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Zhang MM, Yuan B, Wang YT, Zhang FL, Liu CG, Zhao XQ. Differential Protein Expression in Set5p-Mediated Acetic Acid Stress Response and Novel Targets for Engineering Yeast Stress Tolerance. J Proteome Res 2024; 23:2986-2998. [PMID: 38396335 DOI: 10.1021/acs.jproteome.3c00617] [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: 02/25/2024]
Abstract
Acetic acid is a prevalent inhibitor in lignocellulosic hydrolysate, which represses microbial growth and bioproduction. Histone modification and chromatin remodeling have been revealed to be critical for regulating eukaryotic metabolism. However, related studies in chronic acetic acid stress responses remain unclear. Our previous studies revealed that overexpression of the histone H4 methyltransferase Set5p enhanced acetic acid stress tolerance of the budding yeast Saccharomyces cerevisiae. In this study, we examined the role of Set5p in acetic acid stress by analyzing global protein expression. Significant activation of intracellular protein expression under the stress was discovered, and the functions of the differential proteins were mainly involved in chromatin modification, signal transduction, and carbohydrate metabolism. Notably, a substantial increase of Set5p expression was observed in response to acetic acid stress. Functional studies demonstrated that the restriction of the telomere capping protein Rtc3p, as well as Ies3p and Taf14p, which are related to chromatin regulation, was critical for yeast stress response. This study enriches the understanding of the epigenetic regulatory mechanisms underlying yeast stress response mediated by histone-modifying enzymes. The results also benefit the development of robust yeast strains for lignocellulosic bioconversion.
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Affiliation(s)
- Ming-Ming Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bing Yuan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ya-Ting Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Feng-Li Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Jenkins Sánchez LR, Sips LM, Van Bogaert INA. Just passing through: Deploying aquaporins in microbial cell factories. Biotechnol Prog 2024:e3497. [PMID: 39051848 DOI: 10.1002/btpr.3497] [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: 02/29/2024] [Revised: 07/05/2024] [Accepted: 07/10/2024] [Indexed: 07/27/2024]
Abstract
As microbial membranes are naturally impermeable to even the smallest biomolecules, transporter proteins are physiologically essential for normal cell functioning. This makes transporters a key target area for engineering enhanced cell factories. As part of the wider cellular transportome, aquaporins (AQPs) are responsible for transporting small polar solutes, encompassing many compounds which are of great interest for industrial biotechnology, including cell feedstocks, numerous commercially relevant polyols and even weak organic acids. In this review, examples of cell factory engineering by targeting AQPs are presented. These AQP modifications aid in redirecting carbon fluxes and boosting bioconversions either by enhanced feedstock uptake, improved intermediate retention, increasing product export into the media or superior cell viability against stressors with applications in both bacterial and yeast production platforms. Additionally, the future potential for AQP deployment and targeting is discussed, showcasing hurdles and considerations of this strategy as well as recent advances and future directions in the field. By leveraging the natural diversity of AQPs and breakthroughs in channel protein engineering, these transporters are poised to be promising tools capable of enhancing a wide variety of biotechnological processes.
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Affiliation(s)
- Liam Richard Jenkins Sánchez
- BioPort Group, Centre for Synthetic Biology, Department of Biotechnology, Faculty of Bio-science Engineering, Ghent University, Ghent, Belgium
| | - Lobke Maria Sips
- BioPort Group, Centre for Synthetic Biology, Department of Biotechnology, Faculty of Bio-science Engineering, Ghent University, Ghent, Belgium
| | - Inge Noëlle Adriënne Van Bogaert
- BioPort Group, Centre for Synthetic Biology, Department of Biotechnology, Faculty of Bio-science Engineering, Ghent University, Ghent, Belgium
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Jang YB, Kim JY, Bahn YS. Unraveling the cryptic functions of mitogen-activated protein kinases Cpk2 and Mpk2 in Cryptococcus neoformans. mBio 2024; 15:e0115624. [PMID: 38874410 PMCID: PMC11253600 DOI: 10.1128/mbio.01156-24] [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: 04/15/2024] [Accepted: 04/30/2024] [Indexed: 06/15/2024] Open
Abstract
Mitogen-activated protein kinase (MAPK) pathways are fundamental to the regulation of biological processes in eukaryotic organisms. The basidiomycete Cryptococcus neoformans, known for causing fungal meningitis worldwide, possesses five MAPKs. Among these, Cpk1, Hog1, and Mpk1 have established roles in sexual reproduction, stress responses, and cell wall integrity. However, the roles of Cpk2 and Mpk2 are less understood. Our study elucidates the functional interplay between the Cpk1/Cpk2 and Mpk1/Mpk2 MAPK pathways in C. neoformans. We discovered that CPK2 overexpression compensates for cpk1Δ mating deficiencies via the Mat2 transcription factor, revealing functional redundancy between Cpk1 and Cpk2. We also found that Mpk2 is phosphorylated in response to cell wall stress, a process regulated by the MAPK kinase (MAP2K) Mkk2 and MAP2K kinases (MAP3Ks) Ssk2 and Ste11. Overexpression of MPK2 partially restores cell wall integrity in mpk1Δ by influencing key cell wall components, such as chitin and the polysaccharide capsule. Contrarily, MPK2 overexpression cannot restore thermotolerance and cell membrane integrity in mpk1Δ. These results suggest that Mpk1 and Mpk2 have redundant and opposing roles in the cellular response to cell wall and membrane stresses. Most notably, the dual deletion of MPK1 and MPK2 restores wild-type mating efficiency in cpk1Δ mutants via upregulation of the mating-regulating transcription factors MAT2 and ZNF2, suggesting that the Mpk1 and Mpk2 cooperate to negatively regulate the pheromone-responsive Cpk1 MAPK pathway. Our research collectively underscores a sophisticated regulatory network of cryptococcal MAPK signaling pathways that intricately govern sexual reproduction and cell wall integrity, thereby controlling fungal development and pathogenicity.IMPORTANCEIn the realm of fungal biology, our study on Cryptococcus neoformans offers pivotal insights into the roles of specific proteins called mitogen-activated protein kinases (MAPKs). Here, we discovered the cryptic functions of Cpk2 and Mpk2, two MAPKs previously overshadowed by their dominant counterparts Cpk1 and Mpk1, respectively. Our findings reveal that these "underdog" proteins are not just backup players; they play crucial roles in vital processes like mating and cell wall maintenance in C. neoformans. Their ability to step in and compensate when their dominant counterparts are absent showcases the adaptability of C. neoformans. This newfound understanding not only enriches our knowledge of fungal MAPK mechanisms but also underscores the intricate balance and interplay of proteins in ensuring the organism's survival and adaptability.
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Affiliation(s)
- Yu-Byeong Jang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Jin-Young Kim
- Division of Life Science, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Yong-Sun Bahn
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
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Cámara E, Mormino M, Siewers V, Nygård Y. Saccharomyces cerevisiae strains performing similarly during fermentation of lignocellulosic hydrolysates show pronounced differences in transcriptional stress responses. Appl Environ Microbiol 2024; 90:e0233023. [PMID: 38587374 PMCID: PMC11107148 DOI: 10.1128/aem.02330-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/14/2024] [Indexed: 04/09/2024] Open
Abstract
Improving our understanding of the transcriptional changes of Saccharomyces cerevisiae during fermentation of lignocellulosic hydrolysates is crucial for the creation of more efficient strains to be used in biorefineries. We performed RNA sequencing of a CEN.PK laboratory strain, two industrial strains (KE6-12 and Ethanol Red), and two wild-type isolates of the LBCM collection when cultivated anaerobically in wheat straw hydrolysate. Many of the differently expressed genes identified among the strains have previously been reported to be important for tolerance to lignocellulosic hydrolysates or inhibitors therein. Our study demonstrates that stress responses typically identified during aerobic conditions such as glutathione metabolism, osmotolerance, and detoxification processes also are important for anaerobic processes. Overall, the transcriptomic responses were largely strain dependent, and we focused our study on similarities and differences in the transcriptomes of the LBCM strains. The expression of sugar transporter-encoding genes was higher in LBCM31 compared with LBCM109 that showed high expression of genes involved in iron metabolism and genes promoting the accumulation of sphingolipids, phospholipids, and ergosterol. These results highlight different evolutionary adaptations enabling S. cerevisiae to strive in lignocellulosic hydrolysates and suggest novel gene targets for improving fermentation performance and robustness. IMPORTANCE The need for sustainable alternatives to oil-based production of biochemicals and biofuels is undisputable. Saccharomyces cerevisiae is the most commonly used industrial fermentation workhorse. The fermentation of lignocellulosic hydrolysates, second-generation biomass unsuited for food and feed, is still hampered by lowered productivities as the raw material is inhibitory for the cells. In order to map the genetic responses of different S. cerevisiae strains, we performed RNA sequencing of a CEN.PK laboratory strain, two industrial strains (KE6-12 and Ethanol Red), and two wild-type isolates of the LBCM collection when cultivated anaerobically in wheat straw hydrolysate. While the response to inhibitors of S. cerevisiae has been studied earlier, this has in previous studies been done in aerobic conditions. The transcriptomic analysis highlights different evolutionary adaptations among the different S. cerevisiae strains and suggests novel gene targets for improving fermentation performance and robustness.
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Affiliation(s)
- Elena Cámara
- Division of Industrial Biotechnology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Maurizio Mormino
- Division of Industrial Biotechnology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Verena Siewers
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Yvonne Nygård
- Division of Industrial Biotechnology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- VTT Technical Research Centre of Finland, Espoo, Finland
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Zbieralski K, Staszewski J, Konczak J, Lazarewicz N, Nowicka-Kazmierczak M, Wawrzycka D, Maciaszczyk-Dziubinska E. Multilevel Regulation of Membrane Proteins in Response to Metal and Metalloid Stress: A Lesson from Yeast. Int J Mol Sci 2024; 25:4450. [PMID: 38674035 PMCID: PMC11050377 DOI: 10.3390/ijms25084450] [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: 03/07/2024] [Revised: 04/06/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
In the face of flourishing industrialization and global trade, heavy metal and metalloid contamination of the environment is a growing concern throughout the world. The widespread presence of highly toxic compounds of arsenic, antimony, and cadmium in nature poses a particular threat to human health. Prolonged exposure to these toxins has been associated with severe human diseases, including cancer, diabetes, and neurodegenerative disorders. These toxins are known to induce analogous cellular stresses, such as DNA damage, disturbance of redox homeostasis, and proteotoxicity. To overcome these threats and improve or devise treatment methods, it is crucial to understand the mechanisms of cellular detoxification in metal and metalloid stress. Membrane proteins are key cellular components involved in the uptake, vacuolar/lysosomal sequestration, and efflux of these compounds; thus, deciphering the multilevel regulation of these proteins is of the utmost importance. In this review, we summarize data on the mechanisms of arsenic, antimony, and cadmium detoxification in the context of membrane proteome. We used yeast Saccharomyces cerevisiae as a eukaryotic model to elucidate the complex mechanisms of the production, regulation, and degradation of selected membrane transporters under metal(loid)-induced stress conditions. Additionally, we present data on orthologues membrane proteins involved in metal(loid)-associated diseases in humans.
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Affiliation(s)
| | | | | | | | | | | | - Ewa Maciaszczyk-Dziubinska
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland; (K.Z.); (J.S.); (J.K.); (N.L.); (M.N.-K.); (D.W.)
