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Zhao X, Li W, Li X, Jia Z, Song S, Zhao Q. The Effect of Bacterial AHL on the Cyclic Adenosine Monophosphate Content in Plants According to High-Performance Liquid Chromatography. Molecules 2024; 29:1074. [PMID: 38474586 DOI: 10.3390/molecules29051074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/10/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Cyclic adenosine monophosphate (cAMP) is an important second messenger in cells, mediating various stimulation signals such as the growth and development of organisms and stress and participating in regulating various biological processes of cells. This article explores the quantitative determination of cAMP in plants using High-Performance Liquid Chromatography (HPLC) and applies this method to analyzing the changes in cAMP content during the process of plant response to the bacterial quorum sensing signal N-acyl homoserine lactone (AHL). Research has shown that the optimal detection conditions for HPLC are as follows: the chromatographic column is Venusil MP C18 (2), the mobile phase is methanol-water (0.1% trifluoroacetic acid) (v:v, 10:90), the detection wavelength is 259 nm, the column temperature is 35 °C, and the flow rate is 0.8 mL/min. The precision of the standard sample of this method is 98.21%, the precision of the sample is 98.87%, and the recovery rate is 101.067%. The optimal extraction conditions for cAMP in Arabidopsis are to use 15% methanol ultrasonic extraction for 10 min, followed by a 40 °C water bath for 4 h. Bacterial AHL signal processing can significantly stimulate an increase in cAMP levels in Arabidopsis leaves and roots. The establishment of HPLC detection methods for the cAMP content in plants is of great significance for in-depth research on the signal transduction mechanisms of plant-bacterial interactions.
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Affiliation(s)
- Xuemeng Zhao
- School of Biological Science and Engineering, Hebei University of Economics and Business, Shijiazhuang 050061, China
- Biology Institute, Hebei Academy of Sciences, Shijiazhuang 050051, China
| | - Wen Li
- Biology Institute, Hebei Academy of Sciences, Shijiazhuang 050051, China
| | - Xiliu Li
- Biology Institute, Hebei Academy of Sciences, Shijiazhuang 050051, China
| | - Zhenhua Jia
- Biology Institute, Hebei Academy of Sciences, Shijiazhuang 050051, China
- Hebei Technology Innovation Center of Microbiological Control on Main Crop Disease, Shijiazhuang 050051, China
| | - Shuishan Song
- Biology Institute, Hebei Academy of Sciences, Shijiazhuang 050051, China
- Hebei Technology Innovation Center of Microbiological Control on Main Crop Disease, Shijiazhuang 050051, China
| | - Qian Zhao
- Biology Institute, Hebei Academy of Sciences, Shijiazhuang 050051, China
- Hebei Technology Innovation Center of Microbiological Control on Main Crop Disease, Shijiazhuang 050051, China
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2
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Marotta NJ, Weinert EE. Insights into the metabolism, signaling, and physiological effects of 2',3'-cyclic nucleotide monophosphates in bacteria. Crit Rev Biochem Mol Biol 2023; 58:118-131. [PMID: 38064689 PMCID: PMC10877235 DOI: 10.1080/10409238.2023.2290473] [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: 10/06/2023] [Accepted: 11/20/2023] [Indexed: 02/03/2024]
Abstract
2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) have been discovered within both prokaryotes and eukaryotes in the past decade and a half, raising questions about their conserved existence in cells. In plants and mammals, wounding has been found to cause increased levels of 2',3'-cNMPs. Roles for 2',3'-cNMPs in plant immunity suggest that their regulation may be valuable for both plant hosts and microbial pathogens. In support of this hypothesis, a plethora of microbial enzymes have been found with activities related to these molecules. Studies in bacteria suggest that 2',3'-cNMPs are also produced in response to cellular stress and modulate expression of numerous genes. 2',3'-cNMP levels affect bacterial phenotypes, including biofilm formation, motility, and growth. Within E. coli and Salmonella enterica, 2',3'-cNMPs are produced by RNA degradation by RNase I, highlighting potential roles for Type 2 RNases producing 2',3'-cNMPs in a range of organisms. Development of cellular tools to modulate 2',3'-cNMP levels in bacteria has allowed for interrogation of the effects of 2',3'-cNMP concentration on bacterial transcriptomes and physiology. Pull-downs of cellular 2',3'-cNMP binding proteins have identified the ribosome and in vitro studies demonstrated that 2',3'-cNMPs decrease translation, suggesting a direct mechanism for 2',3-cNMP-dependent control of bacterial phenotypes. Future studies dissecting the cellular roles of 2',3'-cNMPs will highlight novel signaling pathways within prokaryotes and which can potentially be engineered to control bacterial physiology.
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Affiliation(s)
- Nick J. Marotta
- Graduate Program in Molecular, Cellular, and Integrative
Biosciences, Penn State University, University Park, PA, 16803, USA
| | - Emily E. Weinert
- Department of Biochemistry and Molecular Biology, Penn
State University, University Park, PA, 16803, USA
- Department of Chemistry, Penn State University, University
Park, PA, 16803, USA
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3
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Wong A, Chi W, Yu J, Bi C, Tian X, Yang Y, Gehring C. Plant adenylate cyclases have come full circle. NATURE PLANTS 2023; 9:1389-1397. [PMID: 37709954 DOI: 10.1038/s41477-023-01486-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 07/07/2023] [Indexed: 09/16/2023]
Abstract
In bacteria, fungi and animals, 3'-5'-cyclic adenosine monophosphate (cAMP) and adenylate cyclases (ACs), enzymes that catalyse the formation of 3',5'-cAMP from ATP, are recognized as key signalling components. In contrast, the presence of cAMP and its biological roles in higher plants have long been a matter of controversy due to the generally lower amounts in plant tissues compared with that in animal and bacterial cells, and a lack of clarity on the molecular nature of the generating and degrading enzymes, as well as downstream effectors. While treatment with 3',5'-cAMP elicited many plant responses, ACs were, however, somewhat elusive. This changed when systematic searches with amino acid motifs deduced from the conserved catalytic centres of annotated ACs from animals and bacteria identified candidate proteins in higher plants that were subsequently shown to have AC activities in vitro and in vivo. The identification of active ACs moonlighting within complex multifunctional proteins is consistent with their roles as molecular tuners and regulators of cellular and physiological functions. Furthermore, the increasing number of ACs identified as part of proteins with different domain architectures suggests that there are many more hidden ACs in plant proteomes and they may affect a multitude of mechanisms and processes at the molecular and systems levels.
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Affiliation(s)
- Aloysius Wong
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China.
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang Province, China.
- Zhejiang Bioinformatics Internatiosnal Science and Technology Cooperation Center, Wenzhou, Zhejiang Province, China.
| | - Wei Chi
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
| | - Jia Yu
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
| | - Chuyun Bi
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang Province, China
- Zhejiang Bioinformatics Internatiosnal Science and Technology Cooperation Center, Wenzhou, Zhejiang Province, China
| | - Xuechen Tian
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang Province, China
- Zhejiang Bioinformatics Internatiosnal Science and Technology Cooperation Center, Wenzhou, Zhejiang Province, China
| | - Yixin Yang
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang Province, China
- Zhejiang Bioinformatics Internatiosnal Science and Technology Cooperation Center, Wenzhou, Zhejiang Province, China
| | - Chris Gehring
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy.
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4
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Locci F, Wang J, Parker JE. TIR-domain enzymatic activities at the heart of plant immunity. CURRENT OPINION IN PLANT BIOLOGY 2023; 74:102373. [PMID: 37150050 DOI: 10.1016/j.pbi.2023.102373] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/15/2023] [Accepted: 04/04/2023] [Indexed: 05/09/2023]
Abstract
Toll/interleukin-1/resistance (TIR) domain proteins contribute to innate immunity in all cellular kingdoms. TIR modules are activated by self-association and in plants, mammals and bacteria, some TIRs have enzymatic functions that are crucial for disease resistance and/or cell death. Many plant TIR-only proteins and pathogen effector-activated TIR-domain NLR receptors are NAD+ hydrolysing enzymes. Biochemical, structural and functional studies established that for both plant TIR-protein types, and certain bacterial TIRs, NADase activity generates bioactive signalling intermediates which promote resistance. A set of plant TIR-catalysed nucleotide isomers was discovered which bind to and activate EDS1 complexes, promoting their interactions with co-functioning helper NLRs. Analysis of TIR enzymes across kingdoms fills an important gap in understanding how pathogen disturbance induces TIR-regulated immune responses.
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Affiliation(s)
- Federica Locci
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, 50829, Germany
| | - Junli Wang
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, 50829, Germany
| | - Jane E Parker
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, 50829, Germany; Cologne-Düsseldorf Cluster of Excellence on Plant Sciences (CEPLAS), 40225, Düsseldorf, Germany.
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5
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Domingo G, Marsoni M, Chiodaroli L, Fortunato S, Bracale M, De Pinto MC, Gehring C, Vannini C. Quantitative phosphoproteomics reveals novel roles of cAMP in plants. Proteomics 2023; 23:e2300165. [PMID: 37264754 DOI: 10.1002/pmic.202300165] [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: 03/27/2023] [Revised: 05/05/2023] [Accepted: 05/23/2023] [Indexed: 06/03/2023]
Abstract
3',5'-cyclic adenosine monophosphate (cAMP) is finally recognized as an essential signaling molecule in plants where cAMP-dependent processes include responses to hormones and environmental stimuli. To better understand the role of 3',5'-cAMP at the systems level, we have undertaken a phosphoproteomic analysis to elucidate the cAMP-dependent response of tobacco BY-2 cells. These cells overexpress a molecular "sponge" that buffers free intracellular cAMP level. The results show that, firstly, in vivo cAMP dampening profoundly affects the plant kinome and notably mitogen-activated protein kinases, receptor-like kinases, and calcium-dependent protein kinases, thereby modulating the cellular responses at the systems level. Secondly, buffering cAMP levels also affects mRNA processing through the modulation of the phosphorylation status of several RNA-binding proteins with roles in splicing, including many serine and arginine-rich proteins. Thirdly, cAMP-dependent phosphorylation targets appear to be conserved among plant species. Taken together, these findings are consistent with an ancient role of cAMP in mRNA processing and cellular programming and suggest that unperturbed cellular cAMP levels are essential for cellular homeostasis and signaling in plant cells.
