1
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Chalivendra S, Shi S, Li X, Kuang Z, Giovinazzo J, Zhang L, Rossi J, Wang J, Saviola AJ, Welty R, Liu S, Vaeth KF, Zhou ZH, Hansen KC, Taliaferro JM, Zhao R. Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast. RNA (NEW YORK, N.Y.) 2024; 30:1070-1088. [PMID: 38688558 PMCID: PMC11251525 DOI: 10.1261/rna.079917.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
The recognition of the 5' splice site (5' ss) is one of the earliest steps of pre-mRNA splicing. To better understand, the mechanism and regulation of 5' ss recognition, we selectively humanized components of the yeast U1 (yU1) snRNP to reveal the function of these components in 5' ss recognition and splicing. We targeted U1C and Luc7, two proteins that interact with and stabilize the yU1 snRNA and the 5' ss RNA duplex. We replaced the zinc-finger (ZnF) domain of yeast U1C (yU1C) with its human counterpart, which resulted in a cold-sensitive growth phenotype and moderate splicing defects. We next added an auxin-inducible degron to yeast Luc7 (yLuc7) protein (to mimic the lack of Luc7Ls in human U1 snRNP). We found that Luc7-depleted yU1 snRNP resulted in the concomitant loss of Prp40 and Snu71 (two other essential yU1 snRNP proteins), and further biochemical analyses suggest a model of how these three proteins interact with each other in the U1 snRNP. The loss of these proteins resulted in a significant growth retardation accompanied by a global suppression of pre-mRNA splicing. The splicing suppression led to mitochondrial dysfunction as revealed by a release of Fe2+ into the growth medium and an induction of mitochondrial reactive oxygen species. Together, these observations indicate that the human U1C ZnF can substitute that of yeast, Luc7 is essential for the incorporation of the Luc7-Prp40-Snu71 trimer into yU1 snRNP, and splicing plays a major role in the regulation of mitochondrial function in yeast.
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Affiliation(s)
- Subbaiah Chalivendra
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Shasha Shi
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Xueni Li
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Zhiling Kuang
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Joseph Giovinazzo
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Lingdi Zhang
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - John Rossi
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Jingxin Wang
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66047, USA
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Robb Welty
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Shiheng Liu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, USA
| | - Katherine F Vaeth
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - J Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
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2
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Zhu J, Zhang K, He Y, Zhang Q, Ran Y, Tan Z, Cui L, Feng Y. Metabolic engineering of Saccharomyces cerevisiae for chelerythrine biosynthesis. Microb Cell Fact 2024; 23:183. [PMID: 38902758 PMCID: PMC11191272 DOI: 10.1186/s12934-024-02448-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 06/03/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Chelerythrine is an important alkaloid used in agriculture and medicine. However, its structural complexity and low abundance in nature hampers either bulk chemical synthesis or extraction from plants. Here, we reconstructed and optimized the complete biosynthesis pathway for chelerythrine from (S)-reticuline in Saccharomyces cerevisiae using genetic reprogramming. RESULTS The first-generation strain Z4 capable of producing chelerythrine was obtained via heterologous expression of seven plant-derived enzymes (McoBBE, TfSMT, AmTDC, EcTNMT, PsMSH, EcP6H, and PsCPR) in S. cerevisiae W303-1 A. When this strain was cultured in the synthetic complete (SC) medium supplemented with 100 µM of (S)-reticuline for 10 days, it produced up to 0.34 µg/L chelerythrine. Furthermore, efficient metabolic engineering was performed by integrating multiple-copy rate-limiting genes (TfSMT, AmTDC, EcTNMT, PsMSH, EcP6H, PsCPR, INO2, and AtATR1), tailoring the heme and NADPH engineering, and engineering product trafficking by heterologous expression of MtABCG10 to enhance the metabolic flux of chelerythrine biosynthesis, leading to a nearly 900-fold increase in chelerythrine production. Combined with the cultivation process, chelerythrine was obtained at a titer of 12.61 mg per liter in a 0.5 L bioreactor, which is over 37,000-fold higher than that of the first-generation recombinant strain. CONCLUSIONS This is the first heterologous reconstruction of the plant-derived pathway to produce chelerythrine in a yeast cell factory. Applying a combinatorial engineering strategy has significantly improved the chelerythrine yield in yeast and is a promising approach for synthesizing functional products using a microbial cell factory. This achievement underscores the potential of metabolic engineering and synthetic biology in revolutionizing natural product biosynthesis.
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Affiliation(s)
- Jiawei Zhu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Kai Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Yuanzhi He
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Qi Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Yanpeng Ran
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Zaigao Tan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Li Cui
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai, 200240, China.
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai, 200240, China.
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3
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Nowrouzi B, Torres-Montero P, Kerkhoven EJ, Martínez JL, Rios-Solis L. Rewiring Saccharomyces cerevisiae metabolism for optimised Taxol® precursors production. Metab Eng Commun 2024; 18:e00229. [PMID: 38098801 PMCID: PMC10716015 DOI: 10.1016/j.mec.2023.e00229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/09/2023] [Accepted: 11/04/2023] [Indexed: 12/17/2023] Open
Abstract
Saccharomyces cerevisiae has been conveniently used to produce Taxol® anticancer drug early precursors. However, the harmful impact of oxidative stress by the first cytochrome P450-reductase enzymes (CYP725A4-POR) of Taxol® pathway has hampered sufficient progress in yeast. Here, we evolved an oxidative stress-resistant yeast strain with three-fold higher titre of their substrate, taxadiene. The performance of the evolved and parent strains were then evaluated in galactose-limited chemostats before and under the oxidative stress by an oxidising agent. The interaction of evolution and oxidative stress was comprehensively evaluated through transcriptomics and metabolite profiles integration in yeast enzyme-constrained genome scale model. Overall, the evolved strain showed improved respiration, reduced overflow metabolites production and oxidative stress re-induction tolerance. The cross-protection mechanism also potentially contributed to better heme, flavin and NADPH availability, essential for CYP725A4 and POR optimal activity in yeast. The results imply that the evolved strain is a robust cell factory for future efforts towards Taxol© production.
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Affiliation(s)
- Behnaz Nowrouzi
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
- Centre for Engineering Biology, The University of Edinburgh, Edinburgh, EH9 3BD, United Kingdom
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Pablo Torres-Montero
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Eduard J. Kerkhoven
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- SciLifeLab, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - José L. Martínez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
- Centre for Engineering Biology, The University of Edinburgh, Edinburgh, EH9 3BD, United Kingdom
- School of Natural and Environmental Sciences, Molecular Biology and Biotechnology Division, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
- Department of Biochemical Engineering, The Advanced Centre for Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, United Kingdom
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4
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Patnaik PK, Nady N, Barlit H, Gülhan A, Labunskyy VM. Lifespan regulation by targeting heme signaling in yeast. GeroScience 2024:10.1007/s11357-024-01218-9. [PMID: 38809391 DOI: 10.1007/s11357-024-01218-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 05/21/2024] [Indexed: 05/30/2024] Open
Abstract
Heme is an essential prosthetic group that serves as a co-factor and a signaling molecule. Heme levels decline with age, and its deficiency is associated with multiple hallmarks of aging, including anemia, mitochondrial dysfunction, and oxidative stress. Dysregulation of heme homeostasis has been also implicated in aging in model organisms suggesting that heme may play an evolutionarily conserved role in controlling lifespan. However, the underlying mechanisms and whether heme homeostasis can be targeted to promote healthy aging remain unclear. Here, we used Saccharomyces cerevisiae as a model to investigate the role of heme in aging. For this, we have engineered a heme auxotrophic yeast strain expressing a plasma membrane-bound heme permease from Caenorhabditis elegans (ceHRG-4). This system can be used to control intracellular heme levels independently of the biosynthetic enzymes by manipulating heme concentration in the media. We observed that heme supplementation leads to a significant extension of yeast replicative lifespan. Our findings revealed that the effect of heme on lifespan is independent of the Hap4 transcription factor. Surprisingly, heme-supplemented cells had impaired growth on YPG medium, which requires mitochondrial respiration to be used, suggesting that these cells are respiratory deficient. Together, our results demonstrate that heme homeostasis is fundamentally important for aging biology, and manipulating heme levels can be used as a promising therapeutic target for promoting longevity.
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Affiliation(s)
- Praveen K Patnaik
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Nour Nady
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Hanna Barlit
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Ali Gülhan
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Vyacheslav M Labunskyy
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA.
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5
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Assalve G, Lunetti P, Zara V, Ferramosca A. Ctp1 and Yhm2: Two Mitochondrial Citrate Transporters to Support Metabolic Flexibility of Saccharomyces cerevisiae. Int J Mol Sci 2024; 25:1870. [PMID: 38339147 PMCID: PMC10855732 DOI: 10.3390/ijms25031870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/28/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
Differently from higher eukaryotic cells, in the yeast Saccharomyces cerevisiae there are two mitochondrial carrier proteins involved in the transport of citrate: Ctp1 and Yhm2. Very little is known about the physiological role of these proteins. Wild-type and mutant yeast strains deleted in CTP1 and YHM2 were grown in media supplemented with a fermentable (glucose) or a nonfermentable (ethanol) carbon source. To assess changes in Ctp1 and Yhm2 mRNA expression levels, real-time PCR was performed after total RNA extraction. In the wild-type strain, the metabolic switch from the exponential to the stationary phase is associated with an increase in the expression level of the two citrate transporters. In addition, the results obtained in the mutant strains suggest that the presence of a single citrate transporter can partially compensate for the absence of the other. Ctp1 and Yhm2 differently contribute to fermentative and respiratory metabolism. Moreover, the two mitochondrial carriers represent a link between the Krebs cycle and the glyoxylate cycle, which play a key role in the metabolic adaptation strategies of S. cerevisiae.
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Affiliation(s)
- Graziana Assalve
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (G.A.); (P.L.); (V.Z.)
- Department of Experimental Medicine, University of Salento, 73100 Lecce, Italy
| | - Paola Lunetti
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (G.A.); (P.L.); (V.Z.)
- Department of Experimental Medicine, University of Salento, 73100 Lecce, Italy
| | - Vincenzo Zara
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (G.A.); (P.L.); (V.Z.)
- Department of Experimental Medicine, University of Salento, 73100 Lecce, Italy
| | - Alessandra Ferramosca
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (G.A.); (P.L.); (V.Z.)
