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Horvath A, Janapala Y, Woodward K, Mahmud S, Cleynen A, Gardiner E, Hannan R, Eyras E, Preiss T, Shirokikh N. Comprehensive translational profiling and STE AI uncover rapid control of protein biosynthesis during cell stress. Nucleic Acids Res 2024; 52:7925-7946. [PMID: 38721779 PMCID: PMC11260467 DOI: 10.1093/nar/gkae365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/21/2024] [Accepted: 04/25/2024] [Indexed: 07/23/2024] Open
Abstract
Translational control is important in all life, but it remains a challenge to accurately quantify. When ribosomes translate messenger (m)RNA into proteins, they attach to the mRNA in series, forming poly(ribo)somes, and can co-localize. Here, we computationally model new types of co-localized ribosomal complexes on mRNA and identify them using enhanced translation complex profile sequencing (eTCP-seq) based on rapid in vivo crosslinking. We detect long disome footprints outside regions of non-random elongation stalls and show these are linked to translation initiation and protein biosynthesis rates. We subject footprints of disomes and other translation complexes to artificial intelligence (AI) analysis and construct a new, accurate and self-normalized measure of translation, termed stochastic translation efficiency (STE). We then apply STE to investigate rapid changes to mRNA translation in yeast undergoing glucose depletion. Importantly, we show that, well beyond tagging elongation stalls, footprints of co-localized ribosomes provide rich insight into translational mechanisms, polysome dynamics and topology. STE AI ranks cellular mRNAs by absolute translation rates under given conditions, can assist in identifying its control elements and will facilitate the development of next-generation synthetic biology designs and mRNA-based therapeutics.
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Affiliation(s)
- Attila Horvath
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
| | - Yoshika Janapala
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
| | - Katrina Woodward
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
| | - Shafi Mahmud
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
| | - Alice Cleynen
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
- Institut Montpelliérain Alexander Grothendieck, Université de Montpellier, CNRS, Montpellier, France
| | - Elizabeth E Gardiner
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The National Platelet Research and Referral Centre, The Australian National University, Canberra, ACT 2601, Australia
| | - Ross D Hannan
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3010, Australia
- Peter MacCallum Cancer Centre, Melbourne 3000, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Australia
- School of Biomedical Sciences, University of Queensland, St Lucia 4067, Australia
| | - Eduardo Eyras
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Centre for Computational Biomedical Sciences, The Australian National University, Canberra, ACT 2601, Australia
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Preiss
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Nikolay E Shirokikh
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
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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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Alfatah M, Lim JJJ, Zhang Y, Naaz A, Cheng TYN, Yogasundaram S, Faidzinn NA, Lin JJ, Eisenhaber B, Eisenhaber F. Uncharacterized yeast gene YBR238C, an effector of TORC1 signaling in a mitochondrial feedback loop, accelerates cellular aging via HAP4- and RMD9-dependent mechanisms. eLife 2024; 12:RP92178. [PMID: 38713053 PMCID: PMC11076046 DOI: 10.7554/elife.92178] [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] [Indexed: 05/08/2024] Open
Abstract
Uncovering the regulators of cellular aging will unravel the complexity of aging biology and identify potential therapeutic interventions to delay the onset and progress of chronic, aging-related diseases. In this work, we systematically compared genesets involved in regulating the lifespan of Saccharomyces cerevisiae (a powerful model organism to study the cellular aging of humans) and those with expression changes under rapamycin treatment. Among the functionally uncharacterized genes in the overlap set, YBR238C stood out as the only one downregulated by rapamycin and with an increased chronological and replicative lifespan upon deletion. We show that YBR238C and its paralog RMD9 oppositely affect mitochondria and aging. YBR238C deletion increases the cellular lifespan by enhancing mitochondrial function. Its overexpression accelerates cellular aging via mitochondrial dysfunction. We find that the phenotypic effect of YBR238C is largely explained by HAP4- and RMD9-dependent mechanisms. Furthermore, we find that genetic- or chemical-based induction of mitochondrial dysfunction increases TORC1 (Target of Rapamycin Complex 1) activity that, subsequently, accelerates cellular aging. Notably, TORC1 inhibition by rapamycin (or deletion of YBR238C) improves the shortened lifespan under these mitochondrial dysfunction conditions in yeast and human cells. The growth of mutant cells (a proxy of TORC1 activity) with enhanced mitochondrial function is sensitive to rapamycin whereas the growth of defective mitochondrial mutants is largely resistant to rapamycin compared to wild type. Our findings demonstrate a feedback loop between TORC1 and mitochondria (the TORC1-MItochondria-TORC1 (TOMITO) signaling process) that regulates cellular aging processes. Hereby, YBR238C is an effector of TORC1 modulating mitochondrial function.
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Affiliation(s)
- Mohammad Alfatah
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Jolyn Jia Jia Lim
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Yizhong Zhang
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Arshia Naaz
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Trishia Yi Ning Cheng
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Sonia Yogasundaram
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Nashrul Afiq Faidzinn
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Jovian Jing Lin
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- LASA – Lausitz Advanced Scientific Applications gGmbHWeißwasserGermany
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- LASA – Lausitz Advanced Scientific Applications gGmbHWeißwasserGermany
- School of Biological Sciences (SBS), Nanyang Technological University (NTU)SingaporeSingapore
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Lewis AG, Carmichael L, Wang RY, Gibney PA. Characterizing a panel of amino acid auxotrophs under auxotrophic starvation conditions. Yeast 2024; 41:5-18. [PMID: 37997284 DOI: 10.1002/yea.3910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/20/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
Auxotrophic strains starving for their cognate nutrient, termed auxotrophic starvation, are characterized by a shorter lifespan, higher glucose wasting phenotype, and inability to accomplish cell cycle arrest when compared to a "natural starvation," where a cell is starving for natural environmental growth-limiting nutrients such as phosphate. Since evidence of this physiological response is limited to only a subset of auxotrophs, we evaluated a panel of auxotrophic mutants to determine whether these responses are characteristic of a broader range of amino acid auxotrophs. Based on the starvation survival kinetics, the panel of strains was grouped into three categories-short-lived strains, strains with survival similar to a prototrophic wild type strain, and long-lived strains. Among the short-lived strains, we observed that the tyrosine, asparagine, threonine, and aspartic acid auxotrophs rapidly decline in viability, with all strains unable to arrest cell cycle progression. The three basic amino acid auxotrophs had a survival similar to a prototrophic strain starving in minimal media. The leucine, tryptophan, methionine, and cysteine auxotrophs displayed the longest lifespan. We also demonstrate how the phenomenon of glucose wasting is limited to only a subset of the tested auxotrophs, namely the asparagine, leucine, and lysine auxotrophs. Furthermore, we observed pleiotropic phenotypes associated with a subgroup of auxotrophs, highlighting the importance of considering unintended phenotypic effects when using auxotrophic strains especially in chronological aging experiments.
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Affiliation(s)
- Alisha G Lewis
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Laurin Carmichael
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Rebecca Y Wang
- Calico Life Sciences LLC, South San Francisco, California, USA
| | - Patrick A Gibney
- Department of Food Science, Cornell University, Ithaca, New York, USA
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Liang J, Tang H, Snyder LF, Youngstrom CE, He BZ. Divergence of TORC1-mediated stress response leads to novel acquired stress resistance in a pathogenic yeast. PLoS Pathog 2023; 19:e1011748. [PMID: 37871123 PMCID: PMC10621968 DOI: 10.1371/journal.ppat.1011748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/02/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023] Open
Abstract
Acquired stress resistance (ASR) enables organisms to prepare for environmental changes that occur after an initial stressor. However, the genetic basis for ASR and how the underlying network evolved remain poorly understood. In this study, we discovered that a short phosphate starvation induces oxidative stress response (OSR) genes in the pathogenic yeast C. glabrata and protects it against a severe H2O2 stress; the same treatment, however, provides little benefit in the low pathogenic-potential relative, S. cerevisiae. This ASR involves the same transcription factors (TFs) as the OSR, but with different combinatorial logics. We show that Target-of-Rapamycin Complex 1 (TORC1) is differentially inhibited by phosphate starvation in the two species and contributes to the ASR via its proximal effector, Sch9. Therefore, evolution of the phosphate starvation-induced ASR involves the rewiring of TORC1's response to phosphate limitation and the repurposing of TF-target gene networks for the OSR using new regulatory logics.
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Affiliation(s)
- Jinye Liang
- Department of Biology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Hanxi Tang
- Department of Biology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Lindsey F. Snyder
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, Iowa, United States of America
| | | | - Bin Z. He
- Department of Biology, The University of Iowa, Iowa City, Iowa, United States of America
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, Iowa, United States of America
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6
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Liang J, Tang H, Snyder LF, Youngstrom CE, He BZ. Divergence of TORC1-mediated Stress Response Leads to Novel Acquired Stress Resistance in a Pathogenic Yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.20.545716. [PMID: 37781605 PMCID: PMC10541095 DOI: 10.1101/2023.06.20.545716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Acquired stress resistance (ASR) enables organisms to prepare for environmental changes that occur after an initial stressor. However, the genetic basis for ASR and how the underlying network evolved remain poorly understood. In this study, we discovered that a short phosphate starvation induces oxidative stress response (OSR) genes in the pathogenic yeast C. glabrata and protects it against a severe H2O2 stress; the same treatment, however, provides little benefit in the low pathogenic-potential relative, S. cerevisiae. This ASR involves the same transcription factors (TFs) as the OSR, but with different combinatorial logics. We show that Target-of-Rapamycin Complex 1 (TORC1) is differentially inhibited by phosphate starvation in the two species and contributes to the ASR via its proximal effector, Sch9. Therefore, evolution of the phosphate starvation-induced ASR involves the rewiring of TORC1's response to phosphate limitation and the repurposing of TF-target gene networks for the OSR using new regulatory logics.
