1
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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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2
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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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3
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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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4
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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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5
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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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6
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Van Damme T, Blancquaert D, Couturon P, Van Der Straeten D, Sandra P, Lynen F. Wounding stress causes rapid increase in concentration of the naturally occurring 2',3'-isomers of cyclic guanosine- and cyclic adenosine monophosphate (cGMP and cAMP) in plant tissues. PHYTOCHEMISTRY 2014; 103:59-66. [PMID: 24735826 DOI: 10.1016/j.phytochem.2014.03.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 02/16/2014] [Accepted: 03/10/2014] [Indexed: 05/21/2023]
Abstract
3',5'-Cyclic guanosine monophosphate (cGMP) and 3',5'-cyclic adenosine monophosphate (cAMP) are well reported second messenger molecules involved in cellular signal transduction, in physiological functions such as neurotransmission in animals and in the modulation of cell growth and differentiation. In plants, 3',5'-cyclic nucleotides have been implicated in the regulation of ion homeostasis, hormone and stress responses. The behavior of the 2',3'-cyclic nucleotide variants is also known in animal tissue but no quantitative information is available about 2',3'-cAMP and 2',3'-cGMP in plant material. A recently developed HILIC-SPE/LC-MS/MS method for the analysis of cyclic nucleotides in blood and animal tissue was therefore adapted to measure 2',3'-cAMP and 2',3'-cGMP concentrations in plant material. Cyclic nucleotide concentrations were measured in Arabidopsis thaliana (Col-0) leaves before and after the application of wounding stress. A significant (∼5-fold) up-regulation of 2',3'-cAMP and 2',3'-cGMP was measured in Arabidopsis leaves compared to the control samples. The results indicate a thus far unreported strong correlation between plant stress and both 2',3'-cAMP and 2',3'-cGMP levels in plant material, and may open new avenues towards understanding the role of cyclic nucleotides in plants.
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Affiliation(s)
- Thomas Van Damme
- Department of Organic Chemistry, Pfizer Analytical Research Center, Ghent University, Krijgslaan 281 S4-bis, B-9000 Ghent, Belgium
| | - Dieter Blancquaert
- Laboratory of Functional Plant Biology, Department of Physiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Pauline Couturon
- Department of Organic Chemistry, Separation Science Group, Ghent University, Krijgslaan 281 S4-bis, B-9000 Ghent, Belgium
| | - Dominique Van Der Straeten
- Laboratory of Functional Plant Biology, Department of Physiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Pat Sandra
- Department of Organic Chemistry, Pfizer Analytical Research Center, Ghent University, Krijgslaan 281 S4-bis, B-9000 Ghent, Belgium; Department of Organic Chemistry, Separation Science Group, Ghent University, Krijgslaan 281 S4-bis, B-9000 Ghent, Belgium
| | - Frédéric Lynen
- Department of Organic Chemistry, Pfizer Analytical Research Center, Ghent University, Krijgslaan 281 S4-bis, B-9000 Ghent, Belgium; Department of Organic Chemistry, Separation Science Group, Ghent University, Krijgslaan 281 S4-bis, B-9000 Ghent, Belgium.
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7
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Lomovatskaya LA, Romanenko AS, Filinova NV, Dudareva LV. Determination of cAMP in plant cells by a modified enzyme immunoassay method. PLANT CELL REPORTS 2011; 30:125-132. [PMID: 21076834 DOI: 10.1007/s00299-010-0950-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 10/29/2010] [Accepted: 10/29/2010] [Indexed: 05/30/2023]
Abstract
Presently, there is no doubt about the functioning of the adenylate cyclase signaling system in plants, but the role of this system in various physiological-biochemical processes has been investigated insufficiently. Cyclic adenosine monophosphate (cAMP), the key component produced by adenylate cyclase, whose concentrations in plant cells vary rather widely, is the indicator of functional activity for this signaling way. In the latter case, in the process of determination of concentrations of this messenger, one encounters difficulties related to insufficient sensitivity of the methods most frequently applied. In this connection, the proposed mechanism is a modification of the method of the enzyme immunoassay (EIA), which is based on immediate measurement of cAMP concentrations in the sample with the use of antibodies. This modification allows us to determine the concentrations of cAMP with the precision of 5 pM, which exceeds the sensitivity of other methods by approximately 10 times. The specificity of the assay has been confirmed by other two independent tests--the capillary electrophoresis and the nuclear magnetic resonance (NMR). It has also been compared to the data obtained with the use of the commercial kit from Sigma-Aldrich. The modification has been tested on such plant objects as in vitro potato plants, and suspension cells of potato and Arabidopsis.