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Affiliation(s)
- Guido Domingo
- Biotechnology and Life Science Department, University of Insubria, Varese, Italy
| | - Milena Marsoni
- Biotechnology and Life Science Department, University of Insubria, Varese, Italy
| | | | | | - Marcella Bracale
- Biotechnology and Life Science Department, University of Insubria, Varese, Italy
| | | | - Chris Gehring
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Candida Vannini
- Biotechnology and Life Science Department, University of Insubria, Varese, Italy
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6
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Chauhan S, Marotta NJ, Karls AC, Weinert EE. Binding of 2',3'-Cyclic Nucleotide Monophosphates to Bacterial Ribosomes Inhibits Translation. ACS CENTRAL SCIENCE 2022; 8:1518-1526. [PMID: 36439312 PMCID: PMC9686202 DOI: 10.1021/acscentsci.2c00681] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Indexed: 06/16/2023]
Abstract
The intracellular small molecules 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) have recently been rediscovered within both prokaryotes and eukaryotes. Studies in bacteria have demonstrated that 2',3'-cNMP levels affect bacterial phenotypes, such as biofilm formation, motility, and growth, and modulate expression of numerous genes, suggesting that 2',3'-cNMP levels are monitored by cells. In this study, 2',3'-cNMP-linked affinity chromatography resins were used to identify Escherichia coli proteins that bind 2',3'-cNMPs, with the top hits including all of the ribosomal proteins, and to confirm direct binding of purified ribosomes. Using in vitro translation assays, we have demonstrated that 2',3'-cNMPs inhibit translation at concentrations found in amino acid-starved cells. In addition, a genetically encoded tool to increase cellular 2',3'-cNMP levels was developed and was demonstrated to decrease E. coli growth rates. Taken together, this work suggests a mechanism for 2',3-cNMP levels to modulate bacterial phenotypes by rapidly affecting translation.
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Affiliation(s)
- Shikha
S. Chauhan
- Department
of Biochemistry and Molecular Biology, Penn
State University, University
Park, Pennsylvania 16802, United States
| | - Nick J. Marotta
- Graduate
Program in Molecular, Cellular, and Integrative Biosciences, Penn State University, University Park, Pennsylvania 16802, United States
| | - Anna C. Karls
- Department
of Microbiology, University of Georgia, Athens, Georgia 30602, United States
| | - Emily E. Weinert
- Department
of Biochemistry and Molecular Biology, Penn
State University, University
Park, Pennsylvania 16802, United States
- Department
of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
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7
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Eastman S, Bayless A, Guo M. The Nucleotide Revolution: Immunity at the Intersection of Toll/Interleukin-1 Receptor Domains, Nucleotides, and Ca 2. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:964-976. [PMID: 35881867 DOI: 10.1094/mpmi-06-22-0132-cr] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The discovery of the enzymatic activity of the toll/interleukin-1 receptor (TIR) domain protein SARM1 five years ago preceded a flood of discoveries regarding the nucleotide substrates and products of TIR domains in plants, animals, bacteria, and archaea. These discoveries into the activity of TIR domains coincide with major advances in understanding the structure and mechanisms of NOD-like receptors and the mutual dependence of pattern recognition receptor- and effector-triggered immunity (PTI and ETI, respectively) in plants. It is quickly becoming clear that TIR domains and TIR-produced nucleotides are ancestral signaling molecules that modulate immunity and that their activity is closely associated with Ca2+ signaling. TIR domain research now bridges the separate disciplines of molecular plant- and animal-microbe interactions, neurology, and prokaryotic immunity. A cohesive framework for understanding the role of enzymatic TIR domains in diverse organisms will help unite the research of these disparate fields. Here, we review known products of TIR domains in plants, animals, bacteria, and archaea and use context gained from animal and prokaryotic TIR domain systems to present a model for TIR domains, nucleotides, and Ca2+ at the intersection of PTI and ETI in plant immunity. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Samuel Eastman
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583, U.S.A
| | - Adam Bayless
- Department of Biology, Colorado State University, Fort Collins, CO 80521, U.S.A
| | - Ming Guo
- Department of Agriculture and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, U.S.A
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8
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Qi L, Kwiatkowski M, Chen H, Hoermayer L, Sinclair S, Zou M, Del Genio CI, Kubeš MF, Napier R, Jaworski K, Friml J. Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. Nature 2022; 611:133-138. [PMID: 36289340 DOI: 10.1038/s41586-022-05369-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 09/20/2022] [Indexed: 02/02/2023]
Abstract
The phytohormone auxin is the major coordinative signal in plant development1, mediating transcriptional reprogramming by a well-established canonical signalling pathway. TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFB) auxin receptors are F-box subunits of ubiquitin ligase complexes. In response to auxin, they associate with Aux/IAA transcriptional repressors and target them for degradation via ubiquitination2,3. Here we identify adenylate cyclase (AC) activity as an additional function of TIR1/AFB receptors across land plants. Auxin, together with Aux/IAAs, stimulates cAMP production. Three separate mutations in the AC motif of the TIR1 C-terminal region, all of which abolish the AC activity, each render TIR1 ineffective in mediating gravitropism and sustained auxin-induced root growth inhibition, and also affect auxin-induced transcriptional regulation. These results highlight the importance of TIR1/AFB AC activity in canonical auxin signalling. They also identify a unique phytohormone receptor cassette combining F-box and AC motifs, and the role of cAMP as a second messenger in plants.
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Affiliation(s)
- Linlin Qi
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Mateusz Kwiatkowski
- Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Huihuang Chen
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Lukas Hoermayer
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Scott Sinclair
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
- Readiness and Response Directorate, Biosecurity New Zealand, Wellington, New Zealand
| | - Minxia Zou
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Charo I Del Genio
- Centre for Fluid and Complex Systems, Coventry University, Coventry, UK
| | - Martin F Kubeš
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Richard Napier
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Krzysztof Jaworski
- Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Jiří Friml
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria.
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9
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Essuman K, Milbrandt J, Dangl JL, Nishimura MT. Shared TIR enzymatic functions regulate cell death and immunity across the tree of life. Science 2022; 377:eabo0001. [DOI: 10.1126/science.abo0001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In the 20th century, researchers studying animal and plant signaling pathways discovered a protein domain shared across diverse innate immune systems: the Toll/Interleukin-1/Resistance-gene (TIR) domain. The TIR domain is found in several protein architectures and was defined as an adaptor mediating protein-protein interactions in animal innate immunity and developmental signaling pathways. However, studies of nerve degeneration in animals, and subsequent breakthroughs in plant, bacterial and archaeal systems, revealed that TIR domains possess enzymatic activities. We provide a synthesis of TIR functions and the role of various related TIR enzymatic products in evolutionarily diverse immune systems. These studies may ultimately guide interventions that would span the tree of life, from treating human neurodegenerative disorders and bacterial infections, to preventing plant diseases.
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Affiliation(s)
- Kow Essuman
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jeffrey Milbrandt
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
- Needleman Center for Neurometabolism and Axonal Therapeutics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Jeffery L. Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marc T. Nishimura
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
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10
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Yu D, Song W, Tan EYJ, Liu L, Cao Y, Jirschitzka J, Li E, Logemann E, Xu C, Huang S, Jia A, Chang X, Han Z, Wu B, Schulze-Lefert P, Chai J. TIR domains of plant immune receptors are 2',3'-cAMP/cGMP synthetases mediating cell death. Cell 2022; 185:2370-2386.e18. [PMID: 35597242 DOI: 10.1016/j.cell.2022.04.032] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/08/2022] [Accepted: 04/26/2022] [Indexed: 12/15/2022]
Abstract
2',3'-cAMP is a positional isomer of the well-established second messenger 3',5'-cAMP, but little is known about the biology of this noncanonical cyclic nucleotide monophosphate (cNMP). Toll/interleukin-1 receptor (TIR) domains of nucleotide-binding leucine-rich repeat (NLR) immune receptors have the NADase function necessary but insufficient to activate plant immune responses. Here, we show that plant TIR proteins, besides being NADases, act as 2',3'-cAMP/cGMP synthetases by hydrolyzing RNA/DNA. Structural data show that a TIR domain adopts distinct oligomers with mutually exclusive NADase and synthetase activity. Mutations specifically disrupting the synthetase activity abrogate TIR-mediated cell death in Nicotiana benthamiana (Nb), supporting an important role for these cNMPs in TIR signaling. Furthermore, the Arabidopsis negative regulator of TIR-NLR signaling, NUDT7, displays 2',3'-cAMP/cGMP but not 3',5'-cAMP/cGMP phosphodiesterase activity and suppresses cell death activity of TIRs in Nb. Our study identifies a family of 2',3'-cAMP/cGMP synthetases and establishes a critical role for them in plant immune responses.
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Affiliation(s)
- Dongli Yu
- Institute of Biochemistry, University of Cologne, Cologne, Germany; Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Wen Song
- Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Eddie Yong Jun Tan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Li Liu
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Yu Cao
- Institute of Biochemistry, University of Cologne, Cologne, Germany; Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jan Jirschitzka
- Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Ertong Li
- Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Elke Logemann
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Chenrui Xu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Shijia Huang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Aolin Jia
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaoyu Chang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhifu Han
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Bin Wu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore.
| | | | - Jijie Chai
- Institute of Biochemistry, University of Cologne, Cologne, Germany; Max Planck Institute for Plant Breeding Research, Cologne, Germany; Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China.
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11
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Thomson M, Liu Y, Nunta K, Cheyne A, Fernandes N, Williams R, Garza-Garcia A, Larrouy-Maumus G. Expression of a novel mycobacterial phosphodiesterase successfully lowers cAMP levels resulting in reduced tolerance to cell wall-targeting antimicrobials. J Biol Chem 2022; 298:102151. [PMID: 35718063 PMCID: PMC9293780 DOI: 10.1016/j.jbc.2022.102151] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 02/09/2023] Open
Abstract
cAMP and antimicrobial susceptibility in mycobacteriaAntimicrobial tolerance, the ability to survive exposure to antimicrobials via transient nonspecific means, promotes the development of antimicrobial resistance (AMR). The study of the molecular mechanisms that result in antimicrobial tolerance is therefore essential for the understanding of AMR. In gram-negative bacteria, the second messenger molecule 3'',5''-cAMP has been previously shown to be involved in AMR. In mycobacteria, however, the role of cAMP in antimicrobial tolerance has been difficult to probe due to its particular complexity. In order to address this difficulty, here, through unbiased biochemical approaches consisting in the fractionation of clear protein lysate from a mycobacterial strain deleted for the known cAMP phosphodiesterase (Rv0805c) combined with mass spectrometry techniques, we identified a novel cyclic nucleotide-degrading phosphodiesterase enzyme (Rv1339) and developed a system to significantly decrease intracellular cAMP levels through plasmid expression of Rv1339 using the constitutive expression system, pVV16. In Mycobacterium smegmatis mc2155, we demonstrate that recombinant expression of Rv1339 reduced cAMP levels threefold and resulted in altered gene expression, impaired bioenergetics, and a disruption in peptidoglycan biosynthesis leading to decreased tolerance to antimicrobials that target cell wall synthesis such as ethambutol, D-cycloserine, and vancomycin. This work increases our understanding of the role of cAMP in mycobacterial antimicrobial tolerance, and our observations suggest that nucleotide signaling may represent a new target for the development of antimicrobial therapies.
