1
|
Krishnan VP, Negi MS, Peesapati R, Vijayraghavan U. Cryptococcus neoformans Slu7 ensures nuclear positioning during mitotic progression through RNA splicing. PLoS Genet 2024; 20:e1011272. [PMID: 38768219 PMCID: PMC11142667 DOI: 10.1371/journal.pgen.1011272] [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: 02/29/2024] [Revised: 05/31/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
The position of the nucleus before it divides during mitosis is variable in different budding yeasts. Studies in the pathogenic intron-rich fungus Cryptococcus neoformans reveal that the nucleus moves entirely into the daughter bud before its division. Here, we report functions of a zinc finger motif containing spliceosome protein C. neoformans Slu7 (CnSlu7) in cell cycle progression. The budding yeast and fission yeast homologs of Slu7 have predominant roles for intron 3' splice site definition during pre-mRNA splicing. Using a conditional knockdown strategy, we show CnSlu7 is an essential factor for viability and is required for efficient cell cycle progression with major role during mitosis. Aberrant nuclear migration, including improper positioning of the nucleus as well as the spindle, were frequently observed in cells depleted of CnSlu7. However, cell cycle delays observed due to Slu7 depletion did not activate the Mad2-dependent spindle assembly checkpoint (SAC). Mining of the global transcriptome changes in the Slu7 knockdown strain identified downregulation of transcripts encoding several cell cycle regulators and cytoskeletal factors for nuclear migration, and the splicing of specific introns of these genes was CnSlu7 dependent. To test the importance of splicing activity of CnSlu7 on nuclear migration, we complemented Slu7 knockdown cells with an intron less PAC1 minigene and demonstrated that the nuclear migration defects were significantly rescued. These findings show that CnSlu7 regulates the functions of diverse cell cycle regulators and cytoskeletal components, ensuring timely cell cycle transitions and nuclear division during mitosis.
Collapse
Affiliation(s)
- Vishnu Priya Krishnan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Manendra Singh Negi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Raghavaram Peesapati
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Usha Vijayraghavan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| |
Collapse
|
2
|
Litsios A, Grys BT, Kraus OZ, Friesen H, Ross C, Masinas MPD, Forster DT, Couvillion MT, Timmermann S, Billmann M, Myers C, Johnsson N, Churchman LS, Boone C, Andrews BJ. Proteome-scale movements and compartment connectivity during the eukaryotic cell cycle. Cell 2024; 187:1490-1507.e21. [PMID: 38452761 PMCID: PMC10947830 DOI: 10.1016/j.cell.2024.02.014] [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: 09/12/2023] [Revised: 12/01/2023] [Accepted: 02/12/2024] [Indexed: 03/09/2024]
Abstract
Cell cycle progression relies on coordinated changes in the composition and subcellular localization of the proteome. By applying two distinct convolutional neural networks on images of millions of live yeast cells, we resolved proteome-level dynamics in both concentration and localization during the cell cycle, with resolution of ∼20 subcellular localization classes. We show that a quarter of the proteome displays cell cycle periodicity, with proteins tending to be controlled either at the level of localization or concentration, but not both. Distinct levels of protein regulation are preferentially utilized for different aspects of the cell cycle, with changes in protein concentration being mostly involved in cell cycle control and changes in protein localization in the biophysical implementation of the cell cycle program. We present a resource for exploring global proteome dynamics during the cell cycle, which will aid in understanding a fundamental biological process at a systems level.
Collapse
Affiliation(s)
- Athanasios Litsios
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Benjamin T Grys
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Oren Z Kraus
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Electrical and Computer Engineering, University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Helena Friesen
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Catherine Ross
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Myra Paz David Masinas
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Duncan T Forster
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Mary T Couvillion
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Stefanie Timmermann
- Institute of Molecular Genetics and Cell Biology, Department of Biology, Ulm University, Ulm 89081, Germany
| | - Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA; Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Chad Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Nils Johnsson
- Institute of Molecular Genetics and Cell Biology, Department of Biology, Ulm University, Ulm 89081, Germany
| | | | - Charles Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; RIKEN Center for Sustainable Resource Science, Wako 351-0198 Saitama, Japan.
