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Holbrook-Smith D, Trouillon J, Sauer U. Metabolomics and Microbial Metabolism: Toward a Systematic Understanding. Annu Rev Biophys 2024; 53:41-64. [PMID: 38109374 DOI: 10.1146/annurev-biophys-030722-021957] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Over the past decades, our understanding of microbial metabolism has increased dramatically. Metabolomics, a family of techniques that are used to measure the quantities of small molecules in biological samples, has been central to these efforts. Advances in analytical chemistry have made it possible to measure the relative and absolute concentrations of more and more compounds with increasing levels of certainty. In this review, we highlight how metabolomics has contributed to understanding microbial metabolism and in what ways it can still be deployed to expand our systematic understanding of metabolism. To that end, we explain how metabolomics was used to (a) characterize network topologies of metabolism and its regulation networks, (b) elucidate the control of metabolic function, and (c) understand the molecular basis of higher-order phenomena. We also discuss areas of inquiry where technological advances should continue to increase the impact of metabolomics, as well as areas where our understanding is bottlenecked by other factors such as the availability of statistical and modeling frameworks that can extract biological meaning from metabolomics data.
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Affiliation(s)
| | - Julian Trouillon
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland;
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland;
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2
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Ding M, Cao S, Xu D, Xia A, Wang Z, Wang W, Duan K, Wu C, Wang Q, Liang J, Wang D, Liu H, Xu JR, Jiang C. A non-pheromone GPCR is essential for meiosis and ascosporogenesis in the wheat scab fungus. Proc Natl Acad Sci U S A 2023; 120:e2313034120. [PMID: 37812726 PMCID: PMC10589705 DOI: 10.1073/pnas.2313034120] [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: 07/30/2023] [Accepted: 09/08/2023] [Indexed: 10/11/2023] Open
Abstract
Meiosis is essential for generating genetic diversity and sexual spores, but the regulation of meiosis and ascosporogenesis is not clear in filamentous fungi, in which dikaryotic and diploid cells formed inside fruiting bodies are not free living and independent of pheromones or pheromone receptors. In this study, Gia1, a non-pheromone GPCR (G protein-coupled receptor) with sexual-specific expression in Fusarium graminearum, is found to be essential for ascosporogenesis. The gia1 mutant was normal in perithecium development, crozier formation, and karyogamy but failed to undergo meiosis, which could be partially rescued by a dominant active mutation in GPA1 and activation of the Gpmk1 pathway. GIA1 orthologs have conserved functions in regulating meiosis and ascosporogenesis in Sordariomycetes. GIA1 has a paralog, GIP1, in F. graminearum and other Hypocreales species which is essential for perithecium formation. GIP1 differed from GIA1 in expression profiles and downstream signaling during sexual reproduction. Whereas the C-terminal tail and IR3 were important for intracellular signaling, the N-terminal region and EL3 of Gia1 were responsible for recognizing its ligand, which is likely a protein enriched in developing perithecia, particularly in the gia1 mutant. Taken together, these results showed that GIA1 encodes a non-pheromone GPCR that regulates the entry into meiosis and ascosporogenesis via the downstream Gpmk1 MAP kinase pathway in F. graminearum and other filamentous ascomycetes.