- Department of Experimental Medicine, University of Salento, 73100 Lecce, Italy
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6
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Patnaik PK, Nady N, Barlit H, Gülhan A, Labunskyy VM. Lifespan regulation by targeting heme signaling in yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576446. [PMID: 38293148 PMCID: PMC10827197 DOI: 10.1101/2024.01.20.576446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Heme is an essential prosthetic group that serves as a co-factor and a signaling molecule. Heme levels decline with age, and its deficiency is associated with multiple hallmarks of aging, including anemia, mitochondrial dysfunction, and oxidative stress. Dysregulation of heme homeostasis has been also implicated in aging in model organisms suggesting that heme may play an evolutionarily conserved role in controlling lifespan. However, the underlying mechanisms and whether heme homeostasis can be targeted to promote healthy aging remain unclear. Here we used Saccharomyces cerevisiae as a model to investigate the role of heme in aging. For this, we have engineered a heme auxotrophic yeast strain expressing a plasma membrane-bound heme permease from Caenorhabditis elegans (ceHRG-4). This system can be used to control intracellular heme levels independently of the biosynthetic enzymes by manipulating heme concentration in the media. We observed that heme supplementation leads to significant lifespan extension in yeast. Our findings revealed that the effect of heme on lifespan is independent of the Hap4 transcription factor. Surprisingly, heme-supplemented cells had impaired growth on YPG medium, which requires mitochondrial respiration to be used, suggesting that these cells are respiratory deficient. Together, our results demonstrate that heme homeostasis is fundamentally important for aging biology and manipulating heme levels can be used as a promising therapeutic target for promoting longevity.
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Affiliation(s)
- Praveen K. Patnaik
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Nour Nady
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Hanna Barlit
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Ali Gülhan
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Vyacheslav M. Labunskyy
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
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7
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Chalivendra S, Shi S, Li X, Kuang Z, Giovinazzo J, Zhang L, Rossi J, Saviola AJ, Wang J, Welty R, Liu S, Vaeth K, Zhou ZH, Hansen KC, Taliaferro JM, Zhao R. Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.15.571893. [PMID: 38168357 PMCID: PMC10760170 DOI: 10.1101/2023.12.15.571893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The recognition of 5' splice site (5' ss) is one of the earliest steps of pre-mRNA splicing. To better understand the mechanism and regulation of 5' ss recognition, we selectively humanized components of the yeast U1 snRNP to reveal the function of these components in 5' ss recognition and splicing. We targeted U1C and Luc7, two proteins that interact with and stabilize the yeast U1 (yU1) snRNA and the 5' ss RNA duplex. We replaced the Zinc-Finger (ZnF) domain of yU1C with its human counterpart, which resulted in cold-sensitive growth phenotype and moderate splicing defects. Next, we added an auxin-inducible degron to yLuc7 protein and found that Luc7-depleted yU1 snRNP resulted in the concomitant loss of PRP40 and Snu71 (two other essential yeast U1 snRNP proteins), and further biochemical analyses suggest a model of how these three proteins interact with each other in the U1 snRNP. The loss of these proteins resulted in a significant growth retardation accompanied by a global suppression of pre-mRNA splicing. The splicing suppression led to mitochondrial dysfunction as revealed by a release of Fe 2+ into the growth medium and an induction of mitochondrial reactive oxygen species. Together, these observations indicate that the human U1C ZnF can substitute that of yeast, Luc7 is essential for the incorporation of the Luc7-Prp40-Snu71 trimer into yeast U1 snRNP, and splicing plays a major role in the regulation of mitochondria function in yeast.
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8
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Liu Y, Zhou Z, Wu S, Ni G, Zhang A, Tsimring LS, Hasty J, Hao N. Enhanced cellular longevity arising from environmental fluctuations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.05.547867. [PMID: 37461504 PMCID: PMC10350066 DOI: 10.1101/2023.07.05.547867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
Cellular longevity is regulated by both genetic and environmental factors. However, the interactions of these factors in the context of aging remain largely unclear. Here, we formulate a mathematical model for dynamic glucose modulation of a core gene circuit in yeast aging, which not only guided the design of pro-longevity interventions, but also revealed the theoretical principles underlying these interventions. We introduce the dynamical systems theory to capture two general means for promoting longevity - the creation of a stable fixed point in the "healthy" state of the cell and the dynamic stabilization of the system around this healthy state through environmental oscillations. Guided by the model, we investigate how both of these can be experimentally realized by dynamically modulating environmental glucose levels. The results establish a paradigm for theoretically analyzing the trajectories and perturbations of aging that can be generalized to aging processes in diverse cell types and organisms.
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Affiliation(s)
- Yuting Liu
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Zhen Zhou
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Songlin Wu
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Gavin Ni
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Alex Zhang
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Lev S. Tsimring
- Synthetic Biology Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Jeff Hasty
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Synthetic Biology Institute, University of California San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Nan Hao
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Synthetic Biology Institute, University of California San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
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9
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Minden S, Aniolek M, Noorman H, Takors R. Mimicked Mixing-Induced Heterogeneities of Industrial Bioreactors Stimulate Long-Lasting Adaption Programs in Ethanol-Producing Yeasts. Genes (Basel) 2023; 14:genes14050997. [PMID: 37239357 DOI: 10.3390/genes14050997] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Commercial-scale bioreactors create an unnatural environment for microbes from an evolutionary point of view. Mixing insufficiencies expose individual cells to fluctuating nutrient concentrations on a second-to-minute scale while transcriptional and translational capacities limit the microbial adaptation time from minutes to hours. This mismatch carries the risk of inadequate adaptation effects, especially considering that nutrients are available at optimal concentrations on average. Consequently, industrial bioprocesses that strive to maintain microbes in a phenotypic sweet spot, during lab-scale development, might suffer performance losses when said adaptive misconfigurations arise during scale-up. Here, we investigated the influence of fluctuating glucose availability on the gene-expression profile in the industrial yeast Ethanol Red™. The stimulus-response experiment introduced 2 min glucose depletion phases to cells growing under glucose limitation in a chemostat. Even though Ethanol Red™ displayed robust growth and productivity, a single 2 min depletion of glucose transiently triggered the environmental stress response. Furthermore, a new growth phenotype with an increased ribosome portfolio emerged after complete adaptation to recurring glucose shortages. The results of this study serve a twofold purpose. First, it highlights the necessity to consider the large-scale environment already at the experimental development stage, even when process-related stressors are moderate. Second, it allowed the deduction of strain engineering guidelines to optimize the genetic background of large-scale production hosts.
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Affiliation(s)
- Steven Minden
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Maria Aniolek
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Henk Noorman
- Royal DSM, 2613 AX Delft, The Netherlands
- Department of Biotechnology, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
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10
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Xue J, Zhou J, Li J, Du G, Chen J, Wang M, Zhao X. Systematic engineering of Saccharomyces cerevisiae for efficient synthesis of hemoglobins and myoglobins. BIORESOURCE TECHNOLOGY 2023; 370:128556. [PMID: 36586429 DOI: 10.1016/j.biortech.2022.128556] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 05/26/2023]
Abstract
Hemoglobin (Hb) and myoglobin (Mb) are kinds of heme-binding proteins that play crucial physiological roles in different organisms. With rapid application development in food processing and biocatalysis, the requirement of biosynthetic Hb and Mb is increasing. However, the production of Hb and Mb is limited by the lower expressional level of globins and insufficient or improper heme supply. After selecting an inducible strategy for the expression of globins, removing the spatial barrier during heme synthesis, increasing the synthesis of 5-aminolevulinate and moderately enhancing heme synthetic rate-limiting steps, the microbial synthesis of bovine and porcine Hb was firstly achieved. Furthermore, an engineered Saccharomyces cerevisiae obtained a higher titer of soybean (108.2 ± 3.5 mg/L) and clover (13.7 ± 0.5 mg/L) Hb and bovine (68.9 ± 1.6 mg/L) and porcine (85.9 ± 5.0 mg/L) Mb. Therefore, this systematic engineering strategy will be useful to produce other hemoproteins or hemoenzymes with high activities.
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Affiliation(s)
- Jike Xue
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jianghua Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Guocheng Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jian Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Miao Wang
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Xinrui Zhao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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11
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Nagar S, Mehta R, Kaur P, Liliah RT, Vancura A. Tolerance to replication stress requires Dun1p kinase and activation of the electron transport chain. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119382. [PMID: 36283478 PMCID: PMC10329874 DOI: 10.1016/j.bbamcr.2022.119382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 09/26/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022]
Abstract
One of the key outcomes of activation of DNA replication checkpoint (DRC) or DNA damage checkpoint (DDC) is the increased synthesis of the deoxyribonucleoside triphosphates (dNTPs), which is a prerequisite for normal progression through the S phase and for effective DNA repair. We have recently shown that DDC increases aerobic metabolism and activates the electron transport chain (ETC) to elevate ATP production and dNTP synthesis by repressing transcription of histone genes, leading to globally altered chromatin architecture and increased transcription of genes encoding enzymes of tricarboxylic acid (TCA) cycle and the ETC. The aim of this study was to determine whether DRC activates ETC. We show here that DRC activates ETC by a checkpoint kinase Dun1p-dependent mechanism. DRC induces transcription of RNR1-4 genes and elevates mtDNA copy number. Inactivation of RRM3 or SGS1, two DNA helicases important for DNA replication, activates DRC but does not render cells dependent on ETC. However, fitness of rrm3Δ and sgs1Δ cells requires Dun1p. The slow growth of rrm3Δdun1Δ and sgs1Δdun1Δ cells can be suppressed by introducing sml1Δ mutation, indicating that the slow growth is due to low levels of dNTPs. Interestingly, inactivation of ETC in dun1Δ cells results in a synthetic growth defect that can be suppressed by sml1Δ mutation, suggesting that ETC is important for dNTP synthesis in the absence of Dun1p function. Together, our results reveal an unexpected connection between ETC, replication stress, and Dun1p kinase.
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Affiliation(s)
- Shreya Nagar
- Department of Biological Sciences, St. John's University, Queens, NY, USA
| | - Riddhi Mehta
- Department of Biological Sciences, St. John's University, Queens, NY, USA
| | - Pritpal Kaur
- Department of Biological Sciences, St. John's University, Queens, NY, USA
| | - Roshini T Liliah
- Department of Biological Sciences, St. John's University, Queens, NY, USA
| | - Ales Vancura
- Department of Biological Sciences, St. John's University, Queens, NY, USA.