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Affiliation(s)
- L A Lomovatskaya
- Laboratory of Phytoimmunology, Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia.
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8
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Ma W, Qi Z, Smigel A, Walker RK, Verma R, Berkowitz GA. Ca2+, cAMP, and transduction of non-self perception during plant immune responses. Proc Natl Acad Sci U S A 2009; 106:20995-1000. [PMID: 19933332 PMCID: PMC2780315 DOI: 10.1073/pnas.0905831106] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Indexed: 01/20/2023] Open
Abstract
Ca(2+) influx is an early signal initiating cytosolic immune responses to pathogen perception in plant cells; molecular components linking pathogen recognition to Ca(2+) influx are not delineated. Work presented here provides insights into this biological system of non-self recognition and response activation. We have recently identified a cyclic nucleotide-activated ion channel as facilitating the Ca(2+) flux that initiates immune signaling in the plant cell cytosol. Work in this report shows that elevation of cAMP is a key player in this signaling cascade. We show that cytosolic Ca(2+) elevation, nitric oxide (NO) and reactive oxygen species generation, as well as immune signaling, lead to a hypersensitive response upon application of pathogens and/or conserved molecules that are components of microbes and are all dependent on cAMP generation. Exogenous cAMP leads to Ca(2+) channel-dependent cytosolic Ca(2+) elevation, NO generation, and defense response gene expression in the absence of the non-self pathogen signal. Inoculation of leaves with a bacterial pathogen leads to cAMP elevation coordinated with Ca(2+) rise. cAMP acts as a secondary messenger in plants; however, no specific protein has been heretofore identified as activated by cAMP in a manner associated with a signaling cascade in plants, as we report here. Our linkage of cAMP elevation in pathogen-inoculated plant leaves to Ca(2+) channels and immune signaling downstream from cytosolic Ca(2+) elevation provides a model for how non-self detection can be transduced to initiate the cascade of events in the cell cytosol that orchestrate pathogen defense responses.
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Affiliation(s)
- Wei Ma
- Agricultural Biotechnology Laboratory, Department of Plant Science, University of Connecticut, 1390 Storrs Road, Storrs, CT 06269-4163
| | - Zhi Qi
- Agricultural Biotechnology Laboratory, Department of Plant Science, University of Connecticut, 1390 Storrs Road, Storrs, CT 06269-4163
| | - Andries Smigel
- Agricultural Biotechnology Laboratory, Department of Plant Science, University of Connecticut, 1390 Storrs Road, Storrs, CT 06269-4163
| | - Robin K. Walker
- Agricultural Biotechnology Laboratory, Department of Plant Science, University of Connecticut, 1390 Storrs Road, Storrs, CT 06269-4163
| | - Rajeev Verma
- Agricultural Biotechnology Laboratory, Department of Plant Science, University of Connecticut, 1390 Storrs Road, Storrs, CT 06269-4163
| | - Gerald A. Berkowitz
- Agricultural Biotechnology Laboratory, Department of Plant Science, University of Connecticut, 1390 Storrs Road, Storrs, CT 06269-4163
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9
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Transduction mechanisms of photoreceptor signals in plant cells. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2009. [DOI: 10.1016/j.jphotochemrev.2009.04.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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10
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Uematsu K, Fukui Y. Role and regulation of cAMP in seed germination of Phacelia tanacetifolia. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2008; 46:768-774. [PMID: 18657429 DOI: 10.1016/j.plaphy.2007.10.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2007] [Indexed: 05/26/2023]
Abstract
Although adenosine 3',5'-cyclic monophosphate (cAMP) is known as a key second messenger in many living organisms, regulating a wide range of cellular responses, its biological function in higher plants is not well understood. In this study, the role and the regulation mechanism of cAMP in seed germination of Phacelia tanacetifolia Benth. were examined. The cAMP level of the seeds incubated under optimal conditions for germination showed a transient elevation before germination. When the seeds were exposed to light or supraoptimal temperature during incubation, elevation of cAMP levels as well as germination of the seeds were inhibited. Addition of membrane-permeable cAMP to the medium restored the germination rates of these seeds, suggesting that cAMP functions during germination. Treatment of the seeds with gibberellin (GA) was also effective to restore the elevation of cAMP levels and germination of the seeds. Uniconazole, a potent inhibitor of GA biosynthesis, blocked elevation of cAMP level under optimal conditions for germination. These results suggest that cAMP plays a role in the regulation of germination and that the cAMP level is regulated by GA in P. tanacetifolia seeds.