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Affiliation(s)
- Mingyu Ding
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, Shaanxi712100, China
| | - Shulin Cao
- Institute of Plant Protection, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu210014, China
| | - Daiying Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, Shaanxi712100, China
| | - Aliang Xia
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, Shaanxi712100, China
| | - Zeyi Wang
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN47907
| | - Wanshan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, Shaanxi712100, China
| | - Kaili Duan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, Shaanxi712100, China
| | - Chenyu Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, Shaanxi712100, China
| | - Qinhu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, Shaanxi712100, China
| | - Jie Liang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, Shaanxi712100, China
| | - Diwen Wang
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN47907
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, Shaanxi712100, China
| | - Jin-Rong Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN47907
| | - Cong Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, Shaanxi712100, China
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3
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Brunnsåker D, Reder GK, Soni NK, Savolainen OI, Gower AH, Tiukova IA, King RD. High-throughput metabolomics for the design and validation of a diauxic shift model. NPJ Syst Biol Appl 2023; 9:11. [PMID: 37029131 PMCID: PMC10082077 DOI: 10.1038/s41540-023-00274-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 03/23/2023] [Indexed: 04/09/2023] Open
Abstract
Saccharomyces cerevisiae is a very well studied organism, yet ∼20% of its proteins remain poorly characterized. Moreover, recent studies seem to indicate that the pace of functional discovery is slow. Previous work has implied that the most probable path forward is via not only automation but fully autonomous systems in which active learning is applied to guide high-throughput experimentation. Development of tools and methods for these types of systems is of paramount importance. In this study we use constrained dynamical flux balance analysis (dFBA) to select ten regulatory deletant strains that are likely to have previously unexplored connections to the diauxic shift. We then analyzed these deletant strains using untargeted metabolomics, generating profiles which were then subsequently investigated to better understand the consequences of the gene deletions in the metabolic reconfiguration of the diauxic shift. We show that metabolic profiles can be utilised to not only gaining insight into cellular transformations such as the diauxic shift, but also on regulatory roles and biological consequences of regulatory gene deletion. We also conclude that untargeted metabolomics is a useful tool for guidance in high-throughput model improvement, and is a fast, sensitive and informative approach appropriate for future large-scale functional analyses of genes. Moreover, it is well-suited for automated approaches due to relative simplicity of processing and the potential to make massively high-throughput.
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Affiliation(s)
- Daniel Brunnsåker
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden.
| | - Gabriel K Reder
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Nikul K Soni
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Otto I Savolainen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
- Department of Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Alexander H Gower
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Ievgeniia A Tiukova
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
- Division of Industrial Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ross D King
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- Alan Turing Institute, London, UK
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4
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High-throughput functional characterization of protein phosphorylation sites in yeast. Nat Biotechnol 2022; 40:382-390. [PMID: 34663920 PMCID: PMC7612524 DOI: 10.1038/s41587-021-01051-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/09/2021] [Indexed: 12/11/2022]
Abstract
Phosphorylation is a critical post-translational modification involved in the regulation of almost all cellular processes. However, fewer than 5% of thousands of recently discovered phosphosites have been functionally annotated. In this study, we devised a chemical genetic approach to study the functional relevance of phosphosites in Saccharomyces cerevisiae. We generated 474 yeast strains with mutations in specific phosphosites that were screened for fitness in 102 conditions, along with a gene deletion library. Of these phosphosites, 42% exhibited growth phenotypes, suggesting that these are more likely functional. We inferred their function based on the similarity of their growth profiles with that of gene deletions and validated a subset by thermal proteome profiling and lipidomics. A high fraction exhibited phenotypes not seen in the corresponding gene deletion, suggestive of a gain-of-function effect. For phosphosites conserved in humans, the severity of the yeast phenotypes is indicative of their human functional relevance. This high-throughput approach allows for functionally characterizing individual phosphosites at scale.
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5
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Schastnaya E, Raguz Nakic Z, Gruber CH, Doubleday PF, Krishnan A, Johns NI, Park J, Wang HH, Sauer U. Extensive regulation of enzyme activity by phosphorylation in Escherichia coli. Nat Commun 2021; 12:5650. [PMID: 34561442 PMCID: PMC8463566 DOI: 10.1038/s41467-021-25988-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/03/2021] [Indexed: 02/08/2023] Open
Abstract
Protein serine/threonine/tyrosine (S/T/Y) phosphorylation is an essential and frequent post-translational modification in eukaryotes, but historically has been considered less prevalent in bacteria because fewer proteins were found to be phosphorylated and most proteins were modified to a lower degree. Recent proteomics studies greatly expanded the phosphoproteome of Escherichia coli to more than 2000 phosphorylation sites (phosphosites), yet mechanisms of action were proposed for only six phosphosites and fitness effects were described for 38 phosphosites upon perturbation. By systematically characterizing functional relevance of S/T/Y phosphorylation in E. coli metabolism, we found 44 of the 52 mutated phosphosites to be functional based on growth phenotypes and intracellular metabolome profiles. By effectively doubling the number of known functional phosphosites, we provide evidence that protein phosphorylation is a major regulation process in bacterial metabolism. Combining in vitro and in vivo experiments, we demonstrate how single phosphosites modulate enzymatic activity and regulate metabolic fluxes in glycolysis, methylglyoxal bypass, acetate metabolism and the split between pentose phosphate and Entner-Doudoroff pathways through mechanisms that include shielding the substrate binding site, limiting structural dynamics, and disrupting interactions relevant for activity in vivo.