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Affiliation(s)
- Jinye Liang
- Biology Department, The University of Iowa, Iowa City, IA 52242
| | - Hanxi Tang
- Biology Department, The University of Iowa, Iowa City, IA 52242
| | - Lindsey F. Snyder
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, IA 52242
| | | | - Bin Z. He
- Biology Department, The University of Iowa, Iowa City, IA 52242
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Sun S, Tranchina D, Gresham D. Parallel proteomics and phosphoproteomics defines starvation signal specific processes in cell quiescence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551843. [PMID: 37577636 PMCID: PMC10418281 DOI: 10.1101/2023.08.03.551843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Cells arrest growth and enter a quiescent state upon nutrient deprivation. However, the molecular processes by which cells respond to different starvation signals to regulate exit from the cell division cycle and initiation of quiescence remains poorly understood. To study the role of protein expression and signaling in quiescence we combined temporal profiling of the proteome and phosphoproteome using stable isotope labeling with amino acids in cell culture (SILAC) in Saccharomyces cerevisiae (budding yeast). We find that carbon and phosphorus starvation signals activate quiescence through largely distinct remodeling of the proteome and phosphoproteome. However, increased expression of mitochondrial proteins is associated with quiescence establishment in response to both starvation signals. Deletion of the putative quiescence regulator RIM15, which encodes a serine-threonine kinase, results in reduced survival of cells starved for phosphorus and nitrogen, but not carbon. However, we identified common protein phosphorylation roles for RIM15 in quiescence that are enriched for RNA metabolism and translation. We also find evidence for RIM15-mediated phosphorylation of some targets, including IGO1, prior to starvation consistent with a functional role for RIM15 in proliferative cells. Finally, our results reveal widespread catabolism of amino acids in response to nitrogen starvation, indicating widespread amino acid recycling via salvage pathways in conditions lacking environmental nitrogen. Our study defines an expanded quiescent proteome and phosphoproteome in yeast, and highlights the multiple coordinated molecular processes at the level of protein expression and phosphorylation that are required for quiescence.
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Affiliation(s)
- Siyu Sun
- Center for Genomics and Systems Biology
- Department of Biology, New York University, New York, NY, 10003, USA
| | - Daniel Tranchina
- Department of Biology, New York University, New York, NY, 10003, USA
- Courant Institute of Mathematical Sciences, New York University, New York, NY, 10003, USA
| | - David Gresham
- Center for Genomics and Systems Biology
- Department of Biology, New York University, New York, NY, 10003, USA
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Fang W, Jiang L, Zhu Y, Yang S, Qiu H, Cheng J, Liang Q, Tu ZC, Ye C. Methionine restriction constrains lipoylation and activates mitochondria for nitrogenic synthesis of amino acids. Nat Commun 2023; 14:2504. [PMID: 37130856 PMCID: PMC10154411 DOI: 10.1038/s41467-023-38289-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 04/21/2023] [Indexed: 05/04/2023] Open
Abstract
Methionine restriction (MR) provides metabolic benefits in many organisms. However, mechanisms underlying the MR-induced effect remain incompletely understood. Here, we show in the budding yeast S. cerevisiae that MR relays a signal of S-adenosylmethionine (SAM) deprivation to adapt bioenergetic mitochondria to nitrogenic anabolism. In particular, decreases in cellular SAM constrain lipoate metabolism and protein lipoylation required for the operation of the tricarboxylic acid (TCA) cycle in the mitochondria, leading to incomplete glucose oxidation with an exit of acetyl-CoA and α-ketoglutarate from the TCA cycle to the syntheses of amino acids, such as arginine and leucine. This mitochondrial response achieves a trade-off between energy metabolism and nitrogenic anabolism, which serves as an effector mechanism promoting cell survival under MR.
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Affiliation(s)
- Wen Fang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Liu Jiang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Yibing Zhu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Sen Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Hong Qiu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Jiou Cheng
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Qingxi Liang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- National R&D Center for Freshwater Fish Processing, Jiangxi Normal University, Nanchang, 330022, China
| | - Zong-Cai Tu
- National R&D Center for Freshwater Fish Processing, Jiangxi Normal University, Nanchang, 330022, China
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, China
| | - Cunqi Ye
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China.
- Kidney Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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Waite KA, Roelofs J. Proteasome granule formation is regulated through mitochondrial respiration and kinase signaling. J Cell Sci 2022; 135:jcs259778. [PMID: 35975718 PMCID: PMC9482347 DOI: 10.1242/jcs.259778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 08/03/2022] [Indexed: 11/20/2022] Open
Abstract
In the yeast Saccharomyces cerevisiae, proteasomes are enriched in cell nuclei, in which they execute important cellular functions. Nutrient stress can change this localization, indicating that proteasomes respond to the metabolic state of the cell. However, the signals that connect these processes remain poorly understood. Carbon starvation triggers a reversible translocation of proteasomes to cytosolic condensates known as proteasome storage granules. Surprisingly, we observed strongly reduced levels of proteasome granules when cells had active cellular respiration prior to starvation. This suggests that the mitochondrial activity of cells is a determining factor in the response of proteasomes to carbon starvation. Consistent with this, upon inhibition of mitochondrial function, we observed that proteasomes relocalize to granules. These links between proteasomes and metabolism involve specific signaling pathways, as we identified a mitogen-activated protein kinase (MAPK) cascade that is critical to the formation of proteasome granules after respiratory growth but not following glycolytic growth. Furthermore, the yeast homolog of AMP kinase, Snf1, is important for proteasome granule formation induced by mitochondrial inhibitors, but it is dispensable for granule formation following carbon starvation. We propose a model in which mitochondrial activity promotes nuclear localization of the proteasome. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
| | - Jeroen Roelofs
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, 3901 Rainbow Blvd., HLSIC 1077, Kansas City, KS 66160-7421, USA
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Askri H, Akrouti I, Rourou S, Kallèl H. Production, purification, and characterization of recombinant rabies virus glycoprotein expressed in PichiaPink™ yeast. BIOTECHNOLOGY REPORTS 2022; 35:e00736. [PMID: 35646619 PMCID: PMC9130087 DOI: 10.1016/j.btre.2022.e00736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/08/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022]
Abstract
The rabies virus glycoprotein was produced in the Pichia pastoris production strains PichiaPink™ . Different carbon sources were found able to support the RABV-G expression under the control of the constitutive GAP promoter. Culture parameters such as oxygen supply, pH or growth rate can affect the yield and the quality of the produced RABV-G. The purified RABV-G was found correctly glycosylated and able to mediate trimeric oligomerization.
The commonly used host for industrial production of recombinant proteins Pichia pastoris, has been used in this work to produce the rabies virus glycoprotein (RABV-G). To allow a constitutive expression and the secretion of the expressed recombinant RABV-G, the PichiaPink™ commercialized expression vectors were modified to contain the constitutive GAP promoter and the α secretion signal sequences. Recombinant PichiaPink™ strains co-expressing the RABV-G and the protein chaperone PDI, have been then generated and screened for the best producer clone. The influence of seven carbon sources on the expression of the RABV-G, has been studied under different culture conditions in shake flask culture. An incubation temperature of 30°C under an agitation rate of 250 rpm in a filling volume of 10:1 flask/culture volume ratio were the optimal conditions for the RABV-G production in shake flask for all screened carbon sources. A bioreactor Fed batch culture has been then carried using glycerol and glucose as they were good carbon sources for cell growth and RABV-G production in shake flask scale. Cells were grown on glycerol during the batch phase then fed with glycerol or glucose defined solutions, a final RABV-G concentration of 2.7 µg/l was obtained with a specific product yield (YP/X) of 0.032 and 0.06 µg/g(DCW) respectively. The use of semi-defined feeding solution enhanced the production and the YP/X to 12.9 µg/l and 0.135 µg/g(DCW) respectively. However, the high cell density favored by these carbon sources resulted in oxygen limitation which influenced the glycosylation pattern of the secreted RABV-G. Alternatively, the use of sucrose as substrate for RABV-G production in large scale culture, resulted in less biomass production and a YP/X of 0.310 µg/g(DCW) was obtained. A cation exchange chromatography was then used for RABV-G purification as one step method. The purified protein was correctly folded and glycosylated and able to adopt trimeric conformation. The knowledges gained through this work offer a valuable insight into the bioprocess design of RABV-G production in Pichia pastoris to obtain a correctly folded protein which can be used during an immunization proposal for subunit Rabies vaccine development.
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Kokina A, Tanilas K, Ozolina Z, Pleiko K, Shvirksts K, Vamza I, Liepins J. Purine Auxotrophic Starvation Evokes Phenotype Similar to Stationary Phase Cells in Budding Yeast. J Fungi (Basel) 2021; 8:29. [PMID: 35049969 PMCID: PMC8780165 DOI: 10.3390/jof8010029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/20/2021] [Accepted: 12/24/2021] [Indexed: 11/25/2022] Open
Abstract
Purine auxotrophy is an abundant trait among eukaryotic parasites and a typical marker for many budding yeast strains. Supplementation with an additional purine source (such as adenine) is necessary to cultivate these strains. If not supplied in adequate amounts, purine starvation sets in. We explored purine starvation effects in a model organism, a budding yeast Saccharomyces cerevisiae ade8 knockout, at the level of cellular morphology, central carbon metabolism, and global transcriptome. We observed that purine-starved cells stopped their cycle in G1/G0 state and accumulated trehalose, and the intracellular concentration of AXP decreased, but adenylate charge remained stable. Cells became tolerant to severe environmental stresses. Intracellular RNA concentration decreased, and massive downregulation of ribosomal biosynthesis genes occurred. We proved that the expression of new proteins during purine starvation is critical for cells to attain stress tolerance phenotype Msn2/4p targets are upregulated in purine-starved cells when compared to cells cultivated in purine-rich media. The overall transcriptomic response to purine starvation resembles that of stationary phase cells. Our results demonstrate that the induction of a strong stress resistance phenotype in budding yeast can be caused not only by natural starvation, but also starvation for metabolic intermediates, such as purines.
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Affiliation(s)
- Agnese Kokina
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia; (Z.O.); (K.S.); (I.V.); (J.L.)
| | - Kristel Tanilas
- Center of Food and Fermentation Technologies, Akadeemia Tee 15A, 12618 Tallinn, Estonia;
| | - Zane Ozolina
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia; (Z.O.); (K.S.); (I.V.); (J.L.)
| | - Karlis Pleiko
- Faculty of Medicine, University of Latvia, Jelgavas 3, LV-1004 Riga, Latvia;
- Laboratory of Precision and Nanomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Karlis Shvirksts
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia; (Z.O.); (K.S.); (I.V.); (J.L.)
| | - Ilze Vamza
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia; (Z.O.); (K.S.); (I.V.); (J.L.)
| | - Janis Liepins
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia; (Z.O.); (K.S.); (I.V.); (J.L.)
