1
|
Creamer DR, Beynon RJ, Hubbard SJ, Ashe MP, Grant CM. Isoform-specific sequestration of protein kinase A fine-tunes intracellular signaling during heat stress. Cell Rep 2024; 43:114360. [PMID: 38865242 DOI: 10.1016/j.celrep.2024.114360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 04/24/2024] [Accepted: 05/30/2024] [Indexed: 06/14/2024] Open
Abstract
Protein kinase A (PKA) is a conserved kinase crucial for fundamental biological processes linked to growth, development, and metabolism. The PKA catalytic subunit is expressed as multiple isoforms in diverse eukaryotes; however, their contribution to ensuring signaling specificity in response to environmental cues remains poorly defined. Catalytic subunit activity is classically moderated via interaction with an inhibitory regulatory subunit. Here, a quantitative mass spectrometry approach is used to examine heat-stress-induced changes in the binding of yeast Tpk1-3 catalytic subunits to the Bcy1 regulatory subunit. We show that Tpk3 is not regulated by Bcy1 binding but, instead, is deactivated upon heat stress via reversible sequestration into cytoplasmic granules. These "Tpk3 granules" are enriched for multiple PKA substrates involved in various metabolic processes, with the Hsp42 sequestrase required for their formation. Hence, regulated sequestration of Tpk3 provides a mechanism to control isoform-specific kinase signaling activity during stress conditions.
Collapse
Affiliation(s)
- Declan R Creamer
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Robert J Beynon
- Centre for Proteome Research, Institute of Systems and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Simon J Hubbard
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Mark P Ashe
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Chris M Grant
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.
| |
Collapse
|
2
|
Obsilova V, Obsil T. The yeast 14-3-3 proteins Bmh1 and Bmh2 regulate key signaling pathways. Front Mol Biosci 2024; 11:1327014. [PMID: 38328397 PMCID: PMC10847541 DOI: 10.3389/fmolb.2024.1327014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024] Open
Abstract
Cell signaling regulates several physiological processes by receiving, processing, and transmitting signals between the extracellular and intracellular environments. In signal transduction, phosphorylation is a crucial effector as the most common posttranslational modification. Selectively recognizing specific phosphorylated motifs of target proteins and modulating their functions through binding interactions, the yeast 14-3-3 proteins Bmh1 and Bmh2 are involved in catabolite repression, carbon metabolism, endocytosis, and mitochondrial retrograde signaling, among other key cellular processes. These conserved scaffolding molecules also mediate crosstalk between ubiquitination and phosphorylation, the spatiotemporal control of meiosis, and the activity of ion transporters Trk1 and Nha1. In humans, deregulation of analogous processes triggers the development of serious diseases, such as diabetes, cancer, viral infections, microbial conditions and neuronal and age-related diseases. Accordingly, the aim of this review article is to provide a brief overview of the latest findings on the functions of yeast 14-3-3 proteins, focusing on their role in modulating the aforementioned processes.
Collapse
Affiliation(s)
- Veronika Obsilova
- Institute of Physiology of the Czech Academy of Sciences, Laboratory of Structural Biology of Signaling Proteins, Division, BIOCEV, Vestec, Czechia
| | - Tomas Obsil
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czechia
| |
Collapse
|
3
|
Zhang Z, Zhong Z, Xiong Y. Sailing in complex nutrient signaling networks: Where I am, where to go, and how to go? MOLECULAR PLANT 2023; 16:1635-1660. [PMID: 37740490 DOI: 10.1016/j.molp.2023.09.012] [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: 05/19/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
To ensure survival and promote growth, sessile plants have developed intricate internal signaling networks tailored in diverse cells and organs with both shared and specialized functions that respond to various internal and external cues. A fascinating question arises: how can a plant cell or organ diagnose the spatial and temporal information it is experiencing to know "where I am," and then is able to make the accurate specific responses to decide "where to go" and "how to go," despite the absence of neuronal systems found in mammals. Drawing inspiration from recent comprehensive investigations into diverse nutrient signaling pathways in plants, this review focuses on the interactive nutrient signaling networks mediated by various nutrient sensors and transducers. We assess and illustrate examples of how cells and organs exhibit specific responses to changing spatial and temporal information within these interactive plant nutrient networks. In addition, we elucidate the underlying mechanisms by which plants employ posttranslational modification codes to integrate different upstream nutrient signals, thereby conferring response specificities to the signaling hub proteins. Furthermore, we discuss recent breakthrough studies that demonstrate the potential of modulating nutrient sensing and signaling as promising strategies to enhance crop yield, even with reduced fertilizer application.
Collapse
Affiliation(s)
- Zhenzhen Zhang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Haixia Institute of Science and Technology, Synthetic Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhaochen Zhong
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Haixia Institute of Science and Technology, Synthetic Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yan Xiong
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Haixia Institute of Science and Technology, Synthetic Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| |
Collapse
|
4
|
Tanahashi R, Nishimura A, Morita F, Nakazawa H, Taniguchi A, Ichikawa K, Nakagami K, Boundy-Mills K, Takagi H. The arginine transporter Can1 acts as a transceptor for regulation of proline utilization in the yeast Saccharomyces cerevisiae. Yeast 2023; 40:333-348. [PMID: 36573467 DOI: 10.1002/yea.3836] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/29/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Proline is the most abundant amino acid in wine and beer, because the yeast Saccharomyces cerevisiae hardly assimilates proline during fermentation processes. Our previous studies showed that arginine induces endocytosis of the proline transporter Put4, resulting in inhibition of proline utilization. We here report a possible role of arginine sensing in the inhibition of proline utilization. We first found that two basic amino acids, ornithine, and lysine, inhibit proline utilization by inducing Put4 endocytosis in a manner similar to arginine, but citrulline does not. Our genetic screening revealed that the arginine transporter Can1 is involved in the inhibition of proline utilization by arginine. Intriguingly, the arginine uptake activity of Can1 was not required for the arginine-dependent inhibition of proline utilization, suggesting that Can1 has a function beyond its commonly known function of transporting arginine. More importantly, our biochemical analyses revealed that Can1 activates signaling cascades of protein kinase A in response to extracellular arginine. Hence, we proposed that Can1 regulates proline utilization by functioning as a transceptor possessing the activity of both a transporter and receptor of arginine.
Collapse
Affiliation(s)
- Ryoya Tanahashi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
- Division for Research Strategy, Institute for Research Initiatives, Nara Institute of Science and Technology, Ikoma, Japan
- Department of Food Science and Technology, University of California Davis, Davis, California, USA
| | - Akira Nishimura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Fumika Morita
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Hayate Nakazawa
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Atsuki Taniguchi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Kazuki Ichikawa
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Kazuki Nakagami
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Kyria Boundy-Mills
- Department of Food Science and Technology, University of California Davis, Davis, California, USA
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| |
Collapse
|
5
|
Wagner ER, Gasch AP. Advances in S. cerevisiae Engineering for Xylose Fermentation and Biofuel Production: Balancing Growth, Metabolism, and Defense. J Fungi (Basel) 2023; 9:786. [PMID: 37623557 PMCID: PMC10455348 DOI: 10.3390/jof9080786] [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: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Genetically engineering microorganisms to produce chemicals has changed the industrialized world. The budding yeast Saccharomyces cerevisiae is frequently used in industry due to its genetic tractability and unique metabolic capabilities. S. cerevisiae has been engineered to produce novel compounds from diverse sugars found in lignocellulosic biomass, including pentose sugars, like xylose, not recognized by the organism. Engineering high flux toward novel compounds has proved to be more challenging than anticipated since simply introducing pathway components is often not enough. Several studies show that the rewiring of upstream signaling is required to direct products toward pathways of interest, but doing so can diminish stress tolerance, which is important in industrial conditions. As an example of these challenges, we reviewed S. cerevisiae engineering efforts, enabling anaerobic xylose fermentation as a model system and showcasing the regulatory interplay's controlling growth, metabolism, and stress defense. Enabling xylose fermentation in S. cerevisiae requires the introduction of several key metabolic enzymes but also regulatory rewiring of three signaling pathways at the intersection of the growth and stress defense responses: the RAS/PKA, Snf1, and high osmolarity glycerol (HOG) pathways. The current studies reviewed here suggest the modulation of global signaling pathways should be adopted into biorefinery microbial engineering pipelines to increase efficient product yields.
Collapse
Affiliation(s)
- Ellen R. Wagner
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Audrey P. Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
| |
Collapse
|
6
|
Zhang B, Zhang Y, Guan R, Du M, Yin X, Zhao W, An S. Trehalase is required for sex pheromone biosynthesis in Helicoverpa armigera. INSECT MOLECULAR BIOLOGY 2022; 31:334-345. [PMID: 35084068 DOI: 10.1111/imb.12762] [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: 09/27/2021] [Revised: 12/08/2021] [Accepted: 01/24/2022] [Indexed: 05/14/2023]
Abstract
Trehalase (Treh) hydrolyzes trehalose to generate glucose and it plays important role in many physiological processes. Acetyl-CoA, the precursor of sex pheromone biosynthesis in the pheromone gland (PG) of Helicoverpa armigera, originates from glucose during glycolysis. However, the function of Treh in sex pheromone biosynthesis remains elusive. In the present study, H. armigera was used as a model to investigate the function of two Trehs (Treh1 and Treh2) in sex pheromone biosynthesis. Results demonstrated that knockdown of HaTreh1 or HaTreh2 in female PGs led to significant decreases in Z11-16:Ald production, female ability to attract males, and successful mating proportions. Pheromone biosynthesis activating neuropeptide (PBAN) treatment triggered HaTreh1 and HaTreh2 activities in the isolated PGs and Sf9 cells. However, the activities of HaTreh1 and HaTreh2 triggered by PBAN were offset by H-89, the specific inhibitor of protein kinase A (PKA). Furthermore, the H-89 treatment significantly decreased the phosphorylation level of Trhe2, which was induced by PBAN. In addition, sugar feeding (5% sugar) increased the enzyme activities of Treh1 and Treh2. In summary, our findings confirmed that PBAN activates Treh1/2 activities by recruiting cAMP/PKA signalling, promotes glycolysis to ensure the supply of acetyl-CoA, and ultimately facilitates sex pheromone biosynthesis and mating behaviour.