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Affiliation(s)
- Evgeniya Schastnaya
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Life Science Zurich PhD Program on Systems Biology, Zurich, Switzerland
| | - Zrinka Raguz Nakic
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Life Science Zurich PhD Program on Systems Biology, Zurich, Switzerland
- Institute of Chemistry and Biotechnology, ZHAW Zurich University of Applied Sciences, Wädenswil, Switzerland
| | - Christoph H Gruber
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Life Science Zurich PhD Program on Systems Biology, Zurich, Switzerland
| | | | - Aarti Krishnan
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Nathan I Johns
- Department of Systems Biology, Columbia University, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY, USA
| | - Jimin Park
- Department of Systems Biology, Columbia University, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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6
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Nalbantoglu S, Karadag A. Metabolomics bridging proteomics along metabolites/oncometabolites and protein modifications: Paving the way toward integrative multiomics. J Pharm Biomed Anal 2021; 199:114031. [PMID: 33857836 DOI: 10.1016/j.jpba.2021.114031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 03/02/2021] [Accepted: 03/16/2021] [Indexed: 02/08/2023]
Abstract
Systems biology adopted functional and integrative multiomics approaches enable to discover the whole set of interacting regulatory components such as genes, transcripts, proteins, metabolites, and metabolite dependent protein modifications. This interactome build up the midpoint of protein-protein/PTM, protein-DNA/RNA, and protein-metabolite network in a cell. As the key drivers in cellular metabolism, metabolites are precursors and regulators of protein post-translational modifications [PTMs] that affect protein diversity and functionality. The precisely orchestrated core pattern of metabolic networks refer to paradigm 'metabolites regulate PTMs, PTMs regulate enzymes, and enzymes modulate metabolites' through a multitude of feedback and feed-forward pathway loops. The concept represents a flawless PTM-metabolite-enzyme(protein) regulomics underlined in reprogramming cancer metabolism. Immense interconnectivity of those biomolecules in their spectacular network of intertwined metabolic pathways makes integrated proteomics and metabolomics an excellent opportunity, and the central component of integrative multiomics framework. It will therefore be of significant interest to integrate global proteome and PTM-based proteomics with metabolomics to achieve disease related altered levels of those molecules. Thereby, present update aims to highlight role and analysis of interacting metabolites/oncometabolites, and metabolite-regulated PTMs loop which may function as translational monitoring biomarkers along the reprogramming continuum of oncometabolism.
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Affiliation(s)
- Sinem Nalbantoglu
- TUBITAK Marmara Research Center, Gene Engineering and Biotechnology Institute, Molecular, Oncology Laboratory, Gebze, Kocaeli, Turkey.
