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Vengayil V, Niphadkar S, Adhikary S, Varahan S, Laxman S. The deubiquitinase Ubp3/Usp10 constrains glucose-mediated mitochondrial repression via phosphate budgeting. eLife 2024; 12:RP90293. [PMID: 39324403 PMCID: PMC11426969 DOI: 10.7554/elife.90293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2024] Open
Abstract
Many cells in high glucose repress mitochondrial respiration, as observed in the Crabtree and Warburg effects. Our understanding of biochemical constraints for mitochondrial activation is limited. Using a Saccharomyces cerevisiae screen, we identified the conserved deubiquitinase Ubp3 (Usp10), as necessary for mitochondrial repression. Ubp3 mutants have increased mitochondrial activity despite abundant glucose, along with decreased glycolytic enzymes, and a rewired glucose metabolic network with increased trehalose production. Utilizing ∆ubp3 cells, along with orthogonal approaches, we establish that the high glycolytic flux in glucose continuously consumes free Pi. This restricts mitochondrial access to inorganic phosphate (Pi), and prevents mitochondrial activation. Contrastingly, rewired glucose metabolism with enhanced trehalose production and reduced GAPDH (as in ∆ubp3 cells) restores Pi. This collectively results in increased mitochondrial Pi and derepression, while restricting mitochondrial Pi transport prevents activation. We therefore suggest that glycolytic flux-dependent intracellular Pi budgeting is a key constraint for mitochondrial repression.
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Affiliation(s)
- Vineeth Vengayil
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem)BangaloreIndia
- Manipal Academy of Higher EducationBangaloreIndia
| | - Shreyas Niphadkar
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem)BangaloreIndia
- Manipal Academy of Higher EducationBangaloreIndia
| | - Swagata Adhikary
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem)BangaloreIndia
- Manipal Academy of Higher EducationBangaloreIndia
| | - Sriram Varahan
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem)BangaloreIndia
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem)BangaloreIndia
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2
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Kumar R, Zhang F, Niphadkar S, Onu C, Vijjamarri AK, Greenberg ML, Laxman S, Hinnebusch AG. Decapping activators Edc3 and Scd6 act redundantly with Dhh1 in post-transcriptional repression of starvation-induced pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.28.610059. [PMID: 39257769 PMCID: PMC11383670 DOI: 10.1101/2024.08.28.610059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Degradation of many yeast mRNAs involves decapping by the Dcp1:Dcp2 complex. Previous studies on decapping activators Edc3 and Scd6 suggested their limited roles in mRNA decay. RNA-seq analysis of mutants lacking one or both proteins revealed that Scd6 and Edc3 have largely redundant activities in targeting numerous mRNAs for degradation that are masked in the single mutants. These transcripts also are frequently targeted by decapping activators Dhh1 and Pat1, and the collective evidence suggests that Scd6/Edc3 act interchangeably to recruit Dhh1 to Dcp2. Ribosome profiling shows that redundancy between Scd6 and Edc3 and their functional interactions with Dhh1 and Pat1 extend to translational repression of particular transcripts, including a cohort of poorly translated mRNAs displaying interdependent regulation by all four factors. Scd6/Edc3 also participate with Dhh1/Pat1 in post-transcriptional repression of proteins required for respiration and catabolism of alternative carbon sources, which are normally expressed only in limiting glucose. Simultaneously eliminating Scd6/Edc3 increases mitochondrial membrane potential and elevates metabolites of the tricarboxylic acid and glyoxylate cycles typically observed only during growth in low glucose. Thus, Scd6/Edc3 act redundantly, in parallel with Dhh1 and in cooperation with Pat1, to adjust gene expression to nutrient availability by controlling mRNA decapping and decay.
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Affiliation(s)
- Rakesh Kumar
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Fan Zhang
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Shreyas Niphadkar
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem) GKVK Post Bellary Road Bangalore 560065
| | - Chisom Onu
- Department of Biological Sciences, Wayne State University, Detroit, MI
| | - Anil Kumar Vijjamarri
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | | | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem) GKVK Post Bellary Road Bangalore 560065
| | - Alan G Hinnebusch
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
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3
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Racine L, Parmentier R, Niphadkar S, Chhun J, Martignoles JA, Delhommeau F, Laxman S, Paldi A. Metabolic adaptation pilots the differentiation of human hematopoietic cells. Life Sci Alliance 2024; 7:e202402747. [PMID: 38802246 PMCID: PMC11130395 DOI: 10.26508/lsa.202402747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/12/2024] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
A continuous supply of energy is an essential prerequisite for survival and represents the highest priority for the cell. We hypothesize that cell differentiation is a process of optimization of energy flow in a changing environment through phenotypic adaptation. The mechanistic basis of this hypothesis is provided by the established link between core energy metabolism and epigenetic covalent modifications of chromatin. This theory predicts that early metabolic perturbations impact subsequent differentiation. To test this, we induced transient metabolic perturbations in undifferentiated human hematopoietic cells using pharmacological inhibitors targeting key metabolic reactions. We recorded changes in chromatin structure and gene expression, as well as phenotypic alterations by single-cell ATAC and RNA sequencing, time-lapse microscopy, and flow cytometry. Our observations suggest that these metabolic perturbations are shortly followed by alterations in chromatin structure, leading to changes in gene expression. We also show that these transient fluctuations alter the differentiation potential of the cells.