Collapse
Affiliation(s)
- Bo Zhang
- State Key Laboratory of Wheat and Maize Crop Science/College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yunhui Zhang
- State Key Laboratory of Wheat and Maize Crop Science/College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Ruobing Guan
- State Key Laboratory of Wheat and Maize Crop Science/College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Mengfang Du
- State Key Laboratory of Wheat and Maize Crop Science/College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Xinming Yin
- State Key Laboratory of Wheat and Maize Crop Science/College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Wenli Zhao
- State Key Laboratory of Wheat and Maize Crop Science/College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Shiheng An
- State Key Laboratory of Wheat and Maize Crop Science/College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| |
Collapse
|
7
|
Foster B, Tyrawa C, Ozsahin E, Lubberts M, Krogerus K, Preiss R, van der Merwe G. Kveik Brewing Yeasts Demonstrate Wide Flexibility in Beer Fermentation Temperature Tolerance and Exhibit Enhanced Trehalose Accumulation. Front Microbiol 2022; 13:747546. [PMID: 35369501 PMCID: PMC8966892 DOI: 10.3389/fmicb.2022.747546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 02/11/2022] [Indexed: 11/25/2022] Open
Abstract
Traditional Norwegian Farmhouse ale yeasts, also known as kveik, have captured the attention of the brewing community in recent years. Kveik were recently reported as fast fermenting thermo- and ethanol tolerant yeasts with the capacity to produce a variety of interesting flavor metabolites. They are a genetically distinct group of domesticated beer yeasts of admixed origin with one parent from the “Beer 1” clade and the other unknown. While kveik are known to ferment wort efficiently at warmer temperatures, their range of fermentation temperatures and corresponding fermentation efficiencies, remain uncharacterized. In addition, the characteristics responsible for their increased thermotolerance remain largely unknown. Here we demonstrate variation in kveik strains at a wide range of fermentation temperatures and show not all kveik strains are equal in fermentation performance and stress tolerance. Furthermore, we uncovered an increased capacity of kveik strains to accumulate intracellular trehalose, which likely contributes to their increased thermo- and ethanol tolerances. Taken together our results present a clearer picture of the future opportunities presented by Norwegian kveik yeasts and offer further insight into their applications in brewing.
Collapse
Affiliation(s)
- Barret Foster
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Caroline Tyrawa
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Emine Ozsahin
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Mark Lubberts
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | | | | | - George van der Merwe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| |
Collapse
|
8
|
Ren L, Hou YP, Zhu YY, Zhao FF, Duan YB, Wu LY, Duan XX, Zhang J, Zhou MG. Validamycin A Enhances the Interaction Between Neutral Trehalase and 14-3-3 Protein Bmh1 in Fusarium graminearum. PHYTOPATHOLOGY 2022; 112:290-298. [PMID: 34156266 DOI: 10.1094/phyto-05-21-0214-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In agriculture, Trehalase is considered the main target of the biological fungicide validamycin A, and the toxicology mechanism of validamycin A is unknown. 14-3-3 proteins, highly conserved proteins, participate in diverse cellular processes, including enzyme activation, protein localization, and acting as a molecular chaperone. In Saccharomyces cerevisiae, the 14-3-3 protein Bmh1could interact with Nth1 to respond to specific external stimuli. Here, we characterized FgNth, FgBmh1, and FgBmh2 in Fusarium graminearum. ΔFgNth, ΔFgBmh1, and ΔFgBmh2 displayed great growth defects and their peripheral tips hyphae generated more branches when compared with wild-type (WT) PH-1. When exposed to validamycin A as well as high osmotic and high temperature stresses, ΔFgNth, ΔFgBmh1, and ΔFgBmh2 showed more tolerance than WT. Both ΔFgNth and ΔFgBmh1 displayed reduced deoxynivalenol production but opposite for ΔFgBmh2, and all three deletion mutants showed reduced virulence on wheat coleoptiles. In addition, coimmunoprecipitation (Co-IP) experiments suggested that FgBmh1 and FgBmh2 both interact with FgNth, but no interaction was detected between FgBmh1 and FgBmh2 in our experiments. Further, validamycin A enhances the interaction between FgBmh1 and FgNth in a positive correlation under concentrations of 1 to 100 μg/ml. In addition, both high osmotic and high temperature stresses promote the interaction between FgBmh1 and FgNth. Co-IP assay also showed that neither FgBmh1 nor FgBmh2 could interact with FgPbs2, a MAPKK kinase in the high-osmolarity glycerol pathway. However, FgBmh2 but not FgBmh1 binds to the heat shock protein FgHsp70 in F. graminearum. Taken together, our results demonstrate that FgNth and FgBmh proteins are involved in growth and responses to external stresses and virulence; and validamycin enhanced the interaction between FgNth and FgBmh1in F. graminearum.
Collapse
Affiliation(s)
- Li Ren
- College of Plant Protection and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yi-Ping Hou
- College of Plant Protection and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yuan-Ye Zhu
- College of Plant Protection and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095 China
| | - Fei-Fei Zhao
- College of Plant Protection and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095 China
| | - Ya-Bing Duan
- College of Plant Protection and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095 China
| | - Luo-Yu Wu
- College of Plant Protection and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095 China
| | - Xiao-Xin Duan
- College of Plant Protection and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jie Zhang
- College of Plant Protection and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095 China
| | - Ming-Guo Zhou
- College of Plant Protection and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095 China
| |
Collapse
|
9
|
Interaction of TOR and PKA Signaling in S. cerevisiae. Biomolecules 2022; 12:biom12020210. [PMID: 35204711 PMCID: PMC8961621 DOI: 10.3390/biom12020210] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 01/13/2023] Open
Abstract
TOR and PKA signaling are the major growth-regulatory nutrient-sensing pathways in S. cerevisiae. A number of experimental findings demonstrated a close relationship between these pathways: Both are responsive to glucose availability. Both regulate ribosome production on the transcriptional level and repress autophagy and the cellular stress response. Sch9, a major downstream effector of TORC1 presumably shares its kinase consensus motif with PKA, and genetic rescue and synthetic defects between PKA and Sch9 have been known for a long time. Further, studies in the first decade of this century have suggested direct regulation of PKA by TORC1. Nonetheless, the contribution of a potential direct cross-talk vs. potential sharing of targets between the pathways has still not been completely resolved. What is more, other findings have in contrast highlighted an antagonistic relationship between the two pathways. In this review, I explore the association between TOR and PKA signaling, mainly by focusing on proteins that are commonly referred to as shared TOR and PKA targets. Most of these proteins are transcription factors which to a large part explain the major transcriptional responses elicited by TOR and PKA upon nutrient shifts. I examine the evidence that these proteins are indeed direct targets of both pathways and which aspects of their regulation are targeted by TOR and PKA. I further explore if they are phosphorylated on shared sites by PKA and Sch9 or when experimental findings point towards regulation via the PP2ASit4/PP2A branch downstream of TORC1. Finally, I critically review data suggesting direct cross-talk between the pathways and its potential mechanism.
Collapse
|
10
|
Van Ende M, Timmermans B, Vanreppelen G, Siscar-Lewin S, Fischer D, Wijnants S, Romero CL, Yazdani S, Rogiers O, Demuyser L, Van Zeebroeck G, Cen Y, Kuchler K, Brunke S, Van Dijck P. The involvement of the Candida glabrata trehalase enzymes in stress resistance and gut colonization. Virulence 2021; 12:329-345. [PMID: 33356857 PMCID: PMC7808424 DOI: 10.1080/21505594.2020.1868825] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 11/28/2020] [Accepted: 12/17/2020] [Indexed: 12/29/2022] Open
Abstract
Candida glabrata is an opportunistic human fungal pathogen and is frequently present in the human microbiome. It has a high relative resistance to environmental stresses and several antifungal drugs. An important component involved in microbial stress tolerance is trehalose. In this work, we characterized the three C. glabrata trehalase enzymes Ath1, Nth1 and Nth2. Single, double and triple deletion strains were constructed and characterized both in vitro and in vivo to determine the role of these enzymes in virulence. Ath1 was found to be located in the periplasm and was essential for growth on trehalose as sole carbon source, while Nth1 on the other hand was important for oxidative stress resistance, an observation which was consistent by the lower survival rate of the NTH1 deletion strain in human macrophages. No significant phenotype was observed for Nth2. The triple deletion strain was unable to establish a stable colonization of the gastrointestinal (GI) tract in mice indicating the importance of having trehalase activity for colonization in the gut.
Collapse
Affiliation(s)
- Mieke Van Ende
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, Leuven, KU Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Bea Timmermans
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, Leuven, KU Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Giel Vanreppelen
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, Leuven, KU Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Sofía Siscar-Lewin
- Department of Microbial Pathogenicity Mechanisms, Hans Knöll Institute, Jena, Germany
| | - Daniel Fischer
- Department of Microbial Pathogenicity Mechanisms, Hans Knöll Institute, Jena, Germany
| | - Stefanie Wijnants
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, Leuven, KU Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Celia Lobo Romero
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, Leuven, KU Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Saleh Yazdani
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, Leuven, KU Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Ona Rogiers
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, Leuven, KU Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Inflammation Research, Ghent, VIB, Belgium
| | - Liesbeth Demuyser
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, Leuven, KU Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Griet Van Zeebroeck
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, Leuven, KU Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Yuke Cen
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, Leuven, KU Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Karl Kuchler
- Medical University of Vienna, Center for Medical Biochemistry, Max Perutz Labs Vienna, Campus Vienna Biocenter, Vienna, Austria
| | - Sascha Brunke
- Department of Microbial Pathogenicity Mechanisms, Hans Knöll Institute, Jena, Germany
| | - Patrick Van Dijck
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, Leuven, KU Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| |
Collapse
|
11
|
Zhou X, Li J, Tang N, Xie H, Fan X, Chen H, Tang M, Xie X. Genome-Wide Analysis of Nutrient Signaling Pathways Conserved in Arbuscular Mycorrhizal Fungi. Microorganisms 2021; 9:1557. [PMID: 34442636 PMCID: PMC8401276 DOI: 10.3390/microorganisms9081557] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 01/03/2023] Open
Abstract
Arbuscular mycorrhizal (AM) fungi form a mutualistic symbiosis with a majority of terrestrial vascular plants. To achieve an efficient nutrient trade with their hosts, AM fungi sense external and internal nutrients, and integrate different hierarchic regulations to optimize nutrient acquisition and homeostasis during mycorrhization. However, the underlying molecular networks in AM fungi orchestrating the nutrient sensing and signaling remain elusive. Based on homology search, we here found that at least 72 gene components involved in four nutrient sensing and signaling pathways, including cAMP-dependent protein kinase A (cAMP-PKA), sucrose non-fermenting 1 (SNF1) protein kinase, target of rapamycin kinase (TOR) and phosphate (PHO) signaling cascades, are well conserved in AM fungi. Based on the knowledge known in model yeast and filamentous fungi, we outlined the possible gene networks functioning in AM fungi. These pathways may regulate the expression of downstream genes involved in nutrient transport, lipid metabolism, trehalase activity, stress resistance and autophagy. The RNA-seq analysis and qRT-PCR results of some core genes further indicate that these pathways may play important roles in spore germination, appressorium formation, arbuscule longevity and sporulation of AM fungi. We hope to inspire further studies on the roles of these candidate genes involved in these nutrient sensing and signaling pathways in AM fungi and AM symbiosis.