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Samakkarn W, Vandecruys P, Moreno MRF, Thevelein J, Ratanakhanokchai K, Soontorngun N. New biomarkers underlying acetic acid tolerance in the probiotic yeast Saccharomyces cerevisiae var. boulardii. Appl Microbiol Biotechnol 2024; 108:153. [PMID: 38240846 PMCID: PMC10799125 DOI: 10.1007/s00253-023-12946-x] [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: 08/15/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 01/22/2024]
Abstract
Evolutionary engineering experiments, in combination with omics technologies, revealed genetic markers underpinning the molecular mechanisms behind acetic acid stress tolerance in the probiotic yeast Saccharomyces cerevisiae var. boulardii. Here, compared to the ancestral Ent strain, evolved yeast strains could quickly adapt to high acetic acid levels (7 g/L) and displayed a shorter lag phase of growth. Bioinformatic-aided whole-genome sequencing identified genetic changes associated with enhanced strain robustness to acetic acid: a duplicated sequence in the essential endocytotic PAN1 gene, mutations in a cell wall mannoprotein (dan4Thr192del), a lipid and fatty acid transcription factor (oaf1Ser57Pro) and a thiamine biosynthetic enzyme (thi13Thr332Ala). Induction of PAN1 and its associated endocytic complex SLA1 and END3 genes was observed following acetic acid treatment in the evolved-resistant strain when compared to the ancestral strain. Genome-wide transcriptomic analysis of the evolved Ent acid-resistant strain (Ent ev16) also revealed a dramatic rewiring of gene expression among genes associated with cellular transport, metabolism, oxidative stress response, biosynthesis/organization of the cell wall, and cell membrane. Some evolved strains also displayed better growth at high acetic acid concentrations and exhibited adaptive metabolic profiles with altered levels of secreted ethanol (4.0-6.4% decrease), glycerol (31.4-78.5% increase), and acetic acid (53.0-60.3% increase) when compared to the ancestral strain. Overall, duplication/mutations and transcriptional alterations are key mechanisms driving improved acetic acid tolerance in probiotic strains. We successfully used adaptive evolutionary engineering to rapidly and effectively elucidate the molecular mechanisms behind important industrial traits to obtain robust probiotic yeast strains for myriad biotechnological applications. KEY POINTS: •Acetic acid adaptation of evolutionary engineered robust probiotic yeast S. boulardii •Enterol ev16 with altered genetic and transcriptomic profiles survives in up to 7 g/L acetic acid •Improved acetic acid tolerance of S. boulardii ev16 with mutated PAN1, DAN4, OAF1, and THI13 genes.
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Affiliation(s)
- Wiwan Samakkarn
- Excellent Research Laboratory for Yeast Innovation, Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Paul Vandecruys
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Heverlee, Belgium
- Center for Microbiology, VIB, Leuven, Flanders, Belgium
| | - Maria Remedios Foulquié Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Heverlee, Belgium
- Center for Microbiology, VIB, Leuven, Flanders, Belgium
| | - Johan Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Heverlee, Belgium
- Center for Microbiology, VIB, Leuven, Flanders, Belgium
- NovelYeast Bv, Open Bio-Incubator, Erasmus High School, (Jette), Brussels, Belgium
| | - Khanok Ratanakhanokchai
- Excellent Research Laboratory for Yeast Innovation, Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Nitnipa Soontorngun
- Excellent Research Laboratory for Yeast Innovation, Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.
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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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Li M, Chu Y, Dong X, Ji H. General mechanisms of weak acid-tolerance and current strategies for the development of tolerant yeasts. World J Microbiol Biotechnol 2023; 40:49. [PMID: 38133718 DOI: 10.1007/s11274-023-03875-y] [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: 11/01/2023] [Accepted: 12/16/2023] [Indexed: 12/23/2023]
Abstract
Yeast cells are often subjected to various types of weak acid stress in the process of industrial production, food processing, and preservation, resulting in growth inhibition and reduced fermentation performance. Under acidic conditions, weak acids enter the near-neutral yeast cytoplasm and dissociate into protons and anions, leading to cytoplasmic acidification and cell damage. Although some yeast strains have developed the ability to survive weak acids, the complexity and diversity of stresses during industrial production still require the application of appropriate strategies for phenotypes improvement. In this review, we summarized current knowledge concerning weak acid stress response and resistance, which may suggest important targets for further construction of more robust strains. We also highlight current feasible strategies for improving the weak acid resistance of yeasts, such as adaptive laboratory evolution, transcription factors engineering, and cell membrane/wall engineering. Moreover, the challenges and perspectives associated with improving the competitiveness of industrial strains are also discussed. This review provides effective strategies for improving the industrial phenotypes of yeast from multiple dimensions in future studies.
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Affiliation(s)
- Mengmeng Li
- Institute of Life Sciences, College of Life and Environmental Science, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China
- Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China
| | - Yunfei Chu
- Institute of Life Sciences, College of Life and Environmental Science, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China
- Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China
| | - Xiameng Dong
- Department of Agriculture and Biotechnology, Wenzhou Vocational College of Science and Technology, Wenzhou, Zhejiang, 325006, PR China.
| | - Hao Ji
- Institute of Life Sciences, College of Life and Environmental Science, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China.
- Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China.
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Dolpatcha S, Phong HX, Thanonkeo S, Klanrit P, Yamada M, Thanonkeo P. Adaptive laboratory evolution under acetic acid stress enhances the multistress tolerance and ethanol production efficiency of Pichia kudriavzevii from lignocellulosic biomass. Sci Rep 2023; 13:21000. [PMID: 38017261 PMCID: PMC10684600 DOI: 10.1038/s41598-023-48408-7] [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: 08/05/2023] [Accepted: 11/26/2023] [Indexed: 11/30/2023] Open
Abstract
Second-generation bioethanol production using lignocellulosic biomass as feedstock requires a highly efficient multistress-tolerant yeast. This study aimed to develop a robust yeast strain of P. kudriavzevii via the adaptive laboratory evolution (ALE) technique. The parental strain of P. kudriavzevii was subjected to repetitive long-term cultivation in medium supplemented with a gradually increasing concentration of acetic acid, the major weak acid liberated during the lignocellulosic pretreatment process. Three evolved P. kudriavzevii strains, namely, PkAC-7, PkAC-8, and PkAC-9, obtained in this study exhibited significantly higher resistance toward multiple stressors, including heat, ethanol, osmotic stress, acetic acid, formic acid, furfural, 5-(hydroxymethyl) furfural (5-HMF), and vanillin. The fermentation efficiency of the evolved strains was also improved, yielding a higher ethanol concentration, productivity, and yield than the parental strain, using undetoxified sugarcane bagasse hydrolysate as feedstock. These findings provide evidence that ALE is a practical approach for increasing the multistress tolerance of P. kudriavzevii for stable and efficient second-generation bioethanol production from lignocellulosic biomass.
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Affiliation(s)
- Sureeporn Dolpatcha
- Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Huynh Xuan Phong
- Department of Microbial Biotechnology, Institute of Food and Biotechnology, Can Tho University, Can Tho, 900000, Vietnam
| | - Sudarat Thanonkeo
- Walai Rukhavej Botanical Research Institute, Mahasarakham University, Maha Sarakham, 44150, Thailand
| | - Preekamol Klanrit
- Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen, 40002, Thailand
- Fermentation Research Center for Value Added Agricultural Products (FerVAAPs), Faculty of Technology, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Mamoru Yamada
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515, Japan
- Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | - Pornthap Thanonkeo
- Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen, 40002, Thailand.
- Fermentation Research Center for Value Added Agricultural Products (FerVAAPs), Faculty of Technology, Khon Kaen University, Khon Kaen, 40002, Thailand.
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10
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Saha N, Swagatika S, Tomar RS. Investigation of the acetic acid stress response in Saccharomyces cerevisiae with mutated H3 residues. MICROBIAL CELL (GRAZ, AUSTRIA) 2023; 10:217-232. [PMID: 37746586 PMCID: PMC10513452 DOI: 10.15698/mic2023.10.806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 09/26/2023]
Abstract
Enhanced levels of acetic acid reduce the activity of yeast strains employed for industrial fermentation-based applications. Therefore, unraveling the genetic factors underlying the regulation of the tolerance and sensitivity of yeast towards acetic acid is imperative for optimising various industrial processes. In this communication, we have attempted to decipher the acetic acid stress response of the previously reported acetic acid-sensitive histone mutants. Revalidation using spot-test assays and growth curves revealed that five of these mutants, viz., H3K18Q, H3S28A, H3K42Q, H3Q68A, and H3F104A, are most sensitive towards the tested acetic acid concentrations. These mutants demonstrated enhanced acetic acid stress response as evidenced by the increased expression levels of AIF1, reactive oxygen species (ROS) generation, chromatin fragmentation, and aggregated actin cytoskeleton. Additionally, the mutants exhibited active cell wall damage response upon acetic acid treatment, as demonstrated by increased Slt2-phosphorylation and expression of cell wall integrity genes. Interestingly, the mutants demonstrated increased sensitivity to cell wall stress-causing agents. Finally, screening of histone H3 N-terminal tail truncation mutants revealed that the tail truncations exhibit general sensitivity to acetic acid stress. Some of these N-terminal tail truncation mutants viz., H3 [del 1-24], H3 [del 1-28], H3 [del 9-24], and H3 [del 25-36] are also sensitive to cell wall stress agents such as Congo red and caffeine suggesting that their enhanced acetic acid sensitivity may be due to cell wall stress induced by acetic acid.
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Affiliation(s)
- Nitu Saha
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, 462066, Madhya Pradesh, India
| | - Swati Swagatika
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, 462066, Madhya Pradesh, India
| | - Raghuvir Singh Tomar
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, 462066, Madhya Pradesh, India
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11
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Zhang J, Wysocki R, Li F, Yu M, Martinoia E, Song WY. Role of ubiquitination in arsenic tolerance in plants. TRENDS IN PLANT SCIENCE 2023; 28:880-892. [PMID: 37002000 DOI: 10.1016/j.tplants.2023.03.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/18/2023] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
Arsenic (As) is harmful to all living organisms, including humans and plants. To limit As uptake and avoid its toxicity, plants employ systems that regulate the uptake of As from the soil and its translocation from roots to grains. Ubiquitination, a highly conserved post-translational modification (PTM) in all eukaryotes, plays crucial roles in modulating As detoxification mechanisms in budding yeast (Saccharomyces cerevisiae), but little is known about its roles in As tolerance and transport in plants. In this opinion article we review recent findings and suggest that ubiquitination plays a crucial role in regulating As transport in plants. We also propose ideas for future research to explore the importance of ubiquitination for enhancing As tolerance in crops.