| | - Abdullah Karadag
- TUBITAK Marmara Research Center, Gene Engineering and Biotechnology Institute, Molecular, Oncology Laboratory, Gebze, Kocaeli, Turkey
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7
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Ochoa D, Jarnuczak AF, Viéitez C, Gehre M, Soucheray M, Mateus A, Kleefeldt AA, Hill A, Garcia-Alonso L, Stein F, Krogan NJ, Savitski MM, Swaney DL, Vizcaíno JA, Noh KM, Beltrao P. The functional landscape of the human phosphoproteome. Nat Biotechnol 2020; 38:365-373. [PMID: 31819260 PMCID: PMC7100915 DOI: 10.1038/s41587-019-0344-3] [Citation(s) in RCA: 221] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 11/05/2019] [Indexed: 12/18/2022]
Abstract
Protein phosphorylation is a key post-translational modification regulating protein function in almost all cellular processes. Although tens of thousands of phosphorylation sites have been identified in human cells, approaches to determine the functional importance of each phosphosite are lacking. Here, we manually curated 112 datasets of phospho-enriched proteins, generated from 104 different human cell types or tissues. We re-analyzed the 6,801 proteomics experiments that passed our quality control criteria, creating a reference phosphoproteome containing 119,809 human phosphosites. To prioritize functional sites, we used machine learning to identify 59 features indicative of proteomic, structural, regulatory or evolutionary relevance and integrate them into a single functional score. Our approach identifies regulatory phosphosites across different molecular mechanisms, processes and diseases, and reveals genetic susceptibilities at a genomic scale. Several regulatory phosphosites were experimentally validated, including identifying a role in neuronal differentiation for phosphosites in SMARCC2, a member of the SWI/SNF chromatin-remodeling complex.
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Affiliation(s)
- David Ochoa
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Andrew F Jarnuczak
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Cristina Viéitez
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Maja Gehre
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Margaret Soucheray
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology and the Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - André Mateus
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Askar A Kleefeldt
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anthony Hill
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Luz Garcia-Alonso
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Frank Stein
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Nevan J Krogan
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology and the Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Danielle L Swaney
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology and the Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Juan A Vizcaíno
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kyung-Min Noh
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Pedro Beltrao
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
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8
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Cui L, Lu H, Lee YH. Challenges and emergent solutions for LC-MS/MS based untargeted metabolomics in diseases. MASS SPECTROMETRY REVIEWS 2018; 37:772-792. [PMID: 29486047 DOI: 10.1002/mas.21562] [Citation(s) in RCA: 186] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 02/02/2018] [Indexed: 05/03/2023]
Abstract
In the past decade, advances in liquid chromatography-mass spectrometry (LC-MS) have revolutionized untargeted metabolomics analyses. By mining metabolomes more deeply, researchers are now primed to uncover key metabolites and their associations with diseases. The employment of untargeted metabolomics has led to new biomarker discoveries and a better mechanistic understanding of diseases with applications in precision medicine. However, many major pertinent challenges remain. First, compound identification has been poor, and left an overwhelming number of unidentified peaks. Second, partial, incomplete metabolomes persist due to factors such as limitations in mass spectrometry data acquisition speeds, wide-range of metabolites concentrations, and cellular/tissue/temporal-specific expression changes that confound our understanding of metabolite perturbations. Third, to contextualize metabolites in pathways and biology is difficult because many metabolites partake in multiple pathways, have yet to be described species specificity, or possess unannotated or more-complex functions that are not easily characterized through metabolomics analyses. From a translational perspective, information related to novel metabolite biomarkers, metabolic pathways, and drug targets might be sparser than they should be. Thankfully, significant progress has been made and novel solutions are emerging, achieved through sustained academic and industrial community efforts in terms of hardware, computational, and experimental approaches. Given the rapidly growing utility of metabolomics, this review will offer new perspectives, increase awareness of the major challenges in LC-MS metabolomics that will significantly benefit the metabolomics community and also the broader the biomedical community metabolomics aspire to serve.