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12
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Ciamponi FE, Procópio DP, Murad NF, Franco TT, Basso TO, Brandão MM. Multi-omics network model reveals key genes associated with p-coumaric acid stress response in an industrial yeast strain. Sci Rep 2022; 12:22466. [PMID: 36577778 PMCID: PMC9797568 DOI: 10.1038/s41598-022-26843-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/21/2022] [Indexed: 12/30/2022] Open
Abstract
The production of ethanol from lignocellulosic sources presents increasingly difficult issues for the global biofuel scenario, leading to increased production costs of current second-generation (2G) ethanol when compared to first-generation (1G) plants. Among the setbacks encountered in industrial processes, the presence of chemical inhibitors from pre-treatment processes severely hinders the potential of yeasts in producing ethanol at peak efficiency. However, some industrial yeast strains have, either naturally or artificially, higher tolerance levels to these compounds. Such is the case of S. cerevisiae SA-1, a Brazilian fuel ethanol industrial strain that has shown high resistance to inhibitors produced by the pre-treatment of cellulosic complexes. Our study focuses on the characterization of the transcriptomic and physiological impact of an inhibitor of this type, p-coumaric acid (pCA), on this strain under chemostat cultivation via RNAseq and quantitative physiological data. It was found that strain SA-1 tend to increase ethanol yield and production rate while decreasing biomass yield when exposed to pCA, in contrast to pCA-susceptible strains, which tend to decrease their ethanol yield and fermentation efficiency when exposed to this substance. This suggests increased metabolic activity linked to mitochondrial and peroxisomal processes. The transcriptomic analysis also revealed a plethora of differentially expressed genes located in co-expressed clusters that are associated with changes in biological pathways linked to biosynthetic and energetical processes. Furthermore, it was also identified 20 genes that act as interaction hubs for these clusters, while also having association with altered pathways and changes in metabolic outputs, potentially leading to the discovery of novel targets for metabolic engineering toward a more robust industrial yeast strain.
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Affiliation(s)
- F. E. Ciamponi
- grid.411087.b0000 0001 0723 2494Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas (Unicamp), Av. Cândido Rondon, 400, Campinas, SP 13083-875 Brazil
| | - D. P. Procópio
- grid.11899.380000 0004 1937 0722Department of Chemical Engineering, University of São Paulo (USP), Av. Prof. Luciano Gualberto, 380, São Paulo, SP 05508-010 Brazil
| | - N. F. Murad
- grid.411087.b0000 0001 0723 2494Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas (Unicamp), Av. Cândido Rondon, 400, Campinas, SP 13083-875 Brazil
| | - T. T. Franco
- grid.411087.b0000 0001 0723 2494School of Chemical Engineering (FEQ), State University of Campinas (Unicamp), Av. Albert Einstein, 500, Campinas, SP 13083-852 Brazil
| | - T. O. Basso
- grid.11899.380000 0004 1937 0722Department of Chemical Engineering, University of São Paulo (USP), Av. Prof. Luciano Gualberto, 380, São Paulo, SP 05508-010 Brazil
| | - M. M. Brandão
- grid.411087.b0000 0001 0723 2494Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas (Unicamp), Av. Cândido Rondon, 400, Campinas, SP 13083-875 Brazil
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13
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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: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [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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14
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Costanza A, Guaragnella N, Bobba A, Manzari C, L'Abbate A, Giudice CL, Picardi E, D'Erchia AM, Pesole G, Giannattasio S. Yeast as a Model to Unravel New BRCA2 Functions in Cell Metabolism. Front Oncol 2022; 12:908442. [PMID: 35734584 PMCID: PMC9207209 DOI: 10.3389/fonc.2022.908442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
Mutations in BRCA2 gene increase the risk for breast cancer and for other cancer types, including pancreatic and prostate cancer. Since its first identification as an oncosupressor in 1995, the best-characterized function of BRCA2 is in the repair of DNA double-strand breaks (DSBs) by homologous recombination. BRCA2 directly interacts with both RAD51 and single-stranded DNA, mediating loading of RAD51 recombinase to sites of single-stranded DNA. In the absence of an efficient homologous recombination pathway, DSBs accumulate resulting in genome instability, thus supporting tumorigenesis. Yet the precise mechanism by which BRCA2 exerts its tumor suppressor function remains unclear. BRCA2 has also been involved in other biological functions including protection of telomere integrity and stalled replication forks, cell cycle progression, transcriptional control and mitophagy. Recently, we and others have reported a role of BRCA2 in modulating cell death programs through a molecular mechanism conserved in yeast and mammals. Here we hypothesize that BRCA2 is a multifunctional protein which exerts specific functions depending on cell stress response pathway. Based on a differential RNA sequencing analysis carried out on yeast cells either growing or undergoing a regulated cell death process, either in the absence or in the presence of BRCA2, we suggest that BRCA2 causes central carbon metabolism reprogramming in response to death stimuli and encourage further investigation on the role of metabolic reprogramming in BRCA2 oncosuppressive function.
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Affiliation(s)
- Alessandra Costanza
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy
| | - Nicoletta Guaragnella
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy.,Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Antonella Bobba
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy
| | - Caterina Manzari
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Alberto L'Abbate
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy
| | - Claudio Lo Giudice
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Ernesto Picardi
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy.,Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Anna Maria D'Erchia
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy.,Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy.,Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Sergio Giannattasio
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy
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15
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Barba‐Aliaga M, Alepuz P. The activator/repressor Hap1 binds to the yeast eIF5A‐encoding gene
TIF51A
to adapt its expression to the mitochondrial functional status. FEBS Lett 2022; 596:1809-1826. [DOI: 10.1002/1873-3468.14366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/12/2022] [Accepted: 04/22/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Marina Barba‐Aliaga
- Instituto de Biotecnología y Biomedicina (Biotecmed) Universitat de València 46100 València Spain
- Departamento de Bioquímica y Biología Molecular Facultad de Ciencias Biológicas Universitat de València 46100 València Spain
| | - Paula Alepuz
- Instituto de Biotecnología y Biomedicina (Biotecmed) Universitat de València 46100 València Spain
- Departamento de Bioquímica y Biología Molecular Facultad de Ciencias Biológicas Universitat de València 46100 València Spain
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16
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Chen X, Li X, Ji B, Wang Y, Ishchuk OP, Vorontsov E, Petranovic D, Siewers V, Engqvist MK. Suppressors of amyloid-β toxicity improve recombinant protein production in yeast by reducing oxidative stress and tuning cellular metabolism. Metab Eng 2022; 72:311-324. [DOI: 10.1016/j.ymben.2022.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/22/2022] [Accepted: 04/25/2022] [Indexed: 12/24/2022]
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17
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Barba-Aliaga M, Alepuz P. Role of eIF5A in Mitochondrial Function. Int J Mol Sci 2022; 23:1284. [PMID: 35163207 PMCID: PMC8835957 DOI: 10.3390/ijms23031284] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 12/17/2022] Open
Abstract
The eukaryotic translation initiation factor 5A (eIF5A) is an evolutionarily conserved protein that binds ribosomes to facilitate the translation of peptide motifs with consecutive prolines or combinations of prolines with glycine and charged amino acids. It has also been linked to other molecular functions and cellular processes, such as nuclear mRNA export and mRNA decay, proliferation, differentiation, autophagy, and apoptosis. The growing interest in eIF5A relates to its association with the pathogenesis of several diseases, including cancer, viral infection, and diabetes. It has also been proposed as an anti-aging factor: its levels decay in aged cells, whereas increasing levels of active eIF5A result in the rejuvenation of the immune and vascular systems and improved brain cognition. Recent data have linked the role of eIF5A in some pathologies with its function in maintaining healthy mitochondria. The eukaryotic translation initiation factor 5A is upregulated under respiratory metabolism and its deficiency reduces oxygen consumption, ATP production, and the levels of several mitochondrial metabolic enzymes, as well as altering mitochondria dynamics. However, although all the accumulated data strongly link eIF5A to mitochondrial function, the precise molecular role and mechanisms involved are still unknown. In this review, we discuss the findings linking eIF5A and mitochondria, speculate about its role in regulating mitochondrial homeostasis, and highlight its potential as a target in diseases related to energy metabolism.
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Affiliation(s)
- Marina Barba-Aliaga
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, 46100 València, Spain
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, 46100 València, Spain
| | - Paula Alepuz
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, 46100 València, Spain
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, 46100 València, Spain
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18
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Tian M, Li Q, Liu Y, Zheng P, Li D, Zhao Y, Wang B, Li C, Wang J, Gao P, Tang Q, Zhang X, Wu H. Relationship between delayed luminescence emission and mitochondrial status in Saccharomyces cerevisiae. Sci Rep 2022; 12:394. [PMID: 35013471 PMCID: PMC8748773 DOI: 10.1038/s41598-021-04290-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/20/2021] [Indexed: 11/09/2022] Open
Abstract
Delayed luminescence (DL) is gradually used in various detection of biological systems as a rapid detection technique, however, its biological mechanism was still not clear. In this study, a new model of DL detection system for liquid biological samples is established to investigate the DL emission of Saccharomyces cerevisiae cells cultured in different glucose concentrations. We analyzed the relationship between the DL emission and cell growth, cell vitality, mitochondrial morphology, mitochondrial DNA (mtDNA) copy number, adenosine triphosphate (ATP), oxygen consumption rate (OCR), as well as mitochondria membrane potential (MMP) in S. cerevisiae cells cultured with 0.01, 0.05, 0.15, 3, 10 and 20 g/L glucose respectively. It was found that the DL emission had strong correlation with mitochondrial morphology, OCR, and MMP. The results suggested that DL is an indicator of mitochondria status under different glucose supply conditions, and may be an effective method to detect mitochondrial metabolism related disorders.