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Affiliation(s)
- Kimio Uematsu
- Department of Applied Biological Chemistry, Laboratory of Biological Chemistry, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, Japan
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11
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Cordell RL, Hill SJ, Ortori CA, Barrett DA. Quantitative profiling of nucleotides and related phosphate-containing metabolites in cultured mammalian cells by liquid chromatography tandem electrospray mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2008; 871:115-24. [PMID: 18650133 DOI: 10.1016/j.jchromb.2008.07.005] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2008] [Revised: 07/08/2008] [Accepted: 07/09/2008] [Indexed: 11/19/2022]
Abstract
A method has been developed for the quantitative profiling of over twenty nucleotides and related phosphorylated species using ion-pair reversed-phase liquid chromatography hyphenated to negative ion tandem electrospray mass spectrometry. The influence of mobile phase pH and ion-pairing agent concentration were assessed to optimise separation and peak shapes. Full quantitative analysis was obtained for the nucleotides by reference to structurally related calibration standards. The developed method was applied to profile changes in nucleotides and related compounds in monolayer cultured Chinese hamster ovary (CHO) cells expressing the beta(2) adrenoceptor when exposed to pharmacological stimuli. These experiments demonstrate the potential of the LC-MS/MS method to detect changes in nucleotide drug targets as well as the simultaneous monitoring of levels of other nucleotides.
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Affiliation(s)
- Rebecca L Cordell
- Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, Nottingham, UK
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12
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Sun G, Yang K, Zhao Z, Guan S, Han X, Gross RW. Shotgun metabolomics approach for the analysis of negatively charged water-soluble cellular metabolites from mouse heart tissue. Anal Chem 2007; 79:6629-40. [PMID: 17665876 PMCID: PMC2981504 DOI: 10.1021/ac070843+] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A shotgun metabolomics approach using MALDI-TOF/TOF mass spectrometry was developed for the rapid analysis of negatively charged water-soluble cellular metabolites. Through the use of neutral organic solvents to inactivate endogenous enzyme activities (i.e., methanol/chloroform/H2O extraction), in conjunction with a matrix having minimal background noise (9-amnioacridine), a set of multiplexed conditions was developed that allowed identification of 285 peaks corresponding to negatively charged metabolites from mouse heart extracts. Identification of metabolite peaks was based on mass accuracy and was confirmed by tandem mass spectrometry for 90 of the identified metabolite peaks. Through multiplexing ionization conditions, new suites of metabolites could be ionized and "spectrometric isolation" of closely neighboring peaks for subsequent tandem mass spectrometric interrogation could be achieved. Moreover, assignments of ions from isomeric metabolites and quantitation of their relative abundance was achieved in many cases through tandem mass spectrometry by identification of diagnostic fragmentation ions (e.g., discrimination of ATP from dGTP). The high sensitivity of this approach facilitated the detection of extremely low abundance metabolites including important signaling metabolites such as IP3, cAMP, and cGMP. Collectively, these results identify a multiplexed MALDI-TOF/TOF MS approach for analysis of negatively charged metabolites in mammalian tissues.
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Affiliation(s)
| | | | | | | | | | - Richard W. Gross
- To whom correspondence should be addressed. Tel.: 314-362-2690. Fax: 314-362-1402.