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Affiliation(s)
- Jie Zhang
- Research Center for Environmental Membrane Biology and Department of Horticulture, Foshan University, Foshan, Guangdong 528000, China
| | - Robert Wysocki
- Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Fangbai Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Min Yu
- Research Center for Environmental Membrane Biology and Department of Horticulture, Foshan University, Foshan, Guangdong 528000, China.
| | - Enrico Martinoia
- Research Center for Environmental Membrane Biology and Department of Horticulture, Foshan University, Foshan, Guangdong 528000, China; Institute of Plant Biology, University Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.
| | - Won-Yong Song
- Research Center for Environmental Membrane Biology and Department of Horticulture, Foshan University, Foshan, Guangdong 528000, China; Department of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
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12
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Mochizuki T, Tanigawa T, Shindo S, Suematsu M, Oguchi Y, Mioka T, Kato Y, Fujiyama M, Hatano E, Yamaguchi M, Chibana H, Abe F. Activation of CWI pathway through high hydrostatic pressure, enhancing glycerol efflux via the aquaglyceroporin Fps1 in Saccharomyces cerevisiae. Mol Biol Cell 2023; 34:ar92. [PMID: 37379203 PMCID: PMC10398897 DOI: 10.1091/mbc.e23-03-0086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/26/2023] [Accepted: 06/22/2023] [Indexed: 06/30/2023] Open
Abstract
The fungal cell wall is the initial barrier for the fungi against diverse external stresses, such as osmolarity changes, harmful drugs, and mechanical injuries. This study explores the roles of osmoregulation and the cell-wall integrity (CWI) pathway in response to high hydrostatic pressure in the yeast Saccharomyces cerevisiae. We demonstrate the roles of the transmembrane mechanosensor Wsc1 and aquaglyceroporin Fps1 in a general mechanism to maintain cell growth under high-pressure regimes. The promotion of water influx into cells at 25 MPa, as evident by an increase in cell volume and a loss of the plasma membrane eisosome structure, activates the CWI pathway through the function of Wsc1. Phosphorylation of Slt2, the downstream mitogen-activated protein kinase, was increased at 25 MPa. Glycerol efflux increases via Fps1 phosphorylation, which is initiated by downstream components of the CWI pathway, and contributes to the reduction in intracellular osmolarity under high pressure. The elucidation of the mechanisms underlying adaptation to high pressure through the well-established CWI pathway could potentially translate to mammalian cells and provide novel insights into cellular mechanosensation.
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Affiliation(s)
- Takahiro Mochizuki
- Department of Chemistry and Biological Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Toshiki Tanigawa
- Department of Chemistry and Biological Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Seiya Shindo
- Department of Chemistry and Biological Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Momoka Suematsu
- Department of Chemistry and Biological Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Yuki Oguchi
- Center for Instrumental Analysis, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Tetsuo Mioka
- Department of Chemistry and Biological Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Yusuke Kato
- Department of Chemistry and Biological Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Mina Fujiyama
- Department of Chemistry and Biological Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Eri Hatano
- Department of Chemistry and Biological Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Masashi Yamaguchi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
| | - Hiroji Chibana
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
| | - Fumiyoshi Abe
- Department of Chemistry and Biological Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
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13
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Wagner ER, Gasch AP. Advances in S. cerevisiae Engineering for Xylose Fermentation and Biofuel Production: Balancing Growth, Metabolism, and Defense. J Fungi (Basel) 2023; 9:786. [PMID: 37623557 PMCID: PMC10455348 DOI: 10.3390/jof9080786] [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: 06/14/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Genetically engineering microorganisms to produce chemicals has changed the industrialized world. The budding yeast Saccharomyces cerevisiae is frequently used in industry due to its genetic tractability and unique metabolic capabilities. S. cerevisiae has been engineered to produce novel compounds from diverse sugars found in lignocellulosic biomass, including pentose sugars, like xylose, not recognized by the organism. Engineering high flux toward novel compounds has proved to be more challenging than anticipated since simply introducing pathway components is often not enough. Several studies show that the rewiring of upstream signaling is required to direct products toward pathways of interest, but doing so can diminish stress tolerance, which is important in industrial conditions. As an example of these challenges, we reviewed S. cerevisiae engineering efforts, enabling anaerobic xylose fermentation as a model system and showcasing the regulatory interplay's controlling growth, metabolism, and stress defense. Enabling xylose fermentation in S. cerevisiae requires the introduction of several key metabolic enzymes but also regulatory rewiring of three signaling pathways at the intersection of the growth and stress defense responses: the RAS/PKA, Snf1, and high osmolarity glycerol (HOG) pathways. The current studies reviewed here suggest the modulation of global signaling pathways should be adopted into biorefinery microbial engineering pipelines to increase efficient product yields.
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Affiliation(s)
- Ellen R. Wagner
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Audrey P. Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
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14
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Romero-Aguilar L, Hernández-Morfín KD, Guerra-Sánchez G, Pardo JP. Metabolic Changes and Antioxidant Response in Ustilago maydis Grown in Acetate. J Fungi (Basel) 2023; 9:749. [PMID: 37504737 PMCID: PMC10381545 DOI: 10.3390/jof9070749] [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: 05/03/2023] [Revised: 06/29/2023] [Accepted: 07/06/2023] [Indexed: 07/29/2023] Open
Abstract
Ustilago maydis is an important model to study intermediary and mitochondrial metabolism, among other processes. U. maydis can grow, at very different rates, on glucose, lactate, glycerol, and ethanol as carbon sources. Under nitrogen starvation and glucose as the only carbon source, this fungus synthesizes and accumulates neutral lipids in the form of lipid droplets (LD). In this work, we studied the accumulation of triacylglycerols in cells cultured in a medium containing acetate, a direct precursor of the acetyl-CoA required for the synthesis of fatty acids. The metabolic adaptation of cells to acetate was studied by measuring the activities of key enzymes involved in glycolysis, gluconeogenesis, and the pentose phosphate pathways. Since growth on acetate induces oxidative stress, the activities of some antioxidant enzymes were also assayed. The results show that cells grown in acetate plus nitrate did not increase the amount of LD, but increased the activities of glutathione reductase, glutathione peroxidase, catalase, and superoxide dismutase, suggesting a higher production of reactive oxygen species in cells growing in acetate. The phosphofructokinase-1 (PFK1) was the enzyme with the lowest specific activity in the glycolytic pathway, suggesting that PFK1 controls the flux of glycolysis. As expected, the activity of the phosphoenolpyruvate carboxykinase, a gluconeogenic enzyme, was present only in the acetate condition. In summary, in the presence of acetate as the only carbon source, U. maydis synthesized fatty acids, which were directed into the production of phospholipids and neutral lipids for biomass generation, but without any excessive accumulation of LD.
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Affiliation(s)
- Lucero Romero-Aguilar
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Interior, Ciudad Universitaria, Coyoacán, Ciudad de México C.P. 04510, Mexico
| | - Katia Daniela Hernández-Morfín
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N Santo Tomás, Miguel Hidalgo, Ciudad de México C.P. 11340, Mexico
| | - Guadalupe Guerra-Sánchez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N Santo Tomás, Miguel Hidalgo, Ciudad de México C.P. 11340, Mexico
| | - Juan Pablo Pardo
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Interior, Ciudad Universitaria, Coyoacán, Ciudad de México C.P. 04510, Mexico
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15
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Nagy L, Vonk P, Künzler M, Földi C, Virágh M, Ohm R, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu X, Nan S, Pareek M, Sahu N, Szathmári B, Varga T, Wu H, Yang X, Merényi Z. Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Stud Mycol 2023; 104:1-85. [PMID: 37351542 PMCID: PMC10282164 DOI: 10.3114/sim.2022.104.01] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/02/2022] [Indexed: 01/09/2024] Open
Abstract
Fruiting bodies (sporocarps, sporophores or basidiomata) of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates their growth, tissue differentiation and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is still limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim at a comprehensive identification of conserved genes related to fruiting body morphogenesis and distil novel functional hypotheses for functionally poorly characterised ones. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported to be involved in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defence, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1 480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10 % of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Citation: Nagy LG, Vonk PJ, Künzler M, Földi C, Virágh M, Ohm RA, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu XB, Nan S, M. Pareek M, Sahu N, Szathmári B, Varga T, Wu W, Yang X, Merényi Z (2023). Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Studies in Mycology 104: 1-85. doi: 10.3114/sim.2022.104.01.
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Affiliation(s)
- L.G. Nagy
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - P.J. Vonk
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands;
| | - M. Künzler
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland;
| | - C. Földi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - M. Virágh
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - R.A. Ohm
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands;
| | - F. Hennicke
- Project Group Genetics and Genomics of Fungi, Chair Evolution of Plants and Fungi, Ruhr-University Bochum, 44780, Bochum, North Rhine-Westphalia, Germany;
| | - B. Bálint
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - Á. Csernetics
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - B. Hegedüs
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - Z. Hou
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - X.B. Liu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - S. Nan
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - M. Pareek
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - N. Sahu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - B. Szathmári
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - T. Varga
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - H. Wu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - X. Yang
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Z. Merényi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
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16
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Li C, Lu J, Yan XJ, Li CW, Lin LC, Xiao DG, Zhang CY. The eisosomes contribute to acid tolerance of yeast by maintaining cell membrane integrity. Food Microbiol 2023; 110:104157. [DOI: 10.1016/j.fm.2022.104157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 09/13/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022]
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17
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Ye PL, Yuan B, Wang XQ, Zhang MM, Zhao XQ. Modification of Phosphorylation Sites in the Yeast Lysine Methyltransferase Set5 Exerts Influences on the Mitogen-Activated Protein Kinase Hog1 under Prolonged Acetic Acid Stress. Microbiol Spectr 2023; 11:e0301122. [PMID: 36975803 PMCID: PMC10100857 DOI: 10.1128/spectrum.03011-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 02/27/2023] [Indexed: 03/29/2023] Open
Abstract
Responses to acetic acid toxicity in the budding yeast Saccharomyces cerevisiae have widespread implications in the biorefinery of lignocellulosic biomass and food preservation. Our previous studies revealed that Set5, the yeast lysine methyltransferase and histone H4 methyltransferase, was involved in acetic acid stress tolerance. However, it is still mysterious how Set5 functions and interacts with the known stress signaling network. Here, we revealed that elevated phosphorylation of Set5 during acetic acid stress is accompanied by enhanced expression of the mitogen-activated protein kinase (MAPK) Hog1. Further experiments uncovered that the phosphomimetic mutation of Set5 endowed yeast cells with improved growth and fermentation performance and altered transcription of specific stress-responsive genes. Intriguingly, Set5 was found to bind the coding region of HOG1 and regulate its transcription, along with increased expression and phosphorylation of Hog1. A protein-protein interaction between Set5 and Hog1 was also revealed. In addition, modification of Set5 phosphosites was shown to regulate reactive oxygen species (ROS) accumulation, which is known to affect yeast acetic acid stress tolerance. The findings in this study imply that Set5 may function together with the central kinase Hog1 to coordinate cell growth and metabolism in response to stress. IMPORTANCE Hog1 is the yeast homolog of p38 MAPK in mammals that is conserved across eukaryotes, and it plays crucial roles in stress tolerance, fungal pathogenesis, and disease treatments. Here, we provide evidence that modification of Set5 phosphorylation sites regulates the expression and phosphorylation of Hog1, which expands current knowledge on upstream regulation of the Hog1 stress signaling network. Set5 and its homologous proteins are present in humans and various eukaryotes. The newly identified effects of Set5 phosphorylation site modifications in this study benefit an in-depth understanding of eukaryotic stress signaling, as well as the treatment of human diseases.