Collapse
Affiliation(s)
- Xiaoqin Zhou
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Jiangyong Li
- Institute for Environmental and Climate Research, Jinan University, Guangzhou 511443, China;
| | - Nianwu Tang
- UMR Interactions Arbres/Microorganismes, Centre INRA-Grand Est-Nancy, 54280 Champenoux, France;
| | - Hongyun Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Xiaoning Fan
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Hui Chen
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Ming Tang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Xianan Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| |
Collapse
|
12
|
Österberg L, Domenzain I, Münch J, Nielsen J, Hohmann S, Cvijovic M. A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism. PLoS Comput Biol 2021; 17:e1008891. [PMID: 33836000 PMCID: PMC8059808 DOI: 10.1371/journal.pcbi.1008891] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 04/21/2021] [Accepted: 03/18/2021] [Indexed: 12/11/2022] Open
Abstract
The interplay between nutrient-induced signaling and metabolism plays an important role in maintaining homeostasis and its malfunction has been implicated in many different human diseases such as obesity, type 2 diabetes, cancer, and neurological disorders. Therefore, unraveling the role of nutrients as signaling molecules and metabolites together with their interconnectivity may provide a deeper understanding of how these conditions occur. Both signaling and metabolism have been extensively studied using various systems biology approaches. However, they are mainly studied individually and in addition, current models lack both the complexity of the dynamics and the effects of the crosstalk in the signaling system. To gain a better understanding of the interconnectivity between nutrient signaling and metabolism in yeast cells, we developed a hybrid model, combining a Boolean module, describing the main pathways of glucose and nitrogen signaling, and an enzyme-constrained model accounting for the central carbon metabolism of Saccharomyces cerevisiae, using a regulatory network as a link. The resulting hybrid model was able to capture a diverse utalization of isoenzymes and to our knowledge outperforms constraint-based models in the prediction of individual enzymes for both respiratory and mixed metabolism. The model showed that during fermentation, enzyme utilization has a major contribution in governing protein allocation, while in low glucose conditions robustness and control are prioritized. In addition, the model was capable of reproducing the regulatory effects that are associated with the Crabtree effect and glucose repression, as well as regulatory effects associated with lifespan increase during caloric restriction. Overall, we show that our hybrid model provides a comprehensive framework for the study of the non-trivial effects of the interplay between signaling and metabolism, suggesting connections between the Snf1 signaling pathways and processes that have been related to chronological lifespan of yeast cells.
Collapse
Affiliation(s)
- Linnea Österberg
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Iván Domenzain
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Julia Münch
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
- BioInnovation Institute, Copenhagen, Denmark
| | - Stefan Hohmann
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Marija Cvijovic
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| |
Collapse
|
13
|
Kahlhofer J, Leon S, Teis D, Schmidt O. The α-arrestin family of ubiquitin ligase adaptors links metabolism with selective endocytosis. Biol Cell 2021; 113:183-219. [PMID: 33314196 DOI: 10.1111/boc.202000137] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/03/2020] [Indexed: 12/14/2022]
Abstract
The regulation of nutrient uptake into cells is important, as it allows to either increase biomass for cell growth or to preserve homoeostasis. A key strategy to adjust cellular nutrient uptake is the reconfiguration of the nutrient transporter repertoire at the plasma membrane by the addition of nutrient transporters through the secretory pathway and by their endocytic removal. In this review, we focus on the mechanisms that regulate selective nutrient transporter endocytosis, which is mediated by the α-arrestin protein family. In the budding yeast Saccharomyces cerevisiae, 14 different α-arrestins (also named arrestin-related trafficking adaptors, ARTs) function as adaptors for the ubiquitin ligase Rsp5. They instruct Rsp5 to ubiquitinate subsets of nutrient transporters to orchestrate their endocytosis. The ART proteins are under multilevel control of the major nutrient sensing systems, including amino acid sensing by the general amino acid control and target of rapamycin pathways, and energy sensing by 5'-adenosine-monophosphate-dependent kinase. The function of the six human α-arrestins is comparably under-characterised. Here, we summarise the current knowledge about the function, regulation and substrates of yeast ARTs and human α-arrestins, and highlight emerging communalities and general principles.
Collapse
Affiliation(s)
- Jennifer Kahlhofer
- Institute for Cell Biology, Biocenter, Medical University Innsbruck, Innsbruck, Austria
| | - Sebastien Leon
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - David Teis
- Institute for Cell Biology, Biocenter, Medical University Innsbruck, Innsbruck, Austria
| | - Oliver Schmidt
- Institute for Cell Biology, Biocenter, Medical University Innsbruck, Innsbruck, Austria
| |
Collapse
|
14
|
Dengler L, Örd M, Schwab LM, Loog M, Ewald JC. Regulation of trehalase activity by multi-site phosphorylation and 14-3-3 interaction. Sci Rep 2021; 11:962. [PMID: 33441790 PMCID: PMC7806596 DOI: 10.1038/s41598-020-80357-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/17/2020] [Indexed: 11/16/2022] Open
Abstract
Protein phosphorylation enables a rapid adjustment of cellular activities to diverse intracellular and environmental stimuli. Many phosphoproteins are targeted on more than one site, which allows the integration of multiple signals and the implementation of complex responses. However, the hierarchy and interplay between multiple phospho-sites are often unknown. Here, we study multi‐site phosphorylation using the yeast trehalase Nth1 and its activator, the 14-3-3 protein Bmh1, as a model. Nth1 is known to be phosphorylated by the metabolic kinase PKA on four serine residues and by the cell cycle kinase CDK on one residue. However, how these five phospho-sites adjust Nth1 activity remains unclear. Using a novel reporter construct, we investigated the contribution of the individual sites for the regulation of the trehalase and its 14-3-3 interactor. In contrast to the constitutively phosphorylated S20 and S83, the weaker sites S21 and S60 are only phosphorylated by increased PKA activity. For binding Bmh1, S83 functions as the high‐affinity “gatekeeper” site, but successful binding of the Bmh1 dimer and thus Nth1 activation requires S60 as a secondary site. Under nutrient-poor conditions with low PKA activity, S60 is not efficiently phosphorylated and the cell cycle dependent phosphorylation of S66 by Cdk1 contributes to Nth1 activity, likely by providing an alternative Bmh1 binding site. Additionally, the PKA sites S20 and S21 modulate the dephosphorylation of Nth1 on downstream Bmh1 sites. In summary, our results expand our molecular understanding of Nth1 regulation and provide a new aspect of the interaction of 14-3-3 proteins with their targets.
Collapse
Affiliation(s)
- Lisa Dengler
- Interfaculty Institute of Cell Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Mihkel Örd
- Institute of Technology, University of Tartu, 50411, Tartu, Estonia
| | - Lucca M Schwab
- Interfaculty Institute of Cell Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Mart Loog
- Institute of Technology, University of Tartu, 50411, Tartu, Estonia
| | - Jennifer C Ewald
- Interfaculty Institute of Cell Biology, University of Tübingen, 72076, Tübingen, Germany.
| |
Collapse
|
15
|
Van Zeebroeck G, Demuyser L, Zhang Z, Cottignie I, Thevelein JM. Nutrient sensing and cAMP signaling in yeast: G-protein coupled receptor versus transceptor activation of PKA. MICROBIAL CELL (GRAZ, AUSTRIA) 2020; 8:17-27. [PMID: 33490229 PMCID: PMC7780724 DOI: 10.15698/mic2021.01.740] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 09/12/2020] [Accepted: 09/17/2020] [Indexed: 11/13/2022]
Abstract
A major signal transduction pathway regulating cell growth and many associated physiological properties as a function of nutrient availability in the yeast Saccharomyces cerevisiae is the protein kinase A (PKA) pathway. Glucose activation of PKA is mediated by G-protein coupled receptor (GPCR) Gpr1, and secondary messenger cAMP. Other nutrients, including nitrogen, phosphate and sulfate, activate PKA in accordingly-starved cells through nutrient transceptors, but apparently without cAMP signaling. We have now used an optimized EPAC-based fluorescence resonance energy transfer (FRET) sensor to precisely monitor in vivo cAMP levels after nutrient addition. We show that GPCR-mediated glucose activation of PKA is correlated with a rapid transient increase in the cAMP level in vivo, whereas nutrient transceptor-mediated activation by nitrogen, phosphate or sulfate, is not associated with any significant increase in cAMP in vivo. We also demonstrate direct physical interaction between the Gap1 amino acid transceptor and the catalytic subunits of PKA, Tpk1, 2 and 3. In addition, we reveal a conserved consensus motif in the nutrient transceptors that is also present in Bcy1, the regulatory subunit of PKA. This suggests that nutrient transceptor activation of PKA may be mediated by direct release of bound PKA catalytic subunits, triggered by the conformational changes occurring during transport of the substrate by the transceptor. Our results support a model in which nutrient transceptors are evolutionary ancestors of GPCRs, employing a more primitive direct signaling mechanism compared to the indirect cAMP second-messenger signaling mechanism used by GPCRs for activation of PKA.
Collapse
Affiliation(s)
- Griet Van Zeebroeck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
- These authors made an equal contribution to this work
| | - Liesbeth Demuyser
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
- These authors made an equal contribution to this work
| | - Zhiqiang Zhang
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Ines Cottignie
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Johan M. Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| |
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
|
Jiang Y, AkhavanAghdam Z, Li Y, Zid BM, Hao N. A protein kinase A-regulated network encodes short- and long-lived cellular memories. Sci Signal 2020; 13:eaay3585. [PMID: 32430291 PMCID: PMC7302112 DOI: 10.1126/scisignal.aay3585] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cells can store memories of prior experiences to modulate their responses to subsequent stresses, as seen for the protein kinase A (PKA)-mediated general stress response in yeast, which is required for resistance against future stressful conditions. Using microfluidics and time-lapse microscopy, we quantitatively analyzed how the cellular memory of stress adaptation is encoded in single yeast cells. We found that cellular memory was biphasic. Short-lived memory was mediated by trehalose synthase and trehalose metabolism. Long-lived memory was mediated by PKA-regulated stress-responsive transcription factors and cytoplasmic messenger ribonucleoprotein granules. Short- and long-lived memory could be selectively induced by different priming input dynamics. Computational modeling revealed how the PKA-mediated regulatory network could encode previous stimuli into memories with distinct dynamics. This biphasic memory-encoding scheme might represent a general strategy to prepare for future challenges in rapidly changing environments.
Collapse
Affiliation(s)
- Yanfei Jiang
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Zohreh AkhavanAghdam
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Yutian Li
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Brian M Zid
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Nan Hao
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
18
|
Kim B, Lee Y, Choi H, Huh WK. The trehalose-6-phosphate phosphatase Tps2 regulates ATG8 transcription and autophagy in Saccharomyces cerevisiae. Autophagy 2020; 17:1013-1027. [PMID: 32240040 DOI: 10.1080/15548627.2020.1746592] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Macroautophagy/autophagy is an important catabolic process for maintaining cellular homeostasis by adapting to various stress conditions. Autophagy is mediated by a double-membrane autophagosome, which sequesters a portion of cytoplasmic components for delivery to the vacuole. Several autophagy-related (ATG) genes play crucial roles in autophagosome formation. The induction of ATG genes must be tightly regulated to maintain a proper autophagic activity, but their regulatory mechanisms are still largely unknown. Here, we report that the trehalose-6-phosphate phosphatase Tps2 functions as a positive regulator of autophagy in Saccharomyces cerevisiae. Cellular trehalose levels do not affect autophagy regulation by Tps2. Loss of Tps2 leads to impaired autophagic flux and reduced ATG8 expre/ssion under nitrogen starvation. In tps2Δ cells, Ume6 is predominantly dephosphorylated and represses ATG8 transcription by binding to its promoter region. Tps2 regulates nuclear translocation and activation of Rim15 kinase, a negative regulator of Ume6, by causing the dissociation of Rim15 from the 14-3-3 proteins Bmh1/2 under nitrogen starvation, suggesting that Rim15 mediates the function of Tps2 as a positive regulator of ATG8 induction. Furthermore, Tps2 plays a crucial role in the dephosphorylation of Ser1061 and Thr1075 residues of Rim15, which is important for controlling the dissociation of Rim15 from Bmh1/2 under nitrogen starvation. Together, our results reveal the role of Tps2 as a positive regulator of autophagy and provide new insight into the regulatory mechanisms of ATG gene expression.Abbreviations: ATG: autophagy-related; ChIP: chromatin immunoprecipitation; Co-IP: co-immunoprecipitation; DAPI: 4',6-diamidino-2-phenylindole; GFP: green fluorescent protein; PKA: protein kinase A; PtdIns3K: phosphatidylinositol 3-kinase; Rim15KI: kinase-inactive Rim15; Rim15-2A: Rim15S1061A,T1075A; TEM: transmission electron microscopy; TORC1: target of rapamycin complex 1.