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Affiliation(s)
- Miao Tian
- ENNOVA Institute of Life Science and Technology, ENN Group, South District of ENN Industrial Park, Langfang, 065001, Hebei, China
| | - Qing Li
- ENNOVA Institute of Life Science and Technology, ENN Group, South District of ENN Industrial Park, Langfang, 065001, Hebei, China
| | - Yang Liu
- ENNOVA Institute of Life Science and Technology, ENN Group, South District of ENN Industrial Park, Langfang, 065001, Hebei, China
| | - Peng Zheng
- ENNOVA Institute of Life Science and Technology, ENN Group, South District of ENN Industrial Park, Langfang, 065001, Hebei, China
| | - Danyu Li
- ENNOVA Institute of Life Science and Technology, ENN Group, South District of ENN Industrial Park, Langfang, 065001, Hebei, China
| | - Yanpeng Zhao
- ENNOVA Institute of Life Science and Technology, ENN Group, South District of ENN Industrial Park, Langfang, 065001, Hebei, China
| | - Bing Wang
- ENNOVA Institute of Life Science and Technology, ENN Group, South District of ENN Industrial Park, Langfang, 065001, Hebei, China
| | - Chenhao Li
- ENNOVA Institute of Life Science and Technology, ENN Group, South District of ENN Industrial Park, Langfang, 065001, Hebei, China
| | - Jing Wang
- ENNOVA Institute of Life Science and Technology, ENN Group, South District of ENN Industrial Park, Langfang, 065001, Hebei, China
| | - Peng Gao
- ENNOVA Institute of Life Science and Technology, ENN Group, South District of ENN Industrial Park, Langfang, 065001, Hebei, China
| | - Qing Tang
- ENNOVA Institute of Life Science and Technology, ENN Group, South District of ENN Industrial Park, Langfang, 065001, Hebei, China
| | - Xiaochun Zhang
- ENNOVA Institute of Life Science and Technology, ENN Group, South District of ENN Industrial Park, Langfang, 065001, Hebei, China
| | - Hong Wu
- ENNOVA Institute of Life Science and Technology, ENN Group, South District of ENN Industrial Park, Langfang, 065001, Hebei, China.
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19
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Flores-Cotera LB, Chávez-Cabrera C, Martínez-Cárdenas A, Sánchez S, García-Flores OU. Deciphering the mechanism by which the yeast Phaffia rhodozyma responds adaptively to environmental, nutritional, and genetic cues. J Ind Microbiol Biotechnol 2021; 48:kuab048. [PMID: 34302341 PMCID: PMC8788774 DOI: 10.1093/jimb/kuab048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/16/2021] [Indexed: 11/13/2022]
Abstract
Phaffia rhodozyma is a basidiomycetous yeast that synthesizes astaxanthin (ASX), which is a powerful and highly valuable antioxidant carotenoid pigment. P. rhodozyma cells accrue ASX and gain an intense red-pink coloration when faced with stressful conditions such as nutrient limitations (e.g., nitrogen or copper), the presence of toxic substances (e.g., antimycin A), or are affected by mutations in the genes that are involved in nitrogen metabolism or respiration. Since cellular accrual of ASX occurs under a wide variety of conditions, this yeast represents a valuable model for studying the growth conditions that entail oxidative stress for yeast cells. Recently, we proposed that ASX synthesis can be largely induced by conditions that lead to reduction-oxidation (redox) imbalances, particularly the state of the NADH/NAD+ couple together with an oxidative environment. In this work, we review the multiple known conditions that elicit ASX synthesis expanding on the data that we formerly examined. When considered alongside the Mitchell's chemiosmotic hypothesis, the study served to rationalize the induction of ASX synthesis and other adaptive cellular processes under a much broader set of conditions. Our aim was to propose an underlying mechanism that explains how a broad range of divergent conditions converge to induce ASX synthesis in P. rhodozyma. The mechanism that links the induction of ASX synthesis with the occurrence of NADH/NAD+ imbalances may help in understanding how other organisms detect any of a broad array of stimuli or gene mutations, and then adaptively respond to activate numerous compensatory cellular processes.
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Affiliation(s)
- Luis B Flores-Cotera
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México city 07360, México
| | - Cipriano Chávez-Cabrera
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México city 07360, México
| | - Anahi Martínez-Cárdenas
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México city 07360, México
| | - Sergio Sánchez
- Department of Molecular Biology and Biotechnology, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México city 04510, México
| | - Oscar Ulises García-Flores
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México city 07360, México
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20
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Cytosolic Quality Control of Mitochondrial Protein Precursors-The Early Stages of the Organelle Biogenesis. Int J Mol Sci 2021; 23:ijms23010007. [PMID: 35008433 PMCID: PMC8745001 DOI: 10.3390/ijms23010007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/12/2022] Open
Abstract
With few exceptions, proteins that constitute the proteome of mitochondria originate outside of this organelle in precursor forms. Such protein precursors follow dedicated transportation paths to reach specific parts of mitochondria, where they complete their maturation and perform their functions. Mitochondrial precursor targeting and import pathways are essential to maintain proper mitochondrial function and cell survival, thus are tightly controlled at each stage. Mechanisms that sustain protein homeostasis of the cytosol play a vital role in the quality control of proteins targeted to the organelle. Starting from their synthesis, precursors are constantly chaperoned and guided to reduce the risk of premature folding, erroneous interactions, or protein damage. The ubiquitin-proteasome system provides proteolytic control that is not restricted to defective proteins but also regulates the supply of precursors to the organelle. Recent discoveries provide evidence that stress caused by the mislocalization of mitochondrial proteins may contribute to disease development. Precursors are not only subject to regulation but also modulate cytosolic machinery. Here we provide an overview of the cellular pathways that are involved in precursor maintenance and guidance at the early cytosolic stages of mitochondrial biogenesis. Moreover, we follow the circumstances in which mitochondrial protein import deregulation disturbs the cellular balance, carefully looking for rescue paths that can restore proteostasis.
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21
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Kaur P, Nagar S, Bhagwat M, Uddin M, Zhu Y, Vancurova I, Vancura A. Activated heme synthesis regulates glycolysis and oxidative metabolism in breast and ovarian cancer cells. PLoS One 2021; 16:e0260400. [PMID: 34807950 PMCID: PMC8608300 DOI: 10.1371/journal.pone.0260400] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 11/09/2021] [Indexed: 12/24/2022] Open
Abstract
Heme is an essential cofactor for enzymes of the electron transport chain (ETC) and ATP synthesis in mitochondrial oxidative phosphorylation (OXPHOS). Heme also binds to and destabilizes Bach1, a transcription regulator that controls expression of several groups of genes important for glycolysis, ETC, and metastasis of cancer cells. Heme synthesis can thus affect pathways through which cells generate energy and precursors for anabolism. In addition, increased heme synthesis may trigger oxidative stress. Since many cancers are characterized by a high glycolytic rate regardless of oxygen availability, targeting glycolysis, ETC, and OXPHOS have emerged as a potential therapeutic strategy. Here, we report that enhancing heme synthesis through exogenous supplementation of heme precursor 5-aminolevulinic acid (ALA) suppresses oxidative metabolism as well as glycolysis and significantly reduces proliferation of both ovarian and breast cancer cells. ALA supplementation also destabilizes Bach1 and inhibits migration of both cell types. Our data indicate that the underlying mechanisms differ in ovarian and breast cancer cells, but involve destabilization of Bach1, AMPK activation, and induction of oxidative stress. In addition, there appears to be an inverse correlation between the activity of oxidative metabolism and ALA sensitivity. Promoting heme synthesis by ALA supplementation may thus represent a promising new anti-cancer strategy, particularly in cancers that are sensitive to altered redox signaling, or in combination with strategies that target the antioxidant systems or metabolic weaknesses of cancer cells.
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Affiliation(s)
- Pritpal Kaur
- Department of Biological Sciences, St. John’s University, New York, United States of America
| | - Shreya Nagar
- Department of Biological Sciences, St. John’s University, New York, United States of America
| | - Madhura Bhagwat
- Department of Biological Sciences, St. John’s University, New York, United States of America
| | - Mohammad Uddin
- Department of Biological Sciences, St. John’s University, New York, United States of America
| | - Yan Zhu
- Department of Biological Sciences, St. John’s University, New York, United States of America
| | - Ivana Vancurova
- Department of Biological Sciences, St. John’s University, New York, United States of America
| | - Ales Vancura
- Department of Biological Sciences, St. John’s University, New York, United States of America
- * E-mail:
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22
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Liu Q, Liu Y, Li G, Savolainen O, Chen Y, Nielsen J. De novo biosynthesis of bioactive isoflavonoids by engineered yeast cell factories. Nat Commun 2021; 12:6085. [PMID: 34667183 PMCID: PMC8526750 DOI: 10.1038/s41467-021-26361-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 09/30/2021] [Indexed: 11/09/2022] Open
Abstract
Isoflavonoids comprise a class of plant natural products with great nutraceutical, pharmaceutical and agricultural significance. Their low abundance in nature and structural complexity however hampers access to these phytochemicals through traditional crop-based manufacturing or chemical synthesis. Microbial bioproduction therefore represents an attractive alternative. Here, we engineer the metabolism of Saccharomyces cerevisiae to become a platform for efficient production of daidzein, a core chemical scaffold for isoflavonoid biosynthesis, and demonstrate its application towards producing bioactive glucosides from glucose, following the screening-reconstruction-application engineering framework. First, we rebuild daidzein biosynthesis in yeast and its production is then improved by 94-fold through screening biosynthetic enzymes, identifying rate-limiting steps, implementing dynamic control, engineering substrate trafficking and fine-tuning competing metabolic processes. The optimized strain produces up to 85.4 mg L-1 of daidzein and introducing plant glycosyltransferases in this strain results in production of bioactive puerarin (72.8 mg L-1) and daidzin (73.2 mg L-1). Our work provides a promising step towards developing synthetic yeast cell factories for de novo biosynthesis of value-added isoflavonoids and the multi-phased framework may be extended to engineer pathways of complex natural products in other microbial hosts.
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Affiliation(s)
- Quanli Liu
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Yi Liu
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Gang Li
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Otto Savolainen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden.,Chalmers Mass Spectrometry Infrastructure, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden.,Institute of Public Health and Clinical Nutrition, University of Eastern Finland, FI-70211, Kuopio, Finland
| | - Yun Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark. .,BioInnovation Institute, Ole Maaløes vej 3, 2200, Copenhagen N, Denmark.
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23
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Ferramosca A, Zara V. Mitochondrial Carriers and Substrates Transport Network: A Lesson from Saccharomyces cerevisiae. Int J Mol Sci 2021; 22:ijms22168496. [PMID: 34445202 PMCID: PMC8395155 DOI: 10.3390/ijms22168496] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 12/12/2022] Open
Abstract
The yeast Saccharomyces cerevisiae is one of the most widely used model organisms for investigating various aspects of basic cellular functions that are conserved in human cells. This organism, as well as human cells, can modulate its metabolism in response to specific growth conditions, different environmental changes, and nutrient depletion. This adaptation results in a metabolic reprogramming of specific metabolic pathways. Mitochondrial carriers play a fundamental role in cellular metabolism, connecting mitochondrial with cytosolic reactions. By transporting substrates across the inner membrane of mitochondria, they contribute to many processes that are central to cellular function. The genome of Saccharomyces cerevisiae encodes 35 members of the mitochondrial carrier family, most of which have been functionally characterized. The aim of this review is to describe the role of the so far identified yeast mitochondrial carriers in cell metabolism, attempting to show the functional connections between substrates transport and specific metabolic pathways, such as oxidative phosphorylation, lipid metabolism, gluconeogenesis, and amino acids synthesis. Analysis of the literature reveals that these proteins transport substrates involved in the same metabolic pathway with a high degree of flexibility and coordination. The understanding of the role of mitochondrial carriers in yeast biology and metabolism could be useful for clarifying unexplored aspects related to the mitochondrial carrier network. Such knowledge will hopefully help in obtaining more insight into the molecular basis of human diseases.