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Affiliation(s)
- Laëtitia Racine
- https://ror.org/02en5vm52 Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, Paris, France
- https://ror.org/046b3cj80 Ecole Pratique des Hautes Etudes, PSL Research University, Paris, France
- AP-HP, SIRIC CURAMUS, Hôpital Saint-Antoine, Service d'Hématologie Biologique, Paris, France
- OPALE Carnot Institute, Paris, France
| | - Romuald Parmentier
- https://ror.org/02en5vm52 Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, Paris, France
- https://ror.org/046b3cj80 Ecole Pratique des Hautes Etudes, PSL Research University, Paris, France
- AP-HP, SIRIC CURAMUS, Hôpital Saint-Antoine, Service d'Hématologie Biologique, Paris, France
- OPALE Carnot Institute, Paris, France
| | - Shreyas Niphadkar
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem), Bangalore, India
| | - Julie Chhun
- https://ror.org/02en5vm52 Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, Paris, France
- https://ror.org/046b3cj80 Ecole Pratique des Hautes Etudes, PSL Research University, Paris, France
- AP-HP, SIRIC CURAMUS, Hôpital Saint-Antoine, Service d'Hématologie Biologique, Paris, France
- OPALE Carnot Institute, Paris, France
| | - Jean-Alain Martignoles
- https://ror.org/02en5vm52 Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, Paris, France
- AP-HP, SIRIC CURAMUS, Hôpital Saint-Antoine, Service d'Hématologie Biologique, Paris, France
- OPALE Carnot Institute, Paris, France
| | - François Delhommeau
- https://ror.org/02en5vm52 Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, Paris, France
- AP-HP, SIRIC CURAMUS, Hôpital Saint-Antoine, Service d'Hématologie Biologique, Paris, France
- OPALE Carnot Institute, Paris, France
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem), Bangalore, India
| | - Andras Paldi
- https://ror.org/02en5vm52 Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, Paris, France
- https://ror.org/046b3cj80 Ecole Pratique des Hautes Etudes, PSL Research University, Paris, France
- AP-HP, SIRIC CURAMUS, Hôpital Saint-Antoine, Service d'Hématologie Biologique, Paris, France
- OPALE Carnot Institute, Paris, France
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4
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Dey P, Rajalaxmi S, Saha P, Thakur PS, Hashmi MA, Lal H, Saini N, Singh N, Ramanathan A. Cold-shock proteome of myoblasts reveals role of RBM3 in promotion of mitochondrial metabolism and myoblast differentiation. Commun Biol 2024; 7:515. [PMID: 38688991 PMCID: PMC11061143 DOI: 10.1038/s42003-024-06196-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
Adaptation to hypothermia is important for skeletal muscle cells under physiological stress and is used for therapeutic hypothermia (mild hypothermia at 32 °C). We show that hypothermic preconditioning at 32 °C for 72 hours improves the differentiation of skeletal muscle myoblasts using both C2C12 and primary myoblasts isolated from 3 month and 18-month-old mice. We analyzed the cold-shock proteome of myoblasts exposed to hypothermia (32 °C for 6 and 48 h) and identified significant changes in pathways related to RNA processing and central carbon, fatty acid, and redox metabolism. The analysis revealed that levels of the cold-shock protein RBM3, an RNA-binding protein, increases with both acute and chronic exposure to hypothermic stress, and is necessary for the enhanced differentiation and maintenance of mitochondrial metabolism. We also show that overexpression of RBM3 at 37 °C is sufficient to promote mitochondrial metabolism, cellular proliferation, and differentiation of C2C12 and primary myoblasts. Proteomic analysis of C2C12 myoblasts overexpressing RBM3 show significant enrichment of pathways involved in fatty acid metabolism, RNA metabolism and the electron transport chain. Overall, we show that the cold-shock protein RBM3 is a critical factor that can be used for controlling the metabolic network of myoblasts.
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Affiliation(s)
- Paulami Dey
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India
- SASTRA Deemed University, Tirumalaisamudram, Thanjavur, 613401, Tamil Nadu, India
| | - Srujanika Rajalaxmi
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India
| | - Pushpita Saha
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India
| | - Purvi Singh Thakur
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India
| | - Maroof Athar Hashmi
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India
- Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Heera Lal
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India
- Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Nistha Saini
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India
| | - Nirpendra Singh
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India
| | - Arvind Ramanathan
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India.
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5
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Das M, Sreedharan S, Shee S, Malhotra N, Nandy M, Banerjee U, Kohli S, Rajmani RS, Chandra N, Seshasayee ASN, Laxman S, Singh A. Cysteine desulfurase (IscS)-mediated fine-tuning of bioenergetics and SUF expression prevents Mycobacterium tuberculosis hypervirulence. SCIENCE ADVANCES 2023; 9:eadh2858. [PMID: 38091389 PMCID: PMC10848736 DOI: 10.1126/sciadv.adh2858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 11/10/2023] [Indexed: 12/18/2023]
Abstract
Iron-sulfur (Fe-S) biogenesis requires multiprotein assembly systems, SUF and ISC, in most prokaryotes. M. tuberculosis (Mtb) encodes a complete SUF system, the depletion of which was bactericidal. The ISC operon is truncated to a single gene iscS (cysteine desulfurase), whose function remains uncertain. Here, we show that MtbΔiscS is bioenergetically deficient and hypersensitive to oxidative stress, antibiotics, and hypoxia. MtbΔiscS resisted killing by nitric oxide (NO). RNA sequencing indicates that IscS is important for expressing regulons of DosR and Fe-S-containing transcription factors, WhiB3 and SufR. Unlike wild-type Mtb, MtbΔiscS could not enter a stable persistent state, continued replicating in mice, and showed hypervirulence. The suf operon was overexpressed in MtbΔiscS during infection in a NO-dependent manner. Suppressing suf expression in MtbΔiscS either by CRISPR interference or upon infection in inducible NO-deficient mice arrests hypervirulence. Together, Mtb redesigned the ISC system to "fine-tune" the expression of SUF machinery for establishing persistence without causing detrimental disease in the host.
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Affiliation(s)
- Mayashree Das
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Sreesa Sreedharan
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore 560065, India
- School of Chemical and Biotechnology, (SASTRA)-Deemed to be University, Thanjavur 613401, India
| | - Somnath Shee
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Nitish Malhotra
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research (TIFR), Bangalore 560065, India
| | - Meghna Nandy
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research (TIFR), Bangalore 560065, India
| | - Ushashi Banerjee
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sakshi Kohli
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Raju S. Rajmani
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Aswin Sai Narain Seshasayee
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research (TIFR), Bangalore 560065, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore 560065, India
| | - Amit Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
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6
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Ramirez-Hincapie S, Birk B, Ternes P, Giri V, Haake V, Herold M, Zickgraf FM, Verlohner A, Huener HA, Kamp H, Driemert P, Landsiedel R, Richling E, Funk-Weyer D, van Ravenzwaay B. A high-throughput metabolomics in vitro platform for the characterization of hepatotoxicity. Cell Biol Toxicol 2023; 39:2899-2917. [PMID: 37138123 PMCID: PMC10693528 DOI: 10.1007/s10565-023-09809-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/27/2023] [Indexed: 05/05/2023]
Abstract
Cell-based metabolomics provides multiparametric physiologically relevant readouts that can be highly advantageous for improved, biologically based decision making in early stages of compound development. Here, we present the development of a 96-well plate LC-MS/MS-based targeted metabolomics screening platform for the classification of liver toxicity modes of action (MoAs) in HepG2 cells. Different parameters of the workflow (cell seeding density, passage number, cytotoxicity testing, sample preparation, metabolite extraction, analytical method, and data processing) were optimized and standardized to increase the efficiency of the testing platform. The applicability of the system was tested with seven substances known to be representative of three different liver toxicity MoAs (peroxisome proliferation, liver enzyme induction, and liver enzyme inhibition). Five concentrations per substance, aimed at covering the complete dose-response curve, were analyzed and 221 uniquely identified metabolites were measured, annotated, and allocated in 12 different metabolite classes such as amino acids, carbohydrates, energy metabolism, nucleobases, vitamins and cofactors, and diverse lipid classes. Multivariate and univariate analyses showed a dose response of the metabolic effects, a clear differentiation between liver toxicity MoAs and resulted in the identification of metabolite patterns specific for each MoA. Key metabolites indicative of both general and mechanistic specific hepatotoxicity were identified. The method presented here offers a multiparametric, mechanistic-based, and cost-effective hepatotoxicity screening that provides MoA classification and sheds light into the pathways involved in the toxicological mechanism. This assay can be implemented as a reliable compound screening platform for improved safety assessment in early compound development pipelines.
