1
|
Diep DTV, Collado J, Hugenroth M, Fausten RM, Percifull L, Wälte M, Schuberth C, Schmidt O, Fernández-Busnadiego R, Bohnert M. A metabolically controlled contact site between vacuoles and lipid droplets in yeast. Dev Cell 2024; 59:740-758.e10. [PMID: 38367622 DOI: 10.1016/j.devcel.2024.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 11/17/2023] [Accepted: 01/18/2024] [Indexed: 02/19/2024]
Abstract
The lipid droplet (LD) organization proteins Ldo16 and Ldo45 affect multiple aspects of LD biology in yeast. They are linked to the LD biogenesis machinery seipin, and their loss causes defects in LD positioning, protein targeting, and breakdown. However, their molecular roles remained enigmatic. Here, we report that Ldo16/45 form a tether complex with Vac8 to create vacuole lipid droplet (vCLIP) contact sites, which can form in the absence of seipin. The phosphatidylinositol transfer protein (PITP) Pdr16 is a further vCLIP-resident recruited specifically by Ldo45. While only an LD subpopulation is engaged in vCLIPs at glucose-replete conditions, nutrient deprivation results in vCLIP expansion, and vCLIP defects impair lipophagy upon prolonged starvation. In summary, Ldo16/45 are multifunctional proteins that control the formation of a metabolically regulated contact site. Our studies suggest a link between LD biogenesis and breakdown and contribute to a deeper understanding of how lipid homeostasis is maintained during metabolic challenges.
Collapse
Affiliation(s)
- Duy Trong Vien Diep
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany
| | - Javier Collado
- Institute of Neuropathology, University Medical Center Göttingen, 37099 Göttingen, Germany
| | - Marie Hugenroth
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany
| | - Rebecca Martina Fausten
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany
| | - Louis Percifull
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany
| | - Mike Wälte
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany
| | - Christian Schuberth
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany
| | - Oliver Schmidt
- Institute of Cell Biology, Biocenter Innsbruck, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Rubén Fernández-Busnadiego
- Institute of Neuropathology, University Medical Center Göttingen, 37099 Göttingen, Germany; Cluster of Excellence "Multiscale Imaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany; Faculty of Physics, University of Göttingen, Göttingen 37077, Germany
| | - Maria Bohnert
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany.
| |
Collapse
|
2
|
Galello F, Bermúdez-Moretti M, Martínez MCO, Rossi S, Portela P. The cAMP-PKA signalling crosstalks with CWI and HOG-MAPK pathways in yeast cell response to osmotic and thermal stress. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:90-105. [PMID: 38495453 PMCID: PMC10941952 DOI: 10.15698/mic2024.03.818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/13/2024] [Accepted: 02/22/2024] [Indexed: 03/19/2024]
Abstract
The yeast Saccharomyces cerevisiae is widely used in food and non-food industries. During industrial fermentation yeast strains are exposed to fluctuations in oxygen concentration, osmotic pressure, pH, ethanol concentration, nutrient availability and temperature. Fermentation performance depends on the ability of the yeast strains to adapt to these changes. Suboptimal conditions trigger responses to the external stimuli to allow homeostasis to be maintained. Stress-specific signalling pathways are activated to coordinate changes in transcription, translation, protein function, and metabolic fluxes while a transient arrest of growth and cell cycle progression occur. cAMP-PKA, HOG-MAPK and CWI signalling pathways are turned on during stress response. Comprehension of the mechanisms involved in the responses and in the adaptation to these stresses during fermentation is key to improving this industrial process. The scope of this review is to outline the advancement of knowledge about the cAMP-PKA signalling and the crosstalk of this pathway with the CWI and HOG-MAPK cascades in response to the environmental challenges heat and hyperosmotic stress.
Collapse
Affiliation(s)
- Fiorella Galello
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET). Buenos Aires, Argentina
| | - Mariana Bermúdez-Moretti
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET). Buenos Aires, Argentina
| | - María Clara Ortolá Martínez
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET). Buenos Aires, Argentina
| | - Silvia Rossi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET). Buenos Aires, Argentina
| | - Paula Portela
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET). Buenos Aires, Argentina
| |
Collapse
|
3
|
Leutert M, Barente AS, Fukuda NK, Rodriguez-Mias RA, Villén J. The regulatory landscape of the yeast phosphoproteome. Nat Struct Mol Biol 2023; 30:1761-1773. [PMID: 37845410 PMCID: PMC10841839 DOI: 10.1038/s41594-023-01115-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 09/05/2023] [Indexed: 10/18/2023]
Abstract
The cellular ability to react to environmental fluctuations depends on signaling networks that are controlled by the dynamic activities of kinases and phosphatases. Here, to gain insight into these stress-responsive phosphorylation networks, we generated a quantitative mass spectrometry-based atlas of early phosphoproteomic responses in Saccharomyces cerevisiae exposed to 101 environmental and chemical perturbations. We report phosphosites on 59% of the yeast proteome, with 18% of the proteome harboring a phosphosite that is regulated within 5 min of stress exposure. We identify shared and perturbation-specific stress response programs, uncover loss of phosphorylation as an integral early event, and dissect the interconnected regulatory landscape of kinase-substrate networks, as we exemplify with target of rapamycin signaling. We further reveal functional organization principles of the stress-responsive phosphoproteome based on phosphorylation site motifs, kinase activities, subcellular localizations, shared functions and pathway intersections. This information-rich map of 25,000 regulated phosphosites advances our understanding of signaling networks.
Collapse
Affiliation(s)
- Mario Leutert
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Anthony S Barente
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Noelle K Fukuda
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| |
Collapse
|
4
|
Wang L, Li A, Fang J, Wang Y, Chen L, Qiao L, Wang W. Enhanced Cell Wall and Cell Membrane Activity Promotes Heat Adaptation of Enterococcus faecium. Int J Mol Sci 2023; 24:11822. [PMID: 37511581 PMCID: PMC10380804 DOI: 10.3390/ijms241411822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/09/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Enterococcus faecium (E. faecium) is widely used in foods and is known as a probiotic to treat or prevent diarrhea in pets and livestock. However, the poor resistance of E. faecium to high temperature processing procedures limits its use. Strain domestication is a low-cost and effective method to obtain high-temperature-resistant strains. In this study, heat treatment was performed from 45 °C to 70 °C and the temperature was gradually increased by 5 °C every 3 days. After domestication, the survival rates of the high temperature adaptation strain RS047-wl under 65 °C water bath for 40 min was 11.5 times higher than WT RS047. Moreover, the saturated fatty acid (SFA) contents in cell membrane and the cell volume significantly increased in the RS047-wl. The combined transcriptomic, metabolomic, and proteomics analysis results showed a significant enhancement of cell wall and membrane synthesis ability in the RS047-wl. In conclusion, one of the main factors contributing to the improved high temperature resistance of RS047-wl was its enhanced ability to synthesize cell wall and membrane, which helped maintain normal cell morphology. Developing a high-temperature-resistant strain and understanding its mechanism enables it to adapt to high temperatures. This lays the groundwork for its future development and application.
Collapse
Affiliation(s)
- Li Wang
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Aike Li
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China
| | - Jun Fang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Yongwei Wang
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China
| | - Lixian Chen
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China
| | - Lin Qiao
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China
| | - Weiwei Wang
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China
| |
Collapse
|
5
|
Zhang L, Li Y, Dong L, Sun K, Liu H, Ma Z, Yan L, Yin Y. MAP Kinase FgHog1 and Importin β FgNmd5 Regulate Calcium Homeostasis in Fusarium graminearum. J Fungi (Basel) 2023; 9:707. [PMID: 37504696 PMCID: PMC10381525 DOI: 10.3390/jof9070707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 07/29/2023] Open
Abstract
Maintaining cellular calcium (Ca2+) homeostasis is essential for many aspects of cellular life. The high-osmolarity glycerol (HOG) mitogen-activated protein kinase (MAPK) pathway responsible for signal integration and transduction plays crucial roles in environmental adaptation, especially in the response to osmotic stress. Hog1 is activated by transient Ca2+ increase in yeast, but the functions of the HOG pathway in Ca2+ homeostasis are largely unknown. We found that the HOG pathway was involved in the regulation of Ca2+ homeostasis in Fusarium graminearum, a devastating fungal pathogen of cereal crops. The deletion mutants of HOG pathway displayed increased sensitivity to Ca2+ and FK506, and elevated intracellular Ca2+ content. Ca2+ treatment induced the phosphorylation of FgHog1, and the phosphorylated FgHog1 was transported into the nucleus by importin β FgNmd5. Moreover, the increased phosphorylation and nuclear accumulation of FgHog1 upon Ca2+ treatment is independent of the calcineurin pathway that is conserved and downstream of the Ca2+ signal. Taken together, this study reported the novel function of FgHog1 in the regulation of Ca2+ homeostasis in F. graminearum, which advance the understanding of the HOG pathway and the association between the HOG and calcineurin pathways in fungi.
Collapse
Affiliation(s)
- Lixin Zhang
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Yiqing Li
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Lanlan Dong
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Kewei Sun
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Hao Liu
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Zhonghua Ma
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Leiyan Yan
- Ningbo Academy of Agricultural Sciences, Ningbo 315040, China
| | - Yanni Yin
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| |
Collapse
|
6
|
Integrative Multiomics Analysis of the Heat Stress Response of Enterococcus faecium. Biomolecules 2023; 13:biom13030437. [PMID: 36979372 PMCID: PMC10046512 DOI: 10.3390/biom13030437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
A continuous heat-adaptation test was conducted for one Enterococcus faecium (E. faecium) strain wild-type (WT) RS047 to obtain a high-temperature-resistant strain. After domestication, the strain was screened with a significantly higher ability of heat resistance. which is named RS047-wl. Then a multi-omics analysis of transcriptomics and metabolomics was used to analyze the mechanism of the heat resistance of the mutant. A total of 98 differentially expressed genes (DEGs) and 115 differential metabolites covering multiple metabolic processes were detected in the mutant, which indicated that the tolerance of heat resistance was regulated by multiple mechanisms. The changes in AgrB, AgrC, and AgrA gene expressions were involved in quorum-sensing (QS) system pathways, which regulate biofilm formation. Second, highly soluble osmotic substances such as putrescine, spermidine, glycine betaine (GB), and trehalose-6P were accumulated for the membrane transport system. Third, organic acids metabolism and purine metabolism were down-regulated. The findings can provide target genes for subsequent genetic modification of E. faecium, and provide indications for screening heat-resistant bacteria, so as to improve the heat-resistant ability of E. faecium for production.