| | - Brenda J Andrews
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| |
Collapse
|
3
|
Su AJ, Yendluri SC, Ünal E. Control of meiotic entry by dual inhibition of a key mitotic transcription factor. eLife 2024; 12:RP90425. [PMID: 38411169 PMCID: PMC10939502 DOI: 10.7554/elife.90425] [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: 02/28/2024] Open
Abstract
The mitosis to meiosis transition requires dynamic changes in gene expression, but whether and how the mitotic transcriptional machinery is regulated during this transition is unknown. In budding yeast, SBF and MBF transcription factors initiate the mitotic gene expression program. Here, we report two mechanisms that work together to restrict SBF activity during meiotic entry: repression of the SBF-specific Swi4 subunit through LUTI-based regulation and inhibition of SBF by Whi5, a functional homolog of the Rb tumor suppressor. We find that untimely SBF activation causes downregulation of early meiotic genes and delays meiotic entry. These defects are largely driven by the SBF-target G1 cyclins, which block the interaction between the central meiotic regulator Ime1 and its cofactor Ume6. Our study provides insight into the role of SWI4LUTI in establishing the meiotic transcriptional program and demonstrates how the LUTI-based regulation is integrated into a larger regulatory network to ensure timely SBF activity.
Collapse
Affiliation(s)
- Amanda J Su
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Siri C Yendluri
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| |
Collapse
|
4
|
Fox J, Cummins B, Moseley RC, Gameiro M, Haase SB. A yeast cell cycle pulse generator model shows consistency with multiple oscillatory and checkpoint mutant datasets. Math Biosci 2024; 367:109102. [PMID: 37939998 PMCID: PMC10842220 DOI: 10.1016/j.mbs.2023.109102] [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: 05/06/2023] [Revised: 09/13/2023] [Accepted: 10/27/2023] [Indexed: 11/10/2023]
Abstract
Modeling biological systems holds great promise for speeding up the rate of discovery in systems biology by predicting experimental outcomes and suggesting targeted interventions. However, this process is dogged by an identifiability issue, in which network models and their parameters are not sufficiently constrained by coarse and noisy data to ensure unique solutions. In this work, we evaluated the capability of a simplified yeast cell-cycle network model to reproduce multiple observed transcriptomic behaviors under genomic mutations. We matched time-series data from both cycling and checkpoint arrested cells to model predictions using an asynchronous multi-level Boolean approach. We showed that this single network model, despite its simplicity, is capable of exhibiting dynamical behavior similar to the datasets in most cases, and we demonstrated the drop in severity of the identifiability issue that results from matching multiple datasets.
Collapse
Affiliation(s)
- Julian Fox
- Department of Mathematical Sciences, Montana State University, Bozeman, MT, USA
| | - Breschine Cummins
- Department of Mathematical Sciences, Montana State University, Bozeman, MT, USA.
| | | | - Marcio Gameiro
- Department of Mathematics, Rutgers University, New Brunswick, NJ, USA
| | | |
Collapse
|
5
|
Su AJ, Yendluri SC, Ünal E. Control of meiotic entry by dual inhibition of a key mitotic transcription factor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533246. [PMID: 36993411 PMCID: PMC10055192 DOI: 10.1101/2023.03.17.533246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
The mitosis to meiosis transition requires dynamic changes in gene expression, but whether and how the mitotic transcriptional machinery is regulated during this transition is unknown. In budding yeast, SBF and MBF transcription factors initiate the mitotic gene expression program. Here, we report two mechanisms that work together to restrict SBF activity during meiotic entry: repression of the SBF-specific Swi4 subunit through LUTI-based regulation and inhibition of SBF by Whi5, a homolog of the Rb tumor suppressor. We find that untimely SBF activation causes downregulation of early meiotic genes and delays meiotic entry. These defects are largely driven by the SBF-target G1 cyclins, which block the interaction between the central meiotic regulator Ime1 and its cofactor Ume6. Our study provides insight into the role of SWI4LUTI in establishing the meiotic transcriptional program and demonstrates how the LUTI-based regulation is integrated into a larger regulatory network to ensure timely SBF activity.
