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Schlarmann P, Sakuragi K, Ikeda A, Yang Y, Sasaki S, Hanaoka K, Araki M, Shibata T, Kanai M, Funato K. The tricalbin family of membrane contact site tethers is involved in the transcriptional responses of S. cerevisiae to glucose. J Biol Chem 2024:107665. [PMID: 39128724 DOI: 10.1016/j.jbc.2024.107665] [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: 03/05/2024] [Revised: 07/24/2024] [Accepted: 08/05/2024] [Indexed: 08/13/2024] Open
Abstract
Cellular organelles maintain areas of close apposition with other organelles at which the cytosolic gap in between them is reduced to a minimum. These membrane contact sites (MCS) are vital for organelle communication and are formed by molecular tethers that physically connect opposing membranes. Although many regulatory pathways are known to converge at MCS, a link between MCS and transcriptional regulation-the primary mechanism through which cells adapt their metabolism to environmental cues-remains largely elusive. In this study, we performed RNA-sequencing on Saccharomyces cerevisiae cells lacking tricalbin proteins (Tcb1, Tcb2, Tcb3), a family of tethering proteins that connect the endoplasmic reticulum with the plasma membrane and Golgi, to investigate if gene expression is altered when MCS are disrupted. Our results indicate that in the tcb1Δ2Δ3Δ strain, pathways responsive to a high-glucose environment, including glycolysis, fermentation, amino acid synthesis, and low-affinity glucose uptake, are upregulated. Conversely, pathways crucial during glucose depletion, such as the tricarboxylic acid (TCA) cycle, respiration, high-affinity glucose uptake, and amino acid uptake are downregulated. In addition, we demonstrate that the altered gene expression of tcb1Δ2Δ3Δ in glucose metabolism correlates with increased growth, glucose consumption, CO2 production, and ethanol generation. In conclusion, our findings reveal that tricalbin protein deletion induces a shift in gene expression patterns mimicking cellular responses to a high-glucose environment. This suggests that MCS play a role in sensing and signaling pathways that modulate gene transcription in response to glucose availability.
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Affiliation(s)
- Philipp Schlarmann
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan
| | - Keiko Sakuragi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan
| | - Atsuko Ikeda
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan
| | - Yujia Yang
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan
| | - Saku Sasaki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan
| | - Kazuki Hanaoka
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan
| | - Misako Araki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan
| | - Tomoko Shibata
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi, Hiroshima 739-0046, Japan
| | - Muneyoshi Kanai
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi, Hiroshima 739-0046, Japan
| | - Kouichi Funato
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan.
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Un Jan Contreras S, Redfern LK, Maguire LW, Promi SI, Gardner CM. Small Interfering RNAs (siRNAs) Negatively Impact Growth and Gene Expression of Environmentally Relevant Bacteria in In Vitro Conditions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:13856-13865. [PMID: 39066708 DOI: 10.1021/acs.est.4c01685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Rising global populations have amplified food scarcity and ushered in the development of genetically modified (GM) crops containing small interference RNAs (siRNAs) that control gene expression to overcome these challenges. The use of RNA interference (RNAi) in agriculture remains controversial due to uncertainty regarding the unintended release of genetic material and downstream nontarget effects, which have not been assessed in environmental bacteria to date. To evaluate the impacts of siRNAs used in agriculture on environmental bacteria, this study assessed microbial growth and viability as well as transcription activity with and without the presence of environmental stressors. Results showed a statistically significant reduction in growth capacity and maximum biomass achieved when bacteria are exposed to siRNAs alone and with additional external stress (p < 0.05). Further transcriptomic analysis demonstrated that nutrient cycling gene activities were found to be consistently and significantly altered following siRNA exposure, particularly among carbon (xylA, FBPase, limEH, Chitinase, rgl, rgh, rgaE, mannanase, ara) and nitrogen (ureC, nasA, narB, narG, nirK) cycling genes (p < 0.05). Decreases in carbon cycling gene transcription profiles were generally significantly enhanced when siRNA exposure was coupled with nutrient or antimicrobial stress. Collectively, findings suggest that certain conditions facilitate the uptake of siRNAs from their surrounding environments that can negatively affect bacterial growth and gene expression activity, with uncertain downstream impacts on ecosystem homeostasis.
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Affiliation(s)
- S Un Jan Contreras
- Department of Civil and Environmental Engineering, Washington State University, 405 Spokane St., Pullman, Washington 99164, United States
| | - L K Redfern
- Department of Bioengineering, Civil Engineering, and Environmental Engineering, Florida Gulf Coast University, 10501 FGCU Blvd., Fort Myers, Florida 33965, United States
| | - L W Maguire
- Maseeh Department of Civil, Architectural, and Environmental Engineering, University of Texas at Austin, 301E E Dean Keeton St c1700, Austin, Texas 78712, United States
| | - S I Promi
- Maseeh Department of Civil, Architectural, and Environmental Engineering, University of Texas at Austin, 301E E Dean Keeton St c1700, Austin, Texas 78712, United States
| | - C M Gardner
- Department of Civil and Environmental Engineering, Washington State University, 405 Spokane St., Pullman, Washington 99164, United States
- Maseeh Department of Civil, Architectural, and Environmental Engineering, University of Texas at Austin, 301E E Dean Keeton St c1700, Austin, Texas 78712, United States
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3
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Ball B, Sukumaran A, Pladwig S, Kazi S, Chan N, Honeywell E, Modrakova M, Geddes-McAlister J. Proteome signatures reveal homeostatic and adaptive oxidative responses by a putative co-chaperone, Wos2, to influence fungal virulence determinants in cryptococcosis. Microbiol Spectr 2024; 12:e0015224. [PMID: 38953322 PMCID: PMC11302251 DOI: 10.1128/spectrum.00152-24] [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: 01/16/2024] [Accepted: 05/27/2024] [Indexed: 07/04/2024] Open
Abstract
The increasing prevalence of invasive fungal pathogens is dramatically changing the clinical landscape of infectious diseases, posing an imminent threat to public health. Specifically, Cryptococcus neoformans, the human opportunistic pathogen, expresses elaborate virulence mechanisms and is equipped with sophisticated adaptation strategies to survive in harsh host environments. This study extensively characterizes Wos2, an Hsp90 co-chaperone homolog, featuring bilateral functioning for both cryptococcal adaptation and the resulting virulence response. In this study, we evaluated the proteome and secretome signatures associated with wos2 deletion in enriched and infection-mimicking conditions to reveal Wos2-dependent regulation of the oxidative stress response through global translational reprogramming. The wos2Δ strain demonstrates defective intracellular and extracellular antioxidant protection systems, measurable through a decreased abundance of critical antioxidant enzymes and reduced growth in the presence of peroxide stress. Additional Wos2-associated stress phenotypes were observed upon fungal challenge with heat shock, osmotic stress, and cell membrane stressors. We demonstrate the importance of Wos2 for intracellular lifestyle of C. neoformans during in vitro macrophage infection and provide evidence for reduced phagosomal replication levels associated with wos2Δ. Accordingly, wos2Δ featured significantly reduced virulence within impacting fungal burden in a murine model of cryptococcosis. Our study highlights a vulnerable point in the fungal chaperone network that offers a therapeutic opportunity to interfere with both fungal virulence and fitness.IMPORTANCEThe global impact of fungal pathogens, both emerging and emerged, is undeniable, and the alarming increase in antifungal resistance rates hampers our ability to protect the global population from deadly infections. For cryptococcal infections, a limited arsenal of antifungals and increasing rates of resistance demand alternative therapeutic strategies, including an anti-virulence approach, which disarms the pathogen of critical virulence factors, empowering the host to remove the pathogens and clear the infection. To this end, we apply state-of-the-art mass spectrometry-based proteomics to evaluate the impact of a recently defined novel co-chaperone, Wos2, toward cryptococcal virulence using in vitro and in vivo models of infection. We explore global proteome and secretome remodeling driven by the protein and uncover the novel role in modulating the fungal oxidative stress response. Complementation of proteome findings with in vitro infectivity assays demonstrated the protective role of Wos2 within the macrophage phagosome, influencing fungal replication and survival. These results underscore differential cryptococcal survivability and weakened patterns of dissemination in the absence of wos2. Overall, our study establishes Wos2 as an important contributor to fungal pathogenesis and warrants further research into critical proteins within global stress response networks as potential druggable targets to reduce fungal virulence and clear infection.
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Affiliation(s)
- Brianna Ball
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Arjun Sukumaran
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Samanta Pladwig
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Samiha Kazi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Norris Chan
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Effie Honeywell
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Manuela Modrakova
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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4
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Panmanee W, Tran MTH, Seye SN, Strome ED. Altered S-AdenosylMethionine availability impacts dNTP pools in Saccharomyces cerevisiae. Yeast 2024; 41:513-524. [PMID: 38961653 DOI: 10.1002/yea.3973] [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: 10/19/2023] [Revised: 04/30/2024] [Accepted: 06/22/2024] [Indexed: 07/05/2024] Open
Abstract
Saccharomyces cerevisiae has long been used as a model organism to study genome instability. The SAM1 and SAM2 genes encode AdoMet synthetases, which generate S-AdenosylMethionine (AdoMet) from Methionine (Met) and ATP. Previous work from our group has shown that deletions of the SAM1 and SAM2 genes cause changes to AdoMet levels and impact genome instability in opposite manners. AdoMet is a key product of methionine metabolism and the major methyl donor for methylation events of proteins, RNAs, small molecules, and lipids. The methyl cycle is interrelated to the folate cycle which is involved in de novo synthesis of purine and pyrimidine deoxyribonucleotides (dATP, dTTP, dCTP, and dGTP). AdoMet also plays a role in polyamine production, essential for cell growth and used in detoxification of reactive oxygen species (ROS) and maintenance of the redox status in cells. This is also impacted by the methyl cycle's role in production of glutathione, another ROS scavenger and cellular protectant. We show here that sam2∆/sam2∆ cells, previously characterized with lower levels of AdoMet and higher genome instability, have a higher level of each dNTP (except dTTP), contributing to a higher overall dNTP pool level when compared to wildtype. Unchecked, these increased levels can lead to multiple types of DNA damage which could account for the genome instability increases in these cells.
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Affiliation(s)
- Warunya Panmanee
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, Kentucky, USA
| | - Men T H Tran
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, Kentucky, USA
| | - Serigne N Seye
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, Kentucky, USA
| | - Erin D Strome
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, Kentucky, USA
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5
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Guo Q, Li J, Wang MR, Zhao M, Zhang G, Tang S, Xiong LB, Gao B, Wang FQ, Wei DZ. Multidimensional engineering of Saccharomyces cerevisiae for the efficient production of heme by exploring the cytotoxicity and tolerance of heme. Metab Eng 2024; 85:46-60. [PMID: 39019249 DOI: 10.1016/j.ymben.2024.07.007] [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: 03/30/2024] [Revised: 06/14/2024] [Accepted: 07/14/2024] [Indexed: 07/19/2024]
Abstract
Heme has attracted considerable attention due to its indispensable biological roles and applications in healthcare and artificial foods. The development and utilization of edible microorganisms instead of animals to produce heme is the most promising method to promote the large-scale industrial production and safe application of heme. However, the cytotoxicity of heme severely restricts its efficient synthesis by microorganisms, and the cytotoxic mechanism is not fully understood. In this study, the effect of heme toxicity on Saccharomyces cerevisiae was evaluated by enhancing its synthesis using metabolic engineering. The results showed that the accumulation of heme after the disruption of heme homeostasis caused serious impairments in cell growth and metabolism, as demonstrated by significantly poor growth, mitochondrial damage, cell deformations, and chapped cell surfaces, and these features which were further associated with substantially elevated reactive oxygen species (ROS) levels within the cell (mainly H2O2 and superoxide anion radicals). To improve cellular tolerance to heme, 5 rounds of laboratory evolution were performed, increasing heme production by 7.3-fold and 4.2-fold in terms of the titer (38.9 mg/L) and specific production capacity (1.4 mg/L/OD600), respectively. Based on comparative transcriptomic analyses, 32 genes were identified as candidates that can be modified to enhance heme production by more than 20% in S. cerevisiae. The combined overexpression of 5 genes (SPS22, REE1, PHO84, HEM4 and CLB2) was shown to be an optimal method to enhance heme production. Therefore, a strain with enhanced heme tolerance and ROS quenching ability (R5-M) was developed that could generate 380.5 mg/L heme with a productivity of 4.2 mg/L/h in fed-batch fermentation, with S. cerevisiae strains being the highest producers reported to date. These findings highlight the importance of improving heme tolerance for the microbial production of heme and provide a solution for efficient heme production by engineered yeasts.
