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Zhang H, Rahman T, Lu S, Adam AP, Wan LQ. Helical vasculogenesis driven by cell chirality. SCIENCE ADVANCES 2024; 10:eadj3582. [PMID: 38381835 PMCID: PMC10881055 DOI: 10.1126/sciadv.adj3582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024]
Abstract
The cellular helical structure is well known for its crucial role in development and disease. Nevertheless, the underlying mechanism governing this phenomenon remains largely unexplored, particularly in recapitulating it in well-controlled engineering systems. Leveraging advanced microfluidics, we present compelling evidence of the spontaneous emergence of helical endothelial tubes exhibiting robust right-handedness governed by inherent cell chirality. To strengthen our findings, we identify a consistent bias toward the same chirality in mouse vascular tissues. Manipulating endothelial cell chirality using small-molecule drugs produces a dose-dependent reversal of the handedness in engineered vessels, accompanied by non-monotonic changes in vascular permeability. Moreover, our three-dimensional cell vertex model provides biomechanical insights into the chiral morphogenesis process, highlighting the role of cellular torque and tissue fluidity in its regulation. Our study unravels an intriguing mechanism underlying vascular chiral morphogenesis, shedding light on the broader implications and distinctive perspectives of tubulogenesis within biological systems.
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Affiliation(s)
- Haokang Zhang
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Tasnif Rahman
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Shuhan Lu
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Alejandro Pablo Adam
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
- Department of Ophthalmology, Albany Medical College, Albany, NY 12208, USA
| | - Leo Q. Wan
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
- Center for Modeling, Simulation and Imaging in Medicine, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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2
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Kotlova ER, Senik SV, Pozhvanov GA, Prokopiev IA, Boldyrev IA, Manzhieva BS, Amigud EY, Puzanskiy RK, Khakulova AA, Serebryakov EB. Uptake and Metabolic Conversion of Exogenous Phosphatidylcholines Depending on Their Acyl Chain Structure in Arabidopsis thaliana. Int J Mol Sci 2023; 25:89. [PMID: 38203257 PMCID: PMC10778594 DOI: 10.3390/ijms25010089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/11/2023] [Accepted: 12/16/2023] [Indexed: 01/12/2024] Open
Abstract
Fungi and plants are not only capable of synthesizing the entire spectrum of lipids de novo but also possess a well-developed system that allows them to assimilate exogenous lipids. However, the role of structure in the ability of lipids to be absorbed and metabolized has not yet been characterized in detail. In the present work, targeted lipidomics of phosphatidylcholines (PCs) and phosphatidylethanolamines (PEs), in parallel with morphological phenotyping, allowed for the identification of differences in the effects of PC molecular species introduced into the growth medium, in particular, typical bacterial saturated (14:0/14:0, 16:0/16:0), monounsaturated (16:0/18:1), and typical for fungi and plants polyunsaturated (16:0/18:2, 18:2/18:2) species, on Arabidopsis thaliana. For comparison, the influence of an artificially synthesized (1,2-di-(3-(3-hexylcyclopentyl)-propanoate)-sn-glycero-3-phosphatidylcholine, which is close in structure to archaeal lipids, was studied. The phenotype deviations stimulated by exogenous lipids included changes in the length and morphology of both the roots and leaves of seedlings. According to lipidomics data, the main trends in response to exogenous lipid exposure were an increase in the proportion of endogenic 18:1/18:1 PC and 18:1_18:2 PC molecular species and a decrease in the relative content of species with C18:3, such as 18:3/18:3 PC and/or 16:0_18:3 PC, 16:1_18:3 PE. The obtained data indicate that exogenous lipid molecules affect plant morphology not only due to their physical properties, which are manifested during incorporation into the membrane, but also due to the participation of exogenous lipid molecules in the metabolism of plant cells. The results obtained open the way to the use of PCs of different structures as cellular regulators.
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Affiliation(s)
- Ekaterina R. Kotlova
- Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint-Petersburg, Russia; (S.V.S.); (G.A.P.); (I.A.P.); (B.S.M.); (E.Y.A.); (R.K.P.)
| | - Svetlana V. Senik
- Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint-Petersburg, Russia; (S.V.S.); (G.A.P.); (I.A.P.); (B.S.M.); (E.Y.A.); (R.K.P.)
| | - Gregory A. Pozhvanov
- Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint-Petersburg, Russia; (S.V.S.); (G.A.P.); (I.A.P.); (B.S.M.); (E.Y.A.); (R.K.P.)
- Department of Botany and Ecology, Faculty of Biology, Herzen State Pedagogical University, 191186 Saint-Petersburg, Russia
| | - Ilya A. Prokopiev
- Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint-Petersburg, Russia; (S.V.S.); (G.A.P.); (I.A.P.); (B.S.M.); (E.Y.A.); (R.K.P.)
| | - Ivan A. Boldyrev
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Bairta S. Manzhieva
- Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint-Petersburg, Russia; (S.V.S.); (G.A.P.); (I.A.P.); (B.S.M.); (E.Y.A.); (R.K.P.)
| | - Ekaterina Ya. Amigud
- Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint-Petersburg, Russia; (S.V.S.); (G.A.P.); (I.A.P.); (B.S.M.); (E.Y.A.); (R.K.P.)
- Department of Botany and Ecology, Faculty of Biology, Herzen State Pedagogical University, 191186 Saint-Petersburg, Russia
| | - Roman K. Puzanskiy
- Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint-Petersburg, Russia; (S.V.S.); (G.A.P.); (I.A.P.); (B.S.M.); (E.Y.A.); (R.K.P.)
| | - Anna A. Khakulova
- Chemical Analysis and Materials Research Core Facility Center, Reseach Park, Saint-Petersburg State University, 199034 Saint-Petersburg, Russia; (A.A.K.); (E.B.S.)
| | - Evgeny B. Serebryakov
- Chemical Analysis and Materials Research Core Facility Center, Reseach Park, Saint-Petersburg State University, 199034 Saint-Petersburg, Russia; (A.A.K.); (E.B.S.)
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3
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Gershfeld NL, Nossal R. Critical point for membrane bilayer formation. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184116. [PMID: 36640998 PMCID: PMC10318949 DOI: 10.1016/j.bbamem.2022.184116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 12/16/2022] [Accepted: 12/22/2022] [Indexed: 01/13/2023]
Abstract
Unilamellar liposomes often are employed in investigations of lipid-protein interactions and the delivery of drugs in therapies for disease. Also, related lipid-containing nanoparticles have been developed as elements of a new class of mRNA vaccines. We show that only unilamellar films form in equilibrium lipid dispersions, at temperature values {T*} that depend on the identities of the lipids (e.g., T* ≈ 29 °C for DMPC). Thermodynamic analysis confirms that films at air-water surfaces can be used to monitor the properties of the lipid vesicles that form in the dispersion. When T > T*, critical exponents describing film properties as T approaches T* are μ ≈ 1.4 and ν ≈ 0.7, which are close to values for the interfacial tension and the correlation length of density fluctuations at fluid interfaces. These results, and observations that within the bilayer the lateral diffusion of fluorescent lipid probes demonstrates increases at T*, suggest that unilamellar vesicles at T* are a transition state between two different multilamellar structures. We generalize the thermodynamic arguments to explain the linkage between lipid structures in the surface and bulk dispersion within more complex samples, showing that dispersions containing total lipid extracts of cell membranes have properties similar to those in dispersions containing single lipids. Information from various independent studies indicates that T* noted for bilayer membranes of a population of cells is identical to the temperature at which the growth or gestation of the cells occurs in vivo. Examples include whole-cell lipid extracts obtained from bacteria, and poikilothermic and homeothermic animals.
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Affiliation(s)
- Norman L Gershfeld
- Section on Molecular Transport, Eunice Kennedy Shriver Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, United States of America
| | - Ralph Nossal
- Section on Integrative Biophysics, Eunice Kennedy Shriver Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, United States of America; Institute for Soft Matter Synthesis and Metrology, Department of Physics, Georgetown University, Washington, DC 20057, United States of America.
