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Mishra S, Welch N, Singh SS, Singh KD, Bellar A, Kumar A, Deutz LN, Hanlon MD, Kant S, Dastidar S, Patel H, Agrawal V, Attaway AH, Musich R, Stark GR, Tedesco FS, Truskey GA, Weiner ID, Karnik SS, Dasarathy S. Ammonia transporter RhBG initiates downstream signaling and functional responses by activating NFκB. Proc Natl Acad Sci U S A 2024; 121:e2314760121. [PMID: 39052834 PMCID: PMC11294993 DOI: 10.1073/pnas.2314760121] [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: 08/30/2023] [Accepted: 06/19/2024] [Indexed: 07/27/2024] Open
Abstract
Transceptors, solute transporters that facilitate intracellular entry of molecules and also initiate intracellular signaling events, have been primarily studied in lower-order species. Ammonia, a cytotoxic endogenous metabolite, is converted to urea in hepatocytes for urinary excretion in mammals. During hyperammonemia, when hepatic metabolism is impaired, nonureagenic ammonia disposal occurs primarily in skeletal muscle. Increased ammonia uptake in skeletal muscle is mediated by a membrane-bound, 12 transmembrane domain solute transporter, Rhesus blood group-associated B glycoprotein (RhBG). We show that in addition to its transport function, RhBG interacts with myeloid differentiation primary response-88 (MyD88) to initiate an intracellular signaling cascade that culminates in activation of NFκB. We also show that ammonia-induced MyD88 signaling is independent of the canonical toll-like receptor-initiated mechanism of MyD88-dependent NFκB activation. In silico, in vitro, and in situ experiments show that the conserved cytosolic J-domain of the RhBG protein interacts with the Toll-interleukin-1 receptor (TIR) domain of MyD88. In skeletal muscle from human patients, human-induced pluripotent stem cell-derived myotubes, and myobundles show an interaction of RhBG-MyD88 during hyperammonemia. Using complementary experimental and multiomics analyses in murine myotubes and mice with muscle-specific RhBG or MyD88 deletion, we show that the RhBG-MyD88 interaction is essential for the activation of NFkB but not ammonia transport. Our studies show a paradigm of substrate-dependent regulation of transceptor function with the potential for modulation of cellular responses in mammalian systems by decoupling transport and signaling functions of transceptors.
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Affiliation(s)
- Saurabh Mishra
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland, OH44195
| | - Nicole Welch
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland, OH44195
- Gastroenterology and Hepatology, Lerner Research Institute, Cleveland, OH44195
| | - Shashi Shekhar Singh
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland, OH44195
| | | | - Annette Bellar
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland, OH44195
| | - Avinash Kumar
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland, OH44195
| | - Lars N. Deutz
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland, OH44195
| | - Maxmillian D. Hanlon
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland, OH44195
| | - Sashi Kant
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland, OH44195
| | - Sumitava Dastidar
- Department of Cell and Developmental Biology, University College London & The Francis Crick Institute, LondonWC1E6DE, UK
| | - Hailee Patel
- Duke Biomedical Engineering, Duke University, Durham, NC27708
| | - Vandana Agrawal
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland, OH44195
| | - Amy H. Attaway
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland, OH44195
- Pulmonary Medicine, Lerner Research Institute, Cleveland, OH44195
| | - Ryan Musich
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland, OH44195
| | - George R. Stark
- Cancer Biology, Lerner Research Institute, Cleveland, OH44195
| | - Francesco Saverio Tedesco
- Department of Cell and Developmental Biology, University College London & The Francis Crick Institute, LondonWC1E6DE, UK
| | | | - I. David Weiner
- Division of Nephrology Hypertension, and Renal Transplantation, University of Florida, Gainesville, FL32610
- Nephrology and Hypertension Section, Gainesville, FL32610
| | - Sadashiva S. Karnik
- Cardiovascular and Metabolic Diseases, Lerner Research Institute, Cleveland, OH44195
| | - Srinivasan Dasarathy
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland, OH44195
- Gastroenterology and Hepatology, Lerner Research Institute, Cleveland, OH44195
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Partipilo M, Jan Slotboom D. The S-component fold: a link between bacterial transporters and receptors. Commun Biol 2024; 7:610. [PMID: 38773269 PMCID: PMC11109136 DOI: 10.1038/s42003-024-06295-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 05/06/2024] [Indexed: 05/23/2024] Open
Abstract
The processes of nutrient uptake and signal sensing are crucial for microbial survival and adaptation. Membrane-embedded proteins involved in these functions (transporters and receptors) are commonly regarded as unrelated in terms of sequence, structure, mechanism of action and evolutionary history. Here, we analyze the protein structural universe using recently developed artificial intelligence-based structure prediction tools, and find an unexpected link between prominent groups of microbial transporters and receptors. The so-called S-components of Energy-Coupling Factor (ECF) transporters, and the membrane domains of sensor histidine kinases of the 5TMR cluster share a structural fold. The discovery of their relatedness manifests a widespread case of prokaryotic "transceptors" (related proteins with transport or receptor function), showcases how artificial intelligence-based structure predictions reveal unchartered evolutionary connections between proteins, and provides new avenues for engineering transport and signaling functions in bacteria.
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Affiliation(s)
- Michele Partipilo
- Department of Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Dirk Jan Slotboom
- Department of Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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Lee B, Hokamp K, Alhussain MM, Bamagoos AA, Fleming AB. The influence of flocculation upon global gene transcription in a yeast CYC8 mutant. Microb Genom 2024; 10:001216. [PMID: 38529898 PMCID: PMC10995634 DOI: 10.1099/mgen.0.001216] [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: 12/05/2023] [Accepted: 02/29/2024] [Indexed: 03/27/2024] Open
Abstract
The transcriptome from a Saccharomyces cerevisiae tup1 deletion mutant was one of the first comprehensive yeast transcriptomes published. Subsequent transcriptomes from tup1 and cyc8 mutants firmly established the Tup1-Cyc8 complex as predominantly acting as a repressor of gene transcription. However, transcriptomes from tup1/cyc8 gene deletion or conditional mutants would all have been influenced by the striking flocculation phenotypes that these mutants display. In this study, we have separated the impact of flocculation from the transcriptome in a cyc8 conditional mutant to reveal those genes (i) subject solely to Cyc8p-dependent regulation, (ii) regulated by flocculation only and (iii) regulated by Cyc8p and further influenced by flocculation. We reveal a more accurate list of Cyc8p-regulated genes that includes newly identified Cyc8p-regulated genes that were masked by the flocculation phenotype and excludes genes which were indirectly influenced by flocculation and not regulated by Cyc8p. Furthermore, we show evidence that flocculation exerts a complex and potentially dynamic influence upon global gene transcription. These data should be of interest to future studies into the mechanism of action of the Tup1-Cyc8 complex and to studies involved in understanding the development of flocculation and its impact upon cell function.
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Affiliation(s)
- Brenda Lee
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Karsten Hokamp
- Department of Genetics, School of Genetics and Microbiology, Smurfit Institute, Trinity College Dublin, Dublin, Ireland
| | - Mohamed M. Alhussain
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Atif A. Bamagoos
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Alastair B. Fleming
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
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4
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Nishimura A. Regulations and functions of proline utilization in yeast Saccharomyces cerevisiae. Biosci Biotechnol Biochem 2024; 88:131-137. [PMID: 37994668 DOI: 10.1093/bbb/zbad165] [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: 10/20/2023] [Accepted: 11/18/2023] [Indexed: 11/24/2023]
Abstract
The quality of alcoholic beverages strongly depends on the metabolic characteristics of the yeast cells being used. To control the aroma and the taste of alcoholic beverages, as well as the production of ethanol in them, it is thus crucial to select yeast cells with the proper characteristics. Grape must contain a high concentration of proline, an amino acid that can potentially be a useful nitrogen source. However, Saccharomyces cerevisiae cannot utilize proline during the wine-making process, resulting in the elevated levels of proline in wine and consequent negative effects on wine quality. In this article, I review and discuss recent discoveries about the inhibitory mechanisms and roles of proline utilization in yeast. The information can help in developing novel yeast strains that can improve fermentation and enhance the quality and production efficiency of wine.
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Affiliation(s)
- Akira Nishimura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
- Institute for Research Initiatives, Nara Institute of Science and Technology, Ikoma, Nara, Japan
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5
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Zhang Z, Zhong Z, Xiong Y. Sailing in complex nutrient signaling networks: Where I am, where to go, and how to go? MOLECULAR PLANT 2023; 16:1635-1660. [PMID: 37740490 DOI: 10.1016/j.molp.2023.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
To ensure survival and promote growth, sessile plants have developed intricate internal signaling networks tailored in diverse cells and organs with both shared and specialized functions that respond to various internal and external cues. A fascinating question arises: how can a plant cell or organ diagnose the spatial and temporal information it is experiencing to know "where I am," and then is able to make the accurate specific responses to decide "where to go" and "how to go," despite the absence of neuronal systems found in mammals. Drawing inspiration from recent comprehensive investigations into diverse nutrient signaling pathways in plants, this review focuses on the interactive nutrient signaling networks mediated by various nutrient sensors and transducers. We assess and illustrate examples of how cells and organs exhibit specific responses to changing spatial and temporal information within these interactive plant nutrient networks. In addition, we elucidate the underlying mechanisms by which plants employ posttranslational modification codes to integrate different upstream nutrient signals, thereby conferring response specificities to the signaling hub proteins. Furthermore, we discuss recent breakthrough studies that demonstrate the potential of modulating nutrient sensing and signaling as promising strategies to enhance crop yield, even with reduced fertilizer application.