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Affiliation(s)
- Pei-Liang Ye
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Bing Yuan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xue-Qing Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ming-Ming Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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18
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A Genome-Wide Phenotypic Analysis of Saccharomyces cerevisiae’s Adaptive Response and Tolerance to Chitosan in Conditions Relevant for Winemaking. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9020172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
In the wine industry, the use of chitosan, a non-toxic biodegradable polysaccharide with antimicrobial properties, has been gaining interest with respect to envisaging the reduction in the use of sulfur dioxide (SO2). Although the mechanisms of toxicity of chitosan against fungal cells have been addressed before, most of the studies undertaken used other sources of chitosan and/or used conditions to solubilize the polymer that were not compatible with winemaking. Herein, the effect of a commercial formulation of chitosan approved for use in winemaking over the growth of the spoilage yeast species Dekkera anomala, Saccharomycodes ludwigii, Zygosaccharomyces bailii, and Pichia anomala was assessed. At the legally allowed concentration of 0.1 g/L, chitosan inhibited the growth of all spoilage yeasts, except for the tested Pichia anomala strains. Interestingly, the highly SO2-tolerant yeasts S. ludwigii and Z. bailii were highly susceptible to chitosan. The growth of commercial Saccharomyces cerevisiae was also impacted by chitosan, in a strain-dependent manner, albeit at higher concentrations. To dissect this differential inhibitory potential and gain further insight into the interaction of chitosan over fungal cells, we explored a chemogenomic analysis to identify all of the S. cerevisiae genes conferring protection against or increasing susceptibility to the commercial formulation of chitosan. Among the genes found to confer protection against chitosan, a high proportion was found to encode proteins required for the assembly and structuring of the cell wall, enzymes involved in the synthesis of plasma membrane lipids, and components of signaling pathways that respond to damages in the plasma membrane (e.g., the Rim101 pathway). The data obtained also suggest that the fungal ribosome and the vacuolar V-ATPase could be directly targeted by chitosan, since the deletion of genes encoding proteins required for the structure and function of these organelles was found to increase tolerance to chitosan. We also demonstrated, for the first time, that the deletion of ITR1, AGP2 and FPS1, encoding plasma membrane transporters, prominently increased the tolerance of S. cerevisiae to chitosan, suggesting that they can serve as carriers for chitosan. Besides providing new insights into the mode of action of chitosan against wine yeasts, this study adds relevant information for its rational use as a substitute/complementary preservative to SO2.
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19
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Lu K, Chen X, Yao X, An Y, Wang X, Qin L, Li X, Wang Z, Liu S, Sun Z, Zhang L, Chen L, Li B, Liu B, Wang W, Ding X, Yang Y, Zhang M, Zou S, Dong H. Phosphorylation of a wheat aquaporin at two sites enhances both plant growth and defense. MOLECULAR PLANT 2022; 15:1772-1789. [PMID: 36207815 DOI: 10.1016/j.molp.2022.10.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 08/30/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Eukaryotic aquaporins share the characteristic of functional multiplicity in transporting distinct substrates and regulating various processes, but the underlying molecular basis for this is largely unknown. Here, we report that the wheat (Triticum aestivum) aquaporin TaPIP2;10 undergoes phosphorylation to promote photosynthesis and productivity and to confer innate immunity against pathogens and a generalist aphid pest. In response to elevated atmospheric CO2 concentrations, TaPIP2;10 is phosphorylated at the serine residue S280 and thereafter transports CO2 into wheat cells, resulting in enhanced photosynthesis and increased grain yield. In response to apoplastic H2O2 induced by pathogen or insect attacks, TaPIP2;10 is phosphorylated at S121 and this phosphorylated form transports H2O2 into the cytoplasm, where H2O2 intensifies host defenses, restricting further attacks. Wheat resistance and grain yield could be simultaneously increased by TaPIP2;10 overexpression or by expressing a TaPIP2;10 phosphomimic with aspartic acid substitutions at S121 and S280, thereby improving both crop productivity and immunity.
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Affiliation(s)
- Kai Lu
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China
| | - Xiaochen Chen
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China
| | - Xiaohui Yao
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China
| | - Yuyan An
- College of Life Sciences, Shaanxi Normal University, Xi'an 710019, China
| | - Xuan Wang
- Institute of Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Lina Qin
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China
| | - Xiaoxu Li
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China
| | - Zuodong Wang
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China
| | - Shuo Liu
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China
| | - Zhimao Sun
- College of Life Sciences, Shaanxi Normal University, Xi'an 710019, China
| | - Liyuan Zhang
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China
| | - Lei Chen
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China
| | - Baoyan Li
- Institute of Plant Protection & Resource and Environment, Yantai Academy of Agricultural Sciences, Yantai 265599, China
| | - Baoyou Liu
- Institute of Plant Protection & Resource and Environment, Yantai Academy of Agricultural Sciences, Yantai 265599, China
| | - Weiyang Wang
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China
| | - Xinhua Ding
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China
| | - Yonghua Yang
- Institute of Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Meixiang Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710019, China.
| | - Shenshen Zou
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China.
| | - Hansong Dong
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China.
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20
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Persson K, Stenberg S, Tamás MJ, Warringer J. Adaptation of the yeast gene knockout collection is near-perfectly predicted by fitness and diminishing return epistasis. G3 (BETHESDA, MD.) 2022; 12:6694849. [PMID: 36083011 PMCID: PMC9635671 DOI: 10.1093/g3journal/jkac240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 08/29/2022] [Indexed: 05/31/2023]
Abstract
Adaptive evolution of clonally dividing cells and microbes is the ultimate cause of cancer and infectious diseases. The possibility of constraining the adaptation of cell populations, by inhibiting proteins enhancing the evolvability, has therefore attracted interest. However, our current understanding of how genes influence adaptation kinetics is limited, partly because accurately measuring adaptation for many cell populations is challenging. We used a high-throughput adaptive laboratory evolution platform to track the adaptation of >18,000 cell populations corresponding to single-gene deletion strains in the haploid yeast deletion collection. We report that the preadaptation fitness of gene knockouts near-perfectly (R2= 0.91) predicts their adaptation to arsenic, leaving at the most a marginal role for dedicated evolvability gene functions. We tracked the adaptation of another >23,000 gene knockout populations to a diverse range of selection pressures and generalized the almost perfect (R2=0.72-0.98) capacity of preadaptation fitness to predict adaptation. We also reconstructed mutations in FPS1, ASK10, and ARR3, which together account for almost all arsenic adaptation in wild-type cells, in gene deletions covering a broad fitness range and show that the predictability of arsenic adaptation can be understood as a by global epistasis, where excluding arsenic is more beneficial to arsenic unfit cells. The paucity of genes with a meaningful evolvability effect on adaptation diminishes the prospects of developing adjuvant drugs aiming to slow antimicrobial and chemotherapy resistance.
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Affiliation(s)
- Karl Persson
- Corresponding author: Department of Biology and Biological Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden.
| | - Simon Stenberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Markus J Tamás
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Jonas Warringer
- Corresponding author: Department of Chemistry and Molecular Biology, University of Gothenburg, PO Box 462, 40530 Gothenburg, Sweden.
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21
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Miao Z, Hao H, Yan R, Wang X, Wang B, Sun J, Li Z, Zhang Y, Sun B. Individualization of Chinese alcoholic beverages: Feasibility towards a regulation of organic acids. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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22
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The NPR/Hal family of protein kinases in yeasts: biological role, phylogeny and regulation under environmental challenges. Comput Struct Biotechnol J 2022; 20:5698-5712. [PMID: 36320937 PMCID: PMC9596735 DOI: 10.1016/j.csbj.2022.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/30/2022] [Accepted: 10/02/2022] [Indexed: 11/30/2022] Open
Abstract
Protein phosphorylation is the most common and versatile post-translational modification occurring in eukaryotes. In yeast, protein phosphorylation is fundamental for maintaining cell growth and adapting to sudden changes in environmental conditions by regulating cellular processes and activating signal transduction pathways. Protein kinases catalyze the reversible addition of phosphate groups to target proteins, thereby regulating their activity. In Saccharomyces cerevisiae, kinases are classified into six major groups based on structural and functional similarities. The NPR/Hal family of kinases comprises nine fungal-specific kinases that, due to lack of similarity with the remaining kinases, were classified to the “Other” group. These kinases are primarily implicated in regulating fundamental cellular processes such as maintaining ion homeostasis and controlling nutrient transporters’ concentration at the plasma membrane. Despite their biological relevance, these kinases remain poorly characterized and explored. This review provides an overview of the information available regarding each of the kinases from the NPR/Hal family, including their known biological functions, mechanisms of regulation, and integration in signaling pathways in S. cerevisiae. Information gathered for non-Saccharomyces species of biotechnological or clinical relevance is also included.
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23
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Zhang J, Liu J, Zheng F, Yu M, Shabala S, Song WY. Comparative Analysis of Arsenic Transport and Tolerance Mechanisms: Evolution from Prokaryote to Higher Plants. Cells 2022; 11:cells11172741. [PMID: 36078150 PMCID: PMC9454679 DOI: 10.3390/cells11172741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/18/2022] Open
Abstract
Arsenic (As) is a toxic metalloid for all living organisms and can cause serious harm to humans. Arsenic is also toxic to plants. To alleviate As toxicity, all living organisms (from prokaryotes to higher plants) have evolved comprehensive mechanisms to reduce cytosolic As concentration through the set of As transporters localized at the plasma and tonoplast membranes, which operate either in arsenite As(III) extrusion out of cells (via ArsB, ACR3, and aquaporins) or by sequestering arsenic into vacuoles (by ABC transporters). In addition, a special arsenate resistance mechanism found in some bacterial systems has evolved in an As hyperaccumulating fern Pteris vittata, which involves transforming arsenate As(V) to an As(V) phosphoglycerate derivative by a glyceraldehyde 3-phosphate dehydrogenase and transporting this complex by an efflux transporter. In the present review, we summarize the evolution of these arsenic resistance mechanisms from prokaryotes to eukaryotes and discuss future approaches that could be utilized to better understand and improve As resistance mechanisms in plants.
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Affiliation(s)
- Jie Zhang
- International Centre for Environmental Membrane Biology, Department of Horticulture, School of Food Science and Engineering, Foshan University, Foshan 528011, China
| | - Jiayou Liu
- International Centre for Environmental Membrane Biology, Department of Horticulture, School of Food Science and Engineering, Foshan University, Foshan 528011, China
| | - Fubin Zheng
- International Centre for Environmental Membrane Biology, Department of Horticulture, School of Food Science and Engineering, Foshan University, Foshan 528011, China
| | - Min Yu
- International Centre for Environmental Membrane Biology, Department of Horticulture, School of Food Science and Engineering, Foshan University, Foshan 528011, China
| | - Sergey Shabala
- International Centre for Environmental Membrane Biology, Department of Horticulture, School of Food Science and Engineering, Foshan University, Foshan 528011, China
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, 7001, Australia
- School of Biological Science, University of Western Australia, Perth 6009, Australia
- Correspondence: (S.S.); (W.-Y.S.)
| | - Won-Yong Song
- International Centre for Environmental Membrane Biology, Department of Horticulture, School of Food Science and Engineering, Foshan University, Foshan 528011, China
- Correspondence: (S.S.); (W.-Y.S.)
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24
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Effects of Inhibitors Generated by Dilute Phosphoric Acid Plus Steam-Exploded Poplar on Saccharomyces cerevisiae Growth. Microorganisms 2022; 10:microorganisms10071456. [PMID: 35889176 PMCID: PMC9318740 DOI: 10.3390/microorganisms10071456] [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: 06/29/2022] [Revised: 07/12/2022] [Accepted: 07/15/2022] [Indexed: 12/03/2022] Open
Abstract
The pretreatment of lignocellulosic biomass is important for efficient bioethanol conversion, but causes undesirable by-products that inhibit microbial growth, conversely affecting the bioconversion efficiency. In this study, the main inhibitors derived from dilute phosphoric acid plus steam-exploded poplar wood were identified as 0.22 g/L furfural, 3.63 g/L acetic acid, 0.08 g/L syringaldehyde, etc., indicating the green nature and low toxicity of the pretreatment process. The effects of the three typical inhibitors (furfural, acetic acid, and syringaldehyde) on Saccharomyces cerevisiae 1517RM growth were analyzed and shown to prolong the lag phase of microbial growth to different degrees. In all the inhibitor groups, the ergosterol secretion was boosted, indicating low cell membrane fluidity and robustness of the strain to an adverse environment. The cell electronegativity and morphology of S. cerevisiae 1517RM also changed under different growth conditions, which was helpful for monitoring the physicochemical properties of cells. Furfural, acetic acid, and syringaldehyde had a synergistic effect on each other, providing an important reference to improving the subsequent ethanol fermentation process.