Collapse
|
7
|
Actin dynamics in protein homeostasis. Biosci Rep 2022; 42:231720. [PMID: 36043949 PMCID: PMC9469105 DOI: 10.1042/bsr20210848] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
Cell homeostasis is maintained in all organisms by the constant adjustment of cell constituents and organisation to account for environmental context. Fine-tuning of the optimal balance of proteins for the conditions, or protein homeostasis, is critical to maintaining cell homeostasis. Actin, a major constituent of the cytoskeleton, forms many different structures which are acutely sensitive to the cell environment. Furthermore, actin structures interact with and are critically important for the function and regulation of multiple factors involved with mRNA and protein production and degradation, and protein regulation. Altogether, actin is a key, if often overlooked, regulator of protein homeostasis across eukaryotes. In this review, we highlight these roles and how they are altered following cell stress, from mRNA transcription to protein degradation.
Collapse
|
8
|
Yeast Protein Kinase A Isoforms: A Means of Encoding Specificity in the Response to Diverse Stress Conditions? Biomolecules 2022; 12:biom12070958. [PMID: 35883514 PMCID: PMC9313097 DOI: 10.3390/biom12070958] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 02/07/2023] Open
Abstract
Eukaryotic cells have developed a complex circuitry of signalling molecules which monitor changes in their intra- and extracellular environments. One of the most widely studied signalling pathways is the highly conserved cyclic AMP (cAMP)/protein kinase A (PKA) pathway, which is a major glucose sensing circuit in the yeast Saccharomyces cerevisiae. PKA activity regulates diverse targets in yeast, positively activating the processes that are associated with rapid cell growth (e.g., fermentative metabolism, ribosome biogenesis and cell division) and negatively regulating the processes that are associated with slow growth, such as respiratory growth, carbohydrate storage and entry into stationary phase. As in higher eukaryotes, yeast has evolved complexity at the level of the PKA catalytic subunit, and Saccharomyces cerevisiae expresses three isoforms, denoted Tpk1-3. Despite evidence for isoform differences in multiple biological processes, the molecular basis of PKA signalling specificity remains poorly defined, and many studies continue to assume redundancy with regards to PKA-mediated regulation. PKA has canonically been shown to play a key role in fine-tuning the cellular response to diverse stressors; however, recent studies have now begun to interrogate the requirement for individual PKA catalytic isoforms in coordinating distinct steps in stress response pathways. In this review, we discuss the known non-redundant functions of the Tpk catalytic subunits and the evolving picture of how these isoforms establish specificity in the response to different stress conditions.
Collapse
|
9
|
Cip1 tunes cell cycle arrest duration upon calcineurin activation. Proc Natl Acad Sci U S A 2022; 119:e2202469119. [PMID: 35653562 DOI: 10.1073/pnas.2202469119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceTo ensure their survival, cells arrest the cell division cycle when they are exposed to environmental stress. The duration of this arrest is dependent upon the time it takes a cell to adapt to a particular environment. How cells adjust the amount of time they remain arrested is not known. This study investigates the role of the phosphatase calcineurin in controlling cell cycle arrest duration in yeast. We show that calcineurin lengthens arrest by prolonging Hog1-dependent activation of the poorly characterized cyclin-dependent kinase inhibitor Cip1. Cip1 only impacts cell cycle arrest in response to stressors that robustly activate calcineurin, suggesting that Cip1 is a context-specific regulator that differentially adjusts the length of arrest depending on the particular stressor.
Collapse
|
10
|
Invergo BM. Accurate, high-coverage assignment of in vivo protein kinases to phosphosites from in vitro phosphoproteomic specificity data. PLoS Comput Biol 2022; 18:e1010110. [PMID: 35560139 PMCID: PMC9132282 DOI: 10.1371/journal.pcbi.1010110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 05/25/2022] [Accepted: 04/15/2022] [Indexed: 12/03/2022] Open
Abstract
Phosphoproteomic experiments routinely observe thousands of phosphorylation sites. To understand the intracellular signaling processes that generated this data, one or more causal protein kinases must be assigned to each phosphosite. However, limited knowledge of kinase specificity typically restricts assignments to a small subset of a kinome. Starting from a statistical model of a high-throughput, in vitro kinase-substrate assay, I have developed an approach to high-coverage, multi-label kinase-substrate assignment called IV-KAPhE (“In vivo-Kinase Assignment for Phosphorylation Evidence”). Tested on human data, IV-KAPhE outperforms other methods of similar scope. Such computational methods generally predict a densely connected kinase-substrate network, with most sites targeted by multiple kinases, pointing either to unaccounted-for biochemical constraints or significant cross-talk and signaling redundancy. I show that such predictions can potentially identify biased kinase-site misannotations within families of closely related kinase isozymes and they provide a robust basis for kinase activity analysis. Proteins can pass around information inside cells about changes in the environment. This process, called intracellular signaling, helps to trigger appropriate cellular responses to environmental changes. One of the main ways information is passed to proteins is through chemical “tagging,” called phosphorylation, by enzymes called protein kinases. We can measure the phosphorylation state of practically all proteins in a cell at any moment. Starting from known cases of phosphorylation by a kinase, many computational methods have been developed to predict if the kinase might tag a certain spot on another protein or if an observed tag was attached by the kinase, with different models for each kinase. I have developed a new method that instead uses a single model to assign one or more kinases to each observed tag, built from the latest large-scale experimental data. This change in focus and unbiased training data allows my method to be significantly more accurate than past methods. I also explored useful applications for my method. For example, I used it to show that much of our knowledge about which kinase is responsible for each tag is probably inaccurately biased towards the commonly studied ones.
Collapse
Affiliation(s)
- Brandon M. Invergo
- Translational Research Exchange @ Exeter, University of Exeter, Exeter, United Kingdom
- * E-mail:
| |
Collapse
|
11
|
Separovich RJ, Wong MW, Bartolec TK, Hamey JJ, Wilkins MR. Site-specific phosphorylation of histone H3K36 methyltransferase Set2p and demethylase Jhd1p is required for stress responses in Saccharomyces cerevisiae. J Mol Biol 2022; 434:167500. [DOI: 10.1016/j.jmb.2022.167500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 01/17/2022] [Accepted: 02/09/2022] [Indexed: 10/19/2022]
|
12
|
Yaakoub H, Sanchez NS, Ongay-Larios L, Courdavault V, Calenda A, Bouchara JP, Coria R, Papon N. The high osmolarity glycerol (HOG) pathway in fungi †. Crit Rev Microbiol 2021; 48:657-695. [PMID: 34893006 DOI: 10.1080/1040841x.2021.2011834] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
While fungi are widely occupying nature, many species are responsible for devastating mycosis in humans. Such niche diversity explains how quick fungal adaptation is necessary to endow the capacity of withstanding fluctuating environments and to cope with host-imposed conditions. Among all the molecular mechanisms evolved by fungi, the most studied one is the activation of the phosphorelay signalling pathways, of which the high osmolarity glycerol (HOG) pathway constitutes one of the key molecular apparatus underpinning fungal adaptation and virulence. In this review, we summarize the seminal knowledge of the HOG pathway with its more recent developments. We specifically described the HOG-mediated stress adaptation, with a particular focus on osmotic and oxidative stress, and point out some lags in our understanding of its involvement in the virulence of pathogenic species including, the medically important fungi Candida albicans, Cryptococcus neoformans, and Aspergillus fumigatus, compared to the model yeast Saccharomyces cerevisiae. Finally, we also highlighted some possible applications of the HOG pathway modifications to improve the fungal-based production of natural products in the industry.
Collapse
Affiliation(s)
- Hajar Yaakoub
- Univ Angers, Univ Brest, GEIHP, SFR ICAT, Angers, France
| | - Norma Silvia Sanchez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Laura Ongay-Larios
- Unidad de Biología Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Vincent Courdavault
- EA2106 "Biomolécules et Biotechnologies Végétales", Université de Tours, Tours, France
| | | | | | - Roberto Coria
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Nicolas Papon
- Univ Angers, Univ Brest, GEIHP, SFR ICAT, Angers, France
| |
Collapse
|
13
|
Mühlhofer M, Peters C, Kriehuber T, Kreuzeder M, Kazman P, Rodina N, Reif B, Haslbeck M, Weinkauf S, Buchner J. Phosphorylation activates the yeast small heat shock protein Hsp26 by weakening domain contacts in the oligomer ensemble. Nat Commun 2021; 12:6697. [PMID: 34795272 PMCID: PMC8602628 DOI: 10.1038/s41467-021-27036-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 11/01/2021] [Indexed: 11/18/2022] Open
Abstract
Hsp26 is a small heat shock protein (sHsp) from S. cerevisiae. Its chaperone activity is activated by oligomer dissociation at heat shock temperatures. Hsp26 contains 9 phosphorylation sites in different structural elements. Our analysis of phospho-mimetic mutations shows that phosphorylation activates Hsp26 at permissive temperatures. The cryo-EM structure of the Hsp26 40mer revealed contacts between the conserved core domain of Hsp26 and the so-called thermosensor domain in the N-terminal part of the protein, which are targeted by phosphorylation. Furthermore, several phosphorylation sites in the C-terminal extension, which link subunits within the oligomer, are sensitive to the introduction of negative charges. In all cases, the intrinsic inhibition of chaperone activity is relieved and the N-terminal domain becomes accessible for substrate protein binding. The weakening of domain interactions within and between subunits by phosphorylation to activate the chaperone activity in response to proteotoxic stresses independent of heat stress could be a general regulation principle of sHsps.