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Affiliation(s)
- Michael Thomson
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Yi Liu
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Kanokkan Nunta
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Ashleigh Cheyne
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Nadia Fernandes
- Imperial BRC Genomics Facility, Imperial College London, London, United Kingdom
| | - Richard Williams
- Imperial BRC Genomics Facility, Imperial College London, London, United Kingdom
| | | | - Gerald Larrouy-Maumus
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom,For correspondence: Gerald Larrouy-Maumus
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12
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TIR domains as two-tiered enzymes to activate plant immunity. Cell 2022; 185:2208-2209. [DOI: 10.1016/j.cell.2022.05.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 05/26/2022] [Accepted: 05/26/2022] [Indexed: 11/17/2022]
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13
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Campos ML. Round and round it goes: a cyclic nucleotide modulates stress responses in plants. PLANT PHYSIOLOGY 2022; 188:1942-1943. [PMID: 35355054 PMCID: PMC8968291 DOI: 10.1093/plphys/kiac004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
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14
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Chodasiewicz M, Kerber O, Gorka M, Moreno JC, Maruri-Lopez I, Minen RI, Sampathkumar A, Nelson ADL, Skirycz A. 2',3'-cAMP treatment mimics the stress molecular response in Arabidopsis thaliana. PLANT PHYSIOLOGY 2022; 188:1966-1978. [PMID: 35043968 PMCID: PMC8968299 DOI: 10.1093/plphys/kiac013] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/01/2021] [Indexed: 05/12/2023]
Abstract
The role of the RNA degradation product 2',3'-cyclic adenosine monophosphate (2',3'-cAMP) is poorly understood. Recent studies have identified 2',3'-cAMP in plant material and determined its role in stress signaling. The level of 2',3'-cAMP increases upon wounding, in the dark, and under heat, and 2',3'-cAMP binding to an RNA-binding protein, Rbp47b, promotes stress granule (SG) assembly. To gain further mechanistic insights into the function of 2',3'-cAMP, we used a multi-omics approach by combining transcriptomics, metabolomics, and proteomics to dissect the response of Arabidopsis (Arabidopsis thaliana) to 2',3'-cAMP treatment. We demonstrated that 2',3'-cAMP is metabolized into adenosine, suggesting that the well-known cyclic nucleotide-adenosine pathway of human cells might also exist in plants. Transcriptomics analysis revealed only minor overlap between 2',3'-cAMP- and adenosine-treated plants, suggesting that these molecules act through independent mechanisms. Treatment with 2',3'-cAMP changed the levels of hundreds of transcripts, proteins, and metabolites, many previously associated with plant stress responses, including protein and RNA degradation products, glucosinolates, chaperones, and SG components. Finally, we demonstrated that 2',3'-cAMP treatment influences the movement of processing bodies, confirming the role of 2',3'-cAMP in the formation and motility of membraneless organelles.
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Affiliation(s)
| | - Olga Kerber
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Michal Gorka
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Juan C Moreno
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Israel Maruri-Lopez
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Romina I Minen
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, USA
| | - Arun Sampathkumar
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Andrew D L Nelson
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, USA
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15
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BdGUCD1 and Cyclic GMP Are Required for Responses of Brachypodium distachyon to Fusarium pseudograminearum in the Mechanism Involving Jasmonate. Int J Mol Sci 2022; 23:ijms23052674. [PMID: 35269814 PMCID: PMC8910563 DOI: 10.3390/ijms23052674] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/26/2022] [Accepted: 02/27/2022] [Indexed: 01/25/2023] Open
Abstract
Guanosine 3′,5′-cyclic monophosphate (cGMP) is an important signaling molecule in plants. cGMP and guanylyl cyclases (GCs), enzymes that catalyze the synthesis of cGMP from GTP, are involved in several physiological processes and responses to environmental factors, including pathogen infections. Using in vitro analysis, we demonstrated that recombinant BdGUCD1 is a protein with high guanylyl cyclase activity and lower adenylyl cyclase activity. In Brachypodium distachyon, infection by Fusarium pseudograminearum leads to changes in BdGUCD1 mRNA levels, as well as differences in endogenous cGMP levels. These observed changes may be related to alarm reactions induced by pathogen infection. As fluctuations in stress phytohormones after infection have been previously described, we performed experiments to determine the relationship between cyclic nucleotides and phytohormones. The results revealed that inhibition of cellular cGMP changes disrupts stress phytohormone content and responses to pathogen. The observations made here allow us to conclude that cGMP is an important element involved in the processes triggered as a result of infection and changes in its levels affect jasmonic acid. Therefore, stimuli-induced transient elevation of cGMP in plants may play beneficial roles in priming an optimized response, likely by triggering the mechanisms of feedback control.
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16
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Duggal Y, Kurasz JE, Fontaine BM, Marotta NJ, Chauhan SS, Karls AC, Weinert EE. Cellular Effects of 2',3'-Cyclic Nucleotide Monophosphates in Gram-Negative Bacteria. J Bacteriol 2022; 204:e0020821. [PMID: 34662237 PMCID: PMC8765455 DOI: 10.1128/jb.00208-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 10/06/2021] [Indexed: 12/13/2022] Open
Abstract
Organismal adaptations to environmental stimuli are governed by intracellular signaling molecules such as nucleotide second messengers. Recent studies have identified functional roles for the noncanonical 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) in both eukaryotes and prokaryotes. In Escherichia coli, 2',3'-cNMPs are produced by RNase I-catalyzed RNA degradation, and these cyclic nucleotides modulate biofilm formation through unknown mechanisms. The present work dissects cellular processes in E. coli and Salmonella enterica serovar Typhimurium that are modulated by 2',3'-cNMPs through the development of cell-permeable 2',3'-cNMP analogs and a 2',3'-cyclic nucleotide phosphodiesterase. Utilization of these chemical and enzymatic tools, in conjunction with phenotypic and transcriptomic investigations, identified pathways regulated by 2',3'-cNMPs, including flagellar motility and biofilm formation, and by oligoribonucleotides with 3'-terminal 2',3'-cyclic phosphates, including responses to cellular stress. Furthermore, interrogation of metabolomic and organismal databases has identified 2',3'-cNMPs in numerous organisms and homologs of the E. coli metabolic proteins that are involved in key eukaryotic pathways. Thus, the present work provides key insights into the roles of these understudied facets of nucleotide metabolism and signaling in prokaryotic physiology and suggest broad roles for 2',3'-cNMPs among bacteria and eukaryotes. IMPORTANCE Bacteria adapt to environmental challenges by producing intracellular signaling molecules that control downstream pathways and alter cellular processes for survival. Nucleotide second messengers serve to transduce extracellular signals and regulate a wide array of intracellular pathways. Recently, 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) were identified as contributing to the regulation of cellular pathways in eukaryotes and prokaryotes. In this study, we define previously unknown cell processes that are affected by fluctuating 2',3'-cNMP levels or RNA oligomers with 2',3'-cyclic phosphate termini in E. coli and Salmonella Typhimurium, providing a framework for studying novel signaling networks in prokaryotes. Furthermore, we utilize metabolomics databases to identify additional prokaryotic and eukaryotic species that generate 2',3'-cNMPs as a resource for future studies.
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Affiliation(s)
- Yashasvika Duggal
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA
| | | | | | - Nick J. Marotta
- Molecular, Cellular and Integrative Biosciences Program, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Shikha S. Chauhan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Anna C. Karls
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Emily E. Weinert
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
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17
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Braun F, Recalde A, Bähre H, Seifert R, Albers SV. Putative Nucleotide-Based Second Messengers in the Archaeal Model Organisms Haloferax volcanii and Sulfolobus acidocaldarius. Front Microbiol 2021; 12:779012. [PMID: 34880846 PMCID: PMC8646023 DOI: 10.3389/fmicb.2021.779012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/01/2021] [Indexed: 12/16/2022] Open
Abstract
Research on nucleotide-based second messengers began in 1956 with the discovery of cyclic adenosine monophosphate (3′,5′-cAMP) by Earl Wilbur Sutherland and his co-workers. Since then, a broad variety of different signaling molecules composed of nucleotides has been discovered. These molecules fulfill crucial tasks in the context of intracellular signal transduction. The vast majority of the currently available knowledge about nucleotide-based second messengers originates from model organisms belonging either to the domain of eukaryotes or to the domain of bacteria, while the archaeal domain is significantly underrepresented in the field of nucleotide-based second messenger research. For several well-stablished eukaryotic and/or bacterial nucleotide-based second messengers, it is currently not clear whether these signaling molecules are present in archaea. In order to shed some light on this issue, this study analyzed cell extracts of two major archaeal model organisms, the euryarchaeon Haloferax volcanii and the crenarchaeon Sulfolobus acidocaldarius, using a modern mass spectrometry method to detect a broad variety of currently known nucleotide-based second messengers. The nucleotides 3′,5′-cAMP, cyclic guanosine monophosphate (3′,5′-cGMP), 5′-phosphoadenylyl-3′,5′-adenosine (5′-pApA), diadenosine tetraphosphate (Ap4A) as well as the 2′,3′-cyclic isomers of all four RNA building blocks (2′,3′-cNMPs) were present in both species. In addition, H. volcanii cell extracts also contain cyclic cytosine monophosphate (3′,5′-cCMP), cyclic uridine monophosphate (3′,5′-cUMP) and cyclic diadenosine monophosphate (3′,5′-c-di-AMP). The widely distributed bacterial second messengers cyclic diguanosine monophosphate (3′,5′-c-di-GMP) and guanosine (penta-)/tetraphosphate [(p)ppGpp] could not be detected. In summary, this study gives a comprehensive overview on the presence of a large set of currently established or putative nucleotide-based second messengers in an eury- and a crenarchaeal model organism.