Collapse
Affiliation(s)
- Bongkeun Kim
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Yongook Lee
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hyojeong Choi
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Won-Ki Huh
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.,Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
| |
Collapse
|
19
|
Plank M, Perepelkina M, Müller M, Vaga S, Zou X, Bourgoint C, Berti M, Saarbach J, Haesendonckx S, Winssinger N, Aebersold R, Loewith R. Chemical Genetics of AGC-kinases Reveals Shared Targets of Ypk1, Protein Kinase A and Sch9. Mol Cell Proteomics 2020; 19:655-671. [PMID: 32102971 PMCID: PMC7124472 DOI: 10.1074/mcp.ra120.001955] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Indexed: 12/22/2022] Open
Abstract
Protein phosphorylation cascades play a central role in the regulation of cell growth and protein kinases PKA, Sch9 and Ypk1 take center stage in regulating this process in S. cerevisiae To understand how these kinases co-ordinately regulate cellular functions we compared the phospho-proteome of exponentially growing cells without and with acute chemical inhibition of PKA, Sch9 and Ypk1. Sites hypo-phosphorylated upon PKA and Sch9 inhibition were preferentially located in RRxS/T-motifs suggesting that many are directly phosphorylated by these enzymes. Interestingly, when inhibiting Ypk1 we not only detected several hypo-phosphorylated sites in the previously reported RxRxxS/T-, but also in an RRxS/T-motif. Validation experiments revealed that neutral trehalase Nth1, a known PKA target, is additionally phosphorylated and activated downstream of Ypk1. Signaling through Ypk1 is therefore more closely related to PKA- and Sch9-signaling than previously appreciated and may perform functions previously only attributed to the latter kinases.
Collapse
Affiliation(s)
- Michael Plank
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland; National Centre of Competence in Research - Chemical Biology, University of Geneva, CH-1211, Geneva, Switzerland.
| | - Mariya Perepelkina
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland
| | - Markus Müller
- National Centre of Competence in Research - Chemical Biology, University of Geneva, CH-1211, Geneva, Switzerland; Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Stefania Vaga
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Xiaoming Zou
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland
| | - Clélia Bourgoint
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland
| | - Marina Berti
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland
| | - Jacques Saarbach
- National Centre of Competence in Research - Chemical Biology, University of Geneva, CH-1211, Geneva, Switzerland; Department of Organic Chemistry, University of Geneva, CH-1211, Geneva, Switzerland
| | - Steven Haesendonckx
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland
| | - Nicolas Winssinger
- National Centre of Competence in Research - Chemical Biology, University of Geneva, CH-1211, Geneva, Switzerland; Department of Organic Chemistry, University of Geneva, CH-1211, Geneva, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, CH-8093 Zürich, Switzerland; Faculty of Science, University of Zurich, CH-8006, Zurich, Switzerland
| | - Robbie Loewith
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland; National Centre of Competence in Research - Chemical Biology, University of Geneva, CH-1211, Geneva, Switzerland.
| |
Collapse
|
20
|
Ciesla M, Skowronek E, Boguta M. Function of TFIIIC, RNA polymerase III initiation factor, in activation and repression of tRNA gene transcription. Nucleic Acids Res 2019; 46:9444-9455. [PMID: 30053100 PMCID: PMC6182151 DOI: 10.1093/nar/gky656] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/10/2018] [Indexed: 01/09/2023] Open
Abstract
Transcription of transfer RNA genes by RNA polymerase III (Pol III) is controlled by general factors, TFIIIB and TFIIIC, and a negative regulator, Maf1. Here we report the interplay between TFIIIC and Maf1 in controlling Pol III activity upon the physiological switch of yeast from fermentation to respiration. TFIIIC directly competes with Pol III for chromatin occupancy as demonstrated by inversely correlated tDNA binding. The association of TFIIIC with tDNA was stronger under unfavorable respiratory conditions and in the presence of Maf1. Induction of tDNA transcription by glucose-activated protein kinase A (PKA) was correlated with the down-regulation of TFIIIC occupancy on tDNA. The conditions that activate the PKA signaling pathway promoted the binding of TFIIIB subunits, Brf1 and Bdp1, with tDNA, but decreased their interaction with TFIIIC. Association of Brf1 and Bdp1 with TFIIIC was much stronger under repressive conditions, potentially restricting TFIIIB recruitment to tDNA and preventing Pol III recruitment. Altogether, we propose a model in which, depending on growth conditions, TFIIIC promotes activation or repression of tDNA transcription.
Collapse
Affiliation(s)
- Malgorzata Ciesla
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Ewa Skowronek
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Magdalena Boguta
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| |
Collapse
|
21
|
Wagner ER, Myers KS, Riley NM, Coon JJ, Gasch AP. PKA and HOG signaling contribute separable roles to anaerobic xylose fermentation in yeast engineered for biofuel production. PLoS One 2019; 14:e0212389. [PMID: 31112537 PMCID: PMC6528989 DOI: 10.1371/journal.pone.0212389] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/29/2019] [Indexed: 12/25/2022] Open
Abstract
Lignocellulosic biomass offers a sustainable source for biofuel production that does not compete with food-based cropping systems. Importantly, two critical bottlenecks prevent economic adoption: many industrially relevant microorganisms cannot ferment pentose sugars prevalent in lignocellulosic medium, leaving a significant amount of carbon unutilized. Furthermore, chemical biomass pretreatment required to release fermentable sugars generates a variety of toxins, which inhibit microbial growth and metabolism, specifically limiting pentose utilization in engineered strains. Here we dissected genetic determinants of anaerobic xylose fermentation and stress tolerance in chemically pretreated corn stover biomass, called hydrolysate. We previously revealed that loss-of-function mutations in the stress-responsive MAP kinase HOG1 and negative regulator of the RAS/Protein Kinase A (PKA) pathway, IRA2, enhances anaerobic xylose fermentation. However, these mutations likely reduce cells' ability to tolerate the toxins present in lignocellulosic hydrolysate, making the strain especially vulnerable to it. We tested the contributions of Hog1 and PKA signaling via IRA2 or PKA negative regulatory subunit BCY1 to metabolism, growth, and stress tolerance in corn stover hydrolysate and laboratory medium with mixed sugars. We found mutations causing upregulated PKA activity increase growth rate and glucose consumption in various media but do not have a specific impact on xylose fermentation. In contrast, mutation of HOG1 specifically increased xylose usage. We hypothesized improving stress tolerance would enhance the rate of xylose consumption in hydrolysate. Surprisingly, increasing stress tolerance did not augment xylose fermentation in lignocellulosic medium in this strain background, suggesting other mechanisms besides cellular stress limit this strain's ability for anaerobic xylose fermentation in hydrolysate.
Collapse
Affiliation(s)
- Ellen R. Wagner
- Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI United States of America
| | - Kevin S. Myers
- Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI United States of America
| | - Nicholas M. Riley
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI United States of America
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI United States of America
- Genome Center of Wisconsin, University of Wisconsin–Madison, Madison, WI United States of America
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison WI United States of America
- Morgridge Institute for Research, Madison, WI United States of America
| | - Audrey P. Gasch
- Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI United States of America
- Genome Center of Wisconsin, University of Wisconsin–Madison, Madison, WI United States of America
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, WI United States of America
| |
Collapse
|
22
|
Karpova EK, Eremina MA, Pirozhkova DS, Gruntenko NE. Stress-related hormones affect carbohydrate metabolism in Drosophila females. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2019; 101:e21540. [PMID: 30793357 DOI: 10.1002/arch.21540] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 06/09/2023]
Abstract
A highly conservative insulin signaling pathway, stable work of which is indicated by carbohydrates metabolism, is also known to play an important role in the control of stress resistance. Here we demonstrate that exposure to heat stress leads to a rise in the levels of trehalose and glucose in females of Drosophila melanogaster, but does not affect the expression level of the trehalase (Treh) gene. We have shown that the rise in juvenile hormone (JH) and dopamine decreases levels of both carbohydrates under the normal conditions but brings them to values close to normal following the stress exposure. The data obtained suggest that (a) dopamine and JH involved in the neuroendocrine stress reaction in D. melanogaster also take part in the regulation of carbohydrates metabolism, tending to normalize it after stress; (b) the regulation of trehalose content under stress does not occur at the level of transcription of the degrading enzyme.
Collapse
Affiliation(s)
- Evgenia K Karpova
- Department of Insects Genetics, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Margarita A Eremina
- Department of Insects Genetics, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Darya S Pirozhkova
- Department of Insects Genetics, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Nataly E Gruntenko
- Department of Insects Genetics, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| |
Collapse
|
23
|
Alblova M, Smidova A, Kalabova D, Lentini Santo D, Obsil T, Obsilova VO. Allosteric activation of yeast enzyme neutral trehalase by calcium and 14-3-3 protein. Physiol Res 2019; 68:147-160. [DOI: 10.33549/physiolres.933950] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Neutral trehalase 1 (Nth1) from Saccharomyces cerevisiae catalyzes disaccharide trehalose hydrolysis and helps yeast to survive adverse conditions, such as heat shock, starvation or oxidative stress. 14-3-3 proteins, master regulators of hundreds of partner proteins, participate in many key cellular processes. Nth1 is activated by phosphorylation followed by 14-3-3 protein (Bmh) binding. The activation mechanism is also potentiated by Ca(2+) binding within the EF-hand-like motif. This review summarizes the current knowledge about trehalases and the molecular and structural basis of Nth1 activation. The crystal structure of fully active Nth1 bound to 14-3-3 protein provided the first high-resolution view of a trehalase from a eukaryotic organism and showed 14-3-3 proteins as structural modulators and allosteric effectors of multi-domain binding partners.
