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Yu X, Li S. Specific regulation of epigenome landscape by metabolic enzymes and metabolites. Biol Rev Camb Philos Soc 2024; 99:878-900. [PMID: 38174803 DOI: 10.1111/brv.13049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
Metabolism includes anabolism and catabolism, which play an essential role in many biological processes. Chromatin modifications are post-translational modifications of histones and nucleic acids that play important roles in regulating chromatin-associated processes such as gene transcription. There is a tight connection between metabolism and chromatin modifications. Many metabolic enzymes and metabolites coordinate cellular activities with alterations in nutrient availability by regulating gene expression through epigenetic mechanisms such as DNA methylation and histone modifications. The dysregulation of gene expression by metabolism and epigenetic modifications may lead to diseases such as diabetes and cancer. Recent studies reveal that metabolic enzymes and metabolites specifically regulate chromatin modifications, including modification types, modification residues and chromatin regions. This specific regulation has been implicated in the development of human diseases, yet the underlying mechanisms are only beginning to be uncovered. In this review, we summarise recent studies of the molecular mechanisms underlying the metabolic regulation of histone and DNA modifications and discuss how they contribute to pathogenesis. We also describe recent developments in technologies used to address the key questions in this field. We hope this will inspire further in-depth investigations of the specific regulatory mechanisms involved, and most importantly will shed lights on the development of more effective disease therapies.
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Affiliation(s)
- Xilan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Shanshan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
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2
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Ma L, Ma J, Tian Y, Li X, Tai B, Xing F. Fus3 Interacts with Gal83, Revealing the MAPK Crosstalk to Snf1/AMPK to Regulate Secondary Metabolic Substrates in Aspergillus flavus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10065-10075. [PMID: 38634532 DOI: 10.1021/acs.jafc.4c01229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Aflatoxins (AFs), highly carcinogenic natural products, are produced by the secondary metabolism of fungi such as Aspergillus flavus. Essential for the fungi to respond to environmental changes and aflatoxin synthesis, the pheromone mitogen-activated protein kinase (MAPK) is a potential regulator of aflatoxin biosynthesis. However, the mechanism by which pheromone MAPK regulates aflatoxin biosynthesis is not clear. Here, we showed Gal83, a new target of Fus3, and identified the pheromone Fus3-MAPK signaling pathway as a regulator of the Snf1/AMPK energy-sensing pathway modulating aflatoxins synthesis substrates. The screening for Fus3 target proteins identified the β subunit of Snf1/AMPK complexes using tandem affinity purification and multiomics. This subunit physically interacted with Fus3 both in vivo and in vitro and received phosphorylation from Fus3. Although the transcript levels of aflatoxin synthesis genes were not noticeably downregulated in both gal83 and fus3 deletion mutant strains, the levels of aflatoxin B1 and its synthesis substrates and gene expression levels of primary metabolizing enzymes were significantly reduced. This suggests that both the Fus3-MAPK and Snf1/AMPK pathways respond to energy signals. In conclusion, all the evidence unlocks a novel pathway of Fus3-MAPK to regulate AFs synthesis substrates by cross-talking with the Snf1/AMPK complexes.
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Affiliation(s)
- Longxue Ma
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences / Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
| | - Junning Ma
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences / Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
| | - Yuanyuan Tian
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences / Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
| | - Xu Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences / Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
| | - Bowen Tai
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences / Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
| | - Fuguo Xing
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences / Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
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3
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Williams TD, Rousseau A. Translation regulation in response to stress. FEBS J 2024. [PMID: 38308808 DOI: 10.1111/febs.17076] [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: 11/09/2023] [Revised: 12/07/2023] [Accepted: 01/22/2024] [Indexed: 02/05/2024]
Abstract
Cell stresses occur in a wide variety of settings: in disease, during industrial processes, and as part of normal day-to-day rhythms. Adaptation to these stresses requires cells to alter their proteome. Cells modify the proteins they synthesize to aid proteome adaptation. Changes in both mRNA transcription and translation contribute to altered protein synthesis. Here, we discuss the changes in translational mechanisms that occur following the onset of stress, and the impact these have on stress adaptation.
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Affiliation(s)
- Thomas D Williams
- MRC-PPU, School of Life Sciences, University of Dundee, UK
- Sir William Dunn School of Pathology, University of Oxford, UK
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4
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Metur SP, Klionsky DJ. Nutrient-dependent signaling pathways that control autophagy in yeast. FEBS Lett 2024; 598:32-47. [PMID: 37758520 PMCID: PMC10841420 DOI: 10.1002/1873-3468.14741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023]
Abstract
Macroautophagy/autophagy is a highly conserved catabolic process vital for cellular stress responses and maintaining equilibrium within the cell. Malfunctioning autophagy has been implicated in the pathogenesis of various diseases, including certain neurodegenerative disorders, diabetes, metabolic diseases, and cancer. Cells face diverse metabolic challenges, such as limitations in nitrogen, carbon, and minerals such as phosphate and iron, necessitating the integration of complex metabolic information. Cells utilize a signal transduction network of sensors, transducers, and effectors to coordinate the execution of the autophagic response, concomitant with the severity of the nutrient-starvation condition. This review presents the current mechanistic understanding of how cells regulate the initiation of autophagy through various nutrient-dependent signaling pathways. Emphasizing findings from studies in yeast, we explore the emerging principles that underlie the nutrient-dependent regulation of autophagy, significantly shaping stress-induced autophagy responses under various metabolic stress conditions.
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Affiliation(s)
- Shree Padma Metur
- Department of Molecular, Cellular and Developmental Biology, Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Daniel J Klionsky
- Department of Molecular, Cellular and Developmental Biology, Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
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5
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Nguyen V, Xue P, Li Y, Zhao H, Lu T. Controlling circuitry underlies the growth optimization of Saccharomyces cerevisiae. Metab Eng 2023; 80:173-183. [PMID: 37739159 PMCID: PMC11089650 DOI: 10.1016/j.ymben.2023.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 08/29/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
Microbial growth emerges from coordinated synthesis of various cellular components from limited resources. In Saccharomyces cerevisiae, cyclic AMP (cAMP)-mediated signaling is shown to orchestrate cellular metabolism; however, it remains unclear quantitatively how the controlling circuit drives resource partition and subsequently shapes biomass growth. Here we combined experiment with mathematical modeling to dissect the signaling-mediated growth optimization of S. cerevisiae. We showed that, through cAMP-mediated control, the organism achieves maximal or nearly maximal steady-state growth during the utilization of multiple tested substrates as well as under perturbations impairing glucose uptake. However, the optimal cAMP concentration varies across cases, suggesting that different modes of resource allocation are adopted for varied conditions. Under settings with nutrient alterations, S. cerevisiae tunes its cAMP level to dynamically reprogram itself to realize rapid adaptation. Moreover, to achieve growth maximization, cells employ additional regulatory systems such as the GCN2-mediated amino acid control. This study establishes a systematic understanding of global resource allocation in S. cerevisiae, providing insights into quantitative yeast physiology as well as metabolic strain engineering for biotechnological applications.
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Affiliation(s)
- Viviana Nguyen
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Pu Xue
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Carl R Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yifei Li
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Huimin Zhao
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Carl R Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Ting Lu
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Carl R Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; National Center for Supercomputing Applications, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
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6
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Wang Y, Li R, Wang D, Qian B, Bian Z, Wei J, Wei X, Xu JR. Regulation of symbiotic interactions and primitive lichen differentiation by UMP1 MAP kinase in Umbilicaria muhlenbergii. Nat Commun 2023; 14:6972. [PMID: 37914724 PMCID: PMC10620189 DOI: 10.1038/s41467-023-42675-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/17/2023] [Indexed: 11/03/2023] Open
Abstract
Lichens are of great ecological importance but mechanisms regulating lichen symbiosis are not clear. Umbilicaria muhlenbergii is a lichen-forming fungus amenable to molecular manipulations and dimorphic. Here, we established conditions conducive to symbiotic interactions and lichen differentiation and showed the importance of UMP1 MAP kinase in lichen development. In the initial biofilm-like symbiotic complexes, algal cells were interwoven with pseudohyphae covered with extracellular matrix. After longer incubation, fungal-algal complexes further differentiated into primitive lichen thalli with a melanized cortex-like and pseudoparenchyma-like tissues containing photoactive algal cells. Mutants deleted of UMP1 were blocked in pseudohyphal growth and development of biofilm-like complexes and primitive lichens. Invasion of dividing mother cells that contributes to algal layer organization in lichens was not observed in the ump1 mutant. Overall, these results showed regulatory roles of UMP1 in symbiotic interactions and lichen development and suitability of U. muhlenbergii as a model for studying lichen symbiosis.
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Affiliation(s)
- Yanyan Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Dept. of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Rong Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Diwen Wang
- Dept. of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Ben Qian
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhuyun Bian
- Dept. of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Jiangchun Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xinli Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jin-Rong Xu
- Dept. of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA.
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7
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Nagy L, Vonk P, Künzler M, Földi C, Virágh M, Ohm R, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu X, Nan S, Pareek M, Sahu N, Szathmári B, Varga T, Wu H, Yang X, Merényi Z. Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Stud Mycol 2023; 104:1-85. [PMID: 37351542 PMCID: PMC10282164 DOI: 10.3114/sim.2022.104.01] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/02/2022] [Indexed: 01/09/2024] Open
Abstract
Fruiting bodies (sporocarps, sporophores or basidiomata) of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates their growth, tissue differentiation and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is still limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim at a comprehensive identification of conserved genes related to fruiting body morphogenesis and distil novel functional hypotheses for functionally poorly characterised ones. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported to be involved in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defence, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1 480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10 % of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Citation: Nagy LG, Vonk PJ, Künzler M, Földi C, Virágh M, Ohm RA, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu XB, Nan S, M. Pareek M, Sahu N, Szathmári B, Varga T, Wu W, Yang X, Merényi Z (2023). Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Studies in Mycology 104: 1-85. doi: 10.3114/sim.2022.104.01.