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Affiliation(s)
- Qidi Guo
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Jiacun Li
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Ming-Rui Wang
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Ming Zhao
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Gege Zhang
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Shuyan Tang
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Liang-Bin Xiong
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Bei Gao
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Feng-Qing Wang
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Dong-Zhi Wei
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
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6
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Ardell S, Martsul A, Johnson MS, Kryazhimskiy S. Environment-independent distribution of mutational effects emerges from microscopic epistasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.18.567655. [PMID: 38014325 PMCID: PMC10680819 DOI: 10.1101/2023.11.18.567655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Predicting how new mutations alter phenotypes is difficult because mutational effects vary across genotypes and environments. Recently discovered global epistasis, where the fitness effects of mutations scale with the fitness of the background genotype, can improve predictions, but how the environment modulates this scaling is unknown. We measured the fitness effects of ~100 insertion mutations in 42 strains of Saccharomyces cerevisiae in six laboratory environments and found that the global-epistasis scaling is nearly invariant across environments. Instead, the environment tunes one global parameter, the background fitness at which most mutations switch sign. As a consequence, the distribution of mutational effects is predictable across genotypes and environments. Our results suggest that the effective dimensionality of genotype-to-phenotype maps across environments is surprisingly low.
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Affiliation(s)
- Sarah Ardell
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA 92093
| | - Alena Martsul
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA 92093
| | - Milo S. Johnson
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sergey Kryazhimskiy
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA 92093
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7
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Renganaath K, Albert FW. Trans-eQTL hotspots shape complex traits by modulating cellular states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.14.567054. [PMID: 38014174 PMCID: PMC10680915 DOI: 10.1101/2023.11.14.567054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Regulatory genetic variation shapes gene expression, providing an important mechanism connecting DNA variation and complex traits. The causal relationships between gene expression and complex traits remain poorly understood. Here, we integrated transcriptomes and 46 genetically complex growth traits in a large cross between two strains of the yeast Saccharomyces cerevisiae. We discovered thousands of genetic correlations between gene expression and growth, suggesting potential functional connections. Local regulatory variation was a minor source of these genetic correlations. Instead, genetic correlations tended to arise from multiple independent trans-acting regulatory loci. Trans-acting hotspots that affect the expression of numerous genes accounted for particularly large fractions of genetic growth variation and of genetic correlations between gene expression and growth. Genes with genetic correlations were enriched for similar biological processes across traits, but with heterogeneous direction of effect. Our results reveal how trans-acting regulatory hotspots shape complex traits by altering cellular states.
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Affiliation(s)
- Kaushik Renganaath
- Department of Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Frank W Albert
- Department of Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis, MN 55455, USA
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8
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Akirtava C, May G, McManus CJ. Deciphering the cis-regulatory landscape of natural yeast Transcript Leaders. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.03.601937. [PMID: 39005336 PMCID: PMC11245039 DOI: 10.1101/2024.07.03.601937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Protein synthesis is a vital process that is highly regulated at the initiation step of translation. Eukaryotic 5' transcript leaders (TLs) contain a variety of cis-regulatory features that influence translation and mRNA stability. However, the relative influences of these features in natural TLs are poorly characterized. To address this, we used massively parallel reporter assays (MPRAs) to quantify RNA levels, ribosome loading, and protein levels from 11,027 natural yeast TLs in vivo and systematically compared the relative impacts of their sequence features on gene expression. We found that yeast TLs influence gene expression over two orders of magnitude. While a leaky scanning model using Kozak contexts and uAUGs explained half of the variance in expression across transcript leaders, the addition of other features explained ~70% of gene expression variation. Our analyses detected key cis-acting sequence features, quantified their effects in vivo, and compared their roles to motifs reported from an in vitro study of ribosome recruitment. In addition, our work quantitated the effects of alternative transcription start site usage on gene expression in yeast. Thus, our study provides new quantitative insights into the roles of TL cis-acting sequences in regulating gene expression.
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Affiliation(s)
- Christina Akirtava
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
- RNA Bioscience Initiative, University of Colorado - Anshutz, Aurora, CO, 80045, USA
| | - Gemma May
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - C Joel McManus
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
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9
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Creamer DR, Beynon RJ, Hubbard SJ, Ashe MP, Grant CM. Isoform-specific sequestration of protein kinase A fine-tunes intracellular signaling during heat stress. Cell Rep 2024; 43:114360. [PMID: 38865242 DOI: 10.1016/j.celrep.2024.114360] [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: 12/22/2023] [Revised: 04/24/2024] [Accepted: 05/30/2024] [Indexed: 06/14/2024] Open
Abstract
Protein kinase A (PKA) is a conserved kinase crucial for fundamental biological processes linked to growth, development, and metabolism. The PKA catalytic subunit is expressed as multiple isoforms in diverse eukaryotes; however, their contribution to ensuring signaling specificity in response to environmental cues remains poorly defined. Catalytic subunit activity is classically moderated via interaction with an inhibitory regulatory subunit. Here, a quantitative mass spectrometry approach is used to examine heat-stress-induced changes in the binding of yeast Tpk1-3 catalytic subunits to the Bcy1 regulatory subunit. We show that Tpk3 is not regulated by Bcy1 binding but, instead, is deactivated upon heat stress via reversible sequestration into cytoplasmic granules. These "Tpk3 granules" are enriched for multiple PKA substrates involved in various metabolic processes, with the Hsp42 sequestrase required for their formation. Hence, regulated sequestration of Tpk3 provides a mechanism to control isoform-specific kinase signaling activity during stress conditions.
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Affiliation(s)
- Declan R Creamer
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Robert J Beynon
- Centre for Proteome Research, Institute of Systems and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Simon J Hubbard
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Mark P Ashe
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Chris M Grant
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.
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Wittmann L, Eigenfeld M, Büchner K, Meiler J, Habisch H, Madl T, Kerpes R, Becker T, Berensmeier S, Schwaminger SP. Millifluidic magnetophoresis-based chip for age-specific fractionation: evaluating the impact of age on metabolomics and gene expression in yeast. LAB ON A CHIP 2024; 24:2987-2998. [PMID: 38739033 DOI: 10.1039/d4lc00185k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
A novel millifluidic process introduces age-based fractionation of S. pastorianus var. carlsbergensis yeast culture through magnetophoresis. Saccharomyces yeast is a model organism for aging research used in various industries. Traditional age-based cell separation methods were labor-intensive, but techniques like magnetic labeling have eased the process by being non-invasive and scalable. Our approach introduces an age-specific fractionation using a 3D-printed millfluidic chip in a two-step process, ensuring efficient cell deflection in the magnetic field and counteracting magnetic induced convection. Among various channel designs, the pinch-shaped channel proved most effective for age differentiation based on magnetically labeled bud scar numbers. Metabolomic analyses revealed changes in certain amino acids and increased NAD+ levels, suggesting metabolic shifts in aging cells. Gene expression studies further underlined these age-related metabolic changes. This innovative platform offers a high-throughput, non-invasive method for age-specific yeast cell fractionation, with potential applications in industries ranging from food and beverages to pharmaceuticals.
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Affiliation(s)
- L Wittmann
- TUM School of Engineering and Design, Chair of Bioseparation Engineering, Technical University of Munich, Boltzmannstr. 15, 85748 Garching, Germany.
| | - M Eigenfeld
- TUM School of Life Science, Chair of Brewing and Beverage Technology, Technical University of Munich, Weihenstephaner Steig 20, 85354 Freising, Germany.
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstr. 6, 8010 Graz, Austria
| | - K Büchner
- TUM School of Life Science, Chair of Brewing and Beverage Technology, Technical University of Munich, Weihenstephaner Steig 20, 85354 Freising, Germany.
| | - J Meiler
- TUM School of Engineering and Design, Chair of Bioseparation Engineering, Technical University of Munich, Boltzmannstr. 15, 85748 Garching, Germany.
| | - H Habisch
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstr. 6, 8010 Graz, Austria
| | - T Madl
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstr. 6, 8010 Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria.
| | - R Kerpes
- TUM School of Life Science, Chair of Brewing and Beverage Technology, Technical University of Munich, Weihenstephaner Steig 20, 85354 Freising, Germany.
| | - T Becker
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstr. 6, 8010 Graz, Austria
- Munich Institute of Integrated Materials, Energy and Process Engineering, Technical University of Munich, Lichtenberstr. 4a, 85748 Garching, Germany
| | - S Berensmeier
- TUM School of Engineering and Design, Chair of Bioseparation Engineering, Technical University of Munich, Boltzmannstr. 15, 85748 Garching, Germany.
- Munich Institute of Integrated Materials, Energy and Process Engineering, Technical University of Munich, Lichtenberstr. 4a, 85748 Garching, Germany
| | - S P Schwaminger
- TUM School of Engineering and Design, Chair of Bioseparation Engineering, Technical University of Munich, Boltzmannstr. 15, 85748 Garching, Germany.
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstr. 6, 8010 Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria.
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11
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Liu Z, Jin T, Qin B, Li R, Shang J, Huang Y. The deletion of ppr2 interferes iron sensing and leads to oxidative stress response in Schizosaccharomyces pombe. Mitochondrion 2024; 76:101875. [PMID: 38499131 DOI: 10.1016/j.mito.2024.101875] [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: 11/07/2023] [Revised: 03/09/2024] [Accepted: 03/15/2024] [Indexed: 03/20/2024]
Abstract
Pentatricopeptide repeat proteins are involved in mitochondrial both transcriptional and posttranscriptional regulation. Schizosaccharomyces pombe Ppr2 is a general mitochondrial translation factor that plays a critical role in the synthesis of all mitochondrial DNA-encoded oxidative phosphorylation subunits, which are essential for mitochondrial respiration. Our previous analysis showed that ppr2 deletion resulted in increased expression of iron uptake genes and caused ferroptosis-like cell death in S. pombe. In the present work, we showed that deletion of ppr2 reduced viability on glycerol- and galactose-containing media.Php4 is a transcription repressor that regulates iron homeostasis in fission yeast. We found that in the ppr2 deletion strain, Php4 was constitutively active and accumulated in the nucleus in the stationary phase. We also found that deletion of ppr2 decreased the ferroptosis-related protein Gpx1 in the mitochondria. Overexpression of Gpx1 improves the viability of Δppr2 cells. We showed that the deletion of ppr2 increased the production of ROS, downregulated heme synthesis and iron-sulfur cluster proteins, and induced stress proteins. Finally, we observed the nuclear accumulation of Pap1-GFP and Sty1-GFP, suggesting that Sty1 and Pap1 in response to cellular stress in the ppr2 deletion strain. These results suggest thatppr2 deletion may cause mitochondrial dysfunction, which is likely to lead to iron-sensing defect and iron starvation response, resulting in perturbation of iron homeostasis and increased hydroxyl radical production. The increased hydroxyl radical production triggers cellular responses in theppr2 deletion strain.
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Affiliation(s)
- Zecheng Liu
- Jiangsu Key Laboratory for Microbes and Functional Genetics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; School of Public Health, Hubei University of Medicine, Shiyan 442000, China
| | - Ting Jin
- Jiangsu Key Laboratory for Microbes and Functional Genetics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Bingxin Qin
- Jiangsu Key Laboratory for Microbes and Functional Genetics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Rongrong Li
- Jiangsu Key Laboratory for Microbes and Functional Genetics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Jinjie Shang
- Jiangsu Key Laboratory for Microbes and Functional Genetics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
| | - Ying Huang
- Jiangsu Key Laboratory for Microbes and Functional Genetics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
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12
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Shen N, Xie H, Liu K, Li X, Wang L, Deng Y, Chen L, Bian Y, Xiao Y. Near-gapless genome and transcriptome analyses provide insights into fruiting body development in Lentinula edodes. Int J Biol Macromol 2024; 263:130610. [PMID: 38447851 DOI: 10.1016/j.ijbiomac.2024.130610] [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: 12/21/2023] [Revised: 03/01/2024] [Accepted: 03/02/2024] [Indexed: 03/08/2024]
Abstract
Fruiting body development in macrofungi is an intensive research subject. In this study, high-quality genomes were assembled for two sexually compatible monokaryons from a heterokaryotic Lentinula edodes strain WX1, and variations in L. edodes genomes were analyzed. Specifically, differential gene expression and allele-specific expression (ASE) were analyzed using the two monokaryotic genomes and transcriptome data from four different stages of fruiting body development in WX1. Results revealed that after aeration, mycelia sensed cell wall stress, pheromones, and a decrease in CO2 concentration, leading to up-regulated expression in genes related to cell adhesion, cell wall remodeling, proteolysis, and lipid metabolism, which may promote primordium differentiation. Aquaporin genes and those related to proteolysis, mitosis, lipid, and carbohydrate metabolism may play important roles in primordium development, while genes related to tissue differentiation and sexual reproduction were active in fruiting body. Several essential genes for fruiting body development were allele-specifically expressed and the two nuclear types could synergistically regulate fruiting body development by dominantly expressing genes with different functions. ASE was probably induced by long terminal repeat-retrotransposons. Findings here contribute to the further understanding of the mechanism of fruiting body development in macrofungi.
