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Li R, Rozum JC, Quail MM, Qasim MN, Sindi SS, Nobile CJ, Albert R, Hernday AD. Inferring gene regulatory networks using transcriptional profiles as dynamical attractors. PLoS Comput Biol 2023; 19:e1010991. [PMID: 37607190 PMCID: PMC10473541 DOI: 10.1371/journal.pcbi.1010991] [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: 03/02/2023] [Revised: 09/01/2023] [Accepted: 07/19/2023] [Indexed: 08/24/2023] Open
Abstract
Genetic regulatory networks (GRNs) regulate the flow of genetic information from the genome to expressed messenger RNAs (mRNAs) and thus are critical to controlling the phenotypic characteristics of cells. Numerous methods exist for profiling mRNA transcript levels and identifying protein-DNA binding interactions at the genome-wide scale. These enable researchers to determine the structure and output of transcriptional regulatory networks, but uncovering the complete structure and regulatory logic of GRNs remains a challenge. The field of GRN inference aims to meet this challenge using computational modeling to derive the structure and logic of GRNs from experimental data and to encode this knowledge in Boolean networks, Bayesian networks, ordinary differential equation (ODE) models, or other modeling frameworks. However, most existing models do not incorporate dynamic transcriptional data since it has historically been less widely available in comparison to "static" transcriptional data. We report the development of an evolutionary algorithm-based ODE modeling approach (named EA) that integrates kinetic transcription data and the theory of attractor matching to infer GRN architecture and regulatory logic. Our method outperformed six leading GRN inference methods, none of which incorporate kinetic transcriptional data, in predicting regulatory connections among TFs when applied to a small-scale engineered synthetic GRN in Saccharomyces cerevisiae. Moreover, we demonstrate the potential of our method to predict unknown transcriptional profiles that would be produced upon genetic perturbation of the GRN governing a two-state cellular phenotypic switch in Candida albicans. We established an iterative refinement strategy to facilitate candidate selection for experimentation; the experimental results in turn provide validation or improvement for the model. In this way, our GRN inference approach can expedite the development of a sophisticated mathematical model that can accurately describe the structure and dynamics of the in vivo GRN.
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Affiliation(s)
- Ruihao Li
- Quantitative and Systems Biology Graduate Program, University of California, Merced, Merced, California, United States of America
| | - Jordan C. Rozum
- Department of Systems Science and Industrial Engineering, Binghamton University (State University of New York), Binghamton, New York, United States of America
| | - Morgan M. Quail
- Quantitative and Systems Biology Graduate Program, University of California, Merced, Merced, California, United States of America
| | - Mohammad N. Qasim
- Quantitative and Systems Biology Graduate Program, University of California, Merced, Merced, California, United States of America
| | - Suzanne S. Sindi
- Department of Applied Mathematics, University of California, Merced, Merced, California, United States of America
| | - Clarissa J. Nobile
- Department of Molecular Cell Biology, University of California, Merced, Merced, California, United States of America
- Health Sciences Research Institute, University of California, Merced, Merced, California, United States of America
| | - Réka Albert
- Department of Physics, Pennsylvania State University, University Park, University Park, Pennsylvania, United States of America
- Department of Biology, Pennsylvania State University, University Park, University Park, Pennsylvania, United States of America
| | - Aaron D. Hernday
- Department of Molecular Cell Biology, University of California, Merced, Merced, California, United States of America
- Health Sciences Research Institute, University of California, Merced, Merced, California, United States of America
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Hollenstein DM, Veis J, Romanov N, Gérecová G, Ogris E, Hartl M, Ammerer G, Reiter W. PP2A Rts1 antagonizes Rck2-mediated hyperosmotic stress signaling in yeast. Microbiol Res 2022; 260:127031. [PMID: 35461031 DOI: 10.1016/j.micres.2022.127031] [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: 09/17/2021] [Revised: 04/03/2022] [Accepted: 04/05/2022] [Indexed: 11/21/2022]
Abstract
In Saccharomyces cerevisiae, impairment of protein phosphatase PP2ARts1 leads to temperature and hyperosmotic stress sensitivity, yet the underlying mechanism and the scope of action of the phosphatase in the stress response remain elusive. Using a quantitative mass spectrometry-based approach we have identified a set of putative substrate proteins that show both hyperosmotic stress- and PP2ARts1-dependent changes in their phosphorylation pattern. A comparative analysis with published MS-shotgun data revealed that the phosphorylation status of many of these sites is regulated by the MAPKAP kinase Rck2, suggesting that the phosphatase antagonizes Rck2 signaling. Detailed gel mobility shift assays and protein-protein interaction analysis strongly indicate that Rck2 activity is directly regulated by PP2ARts1 via a SLiM B56-family interaction motif, revealing how PP2ARts1 influences the response to hyperosmotic stress in Yeast.