Collapse
|
6
|
Arnason TG, MacDonald-Dickinson V, Gaunt MC, Davies GF, Lobanova L, Trost B, Gillespie ZE, Waldner M, Baldwin P, Borrowman D, Marwood H, Vizeacoumar FS, Vizeacoumar FJ, Eskiw CH, Kusalik A, Harkness TAA. Activation of the Anaphase Promoting Complex Reverses Multiple Drug Resistant Cancer in a Canine Model of Multiple Drug Resistant Lymphoma. Cancers (Basel) 2022; 14:cancers14174215. [PMID: 36077749 PMCID: PMC9454423 DOI: 10.3390/cancers14174215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/25/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Multiple drug resistant cancers develop all too soon in patients who received successful cancer treatment. A lack of treatment options often leaves palliative care as the last resort. We tested whether the insulin sensitizer, metformin, known to have anti-cancer activity, could impact canines with drug resistant lymphoma when added to chemotherapy. All canines in the study expressed protein markers of drug resistance and within weeks of receiving metformin, the markers were decreased. A microarray was performed, and from four canines assessed, a common set of 290 elevated genes were discovered in tumor cells compared to control cells. This cluster was enriched with genes that stall the cell cycle, with a large component representing substrates of the Anaphase Promoting Complex (APC), which degrades proteins. One canine entered partial remission. RNAs from this canine showed that APC substrates were decreased during remission and elevated again during relapse, suggesting that the APC was impaired in drug resistant canines and restored when remission occurred. We validated our results in cell lines using APC inhibitors and activators. We conclude that the APC may be a vital guardian of the genome and could delay the onset of multiple drug resistance when activated. Abstract Like humans, canine lymphomas are treated by chemotherapy cocktails and frequently develop multiple drug resistance (MDR). Their shortened clinical timelines and tumor accessibility make canines excellent models to study MDR mechanisms. Insulin-sensitizers have been shown to reduce the incidence of cancer in humans prescribed them, and we previously demonstrated that they also reverse and delay MDR development in vitro. Here, we treated canines with MDR lymphoma with metformin to assess clinical and tumoral responses, including changes in MDR biomarkers, and used mRNA microarrays to determine differential gene expression. Metformin reduced MDR protein markers in all canines in the study. Microarrays performed on mRNAs gathered through longitudinal tumor sampling identified a 290 gene set that was enriched in Anaphase Promoting Complex (APC) substrates and additional mRNAs associated with slowed mitotic progression in MDR samples compared to skin controls. mRNAs from a canine that went into remission showed that APC substrate mRNAs were decreased, indicating that the APC was activated during remission. In vitro validation using canine lymphoma cells selected for resistance to chemotherapeutic drugs confirmed that APC activation restored MDR chemosensitivity, and that APC activity was reduced in MDR cells. This supports the idea that rapidly pushing MDR cells that harbor high loads of chromosome instability through mitosis, by activating the APC, contributes to improved survival and disease-free duration.
Collapse
Affiliation(s)
- Terra G. Arnason
- Division of Endocrinology and Metabolism, Department of Medicine, Saskatoon, SK S7N 0W8, Canada
- Department of Anatomy and Cell Biology, Saskatoon, SK S7N 5E5, Canada
- Department of Anatomy, Physiology and Pharmacology, Saskatoon, SK S7N 5E5, Canada
- Correspondence: (T.G.A.); (T.A.A.H.)
| | - Valerie MacDonald-Dickinson
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, Saskatoon, SK S7N 5B4, Canada
| | - Matthew Casey Gaunt
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, Saskatoon, SK S7N 5B4, Canada
| | - Gerald F. Davies
- Department of Anatomy and Cell Biology, Saskatoon, SK S7N 5E5, Canada
- Department of Biochemistry, Microbiology and Immunology, Saskatoon, SK S7N 5E5, Canada
| | - Liubov Lobanova
- Division of Endocrinology and Metabolism, Department of Medicine, Saskatoon, SK S7N 0W8, Canada
| | - Brett Trost
- Department of Computer Science, Saskatoon, SK S7N 5C9, Canada
| | - Zoe E. Gillespie
- Department of Food and Bioproduct Sciences, Saskatoon, SK S7N 5A8, Canada
| | - Matthew Waldner
- Department of Computer Science, Saskatoon, SK S7N 5C9, Canada
| | - Paige Baldwin
- Department of Anatomy and Cell Biology, Saskatoon, SK S7N 5E5, Canada
| | - Devon Borrowman
- Department of Anatomy and Cell Biology, Saskatoon, SK S7N 5E5, Canada
| | - Hailey Marwood
- Department of Anatomy and Cell Biology, Saskatoon, SK S7N 5E5, Canada
| | - Frederick S. Vizeacoumar
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Franco J. Vizeacoumar
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | | | - Anthony Kusalik
- Department of Computer Science, Saskatoon, SK S7N 5C9, Canada
| | - Troy A. A. Harkness
- Department of Anatomy and Cell Biology, Saskatoon, SK S7N 5E5, Canada
- Department of Biochemistry, Microbiology and Immunology, Saskatoon, SK S7N 5E5, Canada
- Correspondence: (T.G.A.); (T.A.A.H.)