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12
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Differential Physiological Prerequisites and Gene Expression Profiles of Conidial Anastomosis Tube and Germ Tube Formation in Colletotrichum gloeosporioides. J Fungi (Basel) 2021; 7:jof7070509. [PMID: 34202250 PMCID: PMC8306183 DOI: 10.3390/jof7070509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 02/07/2023] Open
Abstract
The conidia of a hemibiotrophic fungus, Colletotrichum gloeosporioides, can conventionally form a germ tube (GT) and develop into a fungal colony. Under certain conditions, they tend to get connected through a conidial anastomosis tube (CAT) to share the nutrients. CAT fusion is believed to be responsible for the generation of genetic variations in few asexual fungi, which appears problematic for effective fungal disease management. The physiological and molecular requirements underlying the GT formation versus CAT fusion remained underexplored. In the present study, we have deciphered the physiological prerequisites for GT formation versus CAT fusion in C. gloeosporioides. GT formation occurred at a high frequency in the presence of nutrients, while CAT fusion was found to be higher in the absence of nutrients. Younger conidia were found to form GT efficiently, while older conidia preferentially formed CAT. Whole transcriptome analysis of GT and CAT revealed highly differential gene expression profiles, wherein 11,050 and 9786 genes were differentially expressed during GT formation and CAT fusion, respectively. A total of 1567 effector candidates were identified; out of them, 102 and 100 were uniquely expressed during GT formation and CAT fusion, respectively. Genes coding for cell wall degrading enzymes, germination, hyphal growth, host-fungus interaction, and virulence were highly upregulated during GT formation. Meanwhile, genes involved in stress response, cell wall remodeling, membrane transport, cytoskeleton, cell cycle, and cell rescue were highly upregulated during CAT fusion. To conclude, the GT formation and CAT fusion were found to be mutually exclusive processes, requiring differential physiological conditions and sets of DEGs in C. gloeosporioides. This study will help in understanding the basic CAT biology in emerging fungal model species of the genus Colletotrichum.
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13
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da Silva J, Honorato da Silva FL, Santos Ribeiro JE, Nóbrega de Melo DJ, Santos FA, Lucena de Medeiros L. Effect of supplementation, temperature and pH on carotenoids and lipids production by Rhodotorula mucilaginosa on sisal bagasse hydrolyzate. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101847] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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Hepowit NL, Pereira KN, Tumolo JM, Chazin WJ, MacGurn JA. Identification of ubiquitin Ser57 kinases regulating the oxidative stress response in yeast. eLife 2020; 9:58155. [PMID: 33074099 PMCID: PMC7647399 DOI: 10.7554/elife.58155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 10/18/2020] [Indexed: 01/26/2023] Open
Abstract
Ubiquitination regulates many different cellular processes, including protein quality control, membrane trafficking, and stress responses. The diversity of ubiquitin functions in the cell is partly due to its ability to form chains with distinct linkages that can alter the fate of substrate proteins in unique ways. The complexity of the ubiquitin code is further enhanced by post-translational modifications on ubiquitin itself, the biological functions of which are not well understood. Here, we present genetic and biochemical evidence that serine 57 (Ser57) phosphorylation of ubiquitin functions in stress responses in Saccharomyces cerevisiae, including the oxidative stress response. We also identify and characterize the first known Ser57 ubiquitin kinases in yeast and human cells, and we report that two Ser57 ubiquitin kinases regulate the oxidative stress response in yeast. These studies implicate ubiquitin phosphorylation at the Ser57 position as an important modifier of ubiquitin function, particularly in response to proteotoxic stress.
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Affiliation(s)
- Nathaniel L Hepowit
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States
| | - Kevin N Pereira
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States
| | - Jessica M Tumolo
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States
| | - Walter J Chazin
- Department of Biochemistry, Vanderbilt University, Nashville, United States
| | - Jason A MacGurn
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States
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15
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Santos SM, Laflin S, Broadway A, Burnet C, Hartheimer J, Rodgers J, Smith DL, Hartman JL. High-resolution yeast quiescence profiling in human-like media reveals complex influences of auxotrophy and nutrient availability. GeroScience 2020; 43:941-964. [PMID: 33015753 PMCID: PMC8110628 DOI: 10.1007/s11357-020-00265-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/03/2020] [Indexed: 12/15/2022] Open
Abstract
Yeast cells survive in stationary phase culture by entering quiescence, which is measured by colony-forming capacity upon nutrient re-exposure. Yeast chronological lifespan (CLS) studies, employing the comprehensive collection of gene knockout strains, have correlated weakly between independent laboratories, which is hypothesized to reflect differential interaction between the deleted genes, auxotrophy, media composition, and other assay conditions influencing quiescence. This hypothesis was investigated by high-throughput quiescence profiling of the parental prototrophic strain, from which the gene deletion strain libraries were constructed, and all possible auxotrophic allele combinations in that background. Defined media resembling human cell culture media promoted long-term quiescence and was used to assess effects of glucose, ammonium sulfate, auxotrophic nutrient availability, target of rapamycin signaling, and replication stress. Frequent, high-replicate measurements of colony-forming capacity from cultures aged past 60 days provided profiles of quiescence phenomena such as gasping and hormesis. Media acidification was assayed in parallel to assess correlation. Influences of leucine, methionine, glucose, and ammonium sulfate metabolism were clarified, and a role for lysine metabolism newly characterized, while histidine and uracil perturbations had less impact. Interactions occurred between glucose, ammonium sulfate, auxotrophy, auxotrophic nutrient limitation, aeration, TOR signaling, and/or replication stress. Weak correlation existed between media acidification and maintenance of quiescence. In summary, experimental factors, uncontrolled across previous genome-wide yeast CLS studies, influence quiescence and interact extensively, revealing quiescence as a complex metabolic and developmental process that should be studied in a prototrophic context, omitting ammonium sulfate from defined media, and employing highly replicable protocols.
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Affiliation(s)
- Sean M Santos
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Samantha Laflin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Audrie Broadway
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Cosby Burnet
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Joline Hartheimer
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - John Rodgers
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Daniel L Smith
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - John L Hartman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
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16
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Metabolic excretion associated with nutrient-growth dysregulation promotes the rapid evolution of an overt metabolic defect. PLoS Biol 2020; 18:e3000757. [PMID: 32833957 PMCID: PMC7470746 DOI: 10.1371/journal.pbio.3000757] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 09/03/2020] [Accepted: 07/20/2020] [Indexed: 01/19/2023] Open
Abstract
In eukaryotes, conserved mechanisms ensure that cell growth is coordinated with nutrient availability. Overactive growth during nutrient limitation ("nutrient-growth dysregulation") can lead to rapid cell death. Here, we demonstrate that cells can adapt to nutrient-growth dysregulation by evolving major metabolic defects. Specifically, when yeast lysine-auxotrophic mutant lys- encountered lysine limitation, an evolutionarily novel stress, cells suffered nutrient-growth dysregulation. A subpopulation repeatedly evolved to lose the ability to synthesize organosulfurs (lys-orgS-). Organosulfurs, mainly reduced glutathione (GSH) and GSH conjugates, were released by lys- cells during lysine limitation when growth was dysregulated, but not during glucose limitation when growth was regulated. Limiting organosulfurs conferred a frequency-dependent fitness advantage to lys-orgS- by eliciting a proper slow growth program, including autophagy. Thus, nutrient-growth dysregulation is associated with rapid organosulfur release, which enables the selection of organosulfur auxotrophy to better tune cell growth to the metabolic environment. We speculate that evolutionarily novel stresses can trigger atypical release of certain metabolites, setting the stage for the evolution of new ecological interactions.
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17
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Selective Eradication of Staphylococcus aureus by the Designer Genetically Programmed Yeast Biocontrol Agent. Antibiotics (Basel) 2020; 9:antibiotics9090527. [PMID: 32824911 PMCID: PMC7559405 DOI: 10.3390/antibiotics9090527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/07/2020] [Accepted: 08/18/2020] [Indexed: 12/29/2022] Open
Abstract
Staphylococcus aureus is a common human pathogen that is particularly often associated with antibiotic resistance. The eradication of this ubiquitous infectious agent from its ecological niches and contaminated surfaces is especially complicated by excessive biofilm formation and persisting cells, which evade the antibacterial activity of conventional antibiotics. Here, we present an alternative view of the problem of specific S. aureus eradication. The constitutive heterologous production of highly specific bacteriolytic protease lysostaphin in yeast Pichia pastoris provides an efficient biocontrol agent, specifically killing S. aureus in coculture. A yeast-based anti-S. aureus probiotic was efficient in a high range of temperatures and target-to-effector ratios, indicating its robustness and versatility in eliminating S. aureus cells. The efficient eradication of S. aureus by live lysostaphin-producing P. pastoris was achieved at high scales, providing a simple, biocompatible and cost-effective strategy for S. aureus lysis in bioproduction and surface decontamination. Future biomedical applications based on designer yeast biocontrol agents require evaluation in in vivo models. However, we believe that this strategy is very promising since it provides highly safe, efficient and selective genetically programmed probiotics and targeted biocontrol agents.
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18
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Wehrs M, Thompson MG, Banerjee D, Prahl JP, Morella NM, Barcelos CA, Moon J, Costello Z, Keasling JD, Shih PM, Tanjore D, Mukhopadhyay A. Investigation of Bar-seq as a method to study population dynamics of Saccharomyces cerevisiae deletion library during bioreactor cultivation. Microb Cell Fact 2020; 19:167. [PMID: 32811554 PMCID: PMC7437010 DOI: 10.1186/s12934-020-01423-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/11/2020] [Indexed: 12/15/2022] Open
Abstract
Background Despite the latest advancements in metabolic engineering for genome editing and characterization of host performance, the successful development of robust cell factories used for industrial bioprocesses and accurate prediction of the behavior of microbial systems, especially when shifting from laboratory-scale to industrial conditions, remains challenging. To increase the probability of success of a scale-up process, data obtained from thoroughly performed studies mirroring cellular responses to typical large-scale stimuli may be used to derive crucial information to better understand potential implications of large-scale cultivation on strain performance. This study assesses the feasibility to employ a barcoded yeast deletion library to assess genome-wide strain fitness across a simulated industrial fermentation regime and aims to understand the genetic basis of changes in strain physiology during industrial fermentation, and the corresponding roles these genes play in strain performance. Results We find that mutant population diversity is maintained through multiple seed trains, enabling large scale fermentation selective pressures to act upon the community. We identify specific deletion mutants that were enriched in all processes tested in this study, independent of the cultivation conditions, which include MCK1, RIM11, MRK1, and YGK3 that all encode homologues of mammalian glycogen synthase kinase 3 (GSK-3). Ecological analysis of beta diversity between all samples revealed significant population divergence over time and showed feed specific consequences of population structure. Further, we show that significant changes in the population diversity during fed-batch cultivations reflect the presence of significant stresses. Our observations indicate that, for this yeast deletion collection, the selection of the feeding scheme which affects the accumulation of the fermentative by-product ethanol impacts the diversity of the mutant pool to a higher degree as compared to the pH of the culture broth. The mutants that were lost during the time of most extreme population selection suggest that specific biological processes may be required to cope with these specific stresses. Conclusions Our results demonstrate the feasibility of Bar-seq to assess fermentation associated stresses in yeast populations under industrial conditions and to understand critical stages of a scale-up process where variability emerges, and selection pressure gets imposed. Overall our work highlights a promising avenue to identify genetic loci and biological stress responses required for fitness under industrial conditions.