Collapse
Affiliation(s)
- Moritz Mühlhofer
- grid.6936.a0000000123222966Center for Protein Assemblies, Department of Chemistry, Technische Universität München, Ernst-Otto-Fischer Str. 8, 85747 Garching, Germany
| | - Carsten Peters
- grid.6936.a0000000123222966Center for Protein Assemblies, Department of Chemistry, Technische Universität München, Ernst-Otto-Fischer Str. 8, 85747 Garching, Germany
| | - Thomas Kriehuber
- grid.6936.a0000000123222966Center for Protein Assemblies, Department of Chemistry, Technische Universität München, Ernst-Otto-Fischer Str. 8, 85747 Garching, Germany ,grid.420061.10000 0001 2171 7500Present Address: Boehringer Ingelheim, Birkendorfer Str. 65, 88397 Biberach an der Riß, Germany
| | - Marina Kreuzeder
- grid.6936.a0000000123222966Center for Protein Assemblies, Department of Chemistry, Technische Universität München, Ernst-Otto-Fischer Str. 8, 85747 Garching, Germany ,grid.5252.00000 0004 1936 973XPresent Address: Ludwig-Maximilians-Universität München, Biozentrum Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - Pamina Kazman
- grid.6936.a0000000123222966Center for Protein Assemblies, Department of Chemistry, Technische Universität München, Ernst-Otto-Fischer Str. 8, 85747 Garching, Germany ,grid.424277.0Present Address: Roche Diagnostics, Nonnenwald 2, 82377 Penzberg, Germany
| | - Natalia Rodina
- grid.6936.a0000000123222966BNMRZ, Department of Chemistry, Technische Universität München, Ernst-Otto-Fischer Str. 2, 85747 Garching, Germany ,Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Bernd Reif
- grid.6936.a0000000123222966BNMRZ, Department of Chemistry, Technische Universität München, Ernst-Otto-Fischer Str. 2, 85747 Garching, Germany ,Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Martin Haslbeck
- grid.6936.a0000000123222966Center for Protein Assemblies, Department of Chemistry, Technische Universität München, Ernst-Otto-Fischer Str. 8, 85747 Garching, Germany
| | - Sevil Weinkauf
- grid.6936.a0000000123222966Center for Protein Assemblies, Department of Chemistry, Technische Universität München, Ernst-Otto-Fischer Str. 8, 85747 Garching, Germany
| | - Johannes Buchner
- Center for Protein Assemblies, Department of Chemistry, Technische Universität München, Ernst-Otto-Fischer Str. 8, 85747, Garching, Germany.
| |
Collapse
|
14
|
Luzarowski M, Vicente R, Kiselev A, Wagner M, Schlossarek D, Erban A, de Souza LP, Childs D, Wojciechowska I, Luzarowska U, Górka M, Sokołowska EM, Kosmacz M, Moreno JC, Brzezińska A, Vegesna B, Kopka J, Fernie AR, Willmitzer L, Ewald JC, Skirycz A. Global mapping of protein-metabolite interactions in Saccharomyces cerevisiae reveals that Ser-Leu dipeptide regulates phosphoglycerate kinase activity. Commun Biol 2021; 4:181. [PMID: 33568709 PMCID: PMC7876005 DOI: 10.1038/s42003-021-01684-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 01/08/2021] [Indexed: 01/30/2023] Open
Abstract
Protein-metabolite interactions are of crucial importance for all cellular processes but remain understudied. Here, we applied a biochemical approach named PROMIS, to address the complexity of the protein-small molecule interactome in the model yeast Saccharomyces cerevisiae. By doing so, we provide a unique dataset, which can be queried for interactions between 74 small molecules and 3982 proteins using a user-friendly interface available at https://promis.mpimp-golm.mpg.de/yeastpmi/ . By interpolating PROMIS with the list of predicted protein-metabolite interactions, we provided experimental validation for 225 binding events. Remarkably, of the 74 small molecules co-eluting with proteins, 36 were proteogenic dipeptides. Targeted analysis of a representative dipeptide, Ser-Leu, revealed numerous protein interactors comprising chaperones, proteasomal subunits, and metabolic enzymes. We could further demonstrate that Ser-Leu binding increases activity of a glycolytic enzyme phosphoglycerate kinase (Pgk1). Consistent with the binding analysis, Ser-Leu supplementation leads to the acute metabolic changes and delays timing of a diauxic shift. Supported by the dipeptide accumulation analysis our work attests to the role of Ser-Leu as a metabolic regulator at the interface of protein degradation and central metabolism.
Collapse
Affiliation(s)
- Marcin Luzarowski
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Rubén Vicente
- grid.418390.70000 0004 0491 976XDepartment of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Andrei Kiselev
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany ,grid.503344.50000 0004 0445 6769Laboratoire de Recherche en Sciences Végétales (LRSV), UPS/CNRS, UMR, Castanet Tolosan, France
| | - Mateusz Wagner
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany ,grid.8505.80000 0001 1010 5103University of Wrocław, Faculty of Biotechnology, Laboratory of Medical Biology, Wrocław, Poland
| | - Dennis Schlossarek
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Alexander Erban
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Leonardo Perez de Souza
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Dorothee Childs
- grid.4709.a0000 0004 0495 846XDepartment of Genome Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Izabela Wojciechowska
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Urszula Luzarowska
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany ,grid.7489.20000 0004 1937 0511Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Michał Górka
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Ewelina M. Sokołowska
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Monika Kosmacz
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany ,grid.45672.320000 0001 1926 5090Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Juan C. Moreno
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany ,grid.45672.320000 0001 1926 5090Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Aleksandra Brzezińska
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Bhavana Vegesna
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Joachim Kopka
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Alisdair R. Fernie
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Lothar Willmitzer
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Jennifer C. Ewald
- grid.10392.390000 0001 2190 1447Interfaculty Institute of Cell Biology, Eberhard Karls University of Tuebingen, Tuebingen, Germany
| | - Aleksandra Skirycz
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany ,grid.5386.8000000041936877XBoyce Thompson Institute, Ithaca, NY USA
| |
Collapse
|
15
|
Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ. Cell 2020; 184:545-559.e22. [PMID: 33357446 PMCID: PMC7836100 DOI: 10.1016/j.cell.2020.12.021] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 08/21/2020] [Accepted: 12/11/2020] [Indexed: 02/02/2023]
Abstract
Biological processes are regulated by intermolecular interactions and chemical modifications that do not affect protein levels, thus escaping detection in classical proteomic screens. We demonstrate here that a global protein structural readout based on limited proteolysis-mass spectrometry (LiP-MS) detects many such functional alterations, simultaneously and in situ, in bacteria undergoing nutrient adaptation and in yeast responding to acute stress. The structural readout, visualized as structural barcodes, captured enzyme activity changes, phosphorylation, protein aggregation, and complex formation, with the resolution of individual regulated functional sites such as binding and active sites. Comparison with prior knowledge, including other ‘omics data, showed that LiP-MS detects many known functional alterations within well-studied pathways. It suggested distinct metabolite-protein interactions and enabled identification of a fructose-1,6-bisphosphate-based regulatory mechanism of glucose uptake in E. coli. The structural readout dramatically increases classical proteomics coverage, generates mechanistic hypotheses, and paves the way for in situ structural systems biology. Dynamic structural proteomic screens detect functional changes at high resolution Detect enzyme activity, phosphorylation, and molecular interactions in situ Generate new molecular hypotheses and increase functional proteomics coverage Enabled discovery of a regulatory mechanism of glucose uptake in E. coli
Collapse
|
16
|
MacGilvray ME, Shishkova E, Place M, Wagner ER, Coon JJ, Gasch AP. Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses. J Proteome Res 2020; 19:3405-3417. [PMID: 32597660 DOI: 10.1021/acs.jproteome.0c00253] [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] [Indexed: 12/14/2022]
Abstract
To cope with sudden changes in the external environment, the budding yeast Saccharomyces cerevisiae orchestrates a multifaceted response that spans many levels of physiology. Several studies have interrogated the transcriptome response to endoplasmic reticulum (ER) stress and the role of regulators such as the Ire1 kinase and Hac1 transcription factors. However, less is known about responses to ER stress at other levels of physiology. Here, we used quantitative phosphoproteomics and computational network inference to uncover the yeast phosphoproteome response to the reducing agent dithiothreitol (DTT) and the upstream signaling network that controls it. We profiled wild-type cells and mutants lacking IRE1 or MAPK kinases MKK1 and MKK2, before and at various times after DTT treatment. In addition to revealing downstream targets of these kinases, our inference approach predicted new regulators in the DTT response, including cell-cycle regulator Cdc28 and osmotic-response kinase Rck2, which we validated computationally. Our results also revealed similarities and surprising differences in responses to different stress conditions, especially in the response of protein kinase A targets. These results have implications for the breadth of signaling programs that can give rise to common stress response signatures.
Collapse
Affiliation(s)
- Matthew E MacGilvray
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Evgenia Shishkova
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Michael Place
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ellen R Wagner
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Departments of Chemistry and Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Morgridge Institute for Research, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Audrey P Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| |
Collapse
|
17
|
Kurdrid P, Phuengcharoen P, Senachak J, Saree S, Hongsthong A. Revealing the key point of the temperature stress response of Arthrospira platensis C1 at the interconnection of C- and N- metabolism by proteome analyses and PPI networking. BMC Mol Cell Biol 2020; 21:43. [PMID: 32532219 PMCID: PMC7291507 DOI: 10.1186/s12860-020-00285-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 05/28/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Growth-temperature stress causes biochemical changes in the cells and reduction of biomass yield. Quantitative proteome of Arthrospira platensis C1 in response to low- and high temperature stresses was previously analysed to elucidate the stress response mechanism. The data highlighted the linkage of signaling proteins and proteins involved in nitrogen and ammonia assimilation, photosynthesis and oxidative stress. RESULTS After phosphoproteome analysis was carried out in this study, the tentative temperature response cascade of A. platensis C1 was drawn based on data integration of quantitative proteome and phosphoproteome analysis and protein-protein interaction (PPI) networks. The integration revealed 31 proteins regulated at the protein-expression and post-translational levels; thus, this group of proteins was designated bi-level regulated proteins. PPI networks were then constructed based on A. platensis C1 gene inference from publicly available interaction data. The key two-component system (TCS) proteins, SPLC1_S082010 and SPLC1_S230960, were identified as bi-level regulated proteins and were linked to SPLC1_S270380 or glutamate synthase, an important enzyme in nitrogen assimilation that synthesizes glutamate from 2-oxoglutarate, which is known as the signal compound that regulates the carbon/nitrogen (C/N) balance of cells. Moreover, the role of the p-site in the PPIs of some phosphoproteins of interest was determined using site-directed mutagenesis and a yeast two-hybrid system. Evidence showing the critical role of the p-site in the PPI was observed for the multi-sensor histidine kinase SPLC1_S041070 (Hik28) and glutamate synthase. PPI subnetwork also showed that the Hik28 involved with the enzymes in fatty acid desaturation and nitrogen metabolism. The effect of Hik28-deletion was validated by fatty acid analysis and measurement of photosynthetic activity under nitrogen depletion. CONCLUSIONS Taken together, the data clearly represents (i) the multi-level regulation of proteins involved in the stress response mechanism and (ii) the key point of the temperature stress response at the interconnection of C- and N- metabolism.