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Affiliation(s)
- Frank Braun
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Freiburg, Germany
| | - Alejandra Recalde
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Freiburg, Germany
| | - Heike Bähre
- Research Core Unit Metabolomics, Hannover Medical School, Hanover, Germany
| | - Roland Seifert
- Research Core Unit Metabolomics, Hannover Medical School, Hanover, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Freiburg, Germany
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18
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Yin X, Liu S, Qin Y, Xing R, Li K, Yu C, Chen X, Li P. Metabonomics analysis of drought resistance of wheat seedlings induced by β-aminobutyric acid-modified chitooligosaccharide derivative. Carbohydr Polym 2021; 272:118437. [PMID: 34420706 DOI: 10.1016/j.carbpol.2021.118437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/30/2021] [Accepted: 07/10/2021] [Indexed: 01/17/2023]
Abstract
Chitooligosaccharide grafted with β-aminobutyric acid based on the idea of bioactive molecular splicing was prepared, and the differences in drought resistance activity before and after grafting were compared. The mechanism was investigated by comparing the differences of the derivative with the Control and Drought about metabolomes. The results showed that the expected derivative was successfully synthesized, named COS-BABA, and had better drought resistance-inducing activity than the raw materials. We suggest that COS-BABA induced drought resistance through second messenger-induced activation of signaling pathways related to traumatic acid and indol-3-lactic acid, which enhanced nucleic acid metabolism to accumulate nucleotides and decreased some amino acids to facilitate protein synthesis. These proteins are regulated to strengthen photosynthesis, resulting in the promotion of carbohydrate metabolism. The accumulation of unsaturated fatty acids stabilized the cell membrane structure and prevented nonstomatal water dissipation. This study provides ideas for the development of more effective drought resistance inducers.
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Affiliation(s)
- Xiujing Yin
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Song Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China.
| | - Yukun Qin
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Ronge Xing
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Kecheng Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Chunlin Yu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Xiaolin Chen
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Pengcheng Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
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19
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Xu R, Guo Y, Peng S, Liu J, Li P, Jia W, Zhao J. Molecular Targets and Biological Functions of cAMP Signaling in Arabidopsis. Biomolecules 2021; 11:biom11050688. [PMID: 34063698 PMCID: PMC8147800 DOI: 10.3390/biom11050688] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 01/11/2023] Open
Abstract
Cyclic AMP (cAMP) is a pivotal signaling molecule existing in almost all living organisms. However, the mechanism of cAMP signaling in plants remains very poorly understood. Here, we employ the engineered activity of soluble adenylate cyclase to induce cellular cAMP elevation in Arabidopsis thaliana plants and identify 427 cAMP-responsive genes (CRGs) through RNA-seq analysis. Induction of cellular cAMP elevation inhibits seed germination, disturbs phytohormone contents, promotes leaf senescence, impairs ethylene response, and compromises salt stress tolerance and pathogen resistance. A set of 62 transcription factors are among the CRGs, supporting a prominent role of cAMP in transcriptional regulation. The CRGs are significantly overrepresented in the pathways of plant hormone signal transduction, MAPK signaling, and diterpenoid biosynthesis, but they are also implicated in lipid, sugar, K+, nitrate signaling, and beyond. Our results provide a basic framework of cAMP signaling for the community to explore. The regulatory roles of cAMP signaling in plant plasticity are discussed.
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Affiliation(s)
- Ruqiang Xu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China
- Correspondence: ; Tel.: +86-0371-6778-5095
| | - Yanhui Guo
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
| | - Song Peng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
| | - Jinrui Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
| | - Panyu Li
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
| | - Wenjing Jia
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
| | - Junheng Zhao
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
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20
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Sun J, Ning Y, Wang L, Wilkins KA, Davies JM. Damage Signaling by Extracellular Nucleotides: A Role for Cyclic Nucleotides in Elevating Cytosolic Free Calcium? FRONTIERS IN PLANT SCIENCE 2021; 12:788514. [PMID: 34925428 PMCID: PMC8675005 DOI: 10.3389/fpls.2021.788514] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 11/10/2021] [Indexed: 05/04/2023]
Abstract
Extracellular ATP (eATP) is now held to be a constitutive damage-associated molecular pattern (DAMP) that is released by wounding, herbivory or pathogen attack. The concentration of eATP must be tightly regulated as either depletion or overload leads to cell death. In Arabidopsis thaliana, sensing of eATP is by two plasma membrane legume-like lectin serine-threonine receptor kinases (P2K1 and P2K2), although other receptors are postulated. The transcriptional response to eATP is dominated by wound- and defense-response genes. Wounding and pathogen attack can involve the cyclic nucleotides cyclic AMP (cAMP) and cyclic GMP (cGMP) which, in common with eATP, can increase cytosolic-free Ca2+ as a second messenger. This perspective on DAMP signaling by eATP considers the possibility that the eATP pathway involves production of cyclic nucleotides to promote opening of cyclic nucleotide-gated channels and so elevates cytosolic-free Ca2+. In silico analysis of P2K1 and P2K2 reveals putative adenylyl and guanylyl kinase sequences that are the hallmarks of "moonlighting" receptors capable of cAMP and cGMP production. Further, an Arabidopsis loss of function cngc mutant was found to have an impaired increase in cytosolic-free Ca2+ in response to eATP. A link between eATP, cyclic nucleotides, and Ca2+ signaling therefore appears credible.
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Affiliation(s)
- Jian Sun
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou, China
| | - Youzheng Ning
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Limin Wang
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Katie A. Wilkins
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Julia M. Davies
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Julia M. Davies,
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21
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Lai JL, Zhang-Xuan D, Xiao-Hui JI, Xue-Gang L. Absorption and interaction mechanisms of uranium & cadmium in purple sweet potato(Ipomoea batatas L.). JOURNAL OF HAZARDOUS MATERIALS 2020; 400:123264. [PMID: 32947695 DOI: 10.1016/j.jhazmat.2020.123264] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 05/19/2023]
Abstract
The purpose of this study was to reveal the absorption and interaction mechanisms of uranium (U) & cadmium (Cd) in corps. Purple sweet potato (Ipomoea batatas L.) was selected as the experimental material. The absorption behavior of U and Cd in this crop and the effects on mineral nutrition were analyzed in a pot experiment. The interactions between U and Cd in purple sweet potato were analyzed using UPLC-MS metabolome analysis. The pot experiment confirmed that the root tuber of the purple sweet potato had accumulated U (1.68-5.16 mg kg-1) and Cd (0.78-2.02 mg kg-1) and would pose a health risk if consumed. Both U and Cd significantly interfered with the mineral nutrient of the roots. Metabolomics revealed that a total of 4865 metabolites were identified in roots. 643 (419 up; 224 down), 526 (332 up; 194 down) and 634 (428 up; 214 down) different metabolites (DEMs) were identified in the U, Cd, and U + Cd exposure groups. Metabolic pathway analysis showed that U and Cd induced the expression of plant hormones (the first messengers) and cyclic nucleotides (cAMP and cGMP, second messengers) in cells and regulated the primary/secondary metabolism of roots to induce resistance to U and Cd toxicity.
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Affiliation(s)
- Jin-Long Lai
- College of Environment and Resources, Southwest University of Science and Technology, Mianyang, 621010, China; School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China; Engineering Research Center of Biomass Materials, Ministry of Education, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Deng Zhang-Xuan
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - J I Xiao-Hui
- College of Environment and Resources, Southwest University of Science and Technology, Mianyang, 621010, China; College of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, 723000, China
| | - Luo Xue-Gang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China; Engineering Research Center of Biomass Materials, Ministry of Education, Southwest University of Science and Technology, Mianyang, 621010, China.
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22
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Kuznetsova AA, Akhmetgalieva AA, Ulyanova VV, Ilinskaya ON, Fedorova OS, Kuznetsov NA. Efficiency of RNA Hydrolysis by Binase from Bacillus pumilus: The Impact of Substrate Structure, Metal Ions, and Low Molecular Weight Nucleotide Compounds. Mol Biol 2020. [DOI: 10.1134/s0026893320050064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Jang GJ, Jang JC, Wu SH. Dynamics and Functions of Stress Granules and Processing Bodies in Plants. PLANTS 2020; 9:plants9091122. [PMID: 32872650 PMCID: PMC7570210 DOI: 10.3390/plants9091122] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 12/23/2022]
Abstract
RNA granules, such as stress granules and processing bodies, can balance the storage, degradation, and translation of mRNAs in diverse eukaryotic organisms. The sessile nature of plants demands highly versatile strategies to respond to environmental fluctuations. In this review, we discuss recent findings of the dynamics and functions of these RNA granules in plants undergoing developmental reprogramming or responding to environmental stresses. Special foci include the dynamic assembly, disassembly, and regulatory roles of these RNA granules in determining the fate of mRNAs.
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Affiliation(s)
- Geng-Jen Jang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan;
| | - Jyan-Chyun Jang
- Department of Horticulture and Crop Science, Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA;
| | - Shu-Hsing Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan;
- Correspondence: ; Tel.: +886-2-2787-1178
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24
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Kosmacz M, Sokołowska EM, Bouzaa S, Skirycz A. Towards a functional understanding of the plant metabolome. CURRENT OPINION IN PLANT BIOLOGY 2020; 55:47-51. [PMID: 32224339 DOI: 10.1016/j.pbi.2020.02.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/22/2020] [Accepted: 02/14/2020] [Indexed: 05/24/2023]
Abstract
Plants are true organic chemists-the chemical diversity of plant metabolomes goes hand in hand with functional diversity. New, often unexpected roles are being reported for both evolutionarily conserved and well-characterised central metabolites such as amino acids, nucleotides, and sugars, and for specialized/secondary metabolites such as carotenoids, glucosinolates, and terpenoids. Our review aims to highlight recent studies reporting novel roles of metabolites and to emphasize the importance of cell-wide identification of metabolite-protein complexes for the comprehensive, functional understanding of the plant metabolome.
