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Capps D, Hunter A, Chiang M, Pracheil T, Liu Z. Ubiquitin-Conjugating Enzymes Ubc1 and Ubc4 Mediate the Turnover of Hap4, a Master Regulator of Mitochondrial Biogenesis in Saccharomyces cerevisiae. Microorganisms 2022; 10:microorganisms10122370. [PMID: 36557625 PMCID: PMC9787919 DOI: 10.3390/microorganisms10122370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 11/21/2022] [Accepted: 11/26/2022] [Indexed: 12/05/2022] Open
Abstract
Mitochondrial biogenesis is tightly regulated in response to extracellular and intracellular signals, thereby adapting yeast cells to changes in their environment. The Hap2/3/4/5 complex is a master transcriptional regulator of mitochondrial biogenesis in yeast. Hap4 is the regulatory subunit of the complex and exhibits increased expression when the Hap2/3/4/5 complex is activated. In cells grown under glucose derepression conditions, both the HAP4 transcript level and Hap4 protein level are increased. As part of an inter-organellar signaling mechanism coordinating gene expression between the mitochondrial and nuclear genomes, the activity of the Hap2/3/4/5 complex is reduced in respiratory-deficient cells, such as ρ0 cells lacking mitochondrial DNA, as a result of reduced Hap4 protein levels. However, the underlying mechanism is unclear. Here, we show that reduced HAP4 expression in ρ0 cells is mediated through both transcriptional and post-transcriptional mechanisms. We show that loss of mitochondrial DNA increases the turnover of Hap4, which requires the 26S proteasome and ubiquitin-conjugating enzymes Ubc1 and Ubc4. Stabilization of Hap4 in the ubc1 ubc4 double mutant leads to increased expression of Hap2/3/4/5-target genes. Our results indicate that mitochondrial biogenesis in yeast is regulated by the functional state of mitochondria partly through ubiquitin/proteasome-dependent turnover of Hap4.
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Tejedor-Sanz S, Stevens ET, Li S, Finnegan P, Nelson J, Knoesen A, Light SH, Ajo-Franklin CM, Marco ML. Extracellular electron transfer increases fermentation in lactic acid bacteria via a hybrid metabolism. eLife 2022; 11:70684. [PMID: 35147079 PMCID: PMC8837199 DOI: 10.7554/elife.70684] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 12/24/2021] [Indexed: 12/11/2022] Open
Abstract
Energy conservation in microorganisms is classically categorized into respiration and fermentation; however, recent work shows some species can use mixed or alternative bioenergetic strategies. We explored the use of extracellular electron transfer for energy conservation in diverse lactic acid bacteria (LAB), microorganisms that mainly rely on fermentative metabolism and are important in food fermentations. The LAB Lactiplantibacillus plantarum uses extracellular electron transfer to increase its NAD+/NADH ratio, generate more ATP through substrate-level phosphorylation, and accumulate biomass more rapidly. This novel, hybrid metabolism is dependent on a type-II NADH dehydrogenase (Ndh2) and conditionally requires a flavin-binding extracellular lipoprotein (PplA) under laboratory conditions. It confers increased fermentation product yield, metabolic flux, and environmental acidification in laboratory media and during kale juice fermentation. The discovery of a single pathway that simultaneously blends features of fermentation and respiration in a primarily fermentative microorganism expands our knowledge of energy conservation and provides immediate biotechnology applications. Bacteria produce the energy they need to live through two processes, respiration and fermentation. While respiration is often more energetically efficient, many bacteria rely on fermentation as their sole means of energy production. Respiration normally depends on the presence of small soluble molecules, such as oxygen, that can diffuse inside the cell, but some bacteria can use metals or other insoluble compounds found outside the cell to perform ‘extracellular electron transfer’. Lactic acid bacteria are a large group of bacteria that have several industrial uses and live in many natural environments. These bacteria survive using fermentation, but they also carry a group of genes needed for extracellular electron transfer. It is unclear whether they use these genes for respiration or if they have a different purpose. Tejedor-Sanz, Stevens et al. used a lactic acid bacterium called Lactiplantibacillus plantarum to study whether and how this group of bacteria use extracellular electron transfer. Analysis of L. plantarum and its effect on its surroundings showed that these bacteria use a hybrid process to produce energy: the cells use aspects of extracellular respiration to increase the yield and efficiency of fermentation. Combining these two approaches may allow L. plantarum to adapt to different environments and grow faster, allowing it to compete against other species. Tejedor-Sanz, Stevens et al. provide new information on a widespread group of bacteria that are often used in food production and industry. The next step will be to understand how the hybrid system is controlled and how it varies among species. Understanding this process could result in new biotechnologies and foods that are healthier, produce less waste, or have different tastes and textures.
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Affiliation(s)
- Sara Tejedor-Sanz
- Department of BioSciences, Rice University, Houston, United States.,Biological Nanostructures Facility, The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Eric T Stevens
- Department of Food Science & Technology, University of California-Davis, Davis, United States
| | - Siiliang Li
- Department of BioSciences, Rice University, Houston, United States
| | - Peter Finnegan
- Department of Food Science & Technology, University of California-Davis, Davis, United States
| | - James Nelson
- Department of Electrical and Computer Engineering, University of California-Davis, Davis, United States
| | - Andre Knoesen
- Department of Electrical and Computer Engineering, University of California-Davis, Davis, United States
| | - Samuel H Light
- Department of Microbiology, University of Chicago, Chicago, United States
| | - Caroline M Ajo-Franklin
- Department of BioSciences, Rice University, Houston, United States.,Biological Nanostructures Facility, The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Maria L Marco
- Department of Food Science & Technology, University of California-Davis, Davis, United States
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3
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Li X, Wang Y, Li G, Liu Q, Pereira R, Chen Y, Nielsen J. Metabolic network remodelling enhances yeast’s fitness on xylose using aerobic glycolysis. Nat Catal 2021. [DOI: 10.1038/s41929-021-00670-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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4
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Kurylenko O, Ruchala J, Kruk B, Vasylyshyn R, Szczepaniak J, Dmytruk K, Sibirny A. The role of Mig1, Mig2, Tup1 and Hap4 transcription factors in regulation of xylose and glucose fermentation in the thermotolerant yeast Ogataea polymorpha. FEMS Yeast Res 2021; 21:6275188. [PMID: 33983391 DOI: 10.1093/femsyr/foab029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 05/07/2021] [Indexed: 01/20/2023] Open
Abstract
Glucose is a preferred carbon source for most living organisms. The metabolism and regulation of glucose utilization are well studied mostly for Saccharomyces cerevisiae. Xylose is the main pentose sugar released from the lignocellulosic biomass, which has a high potential as a renewable feedstock for bioethanol production. The thermotolerant yeast Ogataea (Hansenula) polymorpha, in contrast to S. cerevisiae, is able to metabolize and ferment not only glucose but also xylose. However, in non-conventional yeasts, the regulation of glucose and xylose metabolism remains poorly understood. In this study, we characterize the role of transcriptional factors Mig1, Mig2, Tup1 and Hap4 in the natural xylose-fermenting yeast O. polymorpha. The deletion of MIG1 had no significant influence on ethanol production either from xylose or glucose, however the deletion of both MIG1 and MIG2 reduced the amount of ethanol produced from these sugars. The deletion of HAP4-A and TUP1 genes resulted in increased ethanol production from xylose. Inversely, the overexpression of HAP4-A and TUP1 genes reduced ethanol production during xylose alcoholic fermentation. Thus, HAP4-A and TUP1 are involved in repression of xylose metabolism and fermentation in yeast O. polymorpha and their deletion could be a viable strategy to improve ethanol production from this pentose.
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Affiliation(s)
- Olena Kurylenko
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Justyna Ruchala
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine.,Department of Microbiology and Molecular Genetics, University of Rzeszow, Cwiklinskiej 2D, Building D10, Rzeszow 35-601, Poland
| | - Barbara Kruk
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Cwiklinskiej 2D, Building D10, Rzeszow 35-601, Poland
| | - Roksolana Vasylyshyn
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Justyna Szczepaniak
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Cwiklinskiej 2D, Building D10, Rzeszow 35-601, Poland
| | - Kostyantyn Dmytruk
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Andriy Sibirny
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine.,Department of Microbiology and Molecular Genetics, University of Rzeszow, Cwiklinskiej 2D, Building D10, Rzeszow 35-601, Poland
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5
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Abstract
The budding yeast Saccharomyces cerevisiae is a facultative organism that is able to utilize both anaerobic and aerobic metabolism, depending on the composition of carbon source in the growth medium. When glucose is abundant, yeast catabolizes it to ethanol and other by-products by anaerobic fermentation through the glycolysis pathway. Following glucose exhaustion, cells switch to oxygenic respiration (a.k.a. "diauxic shift"), which allows catabolizing ethanol and the other carbon compounds via the TCA cycle and oxidative phosphorylation in the mitochondria. The diauxic shift is accompanied by elevated reactive oxygen species (ROS) levels and is characterized by activation of ROS defense mechanisms. Traditional measurement of the diauxic shift is done through measuring optical density of cultures grown in a batch at intermediate time points and generating a typical growth curve or by estimating the reduction of glucose and accumulation of ethanol in growth media over time. In this manuscript, we describe a method for determining changes in ROS levels upon yeast growth, using carboxy-H(2)-dichloro-dihydrofluorescein diacetate (carboxy-H(2)-DCFDA). H2-DCFDA is a widely used fluorescent dye for measuring intracellular ROS levels. H2-DCFDA enables a direct measurement of ROS in yeast cells at intermediate time points. The outcome of H2-DCFDA fluorescent readout measurements correlates with the growth curve information, hence providing a clear understanding of the diauxic shift.
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Affiliation(s)
- Abhishek Sinha
- Department of Biology and Environment, University of Haifa at Oranim, Tivon, Israel
- Department of Microbiology, Swami Vivekand University, Sagar, Madhya Pradesh, India
| | - Elah Pick
- Department of Biology and Environment, University of Haifa at Oranim, Tivon, Israel.