Collapse
Affiliation(s)
- M. Alblova
- Department of Structural Biology of Signaling Proteins, Division BIOCEV, Institute of Physiology of the Czech Academy of Sciences, Vestec, Czech Republic.
| | | | | | | | | | | |
Collapse
|
24
|
14-3-3 Proteins: a window for a deeper understanding of fungal metabolism and development. World J Microbiol Biotechnol 2019; 35:24. [PMID: 30666471 DOI: 10.1007/s11274-019-2597-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/14/2019] [Indexed: 01/21/2023]
Abstract
Isoforms of 14-3-3 proteins, similar to their highly conserved homologs in mammals and plants, are both transcriptionally and functionally affected by their extracellular and intracellular environments. These proteins bind to phosphorylated client proteins to modulate their functions in fungi. Since phosphorylation regulates a plethora of different physiological responses in organisms, 14-3-3 proteins play roles in multiple physiological functions, including those controlling metabolisms, cell division, and responses to environmental stimulation. These proteins could also modulate signaling pathways that transduce inputs from the environment and downstream proteins that elicit physiological responses. Increasing evidence supports a prominent role for 14-3-3 proteins in regulating development and metabolism at various levels. In this review, we first provide a brief summary of the molecular structure of 14-3-3 proteins. Second, we discuss the potential roles of 14-3-3 proteins in the regulation of development and metabolism. Third, we review the roles of 14-3-3 proteins in the regulation of their binding partners, including receptors, protein kinases, and some protein kinase substrates. Finally, this review examines recent advances that further elucidate the role of 14-3-3 proteins in signaling transduction in response to environmental stress.
Collapse
|
25
|
Macovei A, Pagano A, Cappuccio M, Gallotti L, Dondi D, De Sousa Araujo S, Fevereiro P, Balestrazzi A. A Snapshot of the Trehalose Pathway During Seed Imbibition in Medicago truncatula Reveals Temporal- and Stress-Dependent Shifts in Gene Expression Patterns Associated With Metabolite Changes. FRONTIERS IN PLANT SCIENCE 2019; 10:1590. [PMID: 31921241 PMCID: PMC6930686 DOI: 10.3389/fpls.2019.01590] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/12/2019] [Indexed: 05/21/2023]
Abstract
Trehalose, a non-reducing disaccharide with multiple functions, among which source of energy and carbon, stress protectant, and signaling molecule, has been mainly studied in relation to plant development and response to stress. The trehalose pathway is conserved among different organisms and is composed of three enzymes: trehalose-6-phosphate synthase (TPS), which converts uridine diphosphate (UDP)-glucose and glucose-6-phosphate to trehalose-6-phosphate (T6P), trehalose-6-phosphatase (TPP), which dephosphorylates T6P to produce trehalose, and trehalase (TRE), responsible for trehalose catabolism. In plants, the trehalose pathway has been mostly studied in resurrection plants and the model plant Arabidopsis thaliana, where 11 AtTPS, 10 AtTPP, and 1 AtTRE genes are present. Here, we aim to investigate the involvement of the trehalose pathway in the early stages of seed germination (specifically, seed imbibition) using the model legume Medicago truncatula as a working system. Since not all the genes belonging to the trehalose pathway had been identified in M. truncatula, we first conducted an in silico analysis using the orthologous gene sequences from A. thaliana. Nine MtTPSs, eight MtTPPs, and a single MtTRE gene were hereby identified. Subsequently, the expression profiles of all the genes (together with the sucrose master-regulator SnRK1) were investigated during seed imbibition with water or stress agents (polyethylene glycol and sodium chloride). The reported data show a temporal distribution and preferential expression of specific TPS and TPP isoforms during seed imbibition with water. Moreover, it was possible to distinguish a small set of genes (e.g., MtTPS1, MtTPS7, MtTPS10, MtTPPA, MtTPPI, MtTRE) having a potential impact as precocious hallmarks of the seed response to stress. When the trehalose levels were measured by high-performance liquid chromatography, a significant decrease was observed during seed imbibition, suggesting that trehalose may act as an energy source rather than osmoprotectant. This is the first report investigating the expression profiles of genes belonging to the trehalose pathway during seed imbibition, thus ascertaining their involvement in the pre-germinative metabolism and their potential as tools to improve seed germination efficiency.
Collapse
Affiliation(s)
- Anca Macovei
- Department of Biology and Biotechnology “L. Spallanzani,” University of Pavia, Pavia, Italy
| | - Andrea Pagano
- Department of Biology and Biotechnology “L. Spallanzani,” University of Pavia, Pavia, Italy
| | - Michela Cappuccio
- Department of Biology and Biotechnology “L. Spallanzani,” University of Pavia, Pavia, Italy
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Green-it Research Unit, Oeiras, Portugal
| | - Lucia Gallotti
- Department of Chemistry, University of Pavia, Pavia, Italy
| | - Daniele Dondi
- Department of Chemistry, University of Pavia, Pavia, Italy
| | - Susana De Sousa Araujo
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Green-it Research Unit, Oeiras, Portugal
| | - Pedro Fevereiro
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Green-it Research Unit, Oeiras, Portugal
- Departamento de Biologia Vegetal, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Alma Balestrazzi
- Department of Biology and Biotechnology “L. Spallanzani,” University of Pavia, Pavia, Italy
- *Correspondence: Alma Balestrazzi,
| |
Collapse
|
26
|
Demuyser L, Van Genechten W, Mizuno H, Colombo S, Van Dijck P. Introducing fluorescence resonance energy transfer-based biosensors for the analysis of cAMP-PKA signalling in the fungal pathogen Candida glabrata. Cell Microbiol 2018; 20:e12863. [PMID: 29845711 DOI: 10.1111/cmi.12863] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 05/10/2018] [Accepted: 05/23/2018] [Indexed: 01/03/2023]
Abstract
The cyclic adenosine monophosphate-protein kinase A (cAMP-PKA) pathway is central to signal transduction in many organisms. In pathogenic fungi such as Candida albicans, this signalling cascade has proven to be involved in several processes, such as virulence, indicating its potential importance in antifungal drug discovery. Candida glabrata is an upcoming pathogen of the same species, yet information regarding the role of cAMP-PKA signalling in virulence is largely lacking. To enable efficient monitoring of cAMP-PKA activity in this pathogen, we here present the usage of two FRET-based biosensors. Both variations in the activity of PKA and the quantity of cAMP can be detected in a time-resolved manner, as we exemplify by glucose-induced activation of the pathway. We also present information on how to adequately process and analyse the data in a mathematically correct and physiologically relevant manner. These sensors will be of great benefit for scientists interested in linking the cAMP-PKA signalling cascade to downstream processes, such as virulence, possibly in a host environment.
Collapse
Affiliation(s)
- Liesbeth Demuyser
- VIB-KU Leuven Center for Microbiology, Flanders, Belgium.,Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
| | - Wouter Van Genechten
- VIB-KU Leuven Center for Microbiology, Flanders, Belgium.,Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium.,Chemistry-Biochemistry Department, Molecular and Structural Biology Section, KU Leuven, Leuven-Heverlee, Belgium
| | - Hideaki Mizuno
- Chemistry-Biochemistry Department, Molecular and Structural Biology Section, KU Leuven, Leuven-Heverlee, Belgium
| | - Sonia Colombo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Patrick Van Dijck
- VIB-KU Leuven Center for Microbiology, Flanders, Belgium.,Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
| |
Collapse
|
27
|
Conrad M, Kankipati HN, Kimpe M, Van Zeebroeck G, Zhang Z, Thevelein JM. The nutrient transceptor/PKA pathway functions independently of TOR and responds to leucine and Gcn2 in a TOR-independent manner. FEMS Yeast Res 2018; 17:3950251. [PMID: 28810702 PMCID: PMC5812495 DOI: 10.1093/femsyr/fox048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/06/2017] [Indexed: 12/25/2022] Open
Abstract
Two nutrient-controlled signalling pathways, the PKA and TOR pathway, play a major role in nutrient regulation of growth as well as growth-correlated properties in yeast. The relationship between the two pathways is not well understood. We have used Gap1 and Pho84 transceptor-mediated activation of trehalase and phosphorylation of fragmented Sch9 as a read-out for rapid nutrient activation of PKA or TORC1, respectively. We have identified conditions in which L-citrulline-induced activation of Sch9 phosphorylation is compromised, but not activation of trehalase: addition of the TORC1 inhibitor, rapamycin and low levels of L-citrulline. The same disconnection was observed for phosphate activation in phosphate-starved cells. The leu2 auxotrophic mutation reduces amino acid activation of trehalase, which is counteracted by deletion of GCN2. Both effects were also independent of TORC1. Our results show that rapid activation of the TOR pathway by amino acids is not involved in rapid activation of the PKA pathway and that effects of Gcn2 inactivation as well as leu2 auxotrophy all act independently of the TOR pathway. Hence, rapid nutrient signalling to PKA and TOR in cells arrested by nutrient starvation acts through parallel pathways.
Collapse
Affiliation(s)
- Michaela Conrad
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Harish Nag Kankipati
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Marlies Kimpe
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Griet Van Zeebroeck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Zhiqiang Zhang
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| |
Collapse
|
28
|
Falcone C, Mazzoni C. RNA stability and metabolism in regulated cell death, aging and diseases. FEMS Yeast Res 2018; 18:4978431. [DOI: 10.1093/femsyr/foy050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/17/2018] [Indexed: 12/13/2022] Open
Affiliation(s)
- Claudio Falcone
- Pasteur Institute-Cenci Bolognetti Foundation, Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185-Rome, Italy
| | - Cristina Mazzoni
- Pasteur Institute-Cenci Bolognetti Foundation, Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185-Rome, Italy
| |
Collapse
|
29
|
Steyfkens F, Zhang Z, Van Zeebroeck G, Thevelein JM. Multiple Transceptors for Macro- and Micro-Nutrients Control Diverse Cellular Properties Through the PKA Pathway in Yeast: A Paradigm for the Rapidly Expanding World of Eukaryotic Nutrient Transceptors Up to Those in Human Cells. Front Pharmacol 2018; 9:191. [PMID: 29662449 PMCID: PMC5890159 DOI: 10.3389/fphar.2018.00191] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 02/20/2018] [Indexed: 12/17/2022] Open
Abstract
The nutrient composition of the medium has dramatic effects on many cellular properties in the yeast Saccharomyces cerevisiae. In addition to the well-known specific responses to starvation for an essential nutrient, like nitrogen or phosphate, the presence of fermentable sugar or a respirative carbon source leads to predominance of fermentation or respiration, respectively. Fermenting and respiring cells also show strong differences in other properties, like storage carbohydrate levels, general stress tolerance and cellular growth rate. However, the main glucose repression pathway, which controls the switch between respiration and fermentation, is not involved in control of these properties. They are controlled by the protein kinase A (PKA) pathway. Addition of glucose to respiring yeast cells triggers cAMP synthesis, activation of PKA and rapid modification of its targets, like storage carbohydrate levels, general stress tolerance and growth rate. However, starvation of fermenting cells in a glucose medium for any essential macro- or micro-nutrient counteracts this effect, leading to downregulation of PKA and its targets concomitant with growth arrest and entrance into G0. Re-addition of the lacking nutrient triggers rapid activation of the PKA pathway, without involvement of cAMP as second messenger. Investigation of the sensing mechanism has revealed that the specific high-affinity nutrient transporter(s) induced during starvation function as transporter-receptors or transceptors for rapid activation of PKA upon re-addition of the missing substrate. In this way, transceptors have been identified for amino acids, ammonium, phosphate, sulfate, iron, and zinc. We propose a hypothesis for regulation of PKA activity by nutrient transceptors to serve as a conceptual framework for future experimentation. Many properties of transceptors appear to be similar to those of classical receptors and nutrient transceptors may constitute intermediate forms in the development of receptors from nutrient transporters during evolution. The nutrient-sensing transceptor system in yeast for activation of the PKA pathway has served as a paradigm for similar studies on candidate nutrient transceptors in other eukaryotes and we succinctly discuss the many examples of transceptors that have already been documented in other yeast species, filamentous fungi, plants, and animals, including the examples in human cells.