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Affiliation(s)
- Zhenzhen Zhang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Haixia Institute of Science and Technology, Synthetic Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhaochen Zhong
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Haixia Institute of Science and Technology, Synthetic Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yan Xiong
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Haixia Institute of Science and Technology, Synthetic Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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6
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Tanahashi R, Nishimura A, Morita F, Nakazawa H, Taniguchi A, Ichikawa K, Nakagami K, Boundy-Mills K, Takagi H. The arginine transporter Can1 acts as a transceptor for regulation of proline utilization in the yeast Saccharomyces cerevisiae. Yeast 2023; 40:333-348. [PMID: 36573467 DOI: 10.1002/yea.3836] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/29/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Proline is the most abundant amino acid in wine and beer, because the yeast Saccharomyces cerevisiae hardly assimilates proline during fermentation processes. Our previous studies showed that arginine induces endocytosis of the proline transporter Put4, resulting in inhibition of proline utilization. We here report a possible role of arginine sensing in the inhibition of proline utilization. We first found that two basic amino acids, ornithine, and lysine, inhibit proline utilization by inducing Put4 endocytosis in a manner similar to arginine, but citrulline does not. Our genetic screening revealed that the arginine transporter Can1 is involved in the inhibition of proline utilization by arginine. Intriguingly, the arginine uptake activity of Can1 was not required for the arginine-dependent inhibition of proline utilization, suggesting that Can1 has a function beyond its commonly known function of transporting arginine. More importantly, our biochemical analyses revealed that Can1 activates signaling cascades of protein kinase A in response to extracellular arginine. Hence, we proposed that Can1 regulates proline utilization by functioning as a transceptor possessing the activity of both a transporter and receptor of arginine.
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Affiliation(s)
- Ryoya Tanahashi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
- Division for Research Strategy, Institute for Research Initiatives, Nara Institute of Science and Technology, Ikoma, Japan
- Department of Food Science and Technology, University of California Davis, Davis, California, USA
| | - Akira Nishimura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Fumika Morita
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Hayate Nakazawa
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Atsuki Taniguchi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Kazuki Ichikawa
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Kazuki Nakagami
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Kyria Boundy-Mills
- Department of Food Science and Technology, University of California Davis, Davis, California, USA
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
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7
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Sulphate Uptake Plays a Major Role in the Production of Sulphur Dioxide by Yeast Cells during Oenological Fermentations. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9030280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Sulphur dioxide (SO2) is mostly used as an antioxidant additive in winemaking, but excessive levels may be harmful to both wine quality and consumers health. During fermentation, yeast Saccharomyces cerevisiae contributes significantly to final SO2 levels, and low-producing strains become especially interesting for the wine industry. Recent evidence implicating the impairment of sulphate transport in the SO2 decrease prompted us to further investigate the sulphate/sulphite metabolic connection in multiple winery yeast strains. Here, we inactivated by CRISPR/Cas9 the high-affinity sulphate permeases (Sul1p and Sul2p) in four strains normally used in winemaking, selected by their different abilities to produce SO2. Mutant strains were then used to perform fermentation assays in different types of natural must, and the final levels of SO2 and other secondary metabolites, crucial for wine organoleptic properties, were further determined for all fermentation products. Overall, data demonstrated the double ΔSUL1/ΔSUL2 inactivation in winery strains significantly decreases the levels of SO2 produced by mutant cells, without however altering both yeast fermentative properties and the ability to release relevant metabolites. Since similar effects were observed in diverse must types for strains with different features, the data strongly support that sulphate assimilation is the determining factor in SO2 production during oenological fermentations.
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8
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Yu Y, Zhong Z, Ma L, Xiang C, Chen J, Huang XY, Xu P, Xiong Y. Sulfate-TOR signaling controls transcriptional reprogramming for shoot apex activation. THE NEW PHYTOLOGIST 2022; 236:1326-1338. [PMID: 36028982 DOI: 10.1111/nph.18441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/14/2022] [Indexed: 06/15/2023]
Abstract
Plants play a primary role for the global sulfur cycle in the earth ecosystems by reduction of inorganic sulfate from the soil to organic sulfur-containing compounds. How plants sense and transduce the sulfate availability to mediate their growth remains largely unclear. The target of rapamycin (TOR) kinase is an evolutionarily conserved master regulator of nutrient sensing and metabolic signaling to control cell proliferation and growth in all eukaryotes. By tissue-specific Western blotting and RNA-sequencing analysis, we investigated sulfate-TOR signal pathway in regulating shoot apex development. Here, we report that inorganic sulfate exhibits high potency activating TOR and cell proliferation to promote true leaf development in Arabidopsis in a glucose-energy parallel pathway. Genetic and metabolite analyses suggest that this sulfate activation of TOR is independent from the sulfate-assimilation process and glucose-energy signaling. Significantly, tissue specific transcriptome analyses uncover previously unknown sulfate-orchestrating genes involved in DNA replication, cell proliferation and various secondary metabolism pathways, which largely depends on TOR signaling. Systematic comparison between the sulfate- and glucose-TOR controlled transcriptome further reveals that TOR kinase, as the central growth integrator, responds to different nutrient signals to control both shared and unique transcriptome networks, therefore, precisely modulates plant proliferation, growth and stress responses.
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Affiliation(s)
- Yongdong Yu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhaochen Zhong
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liuyin Ma
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chengbin Xiang
- Division of Life Sciences and Medicine, Division of Molecular and Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, 230027, China
| | - Jie Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xin-Yuan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ping Xu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yan Xiong
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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9
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Zhang B, Zhang Y, Guan R, Du M, Yin X, Zhao W, An S. Trehalase is required for sex pheromone biosynthesis in Helicoverpa armigera. INSECT MOLECULAR BIOLOGY 2022; 31:334-345. [PMID: 35084068 DOI: 10.1111/imb.12762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/08/2021] [Accepted: 01/24/2022] [Indexed: 05/14/2023]
Abstract
Trehalase (Treh) hydrolyzes trehalose to generate glucose and it plays important role in many physiological processes. Acetyl-CoA, the precursor of sex pheromone biosynthesis in the pheromone gland (PG) of Helicoverpa armigera, originates from glucose during glycolysis. However, the function of Treh in sex pheromone biosynthesis remains elusive. In the present study, H. armigera was used as a model to investigate the function of two Trehs (Treh1 and Treh2) in sex pheromone biosynthesis. Results demonstrated that knockdown of HaTreh1 or HaTreh2 in female PGs led to significant decreases in Z11-16:Ald production, female ability to attract males, and successful mating proportions. Pheromone biosynthesis activating neuropeptide (PBAN) treatment triggered HaTreh1 and HaTreh2 activities in the isolated PGs and Sf9 cells. However, the activities of HaTreh1 and HaTreh2 triggered by PBAN were offset by H-89, the specific inhibitor of protein kinase A (PKA). Furthermore, the H-89 treatment significantly decreased the phosphorylation level of Trhe2, which was induced by PBAN. In addition, sugar feeding (5% sugar) increased the enzyme activities of Treh1 and Treh2. In summary, our findings confirmed that PBAN activates Treh1/2 activities by recruiting cAMP/PKA signalling, promotes glycolysis to ensure the supply of acetyl-CoA, and ultimately facilitates sex pheromone biosynthesis and mating behaviour.