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25
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Zhang X, Nijland JG, Driessen AJM. Combined roles of exporters in acetic acid tolerance in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:67. [PMID: 35717394 PMCID: PMC9206328 DOI: 10.1186/s13068-022-02164-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 06/08/2022] [Indexed: 05/30/2023]
Abstract
Acetic acid is a growth inhibitor generated during alcoholic fermentation and pretreatment of lignocellulosic biomass, a major feedstock to produce bioethanol. An understanding of the acetic acid tolerance mechanisms is pivotal for the industrial production of bioethanol. One of the mechanisms for acetic acid tolerance is transporter-mediated secretion where individual transporters have been implicated. Here, we deleted the transporters Aqr1, Tpo2, and Tpo3, in various combinations, to investigate their combined role in acetic acid tolerance. Single transporter deletions did not impact the tolerance at mild acetic acid stress (20 mM), but at severe stress (50 mM) growth was decreased or impaired. Tpo2 plays a crucial role in acetic acid tolerance, while the AQR1 deletion has a least effect on growth and acetate efflux. Deletion of both Tpo2 and Tpo3 enhanced the severe growth defects at 20 mM acetic acid concomitantly with a reduced rate of acetate secretion, while TPO2 and/or TPO3 overexpression in ∆tpo2∆tpo3∆ restored the tolerance. In the deletion strains, the acetate derived from sugar metabolism accumulated intracellularly, while gene transcription analysis suggests that under these conditions, ethanol metabolism is activated while acetic acid production is reduced. The data demonstrate that Tpo2 and Tpo3 together fulfill an important role in acetate efflux and the acetic acid response.
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Affiliation(s)
- Xiaohuan Zhang
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, Netherlands
| | - Jeroen G Nijland
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, Netherlands
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, Netherlands.
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26
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Kretschmer M, Damoo D, Sun S, Lee CWJ, Croll D, Brumer H, Kronstad J. Organic acids and glucose prime late-stage fungal biotrophy in maize. Science 2022; 376:1187-1191. [PMID: 35679407 DOI: 10.1126/science.abo2401] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Many plant-associated fungi are obligate biotrophs that depend on living hosts to proliferate. However, little is known about the molecular basis of the biotrophic lifestyle, despite the impact of fungi on the environment and food security. In this work, we show that combinations of organic acids and glucose trigger phenotypes that are associated with the late stage of biotrophy for the maize pathogen Ustilago maydis. These phenotypes include the expression of a set of effectors normally observed only during biotrophic development, as well as the formation of melanin associated with sporulation in plant tumors. U. maydis and other hemibiotrophic fungi also respond to a combination of carbon sources with enhanced proliferation. Thus, the response to combinations of nutrients from the host may be a conserved feature of fungal biotrophy.
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Affiliation(s)
- Matthias Kretschmer
- Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Djihane Damoo
- Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Sherry Sun
- Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Christopher W J Lee
- Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Harry Brumer
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - James Kronstad
- Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
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27
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Evaluation of Lignocellulosic Wastewater Valorization with the Oleaginous Yeasts R. kratochvilovae EXF7516 and C. oleaginosum ATCC 20509. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8050204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
During the conversion of lignocellulose, phenolic wastewaters are generated. Therefore, researchers have investigated wastewater valorization processes in which these pollutants are converted to chemicals, i.e., lipids. However, wastewaters are lean feedstocks, so these valorization processes in research typically require the addition of large quantities of sugars and sterilization, which increase costs. This paper investigates a repeated batch fermentation strategy with Rhodotorula kratochvilovae EXF7516 and Cutaneotrichosporon oleaginosum ATCC 20509, without these requirements. The pollutant removal and its conversion to microbial oil were evaluated. Because of the presence of non-monomeric substrates, the ligninolytic enzyme activity was also investigated. The repeated batch fermentation strategy was successful, as more lipids accumulated every cycle, up to a total of 5.4 g/L (23% cell dry weight). In addition, the yeasts consumed up to 87% of monomeric substrates, i.e., sugars, aromatics, and organics acids, and up to 23% of non-monomeric substrates, i.e., partially degraded xylan, lignin, cellulose. Interestingly, lipid production was only observed during the harvest phase of each cycle, as the cells experienced stress, possibly due to oxygen limitation. This work presents the first results on the feasibility of valorizing non-sterilized lignocellulosic wastewater with R. kratochvilovae and C. oleaginosum using a cost-effective repeated batch strategy.
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28
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Gupta A, Rangarajan PN. Histidine is essential for growth of Komagataella phaffii cultured in YPA medium. FEBS Open Bio 2022; 12:1241-1252. [PMID: 35416413 PMCID: PMC9157411 DOI: 10.1002/2211-5463.13408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/26/2022] [Accepted: 04/12/2022] [Indexed: 11/08/2022] Open
Abstract
Komagataella phaffii (a.k.a. Pichia pastoris) requires histidine for optimal growth when cultured in a medium containing yeast extract, peptone (YP) and acetate (YPA). We demonstrate that HIS4-deficient, K. phaffii strain GS115 exhibits a growth defect on YP-media containing acetate, but not on other carbon sources. K. phaffii X33, a prototroph, grows better than K. phaffii GS115 (his4), a histidine auxotroph in YPA. Normal growth of GS115 is restored either by the expression of HIS4 or by culturing in YPA containing ≥0.6 mM histidine. In presence of histidine, expression of several genes is altered including those encoding key subunits of mitochondrial ATP synthase, transporters of amino acids and nutrients, as well as biosynthetic enzymes. Thus, histidine should be included as an essential component for optimal growth of K.phaffii histidine auxotrophs cultured in YPA.
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Affiliation(s)
- Aditi Gupta
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Pundi N Rangarajan
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
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29
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Erian AM, Egermeier M, Marx H, Sauer M. Insights into the glycerol transport of Yarrowia lipolytica. Yeast 2022; 39:323-336. [PMID: 35348234 PMCID: PMC9311158 DOI: 10.1002/yea.3702] [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: 11/24/2021] [Revised: 02/18/2022] [Accepted: 03/07/2022] [Indexed: 12/02/2022] Open
Abstract
Cellular membranes separate cells from the environment and hence, from molecules essential for their survival. To overcome this hurdle, cells developed specialized transport proteins for the transfer of metabolites across these membranes. Crucial metabolites that need to cross the membrane of each living organism, are the carbon sources. While many organisms prefer glucose as a carbon source, the yeast Yarrowia lipolytica seems to favor glycerol over glucose. The fast growth of Y. lipolytica on glycerol and its flexible metabolism renders this yeast a fascinating organism to study the glycerol metabolism. Based on sequence similarities to the known fungal glycerol transporter ScStl1p and glycerol channel ScFps1p, ten proteins of Y. lipolytica were found that are potentially involved in glycerol uptake. To evaluate, which of these proteins is able to transport glycerol in vivo, a complementation assay with a glycerol transport‐deficient strain of Saccharomyces cerevisiae was performed. Six of the ten putative transporters enabled the growth of S. cerevisiae stl1Δ on glycerol and thus, were confirmed as glycerol transporting proteins. Disruption of the transporters in Y. lipolytica abolished its growth on 25 g/L glycerol, but the individual expression of five of the identified glycerol transporters restored growth. Surprisingly, the transporter‐disrupted Y. lipolytica strain retained its ability to grow on high glycerol concentrations. This study provides insight into the glycerol uptake of Y. lipolytica at low glycerol concentrations through the characterization of six glycerol transporters and indicates the existence of further mechanisms active at high glycerol concentrations. Six proteins of Yarrowia lipolytica were identified as glycerol transporters. Two channel proteins and four active transporters facilitated glycerol uptake. Identified transporters are involved in glycerol uptake <25 g/L glycerol. Indication of further glycerol transporters in Y. lipolytica was obtained.
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Affiliation(s)
- Anna M Erian
- CD-Laboratory for Biotechnology of Glycerol, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Michael Egermeier
- CD-Laboratory for Biotechnology of Glycerol, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Hans Marx
- CD-Laboratory for Biotechnology of Glycerol, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Michael Sauer
- CD-Laboratory for Biotechnology of Glycerol, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
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30
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Chen HQ, Xing Q, Cheng C, Zhang MM, Liu CG, Champreda V, Zhao XQ. Identification of Kic1p and Cdc42p as Novel Targets to Engineer Yeast Acetic Acid Stress Tolerance. Front Bioeng Biotechnol 2022; 10:837813. [PMID: 35402407 PMCID: PMC8992792 DOI: 10.3389/fbioe.2022.837813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/09/2022] [Indexed: 11/13/2022] Open
Abstract
Robust yeast strains that are tolerant to multiple stress environments are desired for an efficient biorefinery. Our previous studies revealed that zinc sulfate serves as an important nutrient for stress tolerance of budding yeast Saccharomyces cerevisiae. Acetic acid is a common inhibitor in cellulosic hydrolysate, and the development of acetic acid-tolerant strains is beneficial for lignocellulosic biorefineries. In this study, comparative proteomic studies were performed using S. cerevisiae cultured under acetic acid stress with or without zinc sulfate addition, and novel zinc-responsive proteins were identified. Among the differentially expressed proteins, the protein kinase Kic1p and the small rho-like GTPase Cdc42p, which is required for cell integrity and regulation of cell polarity, respectively, were selected for further studies. Overexpression of KIC1 and CDC42 endowed S. cerevisiae with faster growth and ethanol fermentation under the stresses of acetic acid and mixed inhibitors, as well as in corncob hydrolysate. Notably, the engineered yeast strains showed a 12 h shorter lag phase under the three tested conditions, leading to up to 52.99% higher ethanol productivity than that of the control strain. Further studies showed that the transcription of genes related to stress response was significantly upregulated in the engineered strains under the stress condition. Our results in this study provide novel insights in exploring zinc-responsive proteins for applications of synthetic biology in developing a robust industrial yeast.
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Affiliation(s)
- Hong-Qi Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qi Xing
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Cheng Cheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ming-Ming Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Verawat Champreda
- National Center for Genetic Engineering and Biotechnology, Pathumthani, Thailand
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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31
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Li B, Liu N, Zhao X. Response mechanisms of Saccharomyces cerevisiae to the stress factors present in lignocellulose hydrolysate and strategies for constructing robust strains. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:28. [PMID: 35292082 PMCID: PMC8922928 DOI: 10.1186/s13068-022-02127-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/01/2022] [Indexed: 11/19/2022]
Abstract
Bioconversion of lignocellulosic biomass to biofuels such as bioethanol and high value-added products has attracted great interest in recent decades due to the carbon neutral nature of biomass feedstock. However, there are still many key technical difficulties for the industrial application of biomass bioconversion processes. One of the challenges associated with the microorganism Saccharomyces cerevisiae that is usually used for bioethanol production refers to the inhibition of the yeast by various stress factors. These inhibitive effects seriously restrict the growth and fermentation performance of the strains, resulting in reduced bioethanol production efficiency. Therefore, improving the stress response ability of the strains is of great significance for industrial production of bioethanol. In this article, the response mechanisms of S. cerevisiae to various hydrolysate-derived stress factors including organic acids, furan aldehydes, and phenolic compounds have been reviewed. Organic acids mainly stimulate cells to induce intracellular acidification, furan aldehydes mainly break the intracellular redox balance, and phenolic compounds have a greater effect on membrane homeostasis. These damages lead to inadequate intracellular energy supply and dysregulation of transcription and translation processes, and then activate a series of stress responses. The regulation mechanisms of S. cerevisiae in response to these stress factors are discussed with regard to the cell wall/membrane, energy, amino acids, transcriptional and translational, and redox regulation. The reported key target genes and transcription factors that contribute to the improvement of the strain performance are summarized. Furthermore, the genetic engineering strategies of constructing multilevel defense and eliminating stress effects are discussed in order to provide technical strategies for robust strain construction. It is recommended that robust S. cerevisiae can be constructed with the intervention of metabolic regulation based on the specific stress responses. Rational design with multilevel gene control and intensification of key enzymes can provide good strategies for construction of robust strains.