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Affiliation(s)
- Monika Kosmacz
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Ewelina Maria Sokołowska
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Saad Bouzaa
- Laboratory of Genetic Resources and Biotechnology, Higher National Agronomic School (ENSA), Algiers, Algeria
| | - Aleksandra Skirycz
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany.
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25
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Zambon A, Righi V, Parenti F, Libertini E, Rossi MC, Mucci A. Nucleoside 2',3'-Cyclic Monophosphates in Aphanizomenon flos-aquae Detected through Nuclear Magnetic Resonance and Mass Spectrometry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:12780-12785. [PMID: 31647652 DOI: 10.1021/acs.jafc.9b05991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Aphanizomenon flos-aquae (AFA) cyanobacteria from Klamath Lake (Oregon) are considered a "superfood" due to their broad nutritional profile that has proved to have health-enhancing properties. The AFA metabolome is quite complex. Here, we present a study that, combining multinuclear 1H, 31P, and 13C Nuclear Magnetic Resonance (NMR) spectroscopy and high-resolution mass spectrometry, led to the detection of uncommon phosphorylated metabolites in AFA. We focused our attention on 31P NMR signals at 20 ppm, a chemical shift that usually points to the presence of phosphonates. The molecules contributing to 20 ppm 31P NMR signals revealed, instead, to be nucleoside 2',3'-cyclic monophosphates. These metabolites were fully characterized by multinuclear 1H, 31P, and 13C NMR spectroscopy and high-resolution mass spectrometry.
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Affiliation(s)
- Alfonso Zambon
- Dipartimento di Scienze Chimiche e Geologiche , Università di Modena e Reggio Emilia , Via G. Campi 103 , 41125 Modena , Italy
| | - Valeria Righi
- Dipartimento di Scienze per la Qualità della Vita , Università di Bologna , Campus Rimini, Corso D'Augusto 237 , 49921 Rimini , Italy
| | - Francesca Parenti
- Dipartimento di Scienze Chimiche e Geologiche , Università di Modena e Reggio Emilia , Via G. Campi 103 , 41125 Modena , Italy
| | - Emanuela Libertini
- Dipartimento di Scienze Chimiche e Geologiche , Università di Modena e Reggio Emilia , Via G. Campi 103 , 41125 Modena , Italy
| | - Maria Cecilia Rossi
- Centro Interdipartimentale Grandi Strumenti , Università di Modena e Reggio Emilia , via G. Campi 213/A , 41125 Modena , Italy
| | - Adele Mucci
- Dipartimento di Scienze Chimiche e Geologiche , Università di Modena e Reggio Emilia , Via G. Campi 103 , 41125 Modena , Italy
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Jackson EK, Mi Z, Janesko-Feldman K, Jackson TC, Kochanek PM. 2',3'-cGMP exists in vivo and comprises a 2',3'-cGMP-guanosine pathway. Am J Physiol Regul Integr Comp Physiol 2019; 316:R783-R790. [PMID: 30789788 PMCID: PMC6620655 DOI: 10.1152/ajpregu.00401.2018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/11/2019] [Accepted: 02/19/2019] [Indexed: 01/10/2023]
Abstract
The discovery in 2009 that 2',3'-cAMP exists in biological systems was rapidly followed by identification of 2',3'-cGMP in cell and tissue extracts. To determine whether 2',3'-cGMP exists in mammals under physiological conditions, we used ultraperformance LC-MS/MS to measure 2',3'-cAMP and 2',3'-cGMP in timed urine collections (via direct bladder cannulation) from 25 anesthetized mice. Urinary excretion rates (means ± SE) of 2',3'-cAMP (15.5 ± 1.8 ng/30 min) and 2',3'-cGMP (17.9 ± 1.9 ng/30 min) were similar. Mice also excreted 2'-AMP (3.6 ± 1.1 ng/20 min) and 3'-AMP (9.5 ± 1.2 ng/min), hydrolysis products of 2',3'-cAMP, and 2'-GMP (4.7 ± 1.7 ng/30 min) and 3'-GMP (12.5 ± 1.8 ng/30 min), hydrolysis products of 2',3'-cGMP. To validate that the chromatographic signals were from these endogenous noncanonical nucleotides, we repeated these experiments in mice (n = 18) lacking 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase), an enzyme known to convert 2',3'-cyclic nucleotides to their corresponding 2'-nucleotides. In CNPase-knockout mice, urinary excretions of 2',3'-cAMP, 3'-AMP, 2',3'-cGMP, and 3'-GMP were increased, while urinary excretions of 2'-AMP and 2'-GMP were decreased. Infusions of exogenous 2',3'-cAMP increased urinary excretion of 2',3'-cAMP, 2'-AMP, 3'-AMP, and adenosine, whereas infusions of exogenous 2',3'-cGMP increased excretion of 2',3'-cGMP, 2'-GMP, 3'-GMP, and guanosine. Together, these data suggest the endogenous existence of not only a 2',3'-cAMP-adenosine pathway (2',3'-cAMP → 2'-AMP/3'-AMP → adenosine), which was previously identified, but also a 2',3'-cGMP-guanosine pathway (2',3'-cGMP → 2'-GMP/3'-GMP → guanosine), observed here for the first time. Because it is well known that adenosine and guanosine protect tissues from injury, our data support the concept that both pathways may work together to protect tissues from injury.
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Affiliation(s)
- Edwin K Jackson
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
| | - Zaichuan Mi
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
| | - Keri Janesko-Feldman
- Safar Center for Resuscitation Research, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
| | - Travis C Jackson
- Safar Center for Resuscitation Research, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
| | - Patrick M Kochanek
- Safar Center for Resuscitation Research, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
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Sabetta W, Vandelle E, Locato V, Costa A, Cimini S, Bittencourt Moura A, Luoni L, Graf A, Viggiano L, De Gara L, Bellin D, Blanco E, de Pinto MC. Genetic buffering of cyclic AMP in Arabidopsis thaliana compromises the plant immune response triggered by an avirulent strain of Pseudomonas syringae pv. tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:590-606. [PMID: 30735606 DOI: 10.1111/tpj.14275] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 12/23/2018] [Accepted: 01/24/2019] [Indexed: 05/21/2023]
Abstract
Cyclic AMP plays important roles in different physiological processes, including plant defence responses. However, as little information is known on plant enzymes responsible for cAMP production/degradation, studies of cAMP functions have relied, to date, on non-specific pharmacological approaches. We therefore developed a more reliable approach, producing transgenic Arabidopsis thaliana lines overexpressing the 'cAMP-sponge' (cAS), a genetic tool that specifically buffers cAMP levels. In response to an avirulent strain of Pseudomonas syringae pv. tomato (PstAvrB), cAS plants showed a higher bacterial growth and a reduced hypersensitive cell death in comparison with wild-type (WT) plants. The low cAMP availability after pathogen infection delayed cytosolic calcium elevation, as well as hydrogen peroxide increase and induction of redox systems. The proteomic analysis, performed 24 h post-infection, indicated that a core of 49 proteins was modulated in both genotypes, while 16 and 42 proteins were uniquely modulated in WT and cAS lines, respectively. The involvement of these proteins in the impairment of defence response in cAS plants is discussed in this paper. Moreover, in silico analysis revealed that the promoter regions of the genes coding for proteins uniquely accumulating in WT plants shared the CGCG motif, a target of the calcium-calmodulin-binding transcription factor AtSR1 (Arabidopsis thaliana signal responsive1). Therefore, following pathogen perception, the low free cAMP content, altering timing and levels of defence signals, and likely acting in part through the mis-regulation of AtSR1 activity, affected the speed and strength of the immune response.
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Affiliation(s)
- Wilma Sabetta
- Institute of Biosciences and Bioresources, CNR, Research Division Bari, Via Amendola 165/A, 70126, Bari, Italy
| | - Elodie Vandelle
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Vittoria Locato
- Unit of Food Science and Human Nutrition, University Camps Bio-Medico of Rome, via Alvaro del Portillo, 21, 00128, Rome, Italy
| | - Alex Costa
- Department of Biosciences, University of Milan, Via G. Celoria 26, 20133, Milano, Italy
| | - Sara Cimini
- Unit of Food Science and Human Nutrition, University Camps Bio-Medico of Rome, via Alvaro del Portillo, 21, 00128, Rome, Italy
| | | | - Laura Luoni
- Department of Biosciences, University of Milan, Via G. Celoria 26, 20133, Milano, Italy
| | - Alexander Graf
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Luigi Viggiano
- Department of Biology, University of Bari "Aldo Moro", Via Orabona 4, 70125, Bari, Italy
| | - Laura De Gara
- Unit of Food Science and Human Nutrition, University Camps Bio-Medico of Rome, via Alvaro del Portillo, 21, 00128, Rome, Italy
| | - Diana Bellin
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Emanuela Blanco
- Institute of Biosciences and Bioresources, CNR, Research Division Bari, Via Amendola 165/A, 70126, Bari, Italy
| | - Maria C de Pinto
- Department of Biology, University of Bari "Aldo Moro", Via Orabona 4, 70125, Bari, Italy
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Fontaine BM, Martin KS, Garcia-Rodriguez JM, Jung C, Briggs L, Southwell JE, Jia X, Weinert EE. RNase I regulates Escherichia coli 2',3'-cyclic nucleotide monophosphate levels and biofilm formation. Biochem J 2018; 475:1491-1506. [PMID: 29555843 PMCID: PMC6452634 DOI: 10.1042/bcj20170906] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 03/13/2018] [Accepted: 03/16/2018] [Indexed: 12/15/2022]
Abstract
Regulation of nucleotide and nucleoside concentrations is critical for faithful DNA replication, transcription, and translation in all organisms, and has been linked to bacterial biofilm formation. Unusual 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) recently were quantified in mammalian systems, and previous reports have linked these nucleotides to cellular stress and damage in eukaryotes, suggesting an intriguing connection with nucleotide/nucleoside pools and/or cyclic nucleotide signaling. This work reports the first quantification of 2',3'-cNMPs in Escherichia coli and demonstrates that 2',3'-cNMP levels in E. coli are generated specifically from RNase I-catalyzed RNA degradation, presumably as part of a previously unidentified nucleotide salvage pathway. Furthermore, RNase I and 2',3'-cNMP levels are demonstrated to play an important role in controlling biofilm formation. This work identifies a physiological role for cytoplasmic RNase I and constitutes the first progress toward elucidating the biological functions of bacterial 2',3'-cNMPs.