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Affiliation(s)
- Bo Zhang
- State Key Laboratory of Wheat and Maize Crop Science/College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yunhui Zhang
- State Key Laboratory of Wheat and Maize Crop Science/College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Ruobing Guan
- State Key Laboratory of Wheat and Maize Crop Science/College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Mengfang Du
- State Key Laboratory of Wheat and Maize Crop Science/College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Xinming Yin
- State Key Laboratory of Wheat and Maize Crop Science/College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Wenli Zhao
- State Key Laboratory of Wheat and Maize Crop Science/College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Shiheng An
- State Key Laboratory of Wheat and Maize Crop Science/College of Plant Protection, Henan Agricultural University, Zhengzhou, China
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10
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Local and Systemic Response to Heterogeneous Sulfate Resupply after Sulfur Deficiency in Rice. Int J Mol Sci 2022; 23:ijms23116203. [PMID: 35682882 PMCID: PMC9181796 DOI: 10.3390/ijms23116203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/24/2022] [Accepted: 05/31/2022] [Indexed: 11/29/2022] Open
Abstract
Sulfur (S) is an essential mineral nutrient required for plant growth and development. Plants usually face temporal and spatial variation in sulfur availability, including the heterogeneous sulfate content in soils. As sessile organisms, plants have evolved sophisticated mechanisms to modify their gene expression and physiological processes in order to optimize S acquisition and usage. Such plasticity relies on a complicated network to locally sense S availability and systemically respond to S status, which remains poorly understood. Here, we took advantage of a split-root system and performed transcriptome-wide gene expression analysis on rice plants in S deficiency followed by sulfate resupply. S deficiency altered the expressions of 6749 and 1589 genes in roots and shoots, respectively, accounting for 18.07% and 4.28% of total transcripts detected. Homogeneous sulfate resupply in both split-root halves recovered the expression of 27.06% of S-deficiency-responsive genes in shoots, while 20.76% of S-deficiency-responsive genes were recovered by heterogeneous sulfate resupply with only one split-root half being resupplied with sulfate. The local sulfate resupply response genes with expressions only recovered in the split-root half resupplied with sulfate but not in the other half remained in S deficiency were identified in roots, which were mainly enriched in cellular amino acid metabolic process and root growth and development. Several systemic response genes were also identified in roots, whose expressions remained unchanged in the split-root half resupplied with sulfate but were recovered in the other split-root half without sulfate resupply. The systemic response genes were mainly related to calcium signaling and auxin and ABA signaling. In addition, a large number of S-deficiency-responsive genes exhibited simultaneous local and systemic responses to sulfate resupply, such as the sulfate transporter gene OsSULTR1;1 and the O-acetylserine (thiol) lyase gene, highlighting the existence of a systemic regulation of sulfate uptake and assimilation in S deficiency plants followed by sulfate resupply. Our studies provided a comprehensive transcriptome-wide picture of a local and systemic response to heterogeneous sulfate resupply, which will facilitate an understanding of the systemic regulation of S homeostasis in rice.
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Abstract
As sessile organisms, plants have developed sophisticated mechanism to sense and utilize nutrients from the environment, and modulate their growth and development according to the nutrient availability. Research in the past two decades revealed that nutrient assimilation is not occurring spontaneously, but nutrient signaling networks are complexly regulated and integrate sensing and signaling, gene expression, and metabolism to ensure homeostasis and coordination with plant energy conversion and other processes. Here, we review the importance of the macronutrient sulfur (S) and compare the knowledge of S signaling with other important macronutrients, such as nitrogen (N) and phosphorus (P). We focus on key advances in understanding sulfur sensing and signaling, uptake and assimilation, and we provide new analysis of published literature, to identify core genes regulated by the key transcriptional factor in S starvation response, SLIM1/EIL3, and compare the impact on other nutrient deficiency and stresses on S-related genes.
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Affiliation(s)
- Daniela Ristova
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Stanislav Kopriva
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Zülpicher Str. 47b, 50674 Cologne, Germany
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12
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Abstract
Nutrients are scarce and valuable resources, so plants developed sophisticated mechanisms to optimize nutrient use efficiency. A crucial part of this is monitoring external and internal nutrient levels to adjust processes such as uptake, redistribution, and cellular compartmentation. Measurement of nutrient levels is carried out by primary sensors that typically involve either transceptors or transcription factors. Primary sensors are only now starting to be identified in plants for some nutrients. In particular, for nitrate, there is detailed insight concerning how the external nitrate status is sensed by members of the nitrate transporter 1 (NRT1) family. Potential sensors for other macronutrients such as potassium and sodium have also been identified recently, whereas for micronutrients such as zinc and iron, transcription factor type sensors have been reported. This review provides an overview that interprets and evaluates our current understanding of how plants sense macro and micronutrients in the rhizosphere and root symplast.
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13
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Verma N, Narayan OP, Prasad D, Jogawat A, Panwar SL, Dua M, Johri AK. Functional characterization of a high-affinity iron transporter (PiFTR) from the endophytic fungus Piriformospora indica and its role in plant growth and development. Environ Microbiol 2021; 24:689-706. [PMID: 34227231 DOI: 10.1111/1462-2920.15659] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 11/27/2022]
Abstract
Iron (Fe) is a micronutrient required for plant growth and development; however, most Fe forms in soil are not readily available to plants, resulting in low Fe contents in plants and, thereby, causing Fe deficiency in humans. Biofortification through plant-fungal co-cultivation might be a sustainable approach to increase crop Fe contents. Therefore, we aimed to examine the role of a Piriformospora indica Fe transporter on rice Fe uptake under low Fe conditions. A high-affinity Fe transporter (PiFTR) from P. indica was identified and functionally characterized. PiFTR fulfilled all criteria expected of a functional Fe transporter under Fe-limited conditions. Additionally, PiFTR expression was induced when P. indica was grown under low Fe conditions, and PiFTR complemented a yeast mutant lacking Fe transport. A knockdown (KD) P. indica strain was created via RNA interference to understand the physiological role of PiFTR. We observed that the KD-PiFTR-P. indica strain transported a significantly lower amount of Fe to colonized rice (Oryza sativa) than the wild type (WT) P. indica. WT P. indica-colonized rice plants were healthier and performed significantly better than KD-PiFTR-P. indica-colonized rice plants. Our study offers potential avenues for an agronomically sound amelioration of plant growth in low Fe environments.
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Affiliation(s)
- Nidhi Verma
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Om Prakash Narayan
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Durga Prasad
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Abhimanyu Jogawat
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sneh Lata Panwar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Meenakshi Dua
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Atul Kumar Johri
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
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Narayan OP, Verma N, Jogawat A, Dua M, Johri AK. Sulfur transfer from the endophytic fungus Serendipita indica improves maize growth and requires the sulfate transporter SiSulT. THE PLANT CELL 2021; 33:1268-1285. [PMID: 33793849 DOI: 10.1093/plcell/koab006] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/16/2020] [Indexed: 06/12/2023]
Abstract
A deficiency of the essential macronutrient sulfur leads to stunted plant growth and yield loss; however, an association with a symbiotic fungus can greatly improve nutrient uptake by the host plant. Here, we identified and functionally characterized a high-affinity sulfate transporter from the endophytic fungus Serendipita indica. SiSulT fulfills all the criteria expected of a functional sulfate transporter responding to sulfur limitation: SiSulT expression was induced when S. indica was grown under low-sulfate conditions, and heterologous expression of SiSulT complemented a yeast mutant lacking sulfate transport. We generated a knockdown strain of SiSulT by RNA interference to investigate the consequences of the partial loss of this transporter for the fungus and the host plant (maize, Zea mays) during colonization. Wild-type (WT) S. indica, but not the knockdown strain (kd-SiSulT), largely compensated for low-sulfate availability and supported plant growth. Colonization by WT S. indica also allowed maize roots to allocate precious resources away from sulfate assimilation under low-sulfur conditions, as evidenced by the reduction in expression of most sulfate assimilation genes. Our study illustrates the utility of the endophyte S. indica in sulfur nutrition research and offers potential avenues for agronomically sound amelioration of plant growth in low-sulfate environments.
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Affiliation(s)
- Om Prakash Narayan
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Nidhi Verma
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Abhimanyu Jogawat
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Meenakshi Dua
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Atul Kumar Johri
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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15
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Kawano-Kawada M, Ichimura H, Ohnishi S, Yamamoto Y, Kawasaki Y, Sekito T. Ygr125w/Vsb1-dependent accumulation of basic amino acids into vacuoles of Saccharomyces cerevisiae. Biosci Biotechnol Biochem 2021; 85:1157-1164. [PMID: 33704406 DOI: 10.1093/bbb/zbab015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 01/20/2021] [Indexed: 01/23/2023]
Abstract
The Ygr125w was previously identified as a vacuolar membrane protein by a proteomic analysis. We found that vacuolar levels of basic amino acids drastically decreased in ygr125wΔ cells. Since N- or C-terminally tagged Ygr125w was not functional, an expression plasmid of YGR125w with HA3-tag inserted in its N-terminal hydrophilic region was constructed. Introduction of this plasmid into ygr125w∆ cells restored the vacuolar levels of basic amino acids. We successfully detected the uptake activity of arginine by the vacuolar membrane vesicles depending on HA3-YGR125w expression. A conserved aspartate residue in the predicted first transmembrane helix (D223) was indispensable for the accumulation of basic amino acids. YGR125w has been recently reported as a gene involved in vacuolar storage of arginine; and it is designated as VSB1. Taken together, our findings indicate that Ygr125w/Vsb1 contributes to the uptake of arginine into vacuoles and vacuolar compartmentalization of basic amino acids.