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Affiliation(s)
- Maren Wehrs
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Mitchell G Thompson
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Deepanwita Banerjee
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Jan-Philip Prahl
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Norma M Morella
- Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Carolina A Barcelos
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Jadie Moon
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Zak Costello
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Department of Energy Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK 2970, Horsholm, Denmark.,Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Patrick M Shih
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Plant Biology, University of California-Davis, Davis, CA, 95616, USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA. .,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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19
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Bandara HMHN, Wood DLA, Vanwonterghem I, Hugenholtz P, Cheung BPK, Samaranayake LP. Fluconazole resistance in Candida albicans is induced by Pseudomonas aeruginosa quorum sensing. Sci Rep 2020; 10:7769. [PMID: 32385378 PMCID: PMC7211000 DOI: 10.1038/s41598-020-64761-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/22/2020] [Indexed: 12/16/2022] Open
Abstract
Microorganisms employ quorum sensing (QS) mechanisms to communicate with each other within microbial ecosystems. Emerging evidence suggests that intraspecies and interspecies QS plays an important role in antimicrobial resistance in microbial communities. However, the relationship between interkingdom QS and antimicrobial resistance is largely unknown. Here, we demonstrate that interkingdom QS interactions between a bacterium, Pseudomonas aeruginosa and a yeast, Candida albicans, induce the resistance of the latter to a widely used antifungal fluconazole. Phenotypic, transcriptomic, and proteomic analyses reveal that P. aeruginosa's main QS molecule, N-(3-Oxododecanoyl)-L-homoserine lactone, induces candidal resistance to fluconazole by reversing the antifungal's effect on the ergosterol biosynthesis pathway. Accessory resistance mechanisms including upregulation of C. albicans drug-efflux, regulation of oxidative stress response, and maintenance of cell membrane integrity, further confirm this phenomenon. These findings demonstrate that P. aeruginosa QS molecules may confer protection to neighboring yeasts against azoles, in turn strengthening their co-existence in hostile polymicrobial infection sites.
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Affiliation(s)
- H M H N Bandara
- Oral Microbiology, Bristol Dental School, University of Bristol, Lower Maudlin Street, Bristol, BS1 2LY, UK.
| | - D L A Wood
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - I Vanwonterghem
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - P Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - B P K Cheung
- Faculty of Dentistry, The University of Hong Kong, 34 Hospital Rd, Sai Ying Pun, Hong Kong SAR, China
| | - L P Samaranayake
- College of Dental Medicine, The University of Sharjah, P.O. Box, 27272, Sharjah, UAE
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20
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Proteomic Analysis of Saccharomyces cerevisiae Response to Oxidative Stress Mediated by Cocoa Polyphenols Extract. Molecules 2020; 25:molecules25030452. [PMID: 31973232 PMCID: PMC7037337 DOI: 10.3390/molecules25030452] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/16/2020] [Accepted: 01/20/2020] [Indexed: 12/13/2022] Open
Abstract
The present study addressed the protective effects against oxidative stress (OS) of a cocoa powder extract (CPEX) on the protein expression profile of S. cerevisiae. A proteomic analysis was performed after culture preincubation with CPEX either without stress (−OS) or under stress conditions (+OS) (5 mM of H2O2). LC-MS/MS identified 33 differentially expressed proteins (–OS: 14, +OS: 19) that were included By Gene Ontology analysis in biological processes: biosynthesis of amino acids, carbohydrate metabolism and reactive oxygen species metabolic process. In a gene-knockout strains study, eight proteins were identified as putative candidates for being involved in the protective mechanism of cocoa polyphenols against OS induced by H2O2. CPEX was able to exert its antioxidant activity in yeast mainly through the regulation of: (a) amino acids metabolism proteins by modulating the production of molecules with known antioxidant roles; (b) stress-responsive protein Yhb1, but we were unable to fully understand its down-regulation; (c) protein Prb1, which can act by clipping Histone H3 N-terminal tails that are related to cellular resistance to DNA damaging agents.
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21
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Ribeiro JES, Sant'Ana AMDS, Martini M, Sorce C, Andreucci A, Melo DJND, Silva FLHD. Rhodotorula glutinis cultivation on cassava wastewater for carotenoids and fatty acids generation. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101419] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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22
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Kokina A, Ozolina Z, Liepins J. Purine auxotrophy: Possible applications beyond genetic marker. Yeast 2019; 36:649-656. [PMID: 31334866 DOI: 10.1002/yea.3434] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/12/2019] [Accepted: 07/16/2019] [Indexed: 01/09/2023] Open
Abstract
Exploring new drug candidates or drug targets against many illnesses is necessary as "traditional" treatments lose their effectivity. Cancer and sicknesses caused by protozoan parasites are among these diseases. Cell purine metabolism is an important drug target. Theoretically, inhibiting purine metabolism could stop the proliferation of unwanted cells. Purine metabolism is similar across all eukaryotes. However, some medically important organisms or cell lines rely on their host purine metabolism. Protozoans causing malaria, leishmaniasis, or toxoplasmosis are purine auxotrophs. Some cancer forms have also lost the ability to synthesize purines de novo. Budding yeast can serve as an effective model for eukaryotic purine metabolism, and thus, purine auxotrophic strains could be an important tool. In this review, we present the common principles of purine metabolism in eukaryotes, effects of purine starvation in eukaryotic cells, and purine-starved Saccharomyces cerevisiae as a model for purine depletion-elicited metabolic states with applications in evolution studies and pharmacology. Purine auxotrophic yeast strains behave differently when growing in media with sufficient supplementation with adenine or in media depleted of adenine (starvation). In the latter, they undergo cell cycle arrest at G1/G0 and become stress resistant. Importantly, similar effects have also been observed among parasitic protozoans or cancer cells. We consider that studies on metabolic changes caused by purine auxotrophy could reveal new options for parasite or cancer therapy. Further, knowledge on phenotypic changes will improve the use of auxotrophic strains in high-throughput screening for primary drug candidates.
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Affiliation(s)
- Agnese Kokina
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Zane Ozolina
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Janis Liepins
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
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23
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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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24
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Sima S, Schmauder L, Richter K. Genome-wide analysis of yeast expression data based on a priori generated co-regulation cliques. MICROBIAL CELL 2019; 6:160-176. [PMID: 30854393 PMCID: PMC6402361 DOI: 10.15698/mic2019.03.671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
DNA microarrays are highly sensitive tools to evaluate the gene expression status of organismic samples and standardized array formats exist for many different sample types. Differential expression studies usually utilize the strongest upor downregulated genes to generate networks visualizing the relationships among these genes. To include all yeast genes in one analysis and to get broader information on all cellular responses, we test a priori input of predefined genome-wide expression cliques and subsequent statistical analysis of the expression data. To this end, we generate a set of 72 co-regulation cliques using the information from 3196 microarray experiments. The obtained cliques performed highly significant in gene ontology and transcription factor enrichment analyses. We then tested the clique set on individual microarray experiments reporting on responses to pheromone, glycerol versus glucose based growth and the cellular response to heat. In all cases a highly significant determination of affected expression cliques was possible based on their average expression differences, the positions of their genes within hit rankings (UpRegScore) or the enrichment of the Top200 hits in certain cliques. The 72 cliques were finally used to compare experiments, which reported on the transcriptional response to polyglutamine proteins of different lengths. Using the predefined clique set it is possible to identify with high sensitivity and good significance sample and condition specific changes to gene expression. We thus conclude that an analysis, starting with these 72 preformed expression cliques, can complement traditional microarray analyses by visualizing the entire response on a static genome-wide gene set.
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Affiliation(s)
- Siyuan Sima
- Center for integrated protein research at the Department of Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Lukas Schmauder
- Center for integrated protein research at the Department of Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Klaus Richter
- Center for integrated protein research at the Department of Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
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25
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Swamy KBS, Zhou N. Experimental evolution: its principles and applications in developing stress-tolerant yeasts. Appl Microbiol Biotechnol 2019; 103:2067-2077. [PMID: 30659332 DOI: 10.1007/s00253-019-09616-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/03/2019] [Accepted: 01/03/2019] [Indexed: 10/27/2022]
Abstract
Stress tolerance and resistance in industrial yeast strains are important attributes for cost-effective bioprocessing. The source of stress-tolerant yeasts ranges from extremophilic environments to laboratory engineered strains. However, industrial stress-tolerant yeasts are very rare in nature as the natural environment forces them to evolve traits that optimize survival and reproduction and not the ability to withstand harsh habitat-irrelevant industrial conditions. Experimental evolution is a frequent method used to uncover the mechanisms of evolution and microbial adaption towards environmental stresses. It optimizes biological systems by means of adaptation to environmental stresses and thus has immense power of development of robust stress-tolerant yeasts. This mini-review briefly outlines the basics and implications of evolution experiments and their applications to industrial biotechnology. This work is meant to serve as an introduction to those new to the field of experimental evolution, and as a guide to biologists working in the field of yeast stress response. Future perspectives of experimental evolution for potential biotechnological applications have also been elucidated.
