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Zhang X, Nijland JG, Driessen AJM. Maltose accumulation-induced cell death in Saccharomyces cerevisiae. FEMS Yeast Res 2024; 24:foae012. [PMID: 38565313 PMCID: PMC11037483 DOI: 10.1093/femsyr/foae012] [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: 01/10/2024] [Revised: 03/12/2024] [Accepted: 04/01/2024] [Indexed: 04/04/2024] Open
Abstract
Pretreatment of lignocellulose yields a complex sugar mixture that potentially can be converted into bioethanol and other chemicals by engineered yeast. One approach to overcome competition between sugars for uptake and metabolism is the use of a consortium of specialist strains capable of efficient conversion of single sugars. Here, we show that maltose inhibits cell growth of a xylose-fermenting specialist strain IMX730.1 that is unable to utilize glucose because of the deletion of all hexokinase genes. The growth inhibition cannot be attributed to a competition between maltose and xylose for uptake. The inhibition is enhanced in a strain lacking maltase enzymes (dMalX2) and completely eliminated when all maltose transporters are deleted. High-level accumulation of maltose in the dMalX2 strain is accompanied by a hypotonic-like transcriptional response, while cells are rescued from maltose-induced cell death by the inclusion of an extracellular osmolyte such as sorbitol. These data suggest that maltose-induced cell death is due to high levels of maltose uptake causing hypotonic-like stress conditions and can be prevented through engineering of the maltose transporters. Transporter engineering should be included in the development of stable microbial consortia for the efficient conversion of lignocellulosic feedstocks.
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Affiliation(s)
- Xiaohuan Zhang
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Nijenborgh 7, 9747AG Groningen, the Netherlands
| | - Jeroen G Nijland
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Nijenborgh 7, 9747AG Groningen, the Netherlands
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Nijenborgh 7, 9747AG Groningen, the Netherlands
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2
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Metal ion availability and homeostasis as drivers of metabolic evolution and enzyme function. Curr Opin Genet Dev 2022; 77:101987. [PMID: 36183585 DOI: 10.1016/j.gde.2022.101987] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 01/27/2023]
Abstract
Metal ions are potent catalysts and have been available for cellular biochemistry at all stages of evolution. Growing evidence suggests that metal catalysis was critical for the origin of the very first metabolic reactions. With approximately 80% of modern metabolic pathways being dependent on metal ions, metallocatalysis and homeostasis continue to be essential for intracellular metabolic networks and physiology. However, the genetic network that controls metal ion homeostasis and the impact of metal availability on metabolism is poorly understood. Here, we review recent work on gene and protein evolution relevant for better understanding metal ion biology and its role in metabolism. We highlight the importance of analysing the origin and evolution of enzyme catalysis in the context of catalytically relevant metal ions, summarise unanswered questions essential for developing a comprehensive understanding of metal ion homeostasis and advocate for the consideration of metal ion properties and availability in the design and directed evolution of novel enzymes and pathways.
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Hernández-Ortiz P, Espeso EA. Spatiotemporal dynamics of the calcineurin target CrzA. Cell Signal 2016; 29:168-180. [PMID: 27832964 DOI: 10.1016/j.cellsig.2016.11.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 09/26/2016] [Accepted: 11/05/2016] [Indexed: 01/23/2023]
Abstract
The response of Aspergilli to elevated concentrations of extracellular calcium and manganese, or environmental alkalinization is mediated by CrzA, a calcineurin-responsive transcription factor (TF). CrzA is the effector of a signaling pathway which includes the apical protein's calmodulin and calcineurin, and the protein kinases GskA and CkiA. Preferentially located in the cytoplasm, CrzA is the only element of the pathway modifying its localization under those stress conditions, being imported into nuclei. Remarkably, there is a direct relationship between the nature/intensity of the stimulus and the pace of nuclear import and time of nuclear permanence of CrzA. Alkalinity caused a transient nuclear accumulation of CrzA while high Ca2+ and Mn2+ concentrations generated a long-lasting accumulation. Furthermore, Ca2+ concentrations (below 5mM) that are non-toxic for a crzAΔ mutant promoted full signaling of CrzA. However, micromolar concentrations or a mutation disrupting the interaction of CrzA with the phosphatase complex calcineurin, permitted the visualization of a transient and polarized nuclear accumulation of the TF in a tip-to-base gradient. Overall, these results support a model in which nucleo-cytoplasmic dynamics and transcriptional activity of CrzA are driven by apical signals transmitted by calmodulin and calcineurin. This communication is essential to understand Ca+2-induced stress response in fungi.
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Affiliation(s)
- Patricia Hernández-Ortiz
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Eduardo A Espeso
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain.