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Affiliation(s)
- L.G. Nagy
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - P.J. Vonk
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands;
| | - M. Künzler
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland;
| | - C. Földi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - M. Virágh
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - R.A. Ohm
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands;
| | - F. Hennicke
- Project Group Genetics and Genomics of Fungi, Chair Evolution of Plants and Fungi, Ruhr-University Bochum, 44780, Bochum, North Rhine-Westphalia, Germany;
| | - B. Bálint
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - Á. Csernetics
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - B. Hegedüs
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - Z. Hou
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - X.B. Liu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - S. Nan
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - M. Pareek
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - N. Sahu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - B. Szathmári
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - T. Varga
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - H. Wu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - X. Yang
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Z. Merényi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
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8
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Zhao L, He K, Jiang C, Wang G, Hu S, Wang T, Qian W, Wei Z, Xiong J, Miao W, Yan W. Comparative Genomic and Transcriptomic Profiling Revealed the Molecular Basis of Starch Promoting the Growth and Proliferation of Balantioides coli. Animals (Basel) 2023; 13:ani13101608. [PMID: 37238038 DOI: 10.3390/ani13101608] [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: 03/10/2023] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Carbohydrates are the main source of nutrition for B. coli, supplying energy for cell growth and development. The research aimed at investigating the mechanism of starch on the growth and replication of B. coli. Single-cell separation was used to isolate single trophozoites of B. coli under a stereomicroscope, transcriptomic profiling was conducted based on the SMART-seq2 single-cell RNA-seq method. Comparative genomic analysis was performed on B. coli and eight other ciliates to obtain specific and expanded gene families of B. coli. GO and KEGG enrichment analysis were used to analyze the key genes of B. coli under the action of starch in the present study. The results of single-cell RNA-seq depicts starch affected the growth and replication of B. coli in two ways: (1) the cell cycle was positively promoted by the activation of the cAMP/PKA signaling pathway via glycolysis; (2) the cell autophagy was suppressed through the PI3K/AKT/mTOR pathway. Genes involved in endocytosis, carbohydrate utilization, and the cAMP/PKA signaling pathway were highly enriched in both specific and expanded gene families of B. coli. Starch can be ingested and hydrolyzed into glucose, in turn affecting various biological processes of B. coli. The molecular mechanism of the effect of starch on the growth and proliferation of B. coli by promoting cell cycle and inhibiting the autophagy of trophozoites has been elucidated in our study.
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Affiliation(s)
- Lizhuo Zhao
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Kai He
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
- National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Chuanqi Jiang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Guangying Wang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Suhui Hu
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Tianqi Wang
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Weifeng Qian
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Zhiguo Wei
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wenchao Yan
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
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9
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Lao-Martil D, Schmitz JPJ, Teusink B, van Riel NAW. Elucidating yeast glycolytic dynamics at steady state growth and glucose pulses through kinetic metabolic modeling. Metab Eng 2023; 77:128-142. [PMID: 36963461 DOI: 10.1016/j.ymben.2023.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/12/2023] [Accepted: 03/05/2023] [Indexed: 03/26/2023]
Abstract
Microbial cell factories face changing environments during industrial fermentations. Kinetic metabolic models enable the simulation of the dynamic metabolic response to these perturbations, but their development is challenging due to model complexity and experimental data requirements. An example of this is the well-established microbial cell factory Saccharomyces cerevisiae, for which no consensus kinetic model of central metabolism has been developed and implemented in industry. Here, we aim to bring the academic and industrial communities closer to this consensus model. We developed a physiology informed kinetic model of yeast glycolysis connected to central carbon metabolism by including the effect of anabolic reactions precursors, mitochondria and the trehalose cycle. To parametrize such a large model, a parameter estimation pipeline was developed, consisting of a divide and conquer approach, supplemented with regularization and global optimization. Additionally, we show how this first mechanistic description of a growing yeast cell captures experimental dynamics at different growth rates and under a strong glucose perturbation, is robust to parametric uncertainty and explains the contribution of the different pathways in the network. Such a comprehensive model could not have been developed without using steady state and glucose perturbation data sets. The resulting metabolic reconstruction and parameter estimation pipeline can be applied in the future to study other industrially-relevant scenarios. We show this by generating a hybrid CFD-metabolic model to explore intracellular glycolytic dynamics for the first time. The model suggests that all intracellular metabolites oscillate within a physiological range, except carbon storage metabolism, which is sensitive to the extracellular environment.
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Affiliation(s)
- David Lao-Martil
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Noord-Brabant, 5612AE, the Netherlands
| | - Joep P J Schmitz
- DSM Biotechnology Center, Delft, Zuid-Holland, 2613AX, the Netherlands
| | - Bas Teusink
- Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, Noord-Holland, 1081HZ, the Netherlands
| | - Natal A W van Riel
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Noord-Brabant, 5612AE, the Netherlands; Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Noord-Holland, 1105AZ, the Netherlands.
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10
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Phosphorylation of Jhd2 by the Ras-cAMP-PKA(Tpk2) pathway regulates histone modifications and autophagy. Nat Commun 2022; 13:5675. [PMID: 36167807 PMCID: PMC9515143 DOI: 10.1038/s41467-022-33423-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/16/2022] [Indexed: 11/12/2022] Open
Abstract
Cells need to coordinate gene expression with their metabolic states to maintain cell homeostasis and growth. How cells transduce nutrient availability to appropriate gene expression remains poorly understood. Here we show that glycolysis regulates histone modifications and gene expression by activating protein kinase A (PKA) via the Ras-cyclic AMP pathway. The catalytic subunit of PKA, Tpk2 antagonizes Jhd2-catalyzed H3K4 demethylation by phosphorylating Jhd2 at Ser321 and Ser340 in response to glucose availability. Tpk2-catalyzed Jhd2 phosphorylation impairs its nuclear localization, reduces its binding to chromatin, and promotes its polyubiquitination and degradation by the proteasome. Tpk2-catalyzed Jhd2 phosphorylation also maintains H3K14 acetylation by preventing the binding of histone deacetylase Rpd3 to chromatin. By phosphorylating Jhd2, Tpk2 regulates gene expression, maintains normal chronological life span and promotes autophagy. These results provide a direct connection between metabolism and histone modifications and shed lights on how cells rewire their biological responses to nutrient signals. How cells transduce nutrient availability to appropriate gene expression remains poorly understood. Here the authors show that the nutrient sensor, protein kinase A modulates histone modifications and gene transcription by phosphorylating histone demethylase.
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11
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Nekrakalaya B, Arefian M, Kotimoole CN, Krishna RM, Palliyath GK, Najar MA, Behera SK, Kasaragod S, Santhappan P, Hegde V, Prasad TSK. Towards Phytopathogen Diagnostics? Coconut Bud Rot Pathogen Phytophthora palmivora Mycelial Proteome Analysis Informs Genome Annotation. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:189-203. [PMID: 35353641 DOI: 10.1089/omi.2021.0208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Planetary agriculture stands to benefit immensely from phytopathogen diagnostics, which would enable early detection of pathogens with harmful effects on crops. For example, Phytophthora palmivora is one of the most destructive phytopathogens affecting many economically important tropical crops such as coconut. P. palmivora causes diseases in over 200 host plants, and notably, the bud rot disease in coconut and oil palm, which is often lethal because it is usually detected at advanced stages of infection. Limited availability of large-scale omics datasets for P. palmivora is an important barrier for progress toward phytopathogen diagnostics. We report here the mycelial proteome of P. palmivora using high-resolution mass spectrometry analysis. We identified 8073 proteins in the mycelium. Gene Ontology-based functional classification of detected proteins revealed 4884, 4981, and 3044 proteins, respectively, with roles in biological processes, molecular functions, and cellular components. Proteins such as P-loop, NTPase, and WD40 domains with key roles in signal transduction pathways were identified. KEGG pathway analysis annotated 2467 proteins to various signaling pathways, such as phosphatidylinositol, Ca2+, and mitogen-activated protein kinase, and autophagy and cell cycle. These molecular substrates might possess vital roles in filamentous growth, sporangia formation, degradation of damaged cellular content, and recycling of nutrients in P. palmivora. This large-scale proteomics data and analyses pave the way for new insights on biology, genome annotation, and vegetative growth of the important plant pathogen P. palmivora. They also can help accelerate research on future phytopathogen diagnostics and preventive interventions.
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Affiliation(s)
- Bhagya Nekrakalaya
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Mohammad Arefian
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Chinmaya Narayana Kotimoole
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | | | | | - Mohammad Altaf Najar
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Santosh Kumar Behera
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Sandeep Kasaragod
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | | | - Vinayaka Hegde
- ICAR-Central Plantation Crops Research Institute, Kasaragod, India
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12
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Yu PL, Rollins JA. The cAMP-dependent protein kinase A pathway perturbs autophagy and plays important roles in development and virulence of Sclerotinia sclerotiorum. Fungal Biol 2022; 126:20-34. [DOI: 10.1016/j.funbio.2021.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 09/21/2021] [Accepted: 09/29/2021] [Indexed: 01/15/2023]
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13
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Changes in the distribution of fitness effects and adaptive mutational spectra following a single first step towards adaptation. Nat Commun 2021; 12:5193. [PMID: 34465770 PMCID: PMC8408183 DOI: 10.1038/s41467-021-25440-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/11/2021] [Indexed: 01/17/2023] Open
Abstract
Historical contingency and diminishing returns epistasis have been typically studied for relatively divergent genotypes and/or over long evolutionary timescales. Here, we use Saccharomyces cerevisiae to study the extent of diminishing returns and the changes in the adaptive mutational spectra following a single first adaptive mutational step. We further evolve three clones that arose under identical conditions from a common ancestor. We follow their evolutionary dynamics by lineage tracking and determine adaptive outcomes using fitness assays and whole genome sequencing. We find that diminishing returns manifests as smaller fitness gains during the 2nd step of adaptation compared to the 1st step, mainly due to a compressed distribution of fitness effects. We also find that the beneficial mutational spectra for the 2nd adaptive step are contingent on the 1st step, as we see both shared and diverging adaptive strategies. Finally, we find that adaptive loss-of-function mutations, such as nonsense and frameshift mutations, are less common in the second step of adaptation than in the first step. Analyses of both natural and experimental evolution suggest that adaptation depends on the evolutionary past and adaptive potential decreases over time. Here, by tracking yeast adaptation with DNA barcoding, the authors show that such evolutionary phenomena can be observed even after a single adaptive step.
