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Flores-Cosío G, García-Béjar JA, Sandoval-Nuñez D, Amaya-Delgado L. Stress response and adaptation mechanisms in Kluyveromyces marxianus. ADVANCES IN APPLIED MICROBIOLOGY 2024; 126:27-62. [PMID: 38637106 DOI: 10.1016/bs.aambs.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Kluyveromyces marxianus is a non-Saccharomyces yeast that has gained importance due to its great potential to be used in the food and biotechnology industries. In general, K. marxianus is a known yeast for its ability to assimilate hexoses and pentoses; even this yeast can grow in disaccharides such as sucrose and lactose and polysaccharides such as agave fructans. Otherwise, K. marxianus is an excellent microorganism to produce metabolites of biotechnological interest, such as enzymes, ethanol, aroma compounds, organic acids, and single-cell proteins. However, several studies highlighted the metabolic trait variations among the K. marxianus strains, suggesting genetic diversity within the species that determines its metabolic functions; this diversity can be attributed to its high adaptation capacity against stressful environments. The outstanding metabolic characteristics of K. marxianus have motivated this yeast to be a study model to evaluate its easy adaptability to several environments. This chapter will discuss overview characteristics and applications of K. marxianus and recent insights into the stress response and adaptation mechanisms used by this non-Saccharomyces yeast.
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Affiliation(s)
- G Flores-Cosío
- Industrial Biotechnology Unit, Center for Research and Assistance in Technology and Design of the State of Jalisco, Camino Arenero, Col. El Bajio, C.P., Zapopan Jalisco, A.C, Mexico
| | - J A García-Béjar
- Industrial Biotechnology Unit, Center for Research and Assistance in Technology and Design of the State of Jalisco, Camino Arenero, Col. El Bajio, C.P., Zapopan Jalisco, A.C, Mexico
| | - D Sandoval-Nuñez
- Industrial Biotechnology Unit, Center for Research and Assistance in Technology and Design of the State of Jalisco, Camino Arenero, Col. El Bajio, C.P., Zapopan Jalisco, A.C, Mexico
| | - L Amaya-Delgado
- Industrial Biotechnology Unit, Center for Research and Assistance in Technology and Design of the State of Jalisco, Camino Arenero, Col. El Bajio, C.P., Zapopan Jalisco, A.C, Mexico.
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Liu N, Qin L, Zeng H, Wen A, Miao S. Integrative proteomic-transcriptomic analysis revealed the lifestyles of Lactobacillus paracasei H4-11 and Kluyveromyces marxianus L1-1 under co-cultivation conditions. FOOD SCIENCE AND HUMAN WELLNESS 2023. [DOI: 10.1016/j.fshw.2023.03.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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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.
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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
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Li Y, Long H, Jiang G, Gong X, Yu Z, Huang M, Guan T, Guan Y, Liu X. Analysis of the ethanol stress response mechanism in Wickerhamomyces anomalus based on transcriptomics and metabolomics approaches. BMC Microbiol 2022; 22:275. [PMCID: PMC9664796 DOI: 10.1186/s12866-022-02691-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022] Open
Abstract
Abstract
Background
Wickerhamomyces anomalus (W. anomalus) is a kind of non-Saccharomyces yeast that has a variety of unique physiological characteristics and metabolic features and is widely used in many fields, such as food preservation, biomass energy, and aquaculture feed protein production. However, the mechanism of W. anomalus response to ethanol stress is still unclear, which greatly limits its application in the production of ethanol beverages and ethanol fuels. Therefore, we checked the effects of ethanol stress on the morphology, the growth, and differentially expressed genes (DEGs) and metabolites (DEMs) of W. anomalus.
Results
High concentrations of ethanol (9% ethanol and 12% ethanol) remarkably inhibited the growth of W. anomalus. Energy metabolism, amino acid metabolism, fatty acids metabolism, and nucleic acid metabolism were significantly influenced when exposing to 9% ethanol and 12% ethanolstress, which maybe universal for W. anomalus to response to different concentrations of ethanol stressl Furthermore, extracellular addition of aspartate, glutamate, and arginine significantly abated ethanol damage and improved the survival rate of W. anomalus.