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Affiliation(s)
- Miyuki Kawano-Kawada
- Laboratory of Molecular Physiology and Genetics, Graduate School of Agriculture, Ehime University, Matsuyama, Japan.,Division of Cell-Free Life Sciences, Proteo-Science Center, Ehime University, Matsuyama, Japan.,Advanced Research Support Center (ADRES), Ehime University, Matsuyama, Japan
| | - Haruka Ichimura
- Laboratory of Molecular Physiology and Genetics, Graduate School of Agriculture, Ehime University, Matsuyama, Japan
| | - Shota Ohnishi
- Laboratory of Molecular Physiology and Genetics, Faculty of Agriculture, Ehime University, Matsuyama, Japan
| | - Yusuke Yamamoto
- Laboratory of Molecular Physiology and Genetics, Faculty of Agriculture, Ehime University, Matsuyama, Japan
| | - Yumi Kawasaki
- Laboratory of Molecular Physiology and Genetics, Graduate School of Agriculture, Ehime University, Matsuyama, Japan
| | - Takayuki Sekito
- Laboratory of Molecular Physiology and Genetics, Graduate School of Agriculture, Ehime University, Matsuyama, Japan.,Division of Cell-Free Life Sciences, Proteo-Science Center, Ehime University, Matsuyama, Japan
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16
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Walker ME, Zhang J, Sumby KM, Lee A, Houlès A, Li S, Jiranek V. Sulfate transport mutants affect hydrogen sulfide and sulfite production during alcoholic fermentation. Yeast 2021; 38:367-381. [PMID: 33560525 DOI: 10.1002/yea.3553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 01/18/2021] [Accepted: 01/28/2021] [Indexed: 12/19/2022] Open
Abstract
Hydrogen sulfide is a common wine fault, with a rotten-egg odour, which is directly related to yeast metabolism in response to nitrogen and sulfur availability. In grape juice, sulfate is the most abundant inorganic sulfur compound, which is taken up by yeast through two high-affinity sulfate transporters, Sul1p and Sul2p, and a low affinity transporter, Soa1p. Sulfate contributes to H2 S production under nitrogen limitation, by being reduced via the Sulfur Assimilation Pathway (SAP). Therefore, yeast strains with limited H2 S are highly desirable. We report on the use of toxic analogues of sulfate following ethyl methane sulfate treatment, to isolate six wine yeast mutants that produce no or reduced H2 S and SO2 during fermentation in synthetic and natural juice. Four amino acid substitutions (A99V, G380R, N588K and E856K) in Sul1p were found in all strains except D25-1 which had heterozygous alleles. Two changes were also identified in Sul2p (L268S and A470T). The Sul1p (G380R) and Sul2p (A470T) mutations were chosen for further investigation as these residues are conserved amongst SLC26 membrane proteins (including sulfate permeases). The mutations were introduced into EC1118 using Crispr cas9 technology and shown to reduce accumulation of H2 S and do not result in increased SO2 production during fermentation of model medium (chemically defined grape juice) or Riesling juice. The Sul1p (G380R) and Sul2p (A470T) mutations are newly reported as causal mutations. Our findings contribute to knowledge of the genetic basis of H2 S production as well as the potential use of these strains for winemaking and in yeast breeding programmes.
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Affiliation(s)
- Michelle E Walker
- Department of Wine and Food Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Jin Zhang
- Department of Wine and Food Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Krista M Sumby
- Department of Wine and Food Science, University of Adelaide, Adelaide, South Australia, Australia.,Australian Research Council Training Centre for Innovative Wine Production, Glen Osmond, South Australia, Australia
| | - Andrea Lee
- Department of Wine and Food Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Anne Houlès
- Sciences et Techniques, Université Montpellier 2 (UM2), Montpellier, France
| | - Sijing Li
- Department of Wine and Food Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Vladimir Jiranek
- Department of Wine and Food Science, University of Adelaide, Adelaide, South Australia, Australia.,Australian Research Council Training Centre for Innovative Wine Production, Glen Osmond, South Australia, Australia
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17
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Zhang Z, Cottignie I, Van Zeebroeck G, Thevelein JM. Nutrient transceptors physically interact with the yeast S6/protein kinase B homolog, Sch9, a TOR kinase target. Biochem J 2021; 478:357-375. [PMID: 33394033 PMCID: PMC7850899 DOI: 10.1042/bcj20200722] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/04/2020] [Accepted: 01/04/2021] [Indexed: 12/18/2022]
Abstract
Multiple starvation-induced, high-affinity nutrient transporters in yeast function as receptors for activation of the protein kinase A (PKA) pathway upon re-addition of their substrate. We now show that these transceptors may play more extended roles in nutrient regulation. The Gap1 amino acid, Mep2 ammonium, Pho84 phosphate and Sul1 sulfate transceptors physically interact in vitro and in vivo with the PKA-related Sch9 protein kinase, the yeast homolog of mammalian S6 protein kinase and protein kinase B. Sch9 is a phosphorylation target of TOR and well known to affect nutrient-controlled cellular processes, such as growth rate. Mapping with peptide microarrays suggests specific interaction domains in Gap1 for Sch9 binding. Mutagenesis of the major domain affects the upstart of growth upon the addition of L-citrulline to nitrogen-starved cells to different extents but apparently does not affect in vitro binding. It also does not correlate with the drop in L-citrulline uptake capacity or transceptor activation of the PKA target trehalase by the Gap1 mutant forms. Our results reveal a nutrient transceptor-Sch9-TOR axis in which Sch9 accessibility for phosphorylation by TOR may be affected by nutrient transceptor-Sch9 interaction under conditions of nutrient starvation or other environmental challenges.
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Affiliation(s)
- Zhiqiang Zhang
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Ines Cottignie
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Griet Van Zeebroeck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Johan M. Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
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18
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Yadav B, Jogawat A, Lal SK, Lakra N, Mehta S, Shabek N, Narayan OP. Plant mineral transport systems and the potential for crop improvement. PLANTA 2021; 253:45. [PMID: 33483879 DOI: 10.1007/s00425-020-03551-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 12/22/2020] [Indexed: 05/09/2023]
Abstract
Nutrient transporter genes could be a potential candidate for improving crop plants, with enhanced nutrient uptake leading to increased crop yield by providing tolerance against different biotic and abiotic stresses. The world's food supply is nearing a crisis in meeting the demands of an ever-growing global population, and an increase in both yield and nutrient value of major crops is vitally necessary to meet the increased population demand. Nutrients play an important role in plant metabolism as well as growth and development, and nutrient deficiency results in retarded plant growth and leads to reduced crop yield. A variety of cellular processes govern crop plant nutrient absorption from the soil. Among these, nutrient membrane transporters play an important role in the acquisition of nutrients from soil and transport of these nutrients to their target sites. In addition, as excess nutrient delivery has toxic effects on plant growth, these membrane transporters also play a significant role in the removal of excess nutrients in the crop plant. The key function provided by membrane transporters is the ability to supply the crop plant with an adequate level of tolerance against environmental stresses, such as soil acidity, alkalinity, salinity, drought, and pathogen attack. Membrane transporter genes have been utilized for the improvement of crop plants, with enhanced nutrient uptake leading to increased crop yield by providing tolerance against different biotic and abiotic stresses. Further understanding of the basic mechanisms of nutrient transport in crop plants could facilitate the advanced design of engineered plant crops to achieve increased yield and improve nutrient quality through the use of genetic technologies as well as molecular breeding. This review is focused on nutrient toxicity and tolerance mechanisms in crop plants to aid in understanding and addressing the anticipated global food demand.
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Affiliation(s)
- Bindu Yadav
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Abhimanyu Jogawat
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Shambhu Krishan Lal
- ICAR- Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Nita Lakra
- Department of Biotechnology, CCS HAU, Hisar, India
| | - Sahil Mehta
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Nitzan Shabek
- Department of Plant Biology, University of California, Davis, CA, USA
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19
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Aarabi F, Naake T, Fernie AR, Hoefgen R. Coordinating Sulfur Pools under Sulfate Deprivation. TRENDS IN PLANT SCIENCE 2020; 25:1227-1239. [PMID: 32800669 DOI: 10.1016/j.tplants.2020.07.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/09/2020] [Accepted: 07/14/2020] [Indexed: 05/22/2023]
Abstract
Plants display manifold metabolic changes on sulfate deficiency (S deficiency) with all sulfur-containing pools of primary and secondary metabolism affected. O-Acetylserine (OAS), whose levels are rapidly altered on S deficiency, is correlated tightly with novel regulators of plant sulfur metabolism that have key roles in balancing plant sulfur pools, including the Sulfur Deficiency Induced genes (SDI1 and SDI2), More Sulfur Accumulation1 (MSA1), and GGCT2;1. Despite the importance of OAS in the coordination of S pools under stress, mechanisms of OAS perception and signaling have remained elusive. Here, we put particular focus on the general OAS-responsive genes but also elaborate on the specific roles of SDI1 and SDI2 genes, which downregulate the glucosinolate (GSL) pool size. We also highlight the key open questions in sulfur partitioning.