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Bhondeley M, Liu Z. Mitochondrial Biogenesis Is Positively Regulated by Casein Kinase I Hrr25 Through Phosphorylation of Puf3 in Saccharomyces cerevisiae. Genetics 2020; 215:463-482. [PMID: 32317286 PMCID: PMC7268985 DOI: 10.1534/genetics.120.303191] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 04/20/2020] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial biogenesis requires coordinated expression of genes encoding mitochondrial proteins, which in Saccharomyces cerevisiae is achieved in part via post-transcriptional control by the Pumilio RNA-binding domain protein Puf3 Puf3 binds to the 3'-UTR of many messenger RNAs (mRNAs) that encode mitochondrial proteins, regulating their turnover, translation, and/or mitochondrial targeting. Puf3 hyperphosphorylation correlates with increased mitochondrial biogenesis; however, the kinase responsible for Puf3 phosphorylation is unclear. Here, we show that the casein kinase I protein Hrr25 negatively regulates Puf3 by mediating its phosphorylation. An hrr25 mutation results in reduced phosphorylation of Puf3 in vivo and a puf3 deletion mutation reverses growth defects of hrr25 mutant cells grown on medium with a nonfermentable carbon source. We show that Hrr25 directly phosphorylates Puf3, and that the interaction between Puf3 and Hrr25 is mediated through the N-terminal domain of Puf3 and the kinase domain of Hrr25 We further found that an hrr25 mutation reduces GFP expression from GFP reporter constructs carrying the 3'-UTR of Puf3 targets. Downregulation of GFP expression due to an hrr25 mutation can be reversed either by puf3Δ or by mutations to the Puf3-binding sites in the 3'-UTR of the GFP reporter constructs. Together, our data indicate that Hrr25 is a positive regulator of mitochondrial biogenesis by phosphorylating Puf3 and inhibiting its function in downregulating target mRNAs encoding mitochondrial proteins.
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Affiliation(s)
- Manika Bhondeley
- Department of Biological Sciences, University of New Orleans, Louisiana 70148
| | - Zhengchang Liu
- Department of Biological Sciences, University of New Orleans, Louisiana 70148
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Holland P, Bergenholm D, Börlin CS, Liu G, Nielsen J. Predictive models of eukaryotic transcriptional regulation reveals changes in transcription factor roles and promoter usage between metabolic conditions. Nucleic Acids Res 2019; 47:4986-5000. [PMID: 30976803 PMCID: PMC6547448 DOI: 10.1093/nar/gkz253] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/26/2019] [Accepted: 04/04/2019] [Indexed: 01/08/2023] Open
Abstract
Transcription factors (TF) are central to transcriptional regulation, but they are often studied in relative isolation and without close control of the metabolic state of the cell. Here, we describe genome-wide binding (by ChIP-exo) of 15 yeast TFs in four chemostat conditions that cover a range of metabolic states. We integrate this data with transcriptomics and six additional recently mapped TFs to identify predictive models describing how TFs control gene expression in different metabolic conditions. Contributions by TFs to gene regulation are predicted to be mostly activating, additive and well approximated by assuming linear effects from TF binding signal. Notably, using TF binding peaks from peak finding algorithms gave distinctly worse predictions than simply summing the low-noise and high-resolution TF ChIP-exo reads on promoters. Finally, we discover indications of a novel functional role for three TFs; Gcn4, Ert1 and Sut1 during nitrogen limited aerobic fermentation. In only this condition, the three TFs have correlated binding to a large number of genes (enriched for glycolytic and translation processes) and a negative correlation to target gene transcript levels.
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Affiliation(s)
- Petter Holland
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-41296, Sweden
| | - David Bergenholm
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-41296, Sweden
| | - Christoph S Börlin
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-41296, Sweden
| | - Guodong Liu
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-41296, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-41296, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg SE-41296, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
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8
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Perez-Samper G, Cerulus B, Jariani A, Vermeersch L, Barrajón Simancas N, Bisschops MMM, van den Brink J, Solis-Escalante D, Gallone B, De Maeyer D, van Bael E, Wenseleers T, Michiels J, Marchal K, Daran-Lapujade P, Verstrepen KJ. The Crabtree Effect Shapes the Saccharomyces cerevisiae Lag Phase during the Switch between Different Carbon Sources. mBio 2018; 9:e01331-18. [PMID: 30377274 PMCID: PMC6212832 DOI: 10.1128/mbio.01331-18] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 09/20/2018] [Indexed: 12/16/2022] Open
Abstract
When faced with environmental changes, microbes often enter a temporary growth arrest during which they reprogram the expression of specific genes to adapt to the new conditions. A prime example of such a lag phase occurs when microbes need to switch from glucose to other, less-preferred carbon sources. Despite its industrial relevance, the genetic network that determines the duration of the lag phase has not been studied in much detail. Here, we performed a genome-wide Bar-Seq screen to identify genetic determinants of the Saccharomyces cerevisiae glucose-to-galactose lag phase. The results show that genes involved in respiration, and specifically those encoding complexes III and IV of the electron transport chain, are needed for efficient growth resumption after the lag phase. Anaerobic growth experiments confirmed the importance of respiratory energy conversion in determining the lag phase duration. Moreover, overexpression of the central regulator of respiration, HAP4, leads to significantly shorter lag phases. Together, these results suggest that the glucose-induced repression of respiration, known as the Crabtree effect, is a major determinant of microbial fitness in fluctuating carbon environments.IMPORTANCE The lag phase is arguably one of the prime characteristics of microbial growth. Longer lag phases result in lower competitive fitness in variable environments, and the duration of the lag phase is also important in many industrial processes where long lag phases lead to sluggish, less efficient fermentations. Despite the immense importance of the lag phase, surprisingly little is known about the exact molecular processes that determine its duration. Our study uses the molecular toolbox of S. cerevisiae combined with detailed growth experiments to reveal how the transition from fermentative to respirative metabolism is a key bottleneck for cells to overcome the lag phase. Together, our findings not only yield insight into the key molecular processes and genes that influence lag duration but also open routes to increase the efficiency of industrial fermentations and offer an experimental framework to study other types of lag behavior.
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Affiliation(s)
- Gemma Perez-Samper
- VIB - KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
| | - Bram Cerulus
- VIB - KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
| | - Abbas Jariani
- VIB - KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
| | - Lieselotte Vermeersch
- VIB - KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
| | | | - Markus M M Bisschops
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Joost van den Brink
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | | | - Brigida Gallone
- VIB - KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
| | - Dries De Maeyer
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Elise van Bael
- VIB - KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
| | - Tom Wenseleers
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - Jan Michiels
- VIB - KU Leuven Center for Microbiology, Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Kathleen Marchal
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | | | - Kevin J Verstrepen
- VIB - KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
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9
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Shi X, Zou Y, Chen Y, Ying H. Overexpression of THI4 and HAP4 Improves Glucose Metabolism and Ethanol Production in Saccharomyces cerevisiae. Front Microbiol 2018; 9:1444. [PMID: 29997610 PMCID: PMC6030257 DOI: 10.3389/fmicb.2018.01444] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/11/2018] [Indexed: 12/18/2022] Open
Abstract
Redox homeostasis is essential to the maintenance of cell metabolism. Changes in the redox state cause global metabolic and transcriptional changes. Our previous study indicated that the overexpression of NADH oxidase in Saccharomyces cerevisiae led to increased glucose consumption and ethanol production. Gene expression related to thiamine synthesis and osmotolerance as well as HAP4 expression was increased in response to redox change caused by the overexpression of NADH oxidase. To identify detailed relationships among cofactor levels, thiamine synthesis, expression of HAP4, and osmotolerance, and to determine whether these changes are interdependent, THI4 and HAP4 were overexpressed in S. cerevisiae BY4741. The glucose consumption rate of THI4-overexpressing strain (thi4-OE) was the highest, followed by HAP4-overexpressing strain (hap4-OE) > NADH oxidase-overexpressing strain (nox-OE) > control strain (con), while strain hap4-OE showed the highest concentration of ethanol after 26 h of fermentation. Reduced glycerol production and increased osmotolerance were observed in thi4-OE and hap4-OE, as well as in nox-OE. HAP4 globally regulated thiamine synthesis, biomass synthesis, respiration, and osmotolerance of cells, which conferred the recombinant strain hap4-OE with faster glucose metabolism and enhanced stress resistance. Moreover, overexpression of HAP4 might extend the life span of cells under caloric restriction by lowering the NADH level. Although overexpression of THI4 and HAP4 induced various similar changes at both the metabolic and the transcriptional level, the regulatory effect of THI4 was more limited than that of HAP4, and was restricted to the growth phase of cells. Our findings are expected to benefit the bio-ethanol industry.
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Affiliation(s)
- Xinchi Shi
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,School of Life Sciences, Nantong University, Nantong, China.,State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing, China
| | - Yanan Zou
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing, China
| | - Yong Chen
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing, China
| | - Hanjie Ying
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing, China
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10
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Kumar A, Dandekar JU, Bhat PJ. Fermentative metabolism impedes p53-dependent apoptosis in a Crabtree-positive but not in Crabtree-negative yeast. J Biosci 2017; 42:585-601. [DOI: 10.1007/s12038-017-9717-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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11
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Zhang T, Bu P, Zeng J, Vancura A. Increased heme synthesis in yeast induces a metabolic switch from fermentation to respiration even under conditions of glucose repression. J Biol Chem 2017; 292:16942-16954. [PMID: 28830930 DOI: 10.1074/jbc.m117.790923] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 08/18/2017] [Indexed: 01/13/2023] Open
Abstract
Regulation of mitochondrial biogenesis and respiration is a complex process that involves several signaling pathways and transcription factors as well as communication between the nuclear and mitochondrial genomes. Under aerobic conditions, the budding yeast Saccharomyces cerevisiae metabolizes glucose predominantly by glycolysis and fermentation. We have recently shown that altered chromatin structure in yeast induces respiration by a mechanism that requires transport and metabolism of pyruvate in mitochondria. However, how pyruvate controls the transcriptional responses underlying the metabolic switch from fermentation to respiration is unknown. Here, we report that this pyruvate effect involves heme. We found that heme induces transcription of HAP4, the transcriptional activation subunit of the Hap2/3/4/5p complex, required for growth on nonfermentable carbon sources, in a Hap1p- and Hap2/3/4/5p-dependent manner. Increasing cellular heme levels by inactivating ROX1, which encodes a repressor of many hypoxic genes, or by overexpressing HEM3 or HEM12 induced respiration and elevated ATP levels. Increased heme synthesis, even under conditions of glucose repression, activated Hap1p and the Hap2/3/4/5p complex and induced transcription of HAP4 and genes required for the tricarboxylic acid (TCA) cycle, electron transport chain, and oxidative phosphorylation, leading to a switch from fermentation to respiration. Conversely, inhibiting metabolic flux into the TCA cycle reduced cellular heme levels and HAP4 transcription. Together, our results indicate that the glucose-mediated repression of respiration in budding yeast is at least partly due to the low cellular heme level.