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Affiliation(s)
- Nan Shen
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Haoyu Xie
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Kefang Liu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xinru Li
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Lu Wang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Youjin Deng
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Lianfu Chen
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yinbing Bian
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yang Xiao
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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13
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Saengphing T, Sattayawat P, Kalawil T, Suwannarach N, Kumla J, Yamada M, Panbangred W, Rodrussamee N. Improving furfural tolerance in a xylose-fermenting yeast Spathaspora passalidarum CMUWF1-2 via adaptive laboratory evolution. Microb Cell Fact 2024; 23:80. [PMID: 38481222 PMCID: PMC10936021 DOI: 10.1186/s12934-024-02352-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/01/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Spathaspora passalidarum is a yeast with the highly effective capability of fermenting several monosaccharides in lignocellulosic hydrolysates, especially xylose. However, this yeast was shown to be sensitive to furfural released during pretreatment and hydrolysis processes of lignocellulose biomass. We aimed to improve furfural tolerance in a previously isolated S. passalidarum CMUWF1-2, which presented thermotolerance and no detectable glucose repression, via adaptive laboratory evolution (ALE). RESULTS An adapted strain, AF2.5, was obtained from 17 sequential transfers of CMUWF1-2 in YPD broth with gradually increasing furfural concentration. Strain AF2.5 could tolerate higher concentrations of furfural, ethanol and 5-hydroxymethyl furfuraldehyde (HMF) compared with CMUWF1-2 while maintaining the ability to utilize glucose and other sugars simultaneously. Notably, the lag phase of AF2.5 was 2 times shorter than that of CMUWF1-2 in the presence of 2.0 g/l furfural, which allowed the highest ethanol titers to be reached in a shorter period. To investigate more in-depth effects of furfural, intracellular reactive oxygen species (ROS) accumulation was observed and, in the presence of 2.0 g/l furfural, AF2.5 exhibited 3.41 times less ROS accumulation than CMUWF1-2 consistent with the result from nuclear chromatins diffusion, which the cells number of AF2.5 with diffuse chromatins was also 1.41 and 1.24 times less than CMUWF1-2 at 24 and 36 h, respectively. CONCLUSIONS An enhanced furfural tolerant strain of S. passalidarum was achieved via ALE techniques, which shows faster and higher ethanol productivity than that of the wild type. Not only furfural tolerance but also ethanol and HMF tolerances were improved.
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Affiliation(s)
- Thanyalak Saengphing
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Pachara Sattayawat
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Thitisuda Kalawil
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Nakarin Suwannarach
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Jaturong Kumla
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Mamoru Yamada
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515, Japan
- Life Science, Graduate School of Science and Technology for Innovation, Yamaguchi University, Ube, 755-8611, Japan
- Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | | | - Nadchanok Rodrussamee
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand.
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, 50200, Thailand.
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14
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Mühlhofer M, Offensperger F, Reschke S, Wallmann G, Csaba G, Berchtold E, Riedl M, Blum H, Haslbeck M, Zimmer R, Buchner J. Deletion of the transcription factors Hsf1, Msn2 and Msn4 in yeast uncovers transcriptional reprogramming in response to proteotoxic stress. FEBS Lett 2024; 598:635-657. [PMID: 38366111 DOI: 10.1002/1873-3468.14821] [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: 12/19/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 02/18/2024]
Abstract
The response to proteotoxic stresses such as heat shock allows organisms to maintain protein homeostasis under changing environmental conditions. We asked what happens if an organism can no longer react to cytosolic proteotoxic stress. To test this, we deleted or depleted, either individually or in combination, the stress-responsive transcription factors Msn2, Msn4, and Hsf1 in Saccharomyces cerevisiae. Our study reveals a combination of survival strategies, which together protect essential proteins. Msn2 and 4 broadly reprogram transcription, triggering the response to oxidative stress, as well as biosynthesis of the protective sugar trehalose and glycolytic enzymes, while Hsf1 mainly induces the synthesis of molecular chaperones and reverses the transcriptional response upon prolonged mild heat stress (adaptation).
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Affiliation(s)
- Moritz Mühlhofer
- Center for Protein Assemblies, Department of Bioscience, Technische Universität München, Garching, Germany
| | - Felix Offensperger
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, München, Germany
| | - Sarah Reschke
- Laboratory for Functional Genome Analysis at the Gene Center, LMU München, München, Germany
| | - Georg Wallmann
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, München, Germany
| | - Gergely Csaba
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, München, Germany
| | - Evi Berchtold
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, München, Germany
| | - Maximilian Riedl
- Center for Protein Assemblies, Department of Bioscience, Technische Universität München, Garching, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis at the Gene Center, LMU München, München, Germany
| | - Martin Haslbeck
- Center for Protein Assemblies, Department of Bioscience, Technische Universität München, Garching, Germany
| | - Ralf Zimmer
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, München, Germany
| | - Johannes Buchner
- Center for Protein Assemblies, Department of Bioscience, Technische Universität München, Garching, Germany
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15
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Sillapawattana P, Gruhlke MCH, Seiler TB, Klungsupya P, Charerntantanakul W. Oxidative stress related effect of xenobiotics on eukaryotic model organism, Saccharomyces cerevisiae. Free Radic Biol Med 2024; 212:149-161. [PMID: 38151215 DOI: 10.1016/j.freeradbiomed.2023.12.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 12/29/2023]
Abstract
Ecotoxicological assays have traditionally focused on the effects of chemicals at the individual level by exploiting mortality and reproduction as endpoints. Although these two parameters are ecologically relevant, they rarely provide information regarding the elemental toxic mechanisms. Obviously, the number of xenobiotics used has been rapidly increased. Thus, any established measurement that shortens the actual outcome and, simultaneously provides information about toxic mechanisms is desirable. This research focused on the study of oxidative stress response as a biomarker in the eukaryotic model organism, Saccharomyces cerevisiae. For this, yeast cells were exposed to a set of selected environmentally relevant chemicals via different approaches, including cellular diagnostics, gene expression analysis and chemo-genetic screening. The results demonstrated that at the cellular level, model organisms reacted to different chemicals in distinct manner. For each xenobiotic, the correlation between toxic response of molecular and cellular levels are presented. Namely, the expression of target genes after chemical exposure affected the cellular alteration as evidenced by an elevated level of superoxide dismutase and a reduced amount of glutathione. Furthermore, the results derived from chemo-genetic screening, in which mutants lacking of gene of interest were employed, exhibited more susceptibility to test chemicals in comparison to the wildtype. The response of oxidative stress upon chemical exposure in budding yeast from this study is potentially useful for an establishment of a proper bio-test system which can eventually be linked to adverse effects at an individual level in higher eukaryotes.
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Affiliation(s)
- Panwad Sillapawattana
- Program in Environmental Technology, Faculty of Science, Maejo University, Chiang Mai, Thailand.
| | | | | | - Prapaipat Klungsupya
- Thailand Institute for Scientific and Technological Research (TISTR), Pathum Thani, Thailand
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16
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Zhang B, Xie X, Zhu H, Niu B, Liang D, Chen K, Sun W, Shi D. Solid-state fermentation by S. cerevisiae with high resistance to ferulic acid improves the physicochemical properties of wheat bran and quality of bran-rich Chinese steamed bread. J Food Sci 2024; 89:954-965. [PMID: 38258960 DOI: 10.1111/1750-3841.16930] [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: 09/06/2023] [Revised: 12/02/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024]
Abstract
Wheat bran has numerous health benefits, but its poor processing and sensory properties limit its application in the staple food industry. Fermentation by S. cerevisiae changes the performance of wheat bran. However, high levels of ferulic acid (FA) inhibit S. cerevisiae. The effects of solid-state fermentation of S. cerevisiae with high resistance to FA on the physicochemical properties of wheat bran and the quality of bran-rich Chinese steamed bread (CSB) were investigated. The results showed that the growth of S. cerevisiae was inhibited by FA in a dose-dependent manner. Short-term adaptation strategies efficiently improved the tolerance of S. cerevisiae to FA stress. Compared with the parental strain (PS), fermentation of the short-term adapted strains (adapted strains) significantly increased the FA, total phenol, and soluble dietary fiber content in wheat bran. Wheat bran fermented by the adapted strains had a higher antioxidant capacity than wheat bran fermented by PS. In addition, compared with the PS, the wheat bran fermented by the adapted strains can decrease the hardness, improve the specific volume, and the quality of CSB. Thus, solid-state fermentation of the adapted strain is a potentially effective method to improve the nutritional and physicochemical properties of wheat bran as a cereal food ingredient.
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Affiliation(s)
- Bobo Zhang
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China
- National R&D Center For Frozen Rice&Wheat Products Processing Technology, Zhengzhou, China
- Key Laboratory of Staple Grain Processing, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
- Henan Science and Technology Department, Henan Engineering Research Center of Cold-Chain Food, Zhengzhou, China
| | - Xinhua Xie
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China
- National R&D Center For Frozen Rice&Wheat Products Processing Technology, Zhengzhou, China
| | - Hongshuai Zhu
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China
- National R&D Center For Frozen Rice&Wheat Products Processing Technology, Zhengzhou, China
- Henan Science and Technology Department, Henan Engineering Research Center of Cold-Chain Food, Zhengzhou, China
| | - Bin Niu
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China
- National R&D Center For Frozen Rice&Wheat Products Processing Technology, Zhengzhou, China
- Key Laboratory of Staple Grain Processing, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
- Henan Science and Technology Department, Henan Engineering Research Center of Cold-Chain Food, Zhengzhou, China
| | - Dan Liang
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China
- National R&D Center For Frozen Rice&Wheat Products Processing Technology, Zhengzhou, China
| | - Kai Chen
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China
- National R&D Center For Frozen Rice&Wheat Products Processing Technology, Zhengzhou, China
| | - Wenhong Sun
- Kaifeng Lixing Machinery Equipment Co. Ltd., Kaifeng, China
| | - Dongfeng Shi
- Kaifeng Lixing Machinery Equipment Co. Ltd., Kaifeng, China
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17
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Fu W, Wang S, Ouyang Q, Luo C. A multilayer microfluidic system for studies of the dynamic responses of cellular proteins to oxygen switches at the single-cell level. Integr Biol (Camb) 2024; 16:zyae011. [PMID: 38900168 DOI: 10.1093/intbio/zyae011] [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: 11/17/2023] [Revised: 03/04/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024]
Abstract
Oxygen levels vary in the environment. Oxygen availability has a major effect on almost all organisms, and oxygen is far more than a substrate for energy production. However, less is known about related biological processes under hypoxic conditions and about the adaptations to changing oxygen concentrations. The yeast Saccharomyces cerevisiae can adapt its metabolism for growth under different oxygen concentrations and can grow even under anaerobic conditions. Therefore, we developed a microfluidic device that can generate serial, accurately controlled oxygen concentrations for single-cell studies of multiple yeast strains. This device can construct a broad range of oxygen concentrations, [O2] through on-chip gas-mixing channels from two gases fed to the inlets. Gas diffusion through thin polydimethylsiloxane (PDMS) can lead to the equilibration of [O2] in the medium in the cell culture layer under gas cover regions within 2 min. Here, we established six different and stable [O2] varying between ~0.1 and 20.9% in the corresponding layers of the device designed for multiple parallel single-cell culture of four different yeast strains. Using this device, the dynamic responses of different yeast transcription factors and metabolism-related proteins were studied when the [O2] decreased from 20.9% to serial hypoxic concentrations. We showed that different hypoxic conditions induced varying degrees of transcription factor responses and changes in respiratory metabolism levels. This device can also be used in studies of the aging and physiology of yeast under different oxygen conditions and can provide new insights into the relationship between oxygen and organisms. Integration, innovation and insight: Most living cells are sensitive to the oxygen concentration because they depend on oxygen for survival and proper cellular functions. Here, a composite microfluidic device was designed for yeast single-cell studies at a series of accurately controlled oxygen concentrations. Using this device, we studied the dynamic responses of various transcription factors and proteins to changes in the oxygen concentration. This study is the first to examine protein dynamics and temporal behaviors under different hypoxic conditions at the single yeast cell level, which may provide insights into the processes involved in yeast and even mammalian cells. This device also provides a base model that can be extended to oxygen-related biology and can acquire more information about the complex networks of organisms.