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Affiliation(s)
- Bo Li
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China.,Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Nan Liu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China.,Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xuebing Zhao
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China. .,Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China.
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32
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Ye PL, Wang XQ, Yuan B, Liu CG, Zhao XQ. Manipulating cell flocculation-associated protein kinases in Saccharomyces cerevisiae enables improved stress tolerance and efficient cellulosic ethanol production. BIORESOURCE TECHNOLOGY 2022; 348:126758. [PMID: 35134528 DOI: 10.1016/j.biortech.2022.126758] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
Cell self-flocculation endows yeast strains with improved environmental stress tolerance that benefits bioproduction. Exploration of the metabolic and regulatory network differences between the flocculating and non-flocculating cells is conducive to developing strains with satisfactory fermentation efficiency. In this work, integrated analyses of transcriptome, proteome, and phosphoproteome were performed using flocculating yeast Saccharomyces cerevisiae SPSC01 and its non-flocculating mutant grown under acetic acid stress, and the results revealed prominent changes in protein kinases. Overexpressing the mitogen-activated protein kinase Hog1 upregulated by flocculation led to reduced ROS accumulation and increased glutathione peroxidase activity, leading to improved ethanol production under stress. Among the seven genes encoding protein kinases that were tested, AKL1 showed the best performance when overexpressed, achieving higher ethanol productivity in both corncob hydrolysate and simulated corn stover hydrolysate. These results provide alternative strategies for improving cellulosic ethanol production by engineering key protein kinases in S. cerevisiae.
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Affiliation(s)
- Pei-Liang Ye
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xue-Qing Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bing Yuan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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de Nadal E, Posas F. OUP accepted manuscript. FEMS Yeast Res 2022; 22:6543702. [PMID: 35254447 PMCID: PMC8953452 DOI: 10.1093/femsyr/foac013] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/28/2022] [Accepted: 03/03/2022] [Indexed: 11/15/2022] Open
Affiliation(s)
- Eulàlia de Nadal
- Corresponding author: Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona c/ Baldiri Reixac, 10. 08028 Barcelona - Spain. E-mail:
| | - Francesc Posas
- Corresponding author: Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona c/ Baldiri Reixac, 10. 08028 Barcelona - Spain. E-mail:
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34
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Yaakoub H, Sanchez NS, Ongay-Larios L, Courdavault V, Calenda A, Bouchara JP, Coria R, Papon N. The high osmolarity glycerol (HOG) pathway in fungi †. Crit Rev Microbiol 2021; 48:657-695. [PMID: 34893006 DOI: 10.1080/1040841x.2021.2011834] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
While fungi are widely occupying nature, many species are responsible for devastating mycosis in humans. Such niche diversity explains how quick fungal adaptation is necessary to endow the capacity of withstanding fluctuating environments and to cope with host-imposed conditions. Among all the molecular mechanisms evolved by fungi, the most studied one is the activation of the phosphorelay signalling pathways, of which the high osmolarity glycerol (HOG) pathway constitutes one of the key molecular apparatus underpinning fungal adaptation and virulence. In this review, we summarize the seminal knowledge of the HOG pathway with its more recent developments. We specifically described the HOG-mediated stress adaptation, with a particular focus on osmotic and oxidative stress, and point out some lags in our understanding of its involvement in the virulence of pathogenic species including, the medically important fungi Candida albicans, Cryptococcus neoformans, and Aspergillus fumigatus, compared to the model yeast Saccharomyces cerevisiae. Finally, we also highlighted some possible applications of the HOG pathway modifications to improve the fungal-based production of natural products in the industry.
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Affiliation(s)
- Hajar Yaakoub
- Univ Angers, Univ Brest, GEIHP, SFR ICAT, Angers, France
| | - Norma Silvia Sanchez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Laura Ongay-Larios
- Unidad de Biología Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Vincent Courdavault
- EA2106 "Biomolécules et Biotechnologies Végétales", Université de Tours, Tours, France
| | | | | | - Roberto Coria
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Nicolas Papon
- Univ Angers, Univ Brest, GEIHP, SFR ICAT, Angers, France
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35
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Zhang J, Hamza A, Xie Z, Hussain S, Brestic M, Tahir MA, Ulhassan Z, Yu M, Allakhverdiev SI, Shabala S. Arsenic transport and interaction with plant metabolism: Clues for improving agricultural productivity and food safety. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 290:117987. [PMID: 34425370 DOI: 10.1016/j.envpol.2021.117987] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/12/2021] [Accepted: 08/14/2021] [Indexed: 05/13/2023]
Abstract
Arsenic (As) is a ubiquitous metalloid that is highly toxic to all living organisms. When grown in As-contaminated soils, plants may accumulate significant amounts of As in the grains or edible shoot parts which then enter a food chain. Plant growth and development per se are also both affected by arsenic. These effects are traditionally attributed to As-induced accumulation of reactive oxygen species (ROS) and a consequent lipid peroxidation and damage to cellular membranes. However, this view is oversimplified, as As exposure have a major impact on many metabolic processes in plants, including availability of essential nutrients, photosynthesis, carbohydrate metabolism, lipid metabolism, protein metabolism, and sulfur metabolism. This review is aimed to fill this gap in the knowledge. In addition, the molecular basis of arsenic uptake and transport in plants and prospects of creating low As-accumulating crop species, for both agricultural productivity and food safety, are discussed.
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Affiliation(s)
- Jie Zhang
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, 528000, China
| | - Ameer Hamza
- School of Environment Science and Engineering, China University of Geoscience, Wuhan, 430074, China; College of Agriculture, University of Sargodha, Sargodha, 40100, Pakistan
| | - Zuoming Xie
- School of Environment Science and Engineering, China University of Geoscience, Wuhan, 430074, China
| | - Sajad Hussain
- College of Agronomy, Sichuan Agricultural University, 211-Huimin Road, Wenjiang, Chengdu, 611130, China.
| | - Marian Brestic
- Department of Plant Physiology, Slovak University of Agriculture, Nitra, Slovak Republic
| | - Mukkram Ali Tahir
- College of Agriculture, University of Sargodha, Sargodha, 40100, Pakistan
| | - Zaid Ulhassan
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Laboratory of Spectroscopy Sensing, Zhejiang University, Hangzhou, 310058, China
| | - Min Yu
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, 528000, China
| | - Suleyman I Allakhverdiev
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, 528000, China; K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya St. 35, Moscow, 127276, Russia
| | - Sergey Shabala
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, 528000, China; Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tas7001, Australia.
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36
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Effect of ammonium acetate on alcohol fermentation in cassava-alcohol fermentation process. Microbiol Res 2021; 256:126868. [PMID: 34972024 DOI: 10.1016/j.micres.2021.126868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/02/2021] [Accepted: 09/15/2021] [Indexed: 11/20/2022]
Abstract
The cassava-alcohol fermentation process employing cassava requires nitrogen source to maximize yields by a commercial strain of S. cerevisiae TG1348. In this study, a factorial experimental design was used to assess a suitable nitrogen source for growth and fermentative performance of S. cerevisiae in cassava-ethanol fermentation. The alcohol fermentation time was about 39 h for urea and ammonium acetate, which was 48 h for ammonium chloride and ammonium sulphate. The fermentation time was reduced by 19 % when using urea and ammonium acetate as nitrogen source. Ammonium acetate leaded to the highest alcohol yield, which was 4% higher than for ammonium sulphate. In addition, byproduct formation differed obviously between the nitrogen sources. The glycerol yields were similar for urea, ammonium sulphate and ammonium chloride but were 24 % lower for ammonium acetate. However, glycerol yield for ammonium carbonate was higher than for other nitrogen sources. Clearly, in batch cultures the ammonium acetate not only increased ethanol generation, but also decreased glycerol generation. In order to understand why ammonium acetate promotes alcohol fermentation, acetic acid was added to different nitrogen sources. The weight loss effect of ammonium sulphate adding acetic acid and ammonium acetate as nitrogen source was the same. The fermentation time was shortened by adding acetic acid. And pH was increased by addition of acetic acid when ammonium sulfate and urea were used as nitrogen sources. The results showed that the acetate root plays an important role in ammonium acetate. The results of this study could facilitate the development of new strategies to control fermentation performance.
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Rendulić T, Alves J, Azevedo-Silva J, Soares-Silva I, Casal M. New insights into the acetate uptake transporter (AceTr) family: Unveiling amino acid residues critical for specificity and activity. Comput Struct Biotechnol J 2021; 19:4412-4425. [PMID: 34471488 PMCID: PMC8379382 DOI: 10.1016/j.csbj.2021.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/02/2021] [Accepted: 08/02/2021] [Indexed: 11/25/2022] Open
Abstract
Substrate specificity of Ato1 was engineered by altering its pore size. The L219A and F98A substitutions enable succinic acid transport activity of Ato1. Ato1 E144A substitution causes dominant negative organic acid hypersensitivity. Organic acid hypersensitivity is caused by the hyperactive ATO1 transporter alleles. First report of a fully functional bacterial transporter (SatP) in yeast.
Aiming at improving the transport of biotechnologically relevant carboxylic acids in engineered microbial cell factories, the focus of this work was to study plasma membrane transporters belonging to the Acetate Uptake Transporter (AceTr) family. Ato1 and SatP, members of this family from Saccharomyces cerevisiae and Escherichia coli, respectively, are the main acetate transporters in these species. The analysis of conserved amino acid residues within AceTr family members combined with the study of Ato1 3D model based on SatP, was the rationale for selection of site-directed mutagenesis targets. The library of Ato1-GFP mutant alleles was functionally analysed in the S. cerevisiae IMX1000 strain which shows residual growth in all carboxylic acids tested. A gain of function phenotype was found for mutations in the residues F98 and L219 located at the central constrictive site of the pore, enabling cells to grow on lactic and on succinic acid. This phenotype was associated with an increased transport activity for these substrates. A dominant negative acetic acid hypersensitivity was induced in S. cerevisiae cells expressing the E144A mutant, which was associated with an increased acetic acid uptake. By utilizing computer-assisted 3D-modelling tools we highlight structural features that explain the acquired traits found in the analysed Ato1 mutants. Additionally, we achieved the proper expression of the Escherichia coli SatP, a homologue of Ato1, in S. cerevisiae. To our knowledge, this constitutes the first report of a fully functional bacterial plasma membrane transporter protein in yeast cells.