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Affiliation(s)
| | - Barbara Birk
- BASF SE, Experimental Toxicology and Ecology, Ludwigshafen, Germany
| | | | - Varun Giri
- BASF SE, Experimental Toxicology and Ecology, Ludwigshafen, Germany
| | | | | | | | | | | | | | | | - Robert Landsiedel
- BASF SE, Experimental Toxicology and Ecology, Ludwigshafen, Germany
- Free University of Berlin, Pharmacy, Pharmacology and Toxicology, Berlin, Germany
| | - Elke Richling
- Food Chemistry and Toxicology, Department of Chemistry, University of Kaiserslautern-Landau, Kaiserslautern, Germany
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7
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Prasad A, Sreedharan S, Bakthavachalu B, Laxman S. Eggs of the mosquito Aedes aegypti survive desiccation by rewiring their polyamine and lipid metabolism. PLoS Biol 2023; 21:e3002342. [PMID: 37874799 PMCID: PMC10597479 DOI: 10.1371/journal.pbio.3002342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 09/20/2023] [Indexed: 10/26/2023] Open
Abstract
Upon water loss, some organisms pause their life cycles and escape death. While widespread in microbes, this is less common in animals. Aedes mosquitoes are vectors for viral diseases. Aedes eggs can survive dry environments, but molecular and cellular principles enabling egg survival through desiccation remain unknown. In this report, we find that Aedes aegypti eggs, in contrast to Anopheles stephensi, survive desiccation by acquiring desiccation tolerance at a late developmental stage. We uncover unique proteome and metabolic state changes in Aedes embryos during desiccation that reflect reduced central carbon metabolism, rewiring towards polyamine production, and enhanced lipid utilisation for energy and polyamine synthesis. Using inhibitors targeting these processes in blood-fed mosquitoes that lay eggs, we infer a two-step process of desiccation tolerance in Aedes eggs. The metabolic rewiring towards lipid breakdown and dependent polyamine accumulation confers resistance to desiccation. Furthermore, rapid lipid breakdown is required to fuel energetic requirements upon water reentry to enable larval hatching and survival upon rehydration. This study is fundamental to understanding Aedes embryo survival and in controlling the spread of these mosquitoes.
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Affiliation(s)
- Anjana Prasad
- Tata Institute for Genetics and Society (TIGS) Centre at inStem, Bangalore, India
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem), Bangalore, India
| | - Sreesa Sreedharan
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem), Bangalore, India
- SASTRA University, Thirumalaisamudram, Thanjavur, India
| | - Baskar Bakthavachalu
- Tata Institute for Genetics and Society (TIGS) Centre at inStem, Bangalore, India
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Mandi, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem), Bangalore, India
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8
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Shee S, Veetil RT, Mohanraj K, Das M, Malhotra N, Bandopadhyay D, Beig H, Birua S, Niphadkar S, Nagarajan SN, Sinha VK, Thakur C, Rajmani RS, Chandra N, Laxman S, Singh M, Samal A, Seshasayee AN, Singh A. Biosensor-integrated transposon mutagenesis reveals rv0158 as a coordinator of redox homeostasis in Mycobacterium tuberculosis. eLife 2023; 12:e80218. [PMID: 37642294 PMCID: PMC10501769 DOI: 10.7554/elife.80218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/25/2023] [Indexed: 08/31/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is evolutionarily equipped to resist exogenous reactive oxygen species (ROS) but shows vulnerability to an increase in endogenous ROS (eROS). Since eROS is an unavoidable consequence of aerobic metabolism, understanding how Mtb manages eROS levels is essential yet needs to be characterized. By combining the Mrx1-roGFP2 redox biosensor with transposon mutagenesis, we identified 368 genes (redoxosome) responsible for maintaining homeostatic levels of eROS in Mtb. Integrating redoxosome with a global network of transcriptional regulators revealed a hypothetical protein (Rv0158) as a critical node managing eROS in Mtb. Disruption of rv0158 (rv0158 KO) impaired growth, redox balance, respiration, and metabolism of Mtb on glucose but not on fatty acids. Importantly, rv0158 KO exhibited enhanced growth on propionate, and the Rv0158 protein directly binds to methylmalonyl-CoA, a key intermediate in propionate catabolism. Metabolite profiling, ChIP-Seq, and gene-expression analyses indicate that Rv0158 manages metabolic neutralization of propionate toxicity by regulating the methylcitrate cycle. Disruption of rv0158 enhanced the sensitivity of Mtb to oxidative stress, nitric oxide, and anti-TB drugs. Lastly, rv0158 KO showed poor survival in macrophages and persistence defect in mice. Our results suggest that Rv0158 is a metabolic integrator for carbon metabolism and redox balance in Mtb.
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Affiliation(s)
- Somnath Shee
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | | | - Karthikeyan Mohanraj
- The Institute of Mathematical Sciences, A CI of Homi Bhabha National InstituteChennaiIndia
| | - Mayashree Das
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | | | | | - Hussain Beig
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | - Shalini Birua
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | - Shreyas Niphadkar
- Institute for Stem Cell Science and Regenerative MedicineBangaloreIndia
| | - Sathya Narayanan Nagarajan
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | - Vikrant Kumar Sinha
- Molecular Biophysics Unit, Indian Institute of Science BangaloreBangaloreIndia
| | - Chandrani Thakur
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
| | - Raju S Rajmani
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative MedicineBangaloreIndia
| | - Mahavir Singh
- Molecular Biophysics Unit, Indian Institute of Science BangaloreBangaloreIndia
| | - Areejit Samal
- The Institute of Mathematical Sciences, A CI of Homi Bhabha National InstituteChennaiIndia
| | | | - Amit Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
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9
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Saini N, Naaz A, Metur SP, Gahlot P, Walvekar A, Dutta A, Davathamizhan U, Sarin A, Laxman S. Methionine uptake via the SLC43A2 transporter is essential for regulatory T-cell survival. Life Sci Alliance 2022; 5:5/12/e202201663. [PMID: 36260753 PMCID: PMC9463494 DOI: 10.26508/lsa.202201663] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/30/2022] [Accepted: 08/30/2022] [Indexed: 11/24/2022] Open
Abstract
Regulatory T cells survive after IL-2 withdrawal by taking up and using methionine through the SLC43A2 transporter in a Notch1-dependent manner. Cell death, survival, or growth decisions in T-cell subsets depend on interplay between cytokine-dependent and metabolic processes. The metabolic requirements of T-regulatory cells (Tregs) for their survival and how these are satisfied remain unclear. Herein, we identified a necessary requirement of methionine uptake and usage for Tregs survival upon IL-2 deprivation. Activated Tregs have high methionine uptake and usage to S-adenosyl methionine, and this uptake is essential for Tregs survival in conditions of IL-2 deprivation. We identify a solute carrier protein SLC43A2 transporter, regulated in a Notch1-dependent manner that is necessary for this methionine uptake and Tregs viability. Collectively, we uncover a specifically regulated mechanism of methionine import in Tregs that is required for cells to adapt to cytokine withdrawal. We highlight the need for methionine availability and metabolism in contextually regulating cell death in this immunosuppressive population of T cells.