Collapse
Affiliation(s)
- Pavinee Kurdrid
- Biochemical Engineering and Systems Biology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at King Mongkut's University of Technology Thonburi, Mailing Address: IBEG/BIOTEC@KMUTT, 49 Soi Thian Thale 25, Tha Kham, Bang Khun Thian, Bangkok, 10150, Thailand
| | - Phutnichar Phuengcharoen
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, 49 Soi Thian Thale 25, Tha Kham, Bang Khun Thian, Bangkok, 10150, Thailand
| | - Jittisak Senachak
- Biochemical Engineering and Systems Biology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at King Mongkut's University of Technology Thonburi, Mailing Address: IBEG/BIOTEC@KMUTT, 49 Soi Thian Thale 25, Tha Kham, Bang Khun Thian, Bangkok, 10150, Thailand
| | - Sirilak Saree
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, 49 Soi Thian Thale 25, Tha Kham, Bang Khun Thian, Bangkok, 10150, Thailand
| | - Apiradee Hongsthong
- Biochemical Engineering and Systems Biology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at King Mongkut's University of Technology Thonburi, Mailing Address: IBEG/BIOTEC@KMUTT, 49 Soi Thian Thale 25, Tha Kham, Bang Khun Thian, Bangkok, 10150, Thailand.
| |
Collapse
|
18
|
Kuechler ER, Budzyńska PM, Bernardini JP, Gsponer J, Mayor T. Distinct Features of Stress Granule Proteins Predict Localization in Membraneless Organelles. J Mol Biol 2020; 432:2349-2368. [PMID: 32105731 DOI: 10.1016/j.jmb.2020.02.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 12/31/2022]
Abstract
Recently generated proteomic data provides unprecedented insight into stress granule composition and stands as fruitful ground for further analysis. Stress granules are stress-induced biological assemblies that are of keen interest due to being linked to both long-term cell viability and a variety of protein aggregation-based diseases. Herein, we compile recently published stress granule composition data, formed specifically through heat and oxidative stress, for both mammalian (Homo sapiens) and yeast (Saccharomyces cerevisiae) cells. Interrogation of the data reveals that stress granule proteins are enriched in features that favor protein liquid-liquid phase separation, being highly disordered, soluble, and abundant while maintaining a high level of protein-protein interactions under basal conditions. Furthermore, these "stress granuleomes" are shown to be enriched for multidomained, RNA-binding proteins with increased potential for post-translational modifications. Findings are consistent with the notion that stress granule formation is driven by protein liquid-liquid phase separation. Furthermore, stress granule proteins appear poised near solubility limits while possessing the ability to dynamically alter their phase behavior in response to external threat. Interestingly, several features, such as protein disorder, are more prominent among stress granule proteins that share homologs between yeast and mammalian systems also found within stress-induced foci. We culminate results from our stress granule analysis into novel predictors for granule incorporation and validate the mammalian predictor's performance against multiple types of membraneless condensates and by colocalization microscopy.
Collapse
Affiliation(s)
- Erich R Kuechler
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Paulina M Budzyńska
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Jonathan P Bernardini
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Jörg Gsponer
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
| | - Thibault Mayor
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
| |
Collapse
|
19
|
Storey AJ, Hardman RE, Byrum SD, Mackintosh SG, Edmondson RD, Wahls WP, Tackett AJ, Lewis JA. Accurate and Sensitive Quantitation of the Dynamic Heat Shock Proteome Using Tandem Mass Tags. J Proteome Res 2020; 19:1183-1195. [PMID: 32027144 DOI: 10.1021/acs.jproteome.9b00704] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cells respond to environmental perturbations and insults through modulating protein abundance and function. However, the majority of studies have focused on changes in RNA abundance because quantitative transcriptomics has historically been more facile than quantitative proteomics. Modern Orbitrap mass spectrometers now provide sensitive and deep proteome coverage, allowing direct, global quantification of not only protein abundance but also post-translational modifications (PTMs) that regulate protein activity. We implemented and validated using the well-characterized heat shock response of budding yeast, a tandem mass tagging (TMT), triple-stage mass spectrometry (MS3) strategy to measure global changes in the proteome during the yeast heat shock response over nine time points. We report that basic-pH, ultra-high performance liquid chromatography (UPLC) fractionation of tryptic peptides yields superfractions of minimal redundancy, a crucial requirement for deep coverage and quantification by subsequent LC-MS3. We quantified 2275 proteins across three biological replicates and found that differential expression peaked near 90 min following heat shock (with 868 differentially expressed proteins at 5% false discovery rate). The sensitivity of the approach also allowed us to detect changes in the relative abundance of ubiquitination and phosphorylation PTMs over time. Remarkably, relative quantification of post-translationally modified peptides revealed striking evidence of regulation of the heat shock response by protein PTMs. These data demonstrate that the high precision of TMT-MS3 enables peptide-level quantification of samples, which can reveal important regulation of protein abundance and regulatory PTMs under various experimental conditions.
Collapse
Affiliation(s)
- Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Rebecca E Hardman
- Interdisciplinary Graduate Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, Arkansas 72701, United States.,Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Rick D Edmondson
- College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Wayne P Wahls
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Jeffrey A Lewis
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
| |
Collapse
|
20
|
Yan J, Long Y, Zhou T, Ren J, Li Q, Song G, Cui Z. Dynamic Phosphoproteome Profiling of Zebrafish Embryonic Fibroblasts during Cold Acclimation. Proteomics 2020; 20:e1900257. [PMID: 31826332 DOI: 10.1002/pmic.201900257] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 11/24/2019] [Indexed: 11/09/2022]
Abstract
Temperature affects almost all aspects of the fish life. To cope with low temperature, fish have evolved the ability of cold acclimation for survival. However, intracellular signaling events underlying cold acclimation in fish remain largely unknown. Here, the formation of cold acclimation in zebrafish embryonic fibroblasts (ZF4) is monitored and the phosphorylation events during the process are investigated through a large-scale quantitative phosphoproteomic approach. In total, 11 474 phosphorylation sites are identified on 4066 proteins and quantified 5772 phosphosites on 2519 proteins. Serine, threonine, and tyrosine (Ser/Thr/Tyr) phosphorylation accounted for 85.5%, 13.3%, and 1.2% of total phosphosites, respectively. Among all phosphosites, 702 phosphosites on 510 proteins show differential regulation during cold acclimation of ZF4 cells. These phosphosites are divided into six clusters according to their dynamic changes during cold exposure. Kinase-substrate prediction reveals that mitogen-activated protein kinase (MAPK) among the kinase groups is predominantly responsible for phosphorylation of these phosphosites. The differentially regulated phosphoproteins are functionally associated with various cellular processes such as regulation of actin cytoskeleton and MAPK signaling pathway. These data enrich the database of protein phosphorylation sites in zebrafish and provide key clues for the elucidation of intracellular signaling networks during cold acclimation of fish.
Collapse
Affiliation(s)
- Junjun Yan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong Long
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan, 430072, China
| | - Tong Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Ren
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan, 430072, China
| | - Guili Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan, 430072, China
| | - Zongbin Cui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan, 430072, China.,The Innovative Academy of Seed Design, Chinese Academy of Sciences, Hubei, Wuhan, 430072, China
| |
Collapse
|
21
|
Janschitz M, Romanov N, Varnavides G, Hollenstein DM, Gérecová G, Ammerer G, Hartl M, Reiter W. Novel interconnections of HOG signaling revealed by combined use of two proteomic software packages. Cell Commun Signal 2019; 17:66. [PMID: 31208443 PMCID: PMC6572760 DOI: 10.1186/s12964-019-0381-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 06/04/2019] [Indexed: 12/12/2022] Open
Abstract
Modern quantitative mass spectrometry (MS)-based proteomics enables researchers to unravel signaling networks by monitoring proteome-wide cellular responses to different stimuli. MS-based analysis of signaling systems usually requires an integration of multiple quantitative MS experiments, which remains challenging, given that the overlap between these datasets is not necessarily comprehensive. In a previous study we analyzed the impact of the yeast mitogen-activated protein kinase (MAPK) Hog1 on the hyperosmotic stress-affected phosphorylome. Using a combination of a series of hyperosmotic stress and kinase inhibition experiments, we identified a broad range of direct and indirect substrates of the MAPK. Here we re-evaluate this extensive MS dataset and demonstrate that a combined analysis based on two software packages, MaxQuant and Proteome Discoverer, increases the coverage of Hog1-target proteins by 30%. Using protein-protein proximity assays we show that the majority of new targets gained by this analysis are indeed Hog1-interactors. Additionally, kinetic profiles indicate differential trends of Hog1-dependent versus Hog1-independent phosphorylation sites. Our findings highlight a previously unrecognized interconnection between Hog1 signaling and the RAM signaling network, as well as sphingolipid homeostasis.