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Affiliation(s)
- Fayezeh Aarabi
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Thomas Naake
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
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20
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Van Zeebroeck G, Demuyser L, Zhang Z, Cottignie I, Thevelein JM. Nutrient sensing and cAMP signaling in yeast: G-protein coupled receptor versus transceptor activation of PKA. MICROBIAL CELL (GRAZ, AUSTRIA) 2020; 8:17-27. [PMID: 33490229 PMCID: PMC7780724 DOI: 10.15698/mic2021.01.740] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 09/12/2020] [Accepted: 09/17/2020] [Indexed: 11/13/2022]
Abstract
A major signal transduction pathway regulating cell growth and many associated physiological properties as a function of nutrient availability in the yeast Saccharomyces cerevisiae is the protein kinase A (PKA) pathway. Glucose activation of PKA is mediated by G-protein coupled receptor (GPCR) Gpr1, and secondary messenger cAMP. Other nutrients, including nitrogen, phosphate and sulfate, activate PKA in accordingly-starved cells through nutrient transceptors, but apparently without cAMP signaling. We have now used an optimized EPAC-based fluorescence resonance energy transfer (FRET) sensor to precisely monitor in vivo cAMP levels after nutrient addition. We show that GPCR-mediated glucose activation of PKA is correlated with a rapid transient increase in the cAMP level in vivo, whereas nutrient transceptor-mediated activation by nitrogen, phosphate or sulfate, is not associated with any significant increase in cAMP in vivo. We also demonstrate direct physical interaction between the Gap1 amino acid transceptor and the catalytic subunits of PKA, Tpk1, 2 and 3. In addition, we reveal a conserved consensus motif in the nutrient transceptors that is also present in Bcy1, the regulatory subunit of PKA. This suggests that nutrient transceptor activation of PKA may be mediated by direct release of bound PKA catalytic subunits, triggered by the conformational changes occurring during transport of the substrate by the transceptor. Our results support a model in which nutrient transceptors are evolutionary ancestors of GPCRs, employing a more primitive direct signaling mechanism compared to the indirect cAMP second-messenger signaling mechanism used by GPCRs for activation of PKA.
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Affiliation(s)
- Griet Van Zeebroeck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
- These authors made an equal contribution to this work
| | - Liesbeth Demuyser
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
- These authors made an equal contribution to this work
| | - Zhiqiang Zhang
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Ines Cottignie
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Johan M. Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
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21
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tRNA wobble-uridine modifications as amino acid sensors and regulators of cellular metabolic state. Curr Genet 2019; 66:475-480. [PMID: 31758251 DOI: 10.1007/s00294-019-01045-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/10/2019] [Accepted: 11/13/2019] [Indexed: 12/24/2022]
Abstract
Cells must appropriately sense available nutrients and accordingly regulate their metabolic outputs, to survive. This mini-review considers the idea that conserved chemical modifications of wobble (U34) position tRNA uridines enable cells to sense nutrients and regulate their metabolic state. tRNA wobble uridines are chemically modified at the 2- and 5- positions, with a thiol (s2), and (commonly) a methoxycarbonylmethyl (mcm5) modification, respectively. These modifications reflect sulfur amino acid (methionine and cysteine) availability. The loss of these modifications has minor translation defects. However, they result in striking phenotypes consistent with an altered metabolic state. Using yeast, we recently discovered that the s2 modification regulates overall carbon and nitrogen metabolism, dependent on methionine availability. The loss of this modification results in rewired carbon (glucose) metabolism. Cells have reduced carbon flux towards the pentose phosphate pathway and instead increased flux towards storage carbohydrates-primarily trehalose, along with reduced nucleotide synthesis, and perceived amino acid starvation signatures. Remarkably, this metabolic rewiring in the s2U mutants is caused by mechanisms leading to intracellular phosphate limitation. Thus this U34 tRNA modification responds to methionine availability and integratively regulates carbon and nitrogen homeostasis, wiring cells to a 'growth' state. We interpret the importance of U34 modifications in the context of metabolic sensing and anabolism, emphasizing their intimate coupling to methionine metabolism.
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22
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Takahashi H. Sulfate transport systems in plants: functional diversity and molecular mechanisms underlying regulatory coordination. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4075-4087. [PMID: 30907420 DOI: 10.1093/jxb/erz132] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 03/19/2019] [Indexed: 06/09/2023]
Abstract
Sulfate transporters are integral membrane proteins controlling the flux of sulfate (SO42-) entering the cells and subcellular compartments across the membrane lipid bilayers. Sulfate uptake is a dynamic biological process that occurs in multiple cell layers and organs in plants. In vascular plants, sulfate ions are taken up from the soil environment to the outermost cell layers of roots and horizontally transferred to the vascular tissues for further distribution to distant organs. The amount of sulfate ions being metabolized in the cytosol and chloroplast/plastid or temporarily stored in the vacuole depends on expression levels and functionalities of sulfate transporters bound specifically to the plasma membrane, chloroplast/plastid envelopes, and tonoplast membrane. The entire system for sulfate homeostasis, therefore, requires different types of sulfate transporters to be expressed and coordinately regulated in specific organs, cell types, and subcellular compartments. Transcriptional and post-transcriptional regulatory mechanisms control the expression levels and functions of sulfate transporters to optimize sulfate uptake and internal distribution in response to sulfate availability and demands for synthesis of organic sulfur metabolites. This review article provides an overview of sulfate transport systems and discusses their regulatory aspects investigated in the model plant species Arabidopsis thaliana.
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Affiliation(s)
- Hideki Takahashi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
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23
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Gupta R, Walvekar AS, Liang S, Rashida Z, Shah P, Laxman S. A tRNA modification balances carbon and nitrogen metabolism by regulating phosphate homeostasis. eLife 2019; 8:e44795. [PMID: 31259691 PMCID: PMC6688859 DOI: 10.7554/elife.44795] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 06/30/2019] [Indexed: 12/21/2022] Open
Abstract
Cells must appropriately sense and integrate multiple metabolic resources to commit to proliferation. Here, we report that S. cerevisiae cells regulate carbon and nitrogen metabolic homeostasis through tRNA U34-thiolation. Despite amino acid sufficiency, tRNA-thiolation deficient cells appear amino acid starved. In these cells, carbon flux towards nucleotide synthesis decreases, and trehalose synthesis increases, resulting in a starvation-like metabolic signature. Thiolation mutants have only minor translation defects. However, in these cells phosphate homeostasis genes are strongly down-regulated, resulting in an effectively phosphate-limited state. Reduced phosphate enforces a metabolic switch, where glucose-6-phosphate is routed towards storage carbohydrates. Notably, trehalose synthesis, which releases phosphate and thereby restores phosphate availability, is central to this metabolic rewiring. Thus, cells use thiolated tRNAs to perceive amino acid sufficiency, balance carbon and amino acid metabolic flux and grow optimally, by controlling phosphate availability. These results further biochemically explain how phosphate availability determines a switch to a 'starvation-state'.
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Affiliation(s)
- Ritu Gupta
- Institute for Stem Cell Science and Regenerative Medicine (inStem)BangaloreIndia
| | - Adhish S Walvekar
- Institute for Stem Cell Science and Regenerative Medicine (inStem)BangaloreIndia
| | - Shun Liang
- Department of GeneticsRutgers UniversityPiscatawayUnited States
| | - Zeenat Rashida
- Institute for Stem Cell Science and Regenerative Medicine (inStem)BangaloreIndia
- Manipal Academy of Higher EducationManipalIndia
| | - Premal Shah
- Department of GeneticsRutgers UniversityPiscatawayUnited States
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem)BangaloreIndia
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24
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Abstract
Cell nutrition, detoxification, signalling, homeostasis and response to drugs, processes related to cell growth, differentiation and survival are all mediated by plasma membrane (PM) proteins called transporters. Despite their distinct fine structures, mechanism of function, energetic requirements, kinetics and substrate specificities, all transporters are characterized by a main hydrophobic body embedded in the PM as a series of tightly packed, often intertwined, α-helices that traverse the lipid bilayer in a zigzag mode, connected with intracellular or extracellular loops and hydrophilic N- and C-termini. Whereas longstanding genetic, biochemical and biophysical evidence suggests that specific transmembrane segments, and also their connecting loops, are responsible for substrate recognition and transport dynamics, emerging evidence also reveals the functional importance of transporter N- and C-termini, in respect to transport catalysis, substrate specificity, subcellular expression, stability and signalling. This review highlights selected prototypic examples of transporters in which their termini play important roles in their functioning.
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Affiliation(s)
- Emmanuel Mikros
- Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis, 15771 Athens, Greece
| | - George Diallinas
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15781 Athens, Greece
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25
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Caza M, Kronstad JW. The cAMP/Protein Kinase a Pathway Regulates Virulence and Adaptation to Host Conditions in Cryptococcus neoformans. Front Cell Infect Microbiol 2019; 9:212. [PMID: 31275865 PMCID: PMC6592070 DOI: 10.3389/fcimb.2019.00212] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 05/31/2019] [Indexed: 12/28/2022] Open
Abstract
Nutrient sensing is critical for adaptation of fungi to environmental and host conditions. The conserved cAMP/PKA signaling pathway contributes to adaptation by sensing the availability of key nutrients such as glucose and directing changes in gene expression and metabolism. Interestingly, the cAMP/PKA pathway in fungal pathogens also influences the expression of virulence determinants in response to nutritional and host signals. For instance, protein kinase A (PKA) in the human pathogen Cryptococcus neoformans plays a central role in orchestrating phenotypic changes, such as capsule elaboration and melanin production, that directly impact disease development. In this review, we focus first on insights into the role of the cAMP/PKA pathway in nutrient sensing for the model yeast Saccharomyces cerevisiae to provide a foundation for understanding the pathway in C. neoformans. We then discuss key features of cAMP/PKA signaling in C. neoformans including new insights emerging from the analysis of transcriptional and proteomic changes in strains with altered PKA activity and expression. Finally, we highlight recent studies that connect the cAMP/PKA pathway to cell surface remodeling and the formation of titan cells.
