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Hengardi MT, Liang C, Madivannan K, Yang LK, Koduru L, Kanagasundaram Y, Arumugam P. Reversing the directionality of reactions between non-oxidative pentose phosphate pathway and glycolytic pathway boosts mycosporine-like amino acid production in Saccharomyces cerevisiae. Microb Cell Fact 2024; 23:121. [PMID: 38725068 PMCID: PMC11080194 DOI: 10.1186/s12934-024-02365-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/15/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND Mycosporine-like amino acids (MAAs) are a class of strongly UV-absorbing compounds produced by cyanobacteria, algae and corals and are promising candidates for natural sunscreen components. Low MAA yields from natural sources, coupled with difficulties in culturing its native producers, have catalyzed synthetic biology-guided approaches to produce MAAs in tractable microbial hosts like Escherichia coli, Saccharomyces cerevisiae and Corynebacterium glutamicum. However, the MAA titres obtained in these hosts are still low, necessitating a thorough understanding of cellular factors regulating MAA production. RESULTS To delineate factors that regulate MAA production, we constructed a shinorine (mycosporine-glycine-serine) producing yeast strain by expressing the four MAA biosynthetic enzymes from Nostoc punctiforme in Saccharomyces cerevisiae. We show that shinorine is produced from the pentose phosphate pathway intermediate sedoheptulose 7-phosphate (S7P), and not from the shikimate pathway intermediate 3-dehydroquinate (3DHQ) as previously suggested. Deletions of transaldolase (TAL1) and phosphofructokinase (PFK1/PFK2) genes boosted S7P/shinorine production via independent mechanisms. Unexpectedly, the enhanced S7P/shinorine production in the PFK mutants was not entirely due to increased flux towards the pentose phosphate pathway. We provide multiple lines of evidence in support of a reversed pathway between glycolysis and the non-oxidative pentose phosphate pathway (NOPPP) that boosts S7P/shinorine production in the phosphofructokinase mutant cells. CONCLUSION Reversing the direction of flux between glycolysis and the NOPPP offers a novel metabolic engineering strategy in Saccharomyces cerevisiae.
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Affiliation(s)
- Miselle Tiana Hengardi
- Agency for Science, Technology and Research (A*STAR), Singapore Institute of Food and Biotechnology Innovation, 31 Biopolis Way, Singapore, 138869, Singapore.
- NUS Graduate School for Integrated Sciences and Engineering, National University of Singapore, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore.
| | - Cui Liang
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
| | - Keshiniy Madivannan
- Innovation & Enterprise, Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, Singapore, 138632, Singapore
| | - Lay Kien Yang
- Agency for Science, Technology and Research (A*STAR), Singapore Institute of Food and Biotechnology Innovation, 31 Biopolis Way, Singapore, 138869, Singapore
| | - Lokanand Koduru
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Yoganathan Kanagasundaram
- Agency for Science, Technology and Research (A*STAR), Singapore Institute of Food and Biotechnology Innovation, 31 Biopolis Way, Singapore, 138869, Singapore
| | - Prakash Arumugam
- Agency for Science, Technology and Research (A*STAR), Singapore Institute of Food and Biotechnology Innovation, 31 Biopolis Way, Singapore, 138869, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
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Paul S, Todd OA, Eichelberger KR, Tkaczyk C, Sellman BR, Noverr MC, Cassat JE, Fidel PL, Peters BM. A fungal metabolic regulator underlies infectious synergism during Candida albicans - Staphylococcus aureus intra-abdominal co-infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580531. [PMID: 38405692 PMCID: PMC10888754 DOI: 10.1101/2024.02.15.580531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Candida albicans and Staphylococcus aureus are two commonly associated pathogens that cause nosocomial infections with high morbidity and mortality. Our prior and current work using a murine model of polymicrobial intra-abdominal infection (IAI) uncovered synergistic lethality that was driven by Candida -induced upregulation of functional S. aureus ⍺-toxin leading to polymicrobial sepsis and organ damage. In order to determine the candidal effector(s) mediating enhanced virulence, an unbiased screen of C. albicans transcription factor mutants was undertaken and revealed that zcf13 Δ/Δ failed to drive augmented ⍺-toxin or lethal synergism during co-infection. Using a combination of transcriptional and phenotypic profiling approaches, ZCF13 was shown to regulate genes involved in pentose metabolism, including RBK1 and HGT7 that contribute to fungal ribose catabolism and uptake, respectively. Subsequent experiments revealed that ribose inhibited the staphylococcal agr quorum sensing system and concomitantly repressed toxicity. Unlike wild-type C. albicans , zcf13 Δ/Δ was unable to effectively utilize ribose during co-culture or co-infection leading to exogenous ribose accumulation and agr repression. Forced expression of RBK1 and HGT7 in the zcf13 Δ/Δ mutant fully restored pathogenicity during co-infection. Collectively, our results detail the interwoven complexities of cross-kingdom interactions and highlight how intermicrobial metabolism impacts polymicrobial disease pathogenesis with devastating consequences for the host.
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Byeon H, An Y, Kim T, Rayamajhi V, Lee J, Shin H, Jung S. Effects of Four Organic Carbon Sources on the Growth and Astaxanthin Accumulation of Haematococcus lacustris. Life (Basel) 2023; 14:29. [PMID: 38255645 PMCID: PMC10820012 DOI: 10.3390/life14010029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
The microalga Haematococcus lacustris has a complex life cycle and a slow growth rate, hampering its mass cultivation. Culture of microalgae with organic carbon sources can increase the growth rate. Few studies have evaluated the effects of organic carbon sources on H. lacustris. We compared the vegetative and inductive stages of H. lacustris under autotrophic and mixotrophic conditions using four organic carbon sources: sodium acetate, glycerol, sodium gluconate, and ribose, each at various concentrations (0.325, 0.65, 1.3, and 2.6 g/L). The cell density was increased by 1.3 g/L of glycerol in the vegetative stage. The rapid transition to the inductive stage under nitrogen-depletion conditions caused by 1.3 or 2.6 g/L sodium acetate promoted the accumulation of astaxanthin. The production of astaxanthin by H. lacustris in mass culture using organic carbon sources could increase profitability.
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Affiliation(s)
- Huijeong Byeon
- Department of Biology, Soonchunhyang University, Asan 31538, Chungcheongnam-do, Republic of Korea; (H.B.)
| | - Yunji An
- Department of Biology, Soonchunhyang University, Asan 31538, Chungcheongnam-do, Republic of Korea; (H.B.)
| | - Taesoo Kim
- Department of Biology, Soonchunhyang University, Asan 31538, Chungcheongnam-do, Republic of Korea; (H.B.)
| | - Vijay Rayamajhi
- Department of Biology, Soonchunhyang University, Asan 31538, Chungcheongnam-do, Republic of Korea; (H.B.)
| | - Jihyun Lee
- Korea Fisheries Resources Agency East Sea Branch, Samho-ro, Buk-gu, Pohang 37601, Gyungsangbuk-do, Republic of Korea
| | - HyunWoung Shin
- Department of Biology, Soonchunhyang University, Asan 31538, Chungcheongnam-do, Republic of Korea; (H.B.)
- AlgaeBio, Inc., Asan 31459, Chungcheongnam-do, Republic of Korea
| | - SangMok Jung
- Research Institute for Basic Science, Soonchunhyang University, Asan 31538, Chungcheongnam-do, Republic of Korea
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4
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Remines M, Schoonover M, Knox Z, Kenwright K, Hoffert KM, Coric A, Mead J, Ampfer J, Seye S, Strome ED. Profiling The Compendium Of Changes In Saccharomyces cerevisiae Due To Mutations That Alter Availability Of The Main Methyl Donor S-Adenosylmethionine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544294. [PMID: 37333147 PMCID: PMC10274911 DOI: 10.1101/2023.06.09.544294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The SAM1 and SAM2 genes encode for S-AdenosylMethionine (AdoMet) synthetase enzymes, with AdoMet serving as the main methyl donor. We have previously shown that independent deletion of these genes alters chromosome stability and AdoMet concentrations in opposite ways in S. cerevisiae. To characterize other changes occurring in these mutants, we grew wildtype, sam1∆/sam1∆, and sam2∆/sam2∆ strains in 15 different Phenotypic Microarray plates with different components, equal to 1440 wells, and measured for growth variations. RNA-Sequencing was also carried out on these strains and differential gene expression determined for each mutant. In this study, we explore how the phenotypic growth differences are linked to the altered gene expression, and thereby predict the mechanisms by which loss of the SAM genes and subsequent AdoMet level changes, impact S. cerevisiae pathways and processes. We present six stories, discussing changes in sensitivity or resistance to azoles, cisplatin, oxidative stress, arginine biosynthesis perturbations, DNA synthesis inhibitors, and tamoxifen, to demonstrate the power of this novel methodology to broadly profile changes due to gene mutations. The large number of conditions that result in altered growth, as well as the large number of differentially expressed genes with wide-ranging functionality, speaks to the broad array of impacts that altering methyl donor abundance can impart, even when the conditions tested were not specifically selected as targeting known methyl involving pathways. Our findings demonstrate that some cellular changes are directly related to AdoMet-dependent methyltransferases and AdoMet availability, some are directly linked to the methyl cycle and its role is production of several important cellular components, and others reveal impacts of SAM gene mutations on previously unconnected pathways.
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Affiliation(s)
- McKayla Remines
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Makailyn Schoonover
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Zoey Knox
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Kailee Kenwright
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Kellyn M. Hoffert
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Amila Coric
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - James Mead
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Joseph Ampfer
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Serigne Seye
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Erin D. Strome
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
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5
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Reichling S, Doubleday PF, Germade T, Bergmann A, Loewith R, Sauer U, Holbrook-Smith D. Dynamic metabolome profiling uncovers potential TOR signaling genes. eLife 2023; 12:84295. [PMID: 36598488 PMCID: PMC9812406 DOI: 10.7554/elife.84295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/18/2022] [Indexed: 01/05/2023] Open
Abstract
Although the genetic code of the yeast Saccharomyces cerevisiae was sequenced 25 years ago, the characterization of the roles of genes within it is far from complete. The lack of a complete mapping of functions to genes hampers systematic understanding of the biology of the cell. The advent of high-throughput metabolomics offers a unique approach to uncovering gene function with an attractive combination of cost, robustness, and breadth of applicability. Here, we used flow-injection time-of-flight mass spectrometry to dynamically profile the metabolome of 164 loss-of-function mutants in TOR and receptor or receptor-like genes under a time course of rapamycin treatment, generating a dataset with >7000 metabolomics measurements. In order to provide a resource to the broader community, those data are made available for browsing through an interactive data visualization app hosted at https://rapamycin-yeast.ethz.ch. We demonstrate that dynamic metabolite responses to rapamycin are more informative than steady-state responses when recovering known regulators of TOR signaling, as well as identifying new ones. Deletion of a subset of the novel genes causes phenotypes and proteome responses to rapamycin that further implicate them in TOR signaling. We found that one of these genes, CFF1, was connected to the regulation of pyrimidine biosynthesis through URA10. These results demonstrate the efficacy of the approach for flagging novel potential TOR signaling-related genes and highlight the utility of dynamic perturbations when using functional metabolomics to deliver biological insight.