Collapse
Affiliation(s)
- Marion Janschitz
- Department of Biochemistry, Max F. Perutz Laboratories, Vienna BioCenter, Vienna, Austria
- Children’s Cancer Research Institute, St. Anna Kinderspital, Vienna, Austria
| | - Natalie Romanov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Current Address: Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Gina Varnavides
- Mass Spectrometry Facility, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter, Vienna, Austria
| | | | - Gabriela Gérecová
- Department of Biochemistry, Max F. Perutz Laboratories, Vienna BioCenter, Vienna, Austria
| | - Gustav Ammerer
- Department of Biochemistry, Max F. Perutz Laboratories, Vienna BioCenter, Vienna, Austria
| | - Markus Hartl
- Department of Biochemistry, Max F. Perutz Laboratories, Vienna BioCenter, Vienna, Austria
- Mass Spectrometry Facility, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Wolfgang Reiter
- Mass Spectrometry Facility, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter, Vienna, Austria
| |
Collapse
|
22
|
Pfammatter S, Bonneil E, McManus FP, Thibault P. Accurate Quantitative Proteomic Analyses Using Metabolic Labeling and High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS). J Proteome Res 2019; 18:2129-2138. [DOI: 10.1021/acs.jproteome.9b00021] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
23
|
Kubiniok P, Finicle BT, Piffaretti F, McCracken AN, Perryman M, Hanessian S, Edinger AL, Thibault P. Dynamic Phosphoproteomics Uncovers Signaling Pathways Modulated by Anti-oncogenic Sphingolipid Analogs. Mol Cell Proteomics 2019; 18:408-422. [PMID: 30482847 PMCID: PMC6398214 DOI: 10.1074/mcp.ra118.001053] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/23/2018] [Indexed: 12/31/2022] Open
Abstract
The anti-neoplastic sphingolipid analog SH-BC-893 starves cancer cells to death by down-regulating cell surface nutrient transporters and blocking lysosomal trafficking events. These effects are mediated by the activation of protein phosphatase 2A (PP2A). To identify putative PP2A substrates, we used quantitative phosphoproteomics to profile the temporal changes in protein phosphorylation in FL5.12 cells following incubation with SH-BC-893 or the specific PP2A inhibitor LB-100. These analyses enabled the profiling of more than 15,000 phosphorylation sites, of which 958 sites on 644 proteins were dynamically regulated. We identified 114 putative PP2A substrates including several nutrient transporter proteins, GTPase regulators (e.g. Agap2, Git1), and proteins associated with actin cytoskeletal remodeling (e.g. Vim, Pxn). To identify SH-BC-893-induced cell signaling events that disrupt lysosomal trafficking, we compared phosphorylation profiles in cells treated with SH-BC-893 or C2-ceramide, a non-vacuolating sphingolipid that does not impair lysosomal fusion. These analyses combined with functional assays uncovered the differential regulation of Akt and Gsk3b by SH-BC-893 (vacuolating) and C2-ceramide (non-vacuolating). Dynamic phosphoproteomics of cells treated with compounds affecting PP2A activity thus enabled the correlation of cell signaling with phenotypes to rationalize their mode of action.
Collapse
Affiliation(s)
- Peter Kubiniok
- From the ‡Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada
- §Department of Chemistry, Université de Montréal, Quebec, H3C 3J7, Canada
| | - Brendan T Finicle
- ¶Department of Developmental and Cell Biology, University of California Irvine, Irvine CA 92697
| | - Fanny Piffaretti
- From the ‡Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada
| | - Alison N McCracken
- ¶Department of Developmental and Cell Biology, University of California Irvine, Irvine CA 92697
| | - Michael Perryman
- §Department of Chemistry, Université de Montréal, Quebec, H3C 3J7, Canada
| | - Stephen Hanessian
- §Department of Chemistry, Université de Montréal, Quebec, H3C 3J7, Canada
| | - Aimee L Edinger
- ¶Department of Developmental and Cell Biology, University of California Irvine, Irvine CA 92697;
| | - Pierre Thibault
- From the ‡Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada;
- §Department of Chemistry, Université de Montréal, Quebec, H3C 3J7, Canada
- ‖Department of Biochemistry, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada
| |
Collapse
|
24
|
Ming M, Wang X, Lian L, Zhang H, Gao W, Zhu B, Lou D. Metabolic responses ofSaccharomyces cerevisiaeto ethanol stress using gas chromatography-mass spectrometry. Mol Omics 2019; 15:216-221. [DOI: 10.1039/c9mo00055k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Metabolic responses ofSaccharomyces cerevisiaeunder ethanol stress by a metabolomics method based on GC-MS.
Collapse
Affiliation(s)
- Ming Ming
- Department of Analytical Chemistry
- Jilin Institute of Chemical Technology
- Jilin
- P. R. China
| | - Xiyue Wang
- Department of Analytical Chemistry
- Jilin Institute of Chemical Technology
- Jilin
- P. R. China
| | - Lili Lian
- Department of Analytical Chemistry
- Jilin Institute of Chemical Technology
- Jilin
- P. R. China
| | - Hao Zhang
- Department of Analytical Chemistry
- Jilin Institute of Chemical Technology
- Jilin
- P. R. China
| | - Wenxiu Gao
- Department of Analytical Chemistry
- Jilin Institute of Chemical Technology
- Jilin
- P. R. China
| | - Bo Zhu
- Department of Analytical Chemistry
- Jilin Institute of Chemical Technology
- Jilin
- P. R. China
| | - Dawei Lou
- Department of Analytical Chemistry
- Jilin Institute of Chemical Technology
- Jilin
- P. R. China
| |
Collapse
|
25
|
Li S, Yu H, Liu Y, Zhang X, Ma F. The lipid strategies in Cunninghamella echinulata for an allostatic response to temperature changes. Process Biochem 2019. [DOI: 10.1016/j.procbio.2018.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
26
|
Kawata K, Yugi K, Hatano A, Kokaji T, Tomizawa Y, Fujii M, Uda S, Kubota H, Matsumoto M, Nakayama KI, Kuroda S. Reconstruction of global regulatory network from signaling to cellular functions using phosphoproteomic data. Genes Cells 2018; 24:82-93. [PMID: 30417516 DOI: 10.1111/gtc.12655] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/04/2018] [Accepted: 11/05/2018] [Indexed: 12/21/2022]
Abstract
Cellular signaling regulates various cellular functions via protein phosphorylation. Phosphoproteomic data potentially include information for a global regulatory network from signaling to cellular functions, but a procedure to reconstruct this network using such data has yet to be established. In this paper, we provide a procedure to reconstruct a global regulatory network from signaling to cellular functions from phosphoproteomic data by integrating prior knowledge of cellular functions and inference of the kinase-substrate relationships (KSRs). We used phosphoproteomic data from insulin-stimulated Fao hepatoma cells and identified protein phosphorylation regulated by insulin specifically over-represented in cellular functions in the KEGG database. We inferred kinases for protein phosphorylation by KSRs, and connected the kinases in the insulin signaling layer to the phosphorylated proteins in the cellular functions, revealing that the insulin signal is selectively transmitted via the Pi3k-Akt and Erk signaling pathways to cellular adhesions and RNA maturation, respectively. Thus, we provide a method to reconstruct global regulatory network from signaling to cellular functions based on phosphoproteomic data.
Collapse
Affiliation(s)
- Kentaro Kawata
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Japan
| | - Katsuyuki Yugi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Japan.,YCI Laboratory for Trans-Omics, Young Chief Investigator Program, RIKEN Center for Integrative Medical Science, Yokohama, Japan.,Institute for Advanced Biosciences, Keio University, Fujisawa, Japan.,PRESTO, Japan Science and Technology Agency, Yokohama, Japan
| | - Atsushi Hatano
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Japan
| | - Toshiya Kokaji
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
| | - Yoko Tomizawa
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Japan
| | - Masashi Fujii
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Japan.,Molecular Genetics Research Laboratory, Graduate School of Science, University of Tokyo, Bunkyo-ku, Japan
| | - Shinsuke Uda
- Division of Integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Kubota
- Division of Integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Masaki Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Shinya Kuroda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Bunkyo-ku, Japan
| |
Collapse
|
27
|
Chen Y, Zhang X, Zhang M, Zhu J, Wu Z, Zheng X. A transcriptome analysis of the ameliorate effect of Cyclocarya paliurus triterpenoids on ethanol stress in Saccharomyces cerevisiae. World J Microbiol Biotechnol 2018; 34:182. [PMID: 30478689 DOI: 10.1007/s11274-018-2561-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 11/17/2018] [Indexed: 11/24/2022]
Abstract
Saccharomyces cerevisiae (S. cerevisiae) plays a critical role in ethanol fermentation. However, during the fermentation, yeast cells are exposed to the accumulation of ethanol, which significantly affect the cell growth and the target product yield. In the present work, we employed RNA-sequence (RNA-seq) to investigate the ameliorate effect of Cyclocarya paliurus (C. paliurus) triterpenoids on S. cerevisiae under the ethanol stress. After C. paliurus triterpenoids intervention (0.3% v/v), 84 differentially expressed genes (DEGs) were identified, including 39 up-regulated and 45 down-regulated genes. The addition of triterpenoids decreased the filamentous and invasive growth of cells, and benefit to the redox balance and glycolysis. This study offers a global view through transcriptome analysis to understand the molecular response to ethanol in Sc131 by the treatment of C. paliurus triterpenoids, which may be helpful to enhance ethanol tolerance of S. cerevisiae in the fermentation of Chinese fruit wine.