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14
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Casting iron into the cell fate mold. Biochem J 2021; 478:1879-1883. [PMID: 34029365 DOI: 10.1042/bcj20210108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 11/17/2022]
Abstract
This commentary discusses general concepts introduced in the article 'Bulk autophagy induction and life extension is achieved when iron is the only limited nutrient in Saccharomyces cerevisiae' by Montella-Manuel et al. (Biochem J (2021) 478: 811-837). Montella-Manuel et al. show that like central carbon metabolism, iron metabolism is also closely implicated in autophagy-mediated life extension via the TORC2 activator Ypk1p and the iron regulator Aft1p. While not being an iron-sulfur cluster protein, Aft1p interacts with such proteins and thus senses the redox status of the cell, which, similar to amino acids and AMP, reports its energetic status. Furthermore, glucose and iron deficiencies are interrelated as the diauxic shift in glucose depleted cells requires iron uptake for activating respiration in the absence of fermentation.
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15
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Baro Graf C, Ritagliati C, Stival C, Luque GM, Gentile I, Buffone MG, Krapf D. Everything you ever wanted to know about PKA regulation and its involvement in mammalian sperm capacitation. Mol Cell Endocrinol 2020; 518:110992. [PMID: 32853743 DOI: 10.1016/j.mce.2020.110992] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 12/29/2022]
Abstract
The 3', 5'-cyclic adenosine monophosphate (cAMP) dependent protein kinase (PKA) is a tetrameric holoenzyme comprising a set of two regulatory subunits (PKA-R) and two catalytic (PKA-C) subunits. The PKA-R subunits act as sensors of cAMP and allow PKA-C activity. One of the first signaling events observed during mammalian sperm capacitation is PKA activation. Thus, understanding how PKA activity is restricted in space and time is crucial to decipher the critical steps of sperm capacitation. It is widely accepted that PKA specificity depends on several levels of regulation. Anchoring proteins play a pivotal role in achieving proper localization signaling, subcellular targeting and cAMP microdomains. These multi-factorial regulation steps are necessary for a precise spatio-temporal activation of PKA. Here we discuss recent understanding of regulatory mechanisms of PKA in mammalian sperm, such as post-translational modifications, in the context of its role as the master orchestrator of molecular events conducive to capacitation.
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Affiliation(s)
- Carolina Baro Graf
- Laboratory of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario, Argentina; Laboratorio de Medicina Reproductiva (LMR), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Carla Ritagliati
- Laboratory of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario, Argentina
| | - Cintia Stival
- Laboratory of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario, Argentina
| | - Guillermina M Luque
- Laboratory of Cellular and Molecular Reproductive Biology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Buenos Aires, Argentina
| | - Iñaki Gentile
- Laboratory of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario, Argentina
| | - Mariano G Buffone
- Laboratory of Cellular and Molecular Reproductive Biology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Buenos Aires, Argentina
| | - Dario Krapf
- Laboratory of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario, Argentina; Laboratorio de Medicina Reproductiva (LMR), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
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16
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Wang Y, Wei X, Bian Z, Wei J, Xu JR. Coregulation of dimorphism and symbiosis by cyclic AMP signaling in the lichenized fungus Umbilicaria muhlenbergii. Proc Natl Acad Sci U S A 2020; 117:23847-23858. [PMID: 32873646 PMCID: PMC7519320 DOI: 10.1073/pnas.2005109117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Umbilicaria muhlenbergii is the only known dimorphic lichenized fungus that grows in the hyphal form in lichen thalli but as yeast cells in axenic cultures. However, the regulation of yeast-to-hypha transition and its relationship to the establishment of symbiosis are not clear. In this study, we show that nutrient limitation and hyperosmotic stress trigger the dimorphic change in U. muhlenbergii Contact with algal cells of its photobiont Trebouxia jamesii induced pseudohyphal growth. Treatments with the cAMP diphosphoesterase inhibitor IBMX (3-isobutyl-1-methylxanthine) induced pseudohyphal/hyphal growth and resulted in the differentiation of heavily melanized, lichen cortex-like structures in culture, indicating the role of cAMP signaling in regulating dimorphism. To confirm this observation, we identified and characterized two Gα subunits UmGPA2 and UmGPA3 Whereas deletion of UmGPA2 had only a minor effect on pseudohyphal growth, the ΔUmgpa3 mutant was defective in yeast-to-pseudohypha transition induced by hyperosmotic stress or T. jamesii cells. IBMX treatment suppressed the defect of ΔUmgpa3 in pseudohyphal growth. Transformants expressing the UmGPA3G45V or UmGPA3Q208L dominant active allele were enhanced in the yeast-to-pseudohypha transition and developed pseudohyphae under conditions noninducible to the wild type. Interestingly, T. jamesii cells in close contact with pseudohyphae of UmGPA3G45V and UmGPA3Q208L transformants often collapsed and died after coincubation for over 72 h, indicating that improperly regulated pseudohyphal growth due to dominant active mutations may disrupt the initial establishment of symbiotic interaction between the photobiont and mycobiont. Taken together, these results show that the cAMP-PKA pathway plays a critical role in regulating dimorphism and symbiosis in U. muhlenbergii.
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Affiliation(s)
- Yanyan Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Xinli Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Zhuyun Bian
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Jiangchun Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Jin-Rong Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
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17
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Dahiya R, Mohammad T, Alajmi MF, Rehman MT, Hasan GM, Hussain A, Hassan MI. Insights into the Conserved Regulatory Mechanisms of Human and Yeast Aging. Biomolecules 2020; 10:E882. [PMID: 32526825 PMCID: PMC7355435 DOI: 10.3390/biom10060882] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 05/22/2020] [Accepted: 05/27/2020] [Indexed: 12/12/2022] Open
Abstract
Aging represents a significant biological process having strong associations with cancer, diabetes, and neurodegenerative and cardiovascular disorders, which leads to progressive loss of cellular functions and viability. Astonishingly, age-related disorders share several genetic and molecular mechanisms with the normal aging process. Over the last three decades, budding yeast Saccharomyces cerevisiae has emerged as a powerful yet simple model organism for aging research. Genetic approaches using yeast RLS have led to the identification of hundreds of genes impacting lifespan in higher eukaryotes. Numerous interventions to extend yeast lifespan showed an analogous outcome in multi-cellular eukaryotes like fruit flies, nematodes, rodents, and humans. We collected and analyzed a multitude of observations from published literature and provide the contribution of yeast in the understanding of aging hallmarks most applicable to humans. Here, we discuss key pathways and molecular mechanisms that underpin the evolutionarily conserved aging process and summarize the current understanding and clinical applicability of its trajectories. Gathering critical information on aging biology would pave the way for future investigation targeted at the discovery of aging interventions.
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Affiliation(s)
- Rashmi Dahiya
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India;
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India;
| | - Mohamed F. Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.F.A.); (M.T.R.); (A.H.)
| | - Md. Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.F.A.); (M.T.R.); (A.H.)
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj 11942, Saudi Arabia;
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.F.A.); (M.T.R.); (A.H.)
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India;
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18
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Osiro KO, Borgström C, Brink DP, Fjölnisdóttir BL, Gorwa-Grauslund MF. Exploring the xylose paradox in Saccharomyces cerevisiae through in vivo sugar signalomics of targeted deletants. Microb Cell Fact 2019; 18:88. [PMID: 31122246 PMCID: PMC6532234 DOI: 10.1186/s12934-019-1141-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 05/17/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There have been many successful strategies to implement xylose metabolism in Saccharomyces cerevisiae, but no effort has so far enabled xylose utilization at rates comparable to that of glucose (the preferred sugar of this yeast). Many studies have pointed towards the engineered yeast not sensing that xylose is a fermentable carbon source despite growing and fermenting on it, which is paradoxical. We have previously used fluorescent biosensor strains to in vivo monitor the sugar signalome in yeast engineered with xylose reductase and xylitol dehydrogenase (XR/XDH) and have established that S. cerevisiae senses high concentrations of xylose with the same signal as low concentration of glucose, which may explain the poor utilization. RESULTS In the present study, we evaluated the effects of three deletions (ira2∆, isu1∆ and hog1∆) that have recently been shown to display epistatic effects on a xylose isomerase (XI) strain. Through aerobic and anaerobic characterization, we showed that the proposed effects in XI strains were for the most part also applicable in the XR/XDH background. The ira2∆isu1∆ double deletion led to strains with the highest specific xylose consumption- and ethanol production rates but also the lowest biomass titre. The signalling response revealed that ira2∆isu1∆ changed the low glucose-signal in the background strain to a simultaneous signalling of high and low glucose, suggesting that engineering of the signalome can improve xylose utilization. CONCLUSIONS The study was able to correlate the previously proposed beneficial effects of ira2∆, isu1∆ and hog1∆ on S. cerevisiae xylose uptake, with a change in the sugar signalome. This is in line with our previous hypothesis that the key to resolve the xylose paradox lies in the sugar sensing and signalling networks. These results indicate that the future engineering targets for improved xylose utilization should probably be sought not in the metabolic networks, but in the signalling ones.