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4
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Jiménez-Gutiérrez E, Fernández-Acero T, Alonso-Rodríguez E, Molina M, Martín H. Neomycin Interferes with Phosphatidylinositol-4,5-Bisphosphate at the Yeast Plasma Membrane and Activates the Cell Wall Integrity Pathway. Int J Mol Sci 2022; 23:ijms231911034. [PMID: 36232332 PMCID: PMC9569482 DOI: 10.3390/ijms231911034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/20/2022] Open
Abstract
The cell wall integrity pathway (CWI) is a MAPK-mediated signaling route essential for yeast cell response to cell wall damage, regulating distinct aspects of fungal physiology. We have recently proven that the incorporation of a genetic circuit that operates as a signal amplifier into this pathway allows for the identification of novel elements involved in CWI signaling. Here, we show that the strong growth inhibition triggered by pathway hyperactivation in cells carrying the “Integrity Pathway Activation Circuit” (IPAC) also allows the easy identification of new stimuli. By using the IPAC, we have found various chemical agents that activate the CWI pathway, including the aminoglycoside neomycin. Cells lacking key components of this pathway are sensitive to this antibiotic, due to the disruption of signaling upon neomycin stimulation. Neomycin reduces both phosphatidylinositol-4,5-bisphosphate (PIP2) availability at the plasma membrane and myriocin-induced TORC2-dependent Ypk1 phosphorylation, suggesting a strong interference with plasma membrane homeostasis, specifically with PIP2. The neomycin-induced transcriptional profile involves not only genes related to stress and cell wall biogenesis, but also to amino acid metabolism, reflecting the action of this antibiotic on the yeast ribosome.
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Affiliation(s)
| | | | | | - María Molina
- Correspondence: (M.M.); (H.M.); Tel.: +34-91-394-1888 (M.M. & H.M.)
| | - Humberto Martín
- Correspondence: (M.M.); (H.M.); Tel.: +34-91-394-1888 (M.M. & H.M.)
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5
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Wong CW, Han HW, Hsu SH. Changes of cell membrane fluidity for mesenchymal stem cell spheroids on biomaterial surfaces. World J Stem Cells 2022; 14:616-632. [PMID: 36157913 PMCID: PMC9453270 DOI: 10.4252/wjsc.v14.i8.616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 05/02/2022] [Accepted: 07/11/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The therapeutic potential of mesenchymal stem cells (MSCs) in the form of three-dimensional spheroids has been extensively demonstrated. The underlying mechanisms for the altered cellular behavior of spheroids have also been investigated. Cell membrane fluidity is a critically important physical property for the regulation of cell behavior, but it has not been studied for the spheroid-forming cells to date.
AIM To explore the association between cell membrane fluidity and the morphological changes of MSC spheroids on the surface of biomaterials to elucidate the role of membrane fluidity during the spheroid-forming process of MSCs.
METHODS We generated three-dimensional (3D) MSC spheroids on the surface of various culture substrates including chitosan (CS), CS-hyaluronan (CS-HA), and polyvinyl alcohol (PVA) substrates. The cell membrane fluidity and cell morphological change were examined by a time-lapse recording system as well as a high-resolution 3D cellular image explorer. MSCs and normal/cancer cells were pre-stained with fluorescent dyes and co-cultured on the biomaterials to investigate the exchange of cell membrane during the formation of heterogeneous cellular spheroids.
RESULTS We discovered that vesicle-like bubbles randomly appeared on the outer layer of MSC spheroids cultured on different biomaterial surfaces. The average diameter of the vesicle-like bubbles of MSC spheroids on CS-HA at 37 °C was approximately 10 μm, smaller than that on PVA substrates (approximately 27 μm). Based on time-lapse images, these unique bubbles originated from the dynamic movement of the cell membrane during spheroid formation, which indicated an increment of membrane fluidity for MSCs cultured on these substrates. Moreover, the membrane interaction in two different types of cells with similar membrane fluidity may further induce a higher level of membrane translocation during the formation of heterogeneous spheroids.
CONCLUSION Changes in cell membrane fluidity may be a novel path to elucidate the complicated physiological alterations in 3D spheroid-forming cells.
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Affiliation(s)
- Chui-Wei Wong
- National Taiwan University, Institute of Polymer Science and Engineering, Taipei 10617, Taiwan
| | - Hao-Wei Han
- National Taiwan University, Institute of Polymer Science and Engineering, Taipei 10617, Taiwan
| | - Shan-hui Hsu
- National Taiwan University, Institute of Polymer Science and Engineering, Taipei 10617, Taiwan
- National Health Research Institutes, Institute of Cellular and System Medicine, Miaoli 350, Taiwan
- National Taiwan University, Research and Development Center for Medical Devices, Taipei 10617, Taiwan
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6
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Liu C, Shi K, Lyu K, Liu D, Wang X. The toxicity of neodymium and genome-scale genetic screen of neodymium-sensitive gene deletion mutations in the yeast Saccharomyces cerevisiae. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:41439-41454. [PMID: 35088271 DOI: 10.1007/s11356-021-18100-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
The wide usage of neodymium (Nd) in industry, agriculture, and medicine has made it become an emerging pollutant in the environment. Increasing Nd pollution has potential hazards to plants, animals, and microorganisms. Thus, it is necessary to study the toxicity of Nd and the mechanism of Nd transportation and detoxification in microorganisms. Through genome-scale screening, we identified 70 yeast monogene deletion mutations sensitive to Nd ions. These genes are mainly involved in metabolism, transcription, protein synthesis, cell cycle, DNA processing, protein folding, modification, and cell transport processes. Furthermore, the regulatory networks of Nd toxicity were identified by using the protein interaction group analysis. These networks are associated with various signal pathways, including calcium ion transport, phosphate pathways, vesicular transport, and cell autophagy. In addition, the content of Nd ions in yeast was detected by an inductively coupled plasma mass spectrometry, and most of these Nd-sensitive mutants showed an increased intracellular Nd content. In all, our results provide the basis for understanding the molecular mechanisms of detoxifying Nd ions in yeast cells, which will be useful for future studies on Nd-related issues in the environment, agriculture, and human health.
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Affiliation(s)
- Chengkun Liu
- School of Life Sciences, Shandong University of Technology, Zibo, 255049, Shandong, China
| | - Kailun Shi
- School of Life Sciences, Shandong University of Technology, Zibo, 255049, Shandong, China
| | - Keliang Lyu
- School of Life Sciences, Shandong University of Technology, Zibo, 255049, Shandong, China
| | - Dongwu Liu
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255049, China
| | - Xue Wang
- School of Life Sciences, Shandong University of Technology, Zibo, 255049, Shandong, China
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7
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Yeast cells actively tune their membranes to phase separate at temperatures that scale with growth temperatures. Proc Natl Acad Sci U S A 2022; 119:2116007119. [PMID: 35046036 PMCID: PMC8795566 DOI: 10.1073/pnas.2116007119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2021] [Indexed: 02/06/2023] Open
Abstract
Phase separation in membranes creates domains enriched in specific components. To date, the best example of micrometer-scale phase separation in the membrane of an unperturbed, living cell occurs in a yeast (Saccharomyces cerevisiae) organelle called the vacuole. Recent studies indicate that the phases are functionally important, enabling yeast survival during periods of stress. We discovered that yeast regulate this phase transition; the temperature at which membrane components mix into a single phase is ∼15 °C above the growth temperature. To maintain this offset, yeast may tune the level of ergosterol (a molecule that is structurally similar to cholesterol) in their membranes. Surprisingly, depleting sterols in vacuole membranes causes them to phase separate, in contrast to previous assumptions. Membranes of vacuoles, the lysosomal organelles of Saccharomyces cerevisiae (budding yeast), undergo extraordinary changes during the cell’s normal growth cycle. The cycle begins with a stage of rapid cell growth. Then, as glucose becomes scarce, growth slows, and vacuole membranes phase separate into micrometer-scale domains of two liquid phases. Recent studies suggest that these domains promote yeast survival by organizing membrane proteins that play key roles in a central signaling pathway conserved among eukaryotes (TORC1). An outstanding question in the field has been whether cells regulate phase transitions in response to new physical conditions and how this occurs. Here, we measure transition temperatures and find that after an increase of roughly 15 °C, vacuole membranes appear uniform, independent of growth temperature. Moreover, populations of cells grown at a single temperature regulate this transition to occur over a surprisingly narrow temperature range. Remarkably, the transition temperature scales linearly with the growth temperature, demonstrating that the cells physiologically adapt to maintain proximity to the transition. Next, we ask how yeast adjust their membranes to achieve phase separation. We isolate vacuoles from yeast during the rapid stage of growth, when their membranes do not natively exhibit domains. Ergosterol is the major sterol in yeast. We find that domains appear when ergosterol is depleted, contradicting the prevalent assumption that increases in sterol concentration generally cause membrane phase separation in vivo, but in agreement with previous studies using artificial and cell-derived membranes.