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13
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Riondet C, Morel S, Alcaraz G. Determination of total ribonucleotide pool in plant materials by high-pH anion-exchange high-performance liquid chromatography following extraction with potassium hydroxide. J Chromatogr A 2005; 1077:120-7. [PMID: 16001547 DOI: 10.1016/j.chroma.2005.04.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A new, improved method that only requires a potassium hydroxide extraction procedure is presented for the analysis of a full nucleotide pool in plant materials. Quantification was performed by high-pH anion-exchange chromatography (HPAEC) with UV detection after a potassium hydroxide extraction, and allowed the quantification of 13 linear ribonucleotides in a single run. The method has been validated by comparison of six extraction methods and also by measurement of the intracellular nucleotide levels of three plant species (cell cultures and leaves). The evolution of the nucleotide pool of Nicotiana tabacum cell culture during growth has also been measured, and showed an increase in the pool until the fifth day, where the growth rate reaches a maximum, after which a decrease was observed.
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Affiliation(s)
- Christophe Riondet
- Laboratoire de Physiologie et de Biochimie Végétale, UMR 692 INRA-ENESAD-Université de Bourgogne, ENESAD 26, Boulevard Dr. Petitjean, B.P. 87999, 21079 Dijon, France
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14
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Skirycz A, Świędrych A, Szopa J. Expression of human dopamine receptor in potato (Solanum tuberosum) results in altered tuber carbon metabolism. BMC PLANT BIOLOGY 2005; 5:1. [PMID: 16080795 PMCID: PMC549537 DOI: 10.1186/1471-2229-5-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2004] [Accepted: 02/09/2005] [Indexed: 05/05/2023]
Abstract
BACKGROUND Even though the catecholamines (dopamine, norepinephrine and epinephrine) have been detected in plants their role is poorly documented. Correlations between norepinephrine, soluble sugars and starch concentration have been recently reported for potato plants over-expressing tyrosine decarboxylase, the enzyme mediating the first step of catecholamine synthesis. More recently norepinephrine level was shown to significantly increase after osmotic stress, abscisic acid treatment and wounding. Therefore, it is possible that catecholamines might play a role in plant stress responses by modulating primary carbon metabolism, possibly by a mechanism similar to that in animal cells. Since to date no catecholamine receptor has been identified in plants we transformed potato plants with a cDNA encoding human dopamine receptor (HD1). RESULTS Tuber analysis of transgenic plants revealed changes in the activities of key enzymes mediating sucrose to starch conversion (ADP-glucose phosphorylase and sucrose synthase) and sucrose synthesis (sucrose phosphate synthase) leading to altered content of both soluble sugars and starch. Surprisingly the catecholamine level measured in transgenic plants was significantly increased; the reason for this is as yet unknown. However the presence of the receptor affected a broader range of enzyme activities than those affected by the massive accumulation of norepinephrine reported for plants over-expressing tyrosine decarboxylase. Therefore, it is suggested that the presence of the exogenous receptor activates catecholamine cAMP signalling in plants. CONCLUSIONS Our data support the possible involvement of catecholamines in regulating plant carbon metabolism via cAMP signalling pathway.