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Affiliation(s)
- Mélissa Caza
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - James W Kronstad
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
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26
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Rutherford JC, Bahn YS, van den Berg B, Heitman J, Xue C. Nutrient and Stress Sensing in Pathogenic Yeasts. Front Microbiol 2019; 10:442. [PMID: 30930866 PMCID: PMC6423903 DOI: 10.3389/fmicb.2019.00442] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 02/20/2019] [Indexed: 12/23/2022] Open
Abstract
More than 1.5 million fungal species are estimated to live in vastly different environmental niches. Despite each unique host environment, fungal cells sense certain fundamentally conserved elements, such as nutrients, pheromones and stress, for adaptation to their niches. Sensing these extracellular signals is critical for pathogens to adapt to the hostile host environment and cause disease. Hence, dissecting the complex extracellular signal-sensing mechanisms that aid in this is pivotal and may facilitate the development of new therapeutic approaches to control fungal infections. In this review, we summarize the current knowledge on how two important pathogenic yeasts, Candida albicans and Cryptococcus neoformans, sense nutrient availability, such as carbon sources, amino acids, and ammonium, and different stress signals to regulate their morphogenesis and pathogenicity in comparison with the non-pathogenic model yeast Saccharomyces cerevisiae. The molecular interactions between extracellular signals and their respective sensory systems are described in detail. The potential implication of analyzing nutrient and stress-sensing systems in antifungal drug development is also discussed.
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Affiliation(s)
- Julian C Rutherford
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Yong-Sun Bahn
- Department of Biotechnology, Yonsei University, Seoul, South Korea
| | - Bert van den Berg
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, United States
| | - Chaoyang Xue
- Public Health Research Institute, Rutgers University, Newark, NJ, United States.,Department of Molecular Genetics, Biochemistry and Microbiology, Rutgers University, Newark, NJ, United States
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27
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The Complete Pathway for Thiosulfate Utilization in Saccharomyces cerevisiae. Appl Environ Microbiol 2018; 84:AEM.01241-18. [PMID: 30217845 DOI: 10.1128/aem.01241-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/02/2018] [Indexed: 11/20/2022] Open
Abstract
Saccharomyces cerevisiae is known to grow with thiosulfate as a sulfur source, and it produces more ethanol when using thiosulfate than using sulfate. Here, we report how it assimilates thiosulfate. S. cerevisiae absorbed thiosulfate into the cell through two sulfate permeases, Sul1 and Sul2. Two rhodaneses, Rdl1 and Rdl2, converted thiosulfate to a persulfide and sulfite. The persulfide was reduced by cellular thiols to H2S, and sulfite was reduced by sulfite reductase to H2S. Cysteine synthase incorporated H2S into O-acetyl-l-homoserine to produce l-homocysteine, which is the precursor for cysteine and methionine in S. cerevisiae Several other rhodaneses replaced Rdl1 and Rdl2 for thiosulfate utilization in the yeast. Thus, any organisms with the sulfate assimilation system potentially could use thiosulfate as a sulfur source, since rhodaneses are common in most organisms.IMPORTANCE The complete pathway of thiosulfate assimilation in baker's yeast is determined. The finding reveals the extensive overlap between sulfate and thiosulfate assimilation. Rhodanese is the only additional enzyme for thiosulfate utilization. The common presence of rhodanese in most organisms, including Bacteria, Archaea, and Eukarya, suggests that most organisms with the sulfate assimilation system also use thiosulfate. Since it takes less energy to reduce thiosulfate than sulfate for assimilation, thiosulfate has the potential to become a choice of sulfur in optimized media for industrial fermentation.
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28
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Kawano Y, Suzuki K, Ohtsu I. Current understanding of sulfur assimilation metabolism to biosynthesize L-cysteine and recent progress of its fermentative overproduction in microorganisms. Appl Microbiol Biotechnol 2018; 102:8203-8211. [PMID: 30046857 DOI: 10.1007/s00253-018-9246-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/12/2018] [Accepted: 07/13/2018] [Indexed: 12/01/2022]
Abstract
To all organisms, sulfur is an essential and important element. The assimilation of inorganic sulfur molecules such as sulfate and thiosulfate into organic sulfur compounds such as L-cysteine and L-methionine (essential amino acid for human) is largely contributed by microorganisms. Of these, special attention is given to thiosulfate (S2O32-) assimilation, because thiosulfate relative to often utilized sulfate (SO42-) as a sulfur source is proposed to be more advantageous in microbial growth and biotechnological applications like L-cysteine fermentative overproduction toward industrial manufacturing. In Escherichia coli as well as other many bacteria, the thiosulfate assimilation pathway is known to depend on O-acetyl-L-serine sulfhydrylase B. Recently, another yet-unidentified CysM-independent thiosulfate pathway was found in E. coli. This pathway is expected to consist of the initial part of the thiosulfate to sulfite (SO32-) conversion, and the latter part might be shared with the final part of the known sulfate assimilation pathway [sulfite → sulfide (S2-) → L-cysteine]. The catalysis of thiosulfate to sulfite is at least partly mediated by thiosulfate sulfurtransferase (GlpE). In this mini-review, we introduce updated comprehensive information about sulfur assimilation in microorganisms, including this topic. Also, we introduce recent advances of the application study about L-cysteine overproduction, including the GlpE overexpression.
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Affiliation(s)
- Yusuke Kawano
- Innovation Medical Research Institute, University of Tsukuba, Tsukuba, Japan
| | - Kengo Suzuki
- Department of Research and Development, Euglena Co., Ltd., Minato-ku, Tokyo, Japan
| | - Iwao Ohtsu
- Innovation Medical Research Institute, University of Tsukuba, Tsukuba, Japan.
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29
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Conrad M, Kankipati HN, Kimpe M, Van Zeebroeck G, Zhang Z, Thevelein JM. The nutrient transceptor/PKA pathway functions independently of TOR and responds to leucine and Gcn2 in a TOR-independent manner. FEMS Yeast Res 2018; 17:3950251. [PMID: 28810702 PMCID: PMC5812495 DOI: 10.1093/femsyr/fox048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/06/2017] [Indexed: 12/25/2022] Open
Abstract
Two nutrient-controlled signalling pathways, the PKA and TOR pathway, play a major role in nutrient regulation of growth as well as growth-correlated properties in yeast. The relationship between the two pathways is not well understood. We have used Gap1 and Pho84 transceptor-mediated activation of trehalase and phosphorylation of fragmented Sch9 as a read-out for rapid nutrient activation of PKA or TORC1, respectively. We have identified conditions in which L-citrulline-induced activation of Sch9 phosphorylation is compromised, but not activation of trehalase: addition of the TORC1 inhibitor, rapamycin and low levels of L-citrulline. The same disconnection was observed for phosphate activation in phosphate-starved cells. The leu2 auxotrophic mutation reduces amino acid activation of trehalase, which is counteracted by deletion of GCN2. Both effects were also independent of TORC1. Our results show that rapid activation of the TOR pathway by amino acids is not involved in rapid activation of the PKA pathway and that effects of Gcn2 inactivation as well as leu2 auxotrophy all act independently of the TOR pathway. Hence, rapid nutrient signalling to PKA and TOR in cells arrested by nutrient starvation acts through parallel pathways.
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Affiliation(s)
- Michaela Conrad
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Harish Nag Kankipati
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Marlies Kimpe
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Griet Van Zeebroeck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Zhiqiang Zhang
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
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30
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Steyfkens F, Zhang Z, Van Zeebroeck G, Thevelein JM. Multiple Transceptors for Macro- and Micro-Nutrients Control Diverse Cellular Properties Through the PKA Pathway in Yeast: A Paradigm for the Rapidly Expanding World of Eukaryotic Nutrient Transceptors Up to Those in Human Cells. Front Pharmacol 2018; 9:191. [PMID: 29662449 PMCID: PMC5890159 DOI: 10.3389/fphar.2018.00191] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 02/20/2018] [Indexed: 12/17/2022] Open
Abstract
The nutrient composition of the medium has dramatic effects on many cellular properties in the yeast Saccharomyces cerevisiae. In addition to the well-known specific responses to starvation for an essential nutrient, like nitrogen or phosphate, the presence of fermentable sugar or a respirative carbon source leads to predominance of fermentation or respiration, respectively. Fermenting and respiring cells also show strong differences in other properties, like storage carbohydrate levels, general stress tolerance and cellular growth rate. However, the main glucose repression pathway, which controls the switch between respiration and fermentation, is not involved in control of these properties. They are controlled by the protein kinase A (PKA) pathway. Addition of glucose to respiring yeast cells triggers cAMP synthesis, activation of PKA and rapid modification of its targets, like storage carbohydrate levels, general stress tolerance and growth rate. However, starvation of fermenting cells in a glucose medium for any essential macro- or micro-nutrient counteracts this effect, leading to downregulation of PKA and its targets concomitant with growth arrest and entrance into G0. Re-addition of the lacking nutrient triggers rapid activation of the PKA pathway, without involvement of cAMP as second messenger. Investigation of the sensing mechanism has revealed that the specific high-affinity nutrient transporter(s) induced during starvation function as transporter-receptors or transceptors for rapid activation of PKA upon re-addition of the missing substrate. In this way, transceptors have been identified for amino acids, ammonium, phosphate, sulfate, iron, and zinc. We propose a hypothesis for regulation of PKA activity by nutrient transceptors to serve as a conceptual framework for future experimentation. Many properties of transceptors appear to be similar to those of classical receptors and nutrient transceptors may constitute intermediate forms in the development of receptors from nutrient transporters during evolution. The nutrient-sensing transceptor system in yeast for activation of the PKA pathway has served as a paradigm for similar studies on candidate nutrient transceptors in other eukaryotes and we succinctly discuss the many examples of transceptors that have already been documented in other yeast species, filamentous fungi, plants, and animals, including the examples in human cells.