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Affiliation(s)
| | - Nerve Zhou
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, P Bag 16, Palapye, Botswana
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26
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Talavera D, Kershaw CJ, Costello JL, Castelli LM, Rowe W, Sims PFG, Ashe MP, Grant CM, Pavitt GD, Hubbard SJ. Archetypal transcriptional blocks underpin yeast gene regulation in response to changes in growth conditions. Sci Rep 2018; 8:7949. [PMID: 29785040 PMCID: PMC5962585 DOI: 10.1038/s41598-018-26170-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 05/01/2018] [Indexed: 01/30/2023] Open
Abstract
The transcriptional responses of yeast cells to diverse stresses typically include gene activation and repression. Specific stress defense, citric acid cycle and oxidative phosphorylation genes are activated, whereas protein synthesis genes are coordinately repressed. This view was achieved from comparative transcriptomic experiments delineating sets of genes whose expression greatly changed with specific stresses. Less attention has been paid to the biological significance of 1) consistent, albeit modest, changes in RNA levels across multiple conditions, and 2) the global gene expression correlations observed when comparing numerous genome-wide studies. To address this, we performed a meta-analysis of 1379 microarray-based experiments in yeast, and identified 1388 blocks of RNAs whose expression changes correlate across multiple and diverse conditions. Many of these blocks represent sets of functionally-related RNAs that act in a coordinated fashion under normal and stress conditions, and map to global cell defense and growth responses. Subsequently, we used the blocks to analyze novel RNA-seq experiments, demonstrating their utility and confirming the conclusions drawn from the meta-analysis. Our results provide a new framework for understanding the biological significance of changes in gene expression: 'archetypal' transcriptional blocks that are regulated in a concerted fashion in response to external stimuli.
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Affiliation(s)
- David Talavera
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.
| | - Christopher J Kershaw
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Joseph L Costello
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.,Department of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Lydia M Castelli
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.,Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield, United Kingdom
| | - William Rowe
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.,Department of Chemistry, Loughborough University, Loughborough, United Kingdom
| | - Paul F G Sims
- Manchester Institute of Biotechnology (MIB), The University of Manchester, Manchester, United Kingdom
| | - Mark P Ashe
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Chris M Grant
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Graham D Pavitt
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.
| | - Simon J Hubbard
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.
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27
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Liu G, Yu L, Fang J, Hu CAA, Yin J, Ni H, Ren W, Duraipandiyan V, Chen S, Al-Dhabi NA, Yin Y. Methionine restriction on oxidative stress and immune response in dss-induced colitis mice. Oncotarget 2018; 8:44511-44520. [PMID: 28562346 PMCID: PMC5546498 DOI: 10.18632/oncotarget.17812] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 04/14/2017] [Indexed: 01/20/2023] Open
Abstract
A strong correlation exists between inflammatory bowel disease (IBD) and oxidative stress involving alterations of several key signaling pathways. It is known that methionine promotes reactive oxygen species (ROS) production; we therefore hypothesize that a methionine restriction diet would reduce ROS production, inflammatory responses, and the course of IBD. We generated a murine colitis model by dextran sodium sulfate (DSS) treatment and tested the effects of the methionine restriction diet. Forty-eight mice were randomly divided into four groups of equal size, which included a control (CON) group, an MR (methionine restriction diet) group, a DSS treated group and an MR-DSS treated group. Mice in the first two groups had unrestricted access to water for one week. Mice in the two DSS-treated groups had unrestricted access to 5% DSS solution supplied in the drinking water for the same period. Mice in the CON and DSS groups were given a basal diet, whereas mice in the MR-DSS and MR groups were fed a 0.14% MR diet. We found that DSS reduced daily weight gain, suppressed antioxidant enzyme expression, increased histopathology scores and activated NF-κB and nuclear factor erythroid 2-related factor 2/Kelch-like ECH-associated protein 1 (Nrf2/Keap1) signaling. We also showed that the MR diet upregulated catalase (CAT), superoxide dismutase (SOD), and glutathione peroxidase (GPx) activities, decreased myeloperoxidase (MPO), TNF-α and IL-1β, and reversed activation of the NF-κB signaling pathway in MR-DSS mice. Taken together, our results imply that the MR diet may be considered as an adjuvant in IBD therapeutics.
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Affiliation(s)
- Gang Liu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Lei Yu
- China Animal Disease Control Center, Beijing 102618, China
| | - Jun Fang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Chien-An Andy Hu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China.,Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine, Albuquerque, New Mexico 87131, USA
| | - Jie Yin
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Hengjia Ni
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Wenkai Ren
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Veeramuthu Duraipandiyan
- Addiriyah Research Chair for Environmental Studies, Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Shuai Chen
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Naif Abdullah Al-Dhabi
- Addiriyah Research Chair for Environmental Studies, Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Yulong Yin
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China.,College of Animal Science, South China Agricultural University, Guangzhou 510642, China.,Laboratory of Animal Nutrition and Human Health, School of Life Sciences, Hunan Normal University, Changsha 410081, China
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28
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Aluru M, McKinney T, Venero AKL, Choudhury S, Torres M. Mitogen-activated protein kinases, Fus3 and Kss1, regulate chronological lifespan in yeast. Aging (Albany NY) 2017; 9:2587-2609. [PMID: 29273704 PMCID: PMC5764394 DOI: 10.18632/aging.101350] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 12/11/2017] [Indexed: 04/19/2023]
Abstract
Using a systems-based approach, we have identified several genes not previously evaluated for a role(s) in chronological aging. Here, we have thoroughly investigated the chronological lifespan (CLS) of three of these genes (FUS3, KSS1 and HOG1) and their protein products, each of which have well-defined cell signaling roles in young cells. The importance of FUS3 and KSS1 in CLS are largely unknown and analyzed here for the first time. Using both qualitative and quantitative CLS assays, we show that deletion of any of the three MAPK's increases yeast lifespan. Furthermore, combined deletion of any MAPK and TOR1, most prominently fus3Δ/tor1Δ, produces a two-stage CLS response ending in lifespan increase greater than that of tor1Δ. Similar effects are achieved upon endogenous expression of a non-activatable form of Fus3. We speculate that the autophagy-promoting role of FUS3, which is inherently antagonistic to the role of TOR1, may in part be responsible for the differential aging phenotype of fus3Δ/tor1Δ. Consistent with this notion we show that nitrogen starvation, which promotes autophagy by deactivating Tor1, results in decreased CLS if FUS3 is deleted. Taken together, these results reveal a previously unrealized effect of mating-specific MAPKs in the chronological lifespan of yeast.
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Affiliation(s)
- Maneesha Aluru
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA 30332, USA
| | - Tori McKinney
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA 30332, USA
| | | | - Shilpa Choudhury
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA 30332, USA
| | - Matthew Torres
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA 30332, USA
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29
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Mosbach A, Edel D, Farmer AD, Widdison S, Barchietto T, Dietrich RA, Corran A, Scalliet G. Anilinopyrimidine Resistance in Botrytis cinerea Is Linked to Mitochondrial Function. Front Microbiol 2017; 8:2361. [PMID: 29250050 PMCID: PMC5714876 DOI: 10.3389/fmicb.2017.02361] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/15/2017] [Indexed: 12/11/2022] Open
Abstract
Crop protection anilinopyrimidine (AP) fungicides were introduced more than 20 years ago for the control of a range of diseases caused by ascomycete plant pathogens, and in particular for the control of gray mold caused by Botrytis cinerea. Although early mode of action studies suggested an inhibition of methionine biosynthesis, the molecular target of this class of fungicides was never fully clarified. Despite AP-specific resistance having been described in B. cinerea field isolates and in multiple other targeted species, the underlying resistance mechanisms were unknown. It was therefore expected that the genetic characterization of resistance mechanisms would permit the identification of the molecular target of these fungicides. In order to explore the widest range of possible resistance mechanisms, AP-resistant B. cinerea UV laboratory mutants were generated and the mutations conferring resistance were determined by combining whole-genome sequencing and reverse genetics. Genetic mapping from a cross between a resistant field isolate and a sensitive reference isolate was used in parallel and led to the identification of an additional molecular determinant not found from the characterized UV mutant collection. Together, these two approaches enabled the characterization of an unrivaled diversity of resistance mechanisms. In total, we report the elucidation of resistance-conferring mutations within nine individual genes, two of which are responsible for almost all instances of AP resistance in the field. All identified resistance-conferring genes encode proteins that are involved in mitochondrial processes, suggesting that APs primarily target the mitochondria. The functions of these genes and their possible interactions are discussed in the context of the potential mode of action for this important class of fungicides.
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Affiliation(s)
| | | | - Andrew D. Farmer
- National Center for Genome Resources, Santa Fe, NM, United States
- Syngenta Biotechnology Inc., Research Triangle Park, NC, United States
| | - Stephanie Widdison
- Syngenta Jealott's Hill International Research Centre, Bracknell, United Kingdom
| | | | | | - Andy Corran
- Syngenta Jealott's Hill International Research Centre, Bracknell, United Kingdom
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30
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Martin-Perez M, Villén J. Determinants and Regulation of Protein Turnover in Yeast. Cell Syst 2017; 5:283-294.e5. [PMID: 28918244 DOI: 10.1016/j.cels.2017.08.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 04/02/2017] [Accepted: 08/09/2017] [Indexed: 10/18/2022]
Abstract
Protein turnover maintains the recycling needs of the proteome, and its malfunction has been linked to aging and age-related diseases. However, not all proteins turnover equally, and the factors that contribute to accelerate or slow down turnover are mostly unknown. We measured turnover rates for 3,160 proteins in exponentially growing yeast and analyzed their dependence on physical, functional, and genetic properties. We found that functional characteristics, including protein localization, complex membership, and connectivity, have greater effect on turnover than sequence elements. We also found that protein turnover and mRNA turnover are correlated. Analysis under nutrient perturbation and osmotic stress revealed that protein turnover highly depends on cellular state and is faster when proteins are being actively used. Finally, stress-induced changes in protein and transcript abundance correlated with changes in protein turnover. This study provides a resource of protein turnover rates and principles to understand the recycling needs of the proteome under basal conditions and perturbation.
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Affiliation(s)
- Miguel Martin-Perez
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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31
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Tao J, Wu QY, Ma YC, Chen YL, Zou CG. Antioxidant response is a protective mechanism against nutrient deprivation in C. elegans. Sci Rep 2017; 7:43547. [PMID: 28230214 PMCID: PMC5322524 DOI: 10.1038/srep43547] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 01/27/2017] [Indexed: 12/21/2022] Open
Abstract
Animals often experience periods of nutrient deprivation; however, the molecular mechanisms by which animals survive starvation remain largely unknown. In the nematode Caenorhabditis elegans, the nuclear receptor DAF-12 acts as a dietary and environmental sensor to orchestrate diverse aspects of development, metabolism, and reproduction. Recently, we have reported that DAF-12 together with co-repressor DIN-1S is required for starvation tolerance by promoting fat mobilization. In this report, we found that genetic inactivation of the DAF-12 signaling promoted the production of reactive oxygen species (ROS) during starvation. ROS mediated systemic necrosis, thereby inducing organismal death. The DAF-12/DIN-1S complex up-regulated the expression of antioxidant genes during starvation. The antioxidant enzyme GST-4 in turn suppressed ROS formation, thereby conferring worm survival. Our findings highlight the importance of antioxidant response in starvation tolerance and provide a novel insight into multiple organisms survive and adapt to periods of nutrient deprivation.