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Affiliation(s)
- Toni Rendulić
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Portugal
| | - João Alves
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Portugal
| | - João Azevedo-Silva
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Portugal
| | - Isabel Soares-Silva
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Portugal
| | - Margarida Casal
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Portugal
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38
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Zhang C, Zhou X, Tong T, Ge J. Acetic acid acting as a signaling molecule in the quorum sensing system increases 2,3-butanediol production in Saccharomyces cerevisiae. Prep Biochem Biotechnol 2021; 52:487-497. [PMID: 34431753 DOI: 10.1080/10826068.2021.1966800] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
2,3-Butanediol (2,3-BD) has been extensively used in chemical syntheses. This study aimed to explore acetic acid as a signaling molecule that activates a quorum sensing (QS) system to promote the production of 2,3-BD. The yield of 2,3-BD is proportional to the cell density. Saccharomyces cerevisiae W141 does not produce 2,3-BD when the cell density is lower than the threshold concentration (OD600 nm = 10 or cell density 4.4 × 108 CFU/mL). When 1.5 g/L acetic acid is added, the yield of 2,3-BD is 3.01 ± 0.04 g/L. Subsequently, S. cerevisiae W141 was cocultured with Acetobacter pasteurianus Huniang 1.01 under the optimal conditions, the acetic acid production was increased by 76.7% and 30.6% compared with the original strain and the strain cultivated with 1.5 g/L acetic acid, and the yield of 2,3-BD was increased by 81.9% and 3.3%, respectively. This difference is due to the activity of acetyl lactic acid synthase (ILV2) and 2,3-BD dehydrogenase (BDH1), as the relative expression of the ilv2 and bdh1 genes is increased. The results showed that the biosynthesis of 2,3-BD was regulated by acetic acid as a signaling molecule. S. cerevisiae is a promising host for producing 2,3-BD for industrial applications.
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Affiliation(s)
- Chi Zhang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China.,Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin, China
| | - Xiaohang Zhou
- College of Basic Medicine, Mudanjiang Medical University, Mudanjiang, China
| | - Tianqi Tong
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China.,Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin, China
| | - Jingping Ge
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China.,Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin, China
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Chaves SR, Rego A, Martins VM, Santos-Pereira C, Sousa MJ, Côrte-Real M. Regulation of Cell Death Induced by Acetic Acid in Yeasts. Front Cell Dev Biol 2021; 9:642375. [PMID: 34249904 PMCID: PMC8264433 DOI: 10.3389/fcell.2021.642375] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/04/2021] [Indexed: 11/15/2022] Open
Abstract
Acetic acid has long been considered a molecule of great interest in the yeast research field. It is mostly recognized as a by-product of alcoholic fermentation or as a product of the metabolism of acetic and lactic acid bacteria, as well as of lignocellulosic biomass pretreatment. High acetic acid levels are commonly associated with arrested fermentations or with utilization as vinegar in the food industry. Due to its obvious interest to industrial processes, research on the mechanisms underlying the impact of acetic acid in yeast cells has been increasing. In the past twenty years, a plethora of studies have addressed the intricate cascade of molecular events involved in cell death induced by acetic acid, which is now considered a model in the yeast regulated cell death field. As such, understanding how acetic acid modulates cellular functions brought about important knowledge on modulable targets not only in biotechnology but also in biomedicine. Here, we performed a comprehensive literature review to compile information from published studies performed with lethal concentrations of acetic acid, which shed light on regulated cell death mechanisms. We present an historical retrospective of research on this topic, first providing an overview of the cell death process induced by acetic acid, including functional and structural alterations, followed by an in-depth description of its pharmacological and genetic regulation. As the mechanistic understanding of regulated cell death is crucial both to design improved biomedical strategies and to develop more robust and resilient yeast strains for industrial applications, acetic acid-induced cell death remains a fruitful and open field of study.
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Affiliation(s)
- Susana R Chaves
- Centre of Biological and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| | - António Rego
- Centre of Biological and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| | - Vítor M Martins
- Centre of Biological and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| | - Cátia Santos-Pereira
- Centre of Biological and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal.,Centre of Biological Engineering (CEB), Department of Biological Engineering, University of Minho, Braga, Portugal
| | - Maria João Sousa
- Centre of Biological and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| | - Manuela Côrte-Real
- Centre of Biological and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
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40
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Guaragnella N, Bettiga M. Acetic acid stress in budding yeast: From molecular mechanisms to applications. Yeast 2021; 38:391-400. [PMID: 34000094 PMCID: PMC8361955 DOI: 10.1002/yea.3651] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/13/2021] [Accepted: 05/11/2021] [Indexed: 12/20/2022] Open
Abstract
Acetic acid stress represents a frequent challenge to counteract for yeast cells under several environmental conditions and industrial bioprocesses. The molecular mechanisms underlying its response have been mostly elucidated in the budding yeast Saccharomyces cerevisiae, where acetic acid can be either a physiological substrate or a stressor. This review will focus on acetic acid stress and its response in the context of cellular transport, pH homeostasis, metabolism and stress‐signalling pathways. This information has been integrated with the results obtained by multi‐omics, synthetic biology and metabolic engineering approaches aimed to identify major cellular players involved in acetic acid tolerance. In the production of biofuels and renewable chemicals from lignocellulosic biomass, the improvement of acetic acid tolerance is a key factor. In this view, how this knowledge could be used to contribute to the development and competitiveness of yeast cell factories for sustainable applications will be also discussed. Acetic acid stress is a frequent challenge for budding yeast. Signalling pathways dissection and system‐wide approaches reveal a complex picture. Cell fitness and adaptation under acid stress conditions is environment dependent. Tolerance to acetic acid is a key factor in yeast‐based industrial biotechnology. There is no ‘magic bullet’: An integrated approach is advantageous to develop performing yeast cell factories.
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Affiliation(s)
- Nicoletta Guaragnella
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari A.Moro, Bari, Italy.,Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Rome, Italy
| | - Maurizio Bettiga
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Bioeconomy Division, EviKrets Biobased Processes Consultants, Landvetter, Sweden
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41
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Hahne K, Rödel G, Ostermann K. A fluorescence-based yeast sensor for monitoring acetic acid. Eng Life Sci 2021; 21:303-313. [PMID: 33976603 PMCID: PMC8092980 DOI: 10.1002/elsc.202000006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 11/18/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022] Open
Abstract
Accumulation of acetic acid indicates an imbalance of the process due to a disturbed composition of the microorganisms. Hence, monitoring the acetic acid concentration is an important parameter to control the biogas process. Here, we describe the generation and validation of a fluorescence-based whole cell sensor for the detection of acetic acid based on the yeast Saccharomyces cerevisiae. Acetic acid induces the transcription of a subset of genes. The 5´-regulatory sequences (5´ URS) of these genes were cloned into a multicopy plasmid to drive the expression of a red fluorescent reporter gene. The 5´ URS of YGP1, encoding a cell wall-related glycoprotein, led to a 20-fold increase of fluorescence upon addition of 30 mM acetic acid to the media. We show that the system allows estimating the approximate concentration of acetic acid in condensation samples from a biogas plant. To avoid plasmid loss and increase the long-term stability of the sensor, we integrated the reporter construct into the yeast genome and tested the suitability of spores for long-term storage of sensor cells. Lowering the reporter gene's copy number resulted in a significant drop of the fluorescence, which can be compensated by applying a yeast pheromone-based signal amplification system.
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Affiliation(s)
- Katja Hahne
- Institute of Genetics, Faculty of BiologyTechnische Universität DresdenDresdenGermany
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav CarusTechnische Universität DresdenDresdenGermany
| | - Gerhard Rödel
- Institute of Genetics, Faculty of BiologyTechnische Universität DresdenDresdenGermany
| | - Kai Ostermann
- Institute of Genetics, Faculty of BiologyTechnische Universität DresdenDresdenGermany
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42
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Improving Acetic Acid and Furfural Resistance of Xylose-Fermenting Saccharomyces cerevisiae Strains by Regulating Novel Transcription Factors Revealed via Comparative Transcriptomic Analysis. Appl Environ Microbiol 2021; 87:AEM.00158-21. [PMID: 33712428 DOI: 10.1128/aem.00158-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/04/2021] [Indexed: 11/20/2022] Open
Abstract
Acetic acid and furfural are the two prevalent inhibitors coexisting with glucose and xylose in lignocellulosic hydrolysate. The transcriptional regulations of Saccharomyces cerevisiae in response to acetic acid (Aa), furfural (Fur), and the mixture of acetic acid and furfural (Aa_Fur) were revealed during mixed glucose and xylose fermentation. Carbohydrate metabolism pathways were significantly enriched in response to Aa, while pathways of xenobiotic biodegradation and metabolism were significantly enriched in response to Fur. In addition to these pathways, other pathways were activated in response to Aa_Fur, i.e., cofactor and vitamin metabolism and lipid metabolism. Overexpression of Haa1p or Tye7p improved xylose consumption rates by nearly 50%, while the ethanol yield was enhanced by nearly 8% under acetic acid and furfural stress conditions. Co-overexpression of Haa1p and Tye7p resulted in a 59% increase in xylose consumption rate and a 12% increase in ethanol yield, revealing the beneficial effects of Haa1p and Tye7p on improving the tolerance of yeast to mixed acetic acid and furfural.IMPORTANCE Inhibitor tolerance is essential for S. cerevisiae when fermenting lignocellulosic hydrolysate with various inhibitors, including weak acids, furans, and phenols. The details regarding how xylose-fermenting S. cerevisiae strains respond to multiple inhibitors during fermenting mixed glucose and xylose are still unknown. This study revealed the transcriptional regulation mechanism of an industrial xylose-fermenting S. cerevisiae strain in response to acetic acid and furfural. The transcription factor Haa1p was found to be involved in both acetic acid and furfural tolerance. In addition to Haa1p, four other transcription factors, Hap4p, Yox1p, Tye7p, and Mga1p, were identified as able to improve the resistance of yeast to these two inhibitors. This study underscores the feasibility of uncovering effective transcription factors for constructing robust strains for lignocellulosic bioethanol production.
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43
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Peetermans A, Foulquié-Moreno MR, Thevelein JM. Mechanisms underlying lactic acid tolerance and its influence on lactic acid production in Saccharomyces cerevisiae. MICROBIAL CELL 2021; 8:111-130. [PMID: 34055965 PMCID: PMC8144909 DOI: 10.15698/mic2021.06.751] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the major bottlenecks in lactic acid production using microbial fermentation is the detrimental influence lactic acid accumulation poses on the lactic acid producing cells. The accumulation of lactic acid results in many negative effects on the cell such as intracellular acidification, anion accumulation, membrane perturbation, disturbed amino acid trafficking, increased turgor pressure, ATP depletion, ROS accumulation, metabolic dysregulation and metal chelation. In this review, the manner in which Saccharomyces cerevisiae deals with these issues will be discussed extensively not only for lactic acid as a singular stress factor but also in combination with other stresses. In addition, different methods to improve lactic acid tolerance in S. cerevisiae using targeted and non-targeted engineering methods will be discussed.
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Affiliation(s)
- Arne Peetermans
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001, Leuven-Heverlee, Flanders, Belgium
| | - María R Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001, Leuven-Heverlee, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001, Leuven-Heverlee, Flanders, Belgium.,NovelYeast bv, Open Bio-Incubator, Erasmus High School, Laarbeeklaan 121, 1090 Brussels (Jette), Belgium
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44
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Analysis of the response of the cell membrane of Saccharomyces cerevisiae during the detoxification of common lignocellulosic inhibitors. Sci Rep 2021; 11:6853. [PMID: 33767301 PMCID: PMC7994549 DOI: 10.1038/s41598-021-86135-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 03/11/2021] [Indexed: 01/31/2023] Open
Abstract
Gaining an in-depth understanding of the response of Saccharomyces cerevisiae to the different inhibitors generated during the pretreatment of lignocellulosic material is driving the development of new strains with higher inhibitor tolerances. The objective of this study is to assess, using flow cytometry, how three common inhibitors (vanillin, furfural, and acetic acid) affect the membrane potential, the membrane permeability and the concentration of reactive oxygen species (ROS) during the different fermentations. The membrane potential decreased during the detoxification phase and reflected on the different mechanisms of the toxicity of the inhibitors. While vanillin and furfural caused a metabolic inhibition and a gradual depolarization, acetic acid toxicity was related to fast acidification of the cytosol, causing an immediate depolarization. In the absence of acetic acid, ethanol increased membrane permeability, indicating a possible acquired tolerance to ethanol due to an adaptive response to acetic acid. The intracellular ROS concentration also increased in the presence of the inhibitors, indicating oxidative stress. Measuring these features with flow cytometry allows a real-time assessment of the stress of a cell culture, which can be used in the development of new yeast strains and to design new propagation strategies to pre-adapt the cell cultures to the inhibitors.