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Affiliation(s)
- Stella Reichling
- Institute of Molecular Systems Biology, ETH ZurichZurichSwitzerland
| | | | - Tomas Germade
- Institute of Molecular Systems Biology, ETH ZurichZurichSwitzerland
| | - Ariane Bergmann
- Department of Molecular Biology, University of GenevaGenevaSwitzerland
| | - Robbie Loewith
- Department of Molecular Biology, University of GenevaGenevaSwitzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH ZurichZurichSwitzerland
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6
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Zhang J, Wang N, Chen W, Zhang W, Zhang H, Yu H, Yi Y. Integrated metabolomics and transcriptomics reveal metabolites difference between wild and cultivated Ophiocordyceps sinensis. Food Res Int 2023; 163:112275. [PMID: 36596185 DOI: 10.1016/j.foodres.2022.112275] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/22/2022] [Accepted: 11/27/2022] [Indexed: 12/05/2022]
Abstract
Ophiocordyceps sinensis is a traditional medicinal fungus endemic to the alpine and high-altitude areas of the Qinghai-Tibet plateau. The scarcity of the wild resource has led to increased attention to artificially cultivated O. sinensis. However, little is known about the metabolic differences and the regulatory mechanisms between cultivated and wild O. sinensis. This study exploited untargeted metabolomics and transcriptomics to uncover the differences in accumulated metabolites and expressed genes between wild and cultivated O. sinensis. Metabolomics results revealed that 368 differentially accumulated metabolites were mainly enriched in biosynthesis of amino acids, biosynthesis of plant secondary metabolites and purine nucleotide metabolism. Cultivated O. sinensis contained more amino acids and derivatives, carbohydrates and derivatives, and phenolic acids than wild O. sinensis, whereas the contents of most nucleosides and nucleotides in wild O. sinensis were significantly higher than in cultivated O. sinensis. Transcriptome analysis indicated that 4430 annotated differentially expressed genes were identified between two types. Integrated metabolomics and transcriptomics analyses suggested that IMPDH, AK, ADSS, guaA and GUK genes might be related to the synthesis of purine nucleotides and nucleosides. Our findings will provide a new insight into the molecular basis of metabolic variations of this medicinal fungus.
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Affiliation(s)
- Jianshuang Zhang
- The State Key Laboratory of Southwest Karst Mountain Biodiversity Conservation of Forestry Administration, School of life sciences, Guizhou Normal University, Guiyang 550025, China; The Key Laboratory of Plant Physiology and Development in Guizhou Province, School of life sciences, Guizhou Normal University, Guiyang 550025, China
| | - Na Wang
- The State Key Laboratory of Southwest Karst Mountain Biodiversity Conservation of Forestry Administration, School of life sciences, Guizhou Normal University, Guiyang 550025, China
| | - Wanxuan Chen
- The Key Laboratory of Plant Physiology and Development in Guizhou Province, School of life sciences, Guizhou Normal University, Guiyang 550025, China
| | - Weiping Zhang
- The State Key Laboratory of Southwest Karst Mountain Biodiversity Conservation of Forestry Administration, School of life sciences, Guizhou Normal University, Guiyang 550025, China
| | - Haoshen Zhang
- The Key Laboratory of Plant Physiology and Development in Guizhou Province, School of life sciences, Guizhou Normal University, Guiyang 550025, China
| | - Hao Yu
- The State Key Laboratory of Southwest Karst Mountain Biodiversity Conservation of Forestry Administration, School of life sciences, Guizhou Normal University, Guiyang 550025, China; The Key Laboratory of Plant Physiology and Development in Guizhou Province, School of life sciences, Guizhou Normal University, Guiyang 550025, China.
| | - Yin Yi
- The State Key Laboratory of Southwest Karst Mountain Biodiversity Conservation of Forestry Administration, School of life sciences, Guizhou Normal University, Guiyang 550025, China; The Key Laboratory of Plant Physiology and Development in Guizhou Province, School of life sciences, Guizhou Normal University, Guiyang 550025, China.
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7
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Hurbain J, Thommen Q, Anquez F, Pfeuty B. Quantitative modeling of pentose phosphate pathway response to oxidative stress reveals a cooperative regulatory strategy. iScience 2022; 25:104681. [PMID: 35856027 PMCID: PMC9287814 DOI: 10.1016/j.isci.2022.104681] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/12/2022] [Accepted: 06/23/2022] [Indexed: 01/22/2023] Open
Abstract
Living cells use signaling and regulatory mechanisms to adapt to environmental stresses. Adaptation to oxidative stress involves the regulation of many enzymes in both glycolysis and pentose phosphate pathways (PPP), so as to support PPP-driven NADPH recycling for antioxidant defense. The underlying regulatory logic is investigated by developing a kinetic modeling approach fueled with metabolomics and 13C-fluxomics datasets from human fibroblast cells. Bayesian parameter estimation and phenotypic analysis of models highlight complementary roles for several metabolite-enzyme regulations. Specifically, carbon flux rerouting into PPP involves a tight coordination between the upregulation of G6PD activity concomitant to a decreased NADPH/NADP+ ratio and the differential control of downward and upward glycolytic fluxes through the joint inhibition of PGI and GAPD enzymes. Such functional interplay between distinct regulatory feedbacks promotes efficient detoxification and homeostasis response over a broad range of stress level, but can also explain paradoxical pertubation phenotypes for instance reported for 6PGD modulation in mammalian cells.
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Affiliation(s)
- Julien Hurbain
- CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, University of Lille, 59000 Lille, France
| | - Quentin Thommen
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, University of Lille, 59000 Lille, France
| | - Francois Anquez
- CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, University of Lille, 59000 Lille, France
| | - Benjamin Pfeuty
- CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, University of Lille, 59000 Lille, France
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Initiation of cytosolic plant purine nucleotide catabolism involves a monospecific xanthosine monophosphate phosphatase. Nat Commun 2021; 12:6846. [PMID: 34824243 PMCID: PMC8616923 DOI: 10.1038/s41467-021-27152-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 11/02/2021] [Indexed: 12/05/2022] Open
Abstract
In plants, guanosine monophosphate (GMP) is synthesized from adenosine monophosphate via inosine monophosphate and xanthosine monophosphate (XMP) in the cytosol. It has been shown recently that the catabolic route for adenylate-derived nucleotides bifurcates at XMP from this biosynthetic route. Dephosphorylation of XMP and GMP by as yet unknown phosphatases can initiate cytosolic purine nucleotide catabolism. Here we show that Arabidopsis thaliana possesses a highly XMP-specific phosphatase (XMPP) which is conserved in vascular plants. We demonstrate that XMPP catalyzes the irreversible entry reaction of adenylate-derived nucleotides into purine nucleotide catabolism in vivo, whereas the guanylates enter catabolism via an unidentified GMP phosphatase and guanosine deaminase which are important to maintain purine nucleotide homeostasis. We also present a crystal structure and mutational analysis of XMPP providing a rationale for its exceptionally high substrate specificity, which is likely required for the efficient catalysis of the very small XMP pool in vivo. Dephosphorylation of xanthosine monophosphate (XMP) initiates purine nucleotide catabolism in plant cells. Here the authors identify an XMP phosphatase from Arabidopsis that channels XMP towards catabolism in vivo and demonstrate the structural basis for its XMP specificity.
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Application of Metabolomics in the Study of Starvation-Induced Autophagy in Saccharomyces cerevisiae: A Scoping Review. J Fungi (Basel) 2021; 7:jof7110987. [PMID: 34829274 PMCID: PMC8619235 DOI: 10.3390/jof7110987] [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: 11/03/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 11/18/2022] Open
Abstract
This scoping review is aimed at the application of the metabolomics platform to dissect key metabolites and their intermediates to observe the regulatory mechanisms of starvation-induced autophagy in Saccharomyces cerevisiae. Four research papers were shortlisted in this review following the inclusion and exclusion criteria. We observed a commonly shared pathway undertaken by S. cerevisiae under nutritional stress. Targeted and untargeted metabolomics was applied in either of these studies using varying platforms resulting in the annotation of several different observable metabolites. We saw a commonly shared pathway undertaken by S. cerevisiae under nutritional stress. Following nitrogen starvation, the concentration of cellular nucleosides was altered as a result of autophagic RNA degradation. Additionally, it is also found that autophagy replenishes amino acid pools to sustain macromolecule synthesis. Furthermore, in glucose starvation, nucleosides were broken down into carbonaceous metabolites that are being funneled into the non-oxidative pentose phosphate pathway. The ribose salvage allows for the survival of starved yeast. Moreover, acute glucose starvation showed autophagy to be involved in maintaining ATP/energy levels. We highlighted the practicality of metabolomics as a tool to better understand the underlying mechanisms involved to maintain homeostasis by recycling degradative products to ensure the survival of S. cerevisiae under starvation. The application of metabolomics has extended the scope of autophagy and provided newer intervention targets against cancer as well as neurodegenerative diseases in which autophagy is implicated.
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Hartleben G, Schorpp K, Kwon Y, Betz B, Tsokanos F, Dantes Z, Schäfer A, Rothenaigner I, Monroy Kuhn JM, Morigny P, Mehr L, Lin S, Seitz S, Tokarz J, Artati A, Adamsky J, Plettenburg O, Lutter D, Irmler M, Beckers J, Reichert M, Hadian K, Zeigerer A, Herzig S, Berriel Diaz M. Combination therapies induce cancer cell death through the integrated stress response and disturbed pyrimidine metabolism. EMBO Mol Med 2021; 13:e12461. [PMID: 33665961 PMCID: PMC8033521 DOI: 10.15252/emmm.202012461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 01/24/2021] [Accepted: 01/27/2021] [Indexed: 01/05/2023] Open
Abstract
By accentuating drug efficacy and impeding resistance mechanisms, combinatorial, multi-agent therapies have emerged as key approaches in the treatment of complex diseases, most notably cancer. Using high-throughput drug screens, we uncovered distinct metabolic vulnerabilities and thereby identified drug combinations synergistically causing a starvation-like lethal catabolic response in tumor cells from different cancer entities. Domperidone, a dopamine receptor antagonist, as well as several tricyclic antidepressants (TCAs), including imipramine, induced cancer cell death in combination with the mitochondrial uncoupler niclosamide ethanolamine (NEN) through activation of the integrated stress response pathway and the catabolic CLEAR network. Using transcriptome and metabolome analyses, we characterized a combinatorial response, mainly driven by the transcription factors CHOP and TFE3, which resulted in cell death through enhanced pyrimidine catabolism as well as reduced pyrimidine synthesis. Remarkably, the drug combinations sensitized human organoid cultures to the standard-of-care chemotherapy paclitaxel. Thus, our combinatorial approach could be clinically implemented into established treatment regimen, which would be further facilitated by the advantages of drug repurposing.
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Gupta R, Laxman S. Cycles, sources, and sinks: Conceptualizing how phosphate balance modulates carbon flux using yeast metabolic networks. eLife 2021; 10:e63341. [PMID: 33544078 PMCID: PMC7864628 DOI: 10.7554/elife.63341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/20/2021] [Indexed: 12/11/2022] Open
Abstract
Phosphates are ubiquitous molecules that enable critical intracellular biochemical reactions. Therefore, cells have elaborate responses to phosphate limitation. Our understanding of long-term transcriptional responses to phosphate limitation is extensive. Contrastingly, a systems-level perspective presenting unifying biochemical concepts to interpret how phosphate balance is critically coupled to (and controls) metabolic information flow is missing. To conceptualize such processes, utilizing yeast metabolic networks we categorize phosphates utilized in metabolism into cycles, sources and sinks. Through this, we identify metabolic reactions leading to putative phosphate sources or sinks. With this conceptualization, we illustrate how mass action driven flux towards sources and sinks enable cells to manage phosphate availability during transient/immediate phosphate limitations. We thereby identify how intracellular phosphate availability will predictably alter specific nodes in carbon metabolism, and determine signature cellular metabolic states. Finally, we identify a need to understand intracellular phosphate pools, in order to address mechanisms of phosphate regulation and restoration.