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24
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Exploration and characterization of hypoxia-inducible endogenous promoters in Aspergillus niger. Appl Microbiol Biotechnol 2021; 105:5529-5539. [PMID: 34254155 DOI: 10.1007/s00253-021-11417-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 05/25/2021] [Accepted: 05/29/2021] [Indexed: 12/13/2022]
Abstract
Aspergillus niger is widely used for the efficient production of organic acids and enzyme preparations. However, this organism lacks basic genetic elements for dynamic control, especially inducible promoters that can respond to specific environmental signals. Since these are desirable for better adaptation of fermentation to large-scale industrial production, herein, we have identified the two first hypoxia-inducible promoters in A. niger, PsrbB and PfhbA. Their performance under high or low oxygen conditions was monitored using two reporter proteins, green fluorescent protein (EGFP) and β-glucuronidase (GUS). For comparison, basal expression of the general strong promoter PgpdA was lower than PsrbB but higher than PfhbA. However, under hypoxia, both promoters showed higher expression than under hyperoxia, and these values were also higher than those observed for PgpdA. For PsrbB, strength under hypoxia was ~2-3 times higher than under hyperoxia (for PfhbA, 3-9 times higher) and ~2.5-5 times higher than for PgpdA (for PfhbA, 2-3 times higher). Promoter truncation analysis showed that the PsrbB fragment -1024 to -588 bp is the core region that determines hypoxia response. KEY POINTS: The first identification of two hypoxia-inducible promoters in A. niger is a promising tool for modulation of target genes under hypoxia. Two reporter genes revealed a different activity and responsiveness to hypoxia of PfhbA and PsrbB promoters, which is relevant for the development of dynamic metabolic regulation of A. niger fermentation. PsrbB promoter truncation and bioinformatics analysis is the foundation for further research.
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25
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Pereira R, Ishchuk OP, Li X, Liu Q, Liu Y, Otto M, Chen Y, Siewers V, Nielsen J. Metabolic Engineering of Yeast. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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26
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Ishchuk OP, Frost AT, Muñiz-Paredes F, Matsumoto S, Laforge N, Eriksson NL, Martínez JL, Petranovic D. Improved production of human hemoglobin in yeast by engineering hemoglobin degradation. Metab Eng 2021; 66:259-267. [PMID: 33984513 DOI: 10.1016/j.ymben.2021.05.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/09/2021] [Accepted: 05/04/2021] [Indexed: 12/23/2022]
Abstract
With the increasing demand for blood transfusions, the production of human hemoglobin (Hb) from sustainable sources is increasingly studied. Microbial production is an attractive option, as it may provide a cheap, safe, and reliable source of this protein. To increase the production of human hemoglobin by the yeast Saccharomyces cerevisiae, the degradation of Hb was reduced through several approaches. The deletion of the genes HMX1 (encoding heme oxygenase), VPS10 (encoding receptor for vacuolar proteases), PEP4 (encoding vacuolar proteinase A), ROX1 (encoding heme-dependent repressor of hypoxic genes) and the overexpression of the HEM3 (encoding porphobilinogen deaminase) and the AHSP (encoding human alpha-hemoglobin-stabilizing protein) genes - these changes reduced heme and Hb degradation and improved heme and Hb production. The reduced hemoglobin degradation was validated by a bilirubin biosensor. During glucose fermentation, the engineered strains produced 18% of intracellular Hb relative to the total yeast protein, which is the highest production of human hemoglobin reported in yeast. This increased hemoglobin production was accompanied with an increased oxygen consumption rate and an increased glycerol yield, which (we speculate) is the yeast's response to rebalance its NADH levels under conditions of oxygen limitation and increased protein-production.
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Affiliation(s)
- Olena P Ishchuk
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, SE41296, Gothenburg, Sweden.
| | - August T Frost
- Department of Biotechnology and Biomedicine, Section for Synthetic Biology, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark
| | - Facundo Muñiz-Paredes
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, SE41296, Gothenburg, Sweden
| | - Saki Matsumoto
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, SE41296, Gothenburg, Sweden
| | - Nathalie Laforge
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, SE41296, Gothenburg, Sweden
| | - Nélida Leiva Eriksson
- Department of Chemistry, Division of Biotechnology, Lund University, 221 00, Lund, Sweden
| | - José L Martínez
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, SE41296, Gothenburg, Sweden; Department of Biotechnology and Biomedicine, Section for Synthetic Biology, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark
| | - Dina Petranovic
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, SE41296, Gothenburg, Sweden; Novo Nordisk Foundation Centre for Biosustainability, Chalmers University of Technology, SE41296, Gothenburg, Sweden.
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27
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Peterson PP, Liu Z. Identification and Characterization of Rapidly Accumulating sch9Δ Suppressor Mutations in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2021; 11:6254187. [PMID: 33901283 DOI: 10.1093/g3journal/jkab134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/14/2021] [Indexed: 01/30/2023]
Abstract
Nutrient sensing is important for cell growth, aging, and longevity. In Saccharomyces cerevisiae, Sch9, an AGC-family protein kinase, is a major nutrient sensing kinase homologous to mammalian Akt and S6 kinase. Sch9 integrates environmental cues with cell growth by functioning downstream of TORC1 and in parallel with the Ras/PKA pathway. Mutations in SCH9 lead to reduced cell growth in dextrose medium; however, reports on the ability of sch9Δ mutants to utilize non-fermentable carbon sources are inconsistent. Here we show that sch9Δ mutant strains cannot grow on non-fermentable carbon sources and rapidly accumulate suppressor mutations, which reverse growth defects of sch9Δ mutants. sch9Δ induces gene expression of three transcription factors required for utilization of non-fermentable carbon sources, Cat8, Adr1, and Hap4, while sch9Δ suppressor mutations, termed sns1 and sns2, strongly decrease the gene expression of those transcription factors. Despite the genetic suppression interactions, both sch9Δ and sns1 (or sns2) homozygous mutants have severe defects in meiosis. By screening mutants defective in sporulation, we identified additional sch9Δ suppressor mutants with mutations in GPB1, GPB2, and MCK1. Using library complementation and genetic analysis, we identified SNS1 and SNS2 to be IRA2 and IRA1, respectively. Furthermore, we discovered that lifespan extension in sch9Δ mutants is dependent on IRA2 and that PKA inactivation greatly increases basal expression of CAT8, ADR1, and HAP4. Our results demonstrate that sch9Δ leads to complete loss of growth on non-fermentable carbon sources and mutations in MCK1 or genes encoding negative regulators of the Ras/PKA pathway reverse sch9Δ mutant phenotypes.
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Affiliation(s)
- Patricia P Peterson
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA
| | - Zhengchang Liu
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA
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28
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Jiang Y, Hao N. Memorizing environmental signals through feedback and feedforward loops. Curr Opin Cell Biol 2021; 69:96-102. [PMID: 33549848 DOI: 10.1016/j.ceb.2020.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/12/2022]
Abstract
Cells in diverse organisms can store the information of previous environmental conditions for long periods of time. This form of cellular memory adjusts the cell's responses to future challenges, providing fitness advantages in fluctuating environments. Many biological functions, including cellular memory, are mediated by specific recurring patterns of interactions among proteins and genes, known as 'network motifs.' In this review, we focus on three well-characterized network motifs - negative feedback loops, positive feedback loops, and feedforward loops, which underlie different types of cellular memories. We describe the latest studies identifying these motifs in various molecular processes and discuss how the topologies and dynamics of these motifs can enable memory encoding and storage.
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Affiliation(s)
- Yanfei Jiang
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Nan Hao
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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29
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Barba-Aliaga M, Villarroel-Vicente C, Stanciu A, Corman A, Martínez-Pastor MT, Alepuz P. Yeast Translation Elongation Factor eIF5A Expression Is Regulated by Nutrient Availability through Different Signalling Pathways. Int J Mol Sci 2020; 22:E219. [PMID: 33379337 PMCID: PMC7794953 DOI: 10.3390/ijms22010219] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/17/2020] [Accepted: 12/24/2020] [Indexed: 12/15/2022] Open
Abstract
Translation elongation factor eIF5A binds to ribosomes to promote peptide bonds between problematic amino acids for the reaction like prolines. eIF5A is highly conserved and essential in eukaryotes, which usually contain two similar but differentially expressed paralogue genes. The human eIF5A-1 isoform is abundant and implicated in some cancer types; the eIF5A-2 isoform is absent in most cells but becomes overexpressed in many metastatic cancers. Several reports have connected eIF5A and mitochondria because it co-purifies with the organelle or its inhibition reduces respiration and mitochondrial enzyme levels. However, the mechanisms of eIF5A mitochondrial function, and whether eIF5A expression is regulated by the mitochondrial metabolism, are unknown. We analysed the expression of yeast eIF5A isoforms Tif51A and Tif51B under several metabolic conditions and in mutants. The depletion of Tif51A, but not Tif51B, compromised yeast growth under respiration and reduced oxygen consumption. Tif51A expression followed dual positive regulation: by high glucose through TORC1 signalling, like other translation factors, to promote growth and by low glucose or non-fermentative carbon sources through Snf1 and heme-dependent transcription factor Hap1 to promote respiration. Upon iron depletion, Tif51A was down-regulated and Tif51B up-regulated. Both were Hap1-dependent. Our results demonstrate eIF5A expression regulation by cellular metabolic status.
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Affiliation(s)
- Marina Barba-Aliaga
- Instituto Biotecmed, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain; (M.B.-A.); (C.V.-V.); (A.S.); (A.C.)
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain;
| | - Carlos Villarroel-Vicente
- Instituto Biotecmed, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain; (M.B.-A.); (C.V.-V.); (A.S.); (A.C.)
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain;
| | - Alice Stanciu
- Instituto Biotecmed, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain; (M.B.-A.); (C.V.-V.); (A.S.); (A.C.)
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain;
| | - Alba Corman
- Instituto Biotecmed, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain; (M.B.-A.); (C.V.-V.); (A.S.); (A.C.)