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Affiliation(s)
- Tiantian Zhang
- From the Department of Biological Sciences, St. John's University, Queens, New York 11439
| | - Pengli Bu
- From the Department of Biological Sciences, St. John's University, Queens, New York 11439
| | - Joey Zeng
- From the Department of Biological Sciences, St. John's University, Queens, New York 11439
| | - Ales Vancura
- From the Department of Biological Sciences, St. John's University, Queens, New York 11439
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12
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Bolotin-Fukuhara M. Thirty years of the HAP2/3/4/5 complex. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 2017; 1860:543-559. [DOI: 10.1016/j.bbagrm.2016.10.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/24/2016] [Accepted: 10/25/2016] [Indexed: 01/22/2023]
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13
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Laera L, Guaragnella N, Ždralević M, Marzulli D, Liu Z, Giannattasio S. The transcription factors ADR1 or CAT8 are required for RTG pathway activation and evasion from yeast acetic acid-induced programmed cell death in raffinose. ACTA ACUST UNITED AC 2016; 3:621-631. [PMID: 28357334 PMCID: PMC5348981 DOI: 10.15698/mic2016.12.549] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Yeast Saccharomyces cerevisiae grown on glucose undergoes programmed cell death (PCD) induced by acetic acid (AA-PCD), but evades PCD when grown in raffinose. This is due to concomitant relief of carbon catabolite repression (CCR) and activation of mitochondrial retrograde signaling, a mitochondria-to-nucleus communication pathway causing up-regulation of various nuclear target genes, such as CIT2, encoding peroxisomal citrate synthase, dependent on the positive regulator RTG2 in response to mitochondrial dysfunction. CCR down-regulates genes mainly involved in mitochondrial respiratory metabolism. In this work, we investigated the relationships between the RTG and CCR pathways in the modulation of AA-PCD sensitivity under glucose repression or de-repression conditions. Yeast single and double mutants lacking RTG2 and/or certain factors regulating carbon source utilization, including MIG1, HXK2, ADR1, CAT8, and HAP4, have been analyzed for their survival and CIT2 expression after acetic acid treatment. ADR1 and CAT8 were identified as positive regulators of RTG-dependent gene transcription. ADR1 and CAT8 interact with RTG2 and with each other in inducing cell resistance to AA-PCD in raffinose and controlling the nature of cell death. In the absence of ADR1 and CAT8, AA-PCD evasion is acquired through activation of an alternative factor/pathway repressed by RTG2, suggesting that RTG2 may play a function in promoting necrotic cell death in repressing conditions when RTG pathway is inactive. Moreover, our data show that simultaneous mitochondrial retrograde pathway activation and SNF1-dependent relief of CCR have a key role in central carbon metabolism reprogramming which modulates the yeast acetic acid-stress response.
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Affiliation(s)
- Luna Laera
- National Research Council of Italy, Institute of Biomembranes and Bioenergetics, Bari, Italy
| | - Nicoletta Guaragnella
- National Research Council of Italy, Institute of Biomembranes and Bioenergetics, Bari, Italy
| | - Maša Ždralević
- National Research Council of Italy, Institute of Biomembranes and Bioenergetics, Bari, Italy
| | - Domenico Marzulli
- National Research Council of Italy, Institute of Biomembranes and Bioenergetics, Bari, Italy
| | - Zhengchang Liu
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, USA
| | - Sergio Giannattasio
- National Research Council of Italy, Institute of Biomembranes and Bioenergetics, Bari, Italy
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Baek SH, Kwon EY, Kim SY, Hahn JS. GSF2 deletion increases lactic acid production by alleviating glucose repression in Saccharomyces cerevisiae. Sci Rep 2016; 6:34812. [PMID: 27708428 DOI: 10.1038/srep34812] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 09/20/2016] [Indexed: 01/02/2023] Open
Abstract
Improving lactic acid (LA) tolerance is important for cost-effective microbial production of LA under acidic fermentation conditions. Previously, we generated LA-tolerant D-LA-producing S. cerevisiae strain JHY5310 by laboratory adaptive evolution of JHY5210. In this study, we performed whole genome sequencing of JHY5310, identifying four loss-of-function mutations in GSF2, SYN8, STM1, and SIF2 genes, which are responsible for the LA tolerance of JHY5310. Among the mutations, a nonsense mutation in GSF2 was identified as the major contributor to the improved LA tolerance and LA production in JHY5310. Deletion of GSF2 in the parental strain JHY5210 significantly improved glucose uptake and D-LA production levels, while derepressing glucose-repressed genes including genes involved in the respiratory pathway. Therefore, more efficient generation of ATP and NAD+ via respiration might rescue the growth defects of the LA-producing strain, where ATP depletion through extensive export of lactate and proton is one of major reasons for the impaired growth. Accordingly, alleviation of glucose repression by deleting MIG1 or HXK2 in JHY5210 also improved D-LA production. GSF2 deletion could be applied to various bioprocesses where increasing biomass yield or respiratory flux is desirable.
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Shi X, Zou Y, Chen Y, Zheng C, Ying H. Overexpression of a Water-Forming NADH Oxidase Improves the Metabolism and Stress Tolerance of Saccharomyces cerevisiae in Aerobic Fermentation. Front Microbiol 2016; 7:1427. [PMID: 27679617 PMCID: PMC5020133 DOI: 10.3389/fmicb.2016.01427] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 08/29/2016] [Indexed: 01/01/2023] Open
Abstract
Redox homeostasis is fundamental to the maintenance of metabolism. Redox imbalance can cause oxidative stress, which affects metabolism and growth. Water-forming NADH oxidase regulates the redox balance by oxidizing cytosolic NADH to NAD+, which relieves cytosolic NADH accumulation through rapid glucose consumption in Saccharomyces cerevisiae, thus decreasing the production of the by product glycerol in industrial ethanol production. Here, we studied the effects of overexpression of a water-forming NADH oxidase from Lactococcus lactis on the stress response of S. cerevisiae in aerobic batch fermentation, and we constructed an interaction network of transcriptional regulation and metabolic networks to study the effects of and mechanisms underlying NADH oxidase regulation. The oxidase-overexpressing strain (NOX) showed increased glucose consumption, growth, and ethanol production, while glycerol production was remarkably lower. Glucose was exhausted by NOX at 26 h, while 18.92 ± 0.94 g/L residual glucose was left in the fermentation broth of the control strain (CON) at this time point. At 29.5 h, the ethanol concentration for NOX peaked at 35.25 ± 1.76 g/L, which was 14.37% higher than that for CON (30.82 ± 1.54 g/L). Gene expression involved in the synthesis of thiamine, which is associated with stress responses in various organisms, was increased in NOX. The transcription factor HAP4 was significantly upregulated in NOX at the late-exponential phase, indicating a diauxic shift in response to starvation. The apoptosis-inducing factor Nuc1 was downregulated while the transcription factor Sok2, which regulates the production of the small signaling molecule ammonia, was upregulated at the late-exponential phase, benefiting young cells on the rim. Reactive oxygen species production was decreased by 10% in NOX, supporting a decrease in apoptosis. The HOG pathway was not activated, although the osmotic stress was truly higher, indicating improved osmotolerance. Thus, the NADH oxidase can regulate the metabolism during aerobic fermentation in S. cerevisiae, thereby protecting cells against several stresses. Our findings indicate its suitability for use in industrial processes.
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Affiliation(s)
- Xinchi Shi
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech UniversityNanjing, China; State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech UniversityNanjing, China
| | - Yanan Zou
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech UniversityNanjing, China; State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech UniversityNanjing, China
| | - Yong Chen
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech UniversityNanjing, China; State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech UniversityNanjing, China; Jiangsu National Synergistic Innovation Center for Advanced MaterialsNanjing, China
| | - Cheng Zheng
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech UniversityNanjing, China; State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech UniversityNanjing, China
| | - Hanjie Ying
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech UniversityNanjing, China; State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech UniversityNanjing, China; Jiangsu National Synergistic Innovation Center for Advanced MaterialsNanjing, China
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Galdieri L, Zhang T, Rogerson D, Vancura A. Reduced Histone Expression or a Defect in Chromatin Assembly Induces Respiration. Mol Cell Biol 2016; 36:1064-77. [PMID: 26787838 DOI: 10.1128/MCB.00770-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 01/07/2016] [Indexed: 12/29/2022] Open
Abstract
Regulation of mitochondrial biogenesis and respiration is a complex process that involves several signaling pathways and transcription factors as well as communication between the nuclear and mitochondrial genomes. Here we show that decreased expression of histones or a defect in nucleosome assembly in the yeast Saccharomyces cerevisiae results in increased mitochondrial DNA (mtDNA) copy numbers, oxygen consumption, ATP synthesis, and expression of genes encoding enzymes of the tricarboxylic acid (TCA) cycle and oxidative phosphorylation (OXPHOS). The metabolic shift from fermentation to respiration induced by altered chromatin structure is associated with the induction of the retrograde (RTG) pathway and requires the activity of the Hap2/3/4/5p complex as well as the transport and metabolism of pyruvate in mitochondria. Together, our data indicate that altered chromatin structure relieves glucose repression of mitochondrial respiration by inducing transcription of the TCA cycle and OXPHOS genes carried by both nuclear and mitochondrial DNA.
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Qin J, Zhou YJ, Krivoruchko A, Huang M, Liu L, Khoomrung S, Siewers V, Jiang B, Nielsen J. Modular pathway rewiring of Saccharomyces cerevisiae enables high-level production of L-ornithine. Nat Commun 2015; 6:8224. [PMID: 26345617 DOI: 10.1038/ncomms9224] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 07/29/2015] [Indexed: 11/29/2022] Open
Abstract
Baker's yeast Saccharomyces cerevisiae is an attractive cell factory for production of chemicals and biofuels. Many different products have been produced in this cell factory by reconstruction of heterologous biosynthetic pathways; however, endogenous metabolism by itself involves many metabolites of industrial interest, and de-regulation of endogenous pathways to ensure efficient carbon channelling to such metabolites is therefore of high interest. Furthermore, many of these may serve as precursors for the biosynthesis of complex natural products, and hence strains overproducing certain pathway intermediates can serve as platform cell factories for production of such products. Here we implement a modular pathway rewiring (MPR) strategy and demonstrate its use for pathway optimization resulting in high-level production of L-ornithine, an intermediate of L-arginine biosynthesis and a precursor metabolite for a range of different natural products. The MPR strategy involves rewiring of the urea cycle, subcellular trafficking engineering and pathway re-localization, and improving precursor supply either through attenuation of the Crabtree effect or through the use of controlled fed-batch fermentations, leading to an L-ornithine titre of 1,041±47 mg l−1 with a yield of 67 mg (g glucose)−1 in shake-flask cultures and a titre of 5.1 g l−1 in fed-batch cultivations. Our study represents the first comprehensive study on overproducing an amino-acid intermediate in yeast, and our results demonstrate the potential to use yeast more extensively for low-cost production of many high-value amino-acid-derived chemicals. The complexity of yeast amino acid metabolism has limited carbon channelling to produce valuable chemical metabolites. Here, the authors implement a yeast customized pathway optimization strategy and demonstrate its use for overproduction of L-ornithine, an intermediate of L-arginine biosynthesis.