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Affiliation(s)
- Neetu Saini
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem), Bengaluru, India
| | - Afsana Naaz
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem), Bengaluru, India
| | - Shree Padma Metur
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem), Bengaluru, India
| | - Pinki Gahlot
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem), Bengaluru, India
| | - Adhish Walvekar
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem), Bengaluru, India
| | - Anupam Dutta
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem), Bengaluru, India
| | | | - Apurva Sarin
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem), Bengaluru, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem), Bengaluru, India
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10
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Bandyopadhyay P, Pramanick I, Biswas R, PS S, Sreedharan S, Singh S, Rajmani RS, Laxman S, Dutta S, Singh A. S-Adenosylmethionine-responsive cystathionine β-synthase modulates sulfur metabolism and redox balance in Mycobacterium tuberculosis. SCIENCE ADVANCES 2022; 8:eabo0097. [PMID: 35749503 PMCID: PMC9232105 DOI: 10.1126/sciadv.abo0097] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/09/2022] [Indexed: 05/10/2023]
Abstract
Methionine and cysteine metabolisms are important for the survival and pathogenesis of Mycobacterium tuberculosis (Mtb). The transsulfuration pathway converts methionine to cysteine and represents an important link between antioxidant and methylation metabolism in diverse organisms. Using a combination of biochemistry and cryo-electron microscopy, we characterized the first enzyme of the transsulfuration pathway, cystathionine β-synthase (MtbCbs) in Mtb. We demonstrated that MtbCbs is a heme-less, pyridoxal-5'-phosphate-containing enzyme, allosterically activated by S-adenosylmethionine (SAM). The atomic model of MtbCbs in its native and SAM-bound conformations revealed a unique mode of SAM-dependent allosteric activation. Further, SAM stabilized MtbCbs by sterically occluding proteasomal degradation, which was crucial for supporting methionine and redox metabolism in Mtb. Genetic deficiency of MtbCbs reduced Mtb survival upon homocysteine overload in vitro, inside macrophages, and in mice coinfected with HIV. Thus, the MtbCbs-SAM axis constitutes an important mechanism of coordinating sulfur metabolism in Mtb.
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Affiliation(s)
- Parijat Bandyopadhyay
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Ishika Pramanick
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Rupam Biswas
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Sabarinath PS
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka 560065, India
| | - Sreesa Sreedharan
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka 560065, India
| | - Shalini Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Raju S. Rajmani
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka 560065, India
| | - Somnath Dutta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Amit Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, Karnataka 560012, India
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11
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A multi-omics analysis reveals that the lysine deacetylase ABHD14B influences glucose metabolism in mammals. J Biol Chem 2022; 298:102128. [PMID: 35700823 PMCID: PMC9270251 DOI: 10.1016/j.jbc.2022.102128] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/30/2022] Open
Abstract
The sirtuins and histone deacetylases are the best characterized members of the lysine deacetylase (KDAC) enzyme family. Recently, we annotated the “orphan” enzyme ABHD14B (α/β-hydrolase domain containing protein # 14B) as a novel KDAC and showed this enzyme’s ability to transfer an acetyl-group from protein lysine residue(s) to coenzyme-A to yield acetyl-coenzyme-A, thereby, expanding the repertoire of this enzyme family. However, the role of ABHD14B in metabolic processes is not fully elucidated. Here, we investigated the role of this enzyme using mammalian cell knockdowns in a combined transcriptomics and metabolomics analysis. We found from these complementary experiments in vivo that the loss of ABHD14B results in significantly altered glucose metabolism, specifically the decreased flux of glucose through glycolysis and the citric acid cycle. Further, we show that depleting hepatic ABHD14B in mice also results in defective systemic glucose metabolism, particularly during fasting. Taken together, our findings illuminate the important metabolic functions that the KDAC ABHD14B plays in mammalian physiology and poses new questions regarding the role of this hitherto cryptic metabolism-regulating enzyme.
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12
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Tripathi A, Anand K, Das M, O'Niel RA, P S S, Thakur C, R L RR, Rajmani RS, Chandra N, Laxman S, Singh A. Mycobacterium tuberculosis requires SufT for Fe-S cluster maturation, metabolism, and survival in vivo. PLoS Pathog 2022; 18:e1010475. [PMID: 35427399 PMCID: PMC9045647 DOI: 10.1371/journal.ppat.1010475] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 04/27/2022] [Accepted: 03/25/2022] [Indexed: 11/18/2022] Open
Abstract
Iron-sulfur (Fe-S) cluster proteins carry out essential cellular functions in diverse organisms, including the human pathogen Mycobacterium tuberculosis (Mtb). The mechanisms underlying Fe-S cluster biogenesis are poorly defined in Mtb. Here, we show that Mtb SufT (Rv1466), a DUF59 domain-containing essential protein, is required for the Fe-S cluster maturation. Mtb SufT homodimerizes and interacts with Fe-S cluster biogenesis proteins; SufS and SufU. SufT also interacts with the 4Fe-4S cluster containing proteins; aconitase and SufR. Importantly, a hyperactive cysteine in the DUF59 domain mediates interaction of SufT with SufS, SufU, aconitase, and SufR. We efficiently repressed the expression of SufT to generate a SufT knock-down strain in Mtb (SufT-KD) using CRISPR interference. Depleting SufT reduces aconitase's enzymatic activity under standard growth conditions and in response to oxidative stress and iron limitation. The SufT-KD strain exhibited defective growth and an altered pool of tricarboxylic acid cycle intermediates, amino acids, and sulfur metabolites. Using Seahorse Extracellular Flux analyzer, we demonstrated that SufT depletion diminishes glycolytic rate and oxidative phosphorylation in Mtb. The SufT-KD strain showed defective survival upon exposure to oxidative stress and nitric oxide. Lastly, SufT depletion reduced the survival of Mtb in macrophages and attenuated the ability of Mtb to persist in mice. Altogether, SufT assists in Fe-S cluster maturation and couples this process to bioenergetics of Mtb for survival under low and high demand for Fe-S clusters.
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Affiliation(s)
- Ashutosh Tripathi
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Kushi Anand
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Mayashree Das
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Ruchika Annie O'Niel
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India
| | - Sabarinath P S
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India
| | - Chandrani Thakur
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Raghunatha Reddy R L
- Regional Horticultural Research and Extension Centre (RHREK), GKVK, Bengaluru, India
| | - Raju S Rajmani
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India
| | - Amit Singh
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
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13
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Rashida Z, Srinivasan R, Cyanam M, Laxman S. Kog1/Raptor mediates metabolic rewiring during nutrient limitation by controlling SNF1/AMPK activity. SCIENCE ADVANCES 2021; 7:eabe5544. [PMID: 33853774 PMCID: PMC8046376 DOI: 10.1126/sciadv.abe5544] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 02/26/2021] [Indexed: 05/04/2023]
Abstract
In changing environments, cells modulate resource budgeting through distinct metabolic routes to control growth. Accordingly, the TORC1 and SNF1/AMPK pathways operate contrastingly in nutrient replete or limited environments to maintain homeostasis. The functions of TORC1 under glucose and amino acid limitation are relatively unknown. We identified a modified form of the yeast TORC1 component Kog1/Raptor, which exhibits delayed growth exclusively during glucose and amino acid limitations. Using this, we found a necessary function for Kog1 in these conditions where TORC1 kinase activity is undetectable. Metabolic flux and transcriptome analysis revealed that Kog1 controls SNF1-dependent carbon flux apportioning between glutamate/amino acid biosynthesis and gluconeogenesis. Kog1 regulates SNF1/AMPK activity and outputs and mediates a rapamycin-independent activation of the SNF1 targets Mig1 and Cat8. This enables effective glucose derepression, gluconeogenesis activation, and carbon allocation through different pathways. Therefore, Kog1 centrally regulates metabolic homeostasis and carbon utilization during nutrient limitation by managing SNF1 activity.