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Affiliation(s)
- Liang Cui
- Translational 'Omics and Biomarkers Group, KK Research Centre, KK Women's and Children's Hospital, Singapore, Singapore
- Infectious Diseases-Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Haitao Lu
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Yie Hou Lee
- Translational 'Omics and Biomarkers Group, KK Research Centre, KK Women's and Children's Hospital, Singapore, Singapore
- OBGYN-Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
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9
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MacGilvray ME, Shishkova E, Chasman D, Place M, Gitter A, Coon JJ, Gasch AP. Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response. PLoS Comput Biol 2018; 13:e1006088. [PMID: 29738528 PMCID: PMC5940180 DOI: 10.1371/journal.pcbi.1006088] [Citation(s) in RCA: 18] [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: 08/17/2017] [Accepted: 03/13/2018] [Indexed: 11/18/2022] Open
Abstract
Cells respond to stressful conditions by coordinating a complex, multi-faceted response that spans many levels of physiology. Much of the response is coordinated by changes in protein phosphorylation. Although the regulators of transcriptome changes during stress are well characterized in Saccharomyces cerevisiae, the upstream regulatory network controlling protein phosphorylation is less well dissected. Here, we developed a computational approach to infer the signaling network that regulates phosphorylation changes in response to salt stress. We developed an approach to link predicted regulators to groups of likely co-regulated phospho-peptides responding to stress, thereby creating new edges in a background protein interaction network. We then use integer linear programming (ILP) to integrate wild type and mutant phospho-proteomic data and predict the network controlling stress-activated phospho-proteomic changes. The network we inferred predicted new regulatory connections between stress-activated and growth-regulating pathways and suggested mechanisms coordinating metabolism, cell-cycle progression, and growth during stress. We confirmed several network predictions with co-immunoprecipitations coupled with mass-spectrometry protein identification and mutant phospho-proteomic analysis. Results show that the cAMP-phosphodiesterase Pde2 physically interacts with many stress-regulated transcription factors targeted by PKA, and that reduced phosphorylation of those factors during stress requires the Rck2 kinase that we show physically interacts with Pde2. Together, our work shows how a high-quality computational network model can facilitate discovery of new pathway interactions during osmotic stress. Cells sense and respond to stressful environments by utilizing complex signaling networks that integrate diverse signals to coordinate a multi-faceted physiological response. Much of this response is controlled by post-translational protein phosphorylation. Although many regulators that mediate changes in protein phosphorylation are known, how these regulators inter-connect in a single regulatory network that can transmit cellular signals is not known. It is also unclear how regulators that promote growth and regulators that activate the stress response interconnect to reorganize resource allocation during stress. Here, we developed an integrated experimental and computational workflow to infer the signaling network that regulates phosphorylation changes during osmotic stress in the budding yeast Saccharomyces cerevisiae. The workflow integrates data measuring protein phosphorylation changes in response to osmotic stress with known physical interactions between yeast proteins from large-scale datasets, along with other information about how regulators recognize their targets. The resulting network suggested new signaling connections between regulators and pathways, including those involved in regulating growth and defense, and predicted new regulators involved in stress defense. Our work highlights the power of using network inference to deliver new insight on how cells coordinate a diverse adaptive strategy to stress.
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Affiliation(s)
- Matthew E. MacGilvray
- Laboratory of Genetics, University of Wisconsin—Madison, Madison, WI, United States of America
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin—Madison, Madison, WI, United States of America
| | - Deborah Chasman
- Wisconsin Institute for Discovery, University of Wisconsin–Madison, Madison, WI, United States of America
| | - Michael Place
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Anthony Gitter
- Department of Biostatistics and Medical Informatics, University of Wisconsin -Madison, Madison, WI, United States of America
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Joshua J. Coon
- Department of Biomolecular Chemistry, University of Wisconsin—Madison, Madison, WI, United States of America
- Morgridge Institute for Research, Madison, WI, United States of America
- Department of Chemistry, University of Wisconsin -Madison, Madison, WI, United States of America
- Genome Center of Wisconsin, Madison, WI, United States of America
| | - Audrey P. Gasch
- Laboratory of Genetics, University of Wisconsin—Madison, Madison, WI, United States of America
- Department of Chemistry, University of Wisconsin -Madison, Madison, WI, United States of America
- * E-mail:
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10
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Gonçalves E, Sciacovelli M, Costa ASH, Tran MGB, Johnson TI, Machado D, Frezza C, Saez-Rodriguez J. Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells. Metab Eng 2018; 45:149-157. [PMID: 29191787 PMCID: PMC5805855 DOI: 10.1016/j.ymben.2017.11.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/15/2017] [Accepted: 11/24/2017] [Indexed: 12/31/2022]
Abstract
Deregulated signal transduction and energy metabolism are hallmarks of cancer and both play a fundamental role in tumorigenesis. While it is increasingly recognised that signalling and metabolism are highly interconnected, the underpinning mechanisms of their co-regulation are still largely unknown. Here we designed and acquired proteomics, phosphoproteomics, and metabolomics experiments in fumarate hydratase (FH) deficient cells and developed a computational modelling approach to identify putative regulatory phosphorylation-sites of metabolic enzymes. We identified previously reported functionally relevant phosphosites and potentially novel regulatory residues in enzymes of the central carbon metabolism. In particular, we showed that pyruvate dehydrogenase (PDHA1) enzymatic activity is inhibited by increased phosphorylation in FH-deficient cells, restricting carbon entry from glucose to the tricarboxylic acid cycle. Moreover, we confirmed PDHA1 phosphorylation in human FH-deficient tumours. Our work provides a novel approach to investigate how post-translational modifications of enzymes regulate metabolism and could have important implications for understanding the metabolic transformation of FH-deficient cancers with potential clinical applications.