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Affiliation(s)
- Ritu Gupta
- Institute for Stem Cell Science and Regenerative Medicine (inStem)BangaloreIndia
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem)BangaloreIndia
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12
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Ruchala J, Sibirny AA. Pentose metabolism and conversion to biofuels and high-value chemicals in yeasts. FEMS Microbiol Rev 2020; 45:6034013. [PMID: 33316044 DOI: 10.1093/femsre/fuaa069] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
Pentose sugars are widespread in nature and two of them, D-xylose and L-arabinose belong to the most abundant sugars being the second and third by abundance sugars in dry plant biomass (lignocellulose) and in general on planet. Therefore, it is not surprising that metabolism and bioconversion of these pentoses attract much attention. Several different pathways of D-xylose and L-arabinose catabolism in bacteria and yeasts are known. There are even more common and really ubiquitous though not so abundant pentoses, D-ribose and 2-deoxy-D-ribose, the constituents of all living cells. Thus, ribose metabolism is example of endogenous metabolism whereas metabolism of other pentoses, including xylose and L-arabinose, represents examples of the metabolism of foreign exogenous compounds which normally are not constituents of yeast cells. As a rule, pentose degradation by the wild-type strains of microorganisms does not lead to accumulation of high amounts of valuable substances; however, productive strains have been obtained by random selection and metabolic engineering. There are numerous reviews on xylose and (less) L-arabinose metabolism and conversion to high value substances; however, they mostly are devoted to bacteria or the yeast Saccharomyces cerevisiae. This review is devoted to reviewing pentose metabolism and bioconversion mostly in non-conventional yeasts, which naturally metabolize xylose. Pentose metabolism in the recombinant strains of S. cerevisiae is also considered for comparison. The available data on ribose, xylose, L-arabinose transport, metabolism, regulation of these processes, interaction with glucose catabolism and construction of the productive strains of high-value chemicals or pentose (ribose) itself are described. In addition, genome studies of the natural xylose metabolizing yeasts and available tools for their molecular research are reviewed. Metabolism of other pentoses (2-deoxyribose, D-arabinose, lyxose) is briefly reviewed.
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Affiliation(s)
- Justyna Ruchala
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Andriy A Sibirny
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
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13
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Paredes P, Larama G, Flores L, Leyton A, Ili CG, Asenjo JA, Chisti Y, Shene C. Temperature Differentially Affects Gene Expression in Antarctic Thraustochytrid Oblongichytrium sp. RT2316-13. Mar Drugs 2020; 18:md18110563. [PMID: 33217919 PMCID: PMC7698632 DOI: 10.3390/md18110563] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/08/2020] [Accepted: 11/11/2020] [Indexed: 01/17/2023] Open
Abstract
Oblongichytrium RT2316-13 synthesizes lipids rich in eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). The content of these fatty acids in the total lipids depended on growth temperature. Sequencing technology was used in this work to examine the thraustochytrid's response to a decrease in growth temperature from 15 °C to 5 °C. Around 4% (2944) of the genes were differentially expressed (DE) and only a few of the DE genes (533 upregulated; 206 downregulated) had significant matches to those in the SwissProt database. Most of the annotated DE genes were related to cell membrane composition (fatty acids, sterols, phosphatidylinositol), the membrane enzymes linked to cell energetics, and membrane structure (cytoskeletal proteins and enzymes). In RT2316-13, the synthesis of long-chain polyunsaturated fatty acids occurred through ω3- and ω6-pathways. Enzymes of the alternative pathways (Δ8-desaturase and Δ9-elongase) were also expressed. The upregulation of the genes coding for a Δ5-desaturase and a Δ5-elongase involved in the synthesis of EPA and DHA, explained the enrichment of total lipid with these two long-chain fatty acids at the low temperature. This molecular response has the potential to be used for producing microbial lipids with a fatty acids profile similar to that of fish oils.
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Affiliation(s)
- Paris Paredes
- Department of Chemical Engineering, Center of Food Biotechnology and Bioseparations, BIOREN, and Centre of Biotechnology and Bioengineering (CeBiB), Universidad de La Frontera, Av. Francisco Salazar 01145, Temuco 4780000, Chile; (P.P.); (L.F.); (A.L.)
| | - Giovanni Larama
- Centro de Modelación y Computación Científica, Universidad de La Frontera, Av. Francisco Salazar 01145, Temuco 4780000, Chile;
| | - Liset Flores
- Department of Chemical Engineering, Center of Food Biotechnology and Bioseparations, BIOREN, and Centre of Biotechnology and Bioengineering (CeBiB), Universidad de La Frontera, Av. Francisco Salazar 01145, Temuco 4780000, Chile; (P.P.); (L.F.); (A.L.)
| | - Allison Leyton
- Department of Chemical Engineering, Center of Food Biotechnology and Bioseparations, BIOREN, and Centre of Biotechnology and Bioengineering (CeBiB), Universidad de La Frontera, Av. Francisco Salazar 01145, Temuco 4780000, Chile; (P.P.); (L.F.); (A.L.)
| | - Carmen Gloria Ili
- Centro de Excelencia en Medicina Traslacional—Scientific and Technological Bioresource Nucleus (CEMT-BIOREN), Universidad de La Frontera, Av. Alemania 0478, Temuco 4810296, Chile;
| | - Juan A. Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, Universidad de Chile, Beauchef 851, Santiago 8370459, Chile;
| | - Yusuf Chisti
- School of Engineering, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand;
| | - Carolina Shene
- Department of Chemical Engineering, Center of Food Biotechnology and Bioseparations, BIOREN, and Centre of Biotechnology and Bioengineering (CeBiB), Universidad de La Frontera, Av. Francisco Salazar 01145, Temuco 4780000, Chile; (P.P.); (L.F.); (A.L.)
- Correspondence: ; Tel.: +56-45-232-5491
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14
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Austin S, Mayer A. Phosphate Homeostasis - A Vital Metabolic Equilibrium Maintained Through the INPHORS Signaling Pathway. Front Microbiol 2020; 11:1367. [PMID: 32765429 PMCID: PMC7381174 DOI: 10.3389/fmicb.2020.01367] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/27/2020] [Indexed: 12/12/2022] Open
Abstract
Cells face major changes in demand for and supply of inorganic phosphate (Pi). Pi is often a limiting nutrient in the environment, particularly for plants and microorganisms. At the same time, the need for phosphate varies, establishing conflicts of goals. Cells experience strong peaks of Pi demand, e.g., during the S-phase, when DNA, a highly abundant and phosphate-rich compound, is duplicated. While cells must satisfy these Pi demands, they must safeguard themselves against an excess of Pi in the cytosol. This is necessary because Pi is a product of all nucleotide-hydrolyzing reactions. An accumulation of Pi shifts the equilibria of these reactions and reduces the free energy that they can provide to drive endergonic metabolic reactions. Thus, while Pi starvation may simply retard growth and division, an elevated cytosolic Pi concentration is potentially dangerous for cells because it might stall metabolism. Accordingly, the consequences of perturbed cellular Pi homeostasis are severe. In eukaryotes, they range from lethality in microorganisms such as yeast (Sethuraman et al., 2001; Hürlimann, 2009), severe growth retardation and dwarfism in plants (Puga et al., 2014; Liu et al., 2015; Wild et al., 2016) to neurodegeneration or renal Fanconi syndrome in humans (Legati et al., 2015; Ansermet et al., 2017). Intracellular Pi homeostasis is thus not only a fundamental topic of cell biology but also of growing interest for medicine and agriculture.
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Affiliation(s)
- Sisley Austin
- Département de Biochimie, Université de Lausanne, Lausanne, Switzerland
| | - Andreas Mayer
- Département de Biochimie, Université de Lausanne, Lausanne, Switzerland
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15
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Wang T, Gnanaprakasam JNR, Chen X, Kang S, Xu X, Sun H, Liu L, Rodgers H, Miller E, Cassel TA, Sun Q, Vicente-Muñoz S, Warmoes MO, Lin P, Piedra-Quintero ZL, Guerau-de-Arellano M, Cassady KA, Zheng SG, Yang J, Lane AN, Song X, Fan TWM, Wang R. Inosine is an alternative carbon source for CD8 +-T-cell function under glucose restriction. Nat Metab 2020; 2:635-647. [PMID: 32694789 PMCID: PMC7371628 DOI: 10.1038/s42255-020-0219-4] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 04/30/2020] [Indexed: 12/15/2022]
Abstract
T cells undergo metabolic rewiring to meet their bioenergetic, biosynthetic and redox demands following antigen stimulation. To fulfil these needs, effector T cells must adapt to fluctuations in environmental nutrient levels at sites of infection and inflammation. Here, we show that effector T cells can utilize inosine, as an alternative substrate, to support cell growth and function in the absence of glucose in vitro. T cells metabolize inosine into hypoxanthine and phosphorylated ribose by purine nucleoside phosphorylase. We demonstrate that the ribose subunit of inosine can enter into central metabolic pathways to provide ATP and biosynthetic precursors, and that cancer cells display diverse capacities to utilize inosine as a carbon source. Moreover, the supplementation with inosine enhances the anti-tumour efficacy of immune checkpoint blockade and adoptive T-cell transfer in solid tumours that are defective in metabolizing inosine, reflecting the capability of inosine to relieve tumour-imposed metabolic restrictions on T cells.
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Affiliation(s)
- Tingting Wang
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Ohio State University, Columbus, OH, USA
| | - J N Rashida Gnanaprakasam
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Ohio State University, Columbus, OH, USA
| | - Xuyong Chen
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Ohio State University, Columbus, OH, USA
| | - Siwen Kang
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Ohio State University, Columbus, OH, USA
| | - Xuequn Xu
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Ohio State University, Columbus, OH, USA
| | - Hua Sun
- The Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Lingling Liu
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Ohio State University, Columbus, OH, USA
| | - Hayley Rodgers
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Ohio State University, Columbus, OH, USA
| | - Ethan Miller
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Ohio State University, Columbus, OH, USA
| | - Teresa A Cassel
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Qiushi Sun
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Sara Vicente-Muñoz
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Marc O Warmoes
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Penghui Lin
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Zayda Lizbeth Piedra-Quintero
- School of Health and Rehabilitation Sciences, Division of Medical Laboratory Science, College of Medicine, Wexner Medical Center, Ohio State University, Columbus, OH, USA
| | - Mireia Guerau-de-Arellano
- School of Health and Rehabilitation Sciences, Division of Medical Laboratory Science, College of Medicine, Wexner Medical Center, Ohio State University, Columbus, OH, USA
| | - Kevin A Cassady
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Ohio State University, Columbus, OH, USA
| | - Song Guo Zheng
- Division of Rheumatology and Immunology, Department of Internal Medicine at Ohio State University of Medicine and Wexner Medical Center, Columbus, OH, USA
| | - Jun Yang
- Department of Surgery, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Xiaotong Song
- The Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA.
- Icell Kealex Therapeutics, Houston, TX, USA.
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA.
| | - Ruoning Wang
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Ohio State University, Columbus, OH, USA.