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Affiliation(s)
- Fenella Steyfkens
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Flanders, Belgium
| | - Zhiqiang Zhang
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Flanders, Belgium
| | - Griet Van Zeebroeck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Flanders, Belgium
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31
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Maruyama-Nakashita A. Metabolic changes sustain the plant life in low-sulfur environments. CURRENT OPINION IN PLANT BIOLOGY 2017; 39:144-151. [PMID: 28759781 DOI: 10.1016/j.pbi.2017.06.015] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/11/2017] [Accepted: 06/24/2017] [Indexed: 05/10/2023]
Abstract
Plants assimilate inorganic sulfate into various organic sulfur (S) compounds, which contributes to the global sulfur cycle in the environment as well as the nutritional supply of this essential element to animals. Plants, to sustain their lives, adapt the flow of their S metabolism to respond to external S status by activating S assimilation and catabolism of stored S compounds, and by repressing the synthesis of secondary S metabolites like glucosinolates. The molecular mechanism of this response has been gradually revealed, including the discovery of several regulatory proteins and enzymes involved in S deficiency responses. Recent progress in this research area and the remaining issues are reviewed here.
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Affiliation(s)
- Akiko Maruyama-Nakashita
- Graduate School of Agricultural Science, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
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32
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Huang CW, Walker ME, Fedrizzi B, Gardner RC, Jiranek V. Hydrogen sulfide and its roles in Saccharomyces cerevisiae in a winemaking context. FEMS Yeast Res 2017; 17:4056150. [DOI: 10.1093/femsyr/fox058] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 07/28/2017] [Indexed: 01/02/2023] Open
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33
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Burgard J, Valli M, Graf AB, Gasser B, Mattanovich D. Biomarkers allow detection of nutrient limitations and respective supplementation for elimination in Pichia pastoris fed-batch cultures. Microb Cell Fact 2017; 16:117. [PMID: 28693509 PMCID: PMC5504661 DOI: 10.1186/s12934-017-0730-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/28/2017] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Industrial processes for recombinant protein production challenge production hosts, such as the yeast Pichia pastoris, on multiple levels. During a common P. pastoris fed-batch process, cells experience strong adaptations to different metabolic states or suffer from environmental stresses due to high cell density cultivation. Additionally, recombinant protein production and nutrient limitations are challenging in these processes. RESULTS Pichia pastoris producing porcine carboxypeptidase B (CpB) was cultivated in glucose or methanol-limited fed-batch mode, and the cellular response was analyzed using microarrays. Thereby, strong transcriptional regulations in transport-, regulatory- and metabolic processes connected to sulfur, phosphorus and nitrogen metabolism became obvious. The induction of these genes was observed in both glucose- and methanol- limited fed batch cultivations, but were stronger in the latter condition. As the transcriptional pattern was indicative for nutrient limitations, we performed fed-batch cultivations where we added the respective nutrients and compared them to non-supplemented cultures regarding cell growth, productivity and expression levels of selected biomarker genes. In the non-supplemented reference cultures we observed a strong increase in transcript levels of up to 89-fold for phosphorus limitation marker genes in the late fed-batch phase. Transcript levels of sulfur limitation marker genes were up to 35-fold increased. By addition of (NH4)2SO4 or (NH4)2HPO4, respectively, we were able to suppress the transcriptional response of the marker genes to levels initially observed at the start of the fed batch. Additionally, supplementation had also a positive impact on biomass generation and recombinant protein production. Supplementation with (NH4)2SO4 led to 5% increase in biomass and 52% higher CpB activity in the supernatant, compared to the non-supplemented reference cultivations. In (NH4)2HPO4 supplemented cultures 9% higher biomass concentrations and 60% more CpB activity were reached. CONCLUSIONS Transcriptional analysis of P. pastoris fed-batch cultivations led to the identification of nutrient limitations in the later phases, and respective biomarker genes for indication of limitations. Supplementation of the cultivation media with those nutrients eliminated the limitations on the transcriptional level, and was also shown to enhance productivity of a recombinant protein. The biomarker genes are versatily applicable to media and process optimization approaches, where tailor-made solutions are envisioned.
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Affiliation(s)
- Jonas Burgard
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Minoska Valli
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Alexandra B. Graf
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
- School of Bioengineering, University of Applied Sciences FH Campus Vienna, Vienna, Austria
| | - Brigitte Gasser
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Diethard Mattanovich
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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34
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Dinkeloo K, Boyd S, Pilot G. Update on amino acid transporter functions and on possible amino acid sensing mechanisms in plants. Semin Cell Dev Biol 2017; 74:105-113. [PMID: 28705659 DOI: 10.1016/j.semcdb.2017.07.010] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 06/30/2017] [Accepted: 07/07/2017] [Indexed: 12/25/2022]
Abstract
Amino acids are essential components of plant metabolism, not only as constituents of proteins, but also as precursors of important secondary metabolites and as carriers of organic nitrogen between the organs of the plant. Transport across intracellular membranes and translocation of amino acids within the plant is mediated by membrane amino acid transporters. The past few years have seen the identification of a new family of amino acid transporters in Arabidopsis, the characterization of intracellular amino acid transporters, and the discovery of new roles for already known proteins. While amino acid metabolism needs to be tightly coordinated with amino acid transport activity and carbohydrate metabolism, no gene involved in amino acid sensing in plants has been unequivocally identified to date. This review aims at summarizing the recent data accumulated on the identity and function of amino acid transporters in plants, and discussing the possible identity of amino acid sensors based on data from other organisms.
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Affiliation(s)
- Kasia Dinkeloo
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA 24060, USA
| | - Shelton Boyd
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA 24060, USA
| | - Guillaume Pilot
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA 24060, USA.
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35
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Schothorst J, Zeebroeck GV, Thevelein JM. Identification of Ftr1 and Zrt1 as iron and zinc micronutrient transceptors for activation of the PKA pathway in Saccharomyces cerevisiae. MICROBIAL CELL 2017; 4:74-89. [PMID: 28357393 PMCID: PMC5349193 DOI: 10.15698/mic2017.03.561] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Multiple types of nutrient transceptors, membrane proteins that combine a
transporter and receptor function, have now been established in a variety of
organisms. However, so far all established transceptors utilize one of the
macronutrients, glucose, amino acids, ammonium, nitrate, phosphate or sulfate,
as substrate. This is also true for the Saccharomyces
cerevisiae transceptors mediating activation of the PKA pathway
upon re-addition of a macronutrient to glucose-repressed cells starved for that
nutrient, re-establishing a fermentable growth medium. We now show that the
yeast high-affinity iron transporter Ftr1 and high-affinity zinc transporter
Zrt1 function as transceptors for the micronutrients iron and zinc.
We show that replenishment of iron to iron-starved cells or zinc to
zinc-starved cells triggers within 1-2 minutes a rapid surge in trehalase
activity, a well-established PKA target. The activation with iron is dependent
on Ftr1 and with zinc on Zrt1, and we show that it is independent of
intracellular iron and zinc levels. Similar to the transceptors for
macronutrients, Ftr1 and Zrt1 are strongly induced upon iron and zinc
starvation, respectively, and they are rapidly downregulated by
substrate-induced endocytosis. Our results suggest that transceptor-mediated
signaling to the PKA pathway may occur in all cases where glucose-repressed
yeast cells have been starved first for an essential nutrient, causing arrest of
growth and low activity of the PKA pathway, and subsequently replenished with
the lacking nutrient to re-establish a fermentable growth medium. The broadness
of the phenomenon also makes it likely that nutrient transceptors use a common
mechanism for signaling to the PKA pathway.