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Affiliation(s)
- Wei Fu
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- College of Life Sciences, Peking University, Beijing, 100871, China
| | - Shujing Wang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China
| | - Qi Ouyang
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China
- School of Physics, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Chunxiong Luo
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China
- Wenzhou Institute University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325001, China
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18
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Mattos LMM, Hottum HM, Pires DC, Segat BB, Horn A, Fernandes C, Pereira MD. Exploring the antioxidant activity of Fe(III), Mn(III)Mn(II), and Cu(II) compounds in Saccharomyces cerevisiae and Galleria mellonella models of study. FEMS Yeast Res 2024; 24:foad052. [PMID: 38124682 PMCID: PMC10776354 DOI: 10.1093/femsyr/foad052] [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: 08/16/2023] [Revised: 11/19/2023] [Accepted: 12/19/2023] [Indexed: 12/23/2023] Open
Abstract
Reactive oxygen species (ROS) are closely related to oxidative stress, aging, and the onset of human diseases. To mitigate ROS-induced damages, extensive research has focused on examining the antioxidative attributes of various synthetic/natural substances. Coordination compounds serving as synthetic antioxidants have emerged as a promising approach to attenuate ROS toxicity. Herein, we investigated the antioxidant potential of a series of Fe(III) (1), Mn(III)Mn(II) (2) and Cu(II) (3) coordination compounds synthesized with the ligand N-(2-hydroxybenzyl)-N-(2-pyridylmethyl)[(3-chloro)(2-hydroxy)]-propylamine in Saccharomyces cerevisiae exposed to oxidative stress. We also assessed the antioxidant potential of these complexes in the alternative model of study, Galleria mellonella. DPPH analysis indicated that these complexes presented moderate antioxidant activity. However, treating Saccharomyces cerevisiae with 1, 2 and 3 increased the tolerance against oxidative stress and extended yeast lifespan. The treatment of yeast cells with these complexes decreased lipid peroxidation and catalase activity in stressed cells, whilst no change in SOD activity was observed. Moreover, these complexes induced the Hsp104 expression. In G. mellonella, complex administration extended larval survival under H2O2 stress and did not affect the insect's life cycle. Our results suggest that the antioxidant potential exhibited by these complexes could be further explored to mitigate various oxidative stress-related disorders.
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Affiliation(s)
- Larissa M M Mattos
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, RJ, Brazil
- Rede de Micologia RJ - FAPERJ
| | - Hyan M Hottum
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, RJ, Brazil
- Rede de Micologia RJ - FAPERJ
| | - Daniele C Pires
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, RJ, Brazil
- Rede de Micologia RJ - FAPERJ
| | - Bruna B Segat
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Adolfo Horn
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Christiane Fernandes
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Marcos D Pereira
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, RJ, Brazil
- Rede de Micologia RJ - FAPERJ
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19
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Oduor CI, Cunningham C, Rustamzade N, Zuromski J, Chin DM, Nixon CP, Kurtis JD, Juliano JJ, Bailey JA. Single cell transcriptional changes across the blood stages of artemisinin resistant K13 C580Y mutant Plasmodium falciparum upon dihydroartemisinin exposure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.570387. [PMID: 38105992 PMCID: PMC10723473 DOI: 10.1101/2023.12.06.570387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Artemisinins have been a cornerstone of malaria control, but resistance in Plasmodium falciparum, due to mutations in the Kelch 13 gene, threaten these advances. Artemisinin exposure results in a dynamic transcriptional response across multiple pathways, but most work has focused on ring stages and ex vivo transcriptional analysis, limiting evaluation of all life cycle stages. We applied single cell RNAseq to two unsynchronized isogenic parasite lines (K13C580 and K13580Y) over 6 hrs after a pulse exposure to dihydroartemisinin (DHA). Transcription was altered across all stages, with the greatest occurring at the early trophozoite and mid ring stage in both lines. This response involved the arrest of metabolic processes and the enhancement of protein trafficking and the unfolded protein response. While similar, the response was enhanced in the K13580Y mutant, which may lead to the dormancy phenomenon upon treatment. Increased surface protein expression was seen in mutant parasites at baseline and upon drug exposure, highlighted by the increased expression of PfEMP1 and GARP, a potential therapeutic target. Antibody targeting GARP maintained anti-parasitic efficacy in mutant parasites. This work provides single cell insight of gene transcription across all life cycle stages revealing transcriptional changes that could initiate dormancy state and mediate survival.
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Affiliation(s)
- Cliff I. Oduor
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI
| | - Clark Cunningham
- Division of Infectious Diseases, Department of Medicine, University of North Carolina, Chapel Hill, NC
| | - Nazrin Rustamzade
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI
| | - Jenna Zuromski
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI
| | - Deborah M. Chin
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI
| | - Christian P. Nixon
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI
| | - Jonathan D. Kurtis
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI
| | - Jonathan J. Juliano
- Division of Infectious Diseases, Department of Medicine, University of North Carolina, Chapel Hill, NC
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina, Chapel Hill, NC
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI
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20
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Chaithanya KV, Sinha H. MKT1 alleles regulate stress responses through posttranscriptional modulation of Puf3 targets in budding yeast. Yeast 2023; 40:616-627. [PMID: 37990816 DOI: 10.1002/yea.3908] [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: 06/29/2023] [Revised: 09/18/2023] [Accepted: 10/29/2023] [Indexed: 11/23/2023] Open
Abstract
MKT1 is a pleiotropic stress response gene identified by several quantitative trait studies with MKT189G as a causal variant, contributing to growth advantage in multiple stress environments. MKT1 has been shown to regulate HO endonuclease posttranscriptionally via the Pbp1-Pab1 complex. RNA-binding protein Puf3 modulates a set of nuclear-encoded mitochondrial transcripts whose expression was found to be affected by MKT1 alleles. This study attempts to relate the MKT1 allele-derived growth advantage with the stability of Puf3 targets during stress and elucidate the roles of Pbp1 and Puf3 in this mechanism. Our results showed that the growth advantage of the MKT189G allele in cycloheximide and H2 O2 was PBP1-dependent, whereas in 4-nitroquinoline 1-oxide, the growth advantage was dependent on both PUF3 and PBP1. We compared the messenger RNA decay kinetics of a set of Puf3 targets in multiple stress environments to understand the allele-specific regulation by MKT1. In oxidative stress, the MKT189G allele modulated the differential expression of nuclear-encoded mitochondrial genes in a PBP1- and PUF3-dependent manner. Additionally, MKT189G stabilised Puf3 targets, namely, COX17, MRS1 and RDL2, in an allele and stress-specific manner. Our results showed that COX17, MRS1 and RDL2 had a stress-specific response in stress environments, with the MKT189G allele contributing to better growth; this response was both PBP1- and PUF3-dependent. Our results indicate that the common allele, MKT189G , regulates stress responses by differentially stabilising Puf3-target mitochondrial genes, which allows for the strain's better growth in stress environments.
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Affiliation(s)
- Koppisetty Viswa Chaithanya
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, IIT Madras, Chennai, Tamil Nadu, India
- Centre for Integrative Biology and Systems Medicine (IBSE), IIT Madras, Chennai, Tamil Nadu, India
| | - Himanshu Sinha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, IIT Madras, Chennai, Tamil Nadu, India
- Centre for Integrative Biology and Systems Medicine (IBSE), IIT Madras, Chennai, Tamil Nadu, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai, Tamil Nadu, India
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21
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Licona-Juárez KC, Bezerra AVS, Oliveira ITC, Massingue CD, Medina HR, Rangel DEN. Congo red induces trans-priming to UV-B radiation in Metarhizium robertsii. Fungal Biol 2023; 127:1544-1550. [PMID: 38097328 DOI: 10.1016/j.funbio.2023.06.005] [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: 04/16/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 12/18/2023]
Abstract
Metarhizium spp. is used as a biocontrol agent but is limited because of low tolerance to abiotic stress. Metarhizium robertsii is an excellent study model of fungal pathogenesis in insects, and its tolerance to different stress conditions has been extensively investigated. Priming is the time-limited pre-exposure of an organism to specific stress conditions that increases adaptive response to subsequent exposures. Congo red is a water-soluble azo dye extensively used in stress assays in fungi. It induces morphological changes and weakens the cell wall at sublethal concentrations. Therefore, this chemical agent has been proposed as a stressor to induce priming against other stress conditions in entomopathogenic fungi. This study aimed to evaluate the capacity of Congo red to induce priming in M. robertsii. Conidia were grown on potato dextrose agar with or without Congo red.The tolerance of conidia produced from mycelia grown in these three conditions was evaluated against stress conditions, including osmotic, oxidative, heat, and UV-B radiation. Conidia produced on medium supplemented with Congo red were significantly more tolerant to UV-B radiation but not to the other stress conditions assayed. Our results suggest that Congo red confers trans-priming to UV-B radiation but not for heat, oxidative, or osmotic stress.
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Affiliation(s)
- Karla Cecilia Licona-Juárez
- Universidade Brasil, São Paulo, SP, 08230-030, Brazil; Laboratorio de Biología Molecular, Tecnológico Nacional de Mexico, A. García Cubas 600, Celaya, Guanajuato, 38010, Mexico
| | | | | | | | - Humberto R Medina
- Laboratorio de Biología Molecular, Tecnológico Nacional de Mexico, A. García Cubas 600, Celaya, Guanajuato, 38010, Mexico
| | - Drauzio E N Rangel
- Universidade Tecnológica Federal do Paraná (UTFPR), Dois Vizinhos, PR, 85660-000, Brazil.
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22
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Kłosowski G, Koim-Puchowska B, Dróżdż-Afelt J, Mikulski D. The Reaction of the Yeast Saccharomyces cerevisiae to Contamination of the Medium with Aflatoxins B 2 and G 1, Ochratoxin A and Zearalenone in Aerobic Cultures. Int J Mol Sci 2023; 24:16401. [PMID: 38003590 PMCID: PMC10671187 DOI: 10.3390/ijms242216401] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
The mechanisms by which yeast cells respond to environmental stress include the production of heat shock proteins (HSPs) and the reduction of oxidative stress. The response of yeast exposed to aflatoxins B2+G1 (AFB2+G1), ochratoxin A (OTA), and zearalenone (ZEA) in aerobic conditions was studied. After 72 h of yeast cultivation in media contaminated with mycotoxins, the growth of yeast biomass, the level of malondialdehyde, and the activity of superoxide dismutase, glutathione S-transferase and glutathione peroxidase were examined; the expression profile of the following heat shock proteins was also determined: HSP31, HSP40, HSP60, HSP70, and HSP104. It was demonstrated that at the tested concentrations, both AFB2+G1 and ZEA inhibited yeast biomass growth. OTA at a concentration of 8.4 [µg/L] raised the MDA level. Intensified lipoperoxidation and increased activity of SOD and GPx were observed, regardless of the level of contamination with ZEA (300 µg/L or 900 µg/L). Increased contamination with AFB2+G1 and OTA caused an increase in the production of most HSPs tested (HSP31, HSP40, HSP70, HSP104). ZEA contamination in the used concentration ranges reduced the production of HSP31. The response of yeast cells to the presence of mycotoxin as a stressor resulted in the expression of certain HSPs, but the response was not systematic, which was manifested in different profiles of protein expression depending on the mycotoxin used. The tested mycotoxins influenced the induction of oxidative stress in yeast cells to varying degrees, which resulted in the activation of mainly SOD without GST mobilization or with a small involvement of GPx.
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Affiliation(s)
- Grzegorz Kłosowski
- Department of Biotechnology, Faculty of Biological Sciences, Kazimierz Wielki University, ul. K. J. Poniatowskiego 12, 85-671 Bydgoszcz, Poland (J.D.-A.); (D.M.)
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23
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Kim YH, Ryu JI, Devare MN, Jung J, Kim JY. The intricate role of Sir2 in oxidative stress response during the post-diauxic phase in Saccharomyces cerevisiae. Front Microbiol 2023; 14:1285559. [PMID: 38029141 PMCID: PMC10666771 DOI: 10.3389/fmicb.2023.1285559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023] Open
Abstract
Silent information regulator 2 (Sir2) is a conserved NAD+-dependent histone deacetylase crucial for regulating cellular stress response and the aging process in Saccharomyces cerevisiae. In this study, we investigated the molecular mechanism underlying how the absence of Sir2 can lead to altered stress susceptibilities in S. cerevisiae under different environmental and physiological conditions. In a glucose-complex medium, the sir2Δ strain showed increased sensitivity to H2O2 compared to the wild-type strain during the post-diauxic phase. In contrast, it displayed increased resistance during the exponential growth phase. Transcriptome analysis of yeast cells in the post-diauxic phase indicated that the sir2Δ mutant expressed several oxidative defense genes at lower levels than the wild-type, potentially accounting for its increased susceptibility to H2O2. Interestingly, however, the sir2Δras2Δ double mutant exhibited greater resistance to H2O2 than the ras2Δ single mutant counterpart. We found that the expression regulation of the cytoplasmic catalase encoded by CTT1 was critical for the increased resistance to H2O2 in the sir2Δras2Δ strain. The expression of the CTT1 gene was influenced by the combined effect of RAS2 deletion and the transcription factor Azf1, whose level was modulated by Sir2. These findings provide insights into the importance of understanding the intricate interactions among various factors contributing to cellular stress response.