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Affiliation(s)
- Benjamin M. Fontaine
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Kevin S. Martin
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | | | - Claire Jung
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Laura Briggs
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Jessica E. Southwell
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Xin Jia
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Emily E. Weinert
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
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Pan L, Meng C, Wang J, Ma X, Fan X, Yang Z, Zhou M, Zhang X. Integrated omics data of two annual ryegrass (Lolium multiflorum L.) genotypes reveals core metabolic processes under drought stress. BMC PLANT BIOLOGY 2018; 18:26. [PMID: 29378511 PMCID: PMC5789592 DOI: 10.1186/s12870-018-1239-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 01/17/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND Annual ryegrass (Lolium multiflorum L.) is a commercially important, widely distributed forage crop that is used in the production of hay and silage worldwide. Drought has been a severe environmental constraint in its production. Nevertheless, only a handful of studies have examined the impact of short-term drought stress on annual ryegrass. The aim of this study was to explore how stress-induced core metabolic processes enhance drought tolerance, or adaptation to drought, in annual ryegrass. RESULTS We profiled the transcriptomes, proteomes, and metabolomes of two annual ryegrass genotypes: the drought-resistant genotype "Abundant 10" and drought-susceptible genotype "Adrenalin 11." We identified differentially expressed metabolites and their corresponding proteins and transcripts that are involved in 23 core metabolic processes, in response to short-term drought stress. Protein-gene-metabolite correlation networks were built to reveal the relationships between the expression of transcripts, proteins, and metabolites in drought-resistant annual ryegrass. Furthermore, integrated metabolic pathways were used to observe changes in enzymes corresponding with levels of amino acids, lipids, carbohydrate conjugates, nucleosides, alkaloids and their derivatives, and pyridines and their derivatives. The resulting omics data underscored the significance of 23 core metabolic processes on the enhancement of drought tolerance or adaptation to drought in annual ryegrass. CONCLUSIONS The regulatory networks were inferred using MCoA and correlation analysis to reveal the relationships among the expression of transcripts, proteins, and metabolites that highlight the corresponding elements of these core metabolic pathways. Our results provide valuable insight into the molecular mechanisms of drought resistance, and represent a promising strategy toward the improvement of drought tolerance in annual ryegrass.
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Affiliation(s)
- Ling Pan
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Chen Meng
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, USA
| | - Xiao Ma
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiaomei Fan
- Vazyme Biotech Co., Ltd, Nanjing State Economy & Technology Development Zone, Red Maple Technology Industrial Park, Nanjing, China
| | - Zhongfu Yang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinquan Zhang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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Isner JC, Maathuis FJM. cGMP signalling in plants: from enigma to main stream. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:93-101. [PMID: 32291024 DOI: 10.1071/fp16337] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 11/25/2016] [Indexed: 05/05/2023]
Abstract
All living organisms communicate with their environment, and part of this dialogue is mediated by secondary messengers such as cyclic guanosine mono phosphate (cGMP). In plants, most of the specific components that allow production and breakdown of cGMP have now been identified apart from cGMP dependent phosphodiesterases, enzymes responsible for cGMP catabolism. Irrespectively, the role of cGMP in plant signal transductions is now firmly established with involvement of this nucleotide in development, stress response, ion homeostasis and hormone function. Within these areas, several consistent themes where cGMP may be particularly relevant are slowly emerging: these include regulation of cation fluxes, for example via cyclic nucleotide gated channels and in stomatal functioning. Many details of signalling pathways that incorporate cGMP remain to be unveiled. These include downstream targets other than a small number of ion channels, in particular cGMP dependent kinases. Improved genomics tools may help in this respect, especially since many proteins involved in cGMP signalling appear to have multiple and often overlapping functional domains which hampers identification on the basis of simple homology searches. Another open question regards the topographical distribution of cGMP signals are they cell limited? Does long distance cGMP signalling occur and if so, by what mechanisms? The advent of non-disruptive fluorescent reporters with high spatial and temporal resolution will provide a tool to accelerate progress in all these areas. Automation can facilitate large scale screens of mutants or the action of effectors that impact on cGMP signalling.
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Affiliation(s)
- Jean-Charles Isner
- School of Biological Sciences, Life Sciences Building, University of Bristol, Woodland Road, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
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31
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Jackson EK. Discovery and Roles of 2',3'-cAMP in Biological Systems. Handb Exp Pharmacol 2017; 238:229-252. [PMID: 26721674 DOI: 10.1007/164_2015_40] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In 2009, investigators using ultra-performance liquid chromatography-tandem mass spectrometry to measure, by selected reaction monitoring, 3',5'-cAMP in the renal venous perfusate from isolated, perfused kidneys detected a large signal at the same m/z transition (330 → 136) as 3',5'-cAMP but at a different retention time. Follow-up experiments demonstrated that this signal was due to a positional isomer of 3',5'-cAMP, namely, 2',3'-cAMP. Soon thereafter, investigative teams reported the detection of 2',3'-cAMP and other 2',3'-cNMPs (2',3'-cGMP, 2',3'-cCMP, and 2',3'-cUMP) in biological systems ranging from bacteria to plants to animals to humans. Injury appears to be the major stimulus for the release of these unique noncanonical cNMPs, which likely are formed by the breakdown of RNA. In mammalian cells in culture, in intact rat and mouse kidneys, and in mouse brains in vivo, 2',3'-cAMP is metabolized to 2'-AMP and 3'-AMP; and these AMPs are subsequently converted to adenosine. In rat and mouse kidneys and mouse brains, injury releases 2',3'-cAMP, 2'-AMP, and 3'-AMP into the extracellular compartment; and in humans, traumatic brain injury is associated with large increases in 2',3'-cAMP, 2'-AMP, 3'-AMP, and adenosine in the cerebrospinal fluid. These findings motivate the extracellular 2',3'-cAMP-adenosine pathway hypothesis: intracellular production of 2',3'-cAMP → export of 2',3'-cAMP → extracellular metabolism of 2',3'-cAMP to 2'-AMP and 3'-AMP → extracellular metabolism of 2'-AMP and 3'-AMP to adenosine. Since 2',3'-cAMP has been shown to activate mitochondrial permeability transition pores (mPTPs) leading to apoptosis and necrosis and since adenosine is generally tissue protective, the extracellular 2',3'-cAMP-adenosine pathway may be a protective mechanism [i.e., removes 2',3'-cAMP (an intracellular toxin) and forms adenosine (a tissue protectant)]. This appears to be the case in the brain where deficiency in CNPase (the enzyme that metabolizes 2',3'-cAMP to 2-AMP) leads to increased susceptibility to brain injury and neurological diseases. Surprisingly, CNPase deficiency in the kidney actually protects against acute kidney injury, perhaps by preventing the formation of 2'-AMP (which turns out to be a renal vasoconstrictor) and by augmenting the mitophagy of damaged mitochondria. With regard to 2',3'-cNMPs and their downstream metabolites, there is no doubt much more to be discovered.
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Affiliation(s)
- Edwin K Jackson
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, 100 Technology Drive, Room 514, Pittsburgh, PA, 15219, USA.
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Gehring C, Turek IS. Cyclic Nucleotide Monophosphates and Their Cyclases in Plant Signaling. FRONTIERS IN PLANT SCIENCE 2017; 8:1704. [PMID: 29046682 PMCID: PMC5632652 DOI: 10.3389/fpls.2017.01704] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/19/2017] [Indexed: 05/19/2023]
Abstract
The cyclic nucleotide monophosphates (cNMPs), and notably 3',5'-cyclic guanosine monophosphate (cGMP) and 3',5'-cyclic adenosine monophosphate (cAMP) are now accepted as key signaling molecules in many processes in plants including growth and differentiation, photosynthesis, and biotic and abiotic defense. At the single molecule level, we are now beginning to understand how cNMPs modify specific target molecules such as cyclic nucleotide-gated channels, while at the systems level, a recent study of the Arabidopsis cNMP interactome has identified novel target molecules with specific cNMP-binding domains. A major advance came with the discovery and characterization of a steadily increasing number of guanylate cyclases (GCs) and adenylate cyclases (ACs). Several of the GCs are receptor kinases and include the brassinosteroid receptor, the phytosulfokine receptor, the Pep receptor, the plant natriuretic peptide receptor as well as a nitric oxide sensor. We foresee that in the near future many more molecular mechanisms and biological roles of GCs and ACs and their catalytic products will be discovered and further establish cNMPs as a key component of plant responses to the environment.
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Affiliation(s)
- Chris Gehring
- Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Ilona S. Turek
- Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Leibniz Institute of Plant Biochemistry, Halle, Germany
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Selection of reference genes suitable for qRT-PCR expression profiling of biotic stress, nutrient deficiency and plant hormone responsive genes in bread wheat. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s40502-017-0282-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Sokurenko Y, Ulyanova V, Zelenikhin P, Kolpakov A, Blokhin D, Müller D, Klochkov V, Ilinskaya O. The Role of Metals in the Reaction Catalyzed by Metal-Ion-Independent Bacillary RNase. Bioinorg Chem Appl 2016; 2016:4121960. [PMID: 28096759 PMCID: PMC5209602 DOI: 10.1155/2016/4121960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/27/2016] [Accepted: 11/02/2016] [Indexed: 11/18/2022] Open
Abstract
Extracellular enzymes of intestinal microbiota are the key agents that affect functional activity of the body as they directly interact with epithelial and immune cells. Several species of the Bacillus genus, like Bacillus pumilus, a common producer of extracellular RNase binase, can populate the intestinal microbiome as a colonizing organism. Without involving metal ions as cofactors, binase depolymerizes RNA by cleaving the 3',5'-phosphodiester bond and generates 2',3'-cyclic guanosine phosphates in the first stage of a catalytic reaction. Maintained in the reaction mixture for more than one hour, such messengers can affect the human intestinal microflora and the human body. In the present study, we found that the rate of 2',3'-cGMP was growing in the presence of transition metals that stabilized the RNA structure. At the same time, transition metal ions only marginally reduced the amount of 2',3'-cGMP, blocking binase recognition sites of guanine at N7 of nucleophilic purine bases.