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Affiliation(s)
- Joep Schothorst
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium. ; Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Griet V Zeebroeck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium. ; Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium. ; Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
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36
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Abstract
Cells need to communicate with their environment in order to obtain nutrients, grow, divide and respond to signals related to adaptation in changing physiological conditions or stress. A very basic question in biology is how cells, especially of those organisms living in rapidly changing habitats, sense their environment. Apparently, this question is of particular importance to all free-living microorganisms. The critical role of receptors, transporters and channels, transmembrane proteins located in the plasma membrane of all types of cells, in signaling environmental changes is well established. A relative newcomer in environment sensing are the so called transceptors, membrane proteins that possess both solute transport and receptor-like signaling activities. Now, the transceptor concept is further enlarged to include micronutrient sensing via the iron and zinc high-affinity transporters of Saccharomyces cerevisiae. Interestingly, what seems to underline the transport and/or sensing function of receptors, transporters and transceptors is ligand-induced conformational alterations recognized by downstream intracellular effectors.
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Affiliation(s)
- George Diallinas
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis 15784, Athens, Greece
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37
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Holt S, Kankipati H, De Graeve S, Van Zeebroeck G, Foulquié-Moreno MR, Lindgreen S, Thevelein JM. Major sulfonate transporter Soa1 in Saccharomyces cerevisiae and considerable substrate diversity in its fungal family. Nat Commun 2017; 8:14247. [PMID: 28165463 PMCID: PMC5303821 DOI: 10.1038/ncomms14247] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 12/12/2016] [Indexed: 11/24/2022] Open
Abstract
Sulfate is a well-established sulfur source for fungi; however, in soils sulfonates and sulfate esters, especially choline sulfate, are often much more prominent. Here we show that Saccharomyces cerevisiae YIL166C(SOA1) encodes an inorganic sulfur (sulfate, sulfite and thiosulfate) transporter that also catalyses sulfonate and choline sulfate uptake. Phylogenetic analysis of fungal SOA1 orthologues and expression of 20 members in the sul1Δ sul2Δ soa1Δ strain, which is deficient in inorganic and organic sulfur compound uptake, reveals that these transporters have diverse substrate preferences for sulfur compounds. We further show that SOA2, a S. cerevisiae SOA1 paralogue found in S. uvarum, S. eubayanus and S. arboricola is likely to be an evolutionary remnant of the uncharacterized open reading frames YOL163W and YOL162W. Our work highlights the importance of sulfonates and choline sulfate as sulfur sources in the natural environment of S. cerevisiae and other fungi by identifying fungal transporters for these compounds. Sulfonates are a major source of sulphur for soil microbes but their cellular uptake is still not fully understood. Here the authors show that Saccharomyces cerevisiae YIL166C(SOA1) encodes for an inorganic sulphur transporter that can also function as a sulfonate and choline sulphate transporter.
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Affiliation(s)
- Sylvester Holt
- Laboratory of Molecular Cell Biology, Department of Biology, KU Leuven, Institute of Botany and Microbiology Kasteelpark Arenberg 31, Flanders, B-3001 Leuven-Heverlee, Belgium.,Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Flanders, B-3001 Leuven-Heverlee, Belgium
| | - Harish Kankipati
- Laboratory of Molecular Cell Biology, Department of Biology, KU Leuven, Institute of Botany and Microbiology Kasteelpark Arenberg 31, Flanders, B-3001 Leuven-Heverlee, Belgium.,Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Flanders, B-3001 Leuven-Heverlee, Belgium
| | - Stijn De Graeve
- Laboratory of Molecular Cell Biology, Department of Biology, KU Leuven, Institute of Botany and Microbiology Kasteelpark Arenberg 31, Flanders, B-3001 Leuven-Heverlee, Belgium.,Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Flanders, B-3001 Leuven-Heverlee, Belgium
| | - Griet Van Zeebroeck
- Laboratory of Molecular Cell Biology, Department of Biology, KU Leuven, Institute of Botany and Microbiology Kasteelpark Arenberg 31, Flanders, B-3001 Leuven-Heverlee, Belgium.,Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Flanders, B-3001 Leuven-Heverlee, Belgium
| | - Maria R Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Department of Biology, KU Leuven, Institute of Botany and Microbiology Kasteelpark Arenberg 31, Flanders, B-3001 Leuven-Heverlee, Belgium.,Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Flanders, B-3001 Leuven-Heverlee, Belgium
| | - Stinus Lindgreen
- Carlsberg Research Laboratory, Gamle Carlsberg Vej 4, 1799 Copenhagen V, Denmark
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Department of Biology, KU Leuven, Institute of Botany and Microbiology Kasteelpark Arenberg 31, Flanders, B-3001 Leuven-Heverlee, Belgium.,Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Flanders, B-3001 Leuven-Heverlee, Belgium
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38
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Volpe V, Giovannetti M, Sun XG, Fiorilli V, Bonfante P. The phosphate transporters LjPT4 and MtPT4 mediate early root responses to phosphate status in non mycorrhizal roots. PLANT, CELL & ENVIRONMENT 2016; 39:660-71. [PMID: 26476189 DOI: 10.1111/pce.12659] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/09/2015] [Accepted: 10/12/2015] [Indexed: 05/23/2023]
Abstract
Arbuscular mycorrhizal (AM) symbiosis improves host plant phosphorous (P) status and elicits the expression of AM-inducible phosphate transporters (PTs) in arbuscule-containing cells, where they control arbuscule morphogenesis and P release. We confirmed such functions for LjPT4 in mycorrhizal Lotus japonicus. Promoter-GUS experiments showed LjPT4 transcription not only in arbusculated cells but also in root tips, in the absence of the fungus: here LjPT4 transcription profile depended on the phosphate level. In addition, quantitative RT-PCR confirmed the expression of Lotus and Medicago truncatula PT4 in the tips of non-mycorrhizal roots. Starting from these observations, we hypothesized that AM-inducible PTs may have a regulatory role in plant development, irrespective of the fungal presence. Firstly, we focused on root development responses to different phosphate treatments in both plants demonstrating that phosphate starvation induced a higher number of lateral roots. By contrast, Lotus PT4i plants and Medicago mtpt4 mutants did not show any differential response to phosphate levels, suggesting that PT4 genes affect early root branching. Phosphate starvation-induced genes and a key auxin receptor, MtTIR1, showed an impaired expression in mtpt4 plants. We suggest PT4 genes as novel components of the P-sensing machinery at the root tip level, independently of AM fungi.
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Affiliation(s)
- Veronica Volpe
- Department of Life Science and Systems Biology, University of Turin, Viale Mattioli 25, I-10125, Torino, Italy
| | - Marco Giovannetti
- Department of Life Science and Systems Biology, University of Turin, Viale Mattioli 25, I-10125, Torino, Italy
| | - Xue-Guang Sun
- Department of Life Science and Systems Biology, University of Turin, Viale Mattioli 25, I-10125, Torino, Italy
| | - Valentina Fiorilli
- Department of Life Science and Systems Biology, University of Turin, Viale Mattioli 25, I-10125, Torino, Italy
| | - Paola Bonfante
- Department of Life Science and Systems Biology, University of Turin, Viale Mattioli 25, I-10125, Torino, Italy
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Function and Regulation of Fungal Amino Acid Transporters: Insights from Predicted Structure. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 892:69-106. [PMID: 26721271 DOI: 10.1007/978-3-319-25304-6_4] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Amino acids constitute a major nutritional source for probably all fungi. Studies of model species such as the yeast Saccharomyces cerevisiae and the filamentous fungus Aspergillus nidulans have shown that they possess multiple amino acid transporters. These proteins belong to a limited number of superfamilies, now defined according to protein fold in addition to sequence criteria, and differ in subcellular location, substrate specificity range, and regulation. Structural models of several of these transporters have recently been built, and the detailed molecular mechanisms of amino acid recognition and translocation are now being unveiled. Furthermore, the particular conformations adopted by some of these transporters in response to amino acid binding appear crucial to promoting their ubiquitin-dependent endocytosis and/or to triggering signaling responses. We here summarize current knowledge, derived mainly from studies on S. cerevisiae and A. nidulans, about the transport activities, regulation, and sensing role of fungal amino acid transporters, in relation to predicted structure.
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40
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Samyn DR, Persson BL. Inorganic Phosphate and Sulfate Transport in S. cerevisiae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 892:253-269. [PMID: 26721277 DOI: 10.1007/978-3-319-25304-6_10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Inorganic ions such as phosphate and sulfate are essential macronutrients required for a broad spectrum of cellular functions and their regulation. In a constantly fluctuating environment microorganisms have for their survival developed specific nutrient sensing and transport systems ensuring that the cellular nutrient needs are met. This chapter focuses on the S. cerevisiae plasma membrane localized transporters, of which some are strongly induced under conditions of nutrient scarcity and facilitate the active uptake of inorganic phosphate and sulfate. Recent advances in studying the properties of the high-affinity phosphate and sulfate transporters by means of site-directed mutagenesis have provided further insight into the molecular mechanisms contributing to substrate selectivity and transporter functionality of this important class of membrane transporters.
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Affiliation(s)
- D R Samyn
- Department of Chemistry and Biomedical Sciences, Centre for Biomaterials Chemistry, Linnaeus University, 391 82, Kalmar, Sweden.
| | - B L Persson
- Department of Chemistry and Biomedical Sciences, Centre for Biomaterials Chemistry, Linnaeus University, 391 82, Kalmar, Sweden
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