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Using stable isotope tracers to monitor membrane dynamics in C. elegans. Chem Phys Lipids 2020; 233:104990. [PMID: 33058817 DOI: 10.1016/j.chemphyslip.2020.104990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 10/06/2020] [Accepted: 10/06/2020] [Indexed: 12/29/2022]
Abstract
Membranes within an animal are composed of phospholipids, cholesterol, and proteins that together form a dynamic barrier. The types of lipids that are found within a membrane bilayer impact its biophysical properties including its fluidity, permeability, and susceptibility to damage. While membrane composition is very stable in healthy adults, aberrant membrane structure is seen in a wide and varied array of diseases as well as during natural aging. Despite the wide-reaching impacts of membrane composition, there is relatively little known about how membrane landscape is established and maintained over time. In vivo biochemical modeling of membrane lipids is needed to understand how these molecules interact in their natural configurations. Here, we have described analytical methods that increase the capacity to map the dynamics of individual membrane phospholipids using different types of mass spectrometry. Specifically, we describe novel stable isotope (13C and 15N) strategies to quantify the turnover of dozens of fatty acid tails and intact phospholipids simultaneously.
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Moniliophthora perniciosa development: key genes involved in stress-mediated cell wall organization and autophagy. Int J Biol Macromol 2020; 154:1022-1035. [PMID: 32194118 DOI: 10.1016/j.ijbiomac.2020.03.125] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 02/29/2020] [Accepted: 03/13/2020] [Indexed: 12/11/2022]
Abstract
Moniliophthora perniciosa is a basidiomycete responsible for the witches' broom disease in cacao (Theobroma cacao L.). Chitin synthase (CHS), chitinase (CHIT) and autophagy (ATG) genes have been associated to stress response preceding the formation of basidiocarp. An analysis of literature mining, interactomics and gene expression was developed to identify the main proteins related to development, cell wall organization and autophagy in M. perniciosa. TORC2 complex elements were identified and were involved in the response to the nutrient starvation during the fungus development stages preceding the basidiocarp formation. This complex interacted with target proteins related to cell wall synthesis and to polarization and cell division (FKS1, CHS, CDC42, ROM2). Autolysis and autophagy processes were associated to CHIT2, ATG8 and to the TORC1 complex (TOR1 and KOG1), which is central in the upstream signalization of the stress response due to nutrient starvation and growth regulation. Other important elements that participate to steps preceding basidiocarp formation were also identified (KOG1, SSZ1, GDI1, FKS1, CCD10, CKS1, CDC42, RHO1, AVO1, BAG7). Similar gene expression patterns during fungus reproductive structure formation and when treated by rapamycin (a nutritional related-autophagy stress agent) were observed: cell division related-genes were repressed while those related to autolysis/autophagy were overexpressed.
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Prieto JA, Estruch F, Córcoles-Sáez I, Del Poeta M, Rieger R, Stenzel I, Randez-Gil F. Pho85 and PI(4,5)P 2 regulate different lipid metabolic pathways in response to cold. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1865:158557. [PMID: 31678512 PMCID: PMC7254492 DOI: 10.1016/j.bbalip.2019.158557] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/25/2019] [Accepted: 10/26/2019] [Indexed: 12/11/2022]
Abstract
Lipid homeostasis allows cells to adjust membrane biophysical properties in response to changes in environmental conditions. In the yeast Saccharomyces cerevisiae, a downward shift in temperature from an optimal reduces membrane fluidity, which triggers a lipid remodeling of the plasma membrane. How changes in membrane fluidity are perceived, and how the abundance and composition of different lipid classes is properly balanced, remain largely unknown. Here, we show that the levels of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2], the most abundant plasma membrane phosphoinositide, drop rapidly in response to a downward shift in temperature. This change triggers a signaling cascade transmitted to cytosolic diphosphoinositol phosphate derivatives, among them 5-PP-IP4 and 1-IP7, that exert regulatory functions on genes involved in the inositol and phospholipids (PLs) metabolism, and inhibit the activity of the protein kinase Pho85. Consistent with this, cold exposure triggers a specific program of neutral lipids and PLs changes. Furthermore, we identified Pho85 as playing a key role in controlling the synthesis of long-chain bases (LCBs) via the Ypk1-Orm2 regulatory circuit. We conclude that Pho85 orchestrates a coordinated response of lipid metabolic pathways that ensure yeast thermal adaptation.
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Affiliation(s)
- Jose A Prieto
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino, 7, 46980 Paterna, Valencia, Spain
| | - Francisco Estruch
- Departament of Biochemistry and Molecular Biology, Universitat de València, Dr. Moliner 50, Burjassot 46100, Spain
| | - Isaac Córcoles-Sáez
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino, 7, 46980 Paterna, Valencia, Spain
| | - Maurizio Del Poeta
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, United States of America; Veterans Administration Medical Center, Northport, NY, United States of America
| | - Robert Rieger
- Proteomics Center, Stony Brook University, Stony Brook, NY, United States of America
| | - Irene Stenzel
- Department of Cellular Biochemistry, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Francisca Randez-Gil
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino, 7, 46980 Paterna, Valencia, Spain.
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11
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Fanning S, Haque A, Imberdis T, Baru V, Barrasa MI, Nuber S, Termine D, Ramalingam N, Ho GPH, Noble T, Sandoe J, Lou Y, Landgraf D, Freyzon Y, Newby G, Soldner F, Terry-Kantor E, Kim TE, Hofbauer HF, Becuwe M, Jaenisch R, Pincus D, Clish CB, Walther TC, Farese RV, Srinivasan S, Welte MA, Kohlwein SD, Dettmer U, Lindquist S, Selkoe D. Lipidomic Analysis of α-Synuclein Neurotoxicity Identifies Stearoyl CoA Desaturase as a Target for Parkinson Treatment. Mol Cell 2019; 73:1001-1014.e8. [PMID: 30527540 PMCID: PMC6408259 DOI: 10.1016/j.molcel.2018.11.028] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 09/05/2018] [Accepted: 11/19/2018] [Indexed: 01/08/2023]
Abstract
In Parkinson's disease (PD), α-synuclein (αS) pathologically impacts the brain, a highly lipid-rich organ. We investigated how alterations in αS or lipid/fatty acid homeostasis affect each other. Lipidomic profiling of human αS-expressing yeast revealed increases in oleic acid (OA, 18:1), diglycerides, and triglycerides. These findings were recapitulated in rodent and human neuronal models of αS dyshomeostasis (overexpression; patient-derived triplication or E46K mutation; E46K mice). Preventing lipid droplet formation or augmenting OA increased αS yeast toxicity; suppressing the OA-generating enzyme stearoyl-CoA-desaturase (SCD) was protective. Genetic or pharmacological SCD inhibition ameliorated toxicity in αS-overexpressing rat neurons. In a C. elegans model, SCD knockout prevented αS-induced dopaminergic degeneration. Conversely, we observed detrimental effects of OA on αS homeostasis: in human neural cells, excess OA caused αS inclusion formation, which was reversed by SCD inhibition. Thus, monounsaturated fatty acid metabolism is pivotal for αS-induced neurotoxicity, and inhibiting SCD represents a novel PD therapeutic approach.