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Affiliation(s)
- Karen O Osiro
- Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Celina Borgström
- Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Daniel P Brink
- Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
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19
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Martins TS, Costa V, Pereira C. Signaling pathways governing iron homeostasis in budding yeast. Mol Microbiol 2018; 109:422-432. [DOI: 10.1111/mmi.14009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Telma S. Martins
- I3S-Instituto de Investigação e Inovação em Saúde; Universidade do Porto; Porto Portugal
- IBMC-Instituto de Biologia Molecular e Celular; Universidade do Porto; Porto Portugal
| | - Vítor Costa
- I3S-Instituto de Investigação e Inovação em Saúde; Universidade do Porto; Porto Portugal
- IBMC-Instituto de Biologia Molecular e Celular; Universidade do Porto; Porto Portugal
- Departamento de Biologia Molecular; Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto; Porto Portugal
| | - Clara Pereira
- I3S-Instituto de Investigação e Inovação em Saúde; Universidade do Porto; Porto Portugal
- IBMC-Instituto de Biologia Molecular e Celular; Universidade do Porto; Porto Portugal
- Departamento de Biologia Molecular; Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto; Porto Portugal
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20
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Liu Y, Yang F, Li S, Dai J, Deng H. Glutaredoxin Deletion Shortens Chronological Life Span in Saccharomyces cerevisiae via ROS-Mediated Ras/PKA Activation. J Proteome Res 2018; 17:2318-2327. [DOI: 10.1021/acs.jproteome.8b00012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yan Liu
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fan Yang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Siying Li
- Department of Biochemistry, University of California, Davis, Davis, California 95616, United States,
| | - Junbiao Dai
- Center for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Centre for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Centre for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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21
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Shwab EK, Juvvadi PR, Waitt G, Soderblom EJ, Moseley MA, Nicely NI, Steinbach WJ. Phosphorylation of Aspergillus fumigatus PkaR impacts growth and cell wall integrity through novel mechanisms. FEBS Lett 2017; 591:3730-3744. [PMID: 29067690 PMCID: PMC5705279 DOI: 10.1002/1873-3468.12886] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/06/2017] [Accepted: 10/11/2017] [Indexed: 11/06/2022]
Abstract
Protein kinase A (PKA) signaling is essential for growth and virulence of the fungal pathogen Aspergillus fumigatus. Little is known concerning the regulation of this pathway in filamentous fungi. Employing liquid chromatography-tandem mass spectroscopy, we identified novel phosphorylation sites on the regulatory subunit PkaR, distinct from those previously identified in mammals and yeasts, and demonstrated the importance of two phosphorylation clusters for hyphal growth and cell wall-stress response. We also identified key differences in the regulation of PKA subcellular localization in A. fumigatus compared with other species. This is the first analysis of the phosphoregulation of a PKA regulatory subunit in a filamentous fungus and uncovers critical mechanistic differences between PKA regulation in filamentous fungi compared with mammals and yeast species, suggesting divergent targeting opportunities.
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Affiliation(s)
- E. Keats Shwab
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Duke University Medical Center, Durham NC, USA
| | - Praveen R. Juvvadi
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Duke University Medical Center, Durham NC, USA
| | - Greg Waitt
- Duke Proteomics and Metabolomics Core Facility, Center for Genomic and Computational Biology, Duke University, Durham NC, USA
| | - Erik J. Soderblom
- Duke Proteomics and Metabolomics Core Facility, Center for Genomic and Computational Biology, Duke University, Durham NC, USA
| | - M. Arthur Moseley
- Duke Proteomics and Metabolomics Core Facility, Center for Genomic and Computational Biology, Duke University, Durham NC, USA
| | - Nathan I. Nicely
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - William J. Steinbach
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Duke University Medical Center, Durham NC, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham NC, USA
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22
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Umekawa M, Ujihara M, Nakai D, Takematsu H, Wakayama M. Ecm33 is a novel factor involved in efficient glucose uptake for nutrition-responsive TORC1 signaling in yeast. FEBS Lett 2017; 591:3721-3729. [PMID: 29029364 DOI: 10.1002/1873-3468.12882] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/03/2017] [Accepted: 10/05/2017] [Indexed: 11/09/2022]
Abstract
Glucose uptake is crucial for providing both an energy source and a signal that regulates cell proliferation. Therefore, it is important to clarify the mechanisms underlying glucose uptake and its transmission to intracellular signaling pathways. In this study, we searched for a novel regulatory factor involved in glucose-induced signaling by using Saccharomyces cerevisiae as a eukaryotic model. Requirement of the extracellular protein Ecm33 in efficient glucose uptake and full activation of the nutrient-responsive TOR kinase complex 1 (TORC1) signaling pathway is shown. Cells lacking Ecm33 elicit a series of starvation-induced pathways even in the presence of extracellular high glucose concentration. This results in delayed cell proliferation, reduced ATP, induction of autophagy, and dephosphorylation of the TORC1 substrates Atg13 and Sch9.
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Affiliation(s)
| | - Masato Ujihara
- Faculty of Life Sciences, Ritsumeikan University, Kyoto, Shiga, Japan
| | - Daiki Nakai
- Faculty of Life Sciences, Ritsumeikan University, Kyoto, Shiga, Japan
| | | | - Mamoru Wakayama
- Faculty of Life Sciences, Ritsumeikan University, Kyoto, Shiga, Japan
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23
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Nystoriak MA, Nieves-Cintrón M, Patriarchi T, Buonarati OR, Prada MP, Morotti S, Grandi E, Fernandes JDS, Forbush K, Hofmann F, Sasse KC, Scott JD, Ward SM, Hell JW, Navedo MF. Ser1928 phosphorylation by PKA stimulates the L-type Ca2+ channel CaV1.2 and vasoconstriction during acute hyperglycemia and diabetes. Sci Signal 2017; 10:10/463/eaaf9647. [PMID: 28119464 DOI: 10.1126/scisignal.aaf9647] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Hypercontractility of arterial myocytes and enhanced vascular tone during diabetes are, in part, attributed to the effects of increased glucose (hyperglycemia) on L-type CaV1.2 channels. In murine arterial myocytes, kinase-dependent mechanisms mediate the increase in CaV1.2 activity in response to increased extracellular glucose. We identified a subpopulation of the CaV1.2 channel pore-forming subunit (α1C) within nanometer proximity of protein kinase A (PKA) at the sarcolemma of murine and human arterial myocytes. This arrangement depended upon scaffolding of PKA by an A-kinase anchoring protein 150 (AKAP150) in mice. Glucose-mediated increases in CaV1.2 channel activity were associated with PKA activity, leading to α1C phosphorylation at Ser1928 Compared to arteries from low-fat diet (LFD)-fed mice and nondiabetic patients, arteries from high-fat diet (HFD)-fed mice and from diabetic patients had increased Ser1928 phosphorylation and CaV1.2 activity. Arterial myocytes and arteries from mice lacking AKAP150 or expressing mutant AKAP150 unable to bind PKA did not exhibit increased Ser1928 phosphorylation and CaV1.2 current density in response to increased glucose or to HFD. Consistent with a functional role for Ser1928 phosphorylation, arterial myocytes and arteries from knockin mice expressing a CaV1.2 with Ser1928 mutated to alanine (S1928A) lacked glucose-mediated increases in CaV1.2 activity and vasoconstriction. Furthermore, the HFD-induced increases in CaV1.2 current density and myogenic tone were prevented in S1928A knockin mice. These findings reveal an essential role for α1C phosphorylation at Ser1928 in stimulating CaV1.2 channel activity and vasoconstriction by AKAP-targeted PKA upon exposure to increased glucose and in diabetes.
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Affiliation(s)
- Matthew A Nystoriak
- Department of Pharmacology, University of California, Davis, Davis, CA 95616, USA
| | | | - Tommaso Patriarchi
- Department of Pharmacology, University of California, Davis, Davis, CA 95616, USA
| | - Olivia R Buonarati
- Department of Pharmacology, University of California, Davis, Davis, CA 95616, USA
| | - Maria Paz Prada
- Department of Pharmacology, University of California, Davis, Davis, CA 95616, USA
| | - Stefano Morotti
- Department of Pharmacology, University of California, Davis, Davis, CA 95616, USA
| | - Eleonora Grandi
- Department of Pharmacology, University of California, Davis, Davis, CA 95616, USA
| | | | - Katherine Forbush
- Howard Hughes Medical Institute and Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Franz Hofmann
- Department of Pharmacology and Toxicology, Technical University of Munich, Munich D80802, Germany
| | | | - John D Scott
- Howard Hughes Medical Institute and Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Sean M Ward
- Department of Physiology and Cell Biology, University of Nevada, Reno, NV 89557, USA
| | - Johannes W Hell
- Department of Pharmacology, University of California, Davis, Davis, CA 95616, USA
| | - Manuel F Navedo
- Department of Pharmacology, University of California, Davis, Davis, CA 95616, USA.
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24
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Marques WL, Raghavendran V, Stambuk BU, Gombert AK. Sucrose and Saccharomyces cerevisiae: a relationship most sweet. FEMS Yeast Res 2015; 16:fov107. [PMID: 26658003 DOI: 10.1093/femsyr/fov107] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2015] [Indexed: 12/16/2022] Open
Abstract
Sucrose is an abundant, readily available and inexpensive substrate for industrial biotechnology processes and its use is demonstrated with much success in the production of fuel ethanol in Brazil. Saccharomyces cerevisiae, which naturally evolved to efficiently consume sugars such as sucrose, is one of the most important cell factories due to its robustness, stress tolerance, genetic accessibility, simple nutrient requirements and long history as an industrial workhorse. This minireview is focused on sucrose metabolism in S. cerevisiae, a rather unexplored subject in the scientific literature. An analysis of sucrose availability in nature and yeast sugar metabolism was performed, in order to understand the molecular background that makes S. cerevisiae consume this sugar efficiently. A historical overview on the use of sucrose and S. cerevisiae by humans is also presented considering sugarcane and sugarbeet as the main sources of this carbohydrate. Physiological aspects of sucrose consumption are compared with those concerning other economically relevant sugars. Also, metabolic engineering efforts to alter sucrose catabolism are presented in a chronological manner. In spite of its extensive use in yeast-based industries, a lot of basic and applied research on sucrose metabolism is imperative, mainly in fields such as genetics, physiology and metabolic engineering.
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Affiliation(s)
- Wesley Leoricy Marques
- Department of Chemical Engineering, University of São Paulo, São Paulo-SP, 05424-970, Brazil School of Food Engineering, University of Campinas, Campinas-SP, 13083-862, Brazil
| | | | - Boris Ugarte Stambuk
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis-SC, 88040-900, Brazil
| | - Andreas Karoly Gombert
- Department of Chemical Engineering, University of São Paulo, São Paulo-SP, 05424-970, Brazil School of Food Engineering, University of Campinas, Campinas-SP, 13083-862, Brazil
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Yi DG, Huh WK. UDP-glucose pyrophosphorylase Ugp1 is involved in oxidative stress response and long-term survival during stationary phase in Saccharomyces cerevisiae. Biochem Biophys Res Commun 2015; 467:657-63. [PMID: 26498530 DOI: 10.1016/j.bbrc.2015.10.090] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 10/18/2015] [Indexed: 11/17/2022]
Abstract
Ugp1, UDP-glucose pyrophosphorylase, plays an important role in carbohydrate metabolism because it provides UDP-glucose that is a pivotal metabolite in several metabolic pathways in Saccharomyces cerevisiae. In this study, we show that a considerable reduction of glycogen and trehalose content in ugp1 knockdown cells is rescued by complementing the expression of Ugp1, indicating that Ugp1 is required for the production of storage carbohydrates. Because of the specific function of trehalose as a stress protectant, Ugp1 expression contributed to oxidative stress response and long-term cell survival during stationary phase. Furthermore, the modulation of Ugp1 level readjusted glycogen and trehalose accumulation in the protein kinase A (PKA)-related gene mutants. The PKA-dependent phenotypes of oxidative stress resistance and long-term cell survival were also alleviated via adjustment of Ugp1 level. Collectively, our data suggest that the regulation of UPG1 influences several PKA-dependent processes by adjusting the levels of various carbohydrates.