Collapse
Affiliation(s)
- Yuhui Chen
- Department of Food Science and Engineering, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Xin Zhang
- Department of Food Science and Engineering, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China.
| | - Man Zhang
- Department of Food Science, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Jieyu Zhu
- Department of Food Science, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Zufang Wu
- Department of Food Science and Engineering, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Xiaojie Zheng
- Department of Agriculture and Biotechnology, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, People's Republic of China
| |
Collapse
|
28
|
Xu T, Li D, He Y, Zhang F, Qiao M, Chen Y. The expression level of CSDAP1 in lung cancer and its clinical significance. Oncol Lett 2018; 16:4361-4366. [PMID: 30214570 PMCID: PMC6126166 DOI: 10.3892/ol.2018.9195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 07/11/2018] [Indexed: 12/02/2022] Open
Abstract
Expression level of messenger RNA (mRNA) of cold shock domain protein A intronless pseudogene (CSDAP1) in lung cancer tissues was studied. Fresh pathological specimens collected from 317 patients with primary lung cancer through surgical resection from January 2007 to January 2012 were selected. Reverse transcription-polymerase chain reaction (RT-PCR) and western blot analysis were used to detect the transcription and translation of CSDAP1 in lung cancer tissues and cancer-adjacent normal tissues, and the results were analyzed in combination with clinicopathological features and prognosis of lung cancer. Among 317 lung cancer specimens, 105 cases (33.1%) had high expression of CSDAP1. Among 138 cases of pulmonary adenocarcinoma, 59 cases had high expression of CSDAP1, and the high expression rate was 42.8%. Among 170 cases of lung squamous cell carcinoma, 46 cases had high expression of CSDAP1, and the high expression rate was 27.5% (P<0.05). Three cases of large cell carcinoma and 9 cases of small cell carcinoma had extremely low expression or had no expression of CSDAP1. Among the 127 lung cancer patients with regional lymph node metastasis, 53 cases (41.7%) had high expression of CSDAP1, while among the 190 lung cancer patients without regional lymph node metastasis, 52 cases (27.4%) had high expression of CSDAP1 (P<0.05). The results also revealed that the expression of CSDAP1 was also related to tumor-node-metastasis (TNM) staging of lung cancer. One-year, three-year and five-year survival rates of lung cancer patients who had no expression of CSDAP1 were relatively high (P<0.05). The results suggested that CSDAP1 may play an important role in the occurrence, development and judgement of prognosis of lung cancer.
Collapse
Affiliation(s)
- Tongbai Xu
- Department of Respiratory Medicine, Tianjin Nankai Hospital, Tianjin 300100, P.R. China
| | - Dongsheng Li
- Department of Respiratory Medicine, Tianjin Nankai Hospital, Tianjin 300100, P.R. China
| | - Yuan He
- Department of Respiratory Medicine, Tianjin Nankai Hospital, Tianjin 300100, P.R. China
| | - Fuliang Zhang
- Department of Respiratory Medicine, Tianjin Nankai Hospital, Tianjin 300100, P.R. China
| | - Man Qiao
- Department of Respiratory Medicine, Tianjin Nankai Hospital, Tianjin 300100, P.R. China
| | - Yanhua Chen
- Department of Respiratory Medicine, Tianjin Nankai Hospital, Tianjin 300100, P.R. China
| |
Collapse
|
29
|
Talavera D, Kershaw CJ, Costello JL, Castelli LM, Rowe W, Sims PFG, Ashe MP, Grant CM, Pavitt GD, Hubbard SJ. Archetypal transcriptional blocks underpin yeast gene regulation in response to changes in growth conditions. Sci Rep 2018; 8:7949. [PMID: 29785040 PMCID: PMC5962585 DOI: 10.1038/s41598-018-26170-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 05/01/2018] [Indexed: 01/30/2023] Open
Abstract
The transcriptional responses of yeast cells to diverse stresses typically include gene activation and repression. Specific stress defense, citric acid cycle and oxidative phosphorylation genes are activated, whereas protein synthesis genes are coordinately repressed. This view was achieved from comparative transcriptomic experiments delineating sets of genes whose expression greatly changed with specific stresses. Less attention has been paid to the biological significance of 1) consistent, albeit modest, changes in RNA levels across multiple conditions, and 2) the global gene expression correlations observed when comparing numerous genome-wide studies. To address this, we performed a meta-analysis of 1379 microarray-based experiments in yeast, and identified 1388 blocks of RNAs whose expression changes correlate across multiple and diverse conditions. Many of these blocks represent sets of functionally-related RNAs that act in a coordinated fashion under normal and stress conditions, and map to global cell defense and growth responses. Subsequently, we used the blocks to analyze novel RNA-seq experiments, demonstrating their utility and confirming the conclusions drawn from the meta-analysis. Our results provide a new framework for understanding the biological significance of changes in gene expression: 'archetypal' transcriptional blocks that are regulated in a concerted fashion in response to external stimuli.
Collapse
Affiliation(s)
- David Talavera
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.
| | - Christopher J Kershaw
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Joseph L Costello
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.,Department of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Lydia M Castelli
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.,Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield, United Kingdom
| | - William Rowe
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.,Department of Chemistry, Loughborough University, Loughborough, United Kingdom
| | - Paul F G Sims
- Manchester Institute of Biotechnology (MIB), The University of Manchester, Manchester, United Kingdom
| | - Mark P Ashe
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Chris M Grant
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Graham D Pavitt
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.
| | - Simon J Hubbard
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.
| |
Collapse
|
30
|
Ren L, Li C, Wang Y, Teng Y, Sun H, Xing B, Yang X, Jiang Y, He F. In Vivo Phosphoproteome Analysis Reveals Kinome Reprogramming in Hepatocellular Carcinoma. Mol Cell Proteomics 2018; 17:1067-1083. [PMID: 29472430 DOI: 10.1074/mcp.ra117.000421] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 02/10/2018] [Indexed: 12/19/2022] Open
Abstract
Aberrant kinases contribute to cancer survival and proliferation. Here, we quantitatively characterized phosphoproteomic changes in an HBx-transgenic mouse model of hepatocellular carcinoma (HCC) using high-resolution mass spectrometry, profiled 22,539 phosphorylation sites on 5431 proteins. Using a strategy to interpret kinase- substrate relations in HCC and to uncover predominant kinases in tumors, our results, revealed elevated kinase activities of Src family kinases (SFKs), PKCs, MAPKs, and ROCK2 in HCC, representatives of which were further validated in cell models and clinical HBV-positive HCC samples. Inhibitor combinations targeting Src and PKCs or ROCK2 both synergized significantly to inhibit cell growth. In addition, we demonstrated that phosphorylation at Src Ser17 directly affects its kinase activity. Our phosphoproteome data facilitated the construction of a detailed molecular landscape in HCC and should serve as a resource for the cancer community. Our strategy is generally applicable to targeted therapeutics, also highlights potential mechanisms of kinase regulation.
Collapse
Affiliation(s)
- Liangliang Ren
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Chaoying Li
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Youliang Wang
- §State Key Laboratory of Proteomics, Genetic Laboratory of Development and Diseases, Institute of Biotechnology, Beijing 100071, China
| | - Yan Teng
- §State Key Laboratory of Proteomics, Genetic Laboratory of Development and Diseases, Institute of Biotechnology, Beijing 100071, China
| | - Huichuan Sun
- ¶Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Baocai Xing
- ‖Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Hepatopancreatobiliary Surgery Department I, Peking University; Cancer Hospital & Institute, Beijing 100042, China
| | - Xiao Yang
- §State Key Laboratory of Proteomics, Genetic Laboratory of Development and Diseases, Institute of Biotechnology, Beijing 100071, China
| | - Ying Jiang
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China;
| | - Fuchu He
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China;
| |
Collapse
|
31
|
Jarnuczak AF, Albornoz MG, Eyers CE, Grant CM, Hubbard SJ. A quantitative and temporal map of proteostasis during heat shock in Saccharomyces cerevisiae. Mol Omics 2018; 14:37-52. [PMID: 29570196 DOI: 10.1039/c7mo00050b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Temperature fluctuation is a common environmental stress that elicits a molecular response in order to maintain intracellular protein levels. Here, for the first time, we report a comprehensive temporal and quantitative study of the proteome during a 240 minute heat stress, using label-free mass spectrometry. We report temporal expression changes of the hallmark heat stress proteins, including many molecular chaperones, tightly coupled to their protein clients. A notable lag of 30 to 120 minutes was evident between transcriptome and proteome levels for differentially expressed genes. This targeted molecular response buffers the global proteome; fewer than 15% of proteins display significant abundance change. Additionally, a parallel study in a Hsp70 chaperone mutant (ssb1Δ) demonstrated a significantly attenuated response, at odds with the modest phenotypic effects that are observed on growth rate. We cast the global changes in temporal protein expression into protein interaction and functional networks, to afford a unique, time-resolved and quantitative description of the heat shock response in an important model organism.
Collapse
Affiliation(s)
- Andrew F Jarnuczak
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester M13 9PT, UK.
| | | | | | | | | |
Collapse
|
32
|
Herrmann M, Ravindran SP, Schwenk K, Cordellier M. Population transcriptomics in Daphnia
: The role of thermal selection. Mol Ecol 2017; 27:387-402. [DOI: 10.1111/mec.14450] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 10/22/2017] [Accepted: 11/02/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Maike Herrmann
- Institute for Environmental Sciences; University Koblenz-Landau; Landau in der Pfalz Germany
| | | | - Klaus Schwenk
- Institute for Environmental Sciences; University Koblenz-Landau; Landau in der Pfalz Germany
| | | |
Collapse
|
33
|
Barraza CE, Solari CA, Marcovich I, Kershaw C, Galello F, Rossi S, Ashe MP, Portela P. The role of PKA in the translational response to heat stress in Saccharomyces cerevisiae. PLoS One 2017; 12:e0185416. [PMID: 29045428 PMCID: PMC5646765 DOI: 10.1371/journal.pone.0185416] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 09/12/2017] [Indexed: 11/18/2022] Open
Abstract
Cellular responses to stress stem from a variety of different mechanisms, including translation arrest and relocation of the translationally repressed mRNAs to ribonucleoprotein particles like stress granules (SGs) and processing bodies (PBs). Here, we examine the role of PKA in the S. cerevisiae heat shock response. Under mild heat stress Tpk3 aggregates and promotes aggregation of eIF4G, Pab1 and eIF4E, whereas severe heat stress leads to the formation of PBs and SGs that contain both Tpk2 and Tpk3 and a larger 48S translation initiation complex. Deletion of TPK2 or TPK3 impacts upon the translational response to heat stress of several mRNAs including CYC1, HSP42, HSP30 and ENO2. TPK2 deletion leads to a robust translational arrest, an increase in SGs/PBs aggregation and translational hypersensitivity to heat stress, whereas TPK3 deletion represses SGs/PBs formation, translational arrest and response for the analyzed mRNAs. Therefore, this work provides evidence indicating that Tpk2 and Tpk3 have opposing roles in translational adaptation during heat stress, and highlight how the same signaling pathway can be regulated to generate strikingly distinct physiological outputs.