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Affiliation(s)
- Saranna Fanning
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Aftabul Haque
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Thibaut Imberdis
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Valeriya Baru
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Silke Nuber
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Termine
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Nagendran Ramalingam
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Gary P H Ho
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Tallie Noble
- Mira Costa College, 1 Barnard Drive, Oceanside, CA 92056, USA
| | - Jackson Sandoe
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Yali Lou
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Dirk Landgraf
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Yelena Freyzon
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Gregory Newby
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Frank Soldner
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Elizabeth Terry-Kantor
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Tae-Eun Kim
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Harald F Hofbauer
- Institute of Molecular Biosciences, BioTechMed-Graz, University of Graz, 8010 Graz, Austria
| | - Michel Becuwe
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - David Pincus
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tobias C Walther
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; HHMI, Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA
| | - Robert V Farese
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Supriya Srinivasan
- Department of Chemical Physiology and The Dorris Neuroscience Center, 1 Barnard Drive, Oceanside, CA 92056, USA; The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Michael A Welte
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Sepp D Kohlwein
- Institute of Molecular Biosciences, BioTechMed-Graz, University of Graz, 8010 Graz, Austria
| | - Ulf Dettmer
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA; HHMI, Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Dennis Selkoe
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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12
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Hokken MWJ, Zoll J, Coolen JPM, Zwaan BJ, Verweij PE, Melchers WJG. Phenotypic plasticity and the evolution of azole resistance in Aspergillus fumigatus; an expression profile of clinical isolates upon exposure to itraconazole. BMC Genomics 2019; 20:28. [PMID: 30626317 PMCID: PMC6327609 DOI: 10.1186/s12864-018-5255-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/15/2018] [Indexed: 01/26/2023] Open
Abstract
Background The prevalence of azole resistance in clinical and environmental Aspergillus fumigatus isolates is rising over the past decades, but the molecular basis of the development of antifungal drug resistance is not well understood. This study focuses on the role of phenotypic plasticity in the evolution of azole resistance in A. fumigatus. When A. fumigatus is challenged with a new stressful environment, phenotypic plasticity may allow A. fumigatus to adjust their physiology to still enable growth and reproduction, therefore allowing the establishment of genetic adaptations through natural selection on the available variation in the mutational and recombinational gene pool. To investigate these short-term physiological adaptations, we conducted time series transcriptome analyses on three clinical A. fumigatus isolates, during incubation with itraconazole. Results After analysis of expression patterns, we identified 3955, 3430, 1207, and 1101 differentially expressed genes (DEGs), after 30, 60, 120 and 240 min of incubation with itraconazole, respectively. We explored the general functions in these gene groups and we identified 186 genes that were differentially expressed during the whole time series. Additionally, we investigated expression patterns of potential novel drug-efflux transporters, genes involved in ergosterol and phospholipid biosynthesis, and the known MAPK proteins of A. fumigatus. Conclusions Our data suggests that A. fumigatus adjusts its transcriptome quickly within 60 min of exposure to itraconazole. Further investigation of these short-term adaptive phenotypic plasticity mechanisms might enable us to understand how the direct response of A. fumigatus to itraconazole promotes survival of the fungus in the patient, before any “hard-wired” genetic mutations arise. Electronic supplementary material The online version of this article (10.1186/s12864-018-5255-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Margriet W J Hokken
- Department of Medical Microbiology, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525GA, Nijmegen, the Netherlands. .,Center of Expertise in Mycology Radboudumc/CWZ, Weg door Jonkerbos 100, 6532 SZ, Nijmegen, the Netherlands.
| | - Jan Zoll
- Department of Medical Microbiology, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525GA, Nijmegen, the Netherlands.,Center of Expertise in Mycology Radboudumc/CWZ, Weg door Jonkerbos 100, 6532 SZ, Nijmegen, the Netherlands
| | - Jordy P M Coolen
- Department of Medical Microbiology, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525GA, Nijmegen, the Netherlands.,Center of Expertise in Mycology Radboudumc/CWZ, Weg door Jonkerbos 100, 6532 SZ, Nijmegen, the Netherlands
| | - Bas J Zwaan
- Department of Plant Sciences, Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Paul E Verweij
- Department of Medical Microbiology, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525GA, Nijmegen, the Netherlands.,Center of Expertise in Mycology Radboudumc/CWZ, Weg door Jonkerbos 100, 6532 SZ, Nijmegen, the Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525GA, Nijmegen, the Netherlands.,Center of Expertise in Mycology Radboudumc/CWZ, Weg door Jonkerbos 100, 6532 SZ, Nijmegen, the Netherlands
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13
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Abstract
Ceramides, important players in signal transduction, interact with multiple cellular pathways, including p53 pathways. However, the relationship between ceramide and p53 is very complex, and mechanisms underlying their coregulation are diverse and not fully characterized. The role of p53, an important cellular regulator and a transcription factor, is linked to its tumor suppressor function. Ceramides are involved in the regulation of fundamental processes in cancer cells including cell death, proliferation, autophagy, and drug resistance. This regulation, however, can be pro-death or pro-survival depending on cancer type, the balance between ceramide species, the rate of their synthesis and utilization, and the availability of a specific array of downstream targets. This chapter highlights the central role of ceramide in sphingolipid metabolism, its role in cancer, specific effectors in ceramide pathways controlled by p53, and coregulation of ceramide and p53 signaling. We discuss the recent studies, which underscore the function of p53 in the regulation of ceramide pathways and the reciprocal regulation of p53 by ceramide. This complex relationship is based on several molecular mechanisms including the p53-dependent transcriptional regulation of enzymes in sphingolipid pathways, the activation of mutant p53 through ceramide-mediated alternative splicing, as well as modulation of the p53 function through direct and indirect effects on p53 coregulators and downstream targets. Further insight into the connections between ceramide and p53 will allow simultaneous targeting of the two pathways with a potential to yield more efficient anticancer therapeutics.
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Affiliation(s)
- Kristen A Jeffries
- Nutrition Research Institute, UNC Chapel Hill, Kannapolis, NC, United States
| | - Natalia I Krupenko
- Nutrition Research Institute, UNC Chapel Hill, Kannapolis, NC, United States; Department of Nutrition, UNC Chapel Hill, Chapel Hill, NC, United States
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14
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Xiao W, Duan X, Lin Y, Cao Q, Li S, Guo Y, Gan Y, Qi X, Zhou Y, Guo L, Qin P, Wang Q, Shui W. Distinct Proteome Remodeling of Industrial Saccharomyces cerevisiae in Response to Prolonged Thermal Stress or Transient Heat Shock. J Proteome Res 2018; 17:1812-1825. [PMID: 29611422 DOI: 10.1021/acs.jproteome.7b00842] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To gain a deep understanding of yeast-cell response to heat stress, multiple laboratory strains have been intensively studied via genome-wide expression analysis for the mechanistic dissection of classical heat-shock response (HSR). However, robust industrial strains of Saccharomyces cerevisiae have hardly been explored in global analysis for elucidation of the mechanism of thermotolerant response (TR) during fermentation. Herein, we employed data-independent acquisition and sequential window acquisition of all theoretical mass spectra based proteomic workflows to characterize proteome remodeling of an industrial strain, ScY01, responding to prolonged thermal stress or transient heat shock. By comparing the proteomic signatures of ScY01 in TR versus HSR as well as the HSR of the industrial strain versus a laboratory strain, our study revealed disparate response mechanisms of ScY01 during thermotolerant growth or under heat shock. In addition, through proteomics data-mining for decoding transcription factor interaction networks followed by validation experiments, we uncovered the functions of two novel transcription factors, Mig1 and Srb2, in enhancing the thermotolerance of the industrial strain. This study has demonstrated that accurate and high-throughput quantitative proteomics not only provides new insights into the molecular basis for complex microbial phenotypes but also pinpoints upstream regulators that can be targeted for improving the desired traits of industrial microorganisms.