| |
Collapse
|
7
|
Motta FC, Moseley RC, Cummins B, Deckard A, Haase SB. Conservation of dynamic characteristics of transcriptional regulatory elements in periodic biological processes. BMC Bioinformatics 2022; 23:94. [PMID: 35300586 PMCID: PMC8932128 DOI: 10.1186/s12859-022-04627-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 03/01/2022] [Indexed: 11/12/2022] Open
Abstract
Background Cell and circadian cycles control a large fraction of cell and organismal physiology by regulating large periodic transcriptional programs that encompass anywhere from 15 to 80% of the genome despite performing distinct functions. In each case, these large periodic transcriptional programs are controlled by gene regulatory networks (GRNs), and it has been shown through genetics and chromosome mapping approaches in model systems that at the core of these GRNs are small sets of genes that drive the transcript dynamics of the GRNs. However, it is unlikely that we have identified all of these core genes, even in model organisms. Moreover, large periodic transcriptional programs controlling a variety of processes certainly exist in important non-model organisms where genetic approaches to identifying networks are expensive, time-consuming, or intractable. Ideally, the core network components could be identified using data-driven approaches on the transcriptome dynamics data already available. Results This study shows that a unified set of quantified dynamic features of high-throughput time series gene expression data are more prominent in the core transcriptional regulators of cell and circadian cycles than in their outputs, in multiple organism, even in the presence of external periodic stimuli. Additionally, we observe that the power to discriminate between core and non-core genes is largely insensitive to the particular choice of quantification of these features. Conclusions There are practical applications of the approach presented in this study for network inference, since the result is a ranking of genes that is enriched for core regulatory elements driving a periodic phenotype. In this way, the method provides a prioritization of follow-up genetic experiments. Furthermore, these findings reveal something unexpected—that there are shared dynamic features of the transcript abundance of core components of unrelated GRNs that control disparate periodic phenotypes.
Collapse
Affiliation(s)
- Francis C Motta
- Department of Mathematical Sciences, Florida Atlantic University, 777 Glades Rd, Boca Raton, FL, 33431, USA.
| | - Robert C Moseley
- Department of Biology, Duke University, 130 Science Drive, Durham, NC, 27708, USA
| | - Bree Cummins
- Department of Mathematical Sciences, Montana State University, P.O. Box 172400, Bozeman, MT, 59717, USA
| | | | - Steven B Haase
- Department of Biology, Duke University, 130 Science Drive, Durham, NC, 27708, USA
| |
Collapse
|
8
|
Zeng L, Huang J, Feng P, Zhao X, Si Z, Long X, Cheng Q, Yi Y. Transcriptomic analysis of formic acid stress response in Saccharomyces cerevisiae. World J Microbiol Biotechnol 2022; 38:34. [PMID: 34989900 DOI: 10.1007/s11274-021-03222-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 12/26/2021] [Indexed: 12/23/2022]
Abstract
Formic acid is a representative small molecule acid in lignocellulosic hydrolysate that can inhibit the growth of Saccharomyces cerevisiae cells during alcohol fermentation. However, the mechanism of formic acid cytotoxicity remains largely unknown. In this study, RNA-Seq technology was used to study the response of S. cerevisiae to formic acid stress at the transcriptional level. Scanning electron microscopy and Fourier transform infrared spectroscopy were conducted to observe the surface morphology of yeast cells. A total of 1504 genes were identified as being differentially expressed, with 797 upregulated and 707 downregulated genes. Transcriptomic analysis showed that most genes related to glycolysis, glycogen synthesis, protein degradation, the cell cycle, the MAPK signaling pathway, and redox regulation were significantly induced under formic acid stress and were involved in protein translation and synthesis amino acid synthesis genes were significantly suppressed. Formic acid stress can induce oxidative stress, inhibit protein biosynthesis, cause cells to undergo autophagy, and activate the intracellular metabolic pathways of energy production. The increase of glycogen and the decrease of energy consumption metabolism may be important in the adaptation of S. cerevisiae to formic acid. In addition, formic acid can also induce sexual reproduction and spore formation. This study through transcriptome analysis has preliminarily reveal the molecular response mechanism of S. cerevisiae to formic acid stress and has provided a basis for further research on methods used to improve the tolerance to cell inhibitors in lignocellulose hydrolysate.
