of ethanol can be achieved in beer. The increase in ethanol concentration as a consequence of the fermentation of high gravity (HG) or very high gravity (VHG) worts promotes deleterious pleiotropic effects on the yeast cells. Moderate concentrations of ethanol (5% v/v) change the enzymatic kinetics of proteins and affect biological processes, such as the cell cycle and metabolism, impacting the reuse of yeast for subsequent fermentation. However, high concentrations of ethanol (> 5% v/v) dramatically alter protein structure, leading to unfolded proteins as well as amorphous protein aggregates. It is noteworthy that the effects of elevated ethanol concentrations generated during beer fermentation resemble those of heat shock stress, with similar responses observed in both situations, such as the activation of proteostasis and protein quality control mechanisms in different cell compartments, including endoplasmic reticulum (ER), mitochondria, and cytosol. Despite the extensive published molecular and biochemical data regarding the roles of proteostasis in different organelles of yeast cells, little is known about how this mechanism impacts beer fermentation and how different proteostasis mechanisms found in ER, mitochondria, and cytosol communicate with each other during ethanol/fermentative stress. Supporting this integrative view, transcriptome data analysis was applied using publicly available information for a lager yeast strain grown under beer production conditions. The transcriptome data indicated upregulation of genes that encode chaperones, co-chaperones, unfolded protein response elements in ER and mitochondria, ubiquitin ligases, proteasome components, N-glycosylation quality control pathway proteins, and components of processing bodies (p-bodies) and stress granules (SGs) during lager beer fermentation. Thus, the main purpose of this hypothesis and theory manuscript is to provide a concise picture of how inter-organellar proteostasis mechanisms are connected with one another and with biological processes that may modulate the viability and/or vitality of yeast populations during HG/VHG beer fermentation and serial repitching.
Collapse
Affiliation(s)
- Bianca de Paula Telini
- Brewing Yeast Research Group, Centro de Biotecnologia da UFRGS, Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Marcelo Menoncin
- Brewing Yeast Research Group, Centro de Biotecnologia da UFRGS, Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Diego Bonatto
- Brewing Yeast Research Group, Centro de Biotecnologia da UFRGS, Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| |
Collapse
|
13
|
Morard M, Macías LG, Adam AC, Lairón-Peris M, Pérez-Torrado R, Toft C, Barrio E. Aneuploidy and Ethanol Tolerance in Saccharomyces cerevisiae. Front Genet 2019; 10:82. [PMID: 30809248 PMCID: PMC6379819 DOI: 10.3389/fgene.2019.00082] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 01/28/2019] [Indexed: 12/31/2022] Open
Abstract
Response to environmental stresses is a key factor for microbial organism growth. One of the major stresses for yeasts in fermentative environments is ethanol. Saccharomyces cerevisiae is the most tolerant species in its genus, but intraspecific ethanol-tolerance variation exists. Although, much effort has been done in the last years to discover evolutionary paths to improve ethanol tolerance, this phenotype is still hardly understood. Here, we selected five strains with different ethanol tolerances, and used comparative genomics to determine the main factors that can explain these phenotypic differences. Surprisingly, the main genomic feature, shared only by the highest ethanol-tolerant strains, was a polysomic chromosome III. Transcriptomic data point out that chromosome III is important for the ethanol stress response, and this aneuploidy can be an advantage to respond rapidly to ethanol stress. We found that chromosome III copy numbers also explain differences in other strains. We show that removing the extra chromosome III copy in an ethanol-tolerant strain, returning to euploidy, strongly compromises its tolerance. Chromosome III aneuploidy appears frequently in ethanol-tolerance evolution experiments, and here, we show that aneuploidy is also used by natural strains to enhance their ethanol tolerance.
Collapse
Affiliation(s)
- Miguel Morard
- Departament de Genètica, Universitat de València, Valencia, Spain.,Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Valencia, Spain
| | - Laura G Macías
- Departament de Genètica, Universitat de València, Valencia, Spain.,Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Valencia, Spain
| | - Ana C Adam
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Valencia, Spain
| | - María Lairón-Peris
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Valencia, Spain
| | - Roberto Pérez-Torrado
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Valencia, Spain
| | - Christina Toft
- Departament de Genètica, Universitat de València, Valencia, Spain.,Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Valencia, Spain
| | - Eladio Barrio
- Departament de Genètica, Universitat de València, Valencia, Spain.,Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Valencia, Spain
| |
Collapse
|
14
|
Navarro-Tapia E, Querol A, Pérez-Torrado R. Membrane fluidification by ethanol stress activates unfolded protein response in yeasts. Microb Biotechnol 2018; 11:465-475. [PMID: 29469174 PMCID: PMC5902320 DOI: 10.1111/1751-7915.13032] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 09/05/2017] [Accepted: 11/05/2017] [Indexed: 11/28/2022] Open
Abstract
The toxic effect of ethanol is one of the most important handicaps for many biotechnological applications of yeasts, such as bioethanol production. Elucidation of ethanol stress response will help to improve yeast performance in biotechnological processes. In the yeast Saccharomyces cerevisiae, ethanol stress has been recently described as an activator of the unfolded protein response (UPR), a conserved intracellular signalling pathway that regulates the transcription of ER homoeostasis‐related genes. However, the signal and activation mechanism has not yet been unravelled. Here, we studied UPR's activation after ethanol stress and observed the upregulation of the key target genes, like INO1, involved in lipid metabolism. We found that inositol content influenced UPR activation after ethanol stress and we observed significant changes in lipid composition, which correlate with a major membrane fluidity alteration by this amphipathic molecule. Then, we explored the hypothesis that membrane fluidity changes cause UPR activation upon ethanol stress by studying UPR response against fluidification or rigidification agents and by studying a mutant, erg2, with altered membrane fluidity. The results suggest that the membrane fluidification effects of ethanol and other agents are the signal for UPR activation, a mechanism that has been proposed in higher eukaryotes.
Collapse
Affiliation(s)
- Elisabet Navarro-Tapia
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, E-46980, Paterna, Valencia, Spain
| | - Amparo Querol
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, E-46980, Paterna, Valencia, Spain
| | - Roberto Pérez-Torrado
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, E-46980, Paterna, Valencia, Spain
| |
Collapse
|