Collapse
Affiliation(s)
- Carla E Barraza
- Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET). Buenos Aires, Argentina
| | - Clara A Solari
- Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET). Buenos Aires, Argentina
| | - Irina Marcovich
- Instituto de Investigaciones en Ingenieria Genetica y Biologia Molecular "Dr. Hector N. Torres", Buenos Aires, Argentina
| | - Christopher Kershaw
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Fiorella Galello
- Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET). Buenos Aires, Argentina
| | - Silvia Rossi
- Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET). Buenos Aires, Argentina
| | - Mark P Ashe
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Paula Portela
- Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET). Buenos Aires, Argentina
| |
Collapse
|
34
|
Bai Y, Chen B, Li M, Zhou Y, Ren S, Xu Q, Chen M, Wang S. FPD: A comprehensive phosphorylation database in fungi. Fungal Biol 2017; 121:869-875. [DOI: 10.1016/j.funbio.2017.06.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 06/09/2017] [Accepted: 06/18/2017] [Indexed: 12/26/2022]
|
35
|
Insights regarding fungal phosphoproteomic analysis. Fungal Genet Biol 2017; 104:38-44. [DOI: 10.1016/j.fgb.2017.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/27/2017] [Accepted: 03/07/2017] [Indexed: 11/19/2022]
|
36
|
Chen Y, Nielsen J. Flux control through protein phosphorylation in yeast. FEMS Yeast Res 2017; 16:fow096. [PMID: 27797916 DOI: 10.1093/femsyr/fow096] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2016] [Indexed: 01/26/2023] Open
Abstract
Protein phosphorylation is one of the most important mechanisms regulating metabolism as it can directly modify metabolic enzymes by the addition of phosphate groups. Attributed to such a rapid and reversible mechanism, cells can adjust metabolism rapidly in response to temporal changes. The yeast Saccharomyces cerevisiae, a widely used cell factory and model organism, is reported to show frequent phosphorylation events in metabolism. Studying protein phosphorylation in S. cerevisiae allows for gaining new insight into the function of regulatory networks, which may enable improved metabolic engineering as well as identify mechanisms underlying human metabolic diseases. Here we collect functional phosphorylation events of 41 enzymes involved in yeast metabolism and demonstrate functional mechanisms and the application of this information in metabolic engineering. From a systems biology perspective, we describe the development of phosphoproteomics in yeast as well as approaches to analysing the phosphoproteomics data. Finally, we focus on integrated analyses with other omics data sets and genome-scale metabolic models. Despite the advances, future studies improving both experimental technologies and computational approaches are imperative to expand the current knowledge of protein phosphorylation in S. cerevisiae.
Collapse
Affiliation(s)
- Yu Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.,Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Kgs. Lyngby, Denmark
| |
Collapse
|
37
|
Kanshin E, Giguère S, Jing C, Tyers M, Thibault P. Machine Learning of Global Phosphoproteomic Profiles Enables Discrimination of Direct versus Indirect Kinase Substrates. Mol Cell Proteomics 2017; 16:786-798. [PMID: 28265048 DOI: 10.1074/mcp.m116.066233] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/13/2017] [Indexed: 12/12/2022] Open
Abstract
Mass spectrometry allows quantification of tens of thousands of phosphorylation sites from minute amounts of cellular material. Despite this wealth of information, our understanding of phosphorylation-based signaling is limited, in part because it is not possible to deconvolute substrate phosphorylation that is directly mediated by a particular kinase versus phosphorylation that is mediated by downstream kinases. Here, we describe a framework for assignment of direct in vivo kinase substrates using a combination of selective chemical inhibition, quantitative phosphoproteomics, and machine learning techniques. Our workflow allows classification of phosphorylation events following inhibition of an analog-sensitive kinase into kinase-independent effects of the inhibitor, direct effects on cognate substrates, and indirect effects mediated by downstream kinases or phosphatases. We applied this method to identify many direct targets of Cdc28 and Snf1 kinases in the budding yeast Saccharomyces cerevisiae Global phosphoproteome analysis of acute time-series demonstrated that dephosphorylation of direct kinase substrates occurs more rapidly compared with indirect substrates, both after inhibitor treatment and under a physiological nutrient shift in wt cells. Mutagenesis experiments revealed a high proportion of functionally relevant phosphorylation sites on Snf1 targets. For example, Snf1 itself was inhibited through autophosphorylation on Ser391 and new phosphosites were discovered that modulate the activity of the Reg1 regulatory subunit of the Glc7 phosphatase and the Gal83 β-subunit of SNF1 complex. This methodology applies to any kinase for which a functional analog sensitive version can be constructed to facilitate the dissection of the global phosphorylation network.
Collapse
Affiliation(s)
- Evgeny Kanshin
- From the ‡Institute for Research in Immunology and Cancer
| | | | - Cheng Jing
- From the ‡Institute for Research in Immunology and Cancer
| | - Mike Tyers
- From the ‡Institute for Research in Immunology and Cancer, .,§Department of Medicine
| | - Pierre Thibault
- From the ‡Institute for Research in Immunology and Cancer, .,¶Department of Chemistry, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada
| |
Collapse
|
38
|
Kubiniok P, Lavoie H, Therrien M, Thibault P. Time-resolved Phosphoproteome Analysis of Paradoxical RAF Activation Reveals Novel Targets of ERK. Mol Cell Proteomics 2017; 16:663-679. [PMID: 28188228 DOI: 10.1074/mcp.m116.065128] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/31/2016] [Indexed: 12/19/2022] Open
Abstract
Small molecules targeting aberrant RAF activity, like vemurafenib (PLX4032), are highly effective against cancers harboring the V600E BRAF mutation and are now approved for clinical use against metastatic melanoma. However, in tissues showing elevated RAS activity and in RAS mutant tumors, these inhibitors stimulate RAF dimerization, resulting in inhibitor resistance and downstream "paradoxical" ERK activation. To understand the global signaling response of cancer cells to RAF inhibitors, we profiled the temporal changes of the phosphoproteome of two colon cancer cell lines (Colo205 and HCT116) that respond differently to vemurafenib. Comprehensive data mining and filtering identified a total of 37,910 phosphorylation sites, 660 of which were dynamically modulated upon treatment with vemurafenib. We established that 83% of these dynamic phosphorylation sites were modulated in accordance with the phospho-ERK profile of the two cell lines. Accordingly, kinase substrate prediction algorithms linked most of these dynamic sites to direct ERK1/2-mediated phosphorylation, supporting a low off-target rate for vemurafenib. Functional classification of target proteins indicated the enrichment of known (nuclear pore, transcription factors, and RAS-RTK signaling) and novel (Rho GTPases signaling and actin cytoskeleton) ERK-controlled functions. Our phosphoproteomic data combined with experimental validation established novel dynamic connections between ERK signaling and the transcriptional regulators TEAD3 (Hippo pathway), MKL1, and MKL2 (Rho serum-response elements pathway). We also confirm that an ERK-docking site found in MKL1 is directly antagonized by overlapping actin binding, defining a novel mechanism of actin-modulated phosphorylation. Altogether, time-resolved phosphoproteomics further documented vemurafenib selectivity and identified novel ERK downstream substrates.
Collapse
Affiliation(s)
- Peter Kubiniok
- From the ‡Institute for Research in Immunology and Cancer and.,Departments of §Chemistry
| | - Hugo Lavoie
- From the ‡Institute for Research in Immunology and Cancer and
| | - Marc Therrien
- From the ‡Institute for Research in Immunology and Cancer and .,‖Pathology and Cell Biology, and
| | - Pierre Thibault
- From the ‡Institute for Research in Immunology and Cancer and .,Departments of §Chemistry.,‡‡Biochemistry, Université de Montréal, C.P. 6128, Succursale Centreville, Montréal, Québec H3C 3J7, Canada
| |
Collapse
|
39
|
Lamoliatte F, McManus FP, Maarifi G, Chelbi-Alix MK, Thibault P. Uncovering the SUMOylation and ubiquitylation crosstalk in human cells using sequential peptide immunopurification. Nat Commun 2017; 8:14109. [PMID: 28098164 PMCID: PMC5253644 DOI: 10.1038/ncomms14109] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 11/30/2016] [Indexed: 12/21/2022] Open
Abstract
Crosstalk between the SUMO and ubiquitin pathways has recently been reported. However, no approach currently exists to determine the interrelationship between these modifications. Here, we report an optimized immunoaffinity method that permits the study of both protein ubiquitylation and SUMOylation from a single sample. This method enables the unprecedented identification of 10,388 SUMO sites in HEK293 cells. The sequential use of SUMO and ubiquitin remnant immunoaffinity purification facilitates the dynamic profiling of SUMOylated and ubiquitylated proteins in HEK293 cells treated with the proteasome inhibitor MG132. Quantitative proteomic analyses reveals crosstalk between substrates that control protein degradation, and highlights co-regulation of SUMOylation and ubiquitylation levels on deubiquitinase enzymes and the SUMOylation of proteasome subunits. The SUMOylation of the proteasome affects its recruitment to promyelocytic leukemia protein (PML) nuclear bodies, and PML lacking the SUMO interacting motif fails to colocalize with SUMOylated proteasome further demonstrating that this motif is required for PML catabolism.