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Affiliation(s)
- Weidi Xiao
- College of Life Sciences , Nankai University , Tianjin 300071 , China
| | - Xiaoxiao Duan
- College of Life Sciences , Nankai University , Tianjin 300071 , China.,Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , Tianjin 300308 , China
| | - Yuping Lin
- Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , Tianjin 300308 , China
| | - Qichen Cao
- Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , Tianjin 300308 , China
| | | | - Yufeng Guo
- Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , Tianjin 300308 , China
| | - Yuman Gan
- Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , Tianjin 300308 , China
| | - Xianni Qi
- Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , Tianjin 300308 , China
| | - Yue Zhou
- Demo Laboratory of Thermofisher Scientific China , Shanghai 200120 , China
| | - Lihai Guo
- AB SCIEX , No. 1 Building, No. 24 Yard, Jiuxianqiao Mid Road , Chaoyang District, Beijing 100015 , China
| | - Peibin Qin
- AB SCIEX , No. 1 Building, No. 24 Yard, Jiuxianqiao Mid Road , Chaoyang District, Beijing 100015 , China
| | - Qinhong Wang
- Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , Tianjin 300308 , China
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15
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Navarro-Tapia E, Querol A, Pérez-Torrado R. Membrane fluidification by ethanol stress activates unfolded protein response in yeasts. Microb Biotechnol 2018; 11:465-475. [PMID: 29469174 PMCID: PMC5902320 DOI: 10.1111/1751-7915.13032] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 09/05/2017] [Accepted: 11/05/2017] [Indexed: 11/28/2022] Open
Abstract
The toxic effect of ethanol is one of the most important handicaps for many biotechnological applications of yeasts, such as bioethanol production. Elucidation of ethanol stress response will help to improve yeast performance in biotechnological processes. In the yeast Saccharomyces cerevisiae, ethanol stress has been recently described as an activator of the unfolded protein response (UPR), a conserved intracellular signalling pathway that regulates the transcription of ER homoeostasis‐related genes. However, the signal and activation mechanism has not yet been unravelled. Here, we studied UPR's activation after ethanol stress and observed the upregulation of the key target genes, like INO1, involved in lipid metabolism. We found that inositol content influenced UPR activation after ethanol stress and we observed significant changes in lipid composition, which correlate with a major membrane fluidity alteration by this amphipathic molecule. Then, we explored the hypothesis that membrane fluidity changes cause UPR activation upon ethanol stress by studying UPR response against fluidification or rigidification agents and by studying a mutant, erg2, with altered membrane fluidity. The results suggest that the membrane fluidification effects of ethanol and other agents are the signal for UPR activation, a mechanism that has been proposed in higher eukaryotes.
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Affiliation(s)
- Elisabet Navarro-Tapia
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, E-46980, Paterna, Valencia, Spain
| | - Amparo Querol
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, E-46980, Paterna, Valencia, Spain
| | - Roberto Pérez-Torrado
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, E-46980, Paterna, Valencia, Spain
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16
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Hallmarks of Reversible Separation of Living, Unperturbed Cell Membranes into Two Liquid Phases. Biophys J 2018; 113:2425-2432. [PMID: 29211996 DOI: 10.1016/j.bpj.2017.09.029] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/15/2017] [Accepted: 09/22/2017] [Indexed: 01/04/2023] Open
Abstract
Controversy has long surrounded the question of whether spontaneous lateral demixing of membranes into coexisting liquid phases can organize proteins and lipids on micron scales within unperturbed, living cells. A clear answer hinges on observation of hallmarks of a reversible phase transition. Here, by directly imaging micron-scale membrane domains of yeast vacuoles both in vivo and cell free, we demonstrate that the domains arise through a phase separation mechanism. The domains are large, have smooth boundaries, and can merge quickly, consistent with fluid phases. Moreover, the domains disappear above a distinct miscibility transition temperature (Tmix) and reappear below Tmix, over multiple heating and cooling cycles. Hence, large-scale membrane organization in living cells under physiologically relevant conditions can be controlled by tuning a single thermodynamic parameter.
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17
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Heinisch JJ, Rodicio R. Protein kinase C in fungi—more than just cell wall integrity. FEMS Microbiol Rev 2017; 42:4562651. [DOI: 10.1093/femsre/fux051] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/19/2017] [Indexed: 11/13/2022] Open
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18
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Dymond MK. Mammalian phospholipid homeostasis: evidence that membrane curvature elastic stress drives homeoviscous adaptation in vivo. J R Soc Interface 2017; 13:rsif.2016.0228. [PMID: 27534697 DOI: 10.1098/rsif.2016.0228] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/25/2016] [Indexed: 12/23/2022] Open
Abstract
Several theories of phospholipid homeostasis have postulated that cells regulate the molecular composition of their bilayer membranes, such that a common biophysical membrane parameter is under homeostatic control. Two commonly cited theories are the intrinsic curvature hypothesis, which states that cells control membrane curvature elastic stress, and the theory of homeoviscous adaptation, which postulates cells control acyl chain packing order (membrane order). In this paper, we present evidence from data-driven modelling studies that these two theories correlate in vivo. We estimate the curvature elastic stress of mammalian cells to be 4-7 × 10(-12) N, a value high enough to suggest that in mammalian cells the preservation of membrane order arises through a mechanism where membrane curvature elastic stress is controlled. These results emerge from analysing the molecular contribution of individual phospholipids to both membrane order and curvature elastic stress in nearly 500 cellular compositionally diverse lipidomes. Our model suggests that the de novo synthesis of lipids is the dominant mechanism by which cells control curvature elastic stress and hence membrane order in vivo These results also suggest that cells can increase membrane curvature elastic stress disproportionately to membrane order by incorporating polyunsaturated fatty acids into lipids.
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Affiliation(s)
- Marcus K Dymond
- Division of Chemistry, School of Pharmacy and Biological Sciences, University of Brighton, Brighton BN2 4GL, UK
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19
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Nasution O, Lee YM, Kim E, Lee Y, Kim W, Choi W. Overexpression ofOLE1enhances stress tolerance and constitutively activates the MAPK HOG pathway inSaccharomyces cerevisiae. Biotechnol Bioeng 2016; 114:620-631. [DOI: 10.1002/bit.26093] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 07/26/2016] [Accepted: 08/28/2016] [Indexed: 01/10/2023]
Affiliation(s)
- Olviyani Nasution
- Interdisciplinary Program of EcoCreative; The Graduate School; Ewha Womans University; Seoul 03766 Korea
| | - Young Mi Lee
- Department of Pharmacology; School of Medicine; Ajou University; Suwon Korea
| | - Eunjung Kim
- Department of Pharmacology; School of Medicine; Ajou University; Suwon Korea
| | - Yeji Lee
- Department of Life Sciences; College of Natural Sciences, Ewha Womans University; Seoul Korea
| | - Wankee Kim
- Department of Pharmacology; School of Medicine; Ajou University; Suwon Korea
| | - Wonja Choi
- Interdisciplinary Program of EcoCreative; The Graduate School; Ewha Womans University; Seoul 03766 Korea
- Department of Life Sciences; College of Natural Sciences, Ewha Womans University; Seoul Korea
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20
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Multiple crosstalk between TOR and the cell integrity MAPK signaling pathway in fission yeast. Sci Rep 2016; 6:37515. [PMID: 27876895 PMCID: PMC5120329 DOI: 10.1038/srep37515] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/28/2016] [Indexed: 02/07/2023] Open
Abstract
In eukaryotic cells, the highly conserved Target of Rapamycin (TOR) and the Mitogen Activated Protein Kinase (MAPK) signaling pathways elicit adaptive responses to extra- and intracellular conditions by regulating essential cellular functions. However, the nature of the functional relationships between both pathways is not fully understood. In the fission yeast Schizosaccharomyces pombe the cell integrity MAPK pathway (CIP) regulates morphogenesis, cell wall structure and ionic homeostasis. We show that the Rab GTPase Ryh1, a TORC2 complex activator, cross-activates the CIP and its core member, the MAPK Pmk1, by two distinct mechanisms. The first one involves TORC2 and its downstream effector, Akt ortholog Gad8, which together with TORC1 target Psk1 increase protein levels of the PKC ortholog Pck2 during cell wall stress or glucose starvation. Also, Ryh1 activates Pmk1 in a TORC2-independent fashion by prompting plasma membrane trafficking and stabilization of upstream activators of the MAPK cascade, including PDK ortholog Ksg1 or Rho1 GEF Rgf1. Besides, stress-activated Pmk1 cross-inhibits Ryh1 signaling by decreasing the GTPase activation cycle, and this ensures cell growth during alterations in phosphoinositide metabolism. Our results reveal a highly intricate cross-regulatory relationship between both pathways that warrants adequate cell adaptation and survival in response to environmental changes.