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Affiliation(s)
- Aleksandra Skirycz
- Institute of Biochemistry and Molecular Biology, University of Wrocław, Przybyszewskiego Street 63/77, 51 – 148 Wrocław, Poland
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Golm, Germany
| | - Anna Świędrych
- Institute of Biochemistry and Molecular Biology, University of Wrocław, Przybyszewskiego Street 63/77, 51 – 148 Wrocław, Poland
| | - Jan Szopa
- Institute of Biochemistry and Molecular Biology, University of Wrocław, Przybyszewskiego Street 63/77, 51 – 148 Wrocław, Poland
- Department of Plant Physiology University of Szczecin, Wąska Street 13, 71–415 Szczecin, Poland
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15
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Cyclic nucleotide binding proteins in the Arabidopsis thaliana and Oryza sativa genomes. BMC Bioinformatics 2005; 6:6. [PMID: 15644130 PMCID: PMC545951 DOI: 10.1186/1471-2105-6-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2004] [Accepted: 01/11/2005] [Indexed: 11/25/2022] Open
Abstract
Background Cyclic nucleotides are ubiquitous intracellular messengers. Until recently, the roles of cyclic nucleotides in plant cells have proven difficult to uncover. With an understanding of the protein domains which can bind cyclic nucleotides (CNB and GAF domains) we scanned the completed genomes of the higher plants Arabidopsis thaliana (mustard weed) and Oryza sativa (rice) for the effectors of these signalling molecules. Results Our analysis found that several ion channels and a class of thioesterases constitute the possible cyclic nucleotide binding proteins in plants. Contrary to some reports, we found no biochemical or bioinformatic evidence for a plant cyclic nucleotide regulated protein kinase, suggesting that cyclic nucleotide functions in plants have evolved differently than in mammals. Conclusion This paper provides a molecular framework for the discussion of cyclic nucleotide function in plants, and resolves a longstanding debate about the presence of a cyclic nucleotide dependent kinase in plants.
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16
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Abstract
The natural occurrence of cyclic nucleotides in higher plants, formerly a topic of fierce debate, is now established, as is the presence of nucleotidyl cyclases and cyclic nucleotide phosphodiesterases capable of their synthesis and breakdown. Here we describe the significant properties of cyclic nucleotides, also outlining their second messenger functions and the history of plant cyclic nucleotide research over its first three decades. Findings of the last five years are detailed within the context of the functional role of cyclic nucleotides in higher plants, with particular emphasis upon nucleotidyl cyclases and cyclic nucleotide-responsive protein kinases, -binding proteins and -gated ion channels, with future objectives and strategies discussed.
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Affiliation(s)
- Russell P Newton
- Biochemistry Group, School of Biological Sciences, Wallace Building, University of Wales Swansea, Singleton Park, Swansea SA2 8PP, UK.
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17
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Donaldson L, Ludidi N, Knight MR, Gehring C, Denby K. Salt and osmotic stress cause rapid increases in Arabidopsis thaliana cGMP levels. FEBS Lett 2004; 569:317-20. [PMID: 15225654 DOI: 10.1016/j.febslet.2004.06.016] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2004] [Revised: 06/07/2004] [Accepted: 06/07/2004] [Indexed: 11/20/2022]
Abstract
A guanylyl cyclase has been recently identified in Arabidopsis but, despite the use of pharmacological inhibitors to infer roles of the second messenger 3',5'-cyclic guanosine monophosphate (cGMP), very few measurements of actual cGMP levels in plants are available. Here, we demonstrate that cGMP levels in Arabidopsis seedlings increase rapidly (< or =5 s) and to different degrees after salt and osmotic stress, and that the increases are prevented by treatment with LY, an inhibitor of soluble guanylyl cyclases. In addition, we provide evidence to suggest that salt stress activates two cGMP signalling pathways - an osmotic, calcium-independent pathway and an ionic, calcium-dependent pathway.
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Affiliation(s)
- Lara Donaldson
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag Rondebosch 7701, South Africa
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18
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Lemtiri-Chlieh F, Berkowitz GA. Cyclic adenosine monophosphate regulates calcium channels in the plasma membrane of Arabidopsis leaf guard and mesophyll cells. J Biol Chem 2004; 279:35306-12. [PMID: 15199067 DOI: 10.1074/jbc.m400311200] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The effect of cAMP on Ca(2+)-permeable channels from Arabidopsis thaliana leaf guard cell and mesophyll cell protoplasts was studied using the patch clamp technique. In the whole cell configuration, dibutyryl cAMP was found to increase a hyperpolarization-activated Ba(2+) conductance (I(Ba)). The increase of I(Ba) was blocked by the addition of GdCl(3). In excised outside-out patches, the addition of dibutyryl cAMP consistently activated a channel with particularly fast gating kinetics. Current/voltage analyses indicated a single channel conductance of approximately 13 picosiemens. In patches where we measured some channel activity prior to cAMP application, the data suggest that cAMP enhances channel activity without affecting the single channel conductance. The cAMP activation of these channels was reversible upon washout. The results obtained with excised patches indicate that the cAMP-activated I(Ba) seen in the whole cell configuration could be explained by a direct effect of cAMP on the Ca(2+) channel itself or a close entity to the channel. This work represents the first demonstration using patch clamp analysis of the presence in plant cell membranes of an ion channel directly activated by cAMP.