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Affiliation(s)
- Jun Tao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan 650091, China
| | - Qin-Yi Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan 650091, China
| | - Yi-Cheng Ma
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan 650091, China
| | - Yuan-Li Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan 650091, China
| | - Cheng-Gang Zou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan 650091, China
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32
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Kuno T, Hirayama-Kurogi M, Ito S, Ohtsuki S. Effect of Intestinal Flora on Protein Expression of Drug-Metabolizing Enzymes and Transporters in the Liver and Kidney of Germ-Free and Antibiotics-Treated Mice. Mol Pharm 2016; 13:2691-701. [DOI: 10.1021/acs.molpharmaceut.6b00259] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Takuya Kuno
- Department
of Pharmaceutical Microbiology, Graduate School of Pharmaceutical
Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Department
of Drug Metabolism and Pharmacokinetics, Drug Safety Research Center,
Tokushima Research Institute, Otsuka Pharmaceutical Co., Ltd., 463-10 Kagasuno, Kawauchi-cho, Tokushima, Tokushima 771-0192, Japan
| | - Mio Hirayama-Kurogi
- Department
of Pharmaceutical Microbiology, Graduate School of Pharmaceutical
Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Department
of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- AMED-CREST, Japan
Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda, Tokyo 100-0004, Japan
| | - Shingo Ito
- Department
of Pharmaceutical Microbiology, Graduate School of Pharmaceutical
Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Department
of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- AMED-CREST, Japan
Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda, Tokyo 100-0004, Japan
| | - Sumio Ohtsuki
- Department
of Pharmaceutical Microbiology, Graduate School of Pharmaceutical
Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Department
of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- AMED-CREST, Japan
Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda, Tokyo 100-0004, Japan
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33
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Campbell K, Vowinckel J, Ralser M. Cell-to-cell heterogeneity emerges as consequence of metabolic cooperation in a synthetic yeast community. Biotechnol J 2016; 11:1169-78. [PMID: 27312776 PMCID: PMC5031204 DOI: 10.1002/biot.201500301] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 06/06/2016] [Accepted: 06/08/2016] [Indexed: 12/20/2022]
Abstract
Cells that grow together respond heterogeneously to stress even when they are genetically similar. Metabolism, a key determinant of cellular stress tolerance, may be one source of this phenotypic heterogeneity, however, this relationship is largely unclear. We used self‐establishing metabolically cooperating (SeMeCo) yeast communities, in which metabolic cooperation can be followed on the basis of genotype, as a model to dissect the role of metabolic cooperation in single‐cell heterogeneity. Cells within SeMeCo communities showed to be highly heterogeneous in their stress tolerance, while the survival of each cell under heat or oxidative stress, was strongly determined by its metabolic specialization. This heterogeneity emerged for all metabolite exchange interactions studied (histidine, leucine, uracil, and methionine) as well as oxidant (H2O2, diamide) and heat stress treatments. In contrast, the SeMeCo community collectively showed to be similarly tolerant to stress as wild‐type populations. Moreover, stress heterogeneity did not establish as sole consequence of metabolic genotype (auxotrophic background) of the single cell, but was observed only for cells that cooperated according to their metabolic capacity. We therefore conclude that phenotypic heterogeneity and cell to cell differences in stress tolerance are emergent properties when cells cooperate in metabolism.
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Affiliation(s)
- Kate Campbell
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Jakob Vowinckel
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom. .,The Francis Crick Institute, Mill Hill laboratory, London, United Kingdom.
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34
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Mesquita VA, Machado MD, Silva CF, Soares EV. Influence of the metabolic state on the tolerance of Pichia kudriavzevii to heavy metals. J Basic Microbiol 2016; 56:1244-1251. [PMID: 27283353 DOI: 10.1002/jobm.201600232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 05/22/2016] [Indexed: 11/09/2022]
Abstract
This work aims to examine the influence of the metabolic state of the yeast Pichia kudriavzevii on the susceptibility to a metals mixture (5 mg L-1 Cd, 10 mg L-1 Pb, and 5 mg L-1 Zn). Cells exposed to the metals mixture in the presence of 25 mmol L-1 glucose displayed a higher loss of membrane integrity and proliferation capacity, compared to cells incubated in the absence of glucose. The analysis of the effect of individual metals revealed that glucose increased the toxic effect of Cd marginally, and of Pb significantly. The increased susceptibility to heavy metals due to glucose was attenuated in the simultaneous presence of a mitochondrial respiration inhibitor such as sodium azide (NaN3 ). ATP-depleted yeast cells, resulting from treatment with the non-metabolizable glucose analogue 2-deoxy-d-glucose, showed an increased susceptibility to heavy metals mixture. Pre-incubation of yeast cells with 1 or 1.5 mmol L-1 Ca2+ reduced significantly (P < 0.05) the loss of membrane integrity induced by the metals mixture. These findings contribute to the understanding of metals mechanisms of toxicity in the non-conventional yeast P. kudriavzevii.
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Affiliation(s)
- Vanessa A Mesquita
- Bioengineering Laboratory-CIETI, Department of Chemical Engineering, ISEP-School of Engineering of Polytechnic Institute of Porto, Porto, 4200-072, Portugal.,Department of Biology, Federal University of Lavras (UFLA), Lavras, Minas Gerais, Brazil
| | - Manuela D Machado
- Bioengineering Laboratory-CIETI, Department of Chemical Engineering, ISEP-School of Engineering of Polytechnic Institute of Porto, Porto, 4200-072, Portugal.,CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
| | - Cristina F Silva
- Department of Biology, Federal University of Lavras (UFLA), Lavras, Minas Gerais, Brazil
| | - Eduardo V Soares
- Bioengineering Laboratory-CIETI, Department of Chemical Engineering, ISEP-School of Engineering of Polytechnic Institute of Porto, Porto, 4200-072, Portugal.,CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
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35
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McIsaac RS, Lewis KN, Gibney PA, Buffenstein R. From yeast to human: exploring the comparative biology of methionine restriction in extending eukaryotic life span. Ann N Y Acad Sci 2016; 1363:155-70. [DOI: 10.1111/nyas.13032] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/25/2016] [Accepted: 01/27/2016] [Indexed: 12/19/2022]
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36
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Lee BC, Kaya A, Gladyshev VN. Methionine restriction and life-span control. Ann N Y Acad Sci 2015; 1363:116-24. [PMID: 26663138 DOI: 10.1111/nyas.12973] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Revised: 10/10/2015] [Accepted: 10/22/2015] [Indexed: 01/04/2023]
Abstract
Dietary restriction (DR) without malnutrition is associated with longevity in various organisms. However, it has also been shown that reduced calorie intake is often ineffective in extending life span. Selecting optimal dietary regimens for DR studies is complicated, as the same regimen may lead to different outcomes depending on genotype and environmental factors. Recent studies suggested that interventions such as moderate protein restriction with or without adequate nutrition (e.g., particular amino acids or carbohydrates) may have additional beneficial effects mediated by certain metabolic and hormonal factors implicated in the biology of aging, regardless of total calorie intake. In particular, it was shown that restriction of a single amino acid, methionine, can mimic the effects of DR and extend life span in various model organisms. We discuss the beneficial effects of a methionine-restricted diet, the molecular pathways involved, and the use of this regimen in longevity interventions.
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Affiliation(s)
- Byung Cheon Lee
- College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Alaattin Kaya
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
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37
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Imam S, Schäuble S, Valenzuela J, de Lomana ALG, Carter W, Price ND, Baliga NS. A refined genome-scale reconstruction of Chlamydomonas metabolism provides a platform for systems-level analyses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:1239-56. [PMID: 26485611 PMCID: PMC4715634 DOI: 10.1111/tpj.13059] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 09/30/2015] [Accepted: 10/09/2015] [Indexed: 05/11/2023]
Abstract
Microalgae have reemerged as organisms of prime biotechnological interest due to their ability to synthesize a suite of valuable chemicals. To harness the capabilities of these organisms, we need a comprehensive systems-level understanding of their metabolism, which can be fundamentally achieved through large-scale mechanistic models of metabolism. In this study, we present a revised and significantly improved genome-scale metabolic model for the widely-studied microalga, Chlamydomonas reinhardtii. The model, iCre1355, represents a major advance over previous models, both in content and predictive power. iCre1355 encompasses a broad range of metabolic functions encoded across the nuclear, chloroplast and mitochondrial genomes accounting for 1355 genes (1460 transcripts), 2394 and 1133 metabolites. We found improved performance over the previous metabolic model based on comparisons of predictive accuracy across 306 phenotypes (from 81 mutants), lipid yield analysis and growth rates derived from chemostat-grown cells (under three conditions). Measurement of macronutrient uptake revealed carbon and phosphate to be good predictors of growth rate, while nitrogen consumption appeared to be in excess. We analyzed high-resolution time series transcriptomics data using iCre1355 to uncover dynamic pathway-level changes that occur in response to nitrogen starvation and changes in light intensity. This approach enabled accurate prediction of growth rates, the cessation of growth and accumulation of triacylglycerols during nitrogen starvation, and the temporal response of different growth-associated pathways to increased light intensity. Thus, iCre1355 represents an experimentally validated genome-scale reconstruction of C. reinhardtii metabolism that should serve as a useful resource for studying the metabolic processes of this and related microalgae.