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21
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Lucas C, Ferreira C, Cazzanelli G, Franco-Duarte R, Tulha J, Roelink H, Conway SJ. Yeast Gup1(2) Proteins Are Homologues of the Hedgehog Morphogens Acyltransferases HHAT(L): Facts and Implications. J Dev Biol 2016; 4:E33. [PMID: 29615596 PMCID: PMC5831804 DOI: 10.3390/jdb4040033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/25/2016] [Accepted: 10/27/2016] [Indexed: 12/16/2022] Open
Abstract
In multiple tissues, the Hedgehog secreted morphogen activates in the receiving cells a pathway involved in cell fate, proliferation and differentiation in the receiving cells. This pathway is particularly important during embryogenesis. The protein HHAT (Hedgehog O-acyltransferase) modifies Hh morphogens prior to their secretion, while HHATL (Hh O-acyltransferase-like) negatively regulates the pathway. HHAT and HHATL are homologous to Saccharomyces cerevisiae Gup2 and Gup1, respectively. In yeast, Gup1 is associated with a high number and diversity of biological functions, namely polarity establishment, secretory/endocytic pathway functionality, vacuole morphology and wall and membrane composition, structure and maintenance. Phenotypes underlying death, morphogenesis and differentiation are also included. Paracrine signalling, like the one promoted by the Hh pathway, has not been shown to occur in microbial communities, despite the fact that large aggregates of cells like biofilms or colonies behave as proto-tissues. Instead, these have been suggested to sense the population density through the secretion of quorum-sensing chemicals. This review focuses on Gup1/HHATL and Gup2/HHAT proteins. We review the functions and physiology associated with these proteins in yeasts and higher eukaryotes. We suggest standardisation of the presently chaotic Gup-related nomenclature, which includes KIAA117, c3orf3, RASP, Skinny, Sightless and Central Missing, in order to avoid the disclosure of otherwise unnoticed information.
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Affiliation(s)
- Cândida Lucas
- CBMA—Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, 4710-054 Braga, Portugal; (G.C.); (R.F.-D.); (J.T.)
| | - Célia Ferreira
- CBMA—Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, 4710-054 Braga, Portugal; (G.C.); (R.F.-D.); (J.T.)
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK;
| | - Giulia Cazzanelli
- CBMA—Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, 4710-054 Braga, Portugal; (G.C.); (R.F.-D.); (J.T.)
| | - Ricardo Franco-Duarte
- CBMA—Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, 4710-054 Braga, Portugal; (G.C.); (R.F.-D.); (J.T.)
| | - Joana Tulha
- CBMA—Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, 4710-054 Braga, Portugal; (G.C.); (R.F.-D.); (J.T.)
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22
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Jonasson EM, Rossio V, Hatakeyama R, Abe M, Ohya Y, Yoshida S. Zds1/Zds2-PP2ACdc55 complex specifies signaling output from Rho1 GTPase. J Cell Biol 2016; 212:51-61. [PMID: 26728856 PMCID: PMC4700482 DOI: 10.1083/jcb.201508119] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Zds1/Zds2–PP2ACdc55 forms a complex with Rho1 GTPase and specifies Rho1 signaling outcome by regulating Rho1 GAPs in budding yeast. Budding yeast Rho1 guanosine triphosphatase (GTPase) plays an essential role in polarized cell growth by regulating cell wall glucan synthesis and actin organization. Upon cell wall damage, Rho1 blocks polarized cell growth and repairs the wounds by activating the cell wall integrity (CWI) Pkc1–mitogen-activated protein kinase (MAPK) pathway. A fundamental question is how active Rho1 promotes distinct signaling outputs under different conditions. Here we identified the Zds1/Zds2–protein phosphatase 2ACdc55 (PP2ACdc55) complex as a novel Rho1 effector that regulates Rho1 signaling specificity. Zds1/Zds2–PP2ACdc55 promotes polarized growth and cell wall synthesis by inhibiting Rho1 GTPase-activating protein (GAP) Lrg1 but inhibits CWI pathway by stabilizing another Rho1 GAP, Sac7, suggesting that active Rho1 is biased toward cell growth over stress response. Conversely, upon cell wall damage, Pkc1–Mpk1 activity inhibits cortical PP2ACdc55, ensuring that Rho1 preferentially activates the CWI pathway for cell wall repair. We propose that PP2ACdc55 specifies Rho1 signaling output and that reciprocal antagonism between Rho1–PP2ACdc55 and Rho1–Pkc1 explains how only one signaling pathway is robustly activated at a time.
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Affiliation(s)
- Erin M Jonasson
- Department of Biology and Rosenstiel Basic Biomedical Sciences Research Center, Brandeis University, Waltham, MA 02454
| | - Valentina Rossio
- Department of Biology and Rosenstiel Basic Biomedical Sciences Research Center, Brandeis University, Waltham, MA 02454
| | - Riko Hatakeyama
- Department of Biology and Rosenstiel Basic Biomedical Sciences Research Center, Brandeis University, Waltham, MA 02454
| | - Mitsuhiro Abe
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8561, Japan
| | - Yoshikazu Ohya
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8561, Japan
| | - Satoshi Yoshida
- Department of Biology and Rosenstiel Basic Biomedical Sciences Research Center, Brandeis University, Waltham, MA 02454 Gunma University Initiative for Advanced Research and Institute for Molecular and Cellular Regulation, Gunma University, Maebashi 371-8512, Japan
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Kołaczkowska A, Kołaczkowski M. Drug resistance mechanisms and their regulation in non-albicans Candida species. J Antimicrob Chemother 2016; 71:1438-50. [PMID: 26801081 DOI: 10.1093/jac/dkv445] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Fungal pathogens use various mechanisms to survive exposure to drugs. Prolonged treatment very often leads to the stepwise acquisition of resistance. The limited number of antifungal therapeutics and their mostly fungistatic rather than fungicidal character facilitates selection of resistant strains. These are able to cope with cytotoxic molecules by acquisition of appropriate mutations, re-wiring gene expression and metabolic adjustments. Recent evidence points to the paramount importance of the permeability barrier and cell wall integrity in the process of adaptation to high drug concentrations. Molecular details of basal and acquired drug resistance are best characterized in the most frequent human fungal pathogen, Candida albicans Effector genes directly related to the acquisition of elevated tolerance of this species to azole and echinocandin drugs are well described. The emergence of high-level drug resistance against intrinsically lower susceptibility to azoles in yeast species other than C. albicans is, however, of particular concern. This is due to their steadily increasing contribution to high mortality rates associated with disseminated infections. Recent findings concerning underlying mechanisms associated with elevated drug resistance suggest a link to cell wall and plasma membrane metabolism in non-albicans Candida species.