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16
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Yang C, Li J, Huang Z, Zhang X, Gao X, Zhu C, Morris PF, Zhang X. Structural and catalytic analysis of two diverse uridine phosphorylases in Phytophthora capsici. Sci Rep 2020; 10:9051. [PMID: 32493959 PMCID: PMC7271239 DOI: 10.1038/s41598-020-65935-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 05/08/2020] [Indexed: 11/09/2022] Open
Abstract
Uridine phosphorylase (UP) is a key enzyme of pyrimidine salvage pathways that enables the recycling of endogenous or exogenous-supplied pyrimidines and plays an important intracellular metabolic role. Here, we biochemically and structurally characterized two evolutionarily divergent uridine phosphorylases, PcUP1 and PcUP2 from the oomycete pathogen Phytophthora capsici. Our analysis of other oomycete genomes revealed that both uridine phosphorylases are present in Phytophthora and Pythium genomes, but only UP2 is seen in Saprolegnia spp. which are basal members of the oomycetes. Moreover, uridine phosphorylases are not found in obligate oomycete pathogens such as Hyaloperonospora arabidopsidis and Albugo spp. PcUP1 and PcUP2 are upregulated 300 and 500 fold respectively, within 90 min after infection of pepper leaves. The crystal structures of PcUP1 in ligand-free and in complex with uracil/ribose-1-phosphate, 2'-deoxyuridine/phosphate and thymidine/phosphate were analyzed. Crystal structure of this uridine phosphorylase showed strict conservation of key residues in the binding pocket. Structure analysis of PcUP1 with bound ligands, and site-directed mutagenesis of key residues provide additional support for the "push-pull" model of catalysis. Our study highlights the importance of pyrimidine salvage during the earliest stages of infection.
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Affiliation(s)
- Cancan Yang
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, 271000, China
| | - Jing Li
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, 271000, China
| | - Zhenling Huang
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, 271000, China
| | - Xuefa Zhang
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, 271000, China
| | - Xiaolei Gao
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, 271000, China
| | - Chunyuang Zhu
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, 271000, China
| | - Paul F Morris
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - XiuGuo Zhang
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, 271000, China.
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17
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Luo X, Meng J, Chen X, Cheng L, Yan S, Gao L, Xue M, Yang Y. Metabolomics-based study reveals the effect of lead (Pb) in the culture environment on Whitmania pigra. Sci Rep 2020; 10:4794. [PMID: 32179862 PMCID: PMC7075881 DOI: 10.1038/s41598-020-61745-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/02/2020] [Indexed: 12/03/2022] Open
Abstract
Whitmania pigra, called Mahuang (MH) in Chinese, has been used as a traditional Chinese medicine for many years and is susceptible to Pb exposure in aquaculture environments. To understand the impact of Pb in the culture environment on MHs, we carried out a 50-day culture of MHs in environments with different levels of Pb pollution. Then, tissue samples of MHs reared in the different Pb-polluted environments were collected and analysed by UPLC-Q/TOF-MS. The results showed that the Pb residue in MHs increased with increasing Pb in the culture environment. There was no significant difference in MH Pb content (P < 0.05) between the low-Pb residue group (PbL) and the blank control group (BC), and those of the middle-Pb residue group (PbM) and the high-Pb residue group (PbH) were significantly different from that of the BC group. Metabolomics results showed significant changes in 24 metabolites in the PbL, PbM and PbH groups, some of which were dose-dependent. These metabolites were mainly lipids, nucleotides, and dipeptides, which are involved in metabolic pathways such as glycerophospholipid metabolism, sphingolipid metabolism, and nucleotide metabolism. Overall, the results proved that metabolomics can be an effective tool to understand the effects of Pb on the metabolic responses of MHs.
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Affiliation(s)
- Xuemei Luo
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Jieqin Meng
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Xiufen Chen
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Liangke Cheng
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Shaopeng Yan
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Luying Gao
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Miao Xue
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Yaojun Yang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China.
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18
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Bhat SY, Qureshi IA. Mutations of key substrate binding residues of leishmanial peptidase T alter its functional and structural dynamics. Biochim Biophys Acta Gen Subj 2020; 1864:129465. [DOI: 10.1016/j.bbagen.2019.129465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 10/15/2019] [Accepted: 10/24/2019] [Indexed: 11/27/2022]
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19
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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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20
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Daignan-Fornier B, Pinson B. Yeast to Study Human Purine Metabolism Diseases. Cells 2019; 8:cells8010067. [PMID: 30658520 PMCID: PMC6356901 DOI: 10.3390/cells8010067] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 02/04/2023] Open
Abstract
Purine nucleotides are involved in a multitude of cellular processes, and the dysfunction of purine metabolism has drastic physiological and pathological consequences. Accordingly, several genetic disorders associated with defective purine metabolism have been reported. The etiology of these diseases is poorly understood and simple model organisms, such as yeast, have proved valuable to provide a more comprehensive view of the metabolic consequences caused by the identified mutations. In this review, we present results obtained with the yeast Saccharomyces cerevisiae to exemplify how a eukaryotic unicellular organism can offer highly relevant information for identifying the molecular basis of complex human diseases. Overall, purine metabolism illustrates a remarkable conservation of genes, functions and phenotypes between humans and yeast.
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Affiliation(s)
- Bertrand Daignan-Fornier
- Université de Bordeaux IBGC UMR 5095 1, rue Camille Saint-Saëns, F-33077 Bordeaux, France.
- Centre National de la Recherche Scientifique IBGC UMR 5095 1, rue Camille Saint-Saëns, F-33077 Bordeaux, France.
| | - Benoît Pinson
- Université de Bordeaux IBGC UMR 5095 1, rue Camille Saint-Saëns, F-33077 Bordeaux, France.
- Centre National de la Recherche Scientifique IBGC UMR 5095 1, rue Camille Saint-Saëns, F-33077 Bordeaux, France.
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21
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Walvekar AS, Srinivasan R, Gupta R, Laxman S. Methionine coordinates a hierarchically organized anabolic program enabling proliferation. Mol Biol Cell 2018; 29:3183-3200. [PMID: 30354837 PMCID: PMC6340205 DOI: 10.1091/mbc.e18-08-0515] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/12/2018] [Accepted: 10/19/2018] [Indexed: 12/21/2022] Open
Abstract
Methionine availability during overall amino acid limitation metabolically reprograms cells to support proliferation, the underlying basis for which remains unclear. Here we construct the organization of this methionine-mediated anabolic program using yeast. Combining comparative transcriptome analysis and biochemical and metabolic flux-based approaches, we discover that methionine rewires overall metabolic outputs by increasing the activity of a key regulatory node. This comprises the pentose phosphate pathway (PPP) coupled with reductive biosynthesis, the glutamate dehydrogenase (GDH)-dependent synthesis of glutamate/glutamine, and pyridoxal-5-phosphate (PLP)-dependent transamination capacity. This PPP-GDH-PLP node provides the required cofactors and/or substrates for subsequent rate-limiting reactions in the synthesis of amino acids and therefore nucleotides. These rate-limiting steps in amino acid biosynthesis are also induced in a methionine-dependent manner. This thereby results in a biochemical cascade establishing a hierarchically organized anabolic program. For this methionine-mediated anabolic program to be sustained, cells co-opt a "starvation stress response" regulator, Gcn4p. Collectively, our data suggest a hierarchical metabolic framework explaining how methionine mediates an anabolic switch.
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Affiliation(s)
- Adhish S. Walvekar
- Institute for Stem Cell biology and Regenerative Medicine (inStem), NCBS-TIFR campus, Bangalore 560065, India
| | - Rajalakshmi Srinivasan
- Institute for Stem Cell biology and Regenerative Medicine (inStem), NCBS-TIFR campus, Bangalore 560065, India
| | - Ritu Gupta
- Institute for Stem Cell biology and Regenerative Medicine (inStem), NCBS-TIFR campus, Bangalore 560065, India
| | - Sunil Laxman
- Institute for Stem Cell biology and Regenerative Medicine (inStem), NCBS-TIFR campus, Bangalore 560065, India
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22
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Xu YF, Lu W, Chen JC, Johnson SA, Gibney PA, Thomas DG, Brown G, May AL, Campagna SR, Yakunin AF, Botstein D, Rabinowitz JD. Discovery and Functional Characterization of a Yeast Sugar Alcohol Phosphatase. ACS Chem Biol 2018; 13:3011-3020. [PMID: 30240188 DOI: 10.1021/acschembio.8b00804] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Sugar alcohols (polyols) exist widely in nature. While some specific sugar alcohol phosphatases are known, there is no known phosphatase for some important sugar alcohols (e.g., sorbitol-6-phosphate). Using liquid chromatography-mass spectrometry-based metabolomics, we screened yeast strains with putative phosphatases of unknown function deleted. We show that the yeast gene YNL010W, which has close homologues in all fungi species and some plants, encodes a sugar alcohol phosphatase. We term this enzyme, which hydrolyzes sorbitol-6-phosphate, ribitol-5-phosphate, and (d)-glycerol-3-phosphate, polyol phosphatase 1 or PYP1. Polyol phosphates are structural analogs of the enediol intermediate of phosphoglucose isomerase (Pgi). We find that sorbitol-6-phosphate and ribitol-5-phosphate inhibit Pgi and that Pyp1 activity is important for yeast to maintain Pgi activity in the presence of environmental sugar alcohols. Pyp1 expression is strongly positively correlated with yeast growth rate, presumably because faster growth requires greater glycolytic and accordingly Pgi flux. Thus, yeast express the previously uncharacterized enzyme Pyp1 to prevent inhibition of glycolysis by sugar alcohol phosphates. Pyp1 may be useful for engineering sugar alcohol production.
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Affiliation(s)
- Yi-Fan Xu
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Wenyun Lu
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
| | - Jonathan C. Chen
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Sarah A. Johnson
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Patrick A. Gibney
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
| | - David G. Thomas
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Amanda L. May
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Shawn R. Campagna
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - David Botstein
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Joshua D. Rabinowitz
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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23
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Yang J, Wang F, Yang D, Zhou K, Liu M, Gao Z, Liu P, Dong Y, Zhang J, Liu Q. Structural and biochemical characterization of the yeast HD domain containing protein YGK1 reveals a metal-dependent nucleoside 5'-monophosphatase. Biochem Biophys Res Commun 2018; 501:674-681. [PMID: 29752939 DOI: 10.1016/j.bbrc.2018.05.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 05/08/2018] [Indexed: 11/24/2022]
Abstract
HD-domain is a conserved domain, with the signature of histidine and aspartic (HD) residues doublets. HD-domain proteins may possess nucleotidase and phosphodiesterase activities, and they play important roles in signaling and nucleotide metabolism. In yeast, HD-domain proteins with nucleotidase activity remained unexplored. Here, we biochemically and structurally characterized two HD domain proteins YGK1 (YGL101W) and YB92 (YBR242W) from Saccharomyces cerevisiae as nucleoside 5'-monophosphatases, with substrate preference for deoxyribonucleoside 5'-monophosphatase over ribonucleoside 5'-monophosphatase. By determining the crystal structure of YGK1, we unveiled that YGK1 structure resembled as the crystal structure of YfbR from E. coli. Size-exclusion chromatography and crosslinking studies suggested that YGK1 and YB92 existed in the form of a dimer, respectively, which were consistent with structural observation of YGK1. Site-directed mutagenesis demonstrated that more extensive conserved residues near the divalent metal coordinating active site were essential for YGK1 activity than previous suggested. The metal coordinating His89 and Asp90, and the neighboring conserved Glu93, Glu114 and Glu145 were individually critical for catalysis. In addition, alignments suggested that three flexible loops with hydrophobic residues might be implicated in substrate selectivity to nucleoside moiety. Together, our comparative structural and mutational studies suggested that YGK1 and YB92 functioned as 5'-nucleotidases in S. cerevisiae.