Collapse
Affiliation(s)
- Lingjie Zeng
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, China
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Liuzhou, 545006, China
| | - Jinxiang Huang
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, China
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Liuzhou, 545006, China
| | - Pixue Feng
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, China
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Liuzhou, 545006, China
| | - Xuemei Zhao
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, China
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Liuzhou, 545006, China
| | - Zaiyong Si
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, China
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Liuzhou, 545006, China
| | - Xiufeng Long
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, China
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Liuzhou, 545006, China
| | - Qianwei Cheng
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, China
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Liuzhou, 545006, China
| | - Yi Yi
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, China.
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Liuzhou, 545006, China.
| |
Collapse
|
9
|
Hollenstein DM, Gérecová G, Romanov N, Ferrari J, Veis J, Janschitz M, Beyer R, Schüller C, Ogris E, Hartl M, Ammerer G, Reiter W. A phosphatase-centric mechanism drives stress signaling response. EMBO Rep 2021; 22:e52476. [PMID: 34558777 PMCID: PMC8567219 DOI: 10.15252/embr.202152476] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 08/27/2021] [Accepted: 09/03/2021] [Indexed: 12/14/2022] Open
Abstract
Changing environmental cues lead to the adjustment of cellular physiology by phosphorylation signaling networks that typically center around kinases as active effectors and phosphatases as antagonistic elements. Here, we report a signaling mechanism that reverses this principle. Using the hyperosmotic stress response in Saccharomyces cerevisiae as a model system, we find that a phosphatase-driven mechanism causes induction of phosphorylation. The key activating step that triggers this phospho-proteomic response is the Endosulfine-mediated inhibition of protein phosphatase 2A-Cdc55 (PP2ACdc55 ), while we do not observe concurrent kinase activation. In fact, many of the stress-induced phosphorylation sites appear to be direct substrates of the phosphatase, rendering PP2ACdc55 the main downstream effector of a signaling response that operates in parallel and independent of the well-established kinase-centric stress signaling pathways. This response affects multiple cellular processes and is required for stress survival. Our results demonstrate how a phosphatase can assume the role of active downstream effectors during signaling and allow re-evaluating the impact of phosphatases on shaping the phosphorylome.
Collapse
Affiliation(s)
- David Maria Hollenstein
- Department of Biochemistry and Cell BiologyMax Perutz LabsVienna BioCenter (VBC)University of ViennaViennaAustria
| | - Gabriela Gérecová
- Department of Biochemistry and Cell BiologyMax Perutz LabsVienna BioCenter (VBC)University of ViennaViennaAustria
| | | | - Jessica Ferrari
- Department of Biochemistry and Cell BiologyMax Perutz LabsVienna BioCenter (VBC)University of ViennaViennaAustria
| | - Jiri Veis
- Department of Biochemistry and Cell BiologyMax Perutz LabsVienna BioCenter (VBC)University of ViennaViennaAustria
- Center for Medical BiochemistryMax Perutz Labs, Vienna BioCenterMedical University of ViennaViennaAustria
| | - Marion Janschitz
- Department of Biochemistry and Cell BiologyMax Perutz LabsVienna BioCenter (VBC)University of ViennaViennaAustria
| | - Reinhard Beyer
- Department of Applied Genetics and Cell Biology (DAGZ)University of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Research Platform Bioactive Microbial Metabolites (BiMM)Tulln a.d. DonauAustria
| | - Christoph Schüller
- Department of Applied Genetics and Cell Biology (DAGZ)University of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Research Platform Bioactive Microbial Metabolites (BiMM)Tulln a.d. DonauAustria
| | - Egon Ogris
- Center for Medical BiochemistryMax Perutz Labs, Vienna BioCenterMedical University of ViennaViennaAustria
| | - Markus Hartl
- Department of Biochemistry and Cell BiologyMax Perutz LabsVienna BioCenter (VBC)University of ViennaViennaAustria
- Mass Spectrometry FacilityMax Perutz Labs, Vienna BioCenterUniversity of ViennaViennaAustria
| | - Gustav Ammerer
- Department of Biochemistry and Cell BiologyMax Perutz LabsVienna BioCenter (VBC)University of ViennaViennaAustria
| | - Wolfgang Reiter
- Department of Biochemistry and Cell BiologyMax Perutz LabsVienna BioCenter (VBC)University of ViennaViennaAustria