Collapse
Affiliation(s)
- Frédéric Lamoliatte
- Institute for Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Station, Centre-ville, Montréal, Québec, Canada H3C 3J7.,Department of Chemistry, Université de Montréal, P.O. Box 6128, Station, Centre-ville, Montréal, Québec, Canada H3C 3J7
| | - Francis P McManus
- Institute for Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Station, Centre-ville, Montréal, Québec, Canada H3C 3J7
| | - Ghizlane Maarifi
- INSERM UMR-S1124, Université Paris Descartes, 75006 Paris, France
| | | | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Station, Centre-ville, Montréal, Québec, Canada H3C 3J7.,Department of Chemistry, Université de Montréal, P.O. Box 6128, Station, Centre-ville, Montréal, Québec, Canada H3C 3J7.,Department of Biochemistry, Université de Montréal, P.O. Box 6128, Station, Centre-ville, Montréal, Québec, Canada H3C 3J7
| |
Collapse
|
40
|
Tian J, Zhang S, Li H. Changes in intracellular metabolism underlying the adaptation of Saccharomyces cerevisiae strains to ethanol stress. ANN MICROBIOL 2017. [DOI: 10.1007/s13213-016-1251-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
|
41
|
Pfammatter S, Bonneil E, Thibault P. Improvement of Quantitative Measurements in Multiplex Proteomics Using High-Field Asymmetric Waveform Spectrometry. J Proteome Res 2016; 15:4653-4665. [PMID: 27723353 DOI: 10.1021/acs.jproteome.6b00745] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Quantitative proteomics using isobaric reagent tandem mass tags (TMT) or isobaric tags for relative and absolute quantitation (iTRAQ) provides a convenient approach to compare changes in protein abundance across multiple samples. However, the analysis of complex protein digests by isobaric labeling can be undermined by the relative large proportion of co-selected peptide ions that lead to distorted reporter ion ratios and affect the accuracy and precision of quantitative measurements. Here, we investigated the use of high-field asymmetric waveform ion mobility spectrometry (FAIMS) in proteomic experiments to reduce sample complexity and improve protein quantification using TMT isobaric labeling. LC-FAIMS-MS/MS analyses of human and yeast protein digests led to significant reductions in interfering ions, which increased the number of quantifiable peptides by up to 68% while significantly improving the accuracy of abundance measurements compared to that with conventional LC-MS/MS. The improvement in quantitative measurements using FAIMS is further demonstrated for the temporal profiling of protein abundance of HEK293 cells following heat shock treatment.
Collapse
Affiliation(s)
- Sibylle Pfammatter
- Institute for Research in Immunology and Cancer, ‡Department of Chemistry, Université de Montréal , C.P. 6128, Succursale centre-ville, Montréal, Québec H3C 3J7, Canada
| | - Eric Bonneil
- Institute for Research in Immunology and Cancer, ‡Department of Chemistry, Université de Montréal , C.P. 6128, Succursale centre-ville, Montréal, Québec H3C 3J7, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, ‡Department of Chemistry, Université de Montréal , C.P. 6128, Succursale centre-ville, Montréal, Québec H3C 3J7, Canada
| |
Collapse
|
42
|
Lahtvee PJ, Kumar R, Hallström BM, Nielsen J. Adaptation to different types of stress converge on mitochondrial metabolism. Mol Biol Cell 2016; 27:2505-14. [PMID: 27307591 PMCID: PMC4966989 DOI: 10.1091/mbc.e16-03-0187] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/08/2016] [Indexed: 01/12/2023] Open
Abstract
Yeast cell factories encounter physical and chemical stresses when used for industrial production of fuels and chemicals. These stresses reduce productivity and increase bioprocess costs. Understanding the mechanisms of the stress response is essential for improving cellular robustness in platform strains. We investigated the three most commonly encountered industrial stresses for yeast (ethanol, salt, and temperature) to identify the mechanisms of general and stress-specific responses under chemostat conditions in which specific growth rate-dependent changes are eliminated. By applying systems-level analysis, we found that most stress responses converge on mitochondrial processes. Our analysis revealed that stress-specific factors differ between applied stresses; however, they are underpinned by an increased ATP demand. We found that when ATP demand increases to high levels, respiration cannot provide sufficient ATP, leading to onset of respirofermentative metabolism. Although stress-specific factors increase ATP demand for cellular growth under stressful conditions, increased ATP demand for cellular maintenance underpins a general stress response and is responsible for the onset of overflow metabolism.
Collapse
Affiliation(s)
- Petri-Jaan Lahtvee
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Rahul Kumar
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Björn M Hallström
- Science for Life Laboratory, Royal Institute of Technology, 171 21, Stockholm, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 412 96 Gothenburg, Sweden Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
| |
Collapse
|
43
|
Nägele T, Fürtauer L, Nagler M, Weiszmann J, Weckwerth W. A Strategy for Functional Interpretation of Metabolomic Time Series Data in Context of Metabolic Network Information. Front Mol Biosci 2016; 3:6. [PMID: 27014700 PMCID: PMC4779852 DOI: 10.3389/fmolb.2016.00006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/19/2016] [Indexed: 12/01/2022] Open
Abstract
The functional connection of experimental metabolic time series data with biochemical network information is an important, yet complex, issue in systems biology. Frequently, experimental analysis of diurnal, circadian, or developmental dynamics of metabolism results in a comprehensive and multidimensional data matrix comprising information about metabolite concentrations, protein levels, and/or enzyme activities. While, irrespective of the type of organism, the experimental high-throughput analysis of the transcriptome, proteome, and metabolome has become a common part of many systems biological studies, functional data integration in a biochemical and physiological context is still challenging. Here, an approach is presented which addresses the functional connection of experimental time series data with biochemical network information which can be inferred, for example, from a metabolic network reconstruction. Based on a time-continuous and variance-weighted regression analysis of experimental data, metabolic functions, i.e., first-order derivatives of metabolite concentrations, were related to time-dependent changes in other biochemically relevant metabolic functions, i.e., second-order derivatives of metabolite concentrations. This finally revealed time points of perturbed dependencies in metabolic functions indicating a modified biochemical interaction. The approach was validated using previously published experimental data on a diurnal time course of metabolite levels, enzyme activities, and metabolic flux simulations. To support and ease the presented approach of functional time series analysis, a graphical user interface including a test data set and a manual is provided which can be run within the numerical software environment Matlab®.
Collapse
Affiliation(s)
- Thomas Nägele
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria; Vienna Metabolomics Center, University of ViennaVienna, Austria
| | - Lisa Fürtauer
- Department of Ecogenomics and Systems Biology, University of Vienna Vienna, Austria
| | - Matthias Nagler
- Department of Ecogenomics and Systems Biology, University of Vienna Vienna, Austria
| | - Jakob Weiszmann
- Department of Ecogenomics and Systems Biology, University of Vienna Vienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria; Vienna Metabolomics Center, University of ViennaVienna, Austria
| |
Collapse
|
44
|
Munna MS, Humayun S, Noor R. Influence of heat shock and osmotic stresses on the growth and viability of Saccharomyces cerevisiae SUBSC01. BMC Res Notes 2015; 8:369. [PMID: 26298101 PMCID: PMC4546815 DOI: 10.1186/s13104-015-1355-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 08/17/2015] [Indexed: 01/11/2023] Open
Abstract
Background With a preceding scrutiny of bacterial cellular responses against heat shock and oxidative stresses, current research further investigated such impact on yeast cell. Present study attempted to observe the influence of high temperature (44–46 °C) on the growth and budding pattern of Saccharomyces cerevisiae SUBSC01. Effect of elevated sugar concentrations as another stress stimulant was also observed. Cell growth was measured through the estimation of the optical density at 600 nm (OD600) and by the enumeration of colony forming units on the agar plates up to 450 min. Results Subsequent transformation in the yeast morphology and the cellular arrangement were noticed. A delayed and lengthy lag phase was observed when yeast strain was grown at 30, 37, and 40 °C, while at 32.5 °C, optimal growth pattern was noticed. Cells were found to lose culturability completely at 46 °C whereby cells without the cytoplasmic contents were also observed under the light microscope. Thus the critical growth temperature was recorded as 45 °C which was the highest temperature at which S. cerevisiae SUBSC01 could grow. However, a complete growth retardation was observed at 45 °C with the high concentrations of dextrose (0.36 g/l) and sucrose (0.18 g/l). Notably, yeast budding was found at 44 and 45 °C up to 270 min of incubation, which was further noticed to be suppressed at 46 °C. Conclusions Present study revealed that the optimal and the critical growth temperatures of S. cerevisiae SUBSC01 were 32.5 and 45 °C, respectively; and also projected on the inhibitory concentrations of sugars on yeast growth at that temperature.
Collapse
Affiliation(s)
- Md Sakil Munna
- Department of Microbiology, Stamford University Bangladesh, 51 Siddeswari Road, Dhaka, 1217, Bangladesh.
| | - Sanjida Humayun
- Department of Microbiology, Stamford University Bangladesh, 51 Siddeswari Road, Dhaka, 1217, Bangladesh.
| | - Rashed Noor
- Department of Microbiology, Stamford University Bangladesh, 51 Siddeswari Road, Dhaka, 1217, Bangladesh.
| |
Collapse
|
45
|
Kanshin E, Tyers M, Thibault P. Sample Collection Method Bias Effects in Quantitative Phosphoproteomics. J Proteome Res 2015; 14:2998-3004. [PMID: 26040406 DOI: 10.1021/acs.jproteome.5b00404] [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] [Indexed: 11/29/2022]
Abstract
Current advances in selective enrichment, fractionation, and MS detection of phosphorylated peptides allowed identification and quantitation of tens of thousands phosphosites from minute amounts of biological material. One of the major challenges in the field is preserving the in vivo phosphorylation state of the proteins throughout the sample preparation workflow. This is typically achieved by using phosphatase inhibitors and denaturing conditions during cell lysis. Here we determine if the upstream cell collection techniques could introduce changes in protein phosphorylation. To evaluate the effect of sample collection protocols on the global phosphorylation status of the cell, we compared different sample workflows by metabolic labeling and quantitative mass spectrometry on Saccharomyces cerevisiae cell cultures. We identified highly similar phosphopeptides for cells harvested in ice cold isotonic phosphate buffer, cold ethanol, trichloroacetic acid, and liquid nitrogen. However, quantitative analyses revealed that the commonly used phosphate buffer unexpectedly activated signaling events. Such effects may introduce systematic bias in phosphoproteomics measurements and biochemical analysis.
Collapse
Affiliation(s)
- Evgeny Kanshin
- †Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec H3C 3J7, Canada
| | - Michael Tyers
- †Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec H3C 3J7, Canada.,‡Department of Medicine, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec H3C 3J7, Canada
| | - Pierre Thibault
- †Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec H3C 3J7, Canada.,§Department of Chemistry, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec H3C 3J7, Canada
| |
Collapse
|