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Affiliation(s)
- Jingsi Yang
- College of Chemistry, Dalian University of Technology, No.2 Linggong Road, Ganjingzi District, Dalian City, Liaolin Province, 116024, People's Republic of China
| | - Fei Wang
- Multi-discipline Center, Institute of High Energy Physics in Chinese Academy of Sciences, Beijing, Beijing, 100049, People's Republic of China
| | - Dan Yang
- Institute of Physical Science and Information Technology, Institute of Health Sciences, Anhui University, Hefei, 230601, People's Republic of China
| | - Ke Zhou
- Multi-discipline Center, Institute of High Energy Physics in Chinese Academy of Sciences, Beijing, Beijing, 100049, People's Republic of China
| | - Min Liu
- Institute of Physical Science and Information Technology, Institute of Health Sciences, Anhui University, Hefei, 230601, People's Republic of China
| | - Zengqiang Gao
- Multi-discipline Center, Institute of High Energy Physics in Chinese Academy of Sciences, Beijing, Beijing, 100049, People's Republic of China
| | - Peng Liu
- Multi-discipline Center, Institute of High Energy Physics in Chinese Academy of Sciences, Beijing, Beijing, 100049, People's Republic of China
| | - Yuhui Dong
- Multi-discipline Center, Institute of High Energy Physics in Chinese Academy of Sciences, Beijing, Beijing, 100049, People's Republic of China.
| | - Jianjun Zhang
- College of Chemistry, Dalian University of Technology, No.2 Linggong Road, Ganjingzi District, Dalian City, Liaolin Province, 116024, People's Republic of China
| | - Quansheng Liu
- Multi-discipline Center, Institute of High Energy Physics in Chinese Academy of Sciences, Beijing, Beijing, 100049, People's Republic of China.
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Quality properties and formation of α-dicarbonyl compounds in abalone muscle (Haliotis discus) as affected by tenderization and baking processes. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2018. [DOI: 10.1007/s11694-018-9765-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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25
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Croft T, James Theoga Raj C, Salemi M, Phinney BS, Lin SJ. A functional link between NAD + homeostasis and N-terminal protein acetylation in Saccharomyces cerevisiae. J Biol Chem 2018; 293:2927-2938. [PMID: 29317496 DOI: 10.1074/jbc.m117.807214] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 12/15/2017] [Indexed: 12/12/2022] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+) is an essential metabolite participating in cellular redox chemistry and signaling, and the complex regulation of NAD+ metabolism is not yet fully understood. To investigate this, we established a NAD+-intermediate specific reporter system to identify factors required for salvage of metabolically linked nicotinamide (NAM) and nicotinic acid (NA). Mutants lacking components of the NatB complex, NAT3 and MDM20, appeared as hits in this screen. NatB is an Nα-terminal acetyltransferase responsible for acetylation of the N terminus of specific Met-retained peptides. In NatB mutants, increased NA/NAM levels were concomitant with decreased NAD+ We identified the vacuolar pool of nicotinamide riboside (NR) as the source of this increased NA/NAM. This NR pool is increased by nitrogen starvation, suggesting NAD+ and related metabolites may be trafficked to the vacuole for recycling. Supporting this, increased NA/NAM release in NatB mutants was abolished by deleting the autophagy protein ATG14 We next examined Tpm1 (tropomyosin), whose function is regulated by NatB-mediated acetylation, and Tpm1 overexpression (TPM1-oe) was shown to restore some NatB mutant defects. Interestingly, although TPM1-oe largely suppressed NA/NAM release in NatB mutants, it did not restore NAD+ levels. We showed that decreased nicotinamide mononucleotide adenylyltransferase (Nma1/Nma2) levels probably caused the NAD+ defects, and NMA1-oe was sufficient to restore NAD+ NatB-mediated N-terminal acetylation of Nma1 and Nma2 appears essential for maintaining NAD+ levels. In summary, our results support a connection between NatB-mediated protein acetylation and NAD+ homeostasis. Our findings may contribute to understanding the molecular basis and regulation of NAD+ metabolism.
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Affiliation(s)
- Trevor Croft
- Department of Microbiology and Molecular Genetics, College of Biological Sciences
| | | | - Michelle Salemi
- Proteomic Core Facility, University of California, Davis, California 95616
| | - Brett S Phinney
- Proteomic Core Facility, University of California, Davis, California 95616
| | - Su-Ju Lin
- Department of Microbiology and Molecular Genetics, College of Biological Sciences.
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Schroeder RY, Zhu A, Eubel H, Dahncke K, Witte CP. The ribokinases of Arabidopsis thaliana and Saccharomyces cerevisiae are required for ribose recycling from nucleotide catabolism, which in plants is not essential to survive prolonged dark stress. THE NEW PHYTOLOGIST 2018; 217:233-244. [PMID: 28921561 DOI: 10.1111/nph.14782] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 08/05/2017] [Indexed: 06/07/2023]
Abstract
Nucleotide catabolism in Arabidopsis thaliana and Saccharomyces cerevisiae leads to the release of ribose, which requires phosphorylation to ribose-5-phosphate mediated by ribokinase (RBSK). We aimed to characterize RBSK in plants and yeast, to quantify the contribution of plant nucleotide catabolism to the ribose pool, and to investigate whether ribose carbon contributes to dark stress survival of plants. We performed a phylogenetic analysis and determined the kinetic constants of plant-expressed Arabidopsis and yeast RBSKs. Using mass spectrometry, several metabolites were quantified in AtRBSK mutants and double mutants with genes of nucleoside catabolism. Additionally, the dark stress performance of several nucleotide metabolism mutants and rbsk was compared. The plant PfkB family of sugar kinases forms nine major clades likely representing distinct biochemical functions, one of them RBSK. Nucleotide catabolism is the dominant ribose source in plant metabolism and is highly induced by dark stress. However, rbsk cannot be discerned from the wild type in dark stress. Interestingly, the accumulation of guanosine in a guanosine deaminase mutant strongly enhances dark stress symptoms. Although nucleotide catabolism contributes to carbon mobilization upon darkness and is the dominant source of ribose, the contribution appears to be of minor importance for dark stress survival.
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Affiliation(s)
- Rebekka Y Schroeder
- Department of Molecular Nutrition and Biochemistry of Plants, Institute of Plant Nutrition, Leibniz University Hannover, Herrenhäuser Str. 2, Hannover, 30419, Germany
| | - Anting Zhu
- Department of Molecular Nutrition and Biochemistry of Plants, Institute of Plant Nutrition, Leibniz University Hannover, Herrenhäuser Str. 2, Hannover, 30419, Germany
| | - Holger Eubel
- Department of Plant Proteomics, Institute of Plant Genetics, Leibniz University Hannover, Herrenhäuser Str. 2, Hannover, 30419, Germany
| | - Kathleen Dahncke
- Dahlem Centre of Plant Sciences, Freie Universität Berlin, Albrecht-Thaer-Weg 6, Berlin, 14195, Germany
| | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Institute of Plant Nutrition, Leibniz University Hannover, Herrenhäuser Str. 2, Hannover, 30419, Germany
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Gurvich Y, Leshkowitz D, Barkai N. Dual role of starvation signaling in promoting growth and recovery. PLoS Biol 2017; 15:e2002039. [PMID: 29236696 PMCID: PMC5728490 DOI: 10.1371/journal.pbio.2002039] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 11/01/2017] [Indexed: 11/19/2022] Open
Abstract
Growing cells are subject to cycles of nutrient depletion and repletion. A shortage of nutrients activates a starvation program that promotes growth in limiting conditions. To examine whether nutrient-deprived cells prepare also for their subsequent recovery, we followed the transcription program activated in budding yeast transferred to low-phosphate media and defined its contribution to cell growth during phosphate limitation and upon recovery. An initial transcription wave was induced by moderate phosphate depletion that did not affect cell growth. A second transcription wave followed when phosphate became growth limiting. The starvation program contributed to growth only in the second, growth-limiting phase. Notably, the early response, activated at moderate depletion, promoted recovery from starvation by increasing phosphate influx upon transfer to rich medium. Our results suggest that cells subject to nutrient depletion prepare not only for growth in the limiting conditions but also for their predicted recovery once nutrients are replenished.
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Affiliation(s)
- Yonat Gurvich
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Dena Leshkowitz
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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28
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Pang N, Chen S. Effects of C5 organic carbon and light on growth and cell activity of Haematococcus pluvialis under mixotrophic conditions. ALGAL RES 2017. [DOI: 10.1016/j.algal.2016.12.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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29
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Pires RH, Cataldi TR, Franceschini LM, Labate MV, Fusco-Almeida AM, Labate CA, Palma MS, Soares Mendes-Giannini MJ. Metabolic profiles of planktonic and biofilm cells of Candida orthopsilosis. Future Microbiol 2016; 11:1299-1313. [PMID: 27662506 DOI: 10.2217/fmb-2016-0025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
AIM This study aims to understand which Candida orthopsilosis protein aids fungus adaptation upon its switching from planktonic growth to biofilm. MATERIALS & METHODS Ion mobility separation within mass spectrometry analysis combination were used. RESULTS Proteins mapped for different biosynthetic pathways showed that selective ribosome autophagy might occur in biofilms. Glucose, used as a carbon source in the glycolytic flux, changed to glycogen and trehalose. CONCLUSION Candida orthopsilosis expresses proteins that combine a variety of mechanisms to provide yeasts with the means to adjust the catalytic properties of enzymes. Adjustment of the enzymes helps modulate the biosynthesis/degradation rates of the available nutrients, in order to control and coordinate the metabolic pathways that enable cells to express an adequate response to nutrient availability.
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Affiliation(s)
- Regina Helena Pires
- Department of Clinical Analysis, Clinical Mycology Laboratory, Faculdade de Ciências Farmacêuticas, UNESP - Univ Estadual Paulista Júlio de Mesquita Filho, FCFAr, Rodovia Araraquara-Jaú, km1, Araraquara 14801-902, SP, Brazil
| | - Thaís Regiani Cataldi
- Department of Genetics, ESALQ/USP - Univ de São Paulo, Laboratory Max Feffer Plant Genetics, Av. Pádua Dias 11, Caixa Postal 83, Piracicaba 13400-970, SP, Brazil
| | - Livia Maria Franceschini
- Department of Genetics, ESALQ/USP - Univ de São Paulo, Laboratory Max Feffer Plant Genetics, Av. Pádua Dias 11, Caixa Postal 83, Piracicaba 13400-970, SP, Brazil
| | - Mônica Veneziano Labate
- Department of Genetics, ESALQ/USP - Univ de São Paulo, Laboratory Max Feffer Plant Genetics, Av. Pádua Dias 11, Caixa Postal 83, Piracicaba 13400-970, SP, Brazil
| | - Ana Marisa Fusco-Almeida
- Department of Clinical Analysis, Clinical Mycology Laboratory, Faculdade de Ciências Farmacêuticas, UNESP - Univ Estadual Paulista Júlio de Mesquita Filho, FCFAr, Rodovia Araraquara-Jaú, km1, Araraquara 14801-902, SP, Brazil
| | - Carlos Alberto Labate
- Department of Genetics, ESALQ/USP - Univ de São Paulo, Laboratory Max Feffer Plant Genetics, Av. Pádua Dias 11, Caixa Postal 83, Piracicaba 13400-970, SP, Brazil
| | - Mario Sérgio Palma
- Department of Biology, Lab. Structural Biology & Zoochemistry, CEIS, Univ Estadual Paulista Júlio de Mesquita Filho, UNESP, Institute of Biosciences, Av. 24-A, 1515. Bela Vista, Rio Claro 13506-900, SP, Brazil
| | - Maria José Soares Mendes-Giannini
- Department of Clinical Analysis, Clinical Mycology Laboratory, Faculdade de Ciências Farmacêuticas, UNESP - Univ Estadual Paulista Júlio de Mesquita Filho, FCFAr, Rodovia Araraquara-Jaú, km1, Araraquara 14801-902, SP, Brazil
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Guo JY, Teng X, Laddha SV, Ma S, Van Nostrand SC, Yang Y, Khor S, Chan CS, Rabinowitz JD, White E. Autophagy provides metabolic substrates to maintain energy charge and nucleotide pools in Ras-driven lung cancer cells. Genes Dev 2016; 30:1704-17. [PMID: 27516533 PMCID: PMC5002976 DOI: 10.1101/gad.283416.116] [Citation(s) in RCA: 263] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 07/22/2016] [Indexed: 12/27/2022]
Abstract
Here, Guo et al. investigate how autophagy maintains mitochondrial function in Ras-driven cancer cells and why autophagy is critical for their survival in starvation. By analyzing mitochondrial genomes from Atg7 wild-type and Atg7-deficient Kras-driven lung tumors, the authors demonstrated that autophagy supports nucleotide pools, which enables survival of Ras-driven cancer cells in starvation. Autophagy degrades and is thought to recycle proteins, other macromolecules, and organelles. In genetically engineered mouse models (GEMMs) for Kras-driven lung cancer, autophagy prevents the accumulation of defective mitochondria and promotes malignancy. Autophagy-deficient tumor-derived cell lines are respiration-impaired and starvation-sensitive. However, to what extent their sensitivity to starvation arises from defective mitochondria or an impaired supply of metabolic substrates remains unclear. Here, we sequenced the mitochondrial genomes of wild-type or autophagy-deficient (Atg7−/−) Kras-driven lung tumors. Although Atg7 deletion resulted in increased mitochondrial mutations, there were too few nonsynonymous mutations to cause generalized mitochondrial dysfunction. In contrast, pulse-chase studies with isotope-labeled nutrients revealed impaired mitochondrial substrate supply during starvation of the autophagy-deficient cells. This was associated with increased reactive oxygen species (ROS), lower energy charge, and a dramatic drop in total nucleotide pools. While starvation survival of the autophagy-deficient cells was not rescued by the general antioxidant N-acetyl-cysteine, it was fully rescued by glutamine or glutamate (both amino acids that feed the TCA cycle and nucleotide synthesis) or nucleosides. Thus, maintenance of nucleotide pools is a critical challenge for starving Kras-driven tumor cells. By providing bioenergetic and biosynthetic substrates, autophagy supports nucleotide pools and thereby starvation survival.