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45
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Fungal X-Intrinsic Protein Aquaporin from Trichoderma atroviride: Structural and Functional Considerations. Biomolecules 2021; 11:biom11020338. [PMID: 33672420 PMCID: PMC7927018 DOI: 10.3390/biom11020338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/12/2021] [Accepted: 02/18/2021] [Indexed: 11/24/2022] Open
Abstract
The major intrinsic protein (MIP) superfamily is a key part of the fungal transmembrane transport network. It facilitates the transport of water and low molecular weight solutes across biomembranes. The fungal uncharacterized X-Intrinsic Protein (XIP) subfamily includes the full protein diversity of MIP. Their biological functions still remain fully hypothetical. The aim of this study is still to deepen the diversity and the structure of the XIP subfamily in light of the MIP counterparts—the aquaporins (AQPs) and aquaglyceroporins (AQGPs)—and to describe for the first time their function in the development, biomass accumulation, and mycoparasitic aptitudes of the fungal bioagent Trichoderma atroviride. The fungus-XIP clade, with one member (TriatXIP), is one of the three clades of MIPs that make up the diversity of T. atroviride MIPs, along with the AQPs (three members) and the AQGPs (three members). TriatXIP resembles those of strict aquaporins, predicting water diffusion and possibly other small polar solutes due to particularly wider ar/R constriction with a Lysine substitution at the LE2 position. The XIP loss of function in ∆TriatXIP mutants slightly delays biomass accumulation but does not impact mycoparasitic activities. ∆TriatMIP forms colonies similar to wild type; however, the hyphae are slightly thinner and colonies produce rare chlamydospores in PDA and specific media, most of which are relatively small and exhibit abnormal morphologies. To better understand the molecular causes of these deviant phenotypes, a wide-metabolic survey of the ∆TriatXIPs demonstrates that the delayed growth kinetic, correlated to a decrease in respiration rate, is caused by perturbations in the pentose phosphate pathway. Furthermore, the null expression of the XIP gene strongly impacts the expression of four expressed MIP-encoding genes of T. atroviride, a plausible compensating effect which safeguards the physiological integrity and life cycle of the fungus. This paper offers an overview of the fungal XIP family in the biocontrol agent T. atroviride which will be useful for further functional analysis of this particular MIP subfamily in vegetative growth and the environmental stress response in fungi. Ultimately, these findings have implications for the ecophysiology of Trichoderma spp. in natural, agronomic, and industrial systems.
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Kłosowski G, Mikulski D. Impact of Lignocellulose Pretreatment By-Products on S. cerevisiae Strain Ethanol Red Metabolism during Aerobic and An-aerobic Growth. Molecules 2021; 26:molecules26040806. [PMID: 33557207 PMCID: PMC7913964 DOI: 10.3390/molecules26040806] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 11/16/2022] Open
Abstract
Understanding the specific response of yeast cells to environmental stress factors is the starting point for selecting the conditions of adaptive culture in order to obtain a yeast line with increased resistance to a given stress factor. The aim of the study was to evaluate the specific cellular response of Saccharomyces cerevisiae strain Ethanol Red to stress caused by toxic by-products generated during the pretreatment of lignocellulose, such as levulinic acid, 5-hydroxymethylfurfural, furfural, ferulic acid, syringaldehyde and vanillin. The presence of 5-hydroxymethylfurfural at the highest analyzed concentration (5704.8 ± 249.3 mg/L) under aerobic conditions induced the overproduction of ergosterol and trehalose. On the other hand, under anaerobic conditions (during the alcoholic fermentation), a decrease in the biosynthesis of these environmental stress indicators was observed. The tested yeast strain was able to completely metabolize 5-hydroxymethylfurfural, furfural, syringaldehyde and vanillin, both under aerobic and anaerobic conditions. Yeast cells reacted to the presence of furan aldehydes by overproducing Hsp60 involved in the control of intracellular protein folding. The results may be helpful in optimizing the process parameters of second-generation ethanol production, in order to reduce the formation and toxic effects of fermentation inhibitors.
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47
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Tulha J, Amorim-Rodrigues M, Esquembre LA, Rauch S, Tamás MJ, Lucas C. Physical, genetic and functional interactions between the eisosome protein Pil1 and the MBOAT O-acyltransferase Gup1. FEMS Yeast Res 2020; 21:6045508. [PMID: 33355361 DOI: 10.1093/femsyr/foaa070] [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: 09/29/2020] [Accepted: 12/21/2020] [Indexed: 11/14/2022] Open
Abstract
The Saccharomyces cerevisiae MBOAT O-acyltransferase Gup1 is involved in many processes, including cell wall and membrane composition and integrity, and acetic acid-induced cell death. Gup1 was previously shown to interact physically with the mitochondrial membrane VDAC (Voltage-Dependent Anion Channel) protein Por1 and the ammonium transceptor Mep2. By co-immunoprecipitation, the eisosome core component Pil1 was identified as a novel physical interaction partner of Gup1. The expression of PIL1 and Pil1 protein levels were found to be unaffected by GUP1 deletion. In ∆gup1 cells, Pil1 was distributed in dots (likely representing eisosomes) in the membrane, identically to wt cells. However, ∆gup1 cells presented 50% less Pil1-GFP dots/eisosomes, suggesting that Gup1 is important for eisosome formation. The two proteins also interact genetically in the maintenance of cell wall integrity, and during arsenite and acetic acid exposure. We show that Δgup1 Δpil1 cells take up more arsenite than wt and are extremely sensitive to arsenite and to acetic acid treatments. The latter causes a severe apoptotic wt-like cell death phenotype, epistatically reverting the ∆gup1 necrotic type of death. Gup1 and Pil1 are thus physically, genetically and functionally connected.
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Affiliation(s)
- Joana Tulha
- Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar 4710-057 Braga, Portugal
| | - Mariana Amorim-Rodrigues
- Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar 4710-057 Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar 4710-057 Braga, Portugal
| | - Lidia Alejo Esquembre
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemihuset 412 96 Gothenburg, Sweden
| | - Sebastien Rauch
- Water Environment Technology, Department of Architecture and Civil and Environmental Engineering, Chalmers University of Technology, S-412 96 Gothenburg, Sweden
| | - Markus J Tamás
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemihuset 412 96 Gothenburg, Sweden
| | - Cândida Lucas
- Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar 4710-057 Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar 4710-057 Braga, Portugal
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48
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Vázquez-Ibarra A, Rodríguez-Martínez G, Guerrero-Serrano G, Kawasaki L, Ongay-Larios L, Coria R. Negative feedback-loop mechanisms regulating HOG- and pheromone-MAPK signaling in yeast. Curr Genet 2020; 66:867-880. [PMID: 32564133 DOI: 10.1007/s00294-020-01089-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/08/2020] [Accepted: 06/10/2020] [Indexed: 11/28/2022]
Abstract
The pheromone response and the high osmolarity glycerol (HOG) pathways are considered the prototypical MAPK signaling systems. They are the best-understood pathways in eukaryotic cells, yet they continue to provide insights in how cells relate with the environment. These systems are subjected to tight regulatory circuits to prevent hyperactivation in length and intensity. Failure to do this may be a matter of life or death specially for unicellular organisms such as Saccharomyces cerevisiae. The signaling pathways are fine-tuned by positive and negative feedback loops exerted by pivotal control elements that allow precise responses to specific stimuli, despite the fact that some elements of the systems are common to different signaling pathways. Here we describe the experimentally proven negative feedback loops that modulate the pheromone response and the HOG pathways. As described in this review, MAP kinases are central mechanistic components of these feedback loops. They have the capacity to modulate basal signaling activity, a fast extranuclear response, and a longer-lasting transcriptional process.
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Affiliation(s)
- Araceli Vázquez-Ibarra
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510, México City, México
| | - Griselda Rodríguez-Martínez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510, México City, México
| | | | - Laura Kawasaki
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510, México City, México
| | - Laura Ongay-Larios
- Unidad de Biología Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510, México City, México
| | - Roberto Coria
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510, México City, México.
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Abstract
Opportunistic pathogens such as Candida species can use carboxylic acids, like acetate and lactate, to survive and successfully thrive in different environmental niches. These nonfermentable substrates are frequently the major carbon sources present in certain human body sites, and their efficient uptake by regulated plasma membrane transporters plays a critical role in such nutrient-limited conditions. Here, we cover the physiology and regulation of these proteins and their potential role in Candida virulence. Opportunistic pathogens such as Candida species can use carboxylic acids, like acetate and lactate, to survive and successfully thrive in different environmental niches. These nonfermentable substrates are frequently the major carbon sources present in certain human body sites, and their efficient uptake by regulated plasma membrane transporters plays a critical role in such nutrient-limited conditions. Here, we cover the physiology and regulation of these proteins and their potential role in Candida virulence. This review also presents an evolutionary analysis of orthologues of the Saccharomyces cerevisiae Jen1 lactate and Ady2 acetate transporters, including a phylogenetic analysis of 101 putative carboxylate transporters in twelve medically relevant Candida species. These proteins are assigned to distinct clades according to their amino acid sequence homology and represent the major carboxylic acid uptake systems in yeast. While Jen transporters belong to the sialate:H+ symporter (SHS) family, the Ady2 homologue members are assigned to the acetate uptake transporter (AceTr) family. Here, we reclassify the later members as ATO (acetate transporter ortholog). The new nomenclature will facilitate the study of these transporters, as well as the analysis of their relevance for Candida pathogenesis.
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50
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Shashkova S, Andersson M, Hohmann S, Leake MC. Correlating single-molecule characteristics of the yeast aquaglyceroporin Fps1 with environmental perturbations directly in living cells. Methods 2020; 193:46-53. [PMID: 32387484 DOI: 10.1016/j.ymeth.2020.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/04/2020] [Accepted: 05/04/2020] [Indexed: 01/09/2023] Open
Abstract
Membrane proteins play key roles at the interface between the cell and its environment by mediating selective import and export of molecules via plasma membrane channels. Despite a multitude of studies on transmembrane channels, understanding of their dynamics directly within living systems is limited. To address this, we correlated molecular scale information from living cells with real time changes to their microenvironment. We employed super-resolved millisecond fluorescence microscopy with a single-molecule sensitivity, to track labelled molecules of interest in real time. We use as example the aquaglyceroporin Fps1 in the yeast Saccharomyces cerevisiae to dissect and correlate its stoichiometry and molecular turnover kinetics with various extracellular conditions. We show that Fps1 resides in multi tetrameric clusters while hyperosmotic and oxidative stress conditions cause Fps1 reorganization. Moreover, we demonstrate that rapid exposure to hydrogen peroxide causes Fps1 degradation. In this way we shed new light on aspects of architecture and dynamics of glycerol-permeable plasma membrane channels.
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Affiliation(s)
| | - Mikael Andersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden.
| | - Stefan Hohmann
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden.
| | - Mark C Leake
- Department of Physics, University of York, YO10 5DD York, UK.
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