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Affiliation(s)
- Anna Kołaczkowska
- Department of Biochemistry, Pharmacology and Toxicology, Wroclaw University of Environmental and Life Sciences, Norwida 31, PL 50-375, Wroclaw, Poland
| | - Marcin Kołaczkowski
- Department of Biophysics, Wroclaw Medical University, Chalubinskiego 10, PL50-368, Wroclaw, Poland
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Córcoles-Sáez I, Hernández ML, Martínez-Rivas JM, Prieto JA, Randez-Gil F. Characterization of the S. cerevisiae inp51 mutant links phosphatidylinositol 4,5-bisphosphate levels with lipid content, membrane fluidity and cold growth. Biochim Biophys Acta Mol Cell Biol Lipids 2015; 1861:213-26. [PMID: 26724696 DOI: 10.1016/j.bbalip.2015.12.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 12/15/2015] [Accepted: 12/18/2015] [Indexed: 11/30/2022]
Abstract
Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] and its derivatives diphosphoinositol phosphates (DPIPs) play key signaling and regulatory roles. However, a direct function of these molecules in lipid and membrane homeostasis remains obscure. Here, we have studied the cold tolerance phenotype of yeast cells lacking the Inp51-mediated phosphoinositide-5-phosphatase. Genetic and biochemical approaches showed that increased metabolism of PI(4,5)P2 reduces the activity of the Pho85 kinase by increasing the levels of the DPIP isomer 1-IP7. This effect was key in the cold tolerance phenotype. Indeed, pho85 mutant cells grew better than the wild-type at 15 °C, and lack of this kinase abolished the inp51-mediated cold phenotype. Remarkably, reduced Pho85 function by loss of Inp51 affected the activity of the Pho85-regulated target Pah1, the yeast phosphatidate phosphatase. Cells lacking Inp51 showed reduced Pah1 abundance, derepression of an INO1-lacZ reporter, decreased content of triacylglycerides and elevated levels of phosphatidate, hallmarks of the pah1 mutant. However, the inp51 phenotype was not associated to low Pah1 activity since deletion of PAH1 caused cold sensitivity. In addition, the inp51 mutant exhibited features not shared by pah1, including a 40%-reduction in total lipid content and decreased membrane fluidity. These changes may influence the activity of membrane-anchored and/or associated proteins since deletion of INP51 slows down the transit to the vacuole of the fluorescent dye FM4-64. In conclusion, our work supports a model in which changes in the PI(4,5)P2 pool affect the 1-IP7 levels modulating the activity of Pho85, Pah1 and likely additional Pho85-controlled targets, and regulate lipid composition and membrane properties.
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Affiliation(s)
- Isaac Córcoles-Sáez
- Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Maria Luisa Hernández
- Instituto de la Grasa, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | | | - Jose A Prieto
- Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Francisca Randez-Gil
- Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain.
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Dawaliby R, Trubbia C, Delporte C, Noyon C, Ruysschaert JM, Van Antwerpen P, Govaerts C. Phosphatidylethanolamine Is a Key Regulator of Membrane Fluidity in Eukaryotic Cells. J Biol Chem 2015; 291:3658-67. [PMID: 26663081 DOI: 10.1074/jbc.m115.706523] [Citation(s) in RCA: 230] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Indexed: 01/10/2023] Open
Abstract
Adequate membrane fluidity is required for a variety of key cellular processes and in particular for proper function of membrane proteins. In most eukaryotic cells, membrane fluidity is known to be regulated by fatty acid desaturation and cholesterol, although some cells, such as insect cells, are almost devoid of sterol synthesis. We show here that insect and mammalian cells present similar microviscosity at their respective physiological temperature. To investigate how both sterols and phospholipids control fluidity homeostasis, we quantified the lipidic composition of insect SF9 and mammalian HEK 293T cells under normal or sterol-modified condition. As expected, insect cells show minimal sterols compared with mammalian cells. A major difference is also observed in phospholipid content as the ratio of phosphatidylethanolamine (PE) to phosphatidylcholine (PC) is inverted (4 times higher in SF9 cells). In vitro studies in liposomes confirm that both cholesterol and PE can increase rigidity of the bilayer, suggesting that both can be used by cells to maintain membrane fluidity. We then show that exogenously increasing the cholesterol amount in SF9 membranes leads to a significant decrease in PE:PC ratio whereas decreasing cholesterol in HEK 293T cells using statin treatment leads to an increase in the PE:PC ratio. In all cases, the membrane fluidity is maintained, indicating that both cell types combine regulation by sterols and phospholipids to control proper membrane fluidity.
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Affiliation(s)
- Rosie Dawaliby
- From the Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, CP 206/02, Bd du Triomphe, 1050 Brussels, Belgium
| | - Cataldo Trubbia
- From the Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, CP 206/02, Bd du Triomphe, 1050 Brussels, Belgium
| | - Cédric Delporte
- Laboratory of Pharmaceutical Chemistry and Analytical Platform of the Faculty of Pharmacy, Faculty of Pharmacy, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Caroline Noyon
- Laboratory of Pharmaceutical Chemistry and Analytical Platform of the Faculty of Pharmacy, Faculty of Pharmacy, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Jean-Marie Ruysschaert
- From the Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, CP 206/02, Bd du Triomphe, 1050 Brussels, Belgium
| | - Pierre Van Antwerpen
- Laboratory of Pharmaceutical Chemistry and Analytical Platform of the Faculty of Pharmacy, Faculty of Pharmacy, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Cédric Govaerts
- From the Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, CP 206/02, Bd du Triomphe, 1050 Brussels, Belgium,
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26
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Zhang C, Wang J, Tao H, Dang X, Wang Y, Chen M, Zhai Z, Yu W, Xu L, Shim WB, Lu G, Wang Z. FvBck1, a component of cell wall integrity MAP kinase pathway, is required for virulence and oxidative stress response in sugarcane Pokkah Boeng pathogen. Front Microbiol 2015; 6:1096. [PMID: 26500635 PMCID: PMC4597114 DOI: 10.3389/fmicb.2015.01096] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 09/22/2015] [Indexed: 11/13/2022] Open
Abstract
Fusarium verticillioides (formerly F. moniliforme) is suggested as one of the causal agents of Pokkah Boeng, a serious disease of sugarcane worldwide. Currently, detailed molecular and physiological mechanism of pathogenesis is unknown. In this study, we focused on cell wall integrity MAPK pathway as one of the potential signaling mechanisms associated with Pokkah Boeng pathogenesis. We identified FvBCK1 gene that encodes a MAP kinase kinase kinase homolog and determined that it is not only required for growth, micro- and macro-conidia production, and cell wall integrity but also for response to osmotic and oxidative stresses. The deletion of FvBCK1 caused a significant reduction in virulence and FB1 production, a possibly carcinogenic mycotoxin produced by the fungus. Moreover, we found the expression levels of three genes, which are known to be involved in superoxide scavenging, were down regulated in the mutant. We hypothesized that the loss of superoxide scavenging capacity was one of the reasons for reduced virulence, but overexpression of catalase or peroxidase gene failed to restore the virulence defect in the deletion mutant. When we introduced Magnaporthe oryzae MCK1 into the FvBck1 deletion mutant, while certain phenotypes were restored, the complemented strain failed to gain full virulence. In summary, FvBck1 plays a diverse role in F. verticillioides, and detailed investigation of downstream signaling pathways will lead to a better understanding of how this MAPK pathway regulates Pokkah Boeng on sugarcane.