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain;
| | - María Teresa Martínez-Pastor
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain;
| | - Paula Alepuz
- Instituto Biotecmed, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain; (M.B.-A.); (C.V.-V.); (A.S.); (A.C.)
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain;
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30
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Li Y, Jiang Y, Paxman J, O'Laughlin R, Klepin S, Zhu Y, Pillus L, Tsimring LS, Hasty J, Hao N. A programmable fate decision landscape underlies single-cell aging in yeast. Science 2020; 369:325-329. [PMID: 32675375 DOI: 10.1126/science.aax9552] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 01/24/2020] [Accepted: 05/13/2020] [Indexed: 12/12/2022]
Abstract
Chromatin instability and mitochondrial decline are conserved processes that contribute to cellular aging. Although both processes have been explored individually in the context of their distinct signaling pathways, the mechanism that determines which process dominates during aging of individual cells is unknown. We show that interactions between the chromatin silencing and mitochondrial pathways lead to an epigenetic landscape of yeast replicative aging with multiple equilibrium states that represent different types of terminal states of aging. The structure of the landscape drives single-cell differentiation toward one of these states during aging, whereby the fate is determined quite early and is insensitive to intracellular noise. Guided by a quantitative model of the aging landscape, we genetically engineered a long-lived equilibrium state characterized by an extended life span.
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Affiliation(s)
- Yang Li
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Yanfei Jiang
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Julie Paxman
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Richard O'Laughlin
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Stephen Klepin
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Yuelian Zhu
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Lorraine Pillus
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.,UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Lev S Tsimring
- BioCircuits Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Jeff Hasty
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.,Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA.,BioCircuits Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Nan Hao
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA. .,BioCircuits Institute, University of California San Diego, La Jolla, CA 92093, USA
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31
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Martinez-Guzman O, Willoughby MM, Saini A, Dietz JV, Bohovych I, Medlock AE, Khalimonchuk O, Reddi AR. Mitochondrial-nuclear heme trafficking in budding yeast is regulated by GTPases that control mitochondrial dynamics and ER contact sites. J Cell Sci 2020; 133:jcs.237917. [PMID: 32265272 DOI: 10.1242/jcs.237917] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 03/24/2020] [Indexed: 12/20/2022] Open
Abstract
Heme is a cofactor and signaling molecule that is essential for much of aerobic life. All heme-dependent processes in eukaryotes require that heme is trafficked from its site of synthesis in the mitochondria to hemoproteins located throughout the cell. However, the mechanisms governing the mobilization of heme out of the mitochondria, and the spatio-temporal dynamics of these processes, are poorly understood. Here, using genetically encoded fluorescent heme sensors, we developed a live-cell assay to monitor heme distribution dynamics between the mitochondrial inner membrane, where heme is synthesized, and the mitochondrial matrix, cytosol and nucleus. Surprisingly, heme trafficking to the nucleus is ∼25% faster than to the cytosol or mitochondrial matrix, which have nearly identical heme trafficking dynamics, potentially supporting a role for heme as a mitochondrial-nuclear retrograde signal. Moreover, we discovered that the heme synthetic enzyme 5-aminolevulinic acid synthase (ALAS, also known as Hem1 in yeast), and GTPases in control of the mitochondrial dynamics machinery (Mgm1 and Dnm1) and ER contact sites (Gem1), regulate the flow of heme between the mitochondria and nucleus. Overall, our results indicate that there are parallel pathways for the distribution of bioavailable heme.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Osiris Martinez-Guzman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Mathilda M Willoughby
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Arushi Saini
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jonathan V Dietz
- Department of Biochemistry and Nebraska Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA
| | - Iryna Bohovych
- Department of Biochemistry and Nebraska Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA
| | - Amy E Medlock
- Department of Biochemistry and Molecular Biology, University of Georgia and Augusta University-University of Georgia Medical Partnership, Athens, GA 30602, USA
| | - Oleh Khalimonchuk
- Department of Biochemistry and Nebraska Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA.,Fred & Pamela Buffett Cancer Center, Omaha, NE 68198, USA
| | - Amit R Reddi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA .,Parker Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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32
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Zhang J, Wang Z, Su T, Sun H, Zhu Y, Qi Q, Wang Q. Tuning the Binding Affinity of Heme-Responsive Biosensor for Precise and Dynamic Pathway Regulation. iScience 2020; 23:101067. [PMID: 32371371 PMCID: PMC7200772 DOI: 10.1016/j.isci.2020.101067] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 02/21/2020] [Accepted: 04/13/2020] [Indexed: 02/06/2023] Open
Abstract
Current challenge for dynamic pathway control in metabolic engineering is enabling the components of the artificial regulatory system to be tunable. Here, we designed and built a heme-responsive regulatory system containing a heme biosensor HrtR and CRISPRi to regulate chemicals production while maintaining the intracellular heme homeostasis. A series of engineered biosensors with varied sensitivity and threshold were obtained by semi-rational design with site saturated mutation of HrtR. The modified metabolite-binding affinity of HrtR was confirmed by heme titration and molecular dynamic simulation. Dynamic regulation pattern of the system was validated by the fluctuation of gene expression and intracellular heme concentration. The efficiency of this regulatory system was proved by improving the 5-aminolevulinic acid (ALA) production to 5.35g/L, the highest yield in batch fermentation of Escherichia coli. This system was also successfully used in improving porphobilinogen (PBG) and porphyrins biosynthesis and can be applied in many other biological processes. Designed and built a heme-responsive regulatory system employing HrtR and CRISPRi Turning the binding affinity of HrtR by site saturation mutations Optimizing the system to achieve dynamic regulation of target genes The system was applied to the ALA, PBG, and porphyrins production
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Affiliation(s)
- Jian Zhang
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao 266237, P. R. China
| | - Zhiguo Wang
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou 311121, P. R. China
| | - Tianyuan Su
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao 266237, P. R. China
| | - Huanhuan Sun
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao 266237, P. R. China
| | - Yuan Zhu
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao 266237, P. R. China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao 266237, P. R. China; CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P. R. China.
| | - Qian Wang
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao 266237, P. R. China.
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33
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Hijazi I, Knupp J, Chang A. Retrograde signaling mediates an adaptive survival response to endoplasmic reticulum stress in Saccharomyces cerevisiae. J Cell Sci 2020; 133:jcs.241539. [PMID: 32005698 DOI: 10.1242/jcs.241539] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/23/2020] [Indexed: 12/11/2022] Open
Abstract
One major cause of endoplasmic reticulum (ER) stress is homeostatic imbalance between biosynthetic protein folding and protein folding capacity. Cells utilize mechanisms such as the unfolded protein response (UPR) to cope with ER stress. Nevertheless, when ER stress is prolonged or severe, cell death may occur, accompanied by production of mitochondrial reactive oxygen species (ROS). Using a yeast model (Saccharomyces cerevisiae), we describe an innate, adaptive response to ER stress to increase select mitochondrial proteins, O2 consumption and cell survival. The mitochondrial response allows cells to resist additional ER stress. The ER stress-induced mitochondrial response is mediated by activation of retrograde (RTG) signaling to enhance anapleurotic reactions of the tricarboxylic acid cycle. Mitochondrial response to ER stress is accompanied by inactivation of the conserved TORC1 pathway, and activation of Snf1/AMPK, the conserved energy sensor and regulator of metabolism. Our results provide new insight into the role of respiration in cell survival in the face of ER stress, and should help in developing therapeutic strategies to limit cell death in disorders linked to ER stress.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Imadeddin Hijazi
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 1105 N University, Ann Arbor, MI 48109, USA
| | - Jeffrey Knupp
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 1105 N University, Ann Arbor, MI 48109, USA
| | - Amy Chang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 1105 N University, Ann Arbor, MI 48109, USA
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34
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Bouchez CL, Yoboue ED, de la Rosa Vargas LE, Salin B, Cuvellier S, Rigoulet M, Duvezin-Caubet S, Devin A. "Labile" heme critically regulates mitochondrial biogenesis through the transcriptional co-activator Hap4p in Saccharomyces cerevisiae. J Biol Chem 2020; 295:5095-5109. [PMID: 32075909 DOI: 10.1074/jbc.ra120.012739] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/13/2020] [Indexed: 01/02/2023] Open
Abstract
Heme (iron protoporphyrin IX) is a well-known prosthetic group for enzymes involved in metabolic pathways such as oxygen transport and electron transfer through the mitochondrial respiratory chain. However, heme has also been shown to be an important regulatory molecule (as "labile" heme) for diverse processes such as translation, kinase activity, and transcription in mammals, yeast, and bacteria. Taking advantage of a yeast strain deficient for heme production that enabled controlled modulation and monitoring of labile heme levels, here we investigated the role of labile heme in the regulation of mitochondrial biogenesis. This process is regulated by the HAP complex in yeast. Using several biochemical assays along with EM and epifluorescence microscopy, to the best of our knowledge, we show for the first time that cellular labile heme is critical for the post-translational regulation of HAP complex activity, most likely through the stability of the transcriptional co-activator Hap4p. Consequently, we found that labile heme regulates mitochondrial biogenesis and cell growth. The findings of our work highlight a new mechanism in the regulation of mitochondrial biogenesis by cellular metabolites.
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Affiliation(s)
- Cyrielle L Bouchez
- CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France.,Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France
| | - Edgar D Yoboue
- CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France.,Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France
| | - Livier E de la Rosa Vargas
- CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France.,Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France
| | - Bénédicte Salin
- CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France.,Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France
| | - Sylvain Cuvellier
- CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France.,Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France
| | - Michel Rigoulet
- CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France.,Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France
| | - Stéphane Duvezin-Caubet
- CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France.,Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France
| | - Anne Devin
- CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France .,Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France
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35
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De novo biosynthesis of 8-hydroxyoctanoic acid via a medium-chain length specific fatty acid synthase and cytochrome P450 in Saccharomyces cerevisiae. Metab Eng Commun 2019; 10:e00111. [PMID: 31867212 PMCID: PMC6906673 DOI: 10.1016/j.mec.2019.e00111] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 11/29/2022] Open
Abstract
Terminally hydroxylated fatty acids or dicarboxylic acids are industrially relevant compounds with broad applications. Here, we present the proof of principle for the de novo biosynthesis of 8-hydroxyoctanoic acid from glucose and ethanol in the yeast Saccharomyces cerevisiae. Toxicity tests with medium-chain length ω-hydroxy fatty acids and dicarboxylic acids revealed little or no growth impairments on yeast cultures even at higher concentrations. The ability of various heterologous cytochrome P450 enzymes in combination with their cognate reductases for ω-hydroxylation of externally fed octanoic acid were compared. Finally, the most efficient P450 enzyme system was expressed in a yeast strain, whose fatty acid synthase was engineered for octanoic acid production, resulting in de novo biosynthesis of 8-hydroxyoctanoic acid up to 3 mg/l. Accumulation of octanoic acid revealed that cytochromes P450 activities were limiting 8-hydroxyoctanoic acid synthesis. The hydroxylation of both externally added and intracellularly produced octanoic acid was strongly dependent on the carbon source used, with ethanol being preferred. We further identified the availability of heme, a cofactor needed for P450 activity, as a limiting factor of 8-hydroxyoctanoic acid biosynthesis. Low toxic effects of medium-chain ω-hydroxy fatty acids on yeast cells . Systematic comparison of cytochrome P450 enzyme activities on octanoic acid . De novo biosynthesis of 8-hydroxyoctanoic acid . Improvement of cytochrome P450 activity with ethanol or by addition of hemin .