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Affiliation(s)
- D M Hollenstein
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - J Veis
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria; Center for Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - N Romanov
- Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - G Gérecová
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - E Ogris
- Center for Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - M Hartl
- Mass Spectrometry Facility, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - G Ammerer
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - W Reiter
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria; Mass Spectrometry Facility, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria.
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3
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Huffaker TB, Ekiz HA, Barba C, Lee SH, Runtsch MC, Nelson MC, Bauer KM, Tang WW, Mosbruger TL, Cox JE, Round JL, Voth WP, O'Connell RM. A Stat1 bound enhancer promotes Nampt expression and function within tumor associated macrophages. Nat Commun 2021; 12:2620. [PMID: 33976173 PMCID: PMC8113251 DOI: 10.1038/s41467-021-22923-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 03/30/2021] [Indexed: 02/03/2023] Open
Abstract
Tumor associated macrophage responses are regulated by distinct metabolic states that affect their function. However, the ability of specific signals in the local tumor microenvironment to program macrophage metabolism remains under investigation. Here, we identify NAMPT, the rate limiting enzyme in NAD salvage synthesis, as a target of STAT1 during cellular activation by interferon gamma, an important driver of macrophage polarization and antitumor responses. We demonstrate that STAT1 occupies a conserved element within the first intron of Nampt, termed Nampt-Regulatory Element-1 (NRE1). Through disruption of NRE1 or pharmacological inhibition, a subset of M1 genes is sensitive to NAMPT activity through its impact on glycolytic processes. scRNAseq is used to profile in vivo responses by NRE1-deficient, tumor-associated leukocytes in melanoma tumors through the creation of a unique mouse strain. Reduced Nampt and inflammatory gene expression are present in specific myeloid and APC populations; moreover, targeted ablation of NRE1 in macrophage lineages results in greater tumor burden. Finally, elevated NAMPT expression correlates with IFNγ responses and melanoma patient survival. This study identifies IFN and STAT1-inducible Nampt as an important factor that shapes the metabolic program and function of tumor associated macrophages.
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Affiliation(s)
- Thomas B Huffaker
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - H Atakan Ekiz
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Cindy Barba
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Soh-Hyun Lee
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Marah C Runtsch
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Morgan C Nelson
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Kaylyn M Bauer
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - William W Tang
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | | | - James E Cox
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
- Metabolomics Core Research Facility, University of Utah, Salt Lake City, UT, USA
| | - June L Round
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Warren P Voth
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, USA.
| | - Ryan M O'Connell
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, USA.
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
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PP2A Functions during Mitosis and Cytokinesis in Yeasts. Int J Mol Sci 2019; 21:ijms21010264. [PMID: 31906018 PMCID: PMC6981662 DOI: 10.3390/ijms21010264] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 12/13/2022] Open
Abstract
Protein phosphorylation is a common mechanism for the regulation of cell cycle progression. The opposing functions of cell cycle kinases and phosphatases are crucial for accurate chromosome segregation and exit from mitosis. Protein phosphatases 2A are heterotrimeric complexes that play essential roles in cell growth, proliferation, and regulation of the cell cycle. Here, we review the function of the protein phosphatase 2A family as the counteracting force for the mitotic kinases. We focus on recent findings in the regulation of mitotic exit and cytokinesis by PP2A phosphatases in S. cerevisiae and other fungal species.