Conclusions
The results obtained in this study provide insights into the mechanisms involved in W. anomalus response to ethanol stress. Therefore, new strategies can be realized to improve the ethanol tolerance of W. anomalus through metabolic engineering.
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Ribeiro RA, Bourbon-Melo N, Sá-Correia I. The cell wall and the response and tolerance to stresses of biotechnological relevance in yeasts. Front Microbiol 2022; 13:953479. [PMID: 35966694 PMCID: PMC9366716 DOI: 10.3389/fmicb.2022.953479] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/11/2022] [Indexed: 01/18/2023] Open
Abstract
In industrial settings and processes, yeasts may face multiple adverse environmental conditions. These include exposure to non-optimal temperatures or pH, osmotic stress, and deleterious concentrations of diverse inhibitory compounds. These toxic chemicals may result from the desired accumulation of added-value bio-products, yeast metabolism, or be present or derive from the pre-treatment of feedstocks, as in lignocellulosic biomass hydrolysates. Adaptation and tolerance to industrially relevant stress factors involve highly complex and coordinated molecular mechanisms occurring in the yeast cell with repercussions on the performance and economy of bioprocesses, or on the microbiological stability and conservation of foods, beverages, and other goods. To sense, survive, and adapt to different stresses, yeasts rely on a network of signaling pathways to modulate the global transcriptional response and elicit coordinated changes in the cell. These pathways cooperate and tightly regulate the composition, organization and biophysical properties of the cell wall. The intricacy of the underlying regulatory networks reflects the major role of the cell wall as the first line of defense against a wide range of environmental stresses. However, the involvement of cell wall in the adaptation and tolerance of yeasts to multiple stresses of biotechnological relevance has not received the deserved attention. This article provides an overview of the molecular mechanisms involved in fine-tuning cell wall physicochemical properties during the stress response of Saccharomyces cerevisiae and their implication in stress tolerance. The available information for non-conventional yeast species is also included. These non-Saccharomyces species have recently been on the focus of very active research to better explore or control their biotechnological potential envisaging the transition to a sustainable circular bioeconomy.
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Affiliation(s)
- Ricardo A. Ribeiro
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Nuno Bourbon-Melo
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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Ramírez-Zamudio GD, Silva LH, Vieira NM, Vilela RS, Assis DE, Assis GJ, Estrada MM, Rodrigues RT, Duarte MS, Chizzotti ML. Effect of short-term dietary protein restriction before slaughter on meat quality and skeletal muscle metabolomic profile in culled ewes. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.104956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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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]
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Tinôco D, da Silveira WB. Kinetic model of ethanol inhibition for Kluyveromyces marxianus CCT 7735 (UFV-3) based on the modified Monod model by Ghose & Tyagi. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00876-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Li P, Tan X, Fu X, Dang Y, Li S. Metabolomic analysis reveals Kluyveromyces marxianus’s stress responses during high-temperature ethanol fermentation. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.01.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Yao S, Hao L, Zhou R, Jin Y, Huang J, Wu C. Co-culture with Tetragenococcus halophilus improved the ethanol tolerance of Zygosaccharomyces rouxii by maintaining cell surface properties. Food Microbiol 2021; 97:103750. [PMID: 33653523 DOI: 10.1016/j.fm.2021.103750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/31/2020] [Accepted: 01/18/2021] [Indexed: 02/08/2023]
Abstract
The accumulation of ethanol has a negative effect on the viability and fermentation performance of microorganisms during the production of fermented foods because of its toxicity. In this study, we investigated the effect of co-culture with Tetragenococcus halophilus on ethanol stress resistance of Zygosaccharomyces rouxii. The result showed that co-culture with T. halophilus promoted cell survival of Z. rouxii under ethanol stress, and the tolerance improved with increasing co-culture time when ethanol content was 8%. Physiological analysis showed that the co-cultured Z. rouxii cells maintained higher intracellular content of trehalose and amino acids including tyrosine, tryptophan, arginine and proline after 8% ethanol stress for 90 min. The membrane integrity analysis and biophysical analysis of the cell surface indicated that the presence of ethanol resulted in cell membrane damage and changes of Young's modulus value and roughness of cell surface. While the co-cultured Z. rouxii cells exhibited better membrane integrity, stiffer and smoother cell surface than single-cultured cells under ethanol stress. As for transcriptomic analyses, the genes involved in unsaturated fatty acid biosynthesis, trehalose biosynthesis, various types of N-glycan biosynthesis, inositol phosphate metabolism, MAPK signaling pathway and tight junction had higher expression in co-cultured Z. rouxii cells with down-regulation of majority of gene expression after stress. And these genes may function in the improvement of ethanol tolerance of Z. rouxii in co-culture.