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Affiliation(s)
- Yulia Sokurenko
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya Str. 18, Kazan 420008, Russia
| | - Vera Ulyanova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya Str. 18, Kazan 420008, Russia
| | - Pavel Zelenikhin
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya Str. 18, Kazan 420008, Russia
| | - Alexey Kolpakov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya Str. 18, Kazan 420008, Russia
| | - Dmitriy Blokhin
- Institute of Physics, Kazan Federal University, Kremlevskaya Str. 16a, Kazan 420008, Russia
| | - Dieter Müller
- Institute for Anatomy and Cell Biology, Justus Liebig University Giessen, Aulweg 123, 35385 Giessen, Germany
| | - Vladimir Klochkov
- Institute of Physics, Kazan Federal University, Kremlevskaya Str. 16a, Kazan 420008, Russia
| | - Olga Ilinskaya
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya Str. 18, Kazan 420008, Russia
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Zhang Y, Agrebi R, Bellows LE, Collet JF, Kaever V, Gründling A. Evolutionary Adaptation of the Essential tRNA Methyltransferase TrmD to the Signaling Molecule 3',5'-cAMP in Bacteria. J Biol Chem 2016; 292:313-327. [PMID: 27881678 PMCID: PMC5217690 DOI: 10.1074/jbc.m116.758896] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 11/21/2016] [Indexed: 11/06/2022] Open
Abstract
The nucleotide signaling molecule 3',5'-cyclic adenosine monophosphate (3',5'-cAMP) plays important physiological roles, ranging from carbon catabolite repression in bacteria to mediating the action of hormones in higher eukaryotes, including human. However, it remains unclear whether 3',5'-cAMP is universally present in the Firmicutes group of bacteria. We hypothesized that searching for proteins that bind 3',5'-cAMP might provide new insight into this question. Accordingly, we performed a genome-wide screen and identified the essential Staphylococcus aureus tRNA m1G37 methyltransferase enzyme TrmD, which is conserved in all three domains of life as a tight 3',5'-cAMP-binding protein. TrmD enzymes are known to use S-adenosyl-l-methionine (AdoMet) as substrate; we have shown that 3',5'-cAMP binds competitively with AdoMet to the S. aureus TrmD protein, indicating an overlapping binding site. However, the physiological relevance of this discovery remained unclear, as we were unable to identify a functional adenylate cyclase in S. aureus and only detected 2',3'-cAMP but not 3',5'-cAMP in cellular extracts. Interestingly, TrmD proteins from Escherichia coli and Mycobacterium tuberculosis, organisms known to synthesize 3',5'-cAMP, did not bind this signaling nucleotide. Comparative bioinformatics, mutagenesis, and biochemical analyses revealed that the highly conserved Tyr-86 residue in E. coli TrmD is essential to discriminate between 3',5'-cAMP and the native substrate AdoMet. Combined with a phylogenetic analysis, these results suggest that amino acids in the substrate binding pocket of TrmD underwent an adaptive evolution to accommodate the emergence of adenylate cyclases and thus the signaling molecule 3',5'-cAMP. Altogether this further indicates that S. aureus does not produce 3',5'-cAMP, which would otherwise competitively inhibit an essential enzyme.
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Affiliation(s)
- Yong Zhang
- From the Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Rym Agrebi
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium.,de Duve Institute, Université Catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium, and
| | - Lauren E Bellows
- From the Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jean-François Collet
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium.,de Duve Institute, Université Catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium, and
| | - Volkhard Kaever
- Research Core Unit Metabolomics, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Angelika Gründling
- From the Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom,
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Liu A, Yu Y, Sheng Q, Zheng XY, Yang JY, Li PY, Shi M, Zhou BC, Zhang YZ, Chen XL. Identification of Four Kinds of 2',3'-cNMPs in Escherichia coli and a Method for Their Preparation. ACS Chem Biol 2016; 11:2414-9. [PMID: 27409357 DOI: 10.1021/acschembio.6b00426] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Four kinds of 2',3'-cNMPs have been identified in animals and plants, and their physiological roles are also suggested. However, in prokaryotes, while 2',3'-cCMP and 2',3'-cUMP are reported, 2',3'-cGMP or 2',3'-cAMP have never been identified from bacteria or archaea. In addition, there has been no biological method to prepare these cyclic nucleotides. During the study of a novel gene LfliZ from deep-sea bacterium Pseudoalteromonas sp. SM9913, we found that the recombinant LfliZ oligomers contained endogenous substrates, which were then identified to be 2',3'-cCMP, 2',3'-cUMP, 2',3'-cGMP, and 2',3'-cAMP, showing the first evidence for the biological existence of four kinds of 2',3'-cNMPs in prokaryotes. In addition, we further developed a biological method to simultaneously prepare four kinds of 2',3'-cNMPs from Escherichia coli through expressing LfliZ.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Yu-Zhong Zhang
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Ulyanova V, Shah Mahmud R, Dudkina E, Vershinina V, Domann E, Ilinskaya O. Phylogenetic distribution of extracellular guanyl-preferring ribonucleases renews taxonomic status of two Bacillus strains. J GEN APPL MICROBIOL 2016; 62:181-8. [PMID: 27373509 DOI: 10.2323/jgam.2016.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The potential of microbial ribonucleases as promising antitumor and antiviral agents, determines today's directions of their study. One direction is connected with biodiversity of RNases. We have analyzed completed and drafted Bacillus genomes deposited in GenBank for the presence of coding regions similar to the gene of an extracellular guanyl-preferring RNase of Bacillus amyloliquefaciens (barnase). Orthologues of the barnase gene were detected in 9 species out of 83. All of these belong to "B. subtilis" group within the genus. B. subtilis itself, as well as some other species within this group, lack such types of RNases. RNases similar to barnase were also found in species of "B. cereus" group as a part of plasmid-encoded S-layer toxins. It was also found that taxonomic states of culture collection strains, which were initially described based on a limited set of phenotypic characteristics, can be misleading and need to be confirmed. Using several approaches such as matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), sequencing of genes for 16S ribosomal RNA and RNA polymerase subunit beta followed by reconstruction of phylogenetic trees, we have re-identified two RNase-secreting Bacillus strains: B. thuringiensis B-388 which should be assigned as B. altitudinis B388 and B. intermedius 7P which should be renamed as B. pumilus 7P. Therefore, small secreted guanyl-preferring RNases are the feature of "B. subtilis" group only, which is characterized by distinctive lifestyle and adaptation strategies to environment.
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Affiliation(s)
- Vera Ulyanova
- Institute of Fundamental Medicine and Biology, Kazan Federal University
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Sabetta W, Vannini C, Sgobba A, Marsoni M, Paradiso A, Ortolani F, Bracale M, Viggiano L, Blanco E, de Pinto MC. Cyclic AMP deficiency negatively affects cell growth and enhances stress-related responses in tobacco Bright Yellow-2 cells. PLANT MOLECULAR BIOLOGY 2016; 90:467-83. [PMID: 26786166 DOI: 10.1007/s11103-016-0431-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 01/05/2016] [Indexed: 05/24/2023]
Abstract
Cyclic adenosine 3',5'-monophosphate (cAMP) is a recognized second messenger; however, knowledge of cAMP involvement in plant physiological processes originates primarily from pharmacological studies. To obtain direct evidence for cAMP function in plants, tobacco Bright Yellow-2 (BY-2) cells were transformed with the cAMP sponge, which is a genetically encoded tool that reduces cAMP availability. BY-2 cells expressing the cAMP sponge (cAS cells), showed low levels of free cAMP and exhibited growth inhibition that was not proportional to the cAMP sponge transcript level. Growth inhibition in cAS cells was closely related to the precocious inhibition of mitosis due to a delay in cell cycle progression. The cAMP deficiency also enhanced antioxidant systems. Remarkable changes occurred in the cAS proteomic profile compared with that of wild-type (WT) cells. Proteins involved in translation, cytoskeletal organization, and cell proliferation were down-regulated, whereas stress-related proteins were up-regulated in cAS cells. These results support the hypothesis that BY-2 cells sense cAMP deficiency as a stress condition. Finally, many proteasome subunits were differentially expressed in cAS cells compared with WT cells, indicating that cAMP signaling broadly affects protein degradation via the ubiquitin/proteasome pathway.
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Affiliation(s)
- Wilma Sabetta
- Istituto di Bioscienze e Biorisorse, CNR, Via G. Amendola 165/A, 70126, Bari, Italy
| | - Candida Vannini
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Via H. J. Dunant 3, 21100, Varese, Italy
| | - Alessandra Sgobba
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro", via E. Orabona 4, 70125, Bari, Italy
| | - Milena Marsoni
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Via H. J. Dunant 3, 21100, Varese, Italy
| | - Annalisa Paradiso
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro", via E. Orabona 4, 70125, Bari, Italy
| | - Francesca Ortolani
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Via H. J. Dunant 3, 21100, Varese, Italy
| | - Marcella Bracale
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Via H. J. Dunant 3, 21100, Varese, Italy
| | - Luigi Viggiano
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro", via E. Orabona 4, 70125, Bari, Italy
| | - Emanuela Blanco
- Istituto di Bioscienze e Biorisorse, CNR, Via G. Amendola 165/A, 70126, Bari, Italy
| | - Maria Concetta de Pinto
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro", via E. Orabona 4, 70125, Bari, Italy.
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Jackson EK, Boison D, Schwarzschild MA, Kochanek PM. Purines: forgotten mediators in traumatic brain injury. J Neurochem 2016; 137:142-53. [PMID: 26809224 DOI: 10.1111/jnc.13551] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 01/13/2016] [Accepted: 01/14/2016] [Indexed: 12/12/2022]
Abstract
Recently, the topic of traumatic brain injury has gained attention in both the scientific community and lay press. Similarly, there have been exciting developments on multiple fronts in the area of neurochemistry specifically related to purine biology that are relevant to both neuroprotection and neurodegeneration. At the 2105 meeting of the National Neurotrauma Society, a session sponsored by the International Society for Neurochemistry featured three experts in the field of purine biology who discussed new developments that are germane to both the pathomechanisms of secondary injury and development of therapies for traumatic brain injury. This included presentations by Drs. Edwin Jackson on the novel 2',3'-cAMP pathway in neuroprotection, Detlev Boison on adenosine in post-traumatic seizures and epilepsy, and Michael Schwarzschild on the potential of urate to treat central nervous system injury. This mini review summarizes the important findings in these three areas and outlines future directions for the development of new purine-related therapies for traumatic brain injury and other forms of central nervous system injury. In this review, novel therapies based on three emerging areas of adenosine-related pathobiology in traumatic brain injury (TBI) were proposed, namely, therapies targeting 1) the 2',3'-cyclic adenosine monophosphate (cAMP) pathway, 2) adenosine deficiency after TBI, and 3) augmentation of urate after TBI.