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Affiliation(s)
- Zeenat Rashida
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Post, Bellary Road, Bangalore 560065, India
- Manipal Academy of Higher Education, Manipal 576104, India
| | - Rajalakshmi Srinivasan
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Post, Bellary Road, Bangalore 560065, India
| | - Meghana Cyanam
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Post, Bellary Road, Bangalore 560065, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Post, Bellary Road, Bangalore 560065, India.
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14
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Walvekar AS, Kadamur G, Sreedharan S, Gupta R, Srinivasan R, Laxman S. Methylated PP2A stabilizes Gcn4 to enable a methionine-induced anabolic program. J Biol Chem 2020; 295:18390-18405. [PMID: 33122193 PMCID: PMC7939465 DOI: 10.1074/jbc.ra120.014248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 10/25/2020] [Indexed: 11/06/2022] Open
Abstract
Methionine, through S-adenosylmethionine, activates a multifaceted growth program in which ribosome biogenesis, carbon metabolism, and amino acid and nucleotide biosynthesis are induced. This growth program requires the activity of the Gcn4 transcription factor (called ATF4 in mammals), which facilitates the supply of metabolic precursors that are essential for anabolism. However, how Gcn4 itself is regulated in the presence of methionine is unknown. Here, we discover that Gcn4 protein levels are increased by methionine, despite conditions of high cell growth and translation (in which the roles of Gcn4 are not well-studied). We demonstrate that this mechanism of Gcn4 induction is independent of transcription, as well as the conventional Gcn2/eIF2α-mediated increased translation of Gcn4. Instead, when methionine is abundant, Gcn4 phosphorylation is decreased, which reduces its ubiquitination and therefore degradation. Gcn4 is dephosphorylated by the protein phosphatase 2A (PP2A); our data show that when methionine is abundant, the conserved methyltransferase Ppm1 methylates and alters the activity of the catalytic subunit of PP2A, shifting the balance of Gcn4 toward a dephosphorylated, stable state. The absence of Ppm1 or the loss of the PP2A methylation destabilizes Gcn4 even when methionine is abundant, leading to collapse of the Gcn4-dependent anabolic program. These findings reveal a novel, methionine-dependent signaling and regulatory axis. Here methionine directs the conserved methyltransferase Ppm1 via its target phosphatase PP2A to selectively stabilize Gcn4. Through this, cells conditionally modify a major phosphatase to stabilize a metabolic master regulator and drive anabolism.
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Affiliation(s)
- Adhish S Walvekar
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India
| | - Ganesh Kadamur
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India
| | - Sreesa Sreedharan
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India; School of Chemical and Biotechnology, SASTRA University, Tanjavur, India
| | - Ritu Gupta
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India
| | | | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India.
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15
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Letertre MPM, Myridakis A, Whiley L, Camuzeaux S, Lewis MR, Chappell KE, Thaikkatil A, Dumas ME, Nicholson JK, Swann JR, Wilson ID. A targeted ultra performance liquid chromatography - Tandem mass spectrometric assay for tyrosine and metabolites in urine and plasma: Application to the effects of antibiotics on mice. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1164:122511. [PMID: 33460909 DOI: 10.1016/j.jchromb.2020.122511] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 12/20/2022]
Abstract
Tyrosine plays a key role in mammalian biochemistry and defects in its metabolism (e.g., tyrosinemia, alkaptonuria etc.) have significant adverse consequences for those affected if left untreated. In addition, gut bacterially-derived p-cresol and its metabolites are of interest as a result of various effects on host xenobiotic metabolism. A fit-for-purpose quantitative ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) assay was developed to target and quantify tyrosine and eleven metabolites in urine and plasma. Dansylation, using dansyl chloride, was used to improve chromatographic and mass spectral properties for tyrosine and nine phenolic metabolites, with detection using positive electrospray ionisation (ESI). The sulfate and glucuronide conjugates of p-cresol, where the phenol group was blocked, were quantified intact, using negative ESI via polarity switching during the same run. Sample preparation for urine and plasma involved deproteinization by solvent precipitation (of acetonitrile:isopropyl alcohol (1:1 v/v)) followed by in situ dansylation in 96 well plates. To minimize sample and solvent usage, and maximize sensitivity, analysis was performed using microbore reversed-phase gradient UPLC on a C8 phase with a 7.5 min. cycle time. The coefficients of variation obtained were <15%, with lower limits of quantification ranging from 5 to 250 nM depending upon the analyte. The method was applied to plasma and urine samples obtained from mice placed on a high tyrosine diet with one subgroup of animals subsequently receiving antibiotics to suppress the gut microbiota. Whilst plasma profiles were largely unaffected by antibiotic treatment clear reductions in the amount of p-cresol sulfate and p-cresol glucuronide excreted in the urine were observed for these mice.
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Affiliation(s)
- Marine P M Letertre
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, SW7 2AZ, UK.
| | - Antonis Myridakis
- Department of Surgery and Cancer, Imperial College London, SW7 2AZ, UK
| | - Luke Whiley
- Australian National Phenome Centre, Health Futures Institute, Murdoch University, Harry Perkins South Building, Perth, WA 6150, Australia; Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Murdoch Perth, WA, 6150, Australia; National Phenome Centre, Dept of metabolism, Digestion and Reproduction, Imperial College London, W12 0NN
| | - Stéphane Camuzeaux
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, SW7 2AZ, UK; National Phenome Centre, Dept of metabolism, Digestion and Reproduction, Imperial College London, W12 0NN
| | - Matthew R Lewis
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, SW7 2AZ, UK; National Phenome Centre, Dept of metabolism, Digestion and Reproduction, Imperial College London, W12 0NN
| | - Katie E Chappell
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, SW7 2AZ, UK; National Phenome Centre, Dept of metabolism, Digestion and Reproduction, Imperial College London, W12 0NN
| | - Annie Thaikkatil
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, SW7 2AZ, UK
| | - Marc-Emmanuel Dumas
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, SW7 2AZ, UK
| | - Jeremy K Nicholson
- Australian National Phenome Centre, Health Futures Institute, Murdoch University, Harry Perkins South Building, Perth, WA 6150, Australia; Institute of Global Health Innovation, Imperial College London, Level 1, Faculty Building South Kensington Campus, London SW72NA, UK
| | - Jonathan R Swann
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, SW7 2AZ, UK; School of Human Development and Health, Faculty of Medicine, University of Southampton, UK
| | - Ian D Wilson
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, SW7 2AZ, UK.