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Aouida M, Eshrif A, Ramotar D. Yeast Lacking the PP2A Phosphatase Regulatory Subunit Rts1 Sensitizes rad51 Mutants to Specific DNA Damaging Agents. Front Genet 2019; 10:1117. [PMID: 31781172 PMCID: PMC6857479 DOI: 10.3389/fgene.2019.01117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 10/16/2019] [Indexed: 11/13/2022] Open
Abstract
Rts1 is a regulatory subunit of the trimeric protein phosphatase 2A phosphatase and it participates in many biological processes by modulating the phosphorylation status of proteins. Consistent with its role, mutants lacking Rts1 display multiple phenotypes. We have previously performed a high throughput screen to search for yeast haploid mutants with altered sensitivity to the anticancer drug bleomycin, which acts by damaging the DNA to produce single and double strand breaks. RTS1 was among the genes that when singly deleted cause sensitivity to bleomycin. We investigate whether Rts1 plays a role in the repair of bleomycin-induced DNA lesions. We show that deletion of the RTS1 gene in the rad51 null background, lacking Rad51 known to be involved in the repair of bleomycin-induced DNA lesions, resulted in double mutants that were sensitized to bleomycin and not to other DNA damaging agents that creates DNA adducts. We further show that Rts1 has the ability to bind to DNA and in its absence cells displayed an increase in the frequency of both spontaneous and bleomycin-induced mutations compared to the parent. This is the first report implicating Rts1 with a role in DNA damage and repair, perhaps regulating the phosphorylation status of one or more proteins involved in the repair of DNA strand breaks.
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Affiliation(s)
- Mustapha Aouida
- College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Abdelmoez Eshrif
- Maisonneuve-Rosemont Hospital, Research Center, Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Dindial Ramotar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar.,Maisonneuve-Rosemont Hospital, Research Center, Department of Medicine, Université de Montréal, Montréal, QC, Canada
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Ariño J, Velázquez D, Casamayor A. Ser/Thr protein phosphatases in fungi: structure, regulation and function. MICROBIAL CELL (GRAZ, AUSTRIA) 2019; 6:217-256. [PMID: 31114794 PMCID: PMC6506691 DOI: 10.15698/mic2019.05.677] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/19/2019] [Accepted: 03/21/2019] [Indexed: 12/12/2022]
Abstract
Reversible phospho-dephosphorylation of proteins is a major mechanism for the control of cellular functions. By large, Ser and Thr are the most frequently residues phosphorylated in eukar-yotes. Removal of phosphate from these amino acids is catalyzed by a large family of well-conserved enzymes, collectively called Ser/Thr protein phosphatases. The activity of these enzymes has an enormous impact on cellular functioning. In this work we pre-sent the members of this family in S. cerevisiae and other fungal species, and review the most recent findings concerning their regu-lation and the roles they play in the most diverse aspects of cell biology.
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Affiliation(s)
- Joaquín Ariño
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Diego Velázquez
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Antonio Casamayor
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
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Promotion of Cell Viability and Histone Gene Expression by the Acetyltransferase Gcn5 and the Protein Phosphatase PP2A in Saccharomyces cerevisiae. Genetics 2016; 203:1693-707. [PMID: 27317677 DOI: 10.1534/genetics.116.189506] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/27/2016] [Indexed: 01/23/2023] Open
Abstract
Histone modifications direct chromatin-templated events in the genome and regulate access to DNA sequence information. There are multiple types of modifications, and a common feature is their dynamic nature. An essential step for understanding their regulation, therefore, lies in characterizing the enzymes responsible for adding and removing histone modifications. Starting with a dosage-suppressor screen in Saccharomyces cerevisiae, we have discovered a functional interaction between the acetyltransferase Gcn5 and the protein phosphatase 2A (PP2A) complex, two factors that regulate post-translational modifications. We find that RTS1, one of two genes encoding PP2A regulatory subunits, is a robust and specific high-copy suppressor of temperature sensitivity of gcn5∆ and a subset of other gcn5∆ phenotypes. Conversely, loss of both PP2A(Rts1) and Gcn5 function in the SAGA and SLIK/SALSA complexes is lethal. RTS1 does not restore global transcriptional defects in gcn5∆; however, histone gene expression is restored, suggesting that the mechanism of RTS1 rescue includes restoration of specific cell cycle transcripts. Pointing to new mechanisms of acetylation-phosphorylation cross-talk, RTS1 high-copy rescue of gcn5∆ growth requires two residues of H2B that are phosphorylated in human cells. These data highlight the potential significance of dynamic phosphorylation and dephosphorylation of these deeply conserved histone residues for cell viability.
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