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Busti S, Mapelli V, Tripodi F, Sanvito R, Magni F, Coccetti P, Rocchetti M, Nielsen J, Alberghina L, Vanoni M. Respiratory metabolism and calorie restriction relieve persistent endoplasmic reticulum stress induced by calcium shortage in yeast. Sci Rep 2016; 6:27942. [PMID: 27305947 PMCID: PMC4910072 DOI: 10.1038/srep27942] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 05/27/2016] [Indexed: 11/26/2022] Open
Abstract
Calcium homeostasis is crucial to eukaryotic cell survival. By acting as an enzyme cofactor and a second messenger in several signal transduction pathways, the calcium ion controls many essential biological processes. Inside the endoplasmic reticulum (ER) calcium concentration is carefully regulated to safeguard the correct folding and processing of secretory proteins. By using the model organism Saccharomyces cerevisiae we show that calcium shortage leads to a slowdown of cell growth and metabolism. Accumulation of unfolded proteins within the calcium-depleted lumen of the endoplasmic reticulum (ER stress) triggers the unfolded protein response (UPR) and generates a state of oxidative stress that decreases cell viability. These effects are severe during growth on rapidly fermentable carbon sources and can be mitigated by decreasing the protein synthesis rate or by inducing cellular respiration. Calcium homeostasis, protein biosynthesis and the unfolded protein response are tightly intertwined and the consequences of facing calcium starvation are determined by whether cellular energy production is balanced with demands for anabolic functions. Our findings confirm that the connections linking disturbance of ER calcium equilibrium to ER stress and UPR signaling are evolutionary conserved and highlight the crucial role of metabolism in modulating the effects induced by calcium shortage.
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Affiliation(s)
- Stefano Busti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- SYSBIO, Centre of Systems Biology, Milan, Italy
| | - Valeria Mapelli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
| | - Farida Tripodi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- SYSBIO, Centre of Systems Biology, Milan, Italy
| | - Rossella Sanvito
- Department of Health Sciences, University of Milano-Bicocca, Milan, Italy
| | - Fulvio Magni
- Department of Health Sciences, University of Milano-Bicocca, Milan, Italy
| | - Paola Coccetti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- SYSBIO, Centre of Systems Biology, Milan, Italy
| | - Marcella Rocchetti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Lilia Alberghina
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- SYSBIO, Centre of Systems Biology, Milan, Italy
| | - Marco Vanoni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- SYSBIO, Centre of Systems Biology, Milan, Italy
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Retrotransposon expression in ethanol-stressed Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2010; 87:1447-54. [PMID: 20393705 DOI: 10.1007/s00253-010-2562-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Revised: 03/08/2010] [Accepted: 03/14/2010] [Indexed: 10/19/2022]
Abstract
There are five retrotransposon families in Saccharomyces cerevisiae, three (Ty1, Ty2, and Ty3) of which are known to be transcriptionally active. Early investigations reported yeast retrotransposons to be stress-induced; however, microarray-based studies do not report retrotransposition-related Gene Ontology (GO) categories in the ethanol stress response of S. cerevisiae. In this study, microarray technology was used to investigate the ethanol stress response of S. cerevisiae W303-1A, and the highest stress-induced GO categories, based on z-score, were found to be retrotransposition-related, namely, Retrotransposition Nucleocapsid and Transposition, RNA-Mediated. Further investigation, involving reanalysis of previously published results on the stress response of S. cerevisiae, identified the absence of annotation for retrotransposon genes and associated GO categories and their omission during the printing of spotted arrays as two reasons why these categories in previous gene expression studies on the ethanol stress response of yeast were not reported.
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Fellenberg K, Busold CH, Witt O, Bauer A, Beckmann B, Hauser NC, Frohme M, Winter S, Dippon J, Hoheisel JD. Systematic interpretation of microarray data using experiment annotations. BMC Genomics 2006; 7:319. [PMID: 17181856 PMCID: PMC1774576 DOI: 10.1186/1471-2164-7-319] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2006] [Accepted: 12/20/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Up to now, microarray data are mostly assessed in context with only one or few parameters characterizing the experimental conditions under study. More explicit experiment annotations, however, are highly useful for interpreting microarray data, when available in a statistically accessible format. RESULTS We provide means to preprocess these additional data, and to extract relevant traits corresponding to the transcription patterns under study. We found correspondence analysis particularly well-suited for mapping such extracted traits. It visualizes associations both among and between the traits, the hereby annotated experiments, and the genes, revealing how they are all interrelated. Here, we apply our methods to the systematic interpretation of radioactive (single channel) and two-channel data, stemming from model organisms such as yeast and drosophila up to complex human cancer samples. Inclusion of technical parameters allows for identification of artifacts and flaws in experimental design. CONCLUSION Biological and clinical traits can act as landmarks in transcription space, systematically mapping the variance of large datasets from the predominant changes down toward intricate details.