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36
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Duvigneau JC, Esterbauer H, Kozlov AV. Role of Heme Oxygenase as a Modulator of Heme-Mediated Pathways. Antioxidants (Basel) 2019; 8:antiox8100475. [PMID: 31614577 PMCID: PMC6827082 DOI: 10.3390/antiox8100475] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/27/2019] [Accepted: 10/07/2019] [Indexed: 02/07/2023] Open
Abstract
The heme oxygenase (HO) system is essential for heme and iron homeostasis and necessary for adaptation to cell stress. HO degrades heme to biliverdin (BV), carbon monoxide (CO) and ferrous iron. Although mostly beneficial, the HO reaction can also produce deleterious effects, predominantly attributed to excessive product formation. Underrated so far is, however, that HO may exert effects additionally via modulation of the cellular heme levels. Heme, besides being an often-quoted generator of oxidative stress, plays also an important role as a signaling molecule. Heme controls the anti-oxidative defense, circadian rhythms, activity of ion channels, glucose utilization, erythropoiesis, and macrophage function. This broad spectrum of effects depends on its interaction with proteins ranging from transcription factors to enzymes. In degrading heme, HO has the potential to exert effects also via modulation of heme-mediated pathways. In this review, we will discuss the multitude of pathways regulated by heme to enlarge the view on HO and its role in cell physiology. We will further highlight the contribution of HO to pathophysiology, which results from a dysregulated balance between heme and the degradation products formed by HO.
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Affiliation(s)
- J Catharina Duvigneau
- Institute for Medical Biochemistry, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria.
| | - Harald Esterbauer
- Department of Laboratory Medicine, Medical University of Vienna, 1210 Vienna, Austria.
| | - Andrey V Kozlov
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, 1200 Vienna, Austria.
- Laboratory of Navigational Redox Lipidomics, Department of Human Pathology, IM Sechenov Moscow State Medical University, 119992 Moscow, Russia.
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37
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Lindahl PA. A comprehensive mechanistic model of iron metabolism in Saccharomyces cerevisiae. Metallomics 2019; 11:1779-1799. [PMID: 31531508 DOI: 10.1039/c9mt00199a] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ironome of budding yeast (circa 2019) consists of approximately 139 proteins and 5 nonproteinaceous species. These proteins were grouped according to location in the cell, type of iron center(s), and cellular function. The resulting 27 groups were used, along with an additional 13 nonprotein components, to develop a mesoscale mechanistic model that describes the import, trafficking, metallation, and regulation of iron within growing yeast cells. The model was designed to be simultaneously mutually autocatalytic and mutually autoinhibitory - a property called autocatinhibitory that should be most realistic for simulating cellular biochemical processes. The model was assessed at the systems' level. General conclusions are presented, including a new perspective on understanding regulatory mechanisms in cellular systems. Some unsettled issues are described. This model, once fully developed, has the potential to mimic the phenotype (at a coarse-grain level) of all iron-related genetic mutations in this simple and well-studied eukaryote.
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Affiliation(s)
- Paul A Lindahl
- Departments of Chemistry and of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-3255, USA.
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38
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Guaragnella N, Coyne LP, Chen XJ, Giannattasio S. Mitochondria-cytosol-nucleus crosstalk: learning from Saccharomyces cerevisiae. FEMS Yeast Res 2019; 18:5066171. [PMID: 30165482 DOI: 10.1093/femsyr/foy088] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/02/2018] [Indexed: 12/16/2022] Open
Abstract
Mitochondria are key cell organelles with a prominent role in both energetic metabolism and the maintenance of cellular homeostasis. Since mitochondria harbor their own genome, which encodes a limited number of proteins critical for oxidative phosphorylation and protein translation, their function and biogenesis strictly depend upon nuclear control. The yeast Saccharomyces cerevisiae has been a unique model for understanding mitochondrial DNA organization and inheritance as well as for deciphering the process of assembly of mitochondrial components. In the last three decades, yeast also provided a powerful tool for unveiling the communication network that coordinates the functions of the nucleus, the cytosol and mitochondria. This crosstalk regulates how cells respond to extra- and intracellular changes either to maintain cellular homeostasis or to activate cell death. This review is focused on the key pathways that mediate nucleus-cytosol-mitochondria communications through both transcriptional regulation and proteostatic signaling. We aim to highlight yeast that likely continues to serve as a productive model organism for mitochondrial research in the years to come.
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Affiliation(s)
- Nicoletta Guaragnella
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Via Amendola 165/A, 70126 Bari, Italy
| | - Liam P Coyne
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
| | - Xin Jie Chen
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
| | - Sergio Giannattasio
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Via Amendola 165/A, 70126 Bari, Italy
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39
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Bu P, Nagar S, Bhagwat M, Kaur P, Shah A, Zeng J, Vancurova I, Vancura A. DNA damage response activates respiration and thereby enlarges dNTP pools to promote cell survival in budding yeast. J Biol Chem 2019; 294:9771-9786. [PMID: 31073026 DOI: 10.1074/jbc.ra118.007266] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/30/2019] [Indexed: 12/13/2022] Open
Abstract
The DNA damage response (DDR) is an evolutionarily conserved process essential for cell survival. Previously, we found that decreased histone expression induces mitochondrial respiration, raising the question whether the DDR also stimulates respiration. Here, using oxygen consumption and ATP assays, RT-qPCR and ChIP-qPCR methods, and dNTP analyses, we show that DDR activation in the budding yeast Saccharomyces cerevisiae, either by genetic manipulation or by growth in the presence of genotoxic chemicals, induces respiration. We observed that this induction is conferred by reduced transcription of histone genes and globally decreased DNA nucleosome occupancy. This globally altered chromatin structure increased the expression of genes encoding enzymes of tricarboxylic acid cycle, electron transport chain, oxidative phosphorylation, elevated oxygen consumption, and ATP synthesis. The elevated ATP levels resulting from DDR-stimulated respiration drove enlargement of dNTP pools; cells with a defect in respiration failed to increase dNTP synthesis and exhibited reduced fitness in the presence of DNA damage. Together, our results reveal an unexpected connection between respiration and the DDR and indicate that the benefit of increased dNTP synthesis in the face of DNA damage outweighs possible cellular damage due to increased oxygen metabolism.
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Affiliation(s)
- Pengli Bu
- From the Departments of Biological Sciences and
| | | | | | | | - Ankita Shah
- Pharmaceutical Sciences, St. John's University, Queens, New York 11439
| | - Joey Zeng
- From the Departments of Biological Sciences and
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40
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Huang J, Ma Z, Zhong G, Sheppard DC, Lu L, Zhang S. The mitochondrial thiamine pyrophosphate transporter TptA promotes adaptation to low iron conditions and virulence in fungal pathogen Aspergillus fumigatus. Virulence 2019; 10:234-247. [PMID: 30880633 PMCID: PMC6527022 DOI: 10.1080/21505594.2019.1596505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Aspergillus fumigatus is the most prevalent airborne fungal pathogen that causes invasive fungal infections in immunosuppressed individuals. Adaptation to iron limited conditions is crucial for A. fumigatus virulence. To identify novel genes that play roles in adaptation to low iron conditions we performed an insertional mutagenesis screen in A. fumigatus. Using this approach, we identified the tptA gene in A. fumigatus, which shares homology with the Saccharomyces cerevisiae thiamine pyrophosphate (ThPP) transporter encoding gene tpc1. Heterologous expression of tpc1 in the tptA deletion mutant completely restored the ThPP auxotrophy phenotype, suggesting that Tpc1 and TptA are functional orthologues. Importantly, TptA was required for adaptation to low iron conditions in A. fumigatus. The ΔtptA mutant had decreased resistance to the iron chelator bathophenanthroline disulfonate (BPS) with severe growth defects. Moreover, loss of tptA decreased the expression of hapX, which is a major transcription factor indispensable for adaptation to iron starvation in A. fumigatus. Overexpression of hapX in the ΔtptA strain greatly rescued the growth defect and siderophore production by A. fumigatus in iron-depleted conditions. Mutagenesis experiments demonstrated that the conserved residues related to ThPP uptake in TptA were also required for low iron adaptation. Furthermore, TptA-mediated adaptation to low iron conditions was found to be dependent on carbon sources. Finally, loss of tptA resulted in the attenuation of virulence in a murine model of aspergillosis. Taken together, this study demonstrated that the mitochondrial ThPP transporter TptA promotes low iron adaptation and virulence in A. fumigatus.