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Affiliation(s)
- Saheed Imam
- Institute for Systems Biology, Seattle, WA, USA
| | - Sascha Schäuble
- Institute for Systems Biology, Seattle, WA, USA
- Jena University Language & Information Engineering (JULIE) Lab, Friedrich-Schiller-University Jena, Jena, Germany
- Research Group Theoretical Systems Biology, Friedrich-Schiller-University Jena, 07743 Jena, Germany
| | | | | | | | - Nathan D. Price
- Institute for Systems Biology, Seattle, WA, USA
- Departments of Bioengineering and Computer Science & Engineering, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Nitin S. Baliga
- Institute for Systems Biology, Seattle, WA, USA
- Departments of Biology and Microbiology, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
- Lawrence Berkeley National Lab, Berkeley, CA
- Correspondence: Nitin S. Baliga, Institute for Systems Biology, 401 Terry Ave N., Seattle, WA 98109, Telephone: 206.732.1266, Fax: 206.732.1299,
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Linder RA, Seidl F, Ha K, Ehrenreich IM. The complex genetic and molecular basis of a model quantitative trait. Mol Biol Cell 2015; 27:209-18. [PMID: 26510497 PMCID: PMC4694759 DOI: 10.1091/mbc.e15-06-0408] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/21/2015] [Indexed: 02/02/2023] Open
Abstract
Sixty‐four genomic loci and seven genes that contribute to heritable variation in a model quantitative trait—resistance to oxidative stress—are identified across three yeast strains. The high‐resolution understanding of this phenotype provides new insight into the genetic and molecular basis of quantitative traits. Quantitative traits are often influenced by many loci with small effects. Identifying most of these loci and resolving them to specific genes or genetic variants is challenging. Yet, achieving such a detailed understanding of quantitative traits is important, as it can improve our knowledge of the genetic and molecular basis of heritable phenotypic variation. In this study, we use a genetic mapping strategy that involves recurrent backcrossing with phenotypic selection to obtain new insights into an ecologically, industrially, and medically relevant quantitative trait—tolerance of oxidative stress, as measured based on resistance to hydrogen peroxide. We examine the genetic basis of hydrogen peroxide resistance in three related yeast crosses and detect 64 distinct genomic loci that likely influence the trait. By precisely resolving or cloning a number of these loci, we demonstrate that a broad spectrum of cellular processes contribute to hydrogen peroxide resistance, including DNA repair, scavenging of reactive oxygen species, stress-induced MAPK signaling, translation, and water transport. Consistent with the complex genetic and molecular basis of hydrogen peroxide resistance, we show two examples where multiple distinct causal genetic variants underlie what appears to be a single locus. Our results improve understanding of the genetic and molecular basis of a highly complex, model quantitative trait.
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Affiliation(s)
- Robert A Linder
- Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089-2910
| | - Fabian Seidl
- Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089-2910
| | - Kimberly Ha
- Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089-2910
| | - Ian M Ehrenreich
- Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089-2910
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Chowdhury R, Chowdhury A, Maranas CD. Using Gene Essentiality and Synthetic Lethality Information to Correct Yeast and CHO Cell Genome-Scale Models. Metabolites 2015; 5:536-70. [PMID: 26426067 PMCID: PMC4693185 DOI: 10.3390/metabo5040536] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 09/04/2015] [Accepted: 09/23/2015] [Indexed: 12/14/2022] Open
Abstract
Essentiality (ES) and Synthetic Lethality (SL) information identify combination of genes whose deletion inhibits cell growth. This information is important for both identifying drug targets for tumor and pathogenic bacteria suppression and for flagging and avoiding gene deletions that are non-viable in biotechnology. In this study, we performed a comprehensive ES and SL analysis of two important eukaryotic models (S. cerevisiae and CHO cells) using a bilevel optimization approach introduced earlier. Information gleaned from this study is used to propose specific model changes to remedy inconsistent with data model predictions. Even for the highly curated Yeast 7.11 model we identified 50 changes (metabolic and GPR) leading to the correct prediction of an additional 28% of essential genes and 36% of synthetic lethals along with a 53% reduction in the erroneous identification of essential genes. Due to the paucity of mutant growth phenotype data only 12 changes were made for the CHO 1.2 model leading to an additional correctly predicted 11 essential and eight non-essential genes. Overall, we find that CHO 1.2 was 76% less accurate than the Yeast 7.11 metabolic model in predicting essential genes. Based on this analysis, 14 (single and double deletion) maximally informative experiments are suggested to improve the CHO cell model by using information from a mouse metabolic model. This analysis demonstrates the importance of single and multiple knockout phenotypes in assessing and improving model reconstructions. The advent of techniques such as CRISPR opens the door for the global assessment of eukaryotic models.
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Affiliation(s)
- Ratul Chowdhury
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, PA 16802, USA.
| | - Anupam Chowdhury
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, PA 16802, USA.
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, PA 16802, USA.
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Comparative transcriptomic analysis reveals similarities and dissimilarities in Saccharomyces cerevisiae wine strains response to nitrogen availability. PLoS One 2015; 10:e0122709. [PMID: 25884705 PMCID: PMC4401569 DOI: 10.1371/journal.pone.0122709] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/12/2015] [Indexed: 11/19/2022] Open
Abstract
Nitrogen levels in grape-juices are of major importance in winemaking ensuring adequate yeast growth and fermentation performance. Here we used a comparative transcriptome analysis to uncover wine yeasts responses to nitrogen availability during fermentation. Gene expression was assessed in three genetically and phenotypically divergent commercial wine strains (CEG, VL1 and QA23), under low (67 mg/L) and high nitrogen (670 mg/L) regimes, at three time points during fermentation (12 h, 24 h and 96 h). Two-way ANOVA analysis of each fermentation condition led to the identification of genes whose expression was dependent on strain, fermentation stage and on the interaction of both factors. The high fermenter yeast strain QA23 was more clearly distinct from the other two strains, by differential expression of genes involved in flocculation, mitochondrial functions, energy generation and protein folding and stabilization. For all strains, higher transcriptional variability due to fermentation stage was seen in the high nitrogen fermentations. A positive correlation between maximum fermentation rate and the expression of genes involved in stress response was observed. The finding of common genes correlated with both fermentation activity and nitrogen up-take underlies the role of nitrogen on yeast fermentative fitness. The comparative analysis of genes differentially expressed between both fermentation conditions at 12 h, where the main difference was the level of nitrogen available, showed the highest variability amongst strains revealing strain-specific responses. Nevertheless, we were able to identify a small set of genes whose expression profiles can quantitatively assess the common response of the yeast strains to varying nitrogen conditions. The use of three contrasting yeast strains in gene expression analysis prompts the identification of more reliable, accurate and reproducible biomarkers that will facilitate the diagnosis of deficiency of this nutrient in the grape-musts and the development of strategies to optimize yeast performance in industrial fermentations.
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Barja G. The mitochondrial free radical theory of aging. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2015; 127:1-27. [PMID: 25149212 DOI: 10.1016/b978-0-12-394625-6.00001-5] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mitochondrial free radical theory of aging is reviewed. Only two parameters currently correlate with species longevity in the right sense: the mitochondrial rate of reactive oxygen species (mitROS) production and the degree of fatty acid unsaturation of tissue membranes. Both are low in long-lived animals. In addition, the best-known manipulation that extends longevity, dietary restriction, also decreases the rate of mitROS production and oxidative damage to mtDNA. The same occurs during protein restriction as well as during methionine restriction. These two manipulations also increase maximum longevity in rodents. The decrease in mitROS generation and oxidative stress that takes place in caloric restriction seems to be due to restriction of a single dietary substance: methionine. The information available supports a mitochondrial free radical theory of aging focused on low generation of endogenous damage and low sensitivity of membranes to oxidation in long-lived animals.
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Affiliation(s)
- Gustavo Barja
- Department of Animal Physiology II, Faculty of Biological Sciences, Complutense University, Madrid Spain
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42
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Systematic identification of signal integration by protein kinase A. Proc Natl Acad Sci U S A 2015; 112:4501-6. [PMID: 25831502 DOI: 10.1073/pnas.1409938112] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Cellular processes and homeostasis control in eukaryotic cells is achieved by the action of regulatory proteins such as protein kinase A (PKA). Although the outbound signals from PKA directed to processes such as metabolism, growth, and aging have been well charted, what regulates this conserved regulator remains to be systematically identified to understand how it coordinates biological processes. Using a yeast PKA reporter assay, we identified genes that influence PKA activity by measuring protein-protein interactions between the regulatory and the two catalytic subunits of the PKA complex in 3,726 yeast genetic-deletion backgrounds grown on two carbon sources. Overall, nearly 500 genes were found to be connected directly or indirectly to PKA regulation, including 80 core regulators, denoting a wide diversity of signals regulating PKA, within and beyond the described upstream linear pathways. PKA regulators span multiple processes, including the antagonistic autophagy and methionine biosynthesis pathways. Our results converge toward mechanisms of PKA posttranslational regulation by lysine acetylation, which is conserved between yeast and humans and that, we show, regulates protein complex formation in mammals and carbohydrate storage and aging in yeast. Taken together, these results show that the extent of PKA input matches with its output, because this kinase receives information from upstream and downstream processes, and highlight how biological processes are interconnected and coordinated by PKA.
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Gomez A, Gomez J, Torres ML, Naudi A, Mota-Martorell N, Pamplona R, Barja G. Cysteine dietary supplementation reverses the decrease in mitochondrial ROS production at complex I induced by methionine restriction. J Bioenerg Biomembr 2015; 47:199-208. [DOI: 10.1007/s10863-015-9608-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/05/2015] [Indexed: 01/24/2023]
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Prielhofer R, Cartwright SP, Graf AB, Valli M, Bill RM, Mattanovich D, Gasser B. Pichia pastoris regulates its gene-specific response to different carbon sources at the transcriptional, rather than the translational, level. BMC Genomics 2015; 16:167. [PMID: 25887254 PMCID: PMC4408588 DOI: 10.1186/s12864-015-1393-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 02/24/2015] [Indexed: 11/20/2022] Open
Abstract
Background The methylotrophic, Crabtree-negative yeast Pichia pastoris is widely used as a heterologous protein production host. Strong inducible promoters derived from methanol utilization genes or constitutive glycolytic promoters are typically used to drive gene expression. Notably, genes involved in methanol utilization are not only repressed by the presence of glucose, but also by glycerol. This unusual regulatory behavior prompted us to study the regulation of carbon substrate utilization in different bioprocess conditions on a genome wide scale. Results We performed microarray analysis on the total mRNA population as well as mRNA that had been fractionated according to ribosome occupancy. Translationally quiescent mRNAs were defined as being associated with single ribosomes (monosomes) and highly-translated mRNAs with multiple ribosomes (polysomes). We found that despite their lower growth rates, global translation was most active in methanol-grown P. pastoris cells, followed by excess glycerol- or glucose-grown cells. Transcript-specific translational responses were found to be minimal, while extensive transcriptional regulation was observed for cells grown on different carbon sources. Due to their respiratory metabolism, cells grown in excess glucose or glycerol had very similar expression profiles. Genes subject to glucose repression were mainly involved in the metabolism of alternative carbon sources including the control of glycerol uptake and metabolism. Peroxisomal and methanol utilization genes were confirmed to be subject to carbon substrate repression in excess glucose or glycerol, but were found to be strongly de-repressed in limiting glucose-conditions (as are often applied in fed batch cultivations) in addition to induction by methanol. Conclusions P. pastoris cells grown in excess glycerol or glucose have similar transcript profiles in contrast to S. cerevisiae cells, in which the transcriptional response to these carbon sources is very different. The main response to different growth conditions in P. pastoris is transcriptional; translational regulation was not transcript-specific. The high proportion of mRNAs associated with polysomes in methanol-grown cells is a major finding of this study; it reveals that high productivity during methanol induction is directly linked to the growth condition and not only to promoter strength. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1393-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roland Prielhofer
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria. .,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190, Vienna, Austria.
| | - Stephanie P Cartwright
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Alexandra B Graf
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190, Vienna, Austria. .,School of Bioengineering, University of Applied Sciences FH Campus Wien, Vienna, Austria.
| | - Minoska Valli
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria. .,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190, Vienna, Austria.
| | - Roslyn M Bill
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Diethard Mattanovich
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria. .,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190, Vienna, Austria.
| | - Brigitte Gasser
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria. .,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190, Vienna, Austria.