Collapse
Affiliation(s)
- Fenella Steyfkens
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Flanders, Belgium
| | - Zhiqiang Zhang
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Flanders, Belgium
| | - Griet Van Zeebroeck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Flanders, Belgium
| |
Collapse
|
30
|
Alblova M, Smidova A, Docekal V, Vesely J, Herman P, Obsilova V, Obsil T. Molecular basis of the 14-3-3 protein-dependent activation of yeast neutral trehalase Nth1. Proc Natl Acad Sci U S A 2017; 114:E9811-E9820. [PMID: 29087344 PMCID: PMC5699087 DOI: 10.1073/pnas.1714491114] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The 14-3-3 proteins, a family of highly conserved scaffolding proteins ubiquitously expressed in all eukaryotic cells, interact with and regulate the function of several hundreds of partner proteins. Yeast neutral trehalases (Nth), enzymes responsible for the hydrolysis of trehalose to glucose, compared with trehalases from other organisms, possess distinct structure and regulation involving phosphorylation at multiple sites followed by binding to the 14-3-3 protein. Here we report the crystal structures of yeast Nth1 and its complex with Bmh1 (yeast 14-3-3 isoform), which, together with mutational and fluorescence studies, indicate that the binding of Nth1 by 14-3-3 triggers Nth1's activity by enabling the proper 3D configuration of Nth1's catalytic and calcium-binding domains relative to each other, thus stabilizing the flexible part of the active site required for catalysis. The presented structure of the Bmh1:Nth1 complex highlights the ability of 14-3-3 to modulate the structure of a multidomain binding partner and to function as an allosteric effector. Furthermore, comparison of the Bmh1:Nth1 complex structure with those of 14-3-3:serotonin N-acetyltransferase and 14-3-3:heat shock protein beta-6 complexes revealed similarities in the 3D structures of bound partner proteins, suggesting the highly conserved nature of 14-3-3 affects the structures of many client proteins.
Collapse
Affiliation(s)
- Miroslava Alblova
- Department of Structural Biology of Signaling Proteins, Division Biotechnology and Biomedicine Center of the Academy of Sciences and Charles University in Vestec (BIOCEV), Institute of Physiology, The Czech Academy of Sciences, Prague 14220, Czech Republic
| | - Aneta Smidova
- Department of Structural Biology of Signaling Proteins, Division Biotechnology and Biomedicine Center of the Academy of Sciences and Charles University in Vestec (BIOCEV), Institute of Physiology, The Czech Academy of Sciences, Prague 14220, Czech Republic
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague 12843, Czech Republic
| | - Vojtech Docekal
- Department of Organic Chemistry, Faculty of Science, Charles University, Prague 12843, Czech Republic
| | - Jan Vesely
- Department of Organic Chemistry, Faculty of Science, Charles University, Prague 12843, Czech Republic
| | - Petr Herman
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Prague 12116, Czech Republic
| | - Veronika Obsilova
- Department of Structural Biology of Signaling Proteins, Division Biotechnology and Biomedicine Center of the Academy of Sciences and Charles University in Vestec (BIOCEV), Institute of Physiology, The Czech Academy of Sciences, Prague 14220, Czech Republic;
| | - Tomas Obsil
- Department of Structural Biology of Signaling Proteins, Division Biotechnology and Biomedicine Center of the Academy of Sciences and Charles University in Vestec (BIOCEV), Institute of Physiology, The Czech Academy of Sciences, Prague 14220, Czech Republic;
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague 12843, Czech Republic
| |
Collapse
|
31
|
Zhao G, Chen Y, Carey L, Futcher B. Cyclin-Dependent Kinase Co-Ordinates Carbohydrate Metabolism and Cell Cycle in S. cerevisiae. Mol Cell 2017; 62:546-57. [PMID: 27203179 DOI: 10.1016/j.molcel.2016.04.026] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 03/17/2016] [Accepted: 04/21/2016] [Indexed: 01/15/2023]
Abstract
Cyclin-dependent kinases (CDKs) control cell division in eukaryotes by phosphorylating proteins involved in division. But successful proliferation requires co-ordination between division and cellular growth in mass. Previous proteomic studies suggested that metabolic proteins, as well as cell division proteins, could potentially be substrates of cyclin-dependent kinases. Here we focus on two metabolic enzymes of the yeast S. cerevisiae, neutral trehalase (Nth1) and glycogen phosphorylase (Gph1), and show that their activities are likely directly controlled by CDK activity, thus allowing co-ordinate regulation of carbohydrate metabolism with cell division processes. In this case, co-ordinate regulation may optimize the decision to undertake a final cell division as nutrients are being exhausted. Co-regulation of cell division processes and metabolic processes by CDK activity may be a general phenomenon important for co-ordinating the cell cycle with growth.
Collapse
Affiliation(s)
- Gang Zhao
- Department of Molecular Genetics & Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yuping Chen
- Department of Molecular Genetics & Microbiology, Stony Brook University, Stony Brook, NY 11794, USA; Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Lucas Carey
- Department of Molecular Genetics & Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Bruce Futcher
- Department of Molecular Genetics & Microbiology, Stony Brook University, Stony Brook, NY 11794, USA.
| |
Collapse
|
32
|
Ewald JC, Kuehne A, Zamboni N, Skotheim JM. The Yeast Cyclin-Dependent Kinase Routes Carbon Fluxes to Fuel Cell Cycle Progression. Mol Cell 2017; 62:532-45. [PMID: 27203178 DOI: 10.1016/j.molcel.2016.02.017] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 10/26/2015] [Accepted: 02/11/2016] [Indexed: 01/12/2023]
Abstract
Cell division entails a sequence of processes whose specific demands for biosynthetic precursors and energy place dynamic requirements on metabolism. However, little is known about how metabolic fluxes are coordinated with the cell division cycle. Here, we examine budding yeast to show that more than half of all measured metabolites change significantly through the cell division cycle. Cell cycle-dependent changes in central carbon metabolism are controlled by the cyclin-dependent kinase (Cdk1), a major cell cycle regulator, and the metabolic regulator protein kinase A. At the G1/S transition, Cdk1 phosphorylates and activates the enzyme Nth1, which funnels the storage carbohydrate trehalose into central carbon metabolism. Trehalose utilization fuels anabolic processes required to reliably complete cell division. Thus, the cell cycle entrains carbon metabolism to fuel biosynthesis. Because the oscillation of Cdk activity is a conserved feature of the eukaryotic cell cycle, we anticipate its frequent use in dynamically regulating metabolism for efficient proliferation.
Collapse
Affiliation(s)
- Jennifer C Ewald
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Andreas Kuehne
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; PhD Program Systems Biology, Life Science Zurich Graduate School, 8057 Zurich, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
33
|
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
|
34
|
Liu Y, von Wirén N. Ammonium as a signal for physiological and morphological responses in plants. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2581-2592. [PMID: 28369490 DOI: 10.1093/jxb/erx086] [Citation(s) in RCA: 177] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Ammonium is a major inorganic nitrogen source for plants. At low external supplies, ammonium promotes plant growth, while at high external supplies it causes toxicity. Ammonium triggers rapid changes in cytosolic pH, in gene expression, and in post-translational modifications of proteins, leading to apoplastic acidification, co-ordinated ammonium uptake, enhanced ammonium assimilation, altered oxidative and phytohormonal status, and reshaped root system architecture. Some of these responses are dependent on AMT-type ammonium transporters and are not linked to a nutritional effect, indicating that ammonium is perceived as a signaling molecule by plant cells. This review summarizes current knowledge of ammonium-triggered physiological and morphological responses and highlights existing and putative mechanisms mediating ammonium signaling and sensing events in plants. We put forward the hypothesis that sensing of ammonium takes place at multiple steps along its transport, storage, and assimilation pathways.
Collapse
Affiliation(s)
- Ying Liu
- Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Stadt Seeland, OT Gatersleben, Germany
| | - Nicolaus von Wirén
- Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Stadt Seeland, OT Gatersleben, Germany
| |
Collapse
|
35
|
Central Role of the Trehalose Biosynthesis Pathway in the Pathogenesis of Human Fungal Infections: Opportunities and Challenges for Therapeutic Development. Microbiol Mol Biol Rev 2017; 81:81/2/e00053-16. [PMID: 28298477 DOI: 10.1128/mmbr.00053-16] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Invasive fungal infections cause significant morbidity and mortality in part due to a limited antifungal drug arsenal. One therapeutic challenge faced by clinicians is the significant host toxicity associated with antifungal drugs. Another challenge is the fungistatic mechanism of action of some drugs. Consequently, the identification of fungus-specific drug targets essential for fitness in vivo remains a significant goal of medical mycology research. The trehalose biosynthetic pathway is found in a wide variety of organisms, including human-pathogenic fungi, but not in humans. Genes encoding proteins involved in trehalose biosynthesis are mechanistically linked to the metabolism, cell wall homeostasis, stress responses, and virulence of Candida albicans, Cryptococcus neoformans, and Aspergillus fumigatus. While there are a number of pathways for trehalose production across the tree of life, the TPS/TPP (trehalose-6-phosphate synthase/trehalose-6-phosphate phosphatase) pathway is the canonical pathway found in human-pathogenic fungi. Importantly, data suggest that proteins involved in trehalose biosynthesis play other critical roles in fungal metabolism and in vivo fitness that remain to be fully elucidated. By further defining the biology and functions of trehalose and its biosynthetic pathway components in pathogenic fungi, an opportunity exists to leverage this pathway as a potent antifungal drug target. The goal of this review is to cover the known roles of this important molecule and its associated biosynthesis-encoding genes in the human-pathogenic fungi studied to date and to employ these data to critically assess the opportunities and challenges facing development of this pathway as a therapeutic target.
Collapse
|
36
|
Schothorst J, Zeebroeck GV, Thevelein JM. Identification of Ftr1 and Zrt1 as iron and zinc micronutrient transceptors for activation of the PKA pathway in Saccharomyces cerevisiae. MICROBIAL CELL 2017; 4:74-89. [PMID: 28357393 PMCID: PMC5349193 DOI: 10.15698/mic2017.03.561] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Multiple types of nutrient transceptors, membrane proteins that combine a
transporter and receptor function, have now been established in a variety of
organisms. However, so far all established transceptors utilize one of the
macronutrients, glucose, amino acids, ammonium, nitrate, phosphate or sulfate,
as substrate. This is also true for the Saccharomyces
cerevisiae transceptors mediating activation of the PKA pathway
upon re-addition of a macronutrient to glucose-repressed cells starved for that
nutrient, re-establishing a fermentable growth medium. We now show that the
yeast high-affinity iron transporter Ftr1 and high-affinity zinc transporter
Zrt1 function as transceptors for the micronutrients iron and zinc.