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Affiliation(s)
- Dae-Gwan Yi
- Department of Biological Sciences, Seoul National University, Seoul 151-747, Republic of Korea
| | - Won-Ki Huh
- Department of Biological Sciences, Seoul National University, Seoul 151-747, Republic of Korea; Institute of Microbiology, Seoul National University, Seoul 151-747, Republic of Korea.
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de Assis LJ, Ries LNA, Savoldi M, dos Reis TF, Brown NA, Goldman GH. Aspergillus nidulans protein kinase A plays an important role in cellulase production. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:213. [PMID: 26690721 PMCID: PMC4683954 DOI: 10.1186/s13068-015-0401-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/30/2015] [Indexed: 05/17/2023]
Abstract
BACKGROUND The production of bioethanol from lignocellulosic feedstocks is dependent on lignocellulosic biomass degradation by hydrolytic enzymes. The main component of lignocellulose is cellulose and different types of organisms are able to secrete cellulases. The filamentous fungus Aspergillus nidulans serves as a model organism to study cellulase production and the available tools allow exploring more in depth the mechanisms governing cellulase production and carbon catabolite repression. RESULTS In A. nidulans, microarray data identified the cAMP-dependent protein kinase A (PkaA) as being involved in the transcriptional modulation and the production of lignocellulolytic enzymes in the presence of cellulose. Deletion of pkaA resulted in increased hydrolytic enzyme secretion, but reduced growth in the presence of lignocellulosic components and various other carbon sources. Furthermore, genes involved in fungal development were increased in the ΔpkaA strain, probably leading to the increased hyphal branching as was observed in this strain. This would allow the secretion of higher amounts of proteins. In addition, the expression of SynA, encoding a V-SNARE synaptobrevin protein involved in secretion, was increased in the ΔpkaA mutant. Deletion of pkaA also resulted in the reduced nuclear localization of the carbon catabolite repressor CreA in the presence of glucose and in partial de-repression when grown on cellulose. PkaA is involved in the glucose signaling pathway as the absence of this protein resulted in reduced glucose uptake and lower hexokinase/glucokinase activity, directing the cell to starvation conditions. Genome-wide transcriptomics showed that the expression of genes encoding proteins involved in fatty acid metabolism, mitochondrial function and in the use of cell storages was increased. CONCLUSIONS This study shows that PkaA is involved in hydrolytic enzyme production in A. nidulans. It appears that this protein kinase blocks the glucose pathway, hence forcing the cell to change to starvation conditions, increasing hydrolytic enzyme secretion and inducing the usage of cellular storages. This work uncovered new regulatory avenues governing the tight interplay between the metabolic states of the cell, which are important for the production of hydrolytic enzymes targeting lignocellulosic biomass. Deletion of pkaA resulted in a strain with increased hydrolytic enzyme secretion and reduced biomass formation.
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Affiliation(s)
- Leandro José de Assis
- />Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N, CEP 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Laure Nicolas Annick Ries
- />Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N, CEP 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Marcela Savoldi
- />Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N, CEP 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Thaila Fernanda dos Reis
- />Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N, CEP 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Neil Andrew Brown
- />Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts AL5 2JQ UK
| | - Gustavo Henrique Goldman
- />Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N, CEP 14040-903, Ribeirão Preto, São Paulo, Brazil
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Regulation of PKA activity by an autophosphorylation mechanism in Saccharomyces cerevisiae. Biochem J 2014; 462:567-79. [DOI: 10.1042/bj20140577] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Post-translational modifications can modulate kinase protein activity. We show that autophosphorylation of catalytic subunit of PKA Tpk1 upon glucose stimulus increases its catalytic efficiency. Our findings describe a new control layer on PKA activity in response to nutrient availability.
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Low YS, Bircham PW, Maass DR, Atkinson PH. Kinetochore genes are required to fully activate secretory pathway expansion in S. cerevisiae under induced ER stress. MOLECULAR BIOSYSTEMS 2014; 10:1790-802. [PMID: 24722431 DOI: 10.1039/c3mb70414a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Basal ER stress occurs when proteins misfold in normal physiological conditions and are corrected by the unfolded protein response (UPR). Elevated ER stress occurs when misfolding is refractory as found in numerous diseases such as atherosclerosis, Type II diabetes and some cancers. In elevated ER stress it is unclear whether cells utilise the same or different networks of genes as in basal levels of ER stress. To probe this question, we used secretory pathway reporters Yip3p-GFP, Erv29p-GFP, Orm2p-GFP and UPREpr-GFP placed on the yeast deletion mutant array (DMA) genetic background. The reporter's expression levels, measured by automated microscopy, at basal versus elevated ER stress induced by the over-expression of CPY* were compared. A novel group of kinetochore genes (CTF19 complex) were found to be uniquely required for full induction of all four ER stress reporters in elevated stress. A follow-up reporter screen was developed by mating the ctf19Δ kinetochore gene deletion strain into the genome-wide XXXp-GFP tagged library then testing with over-expressed CPY*. This screen identified Bcy1p and Bfr1p as possible signalling points that down-regulate the UPR and secretory pathway when kinetochore proteins are absent under elevated stress conditions. Bfr1p appears to be a checkpoint that monitors the integrity of kinetochores at increased levels of ER stress. This study concludes that functional kinetochores are required for full activation of the secretory pathway in elevated ER stress and that the responses to basal and elevated levels of ER stress require different networks of genes.
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Affiliation(s)
- Yee S Low
- School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Wellington, New Zealand.
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The adenylyl cyclase plays a regulatory role in the morphogenetic switch from vegetative to pathogenic lifestyle of Fusarium graminearum on wheat. PLoS One 2014; 9:e91135. [PMID: 24603887 PMCID: PMC3946419 DOI: 10.1371/journal.pone.0091135] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 02/11/2014] [Indexed: 11/19/2022] Open
Abstract
Cyclic 3′,5′-adenosine monophosphate (cAMP) is a nucleotide derived from adenosine triphosphate that acts as a second messenger throughout all kingdoms. Intracellular cAMP levels are synthesized by a membrane-bound protein, the adenylyl cyclase. In order to analyze the function of this gene and the importance of cAMP in the life cycle of the cereal pathogen Fusarium graminearum, the adenylyl cyclase gene (FGSG_01234) was deleted by gene replacement (ΔFgac1). The ΔFgac1 mutant displayed a drastically reduced growth on agar medium which could be rescued by a cAMP analogon. Furthermore, the ΔFgac1 mutant was unable to produce perithecia on detached wheat nodes. However, artificial conditions like carrot agar allowed perithecia development. Pathogenicity towards wheat was drastically reduced in ΔFgac1 compared to the wild type. Point-inoculated spikelets showed only small lesions but no typical head blight disease symptoms. Fluorescence microscopy using dsRed-expressing strains revealed that the ΔFgac1 strain was unable to develop any complex infection structures like lobate appressoria and infection cushions. Instead, hyphal anastomosis occurs frequently. Scanning electron microscopy demonstrated the lack of fungal penetration. Hence, the formation of compound appressoria seems to be essential for infection of wheat. Hyphae on flower leaves produced huge amounts of new conidia, thereby circumventing the infection cycle. This abundant sporulation on wheat epidermis was not observed in wild type. Intriguingly, the Fgac1 deletion mutant was able to infect maize cobs as wild type, indicating that cAMP signaling is not important for maize infection. The ΔFgac1 mutant was unable to produce the mycotoxin deoxynivalenol both in vitro and during wheat infection. In this study, we show that cAMP signaling controls important cellular processes such as development of infection structures, pathogenicity, secondary metabolite production and sexual reproduction. For the first time, we show that cAMP regulates the switch from vegetative to pathogenic lifestyle of F. graminearum on wheat.
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Psy2 targets the PP4 family phosphatase Pph3 to dephosphorylate Mth1 and repress glucose transporter gene expression. Mol Cell Biol 2013; 34:452-63. [PMID: 24277933 DOI: 10.1128/mcb.00279-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The reversible nature of protein phosphorylation dictates that any protein kinase activity must be counteracted by protein phosphatase activity. How phosphatases target specific phosphoprotein substrates and reverse the action of kinases, however, is poorly understood in a biological context. We address this question by elucidating a novel function of the conserved PP4 family phosphatase Pph3-Psy2, the yeast counterpart of the mammalian PP4c-R3 complex, in the glucose-signaling pathway. Our studies show that Pph3-Psy2 specifically targets the glucose signal transducer protein Mth1 via direct binding of the EVH1 domain of the Psy2 regulatory subunit to the polyproline motif of Mth1. This activity is required for the timely dephosphorylation of the downstream transcriptional repressor Rgt1 upon glucose withdrawal, a critical event in the repression of HXT genes, which encode glucose transporters. Pph3-Psy2 dephosphorylates Mth1, an Rgt1 associated corepressor, but does not dephosphorylate Rgt1 at sites associated with inactivation, in vitro. We show that Pph3-Psy2 phosphatase antagonizes Mth1 phosphorylation by protein kinase A (PKA), the major protein kinase activated in response to glucose, in vitro and regulates Mth1 function via putative PKA phosphorylation sites in vivo. We conclude that the Pph3-Psy2 phosphatase modulates Mth1 activity to facilitate precise regulation of HXT gene expression by glucose.