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Petryk N, Zhou YF, Sybirna K, Mucchielli MH, Guiard B, Bao WG, Stasyk OV, Stasyk OG, Krasovska OS, Budin K, Reymond N, Imbeaud S, Coudouel S, Delacroix H, Sibirny A, Bolotin-Fukuhara M. Functional study of the Hap4-like genes suggests that the key regulators of carbon metabolism HAP4 and oxidative stress response YAP1 in yeast diverged from a common ancestor. PLoS One 2014; 9:e112263. [PMID: 25479159 PMCID: PMC4257542 DOI: 10.1371/journal.pone.0112263] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 10/06/2014] [Indexed: 12/05/2022] Open
Abstract
The transcriptional regulator HAP4, induced by respiratory substrates, is involved in the balance between fermentation and respiration in S. cerevisiae. We identified putative orthologues of the Hap4 protein in all ascomycetes, based only on a conserved sixteen amino acid-long motif. In addition to this motif, some of these proteins contain a DNA-binding motif of the bZIP type, while being nonetheless globally highly divergent. The genome of the yeast Hansenula polymorpha contains two HAP4-like genes encoding the protein HpHap4-A which, like ScHap4, is devoid of a bZIP motif, and HpHap4-B which contains it. This species has been chosen for a detailed examination of their respective properties. Based mostly on global gene expression studies performed in the S. cerevisiae HAP4 disruption mutant (ScΔhap4), we show here that HpHap4-A is functionally equivalent to ScHap4, whereas HpHap4-B is not. Moreover HpHAP4-B is able to complement the H2O2 hypersensitivity of the ScYap1 deletant, YAP1 being, in S. cerevisiae, the main regulator of oxidative stress. Finally, a transcriptomic analysis performed in the ScΔyap1 strain overexpressing HpHAP4-B shows that HpHap4-B acts both on oxidative stress response and carbohydrate metabolism in a manner different from both ScYap1 and ScHap4. Deletion of these two genes in their natural host, H. polymorpha, confirms that HpHAP4-A participates in the control of the fermentation/respiration balance, while HpHAP4-B is involved in oxidative stress since its deletion leads to hypersensitivity to H2O2. These data, placed in an evolutionary context, raise new questions concerning the evolution of the HAP4 transcriptional regulation function and suggest that Yap1 and Hap4 have diverged from a unique regulatory protein in the fungal ancestor.
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Affiliation(s)
- Nataliya Petryk
- Institut de Génétique et Microbiologie, IFR Génome 115, Université Paris-Sud and CNRS, Orsay, France
- Institute of Cell Biology, National Academy of Sciences, Lviv, Ukraine
- Centre de Génétique Moléculaire, CNRS, Gif sur Yvette, France
| | - You-Fang Zhou
- Institut de Génétique et Microbiologie, IFR Génome 115, Université Paris-Sud and CNRS, Orsay, France
| | - Kateryna Sybirna
- Institut de Génétique et Microbiologie, IFR Génome 115, Université Paris-Sud and CNRS, Orsay, France
| | - Marie-Hélène Mucchielli
- Gif/Orsay DNA MicroArray Platform, Gif sur Yvette, France
- Centre de Génétique Moléculaire, CNRS, Gif sur Yvette, France
| | - Bernard Guiard
- Centre de Génétique Moléculaire, CNRS, Gif sur Yvette, France
| | - Wei-Guo Bao
- Institut de Génétique et Microbiologie, IFR Génome 115, Université Paris-Sud and CNRS, Orsay, France
| | - Oleh V. Stasyk
- Institute of Cell Biology, National Academy of Sciences, Lviv, Ukraine
| | - Olena G. Stasyk
- Institute of Cell Biology, National Academy of Sciences, Lviv, Ukraine
- Department of Biochemistry, Ivan Franko Lviv National University, Lviv, Ukraine
| | | | - Karine Budin
- Institut de Génétique et Microbiologie, IFR Génome 115, Université Paris-Sud and CNRS, Orsay, France
- Gif/Orsay DNA MicroArray Platform, Gif sur Yvette, France
| | - Nancie Reymond
- Gif/Orsay DNA MicroArray Platform, Gif sur Yvette, France
- Centre de Génétique Moléculaire, CNRS, Gif sur Yvette, France
| | | | | | - Hervé Delacroix
- Gif/Orsay DNA MicroArray Platform, Gif sur Yvette, France
- Centre de Génétique Moléculaire, CNRS, Gif sur Yvette, France
| | - Andriy Sibirny
- Institute of Cell Biology, National Academy of Sciences, Lviv, Ukraine
- University of Rzeszow, Rzeszow, Poland
| | - Monique Bolotin-Fukuhara
- Institut de Génétique et Microbiologie, IFR Génome 115, Université Paris-Sud and CNRS, Orsay, France
- * E-mail:
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Zhou Q, Wang W, He X, Zhu X, Shen Y, Yu Z, Wang X, Qi X, Zhang X, Fan M, Dai Y, Yang S, Yan Q. Mechanistic study on the nuclear modifier gene MSS1 mutation suppressing neomycin sensitivity of the mitochondrial 15S rRNA C1477G mutation in Saccharomyces cerevisiae. PLoS One 2014; 9:e90336. [PMID: 24595024 PMCID: PMC3940847 DOI: 10.1371/journal.pone.0090336] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 01/30/2014] [Indexed: 12/31/2022] Open
Abstract
The phenotypic manifestation of mitochondrial DNA (mtDNA) mutations can be modulated by nuclear genes and environmental factors. However, neither the interaction among these factors nor their underlying mechanisms are well understood. The yeast Saccharomyces cerevisiae mtDNA 15S rRNA C1477G mutation (PR) corresponds to the human 12S rRNA A1555G mutation. Here we report that a nuclear modifier gene mss1 mutation suppresses the neomycin-sensitivity phenotype of a yeast C1477G mutant in fermentable YPD medium. Functional assays show that the mitochondrial function of the yeast C1477G mutant was impaired severely in YPD medium with neomycin. Moreover, the mss1 mutation led to a significant increase in the steady-state level of HAP5 (heme activated protein), which greatly up-regulated the expression of glycolytic transcription factors RAP1, GCR1, and GCR2 and thus stimulated glycolysis. Furthermore, the high expression of the key glycolytic enzyme genes HXK2, PFK1 and PYK1 indicated that enhanced glycolysis not only compensated for the ATP reduction from oxidative phosphorylation (OXPHOS) in mitochondria, but also ensured the growth of the mss1(PR) mutant in YPD medium with neomycin. This study advances our understanding of the phenotypic manifestation of mtDNA mutations.
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Affiliation(s)
- Qiyin Zhou
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Wei Wang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xiangyu He
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xiaoyu Zhu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yaoyao Shen
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhe Yu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xuexiang Wang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xuchen Qi
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xuan Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Mingjie Fan
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yu Dai
- College of Life Sciences, Zhejiang University, Hangzhou, China
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shuxu Yang
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qingfeng Yan
- College of Life Sciences, Zhejiang University, Hangzhou, China
- * E-mail:
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Ghiaci P, Norbeck J, Larsson C. Physiological adaptations of Saccharomyces cerevisiae evolved for improved butanol tolerance. Biotechnol Biofuels 2013; 6:101. [PMID: 23855998 PMCID: PMC3729582 DOI: 10.1186/1754-6834-6-101] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 07/01/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND Butanol is a chemical with potential uses as biofuel and solvent, which can be produced by microbial fermentation. However, the end product toxicity is one of the main obstacles for developing the production process irrespective of the choice of production organism. The long-term goal of the present project is to produce 2-butanol in Saccharomyces cerevisiae. Therefore, unraveling the toxicity mechanisms of solvents such as butanol and understanding the mechanisms by which tolerant strains of S. cerevisiae adapt to them would be an important contribution to the development of a bio-based butanol production process. RESULTS A butanol tolerant S. cerevisiae was achieved through a series of sequential batch cultures with gradual increase of 2-butanol concentration. The final mutant (JBA-mut) tolerates all different alcohols tested at higher concentrations compared to the wild type (JBA-wt). Proteomics analysis of the two strains grown under mild butanol-stress revealed 46 proteins changing their expression by more than 1.5-fold in JBA-mut, 34 of which were upregulated. Strikingly, 21 out of the 34 upregulated proteins were predicted constituents of mitochondria. Among the non-mitochondrial up-regulated proteins, the minor isoform of Glycerol-3-phosphatase (Gpp2) was the most notable, since it was the only tested protein whose overexpression was found to confer butanol tolerance. CONCLUSION The study demonstrates several differences between the butanol tolerant mutant and the wild type. Upregulation of proteins involved in the mitochondrial ATP synthesizing machinery constituents and glycerol biosynthesis seem to be beneficial for a successful adaptation of yeast cells to butanol stress.
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Affiliation(s)
- Payam Ghiaci
- Department of Chemical and Biological Engineering, System and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden
| | - Joakim Norbeck
- Department of Chemical and Biological Engineering, System and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden
| | - Christer Larsson
- Department of Chemical and Biological Engineering, System and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden
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Affiliation(s)
- Francisca Randez-Gil
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, 46980 Paterna, Valencia, Spain;
| | - Isaac Córcoles-Sáez
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, 46980 Paterna, Valencia, Spain;
| | - José A. Prieto
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, 46980 Paterna, Valencia, Spain;
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Winter G, Krömer JO. Fluxomics - connecting ‘omics analysis and phenotypes. Environ Microbiol 2013; 15:1901-16. [DOI: 10.1111/1462-2920.12064] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Revised: 11/21/2012] [Accepted: 11/26/2012] [Indexed: 12/31/2022]
Affiliation(s)
- Gal Winter
- Centre for Microbial Electrosynthesis (CEMES); Advanced Water Management Centre (AWMC); University of Queensland; Brisbane; Qld; Australia
| | - Jens O. Krömer
- Centre for Microbial Electrosynthesis (CEMES); Advanced Water Management Centre (AWMC); University of Queensland; Brisbane; Qld; Australia
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Oud B, Flores CL, Gancedo C, Zhang X, Trueheart J, Daran JM, Pronk JT, van Maris AJA. An internal deletion in MTH1 enables growth on glucose of pyruvate-decarboxylase negative, non-fermentative Saccharomyces cerevisiae. Microb Cell Fact 2012; 11:131. [PMID: 22978798 PMCID: PMC3503853 DOI: 10.1186/1475-2859-11-131] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 09/11/2012] [Indexed: 12/02/2022] Open
Abstract
Background Pyruvate-decarboxylase negative (Pdc-) strains of Saccharomyces cerevisiae combine the robustness and high glycolytic capacity of this yeast with the absence of alcoholic fermentation. This makes Pdc-S. cerevisiae an interesting platform for efficient conversion of glucose towards pyruvate-derived products without formation of ethanol as a by-product. However, Pdc- strains cannot grow on high glucose concentrations and require C2-compounds (ethanol or acetate) for growth under conditions with low glucose concentrations, which hitherto has limited application in industry. Results Genetic analysis of a Pdc- strain previously evolved to overcome these deficiencies revealed a 225bp in-frame internal deletion in MTH1, encoding a transcriptional regulator involved in glucose sensing. This internal deletion contains a phosphorylation site required for degradation, thereby hypothetically resulting in increased stability of the protein. Reverse engineering of this alternative MTH1 allele into a non-evolved Pdc- strain enabled growth on 20 g l-1 glucose and 0.3% (v/v) ethanol at a maximum specific growth rate (0.24 h-1) similar to that of the evolved Pdc- strain (0.23 h-1). Furthermore, the reverse engineered Pdc- strain grew on glucose as sole carbon source, albeit at a lower specific growth rate (0.10 h-1) than the evolved strain (0.20 h-1). The observation that overexpression of the wild-type MTH1 allele also restored growth of Pdc-S. cerevisiae on glucose is consistent with the hypothesis that the internal deletion results in decreased degradation of Mth1. Reduced degradation of Mth1 has been shown to result in deregulation of hexose transport. In Pdc- strains, reduced glucose uptake may prevent intracellular accumulation of pyruvate and/or redox problems, while release of glucose repression due to the MTH1 internal deletion may contribute to alleviation of the C2-compound auxotrophy. Conclusions In this study we have discovered and characterised a mutation in MTH1 enabling Pdc- strains to grow on glucose as the sole carbon source. This successful example of reverse engineering not only increases the understanding of the glucose tolerance of evolved Pdc-S. cerevisiae, but also allows introduction of this portable genetic element into various industrial yeast strains, thereby simplifying metabolic engineering strategies.