- Mass Spectrometry FacilityMax Perutz Labs, Vienna BioCenterUniversity of ViennaViennaAustria
| |
Collapse
|
10
|
Impact of Sickle Cell Trait Hemoglobin on the Intraerythrocytic Transcriptional Program of Plasmodium falciparum. mSphere 2021; 6:e0075521. [PMID: 34668757 PMCID: PMC8527989 DOI: 10.1128/msphere.00755-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sickle-trait hemoglobin (HbAS) confers nearly complete protection from severe, life-threatening falciparum malaria in African children. Despite this clear protection, the molecular mechanisms by which HbAS confers these protective phenotypes remain incompletely understood. As a forward genetic screen for aberrant parasite transcriptional responses associated with parasite neutralization in HbAS red blood cells (RBCs), we performed comparative transcriptomic analyses of Plasmodium falciparum in normal (HbAA) and HbAS erythrocytes during both in vitro cultivation of reference parasite strains and naturally occurring P. falciparum infections in Malian children with HbAA or HbAS. During in vitro cultivation, parasites matured normally in HbAS RBCs, and the temporal expression was largely unperturbed of the highly ordered transcriptional program that underlies the parasite’s maturation throughout the intraerythrocytic development cycle (IDC). However, differential expression analysis identified hundreds of transcripts aberrantly expressed in HbAS, largely occurring late in the IDC. Surprisingly, transcripts encoding members of the Maurer’s clefts were overexpressed in HbAS despite impaired parasite protein export in these RBCs, while parasites in HbAS RBCs underexpressed transcripts associated with the endoplasmic reticulum and those encoding serine repeat antigen proteases that promote parasite egress. Analyses of P. falciparum transcriptomes from 32 children with uncomplicated malaria identified stage-specific differential expression: among infections composed of ring-stage parasites, only cyclophilin 19B was underexpressed in children with HbAS, while trophozoite-stage infections identified a range of differentially expressed transcripts, including downregulation in HbAS of several transcripts associated with severe malaria in collateral studies. Collectively, our comparative transcriptomic screen in vitro and in vivo indicates that P. falciparum adapts to HbAS by altering its protein chaperone and folding machinery, oxidative stress response, and protein export machinery. Because HbAS consistently protects from severe P. falciparum, modulation of these responses may offer avenues by which to neutralize P. falciparum parasites. IMPORTANCE Sickle-trait hemoglobin (HbAS) confers nearly complete protection from severe, life-threatening malaria, yet the molecular mechanisms that underlie HbAS protection from severe malaria remain incompletely understood. Here, we used transcriptome sequencing (RNA-seq) to measure the impact of HbAS on the blood-stage transcriptome of Plasmodium falciparum in in vitro time series experiments and in vivo samples from natural infections. Our in vitro time series data reveal that, during its blood stage, P. falciparum’s gene expression in HbAS is impacted primarily through alterations in the abundance of gene products as opposed to variations in the timing of gene expression. Collectively, our in vitro and in vivo data indicate that P. falciparum adapts to HbAS by altering its protein chaperone and folding machinery, oxidative stress response, and protein export machinery. Due to the persistent association of HbAS and protection from severe disease, these processes that are modified in HbAS may offer strategies to neutralize P. falciparum.
Collapse
|
11
|
Abstract
For cells to replicate, a sufficient supply of biosynthetic precursors is needed, necessitating the concerted action of metabolism and protein synthesis during progressive phases of cell division. A global understanding of which biosynthetic processes are involved and how they are temporally regulated during replication is, however, currently lacking. Here, quantitative multiomics analysis is used to generate a holistic view of the eukaryal cell cycle, using the budding yeast Saccharomyces cerevisiae Protein synthesis and central carbon pathways such as glycolysis and amino acid metabolism are shown to synchronize their respective abundance profiles with division, with pathway-specific changes in metabolite abundance also being reflected by a relative increase in mitochondrial volume, as shown by quantitative fluorescence microscopy. These results show biosynthetic precursor production to be temporally regulated to meet phase-specific demands of eukaryal cell division.
Collapse
|