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Dietary L-methionine restriction decreases oxidative stress in porcine liver mitochondria. Exp Gerontol 2015; 65:35-41. [PMID: 25765145 DOI: 10.1016/j.exger.2015.03.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Revised: 03/06/2015] [Accepted: 03/07/2015] [Indexed: 11/23/2022]
Abstract
Dietary methionine restriction (MetR) has been reported to improve hepatocyte function in mammals. However, the underlying mechanisms remain largely unknown. This study was conducted with a swine model to test the hypothesis that MetR decreases generation of reactive oxygen species (ROS) and attenuates oxidative damage in hepatic mitochondria. Twenty-four 35-day old pigs were fed a control diet or a Met-restricted diet for two weeks. Liver mitochondria were isolated to determine: 8-oxodG in mitochondrial DNA, oxidative-derived proteins markers, including glutamic semialdehyde (GSA), aminoadipic semialdehydes (AASA), carboxyethyl-lysine (CEL), carboxymethyl-lysine (CML), and malondialdehyde lysine (MDAL), mitochondrial H2O2 generation rate; rates of oxygen consumption; free radical leak (FRL); anti-oxidative capacity, electron transport complex activity; and protein abundances of respiratory chain complex subunits (NDUFA9, SDHA, Core 2, and Cox 1), manganese superoxide dismutase (MnSOD), and apoptosis-inducing factor (AIF). Compared with the control, MetR decreased mitochondrial 8-oxodG content, H2O2 generation, FRL (P<0.05), and increased rates of oxygen consumption. Abundances of markers for protein oxidative damage, including GSA, AASA, CEL, and CML, were decreased (P<0.05) by 40%, 30%, 32%, and 28%, respectively, compared with the control. Western blot analysis revealed that MetR decreased (P<0.05) the protein abundances of complex subunits, NDUFA9 and AIF without affecting expression of SDHA, Core 2, Cox 1 or MnSOD. The complex I activity (P<0.05) were lowered in MetR group as compared with that of control. Collectively, our findings indicate that dietary MetR decreases mitochondrial ROS generation primarily via inhibiting complex I activity and ROS generation rather than augmenting anti-oxidative capacity, thereby ameliorating oxidative damage to hepatic mitochondrial DNA and proteins.
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Ortmayr K, Schwaiger M, Hann S, Koellensperger G. An integrated metabolomics workflow for the quantification of sulfur pathway intermediates employing thiol protection with N-ethyl maleimide and hydrophilic interaction liquid chromatography tandem mass spectrometry. Analyst 2015; 140:7687-95. [DOI: 10.1039/c5an01629k] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The developed integrated thiol protection and sample preparation strategy prevents unwanted oxidation and allows accurate profiling of sulfur pathway intermediates.
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Affiliation(s)
- Karin Ortmayr
- Institute of Analytical Chemistry
- University of Vienna
- Faculty of Chemistry
- 1090 Vienna
- Austria
| | - Michaela Schwaiger
- Institute of Analytical Chemistry
- University of Vienna
- Faculty of Chemistry
- 1090 Vienna
- Austria
| | - Stephan Hann
- Department of Chemistry
- University of Natural Resources and Life Sciences (BOKU) Vienna
- 1190 Vienna
- Austria
| | - Gunda Koellensperger
- Institute of Analytical Chemistry
- University of Vienna
- Faculty of Chemistry
- 1090 Vienna
- Austria
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García-Ríos E, López-Malo M, Guillamón JM. Global phenotypic and genomic comparison of two Saccharomyces cerevisiae wine strains reveals a novel role of the sulfur assimilation pathway in adaptation at low temperature fermentations. BMC Genomics 2014; 15:1059. [PMID: 25471357 PMCID: PMC4265444 DOI: 10.1186/1471-2164-15-1059] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 11/26/2014] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The wine industry needs better-adapted yeasts to grow at low temperature because it is interested in fermenting at low temperature to improve wine aroma. Elucidating the response to cold in Saccharomyces cerevisiae is of paramount importance for the selection or genetic improvement of wine strains. RESULTS We followed a global approach by comparing transcriptomic, proteomic and genomic changes in two commercial wine strains, which showed clear differences in their growth and fermentation capacity at low temperature. These strains were selected according to the maximum growth rate in a synthetic grape must during miniaturized batch cultures at different temperatures. The fitness differences of the selected strains were corroborated by directly competing during fermentations at optimum and low temperatures. The up-regulation of the genes of the sulfur assimilation pathway and glutathione biosynthesis suggested a crucial role in better performance at low temperature. The presence of some metabolites of these pathways, such as S-Adenosilmethionine (SAM) and glutathione, counteracted the differences in growth rate at low temperature in both strains. Generally, the proteomic and genomic changes observed in both strains also supported the importance of these metabolic pathways in adaptation at low temperature. CONCLUSIONS This work reveals a novel role of the sulfur assimilation pathway in adaptation at low temperature. We propose that a greater activation of this metabolic route enhances the synthesis of key metabolites, such as glutathione, whose protective effects can contribute to improve the fermentation process.
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Affiliation(s)
- Estéfani García-Ríos
- />Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, Po Box 73E-46100, Paterna Valencia, Spain
| | - María López-Malo
- />Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, Po Box 73E-46100, Paterna Valencia, Spain
- />Biotecnologia Enològica. Departament de Bioquímica i Biotecnologia, Facultat de Enologia, Universitat Rovira i Virgili, Marcel•li Domingo s/n, 43007 Tarragona, Spain
| | - José Manuel Guillamón
- />Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, Po Box 73E-46100, Paterna Valencia, Spain
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48
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Schwabe A, Bruggeman FJ. Single yeast cells vary in transcription activity not in delay time after a metabolic shift. Nat Commun 2014; 5:4798. [DOI: 10.1038/ncomms5798] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 07/25/2014] [Indexed: 11/09/2022] Open
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Rúa J, de Castro C, de Arriaga D, García-Armesto MR, Busto F, del Valle P. Stress in Phycomyces blakesleeanus by glucose starvation and acetate growth: Response of the antioxidant system and reserve carbohydrates. Microbiol Res 2014; 169:788-93. [DOI: 10.1016/j.micres.2013.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 12/05/2013] [Accepted: 12/20/2013] [Indexed: 01/01/2023]
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50
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Rodríguez-Lombardero S, Rodríguez-Belmonte ME, González-Siso MI, Vizoso-Vázquez Á, Valdiglesias V, Laffón B, Cerdán ME. Proteomic analyses reveal that Sky1 modulates apoptosis and mitophagy in Saccharomyces cerevisiae cells exposed to cisplatin. Int J Mol Sci 2014; 15:12573-90. [PMID: 25029545 PMCID: PMC4139861 DOI: 10.3390/ijms150712573] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 07/02/2014] [Accepted: 07/02/2014] [Indexed: 12/11/2022] Open
Abstract
Sky1 is the only member of the SR (Serine–Arginine) protein kinase family in Saccharomyces cerevisiae. When yeast cells are treated with the anti-cancer drug cisplatin, Sky1 kinase activity is necessary to produce the cytotoxic effect. In this study, proteome changes in response to this drug and/or SKY1 deletion have been evaluated in order to understand the role of Sky1 in the response of yeast cells to cisplatin. Results reveal differential expression of proteins previously related to the oxidative stress response, DNA damage, apoptosis and mitophagy. With these precedents, the role of Sky1 in apoptosis, necrosis and mitophagy has been evaluated by flow-cytometry, fluorescence microscopy, biosensors and fluorescence techniques. After cisplatin treatment, an apoptotic-like process diminishes in the ∆sky1 strain in comparison to the wild-type. The treatment does not affect mitophagy in the wild-type strain, while an increase is observed in the ∆sky1 strain. The increased resistance to cisplatin observed in the ∆sky1 strain may be attributable to a decrease of apoptosis and an increase of mitophagy.
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Affiliation(s)
- Silvia Rodríguez-Lombardero
- EXPRELA Group, Department of Cellular and Molecular Biology, University of A Coruña, Campus A Coruña, A Coruña E15071, Spain.
| | - M Esther Rodríguez-Belmonte
- EXPRELA Group, Department of Cellular and Molecular Biology, University of A Coruña, Campus A Coruña, A Coruña E15071, Spain.
| | - M Isabel González-Siso
- EXPRELA Group, Department of Cellular and Molecular Biology, University of A Coruña, Campus A Coruña, A Coruña E15071, Spain.
| | - Ángel Vizoso-Vázquez
- EXPRELA Group, Department of Cellular and Molecular Biology, University of A Coruña, Campus A Coruña, A Coruña E15071, Spain.
| | - Vanessa Valdiglesias
- DICOMOSA Group, Department of Psychology, Area of Psychobiology, University of A Coruña, Campus A Coruña, A Coruña E15071, Spain.
| | - Blanca Laffón
- DICOMOSA Group, Department of Psychology, Area of Psychobiology, University of A Coruña, Campus A Coruña, A Coruña E15071, Spain.
| | - M Esperanza Cerdán
- EXPRELA Group, Department of Cellular and Molecular Biology, University of A Coruña, Campus A Coruña, A Coruña E15071, Spain.
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