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Affiliation(s)
- Kurt Fellenberg
- Department of Functional Genome Analysis, German Cancer Research Center, PO 101949, D-69009 Heidelberg, Germany
| | - Christian H Busold
- Department of Functional Genome Analysis, German Cancer Research Center, PO 101949, D-69009 Heidelberg, Germany
| | - Olaf Witt
- Department of Pediatrics I, University of Göttingen, Robert-Koch-Str. 40, D-37075 Göttingen, Germany
- Experimental Pediatric Oncology, German Cancer Research Center, PO 101949, D-69009 Heidelberg, Germany
| | - Andrea Bauer
- Department of Functional Genome Analysis, German Cancer Research Center, PO 101949, D-69009 Heidelberg, Germany
| | - Boris Beckmann
- Department of Functional Genome Analysis, German Cancer Research Center, PO 101949, D-69009 Heidelberg, Germany
| | | | - Marcus Frohme
- Department of Functional Genome Analysis, German Cancer Research Center, PO 101949, D-69009 Heidelberg, Germany
| | - Stefan Winter
- Institute for Stochastics and Applications, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Jürgen Dippon
- Institute for Stochastics and Applications, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Jörg D Hoheisel
- Department of Functional Genome Analysis, German Cancer Research Center, PO 101949, D-69009 Heidelberg, Germany
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Prado SMD, Cerdán ME, González Siso MI. Isolation and transcriptional regulation of the Kluyveromyces lactis FBA1 (fructose-1,6-bisphosphate aldolase) gene. Can J Microbiol 2004; 50:645-52. [PMID: 15467790 DOI: 10.1139/w04-038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cloning and transcriptional regulation of the KlFBA1 gene that codes for the class II fructose-1,6-bisphosphate aldolase of the yeast Kluyveromyces lactis are described. KlFBA1 mRNA diminishes transiently during the shift from hypoxic to fully aerobic conditions and increases in the reversal shift. This regulation is mediated by heme since expression was higher in a mutant defective in heme biosynthesis. KlFBA1 transcription is not induced by calcium-shortage, low temperature, or at stationary phase. These data suggest that KlFBA1 plays a role in the balance between oxidative and fermentative metabolism and that this gene is differentially regulated in K. lactis and Saccharomyces cerevisiae, i.e., a respiratory vs. fermentative yeast.
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Affiliation(s)
- Silvia M Díaz Prado
- Department of Molecular and Cell Biology, University of A Coruña, Campus da Zapateira s/n, 15071- A Coruña, Spain
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Farina F, Uccelletti D, Goffrini P, Butow RA, Abeijon C, Palleschi C. Alterations of O-glycosylation, cell wall, and mitochondrial metabolism in Kluyveromyces lactis cells defective in KlPmr1p, the Golgi Ca2+-ATPase. Biochem Biophys Res Commun 2004; 318:1031-8. [PMID: 15147977 DOI: 10.1016/j.bbrc.2004.04.127] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2004] [Indexed: 11/16/2022]
Abstract
In yeast the P-type Ca(2+)-ATPase of the Golgi apparatus, Pmr1p, is the most important player in calcium homeostasis. In Kluyveromyces lactis KlPMR1 inactivation leads to pleiotropic phenotypes, including reduced N-glycosylation and altered cell wall morphogenesis. To study the physiology of K. lactis when KlPMR1 was inactivated microarrays containing all Saccharomyces cerevisiae coding sequences were utilized. Alterations in O-glycosylation, consistent with the repression of KlPMT2, were found and a terminal N-acetylglucosamine in the O-glycans was identified. Klpmr1Delta cells showed increased expression of PIRs, proteins involved in cell wall maintenance, suggesting that responses to cell wall weakening take place in K. lactis. We found over-expression of KlPDA1 and KlACS2 genes involved in the Acetyl-CoA synthesis and down-regulation of KlIDP1, KlACO1, and KlSDH2 genes involved in respiratory metabolism. Increases in oxygen consumption and succinate dehydrogenase activity were also observed in mutant cells. The described approach highlighted the unexpected involvement of KlPMR1 in energy-yielding processes.
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Affiliation(s)
- Francesca Farina
- Department of Developmental and Cell Biology, University of Rome La Sapienza, Piazza Aldo Moro 5, 00185 Rome, Italy
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9
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Affiliation(s)
- Ying Liu
- Institute of Human Nutrition, Department of Pediatrics, Columbia University College of Physicians & Surgeons, New York, New York 10032, USA
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