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31
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Kvitek DJ, Sherlock G. Whole genome, whole population sequencing reveals that loss of signaling networks is the major adaptive strategy in a constant environment. PLoS Genet 2013; 9:e1003972. [PMID: 24278038 PMCID: PMC3836717 DOI: 10.1371/journal.pgen.1003972] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 10/08/2013] [Indexed: 12/28/2022] Open
Abstract
Molecular signaling networks are ubiquitous across life and likely evolved to allow organisms to sense and respond to environmental change in dynamic environments. Few examples exist regarding the dispensability of signaling networks, and it remains unclear whether they are an essential feature of a highly adapted biological system. Here, we show that signaling network function carries a fitness cost in yeast evolving in a constant environment. We performed whole-genome, whole-population Illumina sequencing on replicate evolution experiments and find the major theme of adaptive evolution in a constant environment is the disruption of signaling networks responsible for regulating the response to environmental perturbations. Over half of all identified mutations occurred in three major signaling networks that regulate growth control: glucose signaling, Ras/cAMP/PKA and HOG. This results in a loss of environmental sensitivity that is reproducible across experiments. However, adaptive clones show reduced viability under starvation conditions, demonstrating an evolutionary tradeoff. These mutations are beneficial in an environment with a constant and predictable nutrient supply, likely because they result in constitutive growth, but reduce fitness in an environment where nutrient supply is not constant. Our results are a clear example of the myopic nature of evolution: a loss of environmental sensitivity in a constant environment is adaptive in the short term, but maladaptive should the environment change. When a population of organisms is faced with a selective pressure, such as a limiting nutrient, mutations that arise randomly may confer a fitness benefit on the individual carrying that mutation. If that individual reproduces before it is lost from the population, the frequency of that mutation may increase. Over time, many beneficial mutations will arise in a large population, but there are few high resolution experiments tracking the frequency of such mutations in an evolving population. We evolved populations of the baker's yeast in a constant environment in the presence of limiting amounts of sugar, and then used DNA sequencing to identify mutations that reached at least a 1% frequency in the population, and tracked them over time. We identified 120 mutations over three experiments, and determined that the genes and pathways that had gained beneficial mutations were largely reproducible across experiments, and that many of the mutations led to the loss of signaling pathways that usually sense a changing environment, allowing the cell to respond appropriately. When these mutant cells were faced with uncertain environments, the mutations proved to be deleterious. Environmental sensing must carry a fitness cost in a constant environment, but is essential in a changing one.
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Affiliation(s)
- Daniel J. Kvitek
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Gavin Sherlock
- Department of Genetics, Stanford University, Stanford, California, United States of America
- * E-mail:
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Zampar GG, Kümmel A, Ewald J, Jol S, Niebel B, Picotti P, Aebersold R, Sauer U, Zamboni N, Heinemann M. Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast. Mol Syst Biol 2013; 9:651. [PMID: 23549479 PMCID: PMC3693829 DOI: 10.1038/msb.2013.11] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 02/21/2013] [Indexed: 01/16/2023] Open
Abstract
The diauxic shift in Saccharomyces cerevisiae is an ideal model to study how eukaryotic cells readjust their metabolism from glycolytic to gluconeogenic operation. In this work, we generated time-resolved physiological data, quantitative metabolome (69 intracellular metabolites) and proteome (72 enzymes) profiles. We found that the diauxic shift is accomplished by three key events that are temporally organized: (i) a reduction in the glycolytic flux and the production of storage compounds before glucose depletion, mediated by downregulation of phosphofructokinase and pyruvate kinase reactions; (ii) upon glucose exhaustion, the reversion of carbon flow through glycolysis and onset of the glyoxylate cycle operation triggered by an increased expression of the enzymes that catalyze the malate synthase and cytosolic citrate synthase reactions; and (iii) in the later stages of the adaptation, the shutting down of the pentose phosphate pathway with a change in NADPH regeneration. Moreover, we identified the transcription factors associated with the observed changes in protein abundances. Taken together, our results represent an important contribution toward a systems-level understanding of how this adaptation is realized.
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Affiliation(s)
- Guillermo G Zampar
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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33
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Gerbeth C, Mikropoulou D, Meisinger C. From inventory to functional mechanisms. FEBS J 2013; 280:4933-42. [DOI: 10.1111/febs.12445] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/10/2013] [Accepted: 07/22/2013] [Indexed: 11/27/2022]
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Shen S, Hao Z, Gu S, Wang J, Cao Z, Li Z, Wang Q, Li P, Hao J, Dong J. The catalytic subunit of cAMP-dependent protein kinase A StPKA-c contributes to conidiation and early invasion in the phytopathogenic fungus Setosphaeria turcica. FEMS Microbiol Lett 2013; 343:135-44. [PMID: 23557024 DOI: 10.1111/1574-6968.12150] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 03/01/2013] [Accepted: 03/20/2013] [Indexed: 11/30/2022] Open
Abstract
Cyclic adenosine monophosphate (cAMP)-dependent protein kinase A (PKA) is an important mediator of signal transduction in eukaryotic cells. Thus, identifying its function is necessary to understand the cAMP signaling network. StPKA-c, the PKA catalytic subunit gene in Setosphaeria turcica, was investigated by RNA interference technology. Transformant strains M3, M5, and M9 with diverse StPKA-c silencing efficiency were confirmed by reverse transcription polymerase chain reaction and Northern blot. Compared with the wild-type strain 01-23, the transformant strains exhibited increased growth rate and significantly decreased conidium production. In addition, the ratios of spore germination and appressorium formation and penetration were slightly reduced. Relative to the wild-type strain, the transformants demonstrated different colony color, greatly reduced pathogenicity, and similar HT-toxin activity. Further studies showed that the content of intracellular melanin in the transformants significantly decreased, and the transcription of transcriptional factor StMR was down-regulated correspondingly. The transcription and enzyme activity of xylanase was also impaired. Thus, we proposed that StPKA-c was mainly involved in the mycelium growth, conidiation, and pathogenesis of S. turcica. Furthermore, it was positively correlated with the biosyntheses of melanin and xylanase but dispensable for the activity of HT-toxin.
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Affiliation(s)
- Shen Shen
- Mycotoxin and Molecular Plant Pathology Laboratory, Agricultural University of Hebei, Baoding, Hebei Province, China
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35
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Hong KK, Nielsen J. Adaptively evolved yeast mutants on galactose show trade-offs in carbon utilization on glucose. Metab Eng 2013; 16:78-86. [PMID: 23376593 DOI: 10.1016/j.ymben.2013.01.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 12/12/2012] [Accepted: 01/17/2013] [Indexed: 11/25/2022]
Abstract
Adaptive evolution offers many opportunities in metabolic engineering; however, several constraints still exist as evolutionary trade-offs may impose collateral cost to obtain new traits. The application of adaptive evolution for strains development could be further improved by elucidating the molecular mechanisms. In this study, adaptively evolved yeast mutants with improved galactose utilization ability showed impaired glucose utilization. The molecular genetic basis of this trade-off was investigated using a systems biology approach. Transcriptional and metabolic changes resulting from the improvement of galactose utilization were found maintained during growth on glucose. Moreover, glucose repression related genes showed conserved expression patterns during growth on both sugars. Mutations in the RAS2 gene that were identified as beneficial for galactose utilization in evolved mutants exhibited significant correlation with attenuation of glucose utilization. These results indicate that antagonistic pleiotropy is the dominant mechanism in the observed trade-off, and it is likely realized by changes in glucose signaling.
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Affiliation(s)
- Kuk-Ki Hong
- Novo Nordisk Foundation Center for Biosustainability, Department of Chemical and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
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36
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Boussalah N, Touzani R, Souna F, Himri I, Bouakka M, Hakkou A, Ghalem S, Kadiri SE. Antifungal activities of amino acid ester functional pyrazolyl compounds against Fusarium oxysporum f.sp. albedinis and Saccharomyces cerevisiae yeast. JOURNAL OF SAUDI CHEMICAL SOCIETY 2013. [DOI: 10.1016/j.jscs.2011.02.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Aragon AD, Torrez-Martinez N, Edwards JS. Genomic analysis of Saccharomyces cerevisiae isolates that grow optimally with glucose as the sole carbon source. Electrophoresis 2012; 33:3514-20. [PMID: 23135695 DOI: 10.1002/elps.201200172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 07/07/2012] [Accepted: 07/09/2012] [Indexed: 11/07/2022]
Abstract
A population of Saccharomyces cerevisiae was cultured for approximately 450 generations in the presence of high glucose to select for genetic variants that grew optimally under these conditions. Using the parental strain BY4741 as the starting population, an evolved culture was obtained after aerobic growth in a high glucose medium for approximately 450 generations. After the evolution period, three single colony isolates were selected for analysis. Next-generation Ion Torrent sequencing was used to evaluate genetic changes. Greater than 100 deletion/insertion changes were found with approximately half of these effecting genes. Additionally, over 180 SNPs were identified with more than one-quarter of these resulting in a nonsynonymous mutation. Affymetrix DNA microarrays and RNseq analysis were used to determine differences in gene expression in the evolved strains compared to the parental strain. It was established that approximately 900 genes demonstrated significantly altered expression in the evolved strains relative to the parental strain. Many of these genes showed similar alterations in their expression in all three evolved strains. Interestingly, genes with altered expression in the three evolved strains included genes with a role in oxidative metabolism. Overall these results are consistent with the physiological observations of optimal growth with glucose as the carbon source. Namely, the decreased ethanol production suggest that the underlying metabolism switched from fermentation to respiration during the selection for optimal growth on glucose.