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Affiliation(s)
- Jessie Yanxiang Guo
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey 08903, USA; Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey 08901, USA; Department of Chemical Biology, Rutgers Ernest Mario School of Pharmacy, Piscataway, New Jersey 08854, USA
| | - Xin Teng
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Saurabh V Laddha
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey 08903, USA
| | - Sirui Ma
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey 08903, USA
| | | | - Yang Yang
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey 08903, USA
| | - Sinan Khor
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey 08903, USA
| | - Chang S Chan
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey 08903, USA; Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey 08901, USA
| | - Joshua D Rabinowitz
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey 08903, USA; Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Eileen White
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey 08903, USA; Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA
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Engineering a microbial platform for de novo biosynthesis of diverse methylxanthines. Metab Eng 2016; 38:191-203. [PMID: 27519552 DOI: 10.1016/j.ymben.2016.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/24/2016] [Accepted: 08/09/2016] [Indexed: 11/20/2022]
Abstract
Engineered microbial biosynthesis of plant natural products can support manufacturing of complex bioactive molecules and enable discovery of non-naturally occurring derivatives. Purine alkaloids, including caffeine (coffee), theophylline (antiasthma drug), theobromine (chocolate), and other methylxanthines, play a significant role in pharmacology and food chemistry. Here, we engineered the eukaryotic microbial host Saccharomyces cerevisiae for the de novo biosynthesis of methylxanthines. We constructed a xanthine-to-xanthosine conversion pathway in native yeast central metabolism to increase endogenous purine flux for the production of 7-methylxanthine, a key intermediate in caffeine biosynthesis. Yeast strains were further engineered to produce caffeine through expression of several enzymes from the coffee plant. By expressing combinations of different N-methyltransferases, we were able to demonstrate re-direction of flux to an alternate pathway and develop strains that support the production of diverse methylxanthines. We achieved production of 270μg/L, 61μg/L, and 3700μg/L of caffeine, theophylline, and 3-methylxanthine, respectively, in 0.3-L bench-scale batch fermentations. The constructed strains provide an early platform for de novo production of methylxanthines and with further development will advance the discovery and synthesis of xanthine derivatives.
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32
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The transcription factor GCN4 regulates PHM8 and alters triacylglycerol metabolism in Saccharomyces cerevisiae. Curr Genet 2016; 62:841-851. [PMID: 26979516 DOI: 10.1007/s00294-016-0590-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/02/2016] [Accepted: 03/03/2016] [Indexed: 02/01/2023]
Abstract
PHM8 is a very important enzyme in nonpolar lipid metabolism because of its role in triacylglycerol (TAG) biosynthesis under phosphate stress conditions. It is positively regulated by the PHO4 transcription factor under low phosphate conditions; however, its regulation has not been explored under normal physiological conditions. General control nonderepressible (GCN4), a basic leucine-zipper transcription factor activates the transcription of amino acids, purine biosynthesis genes and many stress response genes under various stress conditions. In this study, we demonstrate that the level of TAG is regulated by the transcription factor GCN4. GCN4 directly binds to its consensus recognition sequence (TGACTC) in the PHM8 promoter and controls its expression. The analysis of cells expressing the P PHM8 -lacZ reporter gene showed that mutations (TGACTC-GGGCCC) in the GCN4-binding sequence caused a significant increase in β-galactosidase activity. Mutation in the GCN4 binding sequence causes an increase in PHM8 expression, lysophosphatidic acid phosphatase activity and TAG level. PHM8, in conjunction with DGA1, a mono- and diacylglycerol transferase, controls the level of TAG. These results revealed that GCN4 negatively regulates PHM8 and that deletion of GCN4 causes de-repression of PHM8, which is responsible for the increased TAG content in gcn4∆ cells.
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Responses to phosphate deprivation in yeast cells. Curr Genet 2015; 62:301-7. [PMID: 26615590 DOI: 10.1007/s00294-015-0544-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 11/16/2015] [Accepted: 11/18/2015] [Indexed: 01/10/2023]
Abstract
Inorganic phosphate is an essential nutrient because it is required for the biosynthesis of nucleotides, phospholipids and metabolites in energy metabolism. During phosphate starvation, phosphatases play a major role in phosphate acquisition by hydrolyzing phosphorylated macromolecules. In Saccharomyces cerevisiae, PHM8 (YER037W), a lysophosphatidic acid phosphatase, plays an important role in phosphate acquisition by hydrolyzing lysophosphatidic acid and nucleotide monophosphate that results in accumulation of triacylglycerol and nucleotides under phosphate limiting conditions. Under phosphate limiting conditions, it is transcriptionally regulated by Pho4p, a phosphate-responsive transcription factor. In this review, we focus on triacylglycerol metabolism in transcription factors deletion mutants involved in phosphate metabolism and propose a link between phosphate and triacylglycerol metabolism. Deletion of these transcription factors results in an increase in triacylglycerol level. Based on these observations, we suggest that PHM8 is responsible for the increase in triacylglycerol in phosphate metabolising gene deletion mutants.
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Yadav KK, Singh N, Rajasekharan R. PHO4 transcription factor regulates triacylglycerol metabolism under low-phosphate conditions in Saccharomyces cerevisiae. Mol Microbiol 2015; 98:456-72. [PMID: 26179227 DOI: 10.1111/mmi.13133] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2015] [Indexed: 02/01/2023]
Abstract
In Saccharomyces cerevisiae, PHM8 encodes a phosphatase that catalyses the dephosphorylation of lysophosphatidic acids to monoacylglycerol and nucleotide monophosphate to nucleoside and releases free phosphate. In this report, we investigated the role of PHM8 in triacylglycerol metabolism and its transcriptional regulation by a phosphate responsive transcription factor Pho4p under low-phosphate conditions. We found that the wild-type (BY4741) cells accumulate triacylglycerol and the expression of PHM8 was high under low-phosphate conditions. Overexpression of PHM8 in the wild-type, phm8Δ and quadruple phosphatase mutant (pah1Δdpp1Δlpp1Δapp1Δ) caused an increase in the triacylglycerol levels. However, the introduction of the PHM8 deletion into the quadruple phosphatase mutant resulted in a reduction in triacylglycerol levels and LPA phosphatase activity. The transcriptional activator Pho4p binds to the PHM8 promoter under low-phosphate conditions, activating PHM8 expression, which leads to the formation of monoacylglycerol from LPA. The synthesized monoacylglycerol is acylated to diacylglycerol by Dga1p, which is further acylated to triacylglycerol by the same enzyme.
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Affiliation(s)
- Kamlesh Kumar Yadav
- Lipidomic Centre, Department of Lipid Science, CSIR-Central Food Technological Research Institute (CFTRI), Mysore, Karnataka, 570020, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-CFTRI Campus
| | - Neelima Singh
- Lipidomic Centre, Department of Lipid Science, CSIR-Central Food Technological Research Institute (CFTRI), Mysore, Karnataka, 570020, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-CFTRI Campus
| | - Ram Rajasekharan
- Lipidomic Centre, Department of Lipid Science, CSIR-Central Food Technological Research Institute (CFTRI), Mysore, Karnataka, 570020, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-CFTRI Campus
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35
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Slack M, Wang T, Wang R. T cell metabolic reprogramming and plasticity. Mol Immunol 2015; 68:507-12. [PMID: 26277274 DOI: 10.1016/j.molimm.2015.07.036] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 07/26/2015] [Indexed: 12/21/2022]
Abstract
Upon antigen stimulation, small and quiescent naïve T cells undergo an approximately 24h growth phase followed by rapid proliferation. Depending on the nature of the antigen and cytokine milieu, these proliferating T cells differentiate into distinctive functional subgroups that are essential for appropriate immune defense and regulation. T cells undergo a characteristic metabolic rewiring that fulfills the dramatically increased bioenergetic and biosynthetic demands during the transition between resting, activation and differentiation. Beyond this, T cells are distributed throughout the body and are able to function in a wide range of physio-pathological environments, including some with a dramatic metabolic derangement. As such, T cells must quickly respond to and adapt to fluctuations in environmental nutrient levels. We consider such responsiveness and adaptation in terms of metabolic plasticity, that is, an evolutionarilly selected process which allows T cells to illicit robust immune functions in response to either a continuous or disrupted nutrient supply. In this review, we illustrate the relevant metabolic pathways in T cells and discuss the ability of T cells to change their metabolic substrates in response to changes in the environment.
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Affiliation(s)
- Maria Slack
- Department of Pediatrics, The Ohio State University School of Medicine, Columbus, OH, USA; Division of Allergy and Immunology Nationwide Children's Hospital, Columbus, OH, USA; Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, OH, USA
| | - Tingting Wang
- Center for Childhood Cancer and Blood Disease, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Ruoning Wang
- Center for Childhood Cancer and Blood Disease, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA; Hematology/Oncology & BMT, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University School of Medicine, Columbus, OH, USA.