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Affiliation(s)
- Shangjie Yao
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, 610065, China
| | - Liying Hao
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Rongqing Zhou
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, 610065, China
| | - Yao Jin
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, 610065, China
| | - Jun Huang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, 610065, China
| | - Chongde Wu
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, 610065, China.
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Kluyveromyces marxianus: Current State of Omics Studies, Strain Improvement Strategy and Potential Industrial Implementation. FERMENTATION-BASEL 2020. [DOI: 10.3390/fermentation6040124] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Bioethanol is considered an excellent alternative to fossil fuels, since it importantly contributes to the reduced consumption of crude oil, and to the alleviation of environmental pollution. Up to now, the baker yeast Saccharomyces cerevisiae is the most common eukaryotic microorganism used in ethanol production. The inability of S. cerevisiae to grow on pentoses, however, hinders its effective growth on plant biomass hydrolysates, which contain large amounts of C5 and C12 sugars. The industrial-scale bioprocessing requires high temperature bioreactors, diverse carbon sources, and the high titer production of volatile compounds. These criteria indicate that the search for alternative microbes possessing useful traits that meet the required standards of bioethanol production is necessary. Compared to other yeasts, Kluyveromyces marxianus has several advantages over others, e.g., it could grow on a broad spectrum of substrates (C5, C6 and C12 sugars); tolerate high temperature, toxins, and a wide range of pH values; and produce volatile short-chain ester. K. marxianus also shows a high ethanol production rate at high temperature and is a Crabtree-negative species. These attributes make K. marxianus promising as an industrial host for the biosynthesis of biofuels and other valuable chemicals.
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da Silveira FA, de Oliveira Soares DL, Bang KW, Balbino TR, de Moura Ferreira MA, Diniz RHS, de Lima LA, Brandão MM, Villas-Bôas SG, da Silveira WB. Assessment of ethanol tolerance of Kluyveromyces marxianus CCT 7735 selected by adaptive laboratory evolution. Appl Microbiol Biotechnol 2020; 104:7483-7494. [DOI: 10.1007/s00253-020-10768-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 04/21/2020] [Accepted: 07/02/2020] [Indexed: 12/28/2022]
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Xu Y, Yang H, Brennan CS, Coldea TE, Zhao H. Cellular mechanism for the improvement of multiple stress tolerance in brewer's yeast by potassium ion supplementation. Int J Food Sci Technol 2020. [DOI: 10.1111/ijfs.14491] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Yingchao Xu
- School of Food Science and Engineering South China University of Technology Guangzhou 510640 China
| | - Huirong Yang
- School of Food Science and Engineering South China University of Technology Guangzhou 510640 China
| | - Charles S. Brennan
- Department of Wine, Food and Molecular Biosciences Lincoln University Lincoln 7464 Canterbury New Zealand
| | - Teodora Emilia Coldea
- Faculty of Food Science and Technology University of Agricultural Sciences and Veterinary Medicine Cluj‐Napoca 400372 Romania
| | - Haifeng Zhao
- School of Food Science and Engineering South China University of Technology Guangzhou 510640 China
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Li P, Fu X, Chen M, Zhang L, Li S. Proteomic profiling and integrated analysis with transcriptomic data bring new insights in the stress responses of Kluyveromyces marxianus after an arrest during high-temperature ethanol fermentation. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:49. [PMID: 30899329 PMCID: PMC6408782 DOI: 10.1186/s13068-019-1390-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 02/28/2019] [Indexed: 06/01/2023]
Abstract