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Affiliation(s)
- Edwin K Jackson
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Detlev Boison
- Robert Stone Dow Neurobiology Laboratories, Legacy Research Institute, Portland, Oregon, USA
| | - Michael A Schwarzschild
- Department of Neurology, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Patrick M Kochanek
- Safar Center for Resuscitation Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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Druege U, Franken P, Hajirezaei MR. Plant Hormone Homeostasis, Signaling, and Function during Adventitious Root Formation in Cuttings. FRONTIERS IN PLANT SCIENCE 2016; 7:381. [PMID: 27064322 PMCID: PMC4814496 DOI: 10.3389/fpls.2016.00381] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 03/13/2016] [Indexed: 04/14/2023]
Abstract
Adventitious root (AR) formation in cuttings is a multiphase developmental process, resulting from wounding at the cutting site and isolation from the resource and signal network of the whole plant. Though, promotive effects of auxins are widely used for clonal plant propagation, the regulation and function of plant hormones and their intricate signaling networks during AR formation in cuttings are poorly understood. In this focused review, we discuss our recent publications on the involvement of polar auxin transport (PAT) and transcriptional regulation of auxin and ethylene action during AR formation in petunia cuttings in a broad context. Integrating new findings on cuttings of other plant species and general models on plant hormone networks, a model on the regulation and function of auxin, ethylene, and jasmonate in AR formation of cuttings is presented. PAT and cutting off from the basipetal auxin drain are considered as initial principles generating early accumulation of IAA in the rooting zone. This is expected to trigger a self-regulatory process of auxin canalization and maximization to responding target cells, there inducing the program of AR formation. Regulation of auxin homeostasis via auxin influx and efflux carriers, GH3 proteins and peroxidases, of flavonoid metabolism, and of auxin signaling via AUX/IAA proteins, TOPLESS, ARFs, and SAUR-like proteins are postulated as key processes determining the different phases of AR formation. NO and H2O2 mediate auxin signaling via the cGMP and MAPK cascades. Transcription factors of the GRAS-, AP2/ERF-, and WOX-families link auxin signaling to cell fate specification. Cyclin-mediated governing of the cell cycle, modifications of sugar metabolism and microtubule and cell wall remodeling are considered as important implementation processes of auxin function. Induced by the initial wounding and other abiotic stress factors, up-regulation of ethylene biosynthesis, and signaling via ERFs and early accumulation of jasmonic acid stimulate AR formation, while both pathways are linked to auxin. Future research on the function of candidate genes should consider their tissue-specific role and regulation by environmental factors. Furthermore, the whole cutting should be regarded as a system of physiological units with diverse functions specifically responding to the environment and determining the rooting response.
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Affiliation(s)
- Uwe Druege
- Department Plant Propagation, Leibniz Institute of Vegetable and Ornamental CropsErfurt, Germany
- *Correspondence:
| | - Philipp Franken
- Department Plant Propagation, Leibniz Institute of Vegetable and Ornamental CropsErfurt, Germany
| | - Mohammad R. Hajirezaei
- Department of Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
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Jackson EK, Menshikova EV, Mi Z, Verrier JD, Bansal R, Janesko-Feldman K, Jackson TC, Kochanek PM. Renal 2',3'-Cyclic Nucleotide 3'-Phosphodiesterase Is an Important Determinant of AKI Severity after Ischemia-Reperfusion. J Am Soc Nephrol 2015; 27:2069-81. [PMID: 26574047 DOI: 10.1681/asn.2015040397] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 10/07/2015] [Indexed: 12/31/2022] Open
Abstract
A positional isomer of 3',5'-cAMP, 2',3'-cAMP, is produced by kidneys in response to energy depletion, and renal 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) metabolizes 2',3'-cAMP to 2'-AMP; 2',3'-cAMP is a potent opener of mitochondrial permeability transition pores (mPTPs), which can stimulate autophagy. Because autophagy protects against AKI, it is conceivable that inhibition of CNPase protects against ischemia-reperfusion (IR) -induced AKI. Therefore, we investigated renal outcomes, mitochondrial function, number, area, and autophagy in CNPase-knockout (CNPase(-/-)) versus wild-type (WT) mice using a unique two-kidney, hanging-weight model of renal bilateral IR (20 minutes of ischemia followed by 48 hours of reperfusion). Analysis of urinary purines showed attenuated metabolism of 2',3'-cAMP to 2'-AMP in CNPase(-/-) mice. Neither genotype nor IR affected BP, heart rate, urine volume, or albumin excretion. In WT mice, renal IR reduced (14)C-inulin clearance (index of GFR) and increased renal vascular resistance (measured by transit time nanoprobes) and urinary excretion of kidney injury molecule-1 and neutrophil gelatinase-associated lipocalin. IR did not affect these parameters in CNPase(-/-) mice. Histologic analysis revealed that IR induced severe damage in kidneys from WT mice, whereas histologic changes were minimal after IR in CNPase(-/-) mice. Measurements of renal cardiolipin levels, citrate synthase activity, rotenone-sensitive NADH oxidase activity, and proximal tubular mitochondrial and autophagosome area and number (by transmission electron microscopy) indicted accelerated autophagy/mitophagy in injured CNPase(-/-) mice. We conclude that CNPase deletion attenuates IR-induced AKI, in part by accelerating autophagy with targeted removal of damaged mitochondria.
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Affiliation(s)
- Edwin K Jackson
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania;
| | - Elizabeth V Menshikova
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Zaichuan Mi
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jonathan D Verrier
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Rashmi Bansal
- Department of Neuroscience, University of Connecticut School of Medicine, Farmington, Connecticut; and
| | - Keri Janesko-Feldman
- Safar Center for Resuscitation Research and Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Travis C Jackson
- Safar Center for Resuscitation Research and Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Patrick M Kochanek
- Safar Center for Resuscitation Research and Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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Świeżawska B, Jaworski K, Szewczuk P, Pawełek A, Szmidt-Jaworska A. Identification of a Hippeastrum hybridum guanylyl cyclase responsive to wounding and pathogen infection. JOURNAL OF PLANT PHYSIOLOGY 2015; 189:77-86. [PMID: 26523507 DOI: 10.1016/j.jplph.2015.09.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 09/08/2015] [Accepted: 09/09/2015] [Indexed: 05/21/2023]
Abstract
Guanosine 3',5'-cyclic monophosphate (cGMP) is a critical component of many (patho)physiological processes in plants whilst guanylyl cyclases (GCs) which catalyse the formation of cGMP from GTP have remained somewhat elusive. Consequently, the two major aims are the discovery of novel guanylyl cyclases and the identification of GC/cGMP mediated processes. To identify a novel GC from Hippeastrum hybridum plant and facilitate the preparation of guanylyl cyclase in an amount sufficient for further crystallographic studies, we have constructed an overproduction system for this enzyme. This gene encodes a protein of 256 amino acids, with a calculated molecular mass of 28kD. The predicted amino acid sequence contains all the typical features and shows a high identity to other plant GCs. The GST-HpGC1 was catalytically active in Escherichia coli cells and the purified, recombinant HpGC1 was able to convert GTP to cGMP in the presence of divalent cations. The used overexpression system yields a guanylyl cyclase as 6% of the bacterial cytosolic protein. Besides the identification of HpGC1 as a guanylyl cyclase, the study has shown that the level of HpCG1 mRNA changed during stress conditions. Both mechanical damage and a Peyronellaea curtisii (=Phoma narcissi) fungi infection led to an initial decrease in the HpGC1 transcript level, followed by a substantial increase during the remainder of the 48-h test cycle. Moreover, significant changes in cyclic GMP level were observed, taking the form of oscillations. In conclusion, our data unequivocally identified the product of the HpGC1 gene as a guanylyl cyclase and demonstrates that such an overproduction system can be successfully used in enzyme synthesis. Furthermore, they indicate a link between the causing stimulus (wounding, infection) and guanylyl cyclase expression and the increase in cGMP amplitude. Therefore, it is concluded that appearance of cyclic GMP as a mediator in defense and wound-healing mechanisms provides a clue to the regulation of these processes.
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Abstract
As major contributors to global oxygen levels and producers of fatty acids, carotenoids, sterols, and phycocolloids, algae have significant ecological and commercial roles. Early algal models have contributed much to our understanding of circadian clocks at physiological and biochemical levels. The genetic and molecular approaches that identified clock components in other taxa have not been as widely applied to algae. We review results from seven species: the chlorophytes Chlamydomonas reinhardtii, Ostreococcus tauri, and Acetabularia spp.; the dinoflagellates Lingulodinium polyedrum and Symbiodinium spp.; the euglenozoa Euglena gracilis; and the red alga Cyanidioschyzon merolae. The relative simplicity, experimental tractability, and ecological and evolutionary diversity of algal systems may now make them particularly useful in integrating quantitative data from "omic" technologies (e.g., genomics, transcriptomics, metabolomics, and proteomics) with computational and mathematical methods.
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Affiliation(s)
- Zeenat B Noordally
- SynthSys and School of Biological Sciences, University of Edinburgh , Edinburgh EH9 3BF, United Kingdom
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A facile and sensitive method for quantification of cyclic nucleotide monophosphates in mammalian organs: basal levels of eight cNMPs and identification of 2',3'-cIMP. Biomolecules 2014; 4:1070-92. [PMID: 25513747 PMCID: PMC4279170 DOI: 10.3390/biom4041070] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 11/27/2014] [Accepted: 12/01/2014] [Indexed: 12/25/2022] Open
Abstract
A sensitive, versatile and economical method to extract and quantify cyclic nucleotide monophosphates (cNMPs) using LC-MS/MS, including both 3',5'-cNMPs and 2',3'-cNMPs, in mammalian tissues and cellular systems has been developed. Problems, such as matrix effects from complex biological samples, are addressed and have been optimized. This protocol allows for comparison of multiple cNMPs in the same system and was used to examine the relationship between tissue levels of cNMPs in a panel of rat organs. In addition, the study reports the first identification and quantification of 2',3'-cIMP. The developed method will allow for quantification of cNMPs levels in cells and tissues with varying disease states, which will provide insight into the role(s) and interplay of cNMP signalling pathways.
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