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Tsang F, Lin SJ. Less is more: Nutrient limitation induces cross-talk of nutrient sensing pathways with NAD + homeostasis and contributes to longevity. ACTA ACUST UNITED AC 2015; 10:333-357. [PMID: 27683589 DOI: 10.1007/s11515-015-1367-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nutrient sensing pathways and their regulation grant cells control over their metabolism and growth in response to changing nutrients. Factors that regulate nutrient sensing can also modulate longevity. Reduced activity of nutrient sensing pathways such as glucose-sensing PKA, nitrogen-sensing TOR and S6 kinase homolog Sch9 have been linked to increased life span in the yeast, Saccharomyces cerevisiae, and higher eukaryotes. Recently, reduced activity of amino acid sensing SPS pathway was also shown to increase yeast life span. Life span extension by reduced SPS activity requires enhanced NAD+ (nicotinamide adenine dinucleotide, oxidized form) and nicotinamide riboside (NR, a NAD+ precursor) homeostasis. Maintaining adequate NAD+ pools has been shown to play key roles in life span extension, but factors regulating NAD+ metabolism and homeostasis are not completely understood. Recently, NAD+ metabolism was also linked to the phosphate (Pi)-sensing PHO pathway in yeast. Canonical PHO activation requires Pi-starvation. Interestingly, NAD+ depletion without Pi-starvation was sufficient to induce PHO activation, increasing NR production and mobilization. Moreover, SPS signaling appears to function in parallel with PHO signaling components to regulate NR/NAD+ homeostasis. These studies suggest that NAD+ metabolism is likely controlled by and/or coordinated with multiple nutrient sensing pathways. Indeed, cross-regulation of PHO, PKA, TOR and Sch9 pathways was reported to potentially affect NAD+ metabolism; though detailed mechanisms remain unclear. This review discusses yeast longevity-related nutrient sensing pathways and possible mechanisms of life span extension, regulation of NAD+ homeostasis, and cross-talk among nutrient sensing pathways and NAD+ homeostasis.
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Affiliation(s)
- Felicia Tsang
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Su-Ju Lin
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA 95616, USA
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Kuznetsova E, Nocek B, Brown G, Makarova KS, Flick R, Wolf YI, Khusnutdinova A, Evdokimova E, Jin K, Tan K, Hanson AD, Hasnain G, Zallot R, de Crécy-Lagard V, Babu M, Savchenko A, Joachimiak A, Edwards AM, Koonin EV, Yakunin AF. Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae: BIOCHEMICAL, STRUCTURAL, AND EVOLUTIONARY INSIGHTS. J Biol Chem 2015; 290:18678-98. [PMID: 26071590 DOI: 10.1074/jbc.m115.657916] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Indexed: 12/15/2022] Open
Abstract
The haloacid dehalogenase (HAD)-like enzymes comprise a large superfamily of phosphohydrolases present in all organisms. The Saccharomyces cerevisiae genome encodes at least 19 soluble HADs, including 10 uncharacterized proteins. Here, we biochemically characterized 13 yeast phosphatases from the HAD superfamily, which includes both specific and promiscuous enzymes active against various phosphorylated metabolites and peptides with several HADs implicated in detoxification of phosphorylated compounds and pseudouridine. The crystal structures of four yeast HADs provided insight into their active sites, whereas the structure of the YKR070W dimer in complex with substrate revealed a composite substrate-binding site. Although the S. cerevisiae and Escherichia coli HADs share low sequence similarities, the comparison of their substrate profiles revealed seven phosphatases with common preferred substrates. The cluster of secondary substrates supporting significant activity of both S. cerevisiae and E. coli HADs includes 28 common metabolites that appear to represent the pool of potential activities for the evolution of novel HAD phosphatases. Evolution of novel substrate specificities of HAD phosphatases shows no strict correlation with sequence divergence. Thus, evolution of the HAD superfamily combines the conservation of the overall substrate pool and the substrate profiles of some enzymes with remarkable biochemical and structural flexibility of other superfamily members.
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Affiliation(s)
- Ekaterina Kuznetsova
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Boguslaw Nocek
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Greg Brown
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Kira S Makarova
- the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Robert Flick
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Yuri I Wolf
- the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Anna Khusnutdinova
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Elena Evdokimova
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Ke Jin
- the Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada, and
| | - Kemin Tan
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Andrew D Hanson
- the Horticultural Sciences Department, Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
| | - Ghulam Hasnain
- the Horticultural Sciences Department, Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
| | - Rémi Zallot
- the Horticultural Sciences Department, Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
| | - Valérie de Crécy-Lagard
- the Horticultural Sciences Department, Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
| | - Mohan Babu
- the Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada, and
| | - Alexei Savchenko
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Andrzej Joachimiak
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Aled M Edwards
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada, the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Eugene V Koonin
- the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Alexander F Yakunin
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada,
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Nugroho RH, Yoshikawa K, Shimizu H. Metabolomic analysis of acid stress response in Saccharomyces cerevisiae. J Biosci Bioeng 2015; 120:396-404. [PMID: 25795572 DOI: 10.1016/j.jbiosc.2015.02.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 02/17/2015] [Accepted: 02/19/2015] [Indexed: 12/24/2022]
Abstract
Acid stress has been reported to inhibit cell growth and decrease productivity during bio-production processes. In this study, a metabolomics approach was conducted to understand the effect of lactic acid induced stress on metabolite pools in Saccharomyces cerevisiae. Cells were cultured with lactic acid as the acidulant, with or without initial pH control, i.e., at pH 6 or pH 2.5, respectively. Under conditions of low pH, lactic acid led to a decrease in the intracellular pH and specific growth rate; however, these parameters remained unaltered in the cultures with pH control. Capillary electrophoresis-mass spectrometry followed by a statistical principal component analysis was used to identify the metabolites and measure the increased concentrations of ATP, glutathione and proline during severe acid stress. Addition of proline to the acidified cultures improved the specific growth rates. We hypothesized that addition of proline protected the cells from acid stress by combating acid-induced oxidative stress. Lactic acid diffusion into the cell resulted in intracellular acidification, which elicited an oxidative stress response and resulted in increased glutathione levels.
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Affiliation(s)
- Riyanto Heru Nugroho
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Katsunori Yoshikawa
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
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39
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Xu YF, Lu W, Rabinowitz JD. Avoiding misannotation of in-source fragmentation products as cellular metabolites in liquid chromatography-mass spectrometry-based metabolomics. Anal Chem 2015; 87:2273-81. [PMID: 25591916 DOI: 10.1021/ac504118y] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Liquid chromatography-mass spectrometry (LC-MS) technology allows for rapid quantitation of cellular metabolites, with metabolites identified by mass spectrometry and chromatographic retention time. Recently, with the development of rapid scanning high-resolution high accuracy mass spectrometers and the desire for high throughput screening, minimal or no chromatographic separation has become increasingly popular. When analyzing complex cellular extracts, however, the lack of chromatographic separation could potentially result in misannotation of structurally related metabolites. Here, we show that, even using electrospray ionization, a soft ionization method, in-source fragmentation generates unwanted byproducts of identical mass to common metabolites. For example, nucleotide-triphosphates generate nucleotide-diphosphates, and hexose-phosphates generate triose-phosphates. We evaluated yeast intracellular metabolite extracts and found more than 20 cases of in-source fragments that mimic common metabolites. Accordingly, chromatographic separation is required for accurate quantitation of many common cellular metabolites.
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Affiliation(s)
- Yi-Fan Xu
- Lewis Sigler Institute for Integrative Genomics, Princeton University , Princeton, New Jersey 08544, United States
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40
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Abstract
During nitrogen starvation, a nonselective bulk degradation of cytosolic proteins and organelles including ribosomes, termed macro‐autophagy (hereafter termed autophagy), is induced. The precise mechanism of RNA degradation by this pathway has not been yet elucidated. In this issue of the The EMBO Journal, Huang et al characterize an autophagy‐dependent RNA catabolism in yeast and identify the enzymes responsible for the degradation process.
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Affiliation(s)
- Evelyn Welter
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Zvulun Elazar
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
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Huang H, Kawamata T, Horie T, Tsugawa H, Nakayama Y, Ohsumi Y, Fukusaki E. Bulk RNA degradation by nitrogen starvation-induced autophagy in yeast. EMBO J 2014; 34:154-68. [PMID: 25468960 DOI: 10.15252/embj.201489083] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Autophagy is a catabolic process conserved among eukaryotes. Under nutrient starvation, a portion of the cytoplasm is non-selectively sequestered into autophagosomes. Consequently, ribosomes are delivered to the vacuole/lysosome for destruction, but the precise mechanism of autophagic RNA degradation and its physiological implications for cellular metabolism remain unknown. We characterized autophagy-dependent RNA catabolism using a combination of metabolome and molecular biological analyses in yeast. RNA delivered to the vacuole was processed by Rny1, a T2-type ribonuclease, generating 3'-NMPs that were immediately converted to nucleosides by the vacuolar non-specific phosphatase Pho8. In the cytoplasm, these nucleosides were broken down by the nucleosidases Pnp1 and Urh1. Most of the resultant bases were not re-assimilated, but excreted from the cell. Bulk non-selective autophagy causes drastic perturbation of metabolism, which must be minimized to maintain intracellular homeostasis.
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Affiliation(s)
- Hanghang Huang
- Department of Biotechnology, Osaka University, Suita Osaka, Japan
| | - Tomoko Kawamata
- Frontier Research Center, Tokyo Institute of Technology, Midori-ku Yokohama, Japan
| | - Tetsuro Horie
- Frontier Research Center, Tokyo Institute of Technology, Midori-ku Yokohama, Japan
| | - Hiroshi Tsugawa
- Department of Biotechnology, Osaka University, Suita Osaka, Japan
| | | | - Yoshinori Ohsumi
- Frontier Research Center, Tokyo Institute of Technology, Midori-ku Yokohama, Japan
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42
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Taverniti V, Séraphin B. Elimination of cap structures generated by mRNA decay involves the new scavenger mRNA decapping enzyme Aph1/FHIT together with DcpS. Nucleic Acids Res 2014; 43:482-92. [PMID: 25432955 PMCID: PMC4288156 DOI: 10.1093/nar/gku1251] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Eukaryotic 5' mRNA cap structures participate to the post-transcriptional control of gene expression before being released by the two main mRNA decay pathways. In the 3'-5' pathway, the exosome generates free cap dinucleotides (m7GpppN) or capped oligoribonucleotides that are hydrolyzed by the Scavenger Decapping Enzyme (DcpS) forming m7GMP. In the 5'-3' pathway, the decapping enzyme Dcp2 generates m7GDP. We investigated the fate of m7GDP and m7GpppN produced by RNA decay in extracts and cells. This defined a pathway involving DcpS, NTPs and the nucleoside diphosphate kinase for m7GDP elimination. Interestingly, we identified and characterized in vitro and in vivo a new scavenger decapping enzyme involved in m7GpppN degradation. We show that activities mediating cap elimination identified in yeast are essentially conserved in human. Their alteration may contribute to pathologies, possibly through the interference of cap (di)nucleotide with cellular function.