We show that replenishment of iron to iron-starved cells or zinc to
zinc-starved cells triggers within 1-2 minutes a rapid surge in trehalase
activity, a well-established PKA target. The activation with iron is dependent
on Ftr1 and with zinc on Zrt1, and we show that it is independent of
intracellular iron and zinc levels. Similar to the transceptors for
macronutrients, Ftr1 and Zrt1 are strongly induced upon iron and zinc
starvation, respectively, and they are rapidly downregulated by
substrate-induced endocytosis. Our results suggest that transceptor-mediated
signaling to the PKA pathway may occur in all cases where glucose-repressed
yeast cells have been starved first for an essential nutrient, causing arrest of
growth and low activity of the PKA pathway, and subsequently replenished with
the lacking nutrient to re-establish a fermentable growth medium. The broadness
of the phenomenon also makes it likely that nutrient transceptors use a common
mechanism for signaling to the PKA pathway.
Collapse
Affiliation(s)
- Joep Schothorst
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium. ; Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Griet V Zeebroeck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium. ; Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium. ; Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| |
Collapse
|
37
|
Nakagawa Y, Ogihara H, Mochizuki C, Yamamura H, Iimura Y, Hayakawa M. Development of intra-strain self-cloning procedure for breeding baker's yeast strains. J Biosci Bioeng 2017; 123:319-326. [DOI: 10.1016/j.jbiosc.2016.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/09/2016] [Accepted: 10/12/2016] [Indexed: 10/20/2022]
|
38
|
Kumar R. An account of fungal 14-3-3 proteins. Eur J Cell Biol 2017; 96:206-217. [PMID: 28258766 DOI: 10.1016/j.ejcb.2017.02.006] [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: 02/12/2017] [Revised: 02/21/2017] [Accepted: 02/21/2017] [Indexed: 01/09/2023] Open
Abstract
14-3-3s are a group of relatively low molecular weight, acidic, dimeric, protein(s) conserved from single-celled yeast to multicellular vertebrates including humans. Despite lacking catalytic activity, these proteins have been shown to be involved in multiple cellular processes. Apart from their role in normal cellular physiology, recently these proteins have been implicated in various medical consequences. In this present review, fungal 14-3-3 protein localization, interactions, transcription, regulation, their role in the diverse cellular process including DNA duplication, cell cycle, protein trafficking or secretion, apoptosis, autophagy, cell viability under stress, gene expression, spindle positioning, role in carbon metabolism have been discussed. In the end, I also highlighted various roles of yeasts 14-3-3 proteins in tabular form. Thus this review with primary emphasis on yeast will help in appreciating the significance of 14-3-3 proteins in cell physiology.
Collapse
Affiliation(s)
- Ravinder Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, Maharashtra, India.
| |
Collapse
|
39
|
Function and Regulation of Fungal Amino Acid Transporters: Insights from Predicted Structure. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 892:69-106. [PMID: 26721271 DOI: 10.1007/978-3-319-25304-6_4] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Amino acids constitute a major nutritional source for probably all fungi. Studies of model species such as the yeast Saccharomyces cerevisiae and the filamentous fungus Aspergillus nidulans have shown that they possess multiple amino acid transporters. These proteins belong to a limited number of superfamilies, now defined according to protein fold in addition to sequence criteria, and differ in subcellular location, substrate specificity range, and regulation. Structural models of several of these transporters have recently been built, and the detailed molecular mechanisms of amino acid recognition and translocation are now being unveiled. Furthermore, the particular conformations adopted by some of these transporters in response to amino acid binding appear crucial to promoting their ubiquitin-dependent endocytosis and/or to triggering signaling responses. We here summarize current knowledge, derived mainly from studies on S. cerevisiae and A. nidulans, about the transport activities, regulation, and sensing role of fungal amino acid transporters, in relation to predicted structure.
Collapse
|
40
|
Cytoplasmic mRNA turnover and ageing. Mech Ageing Dev 2015; 152:32-42. [PMID: 26432921 PMCID: PMC4710634 DOI: 10.1016/j.mad.2015.09.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 09/17/2015] [Accepted: 09/27/2015] [Indexed: 12/12/2022]
Abstract
We address the cytoplasmic mRNA decay processes that determine the mRNAs half-life. We briefly describe the major, evolutionary conserved, ageing pathways and mechanisms. We summarize critical findings that link mRNA turnover and ageing modulators.
Messenger RNA (mRNA) turnover that determines the lifetime of cytoplasmic mRNAs is a means to control gene expression under both normal and stress conditions, whereas its impact on ageing and age-related disorders has just become evident. Gene expression control is achieved at the level of the mRNA clearance as well as mRNA stability and accessibility to other molecules. All these processes are regulated by cis-acting motifs and trans-acting factors that determine the rates of translation and degradation of transcripts. Specific messenger RNA granules that harbor the mRNA decay machinery or various factors, involved in translational repression and transient storage of mRNAs, are also part of the mRNA fate regulation. Their assembly and function can be modulated to promote stress resistance to adverse conditions and over time affect the ageing process and the lifespan of the organism. Here, we provide insights into the complex relationships of ageing modulators and mRNA turnover mechanisms.
Collapse
|
41
|
Kankipati HN, Rubio-Texeira M, Castermans D, Diallinas G, Thevelein JM. Sul1 and Sul2 sulfate transceptors signal to protein kinase A upon exit of sulfur starvation. J Biol Chem 2015; 290:10430-46. [PMID: 25724649 PMCID: PMC4400352 DOI: 10.1074/jbc.m114.629022] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Indexed: 11/24/2022] Open
Abstract
Sulfate is an essential nutrient with pronounced regulatory effects on cellular metabolism and proliferation. Little is known, however, about how sulfate is sensed by cells. Sul1 and Sul2 are sulfate transporters in the yeast Saccharomyces cerevisiae, strongly induced upon sulfur starvation and endocytosed upon the addition of sulfate. We reveal Sul1,2-dependent activation of PKA targets upon sulfate-induced exit from growth arrest after sulfur starvation. We provide two major arguments in favor of Sul1 and Sul2 acting as transceptors for signaling to PKA. First, the sulfate analogue, d-glucosamine 2-sulfate, acted as a non-transported agonist of signaling by Sul1 and Sul2. Second, mutagenesis to Gln of putative H+-binding residues, Glu-427 in Sul1 or Glu-443 in Sul2, abolished transport without affecting signaling. Hence, Sul1,2 can function as pure sulfate sensors. Sul1E427Q and Sul2E443Q are also deficient in sulfate-induced endocytosis, which can therefore be uncoupled from signaling. Overall, our data suggest that transceptors can undergo independent conformational changes, each responsible for triggering different downstream processes. The Sul1 and Sul2 transceptors are the first identified plasma membrane sensors for extracellular sulfate. High affinity transporters induced upon starvation for their substrate may generally act as transceptors during exit from starvation.
Collapse
Affiliation(s)
- Harish Nag Kankipati
- From the Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium, the Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium, and
| | - Marta Rubio-Texeira
- From the Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium, the Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium, and
| | - Dries Castermans
- From the Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium, the Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium, and
| | - George Diallinas
- the Faculty of Biology, University of Athens, Panepistimioupolis, Athens 15784, Greece
| | - Johan M Thevelein
- From the Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium, the Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium, and
| |
Collapse
|
42
|
Gao J, van Kleeff PJM, Oecking C, Li KW, Erban A, Kopka J, Hincha DK, de Boer AH. Light modulated activity of root alkaline/neutral invertase involves the interaction with 14-3-3 proteins. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:785-96. [PMID: 25256212 DOI: 10.1111/tpj.12677] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 09/04/2014] [Accepted: 09/10/2014] [Indexed: 05/17/2023]
Abstract
Alkaline/neutral invertases (A/N-Invs) are now recognized as essential proteins in plant life. They catalyze the irreversible breakdown of sucrose into glucose and fructose and thus supply the cells with energy as well as signaling molecules. In this study we report on a mechanism that affects the activity of the cytosolic invertase AtCINV1 (At-A/N-InvG or AT1G35580). We demonstrate that Ser547 at the extreme C-terminus of the AtCINV1 protein is a substrate of calcium-dependent kinases (CPK3 and 21) and that phosphorylation creates a high-affinity binding site for 14-3-3 proteins. The invertase as such has basal activity, but we provide evidence that interaction with 14-3-3 proteins enhances its activity. The analysis of three quadruple 14-3-3 mutants generated from six T-DNA insertion mutants of the non-epsilon family shows both specificity as well as redundancy for this function of 14-3-3 proteins. The strong reduction in hexose levels in the roots of one 14-3-3 quadruple mutant plant is in line with the activating function of 14-3-3 proteins. The physiological relevance of this mechanism that affects A/N-invertase activity is underscored by the light-induced activation and is another example of the central role of 14-3-3 proteins in mediating dark/light signaling. The nature of the light-induced signal that travels from the shoot to root and the question whether this signal is transmitted via cytosolic Ca(++) changes that activate calcium-dependent kinases, await further study.
Collapse
Affiliation(s)
- Jing Gao
- Department of Structural Biology, Faculty of Earth and Life Sciences, Vrije Universiteit, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
43
|
Obsilova V, Kopecka M, Kosek D, Kacirova M, Kylarova S, Rezabkova L, Obsil T. Mechanisms of the 14-3-3 protein function: regulation of protein function through conformational modulation. Physiol Res 2014; 63:S155-64. [PMID: 24564655 DOI: 10.33549/physiolres.932659] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Many aspects of protein function regulation require specific protein-protein interactions to carry out the exact biochemical and cellular functions. The highly conserved members of the 14-3-3 protein family mediate such interactions and through binding to hundreds of other proteins provide multitude of regulatory functions, thus playing key roles in many cellular processes. The 14-3-3 protein binding can affect the function of the target protein in many ways including the modulation of its enzyme activity, its subcellular localization, its structure and stability, or its molecular interactions. In this minireview, we focus on mechanisms of the 14-3-3 protein-dependent regulation of three important 14-3-3 binding partners: yeast neutral trehalase Nth1, regulator of G-protein signaling 3 (RGS3), and phosducin.