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Affiliation(s)
- Bart Oud
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
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Yoboue ED, Devin A. Reactive oxygen species-mediated control of mitochondrial biogenesis. Int J Cell Biol 2012; 2012:403870. [PMID: 22693510 DOI: 10.1155/2012/403870] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 03/29/2012] [Accepted: 03/31/2012] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial biogenesis is a complex process. It necessitates the contribution of both the nuclear and the mitochondrial genomes and therefore crosstalk between the nucleus and mitochondria. It is now well established that cellular mitochondrial content can vary according to a number of stimuli and physiological states in eukaryotes. The knowledge of the actors and signals regulating the mitochondrial biogenesis is thus of high importance. The cellular redox state has been considered for a long time as a key element in the regulation of various processes. In this paper, we report the involvement of the oxidative stress in the regulation of some actors of mitochondrial biogenesis.
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Huberts DHEW, Niebel B, Heinemann M. A flux-sensing mechanism could regulate the switch between respiration and fermentation. FEMS Yeast Res 2011; 12:118-28. [DOI: 10.1111/j.1567-1364.2011.00767.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 10/28/2011] [Accepted: 11/16/2011] [Indexed: 12/20/2022] Open
Affiliation(s)
- Daphne H. E. W. Huberts
- Molecular Systems Biology; Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Groningen; The Netherlands
| | - Bastian Niebel
- Molecular Systems Biology; Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Groningen; The Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology; Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Groningen; The Netherlands
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Raab AM, Hlavacek V, Bolotina N, Lang C. Shifting the fermentative/oxidative balance in Saccharomyces cerevisiae by transcriptional deregulation of Snf1 via overexpression of the upstream activating kinase Sak1p. Appl Environ Microbiol 2011; 77:1981-9. [PMID: 21257817 DOI: 10.1128/AEM.02219-10] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
With the aim to reduce fermentation by-products and to promote respiratory metabolism by shifting the fermentative/oxidative balance, we evaluated the constitutive overexpression of the SAK1 and HAP4 genes in Saccharomyces cerevisiae. Sak1p is one of three kinases responsible for the phosphorylation, and thereby the activation, of the Snf1p complex, while Hap4p is the activator subunit of the Hap2/3/4/5 transcriptional complex. We compared the physiology of a SAK1-overexpressing strain with that of a strain overexpressing the HAP4 gene in wild-type and sdh2 deletion (respiratory-deficient) backgrounds. Both SAK1 and HAP4 overexpressions led to the upregulation of glucose-repressed genes and to reduced by-product formation rates (ethanol and glycerol). SAK1 overexpression had a greater impact on growth rates than did HAP4 overexpression. Elevated transcript levels of SAK1, but not HAP4, resulted in increased biomass yields in batch cultures grown on glucose (aerobic and excess glucose) as well as on nonfermentable carbon sources. SAK1 overexpression, but not the combined overexpression of SAK1 and HAP4 or the overexpression of HAP4 alone, restored growth on ethanol in an sdh2 deletion strain. In glucose-grown shake flask cultures, the sdh2 deletion strain with SAK1 and HAP4 overexpression produced succinic acid at a titer of 8.5 g liter(-1) and a yield of 0.26 mol (mol glucose)(-1) within 216 h. We here report for the first time that a constitutively high level of expression of SAK1 alleviates glucose repression and shifts the fermentative/oxidative balance under both glucose-repressed and -derepressed conditions.
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Cao H, Yue M, Li S, Bai X, Zhao X, Du Y. The impact of MIG1 and/or MIG2 disruption on aerobic metabolism of succinate dehydrogenase negative Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2010; 89:733-8. [PMID: 20938771 DOI: 10.1007/s00253-010-2894-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 09/21/2010] [Accepted: 09/21/2010] [Indexed: 11/29/2022]
Abstract
The zinc finger proteins Mig1 and Mig2 play important roles in glucose repression of Saccharomyces cerevisiae. To investigate whether the alleviation of glucose effect would result in an increase in aerobic succinate production, MIG1 and/or MIG2 were disrupted in a succinate dehydrogenase (SDH)-negative S. cerevisiae strain. Moreover, their impacts on physiology of the SDH-negative S. cerevisiae strain were studied under fully aerobic conditions when glucose was the sole carbon source. Our results showed that the succinate production for the SDH-negative S. cerevisiae was very low even under fully aerobic conditions. Furthermore, deletion of MIG1 and/or MIG2 did not result in an increase in succinate production in the SDH-negative S. cerevisiae strain. However, the synthesis of acetate was significantly affected by MIG1 deletion or in combination with MIG2 deletion. The acetate production for the mig1/mig2 double mutant BS2M was reduced by 69.72% compared to the parent strain B2S. In addition, the amount of ethanol produced by BS2M was slightly decreased. With the mig2 mutant BSM2, the concentrations of pyruvate and glycerol were increased by 26.23% and 15.28%, respectively, compared to the parent strain B2S.
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Affiliation(s)
- Hailong Cao
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, People's Republic of China
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Barros MH, da Cunha FM, Oliveira GA, Tahara EB, Kowaltowski AJ. Yeast as a model to study mitochondrial mechanisms in ageing. Mech Ageing Dev 2010; 131:494-502. [DOI: 10.1016/j.mad.2010.04.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Revised: 04/19/2010] [Accepted: 04/27/2010] [Indexed: 01/08/2023]
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Buschlen S, Amillet JM, Guiard B, Fournier A, Marcireau C, Bolotin-Fukuhara M. The S. Cerevisiae HAP complex, a key regulator of mitochondrial function, coordinates nuclear and mitochondrial gene expression. Comp Funct Genomics 2010; 4:37-46. [PMID: 18629096 PMCID: PMC2447382 DOI: 10.1002/cfg.254] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2002] [Accepted: 12/04/2002] [Indexed: 12/05/2022] Open
Abstract
We have compared Saccharomyces cerevisiae global gene expression in wild-type and mutants (Δhap2 and Δhap4) of the HAP transcriptional complex, which has been shown to be necessary for growth on respiratory substrates. Several hundred ORFs
are under positive or negative control of this complex and we analyse here in detail
the effect of HAP on mitochondria. We found that most of the genes upregulated
in the wild-type strain were involved in organelle functions, but practically none
of the downregulated ones. Nuclear genes encoding the different subunits of the
respiratory chain complexes figure in the genes more expressed in the wild-type than
in the mutants, as expected, but in this group we also found key components of
the mitochondrial translation apparatus. This control of mitochondrial translation
may be one of the means of coordinating mitochondrial and nuclear gene expression
in elaborating the respiratory chain. In addition, HAP controls the nuclear genes
involved in several other mitochondrial processes (import, mitochondrial division)
that define the metabolic state of the cell, but not mitochondrial DNA replication and
transcription. In most cases, a putative CCAAT-binding site is present upstream of the
ORF, while in others no such sites are present, suggesting the control to be indirect.
The large number of genes regulated by the HAP complex, as well as the fact that HAP
also regulates some putative transcriptional activators of unknown function, place this
complex at a hierarchically high position in the global transcriptional regulation of
the cell.
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Affiliation(s)
- S Buschlen
- Laboratoire de Génétique Moléculaire, IGM, Batiment 400. Université Paris Sud, 91405 Orsay Cedex, France
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Pir P, Kirdar B, Hayes A, Onsan ZI, Ulgen KO, Oliver SG. Exometabolic and transcriptional response in relation to phenotype and gene copy number in respiration-related deletion mutants of S. cerevisiae. Yeast 2008; 25:661-72. [PMID: 18727146 DOI: 10.1002/yea.1612] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The transcriptional and metabolic impact of deleting one or both copies of a respiration-related gene has been studied in glucose-limited chemostats. Integration of literature information on phenotype with our exometabolome and transcriptome data enabled the identification of novel relationships between gene copy number, transcriptional regulation and phenotype. We found that the effect of complete respiratory deficiency on transcription was limited to downregulation of genes involved in oxidoreductase activity and iron assimilation. Partial respiratory deficiency had no significant impact on gene transcription. Changes in the copy number of two transcription-factor genes, HAP4 and MIG1, had a major impact on genes involved in mitochondrial function. Regulation of respiratory chain components encoded in the nucleus and mitochondria appears to be divided between Hap4p and Oxa1p, respectively. Similarly, repression of respiration may be imposed by the action of Mig1p and Mba1p on nuclear and mitochondrial gene expression, respectively. However, it is not clear whether Oxa1p and Mba1p regulate mitochondrial gene expression via their interaction with mitochondrial ribosomes or by some indirect means. The phenotype of nuclear petite mutants may not simply be due to the absence of respiration; e.g. Oxa1p or Bcs1p may play a role in the regulation of ribosome assembly in the nucleolus. Integration between respiration and cell growth may also result from the action of a single transcription factor. Thus, Hap4p targets genes that are required for respiration and for fitness in nutrient-limited conditions. This suggests that Hap4p may enable cells to adapt to nutrient limitation as well as diauxy.