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Affiliation(s)
- Valerio Taverniti
- Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de Recherche Scientifique (CNRS) UMR 7104/Institut National de Santé et de Recherche Médicale (INSERM) U964/Université de Strasbourg, 67404 Illkirch, France
| | - Bertrand Séraphin
- Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de Recherche Scientifique (CNRS) UMR 7104/Institut National de Santé et de Recherche Médicale (INSERM) U964/Université de Strasbourg, 67404 Illkirch, France
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43
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Vardi N, Levy S, Gurvich Y, Polacheck T, Carmi M, Jaitin D, Amit I, Barkai N. Sequential Feedback Induction Stabilizes the Phosphate Starvation Response in Budding Yeast. Cell Rep 2014; 9:1122-34. [DOI: 10.1016/j.celrep.2014.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/02/2014] [Accepted: 09/29/2014] [Indexed: 12/14/2022] Open
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44
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Buelto D, Duncan MC. Cellular energetics: actin and myosin abstain from ATP during starvation. Curr Biol 2014; 24:R1004-6. [PMID: 25442847 DOI: 10.1016/j.cub.2014.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Destiney Buelto
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Mara C Duncan
- Department of Cell and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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45
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Walther T, Létisse F, Peyriga L, Alkim C, Liu Y, Lardenois A, Martin-Yken H, Portais JC, Primig M, François J. Developmental stage dependent metabolic regulation during meiotic differentiation in budding yeast. BMC Biol 2014; 12:60. [PMID: 25178389 PMCID: PMC4176597 DOI: 10.1186/s12915-014-0060-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Indexed: 12/12/2022] Open
Abstract
Background The meiotic developmental pathway in yeast enables both differentiation of vegetative cells into haploid spores that ensure long-term survival, and recombination of the parental DNA to create genetic diversity. Despite the importance of proper metabolic regulation for the supply of building blocks and energy, little is known about the reprogramming of central metabolic pathways in meiotically differentiating cells during passage through successive developmental stages. Results Metabolic regulation during meiotic differentiation in budding yeast was analyzed by integrating information on genome-wide transcriptional activity, 26 enzymatic activities in the central metabolism, the dynamics of 67 metabolites, and a metabolic flux analysis at mid-stage meiosis. Analyses of mutants arresting sporulation at defined stages demonstrated that metabolic reprogramming is tightly controlled by the progression through the developmental pathway. The correlation between transcript levels and enzymatic activities in the central metabolism varies significantly in a developmental stage-dependent manner. The complete loss of phosphofructokinase activity at mid-stage meiosis enables a unique setup of the glycolytic pathway which facilitates carbon flux repartitioning into synthesis of spore wall precursors during the co-assimilation of glycogen and acetate. The need for correct homeostasis of purine nucleotides during the meiotic differentiation was demonstrated by the sporulation defect of the AMP deaminase mutant amd1, which exhibited hyper-accumulation of ATP accompanied by depletion of guanosine nucleotides. Conclusions Our systems-level analysis shows that reprogramming of the central metabolism during the meiotic differentiation is controlled at different hierarchical levels to meet the metabolic and energetic needs at successive developmental stages. Electronic supplementary material The online version of this article (doi:10.1186/s12915-014-0060-x) contains supplementary material, which is available to authorized users.
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46
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Kato M, Lin SJ. Regulation of NAD+ metabolism, signaling and compartmentalization in the yeast Saccharomyces cerevisiae. DNA Repair (Amst) 2014; 23:49-58. [PMID: 25096760 DOI: 10.1016/j.dnarep.2014.07.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 06/06/2014] [Accepted: 07/11/2014] [Indexed: 12/21/2022]
Abstract
Pyridine nucleotides are essential coenzymes in many cellular redox reactions in all living systems. In addition to functioning as a redox carrier, NAD(+) is also a required co-substrate for the conserved sirtuin deacetylases. Sirtuins regulate transcription, genome maintenance and metabolism and function as molecular links between cells and their environment. Maintaining NAD(+) homeostasis is essential for proper cellular function and aberrant NAD(+) metabolism has been implicated in a number of metabolic- and age-associated diseases. Recently, NAD(+) metabolism has been linked to the phosphate-responsive signaling pathway (PHO pathway) in the budding yeast Saccharomyces cerevisiae. Activation of the PHO pathway is associated with the production and mobilization of the NAD(+) metabolite nicotinamide riboside (NR), which is mediated in part by PHO-regulated nucleotidases. Cross-regulation between NAD(+) metabolism and the PHO pathway has also been reported; however, detailed mechanisms remain to be elucidated. The PHO pathway also appears to modulate the activities of common downstream effectors of multiple nutrient-sensing pathways (Ras-PKA, TOR, Sch9/AKT). These signaling pathways were suggested to play a role in calorie restriction-mediated beneficial effects, which have also been linked to Sir2 function and NAD(+) metabolism. Here, we discuss the interactions of these pathways and their potential roles in regulating NAD(+) metabolism. In eukaryotic cells, intracellular compartmentalization facilitates the regulation of enzymatic functions and also concentrates or sequesters specific metabolites. Various NAD(+)-mediated cellular functions such as mitochondrial oxidative phosphorylation are compartmentalized. Therefore, we also discuss several key players functioning in mitochondrial, cytosolic and vacuolar compartmentalization of NAD(+) intermediates, and their potential roles in NAD(+) homeostasis. To date, it remains unclear how NAD(+) and NAD(+) intermediates shuttle between different cellular compartments. Together, these studies provide a molecular basis for how NAD(+) homeostasis factors and the interacting signaling pathways confer metabolic flexibility and contribute to maintaining cell fitness and genome stability.
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Affiliation(s)
- Michiko Kato
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, One Shields Ave., Davis, CA 95616, USA
| | - Su-Ju Lin
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, One Shields Ave., Davis, CA 95616, USA.
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47
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Daily expression pattern of protein-encoding genes and small noncoding RNAs in synechocystis sp. strain PCC 6803. Appl Environ Microbiol 2014; 80:5195-206. [PMID: 24928881 DOI: 10.1128/aem.01086-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Many organisms harbor circadian clocks with periods close to 24 h. These cellular clocks allow organisms to anticipate the environmental cycles of day and night by synchronizing circadian rhythms with the rising and setting of the sun. These rhythms originate from the oscillator components of circadian clocks and control global gene expression and various cellular processes. The oscillator of photosynthetic cyanobacteria is composed of three proteins, KaiA, KaiB, and KaiC, linked to a complex regulatory network. Synechocystis sp. strain PCC 6803 possesses the standard cyanobacterial kaiABC gene cluster plus multiple kaiB and kaiC gene copies and antisense RNAs for almost every kai transcript. However, there is no clear evidence of circadian rhythms in Synechocystis sp. PCC 6803 under various experimental conditions. It is also still unknown if and to what extent the multiple kai gene copies and kai antisense RNAs affect circadian timing. Moreover, a large number of small noncoding RNAs whose accumulation dynamics over time have not yet been monitored are known for Synechocystis sp. PCC 6803. Here we performed a 48-h time series transcriptome analysis of Synechocystis sp. PCC 6803, taking into account periodic light-dark phases, continuous light, and continuous darkness. We found that expression of functionally related genes occurred in different phases of day and night. Moreover, we found day-peaking and night-peaking transcripts among the small RNAs; in particular, the amounts of kai antisense RNAs correlated or anticorrelated with those of their respective kai target mRNAs, pointing toward the regulatory relevance of these antisense RNAs. Surprisingly, we observed that the amounts of 16S and 23S rRNAs in this cyanobacterium fluctuated in light-dark periods, showing maximum accumulation in the dark phase. Importantly, the amounts of all transcripts, including small noncoding RNAs, did not show any rhythm under continuous light or darkness, indicating the absence of circadian rhythms in Synechocystis.
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48
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Kato M, Lin SJ. YCL047C/POF1 is a novel nicotinamide mononucleotide adenylyltransferase (NMNAT) in Saccharomyces cerevisiae. J Biol Chem 2014; 289:15577-87. [PMID: 24759102 DOI: 10.1074/jbc.m114.558643] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
NAD(+) is an essential metabolic cofactor involved in various cellular biochemical processes. Nicotinamide riboside (NR) is an endogenously produced key pyridine metabolite that plays important roles in the maintenance of NAD(+) pool. Using a NR-specific cell-based screen, we identified mutants that exhibit altered NR release phenotype. Yeast cells lacking the ORF YCL047C/POF1 release considerably more NR compared with wild type, suggesting that POF1 plays an important role in NR/NAD(+) metabolism. The amino acid sequence of Pof1 indicates that it is a putative nicotinamide mononucleotide adenylyltransferase (NMNAT). Unlike other yeast NMNATs, Pof1 exhibits NMN-specific adenylyltransferase activity. Deletion of POF1 significantly lowers NAD(+) levels and decreases the efficiency of NR utilization, resistance to oxidative stress, and NR-induced life span extension. We also show that NR is constantly produced by multiple nucleotidases and that the intracellular NR pools are likely to be compartmentalized, which contributes to the regulation of NAD(+) homeostasis. Our findings may contribute to the understanding of the molecular basis and regulation of NAD(+) metabolism in higher eukaryotes.
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Affiliation(s)
- Michiko Kato
- From the Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, California 95616
| | - Su-Ju Lin
- From the Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, California 95616
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49
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Linck A, Vu XK, Essl C, Hiesl C, Boles E, Oreb M. On the role of GAPDH isoenzymes during pentose fermentation in engineered Saccharomyces cerevisiae. FEMS Yeast Res 2014; 14:389-98. [PMID: 24456572 DOI: 10.1111/1567-1364.12137] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 01/15/2014] [Accepted: 01/15/2014] [Indexed: 11/28/2022] Open
Abstract
In the metabolic network of the cell, many intermediary products are shared between different pathways. d-Glyceraldehyde-3-phosphate, a glycolytic intermediate, is a substrate of GAPDH but is also utilized by transaldolase and transketolase in the scrambling reactions of the nonoxidative pentose phosphate pathway. Recent efforts to engineer baker's yeast strains capable of utilizing pentose sugars present in plant biomass rely on increasing the carbon flux through this pathway. However, the competition between transaldolase and GAPDH for d-glyceraldehyde-3-phosphate produced in the first transketolase reaction compromises the carbon balance of the pathway, thereby limiting the product yield. Guided by the hypothesis that reduction in GAPDH activity would increase the availability of d-glyceraldehyde-3-phosphate for transaldolase and thereby improve ethanol production during fermentation of pentoses, we performed a comprehensive characterization of the three GAPDH isoenzymes in baker's yeast, Tdh1, Tdh2, and Tdh3 and analyzed the effect of their deletion on xylose utilization by engineered strains. Our data suggest that overexpression of transaldolase is a more promising strategy than reduction in GAPDH activity to increase the flux through the nonoxidative pentose phosphate pathway.
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Affiliation(s)
- Annabell Linck
- Institute for Molecular Bioscience, Goethe University, Frankfurt, Germany
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50
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Cobbold SA, Vaughan AM, Lewis IA, Painter HJ, Camargo N, Perlman DH, Fishbaugher M, Healer J, Cowman AF, Kappe SHI, Llinás M. Kinetic flux profiling elucidates two independent acetyl-CoA biosynthetic pathways in Plasmodium falciparum. J Biol Chem 2013; 288:36338-50. [PMID: 24163372 DOI: 10.1074/jbc.m113.503557] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The malaria parasite Plasmodium falciparum depends on glucose to meet its energy requirements during blood-stage development. Although glycolysis is one of the best understood pathways in the parasite, it is unclear if glucose metabolism appreciably contributes to the acetyl-CoA pools required for tricarboxylic acid metabolism (TCA) cycle and fatty acid biosynthesis. P. falciparum possesses a pyruvate dehydrogenase (PDH) complex that is localized to the apicoplast, a specialized quadruple membrane organelle, suggesting that separate acetyl-CoA pools are likely. Herein, we analyze PDH-deficient parasites using rapid stable-isotope labeling and show that PDH does not appreciably contribute to acetyl-CoA synthesis, tricarboxylic acid metabolism, or fatty acid synthesis in blood stage parasites. Rather, we find that acetyl-CoA demands are supplied through a "PDH-like" enzyme and provide evidence that the branched-chain keto acid dehydrogenase (BCKDH) complex is performing this function. We also show that acetyl-CoA synthetase can be a significant contributor to acetyl-CoA biosynthesis. Interestingly, the PDH-like pathway contributes glucose-derived acetyl-CoA to the TCA cycle in a stage-independent process, whereas anapleurotic carbon enters the TCA cycle via a stage-dependent phosphoenolpyruvate carboxylase/phosphoenolpyruvate carboxykinase process that decreases as the parasite matures. Although PDH-deficient parasites have no blood-stage growth defect, they are unable to progress beyond the oocyst phase of the parasite mosquito stage.
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Affiliation(s)
- Simon A Cobbold
- From the Department of Biochemistry and Molecular Biology and Center for Infectious Disease Dynamics, Pennsylvania State University, State College, Pennsylvania 16802
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