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16
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Srinivasan R, Walvekar AS, Rashida Z, Seshasayee A, Laxman S. Genome-scale reconstruction of Gcn4/ATF4 networks driving a growth program. PLoS Genet 2020; 16:e1009252. [PMID: 33378328 PMCID: PMC7773203 DOI: 10.1371/journal.pgen.1009252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 11/04/2020] [Indexed: 12/13/2022] Open
Abstract
Growth and starvation are considered opposite ends of a spectrum. To sustain growth, cells use coordinated gene expression programs and manage biomolecule supply in order to match the demands of metabolism and translation. Global growth programs complement increased ribosomal biogenesis with sufficient carbon metabolism, amino acid and nucleotide biosynthesis. How these resources are collectively managed is a fundamental question. The role of the Gcn4/ATF4 transcription factor has been best studied in contexts where cells encounter amino acid starvation. However, high Gcn4 activity has been observed in contexts of rapid cell proliferation, and the roles of Gcn4 in such growth contexts are unclear. Here, using a methionine-induced growth program in yeast, we show that Gcn4/ATF4 is the fulcrum that maintains metabolic supply in order to sustain translation outputs. By integrating matched transcriptome and ChIP-Seq analysis, we decipher genome-wide direct and indirect roles for Gcn4 in this growth program. Genes that enable metabolic precursor biosynthesis indispensably require Gcn4; contrastingly ribosomal genes are partly repressed by Gcn4. Gcn4 directly binds promoter-regions and transcribes a subset of metabolic genes, particularly driving lysine and arginine biosynthesis. Gcn4 also globally represses lysine and arginine enriched transcripts, which include genes encoding the translation machinery. The Gcn4 dependent lysine and arginine supply thereby maintains the synthesis of the translation machinery. This is required to maintain translation capacity. Gcn4 consequently enables metabolic-precursor supply to bolster protein synthesis, and drive a growth program. Thus, we illustrate how growth and starvation outcomes are both controlled using the same Gcn4 transcriptional outputs that function in distinct contexts.
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Affiliation(s)
- Rajalakshmi Srinivasan
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK post, Bangalore, India
| | - Adhish S. Walvekar
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK post, Bangalore, India
| | - Zeenat Rashida
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK post, Bangalore, India
| | - Aswin Seshasayee
- National Centre for Biological Sciences–TIFR, GKVK post, Bellary Road, Bangalore, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK post, Bangalore, India
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17
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Bhatia M, Thakur J, Suyal S, Oniel R, Chakraborty R, Pradhan S, Sharma M, Sengupta S, Laxman S, Masakapalli SK, Bachhawat AK. Allosteric inhibition of MTHFR prevents futile SAM cycling and maintains nucleotide pools in one-carbon metabolism. J Biol Chem 2020; 295:16037-16057. [PMID: 32934008 PMCID: PMC7681022 DOI: 10.1074/jbc.ra120.015129] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/12/2020] [Indexed: 01/05/2023] Open
Abstract
Methylenetetrahydrofolate reductase (MTHFR) links the folate cycle to the methionine cycle in one-carbon metabolism. The enzyme is known to be allosterically inhibited by SAM for decades, but the importance of this regulatory control to one-carbon metabolism has never been adequately understood. To shed light on this issue, we exchanged selected amino acid residues in a highly conserved stretch within the regulatory region of yeast MTHFR to create a series of feedback-insensitive, deregulated mutants. These were exploited to investigate the impact of defective allosteric regulation on one-carbon metabolism. We observed a strong growth defect in the presence of methionine. Biochemical and metabolite analysis revealed that both the folate and methionine cycles were affected in these mutants, as was the transsulfuration pathway, leading also to a disruption in redox homeostasis. The major consequences, however, appeared to be in the depletion of nucleotides. 13C isotope labeling and metabolic studies revealed that the deregulated MTHFR cells undergo continuous transmethylation of homocysteine by methyltetrahydrofolate (CH3THF) to form methionine. This reaction also drives SAM formation and further depletes ATP reserves. SAM was then cycled back to methionine, leading to futile cycles of SAM synthesis and recycling and explaining the necessity for MTHFR to be regulated by SAM. The study has yielded valuable new insights into the regulation of one-carbon metabolism, and the mutants appear as powerful new tools to further dissect out the intersection of one-carbon metabolism with various pathways both in yeasts and in humans.
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Affiliation(s)
- Muskan Bhatia
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, S.A.S. Nagar, Punjab, India
| | - Jyotika Thakur
- BioX Center, School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, India
| | - Shradha Suyal
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, S.A.S. Nagar, Punjab, India
| | - Ruchika Oniel
- Institute for Stem Cell Science and Regenerative Medicine (inStem), NCBS-TIFR Campus, Bangalore, India
| | - Rahul Chakraborty
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Shalini Pradhan
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, S.A.S. Nagar, Punjab, India
| | - Shantanu Sengupta
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem), NCBS-TIFR Campus, Bangalore, India
| | - Shyam Kumar Masakapalli
- BioX Center, School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, India
| | - Anand Kumar Bachhawat
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, S.A.S. Nagar, Punjab, India.
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18
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Varahan S, Sinha V, Walvekar A, Krishna S, Laxman S. Resource plasticity-driven carbon-nitrogen budgeting enables specialization and division of labor in a clonal community. eLife 2020; 9:e57609. [PMID: 32876564 PMCID: PMC7467726 DOI: 10.7554/elife.57609] [Citation(s) in RCA: 4] [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: 04/09/2020] [Accepted: 07/31/2020] [Indexed: 11/13/2022] Open
Abstract
Previously, we found that in glucose-limited Saccharomyces cerevisiae colonies, metabolic constraints drive cells into groups exhibiting gluconeogenic or glycolytic states. In that study, threshold amounts of trehalose - a limiting, produced carbon-resource, controls the emergence and self-organization of cells exhibiting the glycolytic state, serving as a carbon source that fuels glycolysis (Varahan et al., 2019). We now discover that the plasticity of use of a non-limiting resource, aspartate, controls both resource production and the emergence of heterogeneous cell states, based on differential metabolic budgeting. In gluconeogenic cells, aspartate is a carbon source for trehalose production, while in glycolytic cells using trehalose for carbon, aspartate is predominantly a nitrogen source for nucleotide synthesis. This metabolic plasticity of aspartate enables carbon-nitrogen budgeting, thereby driving the biochemical self-organization of distinct cell states. Through this organization, cells in each state exhibit true division of labor, providing growth/survival advantages for the whole community.