Collapse
Affiliation(s)
- V Obsilova
- Department of Protein Structure, Institute of Physiology Academy of Sciences of the Czech Republic, Prague, Czech Republic. and
| | | | | | | | | | | | | |
Collapse
|
44
|
Eleutherio E, Panek A, De Mesquita JF, Trevisol E, Magalhães R. Revisiting yeast trehalose metabolism. Curr Genet 2014; 61:263-74. [DOI: 10.1007/s00294-014-0450-1] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 08/21/2014] [Accepted: 08/26/2014] [Indexed: 12/16/2022]
|
45
|
Van Zeebroeck G, Rubio-Texeira M, Schothorst J, Thevelein JM. Specific analogues uncouple transport, signalling, oligo-ubiquitination and endocytosis in the yeast Gap1 amino acid transceptor. Mol Microbiol 2014; 93:213-33. [PMID: 24852066 PMCID: PMC4285233 DOI: 10.1111/mmi.12654] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2014] [Indexed: 12/14/2022]
Abstract
The Saccharomyces cerevisiae amino acid transceptor Gap1 functions as receptor for signalling to the PKA pathway and concomitantly undergoes substrate-induced oligo-ubiquitination and endocytosis. We have identified specific amino acids and analogues that uncouple to certain extent signalling, transport, oligo-ubiquitination and endocytosis. l-lysine, l-histidine and l-tryptophan are transported by Gap1 but do not trigger signalling. Unlike l-histidine, l-lysine triggers Gap1 oligo-ubiquitination without substantial induction of endocytosis. Two transported, non-metabolizable signalling agonists, β-alanine and d-histidine, are strong and weak inducers of Gap1 endocytosis, respectively, but both causing Gap1 oligo-ubiquitination. The non-signalling agonist, non-transported competitive inhibitor of Gap1 transport, l-Asp-γ-l-Phe, induces oligo-ubiquitination but no discernible endocytosis. The Km of l-citrulline transport is much lower than the threshold concentration for signalling and endocytosis. These results show that molecules can be transported without triggering signalling or substantial endocytosis, and that oligo-ubiquitination and endocytosis do not require signalling nor metabolism. Oligo-ubiquitination is required, but apparently not sufficient to trigger endocytosis. In addition, we demonstrate intracellular cross-induction of endocytosis of transport-defective Gap1Y395C by ubiquitination- and endocytosis-deficient Gap1K9R,K16R. Our results support the concept that different substrates bind to partially overlapping binding sites in the same general substrate-binding pocket of Gap1, triggering divergent conformations, resulting in different conformation-induced downstream processes.
Collapse
Affiliation(s)
- Griet Van Zeebroeck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium; Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Leuven-Heverlee, Flanders, B-3001, Belgium
| | | | | | | |
Collapse
|
46
|
Kopecka M, Kosek D, Kukacka Z, Rezabkova L, Man P, Novak P, Obsil T, Obsilova V. Role of the EF-hand-like motif in the 14-3-3 protein-mediated activation of yeast neutral trehalase Nth1. J Biol Chem 2014; 289:13948-61. [PMID: 24713696 PMCID: PMC4022866 DOI: 10.1074/jbc.m113.544551] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 03/20/2014] [Indexed: 01/18/2023] Open
Abstract
Trehalases hydrolyze the non-reducing disaccharide trehalose amassed by cells as a universal protectant and storage carbohydrate. Recently, it has been shown that the activity of neutral trehalase Nth1 from Saccharomyces cerevisiae is mediated by the 14-3-3 protein binding that modulates the structure of both the catalytic domain and the region containing the EF-hand-like motif, whose role in the activation of Nth1 is unclear. In this work, the structure of the Nth1·14-3-3 complex and the importance of the EF-hand-like motif were investigated using site-directed mutagenesis, hydrogen/deuterium exchange coupled to mass spectrometry, chemical cross-linking, and small angle x-ray scattering. The low resolution structural views of Nth1 alone and the Nth1·14-3-3 complex show that the 14-3-3 protein binding induces a significant structural rearrangement of the whole Nth1 molecule. The EF-hand-like motif-containing region forms a separate domain that interacts with both the 14-3-3 protein and the catalytic trehalase domain. The structural integrity of the EF-hand like motif is essential for the 14-3-3 protein-mediated activation of Nth1, and calcium binding, although not required for the activation, facilitates this process by affecting its structure. Our data suggest that the EF-hand like motif-containing domain functions as the intermediary through which the 14-3-3 protein modulates the function of the catalytic domain of Nth1.
Collapse
Affiliation(s)
- Miroslava Kopecka
- From the Institute of Physiology and the Second Faculty of Medicine, Charles University, V Uvalu 84, 150 06 Prague, Czech Republic, and
| | - Dalibor Kosek
- From the Institute of Physiology and the Departments of Physical and Macromolecular Chemistry and
| | - Zdenek Kukacka
- the Institute of Microbiology, Academy of Sciences of the Czech Republic v.v.i., Videnska 1083, 14220 Prague, Czech Republic, Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12843 Prague, Czech Republic
| | - Lenka Rezabkova
- From the Institute of Physiology and the Departments of Physical and Macromolecular Chemistry and
| | - Petr Man
- the Institute of Microbiology, Academy of Sciences of the Czech Republic v.v.i., Videnska 1083, 14220 Prague, Czech Republic, Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12843 Prague, Czech Republic
| | - Petr Novak
- the Institute of Microbiology, Academy of Sciences of the Czech Republic v.v.i., Videnska 1083, 14220 Prague, Czech Republic, Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12843 Prague, Czech Republic
| | - Tomas Obsil
- From the Institute of Physiology and the Departments of Physical and Macromolecular Chemistry and
| | | |
Collapse
|
47
|
Milac AL, Bojarska E, Wypijewska del Nogal A. Decapping Scavenger (DcpS) enzyme: advances in its structure, activity and roles in the cap-dependent mRNA metabolism. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:452-62. [PMID: 24742626 DOI: 10.1016/j.bbagrm.2014.04.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 04/07/2014] [Accepted: 04/08/2014] [Indexed: 01/27/2023]
Abstract
Decapping Scavenger (DcpS) enzyme rids eukaryotic cells of short mRNA fragments containing the 5' mRNA cap structure, which appear in the 3'→5' mRNA decay pathway, following deadenylation and exosome-mediated turnover. The unique structural properties of the cap, which consists of 7-methylguanosine attached to the first transcribed nucleoside by a triphosphate chain (m(7)GpppN), guarantee its resistance to non-specific exonucleases. DcpS enzymes are dimers belonging to the Histidine Triad (HIT) superfamily of pyrophosphatases. The specific hydrolysis of m(7)GpppN by DcpS yields m(7)GMP and NDP. By precluding inhibition of other cap-binding proteins by short m(7)GpppN-containing mRNA fragments, DcpS plays an important role in the cap-dependent mRNA metabolism. Over the past decade, lots of new structural, biochemical and biophysical data on DcpS has accumulated. We attempt to integrate these results, referring to DcpS enzymes from different species. Such a synergistic characteristic of the DcpS structure and activity might be useful for better understanding of the DcpS catalytic mechanism, its regulatory role in gene expression, as well as for designing DcpS inhibitors of potential therapeutic application, e.g. in spinal muscular atrophy.
Collapse
Affiliation(s)
- Adina L Milac
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy (IBAR), Splaiul Independentei 296, 060031, Bucharest 17, Romania
| | - Elzbieta Bojarska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki & Wigury 93, 02-089 Warsaw, Poland.
| | - Anna Wypijewska del Nogal
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki & Wigury 93, 02-089 Warsaw, Poland.
| |
Collapse
|
48
|
Conrad M, Schothorst J, Kankipati HN, Van Zeebroeck G, Rubio-Texeira M, Thevelein JM. Nutrient sensing and signaling in the yeast Saccharomyces cerevisiae. FEMS Microbiol Rev 2014; 38:254-99. [PMID: 24483210 PMCID: PMC4238866 DOI: 10.1111/1574-6976.12065] [Citation(s) in RCA: 419] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 12/23/2013] [Accepted: 01/22/2014] [Indexed: 02/04/2023] Open
Abstract
The yeast Saccharomyces cerevisiae has been a favorite organism for pioneering studies on nutrient-sensing and signaling mechanisms. Many specific nutrient responses have been elucidated in great detail. This has led to important new concepts and insight into nutrient-controlled cellular regulation. Major highlights include the central role of the Snf1 protein kinase in the glucose repression pathway, galactose induction, the discovery of a G-protein-coupled receptor system, and role of Ras in glucose-induced cAMP signaling, the role of the protein synthesis initiation machinery in general control of nitrogen metabolism, the cyclin-controlled protein kinase Pho85 in phosphate regulation, nitrogen catabolite repression and the nitrogen-sensing target of rapamycin pathway, and the discovery of transporter-like proteins acting as nutrient sensors. In addition, a number of cellular targets, like carbohydrate stores, stress tolerance, and ribosomal gene expression, are controlled by the presence of multiple nutrients. The protein kinase A signaling pathway plays a major role in this general nutrient response. It has led to the discovery of nutrient transceptors (transporter receptors) as nutrient sensors. Major shortcomings in our knowledge are the relationship between rapid and steady-state nutrient signaling, the role of metabolic intermediates in intracellular nutrient sensing, and the identity of the nutrient sensors controlling cellular growth.
Collapse
Affiliation(s)
- Michaela Conrad
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| | - Joep Schothorst
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| | - Harish Nag Kankipati
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| | - Griet Van Zeebroeck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| | - Marta Rubio-Texeira
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| |
Collapse
|
49
|
Yeast nutrient transceptors provide novel insight in the functionality of membrane transporters. Curr Genet 2013; 59:197-206. [PMID: 24114446 PMCID: PMC3824880 DOI: 10.1007/s00294-013-0413-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 09/17/2013] [Accepted: 09/30/2013] [Indexed: 11/21/2022]
Abstract
In the yeast Saccharomyces cerevisiae several nutrient transporters have been identified that possess an additional function as nutrient receptor. These transporters are induced when yeast cells are starved for their substrate, which triggers entry into stationary phase and acquirement of a low protein kinase A (PKA) phenotype. Re-addition of the lacking nutrient triggers exit from stationary phase and sudden activation of the PKA pathway, the latter being mediated by the nutrient transceptors. At the same time, the transceptors are ubiquitinated, endocytosed and sorted to the vacuole for breakdown. Investigation of the signaling function of the transceptors has provided a new read-out and new tools for gaining insight into the functionality of transporters. Identification of amino acid residues that bind co-transported ions in symporters has been challenging because the inactivation of transport by site-directed mutagenesis is not conclusive with respect to the cause of the inactivation. The discovery of nontransported agonists of the signaling function in transceptors has shown that transport is not required for signaling. Inactivation of transport with maintenance of signaling in transceptors supports that a true proton-binding residue was mutagenised. Determining the relationship between transport and induction of endocytosis has also been challenging, since inactivation of transport by mutagenesis easily causes loss of all affinity for the substrate. The use of analogues with different combinations of transport and signaling capacities has revealed that transport, ubiquitination and endocytosis can be uncoupled in several unexpected ways. The results obtained are consistent with transporters undergoing multiple substrate-induced conformational changes, which allow interaction with different accessory proteins to trigger specific downstream events.
Collapse
|
50
|
Macakova E, Kopecka M, Kukacka Z, Veisova D, Novak P, Man P, Obsil T, Obsilova V. Structural basis of the 14-3-3 protein-dependent activation of yeast neutral trehalase Nth1. Biochim Biophys Acta Gen Subj 2013; 1830:4491-9. [DOI: 10.1016/j.bbagen.2013.05.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 05/08/2013] [Accepted: 05/20/2013] [Indexed: 10/26/2022]
|