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Affiliation(s)
- Emanuel Gonçalves
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Marco Sciacovelli
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Ana S H Costa
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Maxine Gia Binh Tran
- UCL Division of Surgery and Interventional Science, Specialist Center for Kidney Cancer, Royal Free Hospital, Pond Street, London NW3 2QG, UK
| | - Timothy Isaac Johnson
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Daniel Machado
- European Molecular Biology Laboratory, EMBL, Heidelberg, Germany; Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Christian Frezza
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK.
| | - Julio Saez-Rodriguez
- RWTH Aachen University, Faculty of Medicine, Joint Research Center for Computational Biomedicine, Aachen, Germany.
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11
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Diether M, Sauer U. Towards detecting regulatory protein–metabolite interactions. Curr Opin Microbiol 2017; 39:16-23. [DOI: 10.1016/j.mib.2017.07.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 07/21/2017] [Accepted: 07/27/2017] [Indexed: 01/20/2023]
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12
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Vlastaridis P, Kyriakidou P, Chaliotis A, Van de Peer Y, Oliver SG, Amoutzias GD. Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes. Gigascience 2017; 6:1-11. [PMID: 28327990 PMCID: PMC5466708 DOI: 10.1093/gigascience/giw015] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 12/20/2016] [Indexed: 12/03/2022] Open
Abstract
Background Phosphorylation is the most frequent post-translational modification made to proteins and may regulate protein activity as either a molecular digital switch or a rheostat. Despite the cornucopia of high-throughput (HTP) phosphoproteomic data in the last decade, it remains unclear how many proteins are phosphorylated and how many phosphorylation sites (p-sites) can exist in total within a eukaryotic proteome. We present the first reliable estimates of the total number of phosphoproteins and p-sites for four eukaryotes (human, mouse, Arabidopsis, and yeast). Results In all, 187 HTP phosphoproteomic datasets were filtered, compiled, and studied along with two low-throughput (LTP) compendia. Estimates of the number of phosphoproteins and p-sites were inferred by two methods: Capture-Recapture, and fitting the saturation curve of cumulative redundant vs. cumulative non-redundant phosphoproteins/p-sites. Estimates were also adjusted for different levels of noise within the individual datasets and other confounding factors. We estimate that in total, 13 000, 11 000, and 3000 phosphoproteins and 230 000, 156 000, and 40 000 p-sites exist in human, mouse, and yeast, respectively, whereas estimates for Arabidopsis were not as reliable. Conclusions Most of the phosphoproteins have been discovered for human, mouse, and yeast, while the dataset for Arabidopsis is still far from complete. The datasets for p-sites are not as close to saturation as those for phosphoproteins. Integration of the LTP data suggests that current HTP phosphoproteomics appears to be capable of capturing 70 % to 95 % of total phosphoproteins, but only 40 % to 60 % of total p-sites.
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Affiliation(s)
- Panayotis Vlastaridis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larisa, 41500, Greece
| | - Pelagia Kyriakidou
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larisa, 41500, Greece
| | - Anargyros Chaliotis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larisa, 41500, Greece
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium.,Bioinformatics Institute Ghent, Technologiepark 927, B-9052 Ghent, Belgium.,Department of Genetics, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Stephen G Oliver
- Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Grigoris D Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larisa, 41500, Greece
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