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Affiliation(s)
| | | | | | | | - Jeong-Yoon Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
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24
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Fay JC, Alonso-del-Real J, Miller JH, Querol A. Divergence in the Saccharomyces Species' Heat Shock Response Is Indicative of Their Thermal Tolerance. Genome Biol Evol 2023; 15:evad207. [PMID: 37972247 PMCID: PMC10683043 DOI: 10.1093/gbe/evad207] [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: 07/12/2023] [Revised: 10/27/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023] Open
Abstract
The Saccharomyces species have diverged in their thermal growth profile. Both Saccharomyces cerevisiae and Saccharomyces paradoxus grow at temperatures well above the maximum growth temperature of Saccharomyces kudriavzevii and Saccharomyces uvarum but grow more poorly at lower temperatures. In response to thermal shifts, organisms activate a stress response that includes heat shock proteins involved in protein homeostasis and acquisition of thermal tolerance. To determine whether Saccharomyces species have diverged in their response to temperature, we measured changes in gene expression in response to a 12 °C increase or decrease in temperature for four Saccharomyces species and their six pairwise hybrids. To ensure coverage of subtelomeric gene families, we sequenced, assembled, and annotated a complete S. uvarum genome. In response to heat, the cryophilic species showed a stronger stress response than the thermophilic species, and the hybrids showed a mixture of parental responses that depended on the time point. After an initial strong response indicative of high thermal stress, hybrids with a thermophilic parent resolved their heat shock response to become similar to their thermophilic parent. Within the hybrids, only a small number of temperature-responsive genes showed consistent differences between alleles from the thermophilic and cryophilic species. Our results show that divergence in the heat shock response is mainly a consequence of a strain's thermal tolerance, suggesting that cellular factors that signal heat stress or resolve heat-induced changes are relevant to thermal divergence in the Saccharomyces species.
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Affiliation(s)
- Justin C Fay
- Department of Biology, University of Rochester, Rochester, New York, USA
| | - Javier Alonso-del-Real
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Spain
| | - James H Miller
- Department of Biology, University of Rochester, Rochester, New York, USA
| | - Amparo Querol
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Spain
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25
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Albuini FM, de Castro AG, Campos VJ, Ribeiro LE, Vidigal PMP, de Oliveira Mendes TA, Fietto LG. Transcriptome profiling brings new insights into the ethanol stress responses of Spathaspora passalidarum. Appl Microbiol Biotechnol 2023; 107:6573-6589. [PMID: 37658163 DOI: 10.1007/s00253-023-12730-x] [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: 04/10/2023] [Revised: 08/01/2023] [Accepted: 08/10/2023] [Indexed: 09/03/2023]
Abstract
Spathaspora passalidarum is a xylose-fermenting microorganism promising for the fermentation of lignocellulosic hydrolysates. This yeast is more sensitive to ethanol than Saccharomyces cerevisiae for unclear reasons. An RNA-seq experiment was performed to identify transcriptional changes in S. passalidarum in response to ethanol and gain insights into this phenotype. The results showed the upregulation of genes associated with translation and the downregulation of genes encoding proteins involved in lipid metabolism, transporters, and enzymes from glycolysis and fermentation pathways. Our results also revealed that genes encoding heat-shock proteins and involved in antioxidant response were upregulated, whereas the osmotic stress response of S. passalidarum appears impaired under ethanol stress. A pseudohyphal morphology of S. passalidarum colonies was observed in response to ethanol stress, which suggests that ethanol induces a misperception of nitrogen availability in the environment. Changes in the yeast fatty acid profile were observed only after 12 h of ethanol exposure, coinciding with the recovery of the yeast xylose consumption ability. These findings suggest that the lack of fast membrane lipid adjustments, the halt in nutrient absorption and cellular metabolism, and the failure to induce the expression of osmotic stress-responsive genes are the main aspects underlying the low ethanol tolerance of S. passalidarum. KEY POINTS: • Ethanol stress halts Spathaspora passalidarum metabolism and fermentation • Genes encoding nutrient transporters showed downregulation under ethanol stress • Ethanol induces a pseudohyphal cell shape, suggesting a misperception of nutrients.
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Affiliation(s)
- Fernanda Matias Albuini
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, Viçosa, MG, 36570-900, Brazil
| | - Alex Gazolla de Castro
- Departamento de Microbiologia, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, Viçosa, MG, 36570-900, Brazil
| | - Valquíria Júnia Campos
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, Viçosa, MG, 36570-900, Brazil
| | - Lílian Emídio Ribeiro
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, Viçosa, MG, 36570-900, Brazil
| | - Pedro Marcus Pereira Vidigal
- Núcleo de Análise de Biomoléculas (NuBioMol), Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, Viçosa, MG, 36570-900, Brazil
| | - Tiago Antônio de Oliveira Mendes
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, Viçosa, MG, 36570-900, Brazil
| | - Luciano Gomes Fietto
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, Viçosa, MG, 36570-900, Brazil.
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26
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Zhang H, Yang X, Shen C, Sun J, Lu Y, Hu W, Yao H, Zhao W. Modification of the second PEP4-allele facilitates an industrial Saccharomyces cerevisiae to tolerate tartaric acid stress. Res Microbiol 2023; 174:104109. [PMID: 37517628 DOI: 10.1016/j.resmic.2023.104109] [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: 02/21/2023] [Revised: 06/12/2023] [Accepted: 07/24/2023] [Indexed: 08/01/2023]
Abstract
The practical significance of constructing robust industrial production strains against organic acid stress lies not only in improving fermentation efficiency but also in reducing manufacturing costs. In a previous study, we constructed an industrial Saccharomyces cerevisiae strain by modifying another PEP4-allele of a mutant that already had one PEP4-allele disrupted. This modification enhanced cellular tolerance to citric acid stress during growth. Unlike citric acid, which S. cerevisiae can consume, tartaric acid is often added to grape must during winemaking to increase total acidity and is not metabolizable. The results of the present study indicate that the modification of the second PEP4-allele improves the cellular tolerance of the strain with one PEP4-allele disrupted against tartaric acid stress during growth and contributes to maintaining intracellular pH homeostasis in cells subjected to tartaric acid stress. Moreover, under tartaric acid stress, a significant improvement in glucose-ethanol conversion performance, conferred by the modification of the second PEP4-allele, was observed. This study not only broadens our understanding of the role of the PEP4-allele in cellular regulation but also provides a prospective approach to reducing the concentration of sulfur dioxide used in winemaking.
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Affiliation(s)
- Hongbo Zhang
- College of Life and Environmental Sciences, Shaoxing University, 900 Chengnandadao Road, Shaoxing 312000, People's Republic of China.
| | - Xiaomei Yang
- College of Life and Environmental Sciences, Shaoxing University, 900 Chengnandadao Road, Shaoxing 312000, People's Republic of China.
| | - Chi Shen
- College of Life and Environmental Sciences, Shaoxing University, 900 Chengnandadao Road, Shaoxing 312000, People's Republic of China.
| | - Jianqiu Sun
- College of Life and Environmental Sciences, Shaoxing University, 900 Chengnandadao Road, Shaoxing 312000, People's Republic of China.
| | - Yuhang Lu
- College of Life and Environmental Sciences, Shaoxing University, 900 Chengnandadao Road, Shaoxing 312000, People's Republic of China.
| | - Wanting Hu
- College of Life and Environmental Sciences, Shaoxing University, 900 Chengnandadao Road, Shaoxing 312000, People's Republic of China.
| | - Hongfei Yao
- College of Life and Environmental Sciences, Shaoxing University, 900 Chengnandadao Road, Shaoxing 312000, People's Republic of China.
| | - Wenhao Zhao
- College of Life and Environmental Sciences, Shaoxing University, 900 Chengnandadao Road, Shaoxing 312000, People's Republic of China.
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27
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Chen Y, Yang Y, Cai W, Zeng J, Liu N, Wan Y, Fu G. Research progress of anti-environmental factor stress mechanism and anti-stress tolerance way of Saccharomyces cerevisiae during the brewing process. Crit Rev Food Sci Nutr 2023; 63:12308-12323. [PMID: 35848108 DOI: 10.1080/10408398.2022.2101090] [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: 11/03/2022]
Abstract
Saccharomyces cerevisiae plays a decisive role in the brewing of alcohol products, and the ideal growth and fermentation characteristics can give the pure flavor of alcohol products. However, S. cerevisiae can be affected profoundly by environmental factors during the brewing process, which have negative effects on the growth and fermentation characteristics of S. cerevisiae, and seriously hindered the development of brewing industry. Therefore, we summarized the environmental stress factors (ethanol, organic acids, temperature and osmotic pressure) that affect S. cerevisiae during the brewing process. Their impact mechanisms and the metabolic adaption of S. cerevisiae in response to these stress factors. Of note, S. cerevisiae can increase the ability to resist stress factors by changing the cell membrane components, expressing transcriptional regulatory factors, activating the anti-stress metabolic pathway and enhancing ROS scavenging ability. Meantime, the strategies and methods to improve the stress- tolerant ability of S. cerevisiae during the brewing process were also introduced. Compared with the addition of exogenous anti-stress substances, mutation breeding and protoplast fusion, it appears that adaptive evolution and genetic engineering are able to generate ideal environmental stress tolerance strains of S. cerevisiae and are more in line with the needs of the current brewing industry.
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Affiliation(s)
- Yanru Chen
- State Key Laboratory of Food Science and Technology & College of Food Science and Technology & International Institute of Food Innovation, Nanchang University, Nanchang, PR China
| | - Yili Yang
- China Regional Research Centre, International Centre of Genetic Engineering & Biotechnology, Taizhou, PR China
| | - Wenqin Cai
- State Key Laboratory of Food Science and Technology & College of Food Science and Technology & International Institute of Food Innovation, Nanchang University, Nanchang, PR China
| | - Jiali Zeng
- State Key Laboratory of Food Science and Technology & College of Food Science and Technology & International Institute of Food Innovation, Nanchang University, Nanchang, PR China
| | - Na Liu
- State Key Laboratory of Food Science and Technology & College of Food Science and Technology & International Institute of Food Innovation, Nanchang University, Nanchang, PR China
| | - Yin Wan
- State Key Laboratory of Food Science and Technology & College of Food Science and Technology & International Institute of Food Innovation, Nanchang University, Nanchang, PR China
| | - Guiming Fu
- State Key Laboratory of Food Science and Technology & College of Food Science and Technology & International Institute of Food Innovation, Nanchang University, Nanchang, PR China
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28
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Farley FW, McCully RR, Maslo PB, Yu L, Sheff MA, Sadeghi H, Elion EA. Effects of HSP70 chaperones Ssa1 and Ssa2 on Ste5 scaffold and the mating mitogen-activated protein kinase (MAPK) pathway in Saccharomyces cerevisiae. PLoS One 2023; 18:e0289339. [PMID: 37851593 PMCID: PMC10584130 DOI: 10.1371/journal.pone.0289339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 07/17/2023] [Indexed: 10/20/2023] Open
Abstract
Ste5 is a prototype of scaffold proteins that regulate activation of mitogen-activated protein kinase (MAPK) cascades in all eukaryotes. Ste5 associates with many proteins including Gβγ (Ste4), Ste11 MAPKKK, Ste7 MAPKK, Fus3 and Kss1 MAPKs, Bem1, Cdc24. Here we show that Ste5 also associates with heat shock protein 70 chaperone (Hsp70) Ssa1 and that Ssa1 and its ortholog Ssa2 are together important for Ste5 function and efficient mating responses. The majority of purified overexpressed Ste5 associates with Ssa1. Loss of Ssa1 and Ssa2 has deleterious effects on Ste5 abundance, integrity, and localization particularly when Ste5 is expressed at native levels. The status of Ssa1 and Ssa2 influences Ste5 electrophoresis mobility and formation of high molecular weight species thought to be phosphorylated, ubiquitinylated and aggregated and lower molecular weight fragments. A Ste5 VWA domain mutant with greater propensity to form punctate foci has reduced predicted propensity to bind Ssa1 near the mutation sites and forms more punctate foci when Ssa1 Is overexpressed, supporting a dynamic protein quality control relationship between Ste5 and Ssa1. Loss of Ssa1 and Ssa2 reduces activation of Fus3 and Kss1 MAPKs and FUS1 gene expression and impairs mating shmoo morphogenesis. Surprisingly, ssa1, ssa2, ssa3 and ssa4 single, double and triple mutants can still mate, suggesting compensatory mechanisms exist for folding. Additional analysis suggests Ssa1 is the major Hsp70 chaperone for the mating and invasive growth pathways and reveals several Hsp70-Hsp90 chaperone-network proteins required for mating morphogenesis.
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Affiliation(s)
- Francis W. Farley
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, United States of America
| | - Ryan R. McCully
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, United States of America
| | - Paul B. Maslo
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, United States of America
| | - Lu Yu
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, United States of America
| | - Mark A. Sheff
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, United States of America
| | - Homayoun Sadeghi
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, United States of America
| | - Elaine A. Elion
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, United States of America
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29
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Chen Y, Zhang J, Zhu X, Wang Y, Chen J, Sui B, Teng HH. Unraveling the complexities of Cd-aniline composite pollution: Insights from standalone and joint toxicity assessments in a bacterial community. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 265:115509. [PMID: 37742573 DOI: 10.1016/j.ecoenv.2023.115509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/05/2023] [Accepted: 09/20/2023] [Indexed: 09/26/2023]
Abstract
Cadmium (Cd) and aniline frequently co-occur in industrial settings but have rarely been addressed as composite toxicants in terms of the overall toxicity despite extensive knowledge of the environmental impact of each individual pollutant. In this study, we attempt to assess the relation of individual and combined toxic effects of Cd and aniline using a bacterial consortium cultured from soils as a model system. Results showed that the consortial bacteria exhibited drastically stronger tolerance to stand-alone Cd and aniline in comparison to literature data acquired from single species studies. When occurring simultaneously, the joint toxicity displayed a concentration-dependent behavior that wasn't anticipated based on individual chemical tests. Specifically, additive effects manifested with Cd and aniline at their IC10s, but changed to synergistic when the concentrations increased to IC20, and finally transitioned into antagonistic at IC30s and beyond. In addition, co-occurring aniline appeared to have retarded the cellular accumulation of Cd while increasing the enzymatic activities of superoxide dismutase and catalase relative to that in Cd-alone treatments. Finally, the bacterial community experienced distinct compositional changes under solo and combined toxicities with several genera exhibiting inconsistent behavior between treatments of single and composite toxicants. Findings from this study highlight the complexity of bacterial response to composite pollutions and point to the need for more comprehensive references in risk and toxicology assessment at multi-chemical contamination sites.