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Affiliation(s)
- Pinar Pir
- Department of Chemical Engineering, Boğaziçi University, Bebek, 34342 Istanbul, Turkey
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Dikicioglu D, Pir P, Onsan ZI, Ulgen KO, Kirdar B, Oliver SG. Integration of metabolic modeling and phenotypic data in evaluation and improvement of ethanol production using respiration-deficient mutants of Saccharomyces cerevisiae. Appl Environ Microbiol 2008; 74:5809-16. [PMID: 18586960 DOI: 10.1128/AEM.00009-08] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Flux balance analysis and phenotypic data were used to provide clues to the relationships between the activities of gene products and the phenotypes resulting from the deletion of genes involved in respiratory function in Saccharomyces cerevisiae. The effect of partial or complete respiratory deficiency on the ethanol production and growth characteristics of hap4Delta/hap4Delta, mig1Delta/mig1Delta, qdr3Delta/qdr3Delta, pdr3Delta/pdr3Delta, qcr7Delta/qcr7Delta, cyt1Delta/cyt1Delta, and rip1Delta/rip1Delta mutants grown in microaerated chemostats was investigated. The study provided additional evidence for the importance of the selection of a physiologically relevant objective function, and it may improve quantitative predictions of exchange fluxes, as well as qualitative estimations of changes in intracellular fluxes. Ethanol production was successfully predicted by flux balance analysis in the case of the qdr3Delta/qdr3Delta mutant, with maximization of ethanol production as the objective function, suggesting an additional role for Qdr3p in respiration. The absence of similar changes in estimated intracellular fluxes in the qcr7Delta/qcr7Delta mutant compared to the rip1Delta/rip1Delta and cyt1Delta/cyt1Delta mutants indicated that the effect of the deletion of this subunit of complex III was somehow compensated for. Analysis of predicted flux distributions indicated self-organization of intracellular fluxes to avoid NAD(+)/NADH imbalance in rip1Delta/rip1Delta and cyt1Delta/cyt1Delta mutants, but not the qcr7Delta/qcr7Delta mutant. The flux through the glycerol efflux channel, Fps1p, was estimated to be zero in all strains under the investigated conditions. This indicates that previous strategies for improving ethanol production, such as the overexpression of the glutamate synthase gene GLT1 in a GDH1 deletion background or deletion of the glycerol efflux channel gene FPS1 and overexpression of GLT1, are unnecessary in a respiration-deficient background.
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Badotti F, Dário MG, Alves SL, Cordioli MLA, Miletti LC, de Araujo PS, Stambuk BU. Switching the mode of sucrose utilization by Saccharomyces cerevisiae. Microb Cell Fact 2008; 7:4. [PMID: 18304329 PMCID: PMC2268662 DOI: 10.1186/1475-2859-7-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2007] [Accepted: 02/27/2008] [Indexed: 11/17/2022] Open
Abstract
Background Overflow metabolism is an undesirable characteristic of aerobic cultures of Saccharomyces cerevisiae during biomass-directed processes. It results from elevated sugar consumption rates that cause a high substrate conversion to ethanol and other bi-products, severely affecting cell physiology, bioprocess performance, and biomass yields. Fed-batch culture, where sucrose consumption rates are controlled by the external addition of sugar aiming at its low concentrations in the fermentor, is the classical bioprocessing alternative to prevent sugar fermentation by yeasts. However, fed-batch fermentations present drawbacks that could be overcome by simpler batch cultures at relatively high (e.g. 20 g/L) initial sugar concentrations. In this study, a S. cerevisiae strain lacking invertase activity was engineered to transport sucrose into the cells through a low-affinity and low-capacity sucrose-H+ symport activity, and the growth kinetics and biomass yields on sucrose analyzed using simple batch cultures. Results We have deleted from the genome of a S. cerevisiae strain lacking invertase the high-affinity sucrose-H+ symporter encoded by the AGT1 gene. This strain could still grow efficiently on sucrose due to a low-affinity and low-capacity sucrose-H+ symport activity mediated by the MALx1 maltose permeases, and its further intracellular hydrolysis by cytoplasmic maltases. Although sucrose consumption by this engineered yeast strain was slower than with the parental yeast strain, the cells grew efficiently on sucrose due to an increased respiration of the carbon source. Consequently, this engineered yeast strain produced less ethanol and 1.5 to 2 times more biomass when cultivated in simple batch mode using 20 g/L sucrose as the carbon source. Conclusion Higher cell densities during batch cultures on 20 g/L sucrose were achieved by using a S. cerevisiae strain engineered in the sucrose uptake system. Such result was accomplished by effectively reducing sucrose uptake by the yeast cells, avoiding overflow metabolism, with the concomitant reduction in ethanol production. The use of this modified yeast strain in simpler batch culture mode can be a viable option to more complicated traditional sucrose-limited fed-batch cultures for biomass-directed processes of S. cerevisiae.
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Affiliation(s)
- Fernanda Badotti
- Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, SC 88040-900, Brazil.
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Schuurmans JM, Rossell SL, van Tuijl A, Bakker BM, Hellingwerf KJ, Teixeira de Mattos MJ. Effect of hxk2 deletion and HAP4 overexpression on fermentative capacity in Saccharomyces cerevisiae. FEMS Yeast Res 2007; 8:195-203. [PMID: 18179578 DOI: 10.1111/j.1567-1364.2007.00319.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
To describe the fermentative potential of a yeast cell, the fermentative capacity (FC) has been defined as the specific rate of ethanol and CO2 production under anaerobic conditions. The effect of growth rate on FC of glucose-limited grown Saccharomyces cerevisiae strains with altered expression of two major glycolytic regulators, Hap4p and Hxk2p, was compared with their parent strain. Whereas overproduction of Hap4p behaved similar to the wild-type strain, deletion of hxk2 resulted in a very different FC profile. Most importantly, with maltose as the carbon and energy source, the latter strain expressed an FC twofold that of the wild type. Further analysis at the level of gene expression showed large changes in ADH2 transcripts and to a lesser extent in hexose transporters and genes involved in the glyoxylate cycle. With respect to primary glucose metabolism, a shift in the type of hexose transport to one with high affinity was induced. In accordance with the phenotype of the mutant strain, the maltose transporter was constitutively expressed under glucose-limited conditions and synthesis increased in the presence of maltose.
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Affiliation(s)
- Jasper Merijn Schuurmans
- Department of Molecular Microbial Physiology, Swammerdam Institute of Life Sciences, University of Amsterdam, Nieuwe Achtergracht, Amsterdam, The Netherlands
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Feria-Gervasio D, Mouret JR, Gorret N, Goma G, Guillouet SE. Oleic acid delays and modulates the transition from respiratory to fermentative metabolism in Saccharomyces cerevisiae after exposure to glucose excess. Appl Microbiol Biotechnol 2007; 78:319-31. [PMID: 17909788 DOI: 10.1007/s00253-007-1161-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Revised: 08/07/2007] [Accepted: 08/09/2007] [Indexed: 11/25/2022]
Abstract
This work aimed to study the transition from respiratory to fermentative metabolism in Saccharomyces cerevisiae CEN.PK 113-7D and more specifically to evaluate the implication of the acetyl-coenzymeA-derived carbon transport from cytosol to mitochondria in the onset of the metabolic shift. The strategy consisted in introducing, during aerobic glucose-limited chemostat (D = 0.16 h(-1)), [corrected] a local perturbation around the step to be studied by the addition of cosubstrate and in analyzing the consequences of such a perturbation on the metabolic transition. Oleic acid and L: -carnitine were among the tested cosubstrates because they were known to stimulate enzymes implicated in the acetyl-coenzymeA transport between the different cell compartments, such as the carnitine acetyl transferases. The metabolic transition was then comparatively quantified in sole glucose and in glucose/oleic acid chemostats in presence/absence of L: -carnitine after a pulse of glucose. Feeding the culture with oleic acid (D (ole) = 0.0041 and 0.0073 h(-1)) [corrected] led to a delay in the onset of the metabolic shift (up to 15 min), a 33% decrease in the ethanol production and a redirection of the carbon flux toward biomass production. The data clearly showed a modulation of the carbon distribution among respiration and fermentation, in favor of a decrease in the "short-term" Crabtree effect by the oleic acid.
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Affiliation(s)
- David Feria-Gervasio
- UMR5504, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, CNRS, INRA, INSA, 135 Avenue de Rangueil, 31077, Toulouse Cedex, France
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35
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Schuurmans JM, Boorsma A, Lascaris R, Hellingwerf KJ, Teixeira de Mattos MJ. Physiological and transcriptional characterization of Saccharomyces cerevisiae strains with modified expression of catabolic regulators. FEMS Yeast Res 2007; 8:26-34. [PMID: 17892474 DOI: 10.1111/j.1567-1364.2007.00309.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
A comparative physiological and transcriptional study is presented on wild-type Saccharomyces cerevisiae and mutants with altered levels of catabolic regulators: hxk2Delta lacking hexokinase2, HAP4 / overproducing hap4p and hxk2 Delta HAP4 upward arrow. Relative to the wild-type, HAP4 / showed the same growth rate with some increased yield on glucose, and hxk2Delta grew 28% slower but with a dramatically improved yield. Hxk2 Delta HAP4 / grew 14% slower but showed fully oxidative growth. A higher yield correlated with increased respiration. For both hxk2 Delta strains, glucose repression was suppressed (upregulation of high-affinity sugar transporters, invertase and oxidative phosphorylation). T-profiler analysis showed that genes under control of the hap2/3/4/5-binding motif were significantly altered in expression in all strains. HAP4 overexpression, directly or in hxk2 knockouts, led to repression of the genes containing the Zap1p motif including ZAP1 itself, indicating altered zinc metabolism. Whereas HAP4 overexpression resulted in a shift towards oxidative metabolism only, deletion of HXK2 resulted in a strain that, in addition to being oxidative, almost completely lacked the ability to sense glucose. As the double mutant had an energy efficiency close to the maximum even with excess glucose and was derepressed to a larger extent and over a broader range, the functioning of the two regulators is in general considered to be additive.
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Affiliation(s)
- J Merijn Schuurmans
- Swammerdam Institute for Life Sciences, BioCentrum Amsterdam, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
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Dueñas-Sánchez R, Codón AC, Benítez T. Overexpression of transcriptional factor HAP4 in industrial bakers’ yeast. J Biotechnol 2007. [DOI: 10.1016/j.jbiotec.2007.07.358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Alves-Araújo C, Pacheco A, Almeida MJ, Spencer-Martins I, Leão C, Sousa MJ. Sugar utilization patterns and respiro-fermentative metabolism in the baker's yeast Torulaspora delbrueckii. Microbiology (Reading) 2007; 153:898-904. [PMID: 17322210 DOI: 10.1099/mic.0.2006/003475-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The highly osmo- and cryotolerant yeast species Torulaspora delbrueckii is an important case study among the non-Saccharomyces yeast species. The strain T. delbrueckii PYCC 5321, isolated from traditional corn and rye bread dough in northern Portugal, is considered particularly interesting for the baking industry. This paper reports the sugar utilization patterns of this strain, using media with glucose, maltose and sucrose, alone or in mixtures. Kinetics of growth, biomass and ethanol yields, fermentation and respiration rates, hydrolase activities and sugar uptake rates were used to infer the potential applied relevance of this yeast in comparison to a conventional baker's strain of Saccharomyces cerevisiae. The results showed that both maltase and maltose transport in T. delbrueckii were subject to glucose repression and maltose induction, whereas invertase was subject to glucose control but not dependent on sucrose induction. A comparative analysis of specific sugar consumption rates and transport capacities suggests that the transport step limits both glucose and maltose metabolism. Specific rates of CO(2) production and O(2) consumption showed a significantly higher contribution of respiration to the overall metabolism in T. delbrueckii than in S. cerevisiae. This was reflected in the biomass yields from batch cultures and could represent an asset for the large-scale production of the former species. This work contributes to a better understanding of the physiology of a non-conventional yeast species, with a view to the full exploitation of T. delbrueckii by the baking industry.