BACKGROUND The thermotolerant yeast Kluyveromyces marxianus is a potential candidate for high-temperature fermentation. When K. marxianus was used for high-temperature ethanol fermentation, a fermentation arrest was observed during the late fermentation stage and the stress responses have been investigated based on the integration of RNA-Seq and metabolite data. In order to bring new insights into the cellular responses of K. marxianus after the fermentation arrest during high-temperature ethanol fermentation, quantitative proteomic profiling and integrated analysis with transcriptomic data were performed in this study. RESULTS Samples collected at 14, 16, 18, 20 and 22 h during high-temperature fermentation were subjected to isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic profiling and integrated analysis with transcriptomic data. The correlations between transcripts and proteins for the comparative group 16 h vs 14 h accounted for only 4.20% quantified proteins and 3.23% differentially expressed proteins (DEPs), respectively, much higher percentages of correlations (30.56%-59.11%) were found for other comparative groups (i.e., 18 h vs 14 h, 20 h vs 14 h, and 22 h vs 14 h). According to Spearman correlation tests between transcriptome and proteome (the absolute value of a correlation coefficient between 0.5 and 1 indicates a strong correlation), poor correlations were found for all quantified proteins (R = - 0.0355 to 0.0138), DEPs (R = - 0.0079 to 0.0233) and the DEPs with opposite expression trends to corresponding differentially expressed genes (DEGs) (R = - 0.0478 to 0.0636), whereas stronger correlations were observed in terms of the DEPs with the same expression trends as the correlated DEGs (R = 0.5593 to 0.7080). The results of multiple reaction monitoring (MRM) verification indicate that the iTRAQ results were reliable. After the fermentation arrest, a number of proteins involved in transcription, translation, oxidative phosphorylation and fatty acid metabolism were down-regulated, some molecular chaperones and proteasome proteins were up-regulated, the ATPase activity significantly decreased, and the total fatty acids gradually accumulated. In addition, the contents of palmitic acid, oleic acid, C16, C18, C22 and C24 fatty acids increased by 16.77%, 28.49%, 14.14%, 26.88%, 628.57% and 125.29%, respectively. CONCLUSIONS This study confirmed some biochemical and enzymatic alterations provoked by the stress conditions in the specific case of K. marxianus: such as decreases in transcription, translation and oxidative phosphorylation, alterations in cellular fatty acid composition, and increases in the abundance of molecular chaperones and proteasome proteins. These findings provide potential targets for further metabolic engineering towards improvement of the stress tolerance in K. marxianus.
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Affiliation(s)
- Pengsong Li
- MOST-USDA Joint Research Center for Biofuels, Beijing Engineering Research Center for Biofuels, Institute of New Energy Technology, Tsinghua University, Beijing, 100084 China
| | - Xiaofen Fu
- MOST-USDA Joint Research Center for Biofuels, Beijing Engineering Research Center for Biofuels, Institute of New Energy Technology, Tsinghua University, Beijing, 100084 China
| | - Ming Chen
- MOST-USDA Joint Research Center for Biofuels, Beijing Engineering Research Center for Biofuels, Institute of New Energy Technology, Tsinghua University, Beijing, 100084 China
| | - Lei Zhang
- MOST-USDA Joint Research Center for Biofuels, Beijing Engineering Research Center for Biofuels, Institute of New Energy Technology, Tsinghua University, Beijing, 100084 China
- Agricultural Utilization Research Center, Nutrition and Health Research Institute, COFCO Corporation, No.4 Road, Future Science and Technology Park South, Beiqijia, Changping, Beijing, 102209 China
| | - Shizhong Li
- MOST-USDA Joint Research Center for Biofuels, Beijing Engineering Research Center for Biofuels, Institute of New Energy Technology, Tsinghua University, Beijing, 100084 China
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