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Affiliation(s)
- Yuxuan Chen
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin 30072, China
| | - Jianchao Zhang
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin 30072, China.
| | - Xiangyu Zhu
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin 30072, China
| | - Yuebo Wang
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin 30072, China
| | - Jiubin Chen
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin 30072, China
| | - Biao Sui
- College of Resources and Environment, Jilin Agricultural University, Changchun 130118, China
| | - H Henry Teng
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin 30072, China.
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30
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Duy DL, Kim N. Yeast transcription factor Msn2 binds to G4 DNA. Nucleic Acids Res 2023; 51:9643-9657. [PMID: 37615577 PMCID: PMC10570036 DOI: 10.1093/nar/gkad684] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 08/03/2023] [Accepted: 08/15/2023] [Indexed: 08/25/2023] Open
Abstract
Sequences capable of forming quadruplex or G4 DNA are prevalent in the promoter regions. The transformation from canonical to non-canonical secondary structure apparently regulates transcription of a number of human genes. In the budding yeast Saccharomyces cerevisiae, we identified 37 genes with a G4 motif in the promoters including 20 genes that contain stress response element (STRE) overlapping a G4 motif. STRE is the binding site of stress response regulators Msn2 and Msn4, transcription factors belonging to the C2H2 zinc-finger protein family. We show here that Msn2 binds directly to the G4 DNA structure through its zinc-finger domain with a dissociation constant similar to that of STRE-binding and that, in a stress condition, Msn2 is enriched at G4 DNA-forming loci in the yeast genome. For a large fraction of genes with G4/STRE-containing promoters, treating with G4-ligands led to significant elevations in transcription levels. Such transcriptional elevation was greatly diminished in a msn2Δ msn4Δ background and was partly muted when the G4 motif was disrupted. Taken together, our data suggest that G4 DNA could be an alternative binding site of Msn2 in addition to STRE, and that G4 DNA formation could be an important element of transcriptional regulation in yeast.
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Affiliation(s)
- Duong Long Duy
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Nayun Kim
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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Kimura Y, Tsuji T, Shimizu Y, Watanabe Y, Kimura M, Fujimoto T, Higuchi M. Physicochemical properties of the vacuolar membrane and cellular factors determine formation of vacuolar invaginations. Sci Rep 2023; 13:16187. [PMID: 37759072 PMCID: PMC10533490 DOI: 10.1038/s41598-023-43232-5] [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: 02/26/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023] Open
Abstract
Vacuoles change their morphology in response to stress. In yeast exposed to chronically high temperatures, vacuolar membranes get deformed and invaginations are formed. We show that phase-separation of vacuolar membrane occurred after heat stress leading to the formation of the invagination. In addition, Hfl1, a vacuolar membrane-localized Atg8-binding protein, was found to suppress the excess vacuolar invaginations after heat stress. At that time, Hfl1 formed foci at the neck of the invaginations in wild-type cells, whereas it was efficiently degraded in the vacuole in the atg8Δ mutant. Genetic analysis showed that the endosomal sorting complex required for transport machinery was necessary to form the invaginations irrespective of Atg8 or Hfl1. In contrast, a combined mutation with the vacuole BAR domain protein Ivy1 led to vacuoles in hfl1Δivy1Δ and atg8Δivy1Δ mutants having constitutively invaginated structures; moreover, these mutants showed stress-sensitive phenotypes. Our findings suggest that vacuolar invaginations result from the combination of changes in the physiochemical properties of the vacuolar membrane and other cellular factors.
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Affiliation(s)
- Yoko Kimura
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan.
- Department of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan.
| | - Takuma Tsuji
- Laboratory of Molecular Cell Biology, Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yosuke Shimizu
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Yuki Watanabe
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Masafumi Kimura
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Toyoshi Fujimoto
- Laboratory of Molecular Cell Biology, Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Miyuki Higuchi
- Department of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan
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32
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Yang Y, Pian Y, Li J, Xu L, Lu Z, Dai Y, Li Q. Integrative analysis of genome and transcriptome reveal the genetic basis of high temperature tolerance in pleurotus giganteus (Berk. Karun & Hyde). BMC Genomics 2023; 24:552. [PMID: 37723428 PMCID: PMC10506213 DOI: 10.1186/s12864-023-09669-8] [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: 03/29/2023] [Accepted: 09/11/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Pleurotus giganteus is a commonly cultivated mushroom with notable high temperature resistance, making it significant for the growth of the edible fungi industry in the tropics. Despite its practical importance,, the genetic mechanisms underlying its ability to withstand high temperature tolerance remain elusive. RESULTS In this study, we performed high-quality genome sequencing of a monokaryon isolated from a thermotolerant strain of P. giganteus. The genome size was found to be 40.11 Mb, comprising 17 contigs and 13,054 protein-coding genes. Notably, some genes related to abiotic stress were identified in genome, such as genes regulating heat shock protein, protein kinase activity and signal transduction. These findings provide valuable insights into the genetic basis of P. giganteus' high temperature resistance. Furthermore, the phylogenetic tree showed that P. giganteus was more closely related to P. citrinopileatus than other Pleurotus species. The divergence time between Pleurotus and Lentinus was estimated as 153.9 Mya, and they have a divergence time with Panus at 168.3 Mya, which proved the taxonomic status of P. giganteus at the genome level. Additionally, a comparative transcriptome analysis was conducted between mycelia treated with 40 °C heat shock for 18 h (HS) and an untreated control group (CK). Among the 2,614 differentially expressed genes (DEGs), 1,303 genes were up-regulated and 1,311 were down-regulated in the HS group. The enrichment analysis showed that several genes related to abiotic stress, including heat shock protein, DnaJ protein homologue, ubiquitin protease, transcription factors, DNA mismatch repair proteins, and zinc finger proteins, were significantly up-regulated in the HS group. These genes may play important roles in the high temperature adaptation of P. giganteus. Six DEGs were selected according to fourfold expression changes and were validated by qRT-PCR, laying a good foundation for further gene function analysis. CONCLUSION Our study successfully reported a high-quality genome of P. giganteus and identified genes associated with high-temperature tolerance through an integrative analysis of the genome and transcriptome. This study lays a crucial foundation for understanding the high-temperature tolerance mechanism of P. giganteus, providing valuable insights for genetic modification of P. giganteus strains and the development of high-temperature strains for the edible fungus industry, particularly in tropical regions.
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Affiliation(s)
- Yang Yang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
- Key Laboratory of Low Carbon Green Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou, P. R. China
| | - Yongru Pian
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Key Laboratory of Low Carbon Green Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou, P. R. China
- National Agricultural Experimental Station for Agricultural Environment, Danzhou, China
| | - Jingyi Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Key Laboratory of Low Carbon Green Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou, P. R. China
- National Agricultural Experimental Station for Agricultural Environment, Danzhou, China
| | - Lin Xu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Key Laboratory of Low Carbon Green Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou, P. R. China
- National Agricultural Experimental Station for Agricultural Environment, Danzhou, China
| | - Zhu Lu
- Jilin Academy of Vegetables and Flowers Sciences, Changchun, China
| | - Yueting Dai
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.
| | - Qinfen Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
- Key Laboratory of Low Carbon Green Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou, P. R. China.
- National Agricultural Experimental Station for Agricultural Environment, Danzhou, China.
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Ciccarelli M, Masser AE, Kaimal JM, Planells J, Andréasson C. Genetic inactivation of essential HSF1 reveals an isolated transcriptional stress response selectively induced by protein misfolding. Mol Biol Cell 2023; 34:ar101. [PMID: 37467033 PMCID: PMC10551698 DOI: 10.1091/mbc.e23-05-0153] [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: 05/03/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 07/20/2023] Open
Abstract
Heat Shock Factor 1 (Hsf1) in yeast drives the basal transcription of key proteostasis factors and its activity is induced as part of the core heat shock response. Exploring Hsf1 specific functions has been challenging due to the essential nature of the HSF1 gene and the extensive overlap of target promoters with environmental stress response (ESR) transcription factors Msn2 and Msn4 (Msn2/4). In this study, we constructed a viable hsf1∆ strain by replacing the HSF1 open reading frame with genes that constitutively express Hsp40, Hsp70, and Hsp90 from Hsf1-independent promoters. Phenotypic analysis showed that the hsf1∆ strain grows slowly, is sensitive to heat as well as protein misfolding and accumulates protein aggregates. Transcriptome analysis revealed that the transcriptional response to protein misfolding induced by azetidine-2-carboxylic acid is fully dependent on Hsf1. In contrast, the hsf1∆ strain responded to heat shock through the ESR. Following HS, Hsf1 and Msn2/4 showed functional compensatory induction with stronger activation of the remaining stress pathway when the other branch was inactivated. Thus, we provide a long-overdue genetic test of the function of Hsf1 in yeast using the novel hsf1∆ construct. Our data highlight that the accumulation of misfolded proteins is uniquely sensed by Hsf1-Hsp70 chaperone titration inducing a highly selective transcriptional stress response.
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Affiliation(s)
- Michela Ciccarelli
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-10691 Stockholm, Sweden
| | - Anna E Masser
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-10691 Stockholm, Sweden
| | | | - Jordi Planells
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-10691 Stockholm, Sweden
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-10691 Stockholm, Sweden
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Attfield PV. Crucial aspects of metabolism and cell biology relating to industrial production and processing of Saccharomyces biomass. Crit Rev Biotechnol 2023; 43:920-937. [PMID: 35731243 DOI: 10.1080/07388551.2022.2072268] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/27/2022] [Accepted: 04/21/2022] [Indexed: 12/16/2022]
Abstract
The multitude of applications to which Saccharomyces spp. are put makes these yeasts the most prolific of industrial microorganisms. This review considers biological aspects pertaining to the manufacture of industrial yeast biomass. It is proposed that the production of yeast biomass can be considered in two distinct but interdependent phases. Firstly, there is a cell replication phase that involves reproduction of cells by their transitions through multiple budding and metabolic cycles. Secondly, there needs to be a cell conditioning phase that enables the accrued biomass to withstand the physicochemical challenges associated with downstream processing and storage. The production of yeast biomass is not simply a case of providing sugar, nutrients, and other growth conditions to enable multiple budding cycles to occur. In the latter stages of culturing, it is important that all cells are induced to complete their current budding cycle and subsequently enter into a quiescent state engendering robustness. Both the cell replication and conditioning phases need to be optimized and considered in concert to ensure good biomass production economics, and optimum performance of industrial yeasts in food and fermentation applications. Key features of metabolism and cell biology affecting replication and conditioning of industrial Saccharomyces are presented. Alternatives for growth substrates are discussed, along with the challenges and prospects associated with defining the genetic bases of industrially important phenotypes, and the generation of new yeast strains."I must be cruel only to be kind: Thus bad begins, and worse remains behind." William Shakespeare: Hamlet, Act 3, Scene 4.
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Khotimah H, Astuti RI, Rafi M, Yuliana ND. Metabolomics Study Reveals Biomarker L-Proline as Potential Stress-Protectant Compound for High-Temperature Bioethanol Fermentation by Yeast Pichia kudriavzevii 1P4. Appl Biochem Biotechnol 2023; 195:5180-5198. [PMID: 37103737 DOI: 10.1007/s12010-023-04554-2] [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] [Accepted: 04/18/2023] [Indexed: 04/28/2023]
Abstract
High-temperature ethanol fermentation (> 40 °C) can be applied as effective bioprocess technology to increase ethanol production. Thermotolerant yeast Pichia kudriavzevii 1P4 showed the ability to produce ethanol at optimum 37 °C. Thus, this study evaluated the ethanol productivity of isolate 1P4 at high-temperature ethanol fermentation (42 and 45 °C) and the identification of metabolite biomarkers using untargeted metabolomics with liquid chromatography-tandem mass spectrometry (LC-MS/MS). 1P4 showed tolerance to temperature stress up to 45 °C and thus relevant for high-temperature fermentation. As measured by gas chromatography (GC), bioethanol production of 1P4 at 30, 37, 42, and 45 °C was 5.8 g/l, 7.1 g/l, 5.1 g/l, and 2.8 g/l, respectively. The classification of biomarker compounds was based on orthogonal projection analysis to latent structure discriminant analysis (OPLS-DA), resulting in L-proline being a suspected biomarker compound for isolate 1P4 tolerance against high-temperature stress. Indeed, supplementation of L-proline on fermentation medium supported the growth of 1P4 at high temperatures (> 40 °C) than without L-proline. The bioethanol production with the addition of the L-proline resulted in the highest ethanol concentration (7.15 g/l) at 42 °C. Supplementation of L-proline as a stress-protective compound increased ethanol productivity at high-temperature fermentation of 42 and 45 °C by 36.35% and 83.33%, respectively, compared without the addition of L-proline. Preliminary interpretation of these results indicates that bioprocess engineering through supplementation of stress-protective compounds L-proline increases the fermentation efficiency of isolate 1P4 at higher temperatures (42 °C and 45 °C).