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Affiliation(s)
- C Alves-Araújo
- Center of Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - A Pacheco
- Center of Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - M J Almeida
- Center of Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - I Spencer-Martins
- Centro de Recursos Microbiológicos (CREM), Biotechnology Unit, Faculty of Sciences and Technology, New University of Lisbon, 2829-516 Caparica, Portugal
| | - C Leão
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - M J Sousa
- Center of Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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Abstract
After whole-genome duplication (WGD), deletions return most loci to single copy. However, duplicate loci may survive through selection for increased dosage. Here, we show how the WGD increased copy number of some glycolytic genes could have conferred an almost immediate selective advantage to an ancestor of Saccharomyces cerevisiae, providing a rationale for the success of the WGD. We propose that the loss of other redundant genes throughout the genome resulted in incremental dosage increases for the surviving duplicated glycolytic genes. This increase gave post-WGD yeasts a growth advantage through rapid glucose fermentation; one of this lineage's many adaptations to glucose-rich environments. Our hypothesis is supported by data from enzyme kinetics and comparative genomics. Because changes in gene dosage follow directly from post-WGD deletions, dosage selection can confer an almost instantaneous benefit after WGD, unlike neofunctionalization or subfunctionalization, which require specific mutations. We also show theoretically that increased fermentative capacity is of greatest advantage when glucose resources are both large and dense, an observation potentially related to the appearance of angiosperms around the time of WGD.
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Affiliation(s)
- Gavin C Conant
- Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin, Ireland.
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Abstract
Life in the absence of molecular oxygen requires several adaptations. Traditionally, the switch from respiratory metabolism to fermentation has attracted much attention in Saccharomyces cerevisiae, as this is the basis for the use of this yeast in the production of alcohol and in baking. It has also been clear that under anaerobic conditions the yeast is not able to synthesize sterols and unsaturated fatty acids and that for anaerobic growth these have to be added to the media. More recently it has been found that many more factors play a role. Several other biosynthetic reactions also require molecular oxygen and the yeast must have alternatives for these. In addition, the composition of the cell wall and cell membrane show major differences when aerobic and anaerobic cells are compared. All these changes are reflected by the observation that the transcription of more than 500 genes changes significantly between aerobically and anaerobically growing cultures. In this review we will give an overview of the factors that play a role in the survival in the absence of molecular oxygen.
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Affiliation(s)
- I S Ishtar Snoek
- Institute of Biology, Leiden University, Leiden, The Netherlands.
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40
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Piper PW, Harris NL, MacLean M. Preadaptation to efficient respiratory maintenance is essential both for maximal longevity and the retention of replicative potential in chronologically ageing yeast. Mech Ageing Dev 2006; 127:733-40. [PMID: 16784770 DOI: 10.1016/j.mad.2006.05.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2006] [Accepted: 05/16/2006] [Indexed: 12/16/2022]
Abstract
Only recently have the studies of yeast ageing started to focus on the S288c-derived strains used extensively in genomics and on the longest lifespans. Chronological longevity (stationary (G(0)) survival) of such strains is greater when cells are pre-grown on a respiratory carbon source, as compared to when they are pre-grown on glucose (the latter a respiration-repressing sugar). Prior adaptation to efficient respiratory maintenance also ensures that such chronologically aged yeast cells still display a full replicative lifespan should they reenter the cell cycle. In contrast, cells that are pre-grown on glucose exhibit marked and progressive losses of replicative potential as they age chronologically in stationary phase. Increasing the respiratory activity in glucose-grown cultures by HAP4 gene overexpression increased survival and reversed the loss of replicative potential during a subsequent stationary phase. Adaptation to efficient respiratory maintenance is therefore important, not just for maximal longevity, but also for the maintenance of a full replicative lifespan by chronologically ageing cultures of yeast. In such respiration-adapted cultures, losses of the Sch9 protein kinase or Yca1 caspase both shortened lifespan. In contrast loss of Yap1, the major transcriptional regulator of the oxidative stress response, generated a small increase in chronological lifespan in certain strain backgrounds. It would appear, therefore, that any induction of oxidative stress response genes in chronologically ageing yeast is not operating to generate an increase in longevity, even though such protective effects might be expected from the increased proxidant status of these cells over time.
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Affiliation(s)
- Peter W Piper
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, England.
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41
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Bideaux C, Alfenore S, Cameleyre X, Molina-Jouve C, Uribelarrea JL, Guillouet SE. Minimization of glycerol production during the high-performance fed-batch ethanolic fermentation process in Saccharomyces cerevisiae, using a metabolic model as a prediction tool. Appl Environ Microbiol 2006; 72:2134-40. [PMID: 16517663 PMCID: PMC1393190 DOI: 10.1128/aem.72.3.2134-2140.2006] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
On the basis of knowledge of the biological role of glycerol in the redox balance of Saccharomyces cerevisiae, a fermentation strategy was defined to reduce the surplus formation of NADH, responsible for glycerol synthesis. A metabolic model was used to predict the operating conditions that would reduce glycerol production during ethanol fermentation. Experimental validation of the simulation results was done by monitoring the inlet substrate feeding during fed-batch S. cerevisiae cultivation in order to maintain the respiratory quotient (RQ) (defined as the CO2 production to O2 consumption ratio) value between 4 and 5. Compared to previous fermentations without glucose monitoring, the final glycerol concentration was successfully decreased. Although RQ-controlled fermentation led to a lower maximum specific ethanol production rate, it was possible to reach a high level of ethanol production: 85 g.liter-1 with 1.7 g.liter-1 glycerol in 30 h. We showed here that by using a metabolic model as a tool in prediction, it was possible to reduce glycerol production in a very high-performance ethanolic fermentation process.
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Affiliation(s)
- Carine Bideaux
- Biotechnology and Bioprocess Laboratory, UMR-CNRS 5504, UMR-INRA 792, Département de Génie Biochimique et Alimentaire, Institut National des Sciences Appliquées, 135 Avenue de Rangueil, 31077 Toulouse Cedex, France
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Pir P, Kırdar B, Hayes A, Önsan ZÝ, Ülgen KÖ, Oliver SG. Integrative investigation of metabolic and transcriptomic data. BMC Bioinformatics 2006; 7:203. [PMID: 16611354 PMCID: PMC1481621 DOI: 10.1186/1471-2105-7-203] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2005] [Accepted: 04/12/2006] [Indexed: 11/10/2022] Open
Abstract
Background New analysis methods are being developed to integrate data from transcriptome, proteome, interactome, metabolome, and other investigative approaches. At the same time, existing methods are being modified to serve the objectives of systems biology and permit the interpretation of the huge datasets currently being generated by high-throughput methods. Results Transcriptomic and metabolic data from chemostat fermentors were collected with the aim of investigating the relationship between these two data sets. The variation in transcriptome data in response to three physiological or genetic perturbations (medium composition, growth rate, and specific gene deletions) was investigated using linear modelling, and open reading-frames (ORFs) whose expression changed significantly in response to these perturbations were identified. Assuming that the metabolic profile is a function of the transcriptome profile, expression levels of the different ORFs were used to model the metabolic variables via Partial Least Squares (Projection to Latent Structures – PLS) using PLS toolbox in Matlab. Conclusion The experimental design allowed the analyses to discriminate between the effects which the growth medium, dilution rate, and the deletion of specific genes had on the transcriptome and metabolite profiles. Metabolite data were modelled as a function of the transcriptome to determine their congruence. The genes that are involved in central carbon metabolism of yeast cells were found to be the ORFs with the most significant contribution to the model.
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Affiliation(s)
- Pınar Pir
- Department of Chemical Engineering, Boğaziçi University, Bebek 34342, İstanbul, Turkey
- Centre for the Analysis of Biological Complexity, Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Betül Kırdar
- Department of Chemical Engineering, Boğaziçi University, Bebek 34342, İstanbul, Turkey
| | - Andrew Hayes
- Centre for the Analysis of Biological Complexity, Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Z Ýlsen Önsan
- Department of Chemical Engineering, Boğaziçi University, Bebek 34342, İstanbul, Turkey
| | - Kutlu Ö Ülgen
- Department of Chemical Engineering, Boğaziçi University, Bebek 34342, İstanbul, Turkey
| | - Stephen G Oliver
- Centre for the Analysis of Biological Complexity, Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
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Yeang CH, Mak HC, McCuine S, Workman C, Jaakkola T, Ideker T. Validation and refinement of gene-regulatory pathways on a network of physical interactions. Genome Biol 2005; 6:R62. [PMID: 15998451 PMCID: PMC1175993 DOI: 10.1186/gb-2005-6-7-r62] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2005] [Revised: 05/03/2005] [Accepted: 06/03/2005] [Indexed: 01/10/2023] Open
Abstract
As genome-scale measurements lead to increasingly complex models of gene regulation, systematic approaches are needed to validate and refine these models. Towards this goal, we describe an automated procedure for prioritizing genetic perturbations in order to discriminate optimally between alternative models of a gene-regulatory network. Using this procedure, we evaluate 38 candidate regulatory networks in yeast and perform four high-priority gene knockout experiments. The refined networks support previously unknown regulatory mechanisms downstream of SOK2 and SWI4.
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Affiliation(s)
- Chen-Hsiang Yeang
- Center for Biomolecular Science and Engineering, Baskin School of Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
| | - H Craig Mak
- Department of Bioengineering, University of California at San Diego, La Jolla, CA 92093, USA
| | - Scott McCuine
- Department of Bioengineering, University of California at San Diego, La Jolla, CA 92093, USA
| | - Christopher Workman
- Department of Bioengineering, University of California at San Diego, La Jolla, CA 92093, USA
| | - Tommi Jaakkola
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Trey Ideker
- Department of Bioengineering, University of California at San Diego, La Jolla, CA 92093, USA
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Abstract
Mitochondrial DNA (mtDNA) is essential for cells to maintain respiratory competency and is inherited as a protein-DNA complex called the nucleoid. We have identified 22 mtDNA-associated proteins in yeast, among which is mitochondrial aconitase (Aco1p). We show that this Krebs-cycle enzyme is essential for mtDNA maintenance independent of its catalytic activity. Regulation of ACO1 expression by the HAP and retrograde metabolic signaling pathways directly affects mtDNA maintenance. When constitutively expressed, Aco1p can replace the mtDNA packaging function of the high-mobility-group protein Abf2p. Thus, Aco1p may integrate metabolic signals and mtDNA maintenance.