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Affiliation(s)
- Anthony D Aragon
- UNM Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, NM 87131, USA
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38
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Interactions between the kinetochore complex and the protein kinase A pathway in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2012; 2:831-41. [PMID: 22870406 PMCID: PMC3385989 DOI: 10.1534/g3.112.002675] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 05/16/2012] [Indexed: 11/28/2022]
Abstract
The kinetochore is a large structure composed of multiple protein subcomplexes that connect chromosomes to spindle microtubules to enable accurate chromosome segregation. Significant advances have been made in the identification of kinetochore proteins and elucidation of kinetochore structure; however, comparatively little is known about how cellular signals integrate with kinetochore function. In the budding yeast Saccharomyces cerevisiae, the cyclic AMP protein kinase A signaling pathway promotes cellular growth in response to glucose. In this study, we find that decreasing protein kinase A activity, either by overexpressing negative regulators of the pathway or deleting the upstream effector Ras2, improves the viability of ipl1 and spc24 kinetochore mutants. Ipl1/Aurora B is a highly conserved kinase that corrects attachment of sister kinetochores that have attached to the same spindle pole, whereas Spc24 is a component of the conserved Ndc80 kinetochore complex that attaches directly to microtubules. Unexpectedly, we find that kinetochore mutants have increased phosphorylation levels of protein kinase A substrates, suggesting that the cyclic AMP protein kinase A signaling pathway is stimulated. The increase in protein kinase A activity in kinetochore mutants is not induced by activation of the spindle checkpoint or a metaphase delay because protein kinase A activity remains constant during an unperturbed cell cycle. Finally, we show that lowering protein kinase A activity can rescue the chromosome loss defect of the inner kinetochore ndc10 mutant. Overall, our data suggest that the increased protein kinase A activity in kinetochore mutants is detrimental to cellular growth and chromosome transmission fidelity.
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Acetate regulation of spore formation is under the control of the Ras/cyclic AMP/protein kinase A pathway and carbon dioxide in Saccharomyces cerevisiae. EUKARYOTIC CELL 2012; 11:1021-32. [PMID: 22660623 DOI: 10.1128/ec.05240-11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In Saccharomyces cerevisiae, the Ras/cyclic AMP (cAMP)/protein kinase A (PKA) pathway is a nutrient-sensitive signaling cascade that regulates vegetative growth, carbohydrate metabolism, and entry into meiosis. How this pathway controls later steps of meiotic development is largely unknown. Here, we have analyzed the role of the Ras/cAMP/PKA pathway in spore formation by the meiosis-specific manipulation of Ras and PKA or by the disturbance of cAMP production. We found that the regulation of spore formation by acetate takes place after commitment to meiosis and depends on PKA and appropriate A kinase activation by Ras/Cyr1 adenylyl cyclase but not by activation through the Gpa2/Gpr1 branch. We further discovered that spore formation is regulated by carbon dioxide/bicarbonate, and an analysis of mutants defective in acetate transport (ady2Δ) or carbonic anhydrase (nce103Δ) provided evidence that these metabolites are involved in connecting the nutritional state of the meiotic cell to spore number control. Finally, we observed that the potential PKA target Ady1 is required for the proper localization of the meiotic plaque proteins Mpc70 and Spo74 at spindle pole bodies and for the ability of these proteins to initiate spore formation. Overall, our investigation suggests that the Ras/cAMP/PKA pathway plays a crucial role in the regulation of spore formation by acetate and indicates that the control of meiotic development by this signaling cascade takes places at several steps and is more complex than previously anticipated.
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Vandamme J, Castermans D, Thevelein JM. Molecular mechanisms of feedback inhibition of protein kinase A on intracellular cAMP accumulation. Cell Signal 2012; 24:1610-8. [PMID: 22522182 DOI: 10.1016/j.cellsig.2012.04.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 03/22/2012] [Accepted: 04/04/2012] [Indexed: 01/13/2023]
Abstract
The cAMP-protein kinase A (PKA) pathway is a major signalling pathway in the yeast Saccharomyces cerevisiae, but also in many other eukaryotic cell types, including mammalian cells. Since cAMP plays a crucial role as second messenger in the regulation of this pathway, its levels are strictly controlled, both in the basal condition and after induction by agonists. A major factor in the down-regulation of the cAMP level after stimulation is PKA itself. Activation of PKA triggers feedback down-regulation of the increased cAMP level, stimulating its return to the basal concentration. This is accomplished at different levels. The best documented mechanisms are: inhibition of cAMP synthesis by down-regulation of adenylate cyclase and/or its regulatory proteins, stimulation of cAMP breakdown by phosphodiesterases and spatial regulation of cAMP levels in the cell by A-Kinase Anchoring Proteins (AKAPs). In this review we describe these processes in detail for S. cerevisiae, for cells of mammals and selected other organisms, and we hint at other possible targets for feedback regulation of intracellular cAMP levels.
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Rao S, Schmidt O, Harbauer AB, Schönfisch B, Guiard B, Pfanner N, Meisinger C. Biogenesis of the preprotein translocase of the outer mitochondrial membrane: protein kinase A phosphorylates the precursor of Tom40 and impairs its import. Mol Biol Cell 2012; 23:1618-27. [PMID: 22419819 PMCID: PMC3338429 DOI: 10.1091/mbc.e11-11-0933] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The translocase of the outer mitochondrial membrane (TOM) is essential for the import of proteins into mitochondria. Cytosolic protein kinase A phosphorylates the precursor of the channel-forming protein Tom40 and inhibits its import into mitochondria, thus regulating the biogenesis of the protein entry gate of mitochondria. The preprotein translocase of the outer mitochondrial membrane (TOM) functions as the main entry gate for the import of nuclear-encoded proteins into mitochondria. The major subunits of the TOM complex are the three receptors Tom20, Tom22, and Tom70 and the central channel-forming protein Tom40. Cytosolic kinases have been shown to regulate the biogenesis and activity of the Tom receptors. Casein kinase 2 stimulates the biogenesis of Tom22 and Tom20, whereas protein kinase A (PKA) impairs the receptor function of Tom70. Here we report that PKA exerts an inhibitory effect on the biogenesis of the β-barrel protein Tom40. Tom40 is synthesized as precursor on cytosolic ribosomes and subsequently imported into mitochondria. We show that PKA phosphorylates the precursor of Tom40. The phosphorylated Tom40 precursor is impaired in import into mitochondria, whereas the nonphosphorylated precursor is efficiently imported. We conclude that PKA plays a dual role in the regulation of the TOM complex. Phosphorylation by PKA not only impairs the receptor activity of Tom70, but it also inhibits the biogenesis of the channel protein Tom40.
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Affiliation(s)
- Sanjana Rao
- Institut für Biochemie und Molekularbiologie, Zentrum für Biochemie und Molekulare Zellforschung, Universität Freiburg, 79104 Freiburg, Germany
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Gu J, Wang C, Shih IM, Wang TL, Wang Y, Clarke R, Xuan J. GIST: a Gibbs sampler to identify intracellular signal transduction pathways. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2012; 2011:2434-7. [PMID: 22254833 DOI: 10.1109/iembs.2011.6090677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Identification of intracellular signal transduction pathways plays an important role in understanding the mechanisms of how cells respond to external stimuli. The availability of high throughput microarray expression data and accumulating knowledge of protein-protein interactions have provided us with useful information to infer condition-specific signal transduction pathways. We propose a novel method called Gibbs sampler to Infer Signal Transduction pathways (GIST) to search dys-regulated pathways from large-scale protein-protein interaction networks. GIST incorporates different knowledge sources to extract paths that are highly associated with biological phenotypes or clinical information. One of the most attractive features of GIST is that the algorithm will not only provide the single optimal path according to the defined cost function but also reveal multiple suboptimal paths as alternative solutions, which can be utilized to study the pathway crosstalk. As a proof-of-concept, we test our GIST algorithm on yeast PPI networks and the identified MAPK signaling pathways are well supported by existing biological knowledge. We also apply the GIST algorithm onto a breast cancer patient dataset to show its feasibility of identifying potential pathways for further biological validation.
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Affiliation(s)
- Jinghua Gu
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, USA.
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Mehrabi R, M'barek SB, Saidi A, Abrinbana M, de Wit PJGM, Kema GHJ. MAP kinase phosphorylation and cAMP assessment in fungi. Methods Mol Biol 2012; 835:571-83. [PMID: 22183678 DOI: 10.1007/978-1-61779-501-5_35] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The cyclic AMP (cAMP) signaling and mitogen-activated protein (MAP) kinase pathways are the most important signal transduction pathways in eukaryotes. In many plant pathogenic fungi they play pivotal roles in virulence and development. Identification and understanding the role of signal transduction pathways in regulation of cellular responses require robust biochemical techniques. Determination of both the phosphorylation status of MAPKs and the intracellular levels of cAMP is required to unravel the function of these pathways during adaptation of fungi to environmental stress conditions or when particular fungal genes are disrupted or silenced. Here we describe protocols to determine the phosphorylation status of three different MAPKs including Fus3, Slt2 and Hog1 as well as a protocol to measure the intracellular levels of cAMP levels. These protocols can be adapted for a wide range of fungi.
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Stefan E, Malleshaiah MK, Breton B, Ear PH, Bachmann V, Beyermann M, Bouvier M, Michnick SW. PKA regulatory subunits mediate synergy among conserved G-protein-coupled receptor cascades. Nat Commun 2011; 2:598. [PMID: 22186894 PMCID: PMC3247815 DOI: 10.1038/ncomms1605] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 11/18/2011] [Indexed: 11/09/2022] Open
Abstract
G-protein-coupled receptors sense extracellular chemical or physical stimuli and transmit these signals to distinct trimeric G-proteins. Activated Gα-proteins route signals to interconnected effector cascades, thus regulating thresholds, amplitudes and durations of signalling. Gαs- or Gαi-coupled receptor cascades are mechanistically conserved and mediate many sensory processes, including synaptic transmission, cell proliferation and chemotaxis. Here we show that a central, conserved component of Gαs-coupled receptor cascades, the regulatory subunit type-II (RII) of protein kinase A undergoes adenosine 3′-5′-cyclic monophosphate (cAMP)-dependent binding to Gαi. Stimulation of a mammalian Gαi-coupled receptor and concomitant cAMP-RII binding to Gαi, augments the sensitivity, amplitude and duration of Gαi:βγ activity and downstream mitogen-activated protein kinase signalling, independent of protein kinase A kinase activity. The mechanism is conserved in budding yeast, causing nutrient-dependent modulation of a pheromone response. These findings suggest a direct mechanism by which coincident activation of Gαs-coupled receptors controls the precision of adaptive responses of activated Gαi-coupled receptor cascades. G-protein-coupled receptors sense extracellular cues and transmit the signal to distinct trimeric G-proteins. Stefan et al. show that in response to cAMP, a central and conserved component of the Gαs-coupled receptor cascade, the RII subunit of PKA, specifically binds to and participates in Gαi signaling.