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Affiliation(s)
- Husnul Khotimah
- Graduate School of Biotechnology, IPB University, Bogor, West Java, 16680, Indonesia
| | - Rika Indri Astuti
- Department of Biology, IPB University, Bogor, West Java, 16680, Indonesia.
- Biotechnology Research Center, IPB University, Bogor, West Java, Indonesia.
| | - Mohamad Rafi
- Department of Chemistry, IPB University, Bogor, West Java, 16680, Indonesia
- Advance Research Laboratory, IPB University, Bogor, West Java, 16680, Indonesia
| | - Nancy Dewi Yuliana
- Department of Food Science and Technology, IPB University, Bogor, West Java, 16680, Indonesia
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Neves-da-Rocha J, Santos-Saboya MJ, Lopes MER, Rossi A, Martinez-Rossi NM. Insights and Perspectives on the Role of Proteostasis and Heat Shock Proteins in Fungal Infections. Microorganisms 2023; 11:1878. [PMID: 37630438 PMCID: PMC10456932 DOI: 10.3390/microorganisms11081878] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 08/27/2023] Open
Abstract
Fungi are a diverse group of eukaryotic organisms that infect humans, animals, and plants. To successfully colonize their hosts, pathogenic fungi must continuously adapt to the host's unique environment, e.g., changes in temperature, pH, and nutrient availability. Appropriate protein folding, assembly, and degradation are essential for maintaining cellular homeostasis and survival under stressful conditions. Therefore, the regulation of proteostasis is crucial for fungal pathogenesis. The heat shock response (HSR) is one of the most important cellular mechanisms for maintaining proteostasis. It is activated by various stresses and regulates the activity of heat shock proteins (HSPs). As molecular chaperones, HSPs participate in the proteostatic network to control cellular protein levels by affecting their conformation, location, and degradation. In recent years, a growing body of evidence has highlighted the crucial yet understudied role of stress response circuits in fungal infections. This review explores the role of protein homeostasis and HSPs in fungal pathogenicity, including their contributions to virulence and host-pathogen interactions, as well as the concerted effects between HSPs and the main proteostasis circuits in the cell. Furthermore, we discuss perspectives in the field and the potential for targeting the components of these circuits to develop novel antifungal therapies.
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Affiliation(s)
- João Neves-da-Rocha
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil; (M.J.S.-S.); (M.E.R.L.); (A.R.)
| | | | | | | | - Nilce M. Martinez-Rossi
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil; (M.J.S.-S.); (M.E.R.L.); (A.R.)
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37
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Boronat S, Cabrera M, Vega M, Alcalá J, Salas-Pino S, Daga RR, Ayté J, Hidalgo E. Formation of Transient Protein Aggregate-like Centers Is a General Strategy Postponing Degradation of Misfolded Intermediates. Int J Mol Sci 2023; 24:11202. [PMID: 37446379 DOI: 10.3390/ijms241311202] [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: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
When misfolded intermediates accumulate during heat shock, the protein quality control system promotes cellular adaptation strategies. In Schizosaccharomyces pombe, thermo-sensitive proteins assemble upon stress into protein aggregate-like centers, PACs, to escape from degradation. The role of this protein deposition strategy has been elusive due to the use of different model systems and reporters, and to the addition of artificial inhibitors, which made interpretation of the results difficult. Here, we compare fission and budding yeast model systems, expressing the same misfolding reporters in experiments lacking proteasome or translation inhibitors. We demonstrate that mild heat shock triggers reversible PAC formation, with the collapse of both reporters and chaperones in a process largely mediated by chaperones. This assembly postpones proteasomal degradation of the misfolding reporters, and their Hsp104-dependent disassembly occurs during stress recovery. Severe heat shock induces formation of cytosolic PACs, but also of nuclear structures resembling nucleolar rings, NuRs, presumably to halt nuclear functions. Our study demonstrates that these distantly related yeasts use very similar strategies to adapt and survive to mild and severe heat shock and that aggregate-like formation is a general cellular scheme to postpone protein degradation and facilitate exit from stress.
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Affiliation(s)
- Susanna Boronat
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Margarita Cabrera
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 08003 Barcelona, Spain
- Centro de Biología Molecular Severo Ochoa and Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), 28049 Madrid, Spain
| | - Montserrat Vega
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Jorge Alcalá
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Silvia Salas-Pino
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas-Junta de Andalucía, Carretera de Utrera, km1, 41013 Seville, Spain
| | - Rafael R Daga
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas-Junta de Andalucía, Carretera de Utrera, km1, 41013 Seville, Spain
| | - José Ayté
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Elena Hidalgo
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 08003 Barcelona, Spain
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38
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Fay JC, Alonso-Del-Real J, Miller JH, Querol A. Divergence in the Saccharomyces species' heat shock response is indicative of their thermal tolerance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.04.547718. [PMID: 37461527 PMCID: PMC10349932 DOI: 10.1101/2023.07.04.547718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
The Saccharomyces species have diverged in their thermal growth profile. Both S. cerevisiae and S. paradoxus grow at temperatures well above the maximum growth temperature of S. kudriavzevii and S. uvarum, but grow more poorly at lower temperatures. In response to thermal shifts, organisms activate a stress response that includes heat shock proteins involved in protein homeostasis and acquisition of thermal tolerance. To determine whether Saccharomyces species have diverged in their response to temperature we measured changes in gene expression in response to a 12°C increase or decrease in temperature for four Saccharomyces species and their six pairwise hybrids. To ensure coverage of subtelomeric gene families we sequenced, assembled and annotated a complete S. uvarum genome. All the strains exhibited a stronger response to heat than cold treatment. In response to heat, the cryophilic species showed a stronger response than the thermophilic species. The hybrids showed a mixture of parental stress responses depending on the time point. After the initial response, hybrids with a thermophilic parent were more similar to S. cerevisiae and S. paradoxus, and the S. cerevisiae × S. paradoxus hybrid showed the weakest heat shock response. Within the hybrids a small subset of temperature responsive genes showed species specific responses but most were also hybrid specific. Our results show that divergence in the heat shock response is indicative of a strain's thermal tolerance, suggesting that cellular factors that signal heat stress or resolve heat induced changes are relevant to thermal divergence in the Saccharomyces species.
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Affiliation(s)
- Justin C Fay
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Javier Alonso-Del-Real
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Valencia, Spain
- Present position: Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - James H Miller
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Amparo Querol
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Valencia, Spain
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Jennings MD, Srivastava P, Kershaw CJ, Talavera D, Grant C, Pavitt G. Interaction of the La-related protein Slf1 with colliding ribosomes maintains translation of oxidative-stress responsive mRNAs. Nucleic Acids Res 2023; 51:5755-5773. [PMID: 37070186 PMCID: PMC10287931 DOI: 10.1093/nar/gkad272] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 04/19/2023] Open
Abstract
In response to oxidative stress cells reprogram gene expression to enhance levels of antioxidant enzymes and promote survival. In Saccharomyces cerevisiae the polysome-interacting La-related proteins (LARPs) Slf1 and Sro9 aid adaptation of protein synthesis during stress by undetermined means. To gain insight in their mechanisms of action in stress responses, we determined LARP mRNA binding positions in stressed and unstressed cells. Both proteins bind within coding regions of stress-regulated antioxidant enzyme and other highly translated mRNAs in both optimal and stressed conditions. LARP interaction sites are framed and enriched with ribosome footprints suggesting ribosome-LARP-mRNA complexes are identified. Although stress-induced translation of antioxidant enzyme mRNAs is attenuated in slf1Δ, these mRNAs remain on polysomes. Focusing further on Slf1, we find it binds to both monosomes and disomes following RNase treatment. slf1Δ reduces disome enrichment during stress and alters programmed ribosome frameshifting rates. We propose that Slf1 is a ribosome-associated translational modulator that stabilises stalled/collided ribosomes, prevents ribosome frameshifting and so promotes translation of a set of highly-translated mRNAs that together facilitate cell survival and adaptation to stress.
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Affiliation(s)
- Martin D Jennings
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Priya Srivastava
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Christopher J Kershaw
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - David Talavera
- Division of Cardiovascular Sciences, School of Medical Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Christopher M Grant
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Graham D Pavitt
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, M13 9PT, UK
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40
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Xiao C, Xue S, Pan Y, Liu X, Huang M. Overexpression of genes by stress-responsive promoters increases protein secretion in Saccharomyces cerevisiae. World J Microbiol Biotechnol 2023; 39:203. [PMID: 37209206 DOI: 10.1007/s11274-023-03646-9] [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: 02/15/2023] [Accepted: 05/10/2023] [Indexed: 05/22/2023]
Abstract
Recombinant proteins produced by cell factories are now widely used in various fields. Many efforts have been made to improve the secretion capacity of cell factories to meet the increasing demand for recombinant proteins. Recombinant protein production usually causes cell stress in the endoplasmic reticulum (ER). The overexpression of key genes possibly removes limitations in protein secretion. However, inappropriate gene expression may have negative effects. There is a need for dynamic control of genes adapted to cellular status. In this study, we constructed and characterized synthetic promoters that were inducible under ER stress conditions in Saccharomyces cerevisiae. The unfolded protein response element UPRE2, responding to stress with a wide dynamic range, was assembled with various promoter core regions, resulting in UPR-responsive promoters. Synthetic responsive promoters regulated gene expression by responding to stress level, which reflected the cellular status. The engineered strain using synthetic responsive promoters P4UPRE2 - TDH3 and P4UPRE2 - TEF1 for co-expression of ERO1 and SLY1 had 95% higher α-amylase production compared with the strain using the native promoters PTDH3 and PTEF1. This work showed that UPR-responsive promoters were useful in the metabolic engineering of yeast strains for tuning genes to support efficient protein production.
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Affiliation(s)
- Chufan Xiao
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Songlyu Xue
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Yuyang Pan
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Xiufang Liu
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Mingtao Huang
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China.
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Hung PH, Liao CW, Ko FH, Tsai HK, Leu JY. Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains. iScience 2023; 26:106635. [PMID: 37138775 PMCID: PMC10149407 DOI: 10.1016/j.isci.2023.106635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 02/21/2023] [Accepted: 04/05/2023] [Indexed: 05/05/2023] Open
Abstract
Enhanced phenotypic diversity increases a population's likelihood of surviving catastrophic conditions. Hsp90, an essential molecular chaperone and a central network hub in eukaryotes, has been observed to suppress or enhance the effects of genetic variation on phenotypic diversity in response to environmental cues. Because many Hsp90-interacting genes are involved in signaling transduction pathways and transcriptional regulation, we tested how common Hsp90-dependent differential gene expression is in natural populations. Many genes exhibited Hsp90-dependent strain-specific differential expression in five diverse yeast strains. We further identified transcription factors (TFs) potentially contributing to variable expression. We found that on Hsp90 inhibition or environmental stress, activities or abundances of Hsp90-dependent TFs varied among strains, resulting in differential strain-specific expression of their target genes, which consequently led to phenotypic diversity. We provide evidence that individual strains can readily display specific Hsp90-dependent gene expression, suggesting that the evolutionary impacts of Hsp90 are widespread in nature.
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Affiliation(s)
- Po-Hsiang Hung
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 115, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
- Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Chia-Wei Liao
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Fu-Hsuan Ko
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Huai-Kuang Tsai
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 115, Taiwan
- Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
- Corresponding author
| | - Jun-Yi Leu
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 115, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
- Corresponding author
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Elias D, Tóth Hervay N, Bujdos M, Gbelska Y. Essential Role of CgErg6p in Maintaining Oxidative Stress Tolerance and Iron Homeostasis in Candida glabrata. J Fungi (Basel) 2023; 9:jof9050579. [PMID: 37233290 DOI: 10.3390/jof9050579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023] Open
Abstract
The human pathogenic fungus Candida glabrata is the second leading cause of candidemia, a life-threatening invasive mycosis. Clinical outcomes are complicated by reduced susceptibility of C. glabrata to azoles together with its ability to evolve stable resistance to both azoles and echinocandins following drug exposure. Compared to other Candida spp., C. glabrata displays robust oxidative stress resistance. In this study, we investigated the impact of CgERG6 gene deletion on the oxidative stress response in C. glabrata. CgERG6 gene encodes sterol-24-C-methyltransferase, which is involved in the final steps of ergosterol biosynthesis. Our previous results showed that the Cgerg6Δ mutant has a lower ergosterol content in its membranes. Here, we show that the Cgerg6Δ mutant displays increased susceptibility to oxidative stress inducing agents, such as menadione, hydrogen peroxide and diamide, accompanied with increased intracellular ROS production. The Cgerg6Δ mutant is not able to tolerate higher concentrations of iron in the growth media. We observed increased expression of transcription factors, CgYap1p, CgMsn4p and CgYap5p, together with increased expression of catalase encoding the CgCTA1 gene and vacuolar iron transporter CgCCC1 in the Cgerg6Δ mutant cells. However, it seems that the CgERG6 gene deletion does not influence the function of mitochondria.