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Affiliation(s)
- Xin Jie Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390-9148, USA
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45
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Lei F, Olsson L, Jørgensen SB. Dynamic effects related to steady-state multiplicity in continuous Saccharomyces cerevisiae cultivations. Biotechnol Bioeng 2004; 88:838-48. [PMID: 15538722 DOI: 10.1002/bit.20291] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The behavioral differences between chemostat and productostat cultivation of aerobic glucose-limited Saccharomyces cerevisiae were investigated. Three types of experiments were conducted: a chemostat, where the dilution rate was shifted up or down in stepwise manner; and a productostat, with either stepwise changed or a rampwise increased ethanol setpoint, i.e., an accelero-productostat. The transient responses from chemostat and productostat experiments were interpreted using a simple metabolic flux model. In a productostat it was possible to obtain oxido-reductive steady states at dilution rates far below Dcrit due to a strong repression of the respiratory system. However, these steady states could not be obtained in a chemostat, since a dilution rate shift-down from an oxido-reductive steady state led to a derepression of the respiratory system. It can therefore be concluded that the range of dilution rates where steady-state multiplicity can be obtained differs depending on the operation mode and that this dilution rate multiplicity range may appear larger in a productostat than in a chemostat. A more narrow multiplicity range, however, was obtained when the productostat was operated as an accelero-productostat.
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Affiliation(s)
- Frede Lei
- CAPEC, Department of Chemical Engineering, Building 227, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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46
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Tai SL, Boer VM, Daran-Lapujade P, Walsh MC, de Winde JH, Daran JM, Pronk JT. Two-dimensional transcriptome analysis in chemostat cultures. Combinatorial effects of oxygen availability and macronutrient limitation in Saccharomyces cerevisiae. J Biol Chem 2004; 280:437-47. [PMID: 15496405 DOI: 10.1074/jbc.m410573200] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Genome-wide analysis of transcriptional regulation is generally studied by determining sets of "signature transcripts" that are up- or down-regulated relative to a reference situation when a single culture parameter or genetic modification is changed. This approach is especially relevant for defining small subsets of transcripts for use in high throughput, cost-effective diagnostic analyses. However, this approach may overlook the simultaneous control of transcription by more than one environmental parameter. This study represents the first quantitative assessment of the impact of transcriptional cross-regulation by different environmental parameters. As a model, we compared the response of aerobic as well as anaerobic chemostat cultures of the yeast Saccharomyces cerevisiae to growth limitation by four different macronutrients (carbon, nitrogen, phosphorus, and sulfur). The identity of the growth-limiting nutrient was shown to have a strong impact on the sets of transcripts that responded to oxygen availability and vice versa. We concluded that identification of reliable signature transcripts for specific environmental parameters can be obtained only by combining transcriptome data sets obtained under several sets of reference conditions. Furthermore, the two-dimensional approach to transcriptome analysis is a valuable new tool to study the interaction of different transcriptional regulation systems.
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Affiliation(s)
- Siew Leng Tai
- Kluyver Laboratory of Biotechnology, Delft University of Technology, Julianalaan 67, 2628BC Delft, The Netherlands
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47
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Lascaris R, Piwowarski J, van der Spek H, de Mattos JT, Grivell L, Blom J. Overexpression of HAP4 in glucose-derepressed yeast cells reveals respiratory control of glucose-regulated genes. Microbiology (Reading) 2004; 150:929-934. [PMID: 15073302 DOI: 10.1099/mic.0.26742-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A link between control of respiration and glucose repression in yeast is reported. The HAP4 gene was overexpressed in a Delta mig1 deletion background, generating a mutant in which respiratory function is stimulated and glucose repression is diminished. Although this combination does not result in derepression of genes encoding proteins involved in respiratory function, it nevertheless generates resistance against 2-deoxyglucose and hence contributes to more derepressed growth characteristics. Unexpectedly, overexpression of HAP4 in the Delta mig1 deletion strain causes strong repression of several target genes of the Mig1p repressor. Repression is not restricted to glucose growth conditions and does not require the glucose repressors Mig2p or Hxk2p. It was observed that expression of the SUC2 gene is transiently repressed after glucose is added to respiratory-growing Delta mig1 cells. Additional overexpression of HAP4 prevents release from this novel repressed state. The data presented show that respiratory function controls transcription of genes required for the metabolism of alternative sugars. This respiratory feedback control is suggested to regulate the feed into glycolysis in derepressed conditions.
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Affiliation(s)
- Romeo Lascaris
- Swammerdam Institute for Life Sciences, University of Amsterdam, Kruislaan 318, 1098 SM Amsterdam, The Netherlands
| | - Jan Piwowarski
- Swammerdam Institute for Life Sciences, University of Amsterdam, Kruislaan 318, 1098 SM Amsterdam, The Netherlands
| | - Hans van der Spek
- Swammerdam Institute for Life Sciences, University of Amsterdam, Kruislaan 318, 1098 SM Amsterdam, The Netherlands
| | - Joost Teixeira de Mattos
- Swammerdam Institute for Life Sciences, University of Amsterdam, Kruislaan 318, 1098 SM Amsterdam, The Netherlands
| | - Les Grivell
- Swammerdam Institute for Life Sciences, University of Amsterdam, Kruislaan 318, 1098 SM Amsterdam, The Netherlands
| | - Jolanda Blom
- Swammerdam Institute for Life Sciences, University of Amsterdam, Kruislaan 318, 1098 SM Amsterdam, The Netherlands
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van Maris AJA, Geertman JMA, Vermeulen A, Groothuizen MK, Winkler AA, Piper MDW, van Dijken JP, Pronk JT. Directed evolution of pyruvate decarboxylase-negative Saccharomyces cerevisiae, yielding a C2-independent, glucose-tolerant, and pyruvate-hyperproducing yeast. Appl Environ Microbiol 2004; 70:159-66. [PMID: 14711638 PMCID: PMC321313 DOI: 10.1128/aem.70.1.159-166.2004] [Citation(s) in RCA: 154] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The absence of alcoholic fermentation makes pyruvate decarboxylase-negative (Pdc(-)) strains of Saccharomyces cerevisiae an interesting platform for further metabolic engineering of central metabolism. However, Pdc(-) S. cerevisiae strains have two growth defects: (i) growth on synthetic medium in glucose-limited chemostat cultures requires the addition of small amounts of ethanol or acetate and (ii) even in the presence of a C(2) compound, these strains cannot grow in batch cultures on synthetic medium with glucose. We used two subsequent phenotypic selection strategies to obtain a Pdc(-) strain without these growth defects. An acetate-independent Pdc(-) mutant was obtained via (otherwise) glucose-limited chemostat cultivation by progressively lowering the acetate content in the feed. Transcriptome analysis did not reveal the mechanisms behind the C(2) independence. Further selection for glucose tolerance in shake flasks resulted in a Pdc(-) S. cerevisiae mutant (TAM) that could grow in batch cultures ( micro (max) = 0.20 h(-1)) on synthetic medium, with glucose as the sole carbon source. Although the exact molecular mechanisms underlying the glucose-tolerant phenotype were not resolved, transcriptome analysis of the TAM strain revealed increased transcript levels of many glucose-repressible genes relative to the isogenic wild type in nitrogen-limited chemostat cultures with excess glucose. In pH-controlled aerobic batch cultures, the TAM strain produced large amounts of pyruvate. By repeated glucose feeding, a pyruvate concentration of 135 g liter(-1) was obtained, with a specific pyruvate production rate of 6 to 7 mmol g of biomass(-1) h(-1) during the exponential-growth phase and an overall yield of 0.54 g of pyruvate g of glucose(-1).
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Affiliation(s)
- Antonius J A van Maris
- Department of Biotechnology, Delft University of Technology, NL-2628 BC Delft. BIRD Engineering B.V., NL-3044 CK Rotterdam, The Netherlands
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Bellí G, Molina MM, García-Martínez J, Pérez-Ortín JE, Herrero E. Saccharomyces cerevisiae glutaredoxin 5-deficient cells subjected to continuous oxidizing conditions are affected in the expression of specific sets of genes. J Biol Chem 2004; 279:12386-95. [PMID: 14722110 DOI: 10.1074/jbc.m311879200] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The Saccharomyces cerevisiae GRX5 gene codes for a mitochondrial glutaredoxin involved in the synthesis of iron/sulfur clusters. Its absence prevents respiratory growth and causes the accumulation of iron inside cells and constitutive oxidation of proteins. Null Deltagrx5 mutants were used as an example of continuously oxidized cells, as opposed to situations in which oxidative stress is instantaneously caused by addition of external oxidants. Whole transcriptome analysis was carried out in the mutant cells. The set of genes whose expression was affected by the absence of Grx5 does not significantly overlap with the set of genes affected in respiratory petite mutants. Many Aft1-dependent genes involved in iron utilization that are up-regulated in a frataxin mutant were also up-regulated in the absence of Grx5. BIO5 is another Aft1-dependent gene induced both upon iron deprivation and in Deltagrx5 cells; this links iron and biotin metabolism. Other genes are specifically affected under the oxidative conditions generated by the grx5 mutation. One of these is MLP1, which codes for a homologue of the Slt2 kinase. Cells lacking MLP1 and GRX5 are hypersensitive to oxidative stress caused by external agents and exhibit increased protein oxidation in relation to single mutants. This in turn points to a role for Mlp1 in protection against oxidative stress. The genes of the Hap4 regulon, which are involved in respiratory metabolism, are down-regulated in Deltagrx5 cells. This effect is suppressed by HAP4 overexpression. Inhibition of respiratory metabolism during continuous moderately oxidative conditions could be a protective response by the cell.
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Affiliation(s)
- Gemma Bellí
- Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina, Universitat de Lleida, Rovira Roure 44, 25198-Lleida, Spain
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50
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Abstract
Calorie restriction (CR) extends life span in a wide variety of species. Previously, we showed that calorie restriction increases the replicative life span in yeast by activating Sir2, a highly conserved NAD-dependent deacetylase. Here we test whether CR activates Sir2 by increasing the NAD/NADH ratio or by regulating the level of nicotinamide, a known inhibitor of Sir2. We show that CR decreases NADH levels, and that NADH is a competitive inhibitor of Sir2. A genetic intervention that specifically decreases NADH levels increases life span, validating the model that NADH regulates yeast longevity in response to CR.
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Affiliation(s)
- Su-Ju Lin
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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