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Affiliation(s)
- Jingjing Huang
- a Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences , Nanjing Normal University , Nanjing , China
| | - Zhihua Ma
- a Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences , Nanjing Normal University , Nanjing , China
| | - Guowei Zhong
- b Department of Hygiene Analysis and Detection, School of Public Health , Nanjing Medical University , Nanjing , China
| | - Donald C Sheppard
- c Departments of Medicine, Microbiology & Immunology , McGill University , Montréal , QC , Canada.,d Infectious Diseases and Immunity in Global Health Program , Research Institute of the McGill University Health Centre , Montreal , QC , Canada
| | - Ling Lu
- a Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences , Nanjing Normal University , Nanjing , China
| | - Shizhu Zhang
- a Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences , Nanjing Normal University , Nanjing , China
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41
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Zhu XM, Zhang XX, Cheng RT, Yu HL, Yuan RS, Bu XL, Xu J, Ao P, Chen YC, Xu MJ. Dynamical modelling of secondary metabolism and metabolic switches in Streptomyces xiamenensis 318. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190418. [PMID: 31183155 PMCID: PMC6502367 DOI: 10.1098/rsos.190418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
The production of secondary metabolites, while important for bioengineering purposes, presents a paradox in itself. Though widely existing in plants and bacteria, they have no definite physiological roles. Yet in both native habitats and laboratories, their production appears robust and follows apparent metabolic switches. We show in this work that the enzyme-catalysed process may improve the metabolic stability of the cells. The latter can be responsible for the overall metabolic behaviours such as dynamic metabolic landscape, metabolic switches and robustness, which can in turn affect the genetic formation of the organism in question. Mangrove-derived Streptomyces xiamenensis 318, with a relatively compact genome for secondary metabolism, is used as a model organism in our investigation. Integrated studies via kinetic metabolic modelling, transcriptase measurements and metabolic profiling were performed on this strain. Our results demonstrate that the secondary metabolites increase the metabolic fitness of the organism via stabilizing the underlying metabolic network. And the fluxes directing to NADH, NADPH, acetyl-CoA and glutamate provide the key switches for the overall and secondary metabolism. The information may be helpful for improving the xiamenmycin production on the strain.
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Affiliation(s)
- Xiao-Mei Zhu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
- Shanghai Center for Quantitative Life Sciences and Physics Department, Shanghai University, Shanghai 200444, People's Republic of China
| | - Xing-Xing Zhang
- Shanghai Center for Quantitative Life Sciences and Physics Department, Shanghai University, Shanghai 200444, People's Republic of China
| | - Run-Tan Cheng
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
| | - He-Lin Yu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
| | - Ruo-Shi Yuan
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
| | - Xu-Liang Bu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
- School of Oceanography, State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Jun Xu
- School of Oceanography, State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Ping Ao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
- Shanghai Center for Quantitative Life Sciences and Physics Department, Shanghai University, Shanghai 200444, People's Republic of China
| | - Yong-Cong Chen
- Shanghai Center for Quantitative Life Sciences and Physics Department, Shanghai University, Shanghai 200444, People's Republic of China
| | - Min-Juan Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
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42
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Donegan RK, Moore CM, Hanna DA, Reddi AR. Handling heme: The mechanisms underlying the movement of heme within and between cells. Free Radic Biol Med 2019; 133:88-100. [PMID: 30092350 PMCID: PMC6363905 DOI: 10.1016/j.freeradbiomed.2018.08.005] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 02/02/2023]
Abstract
Heme is an essential cofactor and signaling molecule required for virtually all aerobic life. However, excess heme is cytotoxic. Therefore, heme must be safely transported and trafficked from the site of synthesis in the mitochondria or uptake at the cell surface, to hemoproteins in most subcellular compartments. While heme synthesis and degradation are relatively well characterized, little is known about how heme is trafficked and transported throughout the cell. Herein, we review eukaryotic heme transport, trafficking, and mobilization, with a focus on factors that regulate bioavailable heme. We also highlight the role of gasotransmitters and small molecules in heme mobilization and bioavailability, and heme trafficking at the host-pathogen interface.
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Affiliation(s)
- Rebecca K Donegan
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Courtney M Moore
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - David A Hanna
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Amit R Reddi
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, United States; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States; Parker Petit Institute for Bioengineering & Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, United States.
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43
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da Fonseca-Pereira P, Neri-Silva R, Cavalcanti JHF, Brito DS, Weber APM, Araújo WL, Nunes-Nesi A. Data-Mining Bioinformatics: Connecting Adenylate Transport and Metabolic Responses to Stress. TRENDS IN PLANT SCIENCE 2018; 23:961-974. [PMID: 30287161 DOI: 10.1016/j.tplants.2018.09.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/30/2018] [Accepted: 09/07/2018] [Indexed: 06/08/2023]
Abstract
Adenine nucleotides are essential in countless processes within the cellular metabolism. In plants, ATP is mainly produced in chloroplasts and mitochondria through photophosphorylation and oxidative phosphorylation, respectively. Thus, efficient adenylate transport systems are required for intracellular energy partitioning between the cell organelles. Adenylate carriers present in different subcellular compartments have been previously identified and biochemically characterized in plants. Here, by using data-mining bioinformatics tools, we propose how, and to what extent, these carriers integrate energy metabolism within a plant cell under different environmental conditions. We demonstrate that the expression pattern of the corresponding genes is variable under different environmental conditions, suggesting that specific adenylate carriers have distinct and nonredundant functions in plants.
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Affiliation(s)
- Paula da Fonseca-Pereira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil; These authors contributed equally to this work
| | - Roberto Neri-Silva
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil; These authors contributed equally to this work
| | - João Henrique F Cavalcanti
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil; Max-Panck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Danielle S Brito
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-Universität, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil; Max-Panck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.
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44
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Hanna DA, Hu R, Kim H, Martinez-Guzman O, Torres MP, Reddi AR. Heme bioavailability and signaling in response to stress in yeast cells. J Biol Chem 2018; 293:12378-12393. [PMID: 29921585 DOI: 10.1074/jbc.ra118.002125] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 06/15/2018] [Indexed: 12/28/2022] Open
Abstract
Protoheme (hereafter referred to as heme) is an essential cellular cofactor and signaling molecule that is also potentially cytotoxic. To mitigate heme toxicity, heme synthesis and degradation are tightly coupled to heme utilization in order to limit the intracellular concentration of "free" heme. Such a model, however, would suggest that a readily accessible steady-state, bioavailable labile heme (LH) pool is not required for supporting heme-dependent processes. Using the yeast Saccharomyces cerevisiae as a model and fluorescent heme sensors, site-specific heme chelators, and molecular genetic approaches, we found here that 1) yeast cells preferentially use LH in heme-depleted conditions; 2) sequestration of cytosolic LH suppresses heme signaling; and 3) lead (Pb2+) stress contributes to a decrease in total heme, but an increase in LH, which correlates with increased heme signaling. We also observed that the proteasome is involved in the regulation of the LH pool and that loss of proteasomal activity sensitizes cells to Pb2+ effects on heme homeostasis. Overall, these findings suggest an important role for LH in supporting heme-dependent functions in yeast physiology.
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Affiliation(s)
| | - Rebecca Hu
- From the School of Chemistry and Biochemistry
| | - Hyojung Kim
- From the School of Chemistry and Biochemistry.,School of Biological Sciences, and
| | | | - Matthew P Torres
- School of Biological Sciences, and.,Parker Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Amit R Reddi
- From the School of Chemistry and Biochemistry, .,Parker Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332
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45
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Increased mitochondrial respiration promotes survival from endoplasmic reticulum stress. Cell Death Differ 2018; 26:487-501. [PMID: 29795335 DOI: 10.1038/s41418-018-0133-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 04/20/2018] [Accepted: 05/06/2018] [Indexed: 12/17/2022] Open
Abstract
Protein misfolding in the endoplasmic reticulum (ER) is accompanied by adaptive cellular responses to promote cell survival. We now show that activation of mitochondrial respiration is a critical component of an adaptive ER stress response, requiring the unfolded protein response (UPR) sensor Ire1, and also calcium signaling via calcineurin. In yeast and mammalian cells lacking Ire1 or calcineurin, respiratory activation is impaired in response to ER stress; accumulation of mitochondrial reactive oxygen species (ROS) triggers cell death as abrogation of ROS by antioxidants or loss of the electron transport chain (in yeast) can rescue cells from death. Significantly, cells are rescued from ER stress-induced death by mitochondrial uncoupling by CCCP to increase O2 consumption (and increase the efficiency of electron transfer). Remarkably, genetic and pharmacologic strategies to promote mitochondrial biogenesis and increase O2 consumption also alleviate ER stress-mediated ROS and death in yeast and mammalian cells. Moreover, in a yeast genetic screen, three mitochondrial proteins Mrx9, Mrm1, and Aim19 that increase mitochondrial biogenesis were identified as high copy suppressors of ER stress-mediated cell death. Our results show that enhanced mitochondrial biogenesis, linked to improved efficiency of the electron transport chain, is a powerful strategy to block ROS accumulation and promote cell survival during ER stress in eukaryotic cells.
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Tran Nguyen Hoang P, Ko JK, Gong G, Um Y, Lee SM. Genomic and phenotypic characterization of a refactored xylose-utilizing Saccharomyces cerevisiae strain for lignocellulosic biofuel production. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:268. [PMID: 30288173 PMCID: PMC6162923 DOI: 10.1186/s13068-018-1269-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/21/2018] [Indexed: 05/12/2023]
Abstract
BACKGROUND Engineered strains of Saccharomyces cerevisiae have significantly improved the prospects of biorefinery by improving the bioconversion yields in lignocellulosic bioethanol production and expanding the product profiles to include advanced biofuels and chemicals. However, the lignocellulosic biorefinery concept has not been fully applied using engineered strains in which either xylose utilization or advanced biofuel/chemical production pathways have been upgraded separately. Specifically, high-performance xylose-fermenting strains have rarely been employed as advanced biofuel and chemical production platforms and require further engineering to expand their product profiles. RESULTS In this study, we refactored a high-performance xylose-fermenting S. cerevisiae that could potentially serve as a platform strain for advanced biofuels and biochemical production. Through combinatorial CRISPR-Cas9-mediated rational and evolutionary engineering, we obtained a newly refactored isomerase-based xylose-fermenting strain, XUSE, that demonstrated efficient conversion of xylose into ethanol with a high yield of 0.43 g/g. In addition, XUSE exhibited the simultaneous fermentation of glucose and xylose with negligible glucose inhibition, indicating the potential of this isomerase-based xylose-utilizing strain for lignocellulosic biorefinery. The genomic and transcriptomic analysis of XUSE revealed beneficial mutations and changes in gene expression that are responsible for the enhanced xylose fermentation performance of XUSE. CONCLUSIONS In this study, we developed a high-performance xylose-fermenting S. cerevisiae strain, XUSE, with high ethanol yield and negligible glucose inhibition. Understanding the genomic and transcriptomic characteristics of XUSE revealed isomerase-based engineering strategies for improved xylose fermentation in S. cerevisiae. With high xylose fermentation performance and room for further engineering, XUSE could serve as a promising platform strain for lignocellulosic biorefinery.
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Affiliation(s)
- Phuong Tran Nguyen Hoang
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
- Division of Energy and Environment Technology, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
| | - Ja Kyong Ko
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
| | - Gyeongtaek Gong
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
- Division of Energy and Environment Technology, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
- Division of Energy and Environment Technology, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
- Green School, Korea University, Seoul, 02841 Republic of Korea
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