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Affiliation(s)
- Daniel Elias
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovakia
| | - Nora Tóth Hervay
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovakia
| | - Marek Bujdos
- Faculty of Natural Sciences, Institute of Laboratory Research on Geomaterials, Comenius University in Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovakia
| | - Yvetta Gbelska
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovakia
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Ulrich K. Redox-regulated chaperones in cell stress responses. Biochem Soc Trans 2023:233014. [PMID: 37140269 DOI: 10.1042/bst20221304] [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: 01/30/2023] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 05/05/2023]
Abstract
Proteostasis and redox homeostasis are tightly interconnected and most protein quality control pathways are under direct redox regulation which allow cells to immediately respond to oxidative stress conditions. The activation of ATP-independent chaperones serves as a first line of defense to counteract oxidative unfolding and aggregation of proteins. Conserved cysteine residues evolved as redox-sensitive switches which upon reversible oxidation induce substantial conformational rearrangements and the formation of chaperone-active complexes. In addition to harnessing unfolding proteins, these chaperone holdases interact with ATP-dependent chaperone systems to facilitate client refolding and restoring proteostasis during stress recovery. This minireview gives an insight into highly orchestrated mechanisms regulating the stress-specific activation and inactivation of redox-regulated chaperones and their role in cell stress responses.
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Affiliation(s)
- Kathrin Ulrich
- Institute of Biochemistry, Cellular Biochemistry, University of Cologne, Zuelpicher Str. 47a, 50674 Cologne, Germany
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Gutiérrez-Escobedo G, Vázquez-Franco N, López-Marmolejo A, Luna-Arvizu G, Cañas-Villamar I, Castaño I, De Las Peñas A. Characterization of the Trr/Trx system in the fungal pathogen Candida glabrata. Fungal Genet Biol 2023; 166:103799. [PMID: 37105080 DOI: 10.1016/j.fgb.2023.103799] [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: 02/22/2023] [Revised: 04/07/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023]
Abstract
C. glabrata, an opportunistic fungal pathogen, can adapt and resist to different stress conditions. It is highly resistant to oxidant stress compared to other Candida spp and to the phylogenetically related but non-pathogen Saccharomyces cerevisiae. In this work, we describe the Trx/Trr system of C. glabrata composed of Trr1 and Trr2 (thioredoxin reductases) and Trx2 (thioredoxin) that are localized in the cytoplasm and Trx3 present in the mitochondrion. The transcriptional induction of TRR2 and TRX2 by oxidants depends on Yap1 and Skn7 and TRR1 and TRX3 have a low expression level. Both TRR2 and TRX2 play an important role in the oxidative stress response. The absence of TRX2 causes auxotrophy of methionine and cysteine. Trr1 and Trr2 are necessary for survival at high temperatures and for the chronological life span of C. glabrata. Furthermore, the Trx/Trr system is needed for survival in the presence of neutrophils. The role of TRR1 and TRX3 is not clear, but in the presence of neutrophils, they have non-overlapping functions with their TRR2 and TRX2 paralogues.
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Affiliation(s)
- Guadalupe Gutiérrez-Escobedo
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, #2055, Col. Lomas 4ª Sección, San Luis Potosí 78216, Mexico
| | - Norma Vázquez-Franco
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Universidad Autónoma de Querétaro, Querétaro, Mexico
| | - Ana López-Marmolejo
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, #2055, Col. Lomas 4ª Sección, San Luis Potosí 78216, Mexico
| | - Gabriel Luna-Arvizu
- Department of Biology, Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
| | - Israel Cañas-Villamar
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, #2055, Col. Lomas 4ª Sección, San Luis Potosí 78216, Mexico
| | - Irene Castaño
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, #2055, Col. Lomas 4ª Sección, San Luis Potosí 78216, Mexico
| | - Alejandro De Las Peñas
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, #2055, Col. Lomas 4ª Sección, San Luis Potosí 78216, Mexico.
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Regulation of germline proteostasis by HSF1 and insulin/IGF-1 signaling. Biochem Soc Trans 2023; 51:501-512. [PMID: 36892215 DOI: 10.1042/bst20220616] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 03/10/2023]
Abstract
Protein homeostasis (proteostasis) is essential for cellular function and organismal health and requires the concerted actions of protein synthesis, folding, transport, and turnover. In sexually reproducing organisms, the immortal germline lineage passes genetic information across generations. Accumulating evidence indicates the importance of proteome integrity for germ cells as genome stability. As gametogenesis involves very active protein synthesis and is highly energy-demanding, it has unique requirements for proteostasis regulation and is sensitive to stress and nutrient availability. The heat shock factor 1 (HSF1), a key transcriptional regulator of cellular response to cytosolic and nuclear protein misfolding has evolutionarily conserved roles in germline development. Similarly, insulin/insulin-like growth factor-1 (IGF-1) signaling, a major nutrient-sensing pathway, impacts many aspects of gametogenesis. Here, we focus on HSF1 and IIS to review insights into their roles in germline proteostasis and discuss the implications on gamete quality control during stress and aging.
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Kyriakou M, Christodoulou M, Ioannou A, Fotopoulos V, Koutinas M. Improvement of stress multi-tolerance and bioethanol production by Saccharomyces cerevisiae immobilised on biochar: Monitoring transcription from defence-related genes. Biochem Eng J 2023. [DOI: 10.1016/j.bej.2023.108914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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Su Y, Xu C, Shea J, DeStephanis D, Su Z. Transcriptomic changes in single yeast cells under various stress conditions. BMC Genomics 2023; 24:88. [PMID: 36829151 PMCID: PMC9960639 DOI: 10.1186/s12864-023-09184-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/13/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND The stress response of Saccharomyces cerevisiae has been extensively studied in the past decade. However, with the advent of recent technology in single-cell transcriptome profiling, there is a new opportunity to expand and further understanding of the yeast stress response with greater resolution on a system level. To understand transcriptomic changes in baker's yeast S. cerevisiae cells under stress conditions, we sequenced 117 yeast cells under three stress treatments (hypotonic condition, glucose starvation and amino acid starvation) using a full-length single-cell RNA-Seq method. RESULTS We found that though single cells from the same treatment showed varying degrees of uniformity, technical noise and batch effects can confound results significantly. However, upon careful selection of samples to reduce technical artifacts and account for batch-effects, we were able to capture distinct transcriptomic signatures for different stress conditions as well as putative regulatory relationships between transcription factors and target genes. CONCLUSION Our results show that a full-length single-cell based transcriptomic analysis of the yeast may help paint a clearer picture of how the model organism responds to stress than do bulk cell population-based methods.
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Affiliation(s)
- Yangqi Su
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 28223, Charlotte, NC, USA
| | - Chen Xu
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 28223, Charlotte, NC, USA
| | - Jonathan Shea
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 28223, Charlotte, NC, USA
| | - Darla DeStephanis
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 28223, Charlotte, NC, USA
| | - Zhengchang Su
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 28223, Charlotte, NC, USA.
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The Entomopathogenic Fungus Beauveria bassiana Employs Autophagy as a Persistence and Recovery Mechanism during Conidial Dormancy. mBio 2023; 14:e0304922. [PMID: 36809079 PMCID: PMC10128008 DOI: 10.1128/mbio.03049-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Many filamentous fungi develop a conidiation process as an essential mechanism for their dispersal and survival in natural ecosystems. However, the mechanisms underlying conidial persistence in environments are still not fully understood. Here, we report that autophagy is crucial for conidial lifespans (i.e., viability) and vitality (e.g., stress responses and virulence) in the filamentous mycopathogen Beauveria bassiana. Specifically, Atg11-mediated selective autophagy played an important, but not dominant, role in the total autophagic flux. Furthermore, the aspartyl aminopeptidase Ape4 was found to be involved in conidial vitality during dormancy. Notably, the vacuolar translocation of Ape4 was dependent on its physical interaction with autophagy-related protein 8 (Atg8) and associated with the autophagic role of Atg8, as determined through a truncation assay of a critical carboxyl-tripeptide. These observations revealed that autophagy acted as a subcellular mechanism for conidial recovery during dormancy in environments. In addition, a novel Atg8-dependent targeting route for vacuolar hydrolase was identified, which is essential for conidial exit from a long-term dormancy. These new insights improved our understanding of the roles of autophagy in the physiological ecology of filamentous fungi as well as the molecular mechanisms involved in selective autophagy. IMPORTANCE Conidial environmental persistence is essential for fungal dispersal in ecosystems while also serving as a determinant for the biocontrol efficacy of entomopathogenic fungi during integrated pest management. This study identified autophagy as a mechanism to safeguard conidial lifespans and vitality postmaturation. In this mechanism, the aspartyl aminopeptidase Ape4 translocates into vacuoles via its physical interaction with autophagy-related protein 8 (Atg8) and is involved in conidial vitality during survival. The study revealed that autophagy acted as a subcellular mechanism for maintaining conidial persistence during dormancy, while also documenting an Atg8-dependent targeting route for vacuolar hydrolase during conidial recovery from dormancy. Thus, these observations provided new insight into the roles of autophagy in the physiological ecology of filamentous fungi and documented novel molecular mechanisms involved in selective autophagy.
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Lammel DR, Szymczak A, Bielcik M, Rillig MC. Fungal growth response to recurring heating events is modulated by species interactions. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.1028136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
An increasing frequency of heat events can affect key organisms related to ecosystem functions. Soil saprobic fungi have important roles in carbon and nutrient cycling in soils, and they are clearly affected by heat events. When tested individually, saprobic soil fungi showed a variety of growth responses to a series of two heat events. However, in nature, these fungi rarely grow alone. Coexistence theory predicts that diversity in the response to stressors can influence the outcome of species interactions and growth. This means that the co-cultivation of different fungi may affect their growth response to heat events. To test if recurring heat events affect fungal growth in small synthetic communities, we evaluated fungi previously known to respond to recurring heat events in experimental small communities composed of two and three species. For the fungi growing in pairs, surprisingly, most of the responses could not be predicted by how the isolates responded individually. In some cases, facilitation or increased competition was observed. For the three fungi growing together, results were also not predicted by the individual or pair responses. Both the heat events and the small communities influenced the growth of the fungi and growth properties emerged from the interactions among isolates and the heat stress. We show that not only do environmental conditions influence fungal interactions and growth rates but also that the co-cultivation of different fungi affects the fungal response to recurring heat events. These results indicate that more complex experimental designs are needed to better understand the effects of recurring heat events and climate change on soil fungi.
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50
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Liang P, Li J, Wang Q, Dai Z. Enhancing the thermotolerance and erythritol production of Yarrowia lipolytica by introducing heat-resistant devices. Front Bioeng Biotechnol 2023; 11:1108653. [PMID: 36845173 PMCID: PMC9947466 DOI: 10.3389/fbioe.2023.1108653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 01/20/2023] [Indexed: 02/11/2023] Open
Abstract
Yarrowia lipolytica has been widely used in the food biotech-related industry, where it plays the host's role in producing erythritol. Nevertheless, a temperature of about 28°C-30°C has been estimated as the yeast's optimal growth temperature, leading to the consumption of a considerable quantity of cooling water, especially in summer, which is obligatory for fermentation. Herein is described a method for improving the thermotolerance and erythritol production efficiency at high temperatures of Y. lipolytica. Through screening and testing different heat resistant devices, eight refactored engineered strains showed better growth at higher temperature and the antioxidant properties of the eight engineered strains were also improved. In addition, the erythritol titer, yield and productivity of the strain FOS11-Ctt1 represented the best among the eight strains, reaching at 39.25 g/L, 0.348 g/g glucose, and 0.55 g/L/h respectively, which were increased by 156%, 86% and 161% compared with the control strain, respectively. This study provides insight into an effective heat-resistant device that could enhance the thermotolerance and erythritol production of Y. lipolytica, which might be considered a valued scientific reference for other resistant strains' construction.
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Affiliation(s)
- Peixin Liang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China,National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Jing Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China,National Center of Technology Innovation for Synthetic Biology, Tianjin, China,College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Qinhong Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China,National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Zongjie Dai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China,National Center of Technology Innovation for Synthetic Biology, Tianjin, China,*Correspondence: Zongjie Dai,
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