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Affiliation(s)
- Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria.
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Casado C, González A, Platara M, Ruiz A, Ariño J. The role of the protein kinase A pathway in the response to alkaline pH stress in yeast. Biochem J 2011; 438:523-33. [PMID: 21749328 PMCID: PMC3253439 DOI: 10.1042/bj20110607] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2010] [Revised: 07/11/2011] [Accepted: 07/13/2011] [Indexed: 11/17/2022]
Abstract
Exposure of Saccharomyces cerevisiae to alkaline pH provokes a stress condition that generates a compensatory reaction. In the present study we examined a possible role for the PKA (protein kinase A) pathway in this response. Phenotypic analysis revealed that mutations that activate the PKA pathway (ira1 ira2, bcy1) tend to cause sensitivity to alkaline pH, whereas its deactivation enhances tolerance to this stress. We observed that alkalinization causes a transient decrease in cAMP, the main regulator of the pathway. Alkaline pH causes rapid nuclear localization of the PKA-regulated Msn2 transcription factor which, together with Msn4, mediates a general stress response by binding with STRE (stress response element) sequences in many promoters. Consequently, a synthetic STRE-LacZ reporter shows a rapid induction in response to alkaline stress. A msn2 msn4 mutant is sensitive to alkaline pH, and transcriptomic analysis reveals that after 10 min of alkaline stress, the expression of many induced genes (47%) depends, at least in part, on the presence of Msn2 and Msn4. Taken together, these results demonstrate that inhibition of the PKA pathway by alkaline pH represents a substantial part of the adaptive response to this kind of stress and that this response involves Msn2/Msn4-mediated genome expression remodelling. However, the relevance of attenuation of PKA in high pH tolerance is probably not restricted to regulation of Msn2 function.
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Key Words
- alkaline stress
- gene expression
- msn2
- msn4
- protein kinase a (pka)
- saccharomyces cerevisiae
- transcription factor
- cdre, calcineurin-dependent response element
- cy3, indocarbocyanine
- cy5, indodicarbocyanine
- gap, gtpase activating proteins
- gef, guanine-nucleotide-exchange factor
- gfp, green fluorescent protein
- go, gene ontology
- pka, protein kinase a
- stre, stress response element
- tor, target of rapamycin
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Affiliation(s)
- Carlos Casado
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra 08193, Barcelona, Spain
| | - Asier González
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra 08193, Barcelona, Spain
| | - Maria Platara
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra 08193, Barcelona, Spain
| | - Amparo Ruiz
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra 08193, Barcelona, Spain
| | - Joaquín Ariño
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra 08193, Barcelona, Spain
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The TEA transcription factor Tec1 links TOR and MAPK pathways to coordinate yeast development. Genetics 2011; 189:479-94. [PMID: 21840851 DOI: 10.1534/genetics.111.133629] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In Saccharomyces cerevisiae, the TEA transcription factor Tec1 controls several developmental programs in response to nutrients and pheromones. Tec1 is targeted by the pheromone-responsive Fus3/Kss1 mitogen-activated protein kinase (MAPK) cascade, which destabilizes the transcription factor to ensure efficient mating of sexual partner cells. The regulation of Tec1 by signaling pathways that control cell division and development in response to nutrients, however, is not known. Here, we show that Tec1 protein stability is under control of the nutrient-sensitive target of rapamycin complex 1 (TORC1) signaling pathway via the Tip41-Tap42-Sit4 branch. We further show that degradation of Tec1 upon inhibition of TORC1 by rapamycin does not involve polyubiquitylation and appears to be proteasome independent. However, rapamycin-induced Tec1 degradation depends on the HECT ubiquitin ligase Rsp5, which physically interacts with Tec1 via conserved PxY motives. We further demonstrate that rapamycin and mating pheromone control Tec1 protein stability through distinct mechanisms by targeting different domains of the transcription factor. Finally, we show that Tec1 is a positive regulator of yeast chronological lifespan (CLS), a known TORC1-regulated process. Our findings indicate that in yeast, Tec1 links TORC1 and MAPK signaling pathways to coordinate control of cellular development in response to different stimuli.
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Waltermann C, Klipp E. Information theory based approaches to cellular signaling. Biochim Biophys Acta Gen Subj 2011; 1810:924-32. [PMID: 21798319 DOI: 10.1016/j.bbagen.2011.07.009] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 06/08/2011] [Accepted: 07/13/2011] [Indexed: 01/26/2023]
Abstract
BACKGROUND Cells interact with their environment and they have to react adequately to internal and external changes such changes in nutrient composition, physical properties like temperature or osmolarity and other stresses. More specifically, they must be able to evaluate whether the external change is significant or just in the range of noise. Based on multiple external parameters they have to compute an optimal response. Cellular signaling pathways are considered as the major means of information perception and transmission in cells. SCOPE OF REVIEW Here, we review different attempts to quantify information processing on the level of individual cells. We refer to Shannon entropy, mutual information, and informal measures of signaling pathway cross-talk and specificity. MAJOR CONCLUSIONS Information theory in systems biology has been successfully applied to identification of optimal pathway structures, mutual information and entropy as system response in sensitivity analysis, and quantification of input and output information. GENERAL SIGNIFICANCE While the study of information transmission within the framework of information theory in technical systems is an advanced field with high impact in engineering and telecommunication, its application to biological objects and processes is still restricted to specific fields such as neuroscience, structural and molecular biology. However, in systems biology dealing with a holistic understanding of biochemical systems and cellular signaling only recently a number of examples for the application of information theory have emerged. This article is part of a Special Issue entitled Systems Biology of Microorganisms.
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Alberghina L, Mavelli G, Drovandi G, Palumbo P, Pessina S, Tripodi F, Coccetti P, Vanoni M. Cell growth and cell cycle in Saccharomyces cerevisiae: basic regulatory design and protein-protein interaction network. Biotechnol Adv 2011; 30:52-72. [PMID: 21821114 DOI: 10.1016/j.biotechadv.2011.07.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 06/23/2011] [Accepted: 07/06/2011] [Indexed: 10/18/2022]
Abstract
In this review we summarize the major connections between cell growth and cell cycle in the model eukaryote Saccharomyces cerevisiae. In S. cerevisiae regulation of cell cycle progression is achieved predominantly during a narrow interval in the late G1 phase known as START (Pringle and Hartwell, 1981). At START a yeast cell integrates environmental and internal signals (such as nutrient availability, presence of pheromone, attainment of a critical size, status of the metabolic machinery) and decides whether to enter a new cell cycle or to undertake an alternative developmental program. Several signaling pathways, that act to connect the nutritional status to cellular actions, are briefly outlined. A Growth & Cycle interaction network has been manually curated. More than one fifth of the edges within the Growth & Cycle network connect Growth and Cycle proteins, indicating a strong interconnection between the processes of cell growth and cell cycle. The backbone of the Growth & Cycle network is composed of middle-degree nodes suggesting that it shares some properties with HOT networks. The development of multi-scale modeling and simulation analysis will help to elucidate relevant central features of growth and cycle as well as to identify their system-level properties. Confident collaborative efforts involving different expertises will allow to construct consensus, integrated models effectively linking the processes of cell growth and cell cycle, ultimately contributing to shed more light also on diseases in which an altered proliferation ability is observed, such as cancer.
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Affiliation(s)
- Lilia Alberghina
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy.
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Kim HS, Park SY, Lee S, Adams EL, Czymmek K, Kang S. Loss of cAMP-dependent protein kinase A affects multiple traits important for root pathogenesis by Fusarium oxysporum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:719-732. [PMID: 21261464 DOI: 10.1094/mpmi-11-10-0267] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The soilborne fungal pathogen Fusarium oxysporum causes vascular wilt and root rot diseases in many plant species. We investigated the role of cyclic AMP-dependent protein kinase A of F. oxysporum (FoCPKA) in growth, morphology, and root attachment, penetration, and pathogenesis in Arabidopsis thaliana. Affinity of spore attachment to root surfaces of A. thaliana, observed microscopically and measured by atomic force microscopy, was reduced by a loss-of-function mutation in the gene encoding the catalytic subunit of FoCPKA. The resulting mutants also failed to penetrate into the vascular system of A. thaliana roots and lost virulence. Even when the mutants managed to enter the vascular system via physically wounded roots, the degree of vascular colonization was significantly lower than that of the corresponding wild-type strain O-685 and no noticeable disease symptoms were observed. The mutants also had reduced vegetative growth and spore production, and their hyphal growth patterns were distinct from those of O-685. Coinoculation of O-685 with an focpkA mutant or a strain nonpathogenic to A. thaliana significantly reduced disease severity and the degree of root colonization by O-685. Several experimental tools useful for studying mechanisms of fungal root pathogenesis are also introduced.
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Affiliation(s)
- Hye-Seon Kim
- Department of Plant Pathology, The Pennsylvania State University, University Park, PA, USA
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Brückner S, Mösch HU. Choosing the right lifestyle: adhesion and development in Saccharomyces cerevisiae. FEMS Microbiol Rev 2011; 36:25-58. [PMID: 21521246 DOI: 10.1111/j.1574-6976.2011.00275.x] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The budding yeast Saccharomyces cerevisiae is a eukaryotic microorganism that is able to choose between different unicellular and multicellular lifestyles. The potential of individual yeast cells to switch between different growth modes is advantageous for optimal dissemination, protection and substrate colonization at the population level. A crucial step in lifestyle adaptation is the control of self- and foreign adhesion. For this purpose, S. cerevisiae contains a set of cell wall-associated proteins, which confer adhesion to diverse biotic and abiotic surfaces. Here, we provide an overview of different aspects of S. cerevisiae adhesion, including a detailed description of known lifestyles, recent insights into adhesin structure and function and an outline of the complex regulatory network for adhesin gene regulation. Our review shows that S. cerevisiae is a model system suitable for studying not only the mechanisms and regulation of cell adhesion, but also the role of this process in microbial development, ecology and evolution.
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Affiliation(s)
- Stefan Brückner
- Department of Genetics, Philipps-Universität Marburg, Marburg, Germany
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