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Affiliation(s)
- Sriram Varahan
- InStem - Institute for Stem Cell Science and Regenerative MedicineBangaloreIndia
| | - Vaibhhav Sinha
- Simons Centre for the Study of Living Machines, National Center for Biological Sciences, Tata Institute for Fundamental ResearchBangaloreIndia
- Manipal Academy of Higher EducationManipalIndia
| | - Adhish Walvekar
- InStem - Institute for Stem Cell Science and Regenerative MedicineBangaloreIndia
| | - Sandeep Krishna
- Simons Centre for the Study of Living Machines, National Center for Biological Sciences, Tata Institute for Fundamental ResearchBangaloreIndia
| | - Sunil Laxman
- InStem - Institute for Stem Cell Science and Regenerative MedicineBangaloreIndia
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19
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Bruhn C, Ajazi A, Ferrari E, Lanz MC, Batrin R, Choudhary R, Walvekar A, Laxman S, Longhese MP, Fabre E, Smolka MB, Foiani M. The Rad53 CHK1/CHK2-Spt21 NPAT and Tel1 ATM axes couple glucose tolerance to histone dosage and subtelomeric silencing. Nat Commun 2020; 11:4154. [PMID: 32814778 PMCID: PMC7438486 DOI: 10.1038/s41467-020-17961-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 07/23/2020] [Indexed: 12/14/2022] Open
Abstract
The DNA damage response (DDR) coordinates DNA metabolism with nuclear and non-nuclear processes. The DDR kinase Rad53CHK1/CHK2 controls histone degradation to assist DNA repair. However, Rad53 deficiency causes histone-dependent growth defects in the absence of DNA damage, pointing out unknown physiological functions of the Rad53-histone axis. Here we show that histone dosage control by Rad53 ensures metabolic homeostasis. Under physiological conditions, Rad53 regulates histone levels through inhibitory phosphorylation of the transcription factor Spt21NPAT on Ser276. Rad53-Spt21 mutants display severe glucose dependence, caused by excess histones through two separable mechanisms: dampening of acetyl-coenzyme A-dependent carbon metabolism through histone hyper-acetylation, and Sirtuin-mediated silencing of starvation-induced subtelomeric domains. We further demonstrate that repression of subtelomere silencing by physiological Tel1ATM and Rpd3HDAC activities coveys tolerance to glucose restriction. Our findings identify DDR mutations, histone imbalances and aberrant subtelomeric chromatin as interconnected causes of glucose dependence, implying that DDR kinases coordinate metabolism and epigenetic changes.
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Affiliation(s)
- Christopher Bruhn
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139, Milan, Italy.
| | - Arta Ajazi
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139, Milan, Italy
| | - Elisa Ferrari
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139, Milan, Italy
| | - Michael Charles Lanz
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Renaud Batrin
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Centre de Recherche St Louis, F-75010, Paris, France
| | - Ramveer Choudhary
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139, Milan, Italy
| | - Adhish Walvekar
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, Karnataka, 560065, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, Karnataka, 560065, India
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Edificio U3, Piazza della Scienza 2, 20126, Milan, Italy
| | - Emmanuelle Fabre
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Centre de Recherche St Louis, F-75010, Paris, France
| | - Marcus Bustamente Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Marco Foiani
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139, Milan, Italy.
- Università degli Studi di Milano, Via Festa del Perdono 7, 20122, Milan, Italy.
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20
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Grim CM, Luu GT, Sanchez LM. Staring into the void: demystifying microbial metabolomics. FEMS Microbiol Lett 2020; 366:5519856. [PMID: 31210257 DOI: 10.1093/femsle/fnz135] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/14/2019] [Indexed: 12/18/2022] Open
Abstract
Metabolites give us a window into the chemistry of microbes and are split into two subclasses: primary and secondary. Primary metabolites are required for life whereas secondary metabolites have historically been classified as those appearing after exponential growth and are not necessarily needed for survival. Many microbial species are estimated to produce hundreds of metabolites and can be affected by differing nutrients. Using various analytical techniques, metabolites can be directly detected in order to elucidate their biological significance. Currently, a single experiment can produce anywhere from megabytes to terabytes of data. This big data has motivated scientists to develop informatics tools to help target specific metabolites or sets of metabolites. Broadly, it is imperative to identify clear biological questions before embarking on a study of metabolites (metabolomics). For instance, studying the effect of a transposon insertion on phenazine biosynthesis in Pseudomonas is a very different from asking what molecules are present in a specific banana-derived strain of Pseudomonas. This review is meant to serve as a primer for a 'choose your own adventure' approach for microbiologists with limited mass spectrometry expertise, with a strong focus on liquid chromatography mass spectrometry based workflows developed or optimized within the past five years.
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Affiliation(s)
- Cynthia M Grim
- Department of Pharmaceutical Sciences, University of Ilinois at Chicago, 833 S Wood St, Chicago, IL 60612, USA
| | - Gordon T Luu
- Department of Pharmaceutical Sciences, University of Ilinois at Chicago, 833 S Wood St, Chicago, IL 60612, USA
| | - Laura M Sanchez
- Department of Pharmaceutical Sciences, University of Ilinois at Chicago, 833 S Wood St, Chicago, IL 60612, USA
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21
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Anabolic SIRT4 Exerts Retrograde Control over TORC1 Signaling by Glutamine Sparing in the Mitochondria. Mol Cell Biol 2020; 40:MCB.00212-19. [PMID: 31685549 DOI: 10.1128/mcb.00212-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/28/2019] [Indexed: 12/30/2022] Open
Abstract
Anabolic and catabolic signaling mediated via mTOR and AMPK (AMP-activated kinase) have to be intrinsically coupled to mitochondrial functions for maintaining homeostasis and mitigate cellular/organismal stress. Although glutamine is known to activate mTOR, whether and how differential mitochondrial utilization of glutamine impinges on mTOR signaling has been less explored. Mitochondrial SIRT4, which unlike other sirtuins is induced in a fed state, is known to inhibit catabolic signaling/pathways through the AMPK-PGC1α/SIRT1-peroxisome proliferator-activated receptor α (PPARα) axis and negatively regulate glutamine metabolism via the tricarboxylic acid cycle. However, physiological significance of SIRT4 functions during a fed state is still unknown. Here, we establish SIRT4 as key anabolic factor that activates TORC1 signaling and regulates lipogenesis, autophagy, and cell proliferation. Mechanistically, we demonstrate that the ability of SIRT4 to inhibit anaplerotic conversion of glutamine to α-ketoglutarate potentiates TORC1. Interestingly, we also show that mitochondrial glutamine sparing or utilization is critical for differentially regulating TORC1 under fed and fasted conditions. Moreover, we conclusively show that differential expression of SIRT4 during fed and fasted states is vital for coupling mitochondrial energetics and glutamine utilization with anabolic pathways. These significant findings also illustrate that SIRT4 integrates nutrient inputs with mitochondrial retrograde signals to maintain a balance between anabolic and catabolic pathways.
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22
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Gupta R, Laxman S. Steady-state and Flux-based Trehalose Estimation as an Indicator of Carbon Flow from Gluconeogenesis or Glycolysis. Bio Protoc 2020; 10:e3483. [PMID: 32181267 DOI: 10.21769/bioprotoc.3483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Trehalose (and glycogen) is a major storage carbohydrate in many cells, including S. cerevisiae. Typically, trehalose (a disaccharide of glucose) is synthesized and stored through gluconeogenesis. However, trehalose can also be made directly from glucose, if glucose-6-phosphate is channeled away from glycolysis or pentose phosphate pathway. Therefore, analyzing trehalose synthesis, utilization or its accumulation, can be used as a sentinel read-out for either gluconeogenesis or rewired glucose utilization. However, the steady-state measurements alone of trehalose cannot unambiguously distinguish the nature of carbon flux in a system. Here, we first summarize simple steady-state enzymatic assays to measure trehalose (and glycogen), that will have very wide uses. Subsequently, we describe methods of highly sensitive, quantitative LC-MS/MS based to measure trehalose. We include methods of 13C stable-isotope based pulse-labeling experiments (using different carbon sources) with which to measure rates of trehalose synthesis, from different carbon metabolism pathways. This approach can be used to unambiguously determine the extent of carbon flux into trehalose coming from gluconeogenesis, or directly from glucose/glycolysis. These protocols collectively enable comprehensive steady-state as well as carbon flux based measurements of trehalose. This permits a dissection of carbon flux to distinguish between cells in a gluconeogenic state (conventionally leading to trehalose synthesis), or cells with rewired glucose metabolism (also leading to trehalose synthesis). While the methods presented are optimized for yeast, these methods can be easily adapted to several types of cells, including many microbes.