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Affiliation(s)
- Chengkang Zhang
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Jianqiang Wang
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Hong Tao
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Xie Dang
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Yang Wang
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Miaoping Chen
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Zhenzhen Zhai
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Wenying Yu
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Won-Bo Shim
- Department of Plant Pathology and Microbiology, Texas A&M UniversityCollege Station, TX, USA
| | - Guodong Lu
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Zonghua Wang
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry UniversityFuzhou, China
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27
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Experimental and computational analysis of a large protein network that controls fat storage reveals the design principles of a signaling network. PLoS Comput Biol 2015; 11:e1004264. [PMID: 26020510 PMCID: PMC4447291 DOI: 10.1371/journal.pcbi.1004264] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 04/02/2015] [Indexed: 01/26/2023] Open
Abstract
An approach combining genetic, proteomic, computational, and physiological analysis was used to define a protein network that regulates fat storage in budding yeast (Saccharomyces cerevisiae). A computational analysis of this network shows that it is not scale-free, and is best approximated by the Watts-Strogatz model, which generates “small-world” networks with high clustering and short path lengths. The network is also modular, containing energy level sensing proteins that connect to four output processes: autophagy, fatty acid synthesis, mRNA processing, and MAP kinase signaling. The importance of each protein to network function is dependent on its Katz centrality score, which is related both to the protein’s position within a module and to the module’s relationship to the network as a whole. The network is also divisible into subnetworks that span modular boundaries and regulate different aspects of fat metabolism. We used a combination of genetics and pharmacology to simultaneously block output from multiple network nodes. The phenotypic results of this blockage define patterns of communication among distant network nodes, and these patterns are consistent with the Watts-Strogatz model. We discovered a large protein network that regulates fat storage in budding yeast. This network contains 94 proteins, almost all of which bind to other proteins in the network. To understand the functions of large protein collections such as these, it will be necessary to move away from one-by-one analysis of individual proteins and create computational models of entire networks. This will allow classification of networks into categories and permit researchers to identify key network proteins on theoretical grounds. We show here that the fat regulation network fits a Watts-Strogatz small-world model. This model was devised to explain the clustering phenomena often observed in real networks, but has not been previously applied to signaling networks within cells. The short path length and high clustering coefficients characteristic of the Watts-Strogatz topology allow for rapid communication between distant nodes and for division of the network into modules that perform different functions. The fat regulation network has modules, and it is divisible into subnetworks that span modular boundaries and regulate different aspects of fat metabolism. We experimentally examined communication between nodes within the network using a combination of genetics and pharmacology, and showed that the communication patterns are consistent with the Watts-Strogatz topology.
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Niles BJ, Powers T. TOR complex 2-Ypk1 signaling regulates actin polarization via reactive oxygen species. Mol Biol Cell 2014; 25:3962-72. [PMID: 25253719 PMCID: PMC4244204 DOI: 10.1091/mbc.e14-06-1122] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The evolutionarily conserved mTOR complex 2 (mTORC2) signaling pathway is an important regulator of actin cytoskeletal architecture and, as such, is a candidate target for preventing cancer cell motility and invasion. Remarkably, the precise mechanism(s) by which mTORC2 regulates the actin cytoskeleton have remained elusive. Here we show that in budding yeast, TORC2 and its downstream kinase Ypk1 regulate actin polarization by controlling reactive oxygen species (ROS) accumulation. Specifically, we find that TORC2-Ypk1 regulates actin polarization both by vacuole-related ROS, controlled by the phospholipid flippase kinase Fpk1 and sphingolipids, and by mitochondria-mediated ROS, controlled by the PKA subunit Tpk3. In addition, we find that the protein kinase C (Pkc1)/MAPK cascade, a well-established regulator of actin, acts downstream of Ypk1 to regulate ROS, in part by promoting degradation of the oxidative stress responsive repressor, cyclin C. Furthermore, we show that Ypk1 regulates Pkc1 activity through proper localization of Rom2 at the plasma membrane, which is also dependent on Fpk1 and sphingolipids. Together these findings demonstrate important links between TORC2/Ypk1 signaling, Fpk1, sphingolipids, Pkc1, and ROS as regulators of actin and suggest that ROS may play an important role in mTORC2-dependent dysregulation of the actin cytoskeleton in cancer cells.
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Affiliation(s)
- Brad J Niles
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, Davis, CA 95616
| | - Ted Powers
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, Davis, CA 95616
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29
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Abstract
The heat-shock response in cells, involving increased transcription of a specific set of genes in response to a sudden increase in temperature, is a highly conserved biological response occurring in all organisms. Despite considerable attention to the processes activated during heat shock, less is known about the role of genes in survival of a sudden temperature increase. Saccharomyces cerevisiae genes involved in the maintenance of heat-shock resistance in exponential and stationary phase were identified by screening the homozygous diploid deletants in nonessential genes and the heterozygous diploid mutants in essential genes for survival after a sudden shift in temperature from 30 to 50°. More than a thousand genes were identified that led to altered sensitivity to heat shock, with little overlap between them and those previously identified to affect thermotolerance. There was also little overlap with genes that are activated or repressed during heat-shock, with only 5% of them regulated by the heat-shock transcription factor. The target of rapamycin and protein kinase A pathways, lipid metabolism, vacuolar H+-ATPase, vacuolar protein sorting, and mitochondrial genome maintenance/translation were critical to maintenance of resistance. Mutants affected in l-tryptophan metabolism were heat-shock resistant in both growth phases; those affected in cytoplasmic ribosome biogenesis and DNA double-strand break repair were resistant in stationary phase, and in mRNA catabolic processes in exponential phase. Mutations affecting mitochondrial genome maintenance were highly represented in sensitive mutants. The cell division transcription factor Swi6p and Hac1p involved in the unfolded protein response also play roles in maintenance of heat-shock resistance.
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30
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Negative functional interaction between cell integrity MAPK pathway and Rho1 GTPase in fission yeast. Genetics 2013; 195:421-32. [PMID: 23934882 DOI: 10.1534/genetics.113.154807] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rho1 GTPase is the main activator of cell wall glucan biosynthesis and regulates actin cytoskeleton in fungi, including Schizosaccharomyces pombe. We have obtained a fission yeast thermosensitive mutant strain carrying the rho1-596 allele, which displays reduced Rho1 GTPase activity. This strain has severe cell wall defects and a thermosensitive growth, which is partially suppressed by osmotic stabilization. In a global screening for rho1-596 multicopy suppresors the pmp1+ gene was identified. Pmp1 is a dual specificity phosphatase that negatively regulates the Pmk1 mitogen-activated protein kinase (MAPK) cell integrity pathway. Accordingly, elimination of Pmk1 MAPK partially rescued rho1-596 thermosensitivity, corroborating the unexpected antagonistic functional relationship of these genes. We found that rho1-596 cells displayed increased basal activation of the cell integrity MAPK pathway and therefore were hypersensitive to MgCl2 and FK506. Moreover, the absence of calcineurin was lethal for rho1-596. We found a higher level of calcineurin activity in rho1-596 than in wild-type cells, and overexpression of constitutively active calcineurin partially rescued rho1-596 thermosensitivity. All together our results suggest that loss of Rho1 function causes an increase in the cell integrity MAPK activity, which is detrimental to the cells and turns calcineurin activity essential.
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31
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Checks and balances in membrane phospholipid class and acyl chain homeostasis, the yeast perspective. Prog Lipid Res 2013; 52:374-94. [PMID: 23631861 DOI: 10.1016/j.plipres.2013.04.006] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 03/28/2013] [Accepted: 04/16/2013] [Indexed: 11/24/2022]
Abstract
Glycerophospholipids are the most abundant membrane lipid constituents in most eukaryotic cells. As a consequence, phospholipid class and acyl chain homeostasis are crucial for maintaining optimal physical properties of membranes that in turn are crucial for membrane function. The topic of this review is our current understanding of membrane phospholipid homeostasis in the reference eukaryote Saccharomyces cerevisiae. After introducing the physical parameters of the membrane that are kept in optimal range, the properties of the major membrane phospholipids and their contributions to membrane structure and dynamics are summarized. Phospholipid metabolism and known mechanisms of regulation are discussed, including potential sensors for monitoring membrane physical properties. Special attention is paid to processes that maintain the phospholipid class specific molecular species profiles, and to the interplay between phospholipid class and acyl chain composition when yeast membrane lipid homeostasis is challenged. Based on the reviewed studies, molecular species selectivity of the lipid metabolic enzymes, and mass action in acyl-CoA metabolism are put forward as important intrinsic contributors to membrane lipid homeostasis.
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