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Affiliation(s)
- Ritu Gupta
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Post Bellary Road, Bangalore 560065, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Post Bellary Road, Bangalore 560065, India
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23
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Vengayil V, Rashida Z, Laxman S. The E3 ubiquitin ligase Pib1 regulates effective gluconeogenic shutdown upon glucose availability. J Biol Chem 2019; 294:17209-17223. [PMID: 31604822 PMCID: PMC6873170 DOI: 10.1074/jbc.ra119.009822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/27/2019] [Indexed: 12/31/2022] Open
Abstract
Cells use multiple mechanisms to regulate their metabolic states in response to changes in their nutrient environment. One example is the response of cells to glucose. In Saccharomyces cerevisiae growing in glucose-depleted medium, the re-availability of glucose leads to the down-regulation of gluconeogenesis and the activation of glycolysis, leading to "glucose repression." However, our knowledge of the mechanisms mediating the glucose-dependent down-regulation of the gluconeogenic transcription factors is limited. Using the major gluconeogenic transcription factor Rds2 as a candidate, we identify here a novel role for the E3 ubiquitin ligase Pib1 in regulating the stability and degradation of Rds2. Glucose addition to cells growing under glucose limitation results in a rapid ubiquitination of Rds2, followed by its proteasomal degradation. Through in vivo and in vitro experiments, we establish Pib1 as the ubiquitin E3 ligase that regulates Rds2 ubiquitination and stability. Notably, this Pib1-mediated Rds2 ubiquitination, followed by proteasomal degradation, is specific to the presence of glucose. This Pib1-mediated ubiquitination of Rds2 depends on the phosphorylation state of Rds2, suggesting a cross-talk between ubiquitination and phosphorylation to achieve a metabolic state change. Using stable isotope-based metabolic flux experiments, we find that the loss of Pib1 results in an imbalanced gluconeogenic state, regardless of glucose availability. Pib1 is required for complete glucose repression and enables cells to optimally grow in competitive environments when glucose again becomes available. Our results reveal the existence of a Pib1-mediated regulatory program that mediates glucose repression when glucose availability is restored.
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Affiliation(s)
- Vineeth Vengayil
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Post, Bellary Road, Bangalore 560065, India
- Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Zeenat Rashida
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Post, Bellary Road, Bangalore 560065, India
- Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Post, Bellary Road, Bangalore 560065, India
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24
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Gupta R, Walvekar AS, Liang S, Rashida Z, Shah P, Laxman S. A tRNA modification balances carbon and nitrogen metabolism by regulating phosphate homeostasis. eLife 2019; 8:e44795. [PMID: 31259691 PMCID: PMC6688859 DOI: 10.7554/elife.44795] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 06/30/2019] [Indexed: 12/21/2022] Open
Abstract
Cells must appropriately sense and integrate multiple metabolic resources to commit to proliferation. Here, we report that S. cerevisiae cells regulate carbon and nitrogen metabolic homeostasis through tRNA U34-thiolation. Despite amino acid sufficiency, tRNA-thiolation deficient cells appear amino acid starved. In these cells, carbon flux towards nucleotide synthesis decreases, and trehalose synthesis increases, resulting in a starvation-like metabolic signature. Thiolation mutants have only minor translation defects. However, in these cells phosphate homeostasis genes are strongly down-regulated, resulting in an effectively phosphate-limited state. Reduced phosphate enforces a metabolic switch, where glucose-6-phosphate is routed towards storage carbohydrates. Notably, trehalose synthesis, which releases phosphate and thereby restores phosphate availability, is central to this metabolic rewiring. Thus, cells use thiolated tRNAs to perceive amino acid sufficiency, balance carbon and amino acid metabolic flux and grow optimally, by controlling phosphate availability. These results further biochemically explain how phosphate availability determines a switch to a 'starvation-state'.
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Affiliation(s)
- Ritu Gupta
- Institute for Stem Cell Science and Regenerative Medicine (inStem)BangaloreIndia
| | - Adhish S Walvekar
- Institute for Stem Cell Science and Regenerative Medicine (inStem)BangaloreIndia
| | - Shun Liang
- Department of GeneticsRutgers UniversityPiscatawayUnited States
| | - Zeenat Rashida
- Institute for Stem Cell Science and Regenerative Medicine (inStem)BangaloreIndia
- Manipal Academy of Higher EducationManipalIndia
| | - Premal Shah
- Department of GeneticsRutgers UniversityPiscatawayUnited States
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem)BangaloreIndia
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25
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Varahan S, Walvekar A, Sinha V, Krishna S, Laxman S. Metabolic constraints drive self-organization of specialized cell groups. eLife 2019; 8:e46735. [PMID: 31241462 PMCID: PMC6658198 DOI: 10.7554/elife.46735] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 06/19/2019] [Indexed: 12/30/2022] Open
Abstract
How phenotypically distinct states in isogenic cell populations appear and stably co-exist remains unresolved. We find that within a mature, clonal yeast colony developing in low glucose, cells arrange into metabolically disparate cell groups. Using this system, we model and experimentally identify metabolic constraints sufficient to drive such self-assembly. Beginning in a uniformly gluconeogenic state, cells exhibiting a contrary, high pentose phosphate pathway activity state, spontaneously appear and proliferate, in a spatially constrained manner. Gluconeogenic cells in the colony produce and provide a resource, which we identify as trehalose. Above threshold concentrations of external trehalose, cells switch to the new metabolic state and proliferate. A self-organized system establishes, where cells in this new state are sustained by trehalose consumption, which thereby restrains other cells in the trehalose producing, gluconeogenic state. Our work suggests simple physico-chemical principles that determine how isogenic cells spontaneously self-organize into structured assemblies in complimentary, specialized states.
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Affiliation(s)
- Sriram Varahan
- InStem - Institute for Stem Cell Science and Regenerative MedicineBangaloreIndia
| | - Adhish Walvekar
- InStem - Institute for Stem Cell Science and Regenerative MedicineBangaloreIndia
| | - Vaibhhav Sinha
- Simons Centre for the Study of Living MachinesNational Centre for Biological Sciences-Tata Institute of Fundamental ResearchBangaloreIndia
- Manipal Academy of Higher EducationManipalIndia
| | - Sandeep Krishna
- Simons Centre for the Study of Living MachinesNational Centre for Biological Sciences-Tata Institute of Fundamental ResearchBangaloreIndia
| | - Sunil Laxman
- InStem - Institute for Stem Cell Science and Regenerative MedicineBangaloreIndia
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26
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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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