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Affiliation(s)
- Fouad Lemtiri-Chlieh
- Agricultural Biotechnology Laboratory, Department of Plant Science, University of Connecticut, Storrs, Connecticut 06269-4067, USA
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19
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Zhao J, Guo Y, Fujita K, Sakai K. Involvement of cAMP signaling in elicitor-induced phytoalexin accumulation in Cupressus lusitanica cell cultures. THE NEW PHYTOLOGIST 2004; 161:723-733. [PMID: 33873708 DOI: 10.1111/j.1469-8137.2004.00976.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
• An increasing body of evidence on plant electrophysiology, biochemistry, and molecular biology shows that cAMP exists in higher plants and plays a role in several physiological processes by affecting potassium (K+ ) or calcium (Ca2+ ) fluxes. Our study here reports that cAMP is involved in elicitor-induced accumulation of a phytoalexin, β-thujaplicin, in Cupressus lusitanica cell cultures. • Treatment of C. lusitanica cultured cells with cAMP or its analogues stimulated β-thujaplicin accumulation. Cholera toxin and forskolin, activators of adenylyl cyclase, also stimulated β-thujaplicin accumulation. Enzyme immunoassay showed that after elicitor treatment, cAMP level in the elicited cells quickly increased to about three- to five-fold over the control. Cholera toxin and forskolin also stimulated cAMP accumulation in the absence of elicitor. • However, K+ and Ca2+ channel blockers inhibited the β-thujaplicin accumulation induced by cAMP analogues, suggesting that the cAMP-stimulated β-thujaplicin accumulation may involve Ca2+ and K+ fluxes. Several ionophores mimicked cAMP induction of β-thujaplicin accumulation. • Cross-talk between cAMP treatment and the ethylene signaling pathway was also observed to work in the cell cultures via Ca2+ signaling. The study also indicates an involvement of protein kinase cascades in cAMP signaling processes, leading to both phytoalexin and ethylene production.
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Affiliation(s)
- Jian Zhao
- Laboratory of Forest Chemistry and Biochemistry, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581 Japan
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050 China
| | - Yingqing Guo
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050 China
| | - Koki Fujita
- Laboratory of Forest Chemistry and Biochemistry, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581 Japan
| | - Kokki Sakai
- Laboratory of Forest Chemistry and Biochemistry, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581 Japan
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20
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Tilton GB, Shockey JM, Browse J. Biochemical and Molecular Characterization of ACH2, an Acyl-CoA Thioesterase from Arabidopsis thaliana. J Biol Chem 2004; 279:7487-94. [PMID: 14660652 DOI: 10.1074/jbc.m309532200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
By using computer-based homology searches of the Arabidopsis genome, we identified the gene for ACH2, a putative acyl-CoA thioesterase. With the exception of a unique 129-amino acid N-terminal extension, the ACH2 protein is 17-36% identical to members of a family of acyl-CoA thioesterases that are found in both prokaryotes and eukaryotes. The eukaryotic homologs of ACH2 are peroxisomal acyl-CoA thioesterases that are up-regulated during times of increased fatty acid oxidation, suggesting potential roles in peroxisomal beta-oxidation. We investigated ACH2 to determine whether it has a similar role in the plant cell. Like its eukaryotic homologs, ACH2 carries a putative type 1 peroxisomal targeting sequence (-SKL(COOH)), and maintains all the catalytic residues typical of this family of acyl-CoA thioesterases. Analytical ultracentrifugation of recombinant ACH2-6His shows that it associates as a 196-kDa homotetramer in vitro, a result that is significant in light of the cooperative kinetics demonstrated by ACH2-6His in vitro. The cooperative effects are most pronounced with medium chain acyl-CoAs, where the Hill coefficient is 3.8 for lauroyl-CoA, but decrease for long chain acyl-CoAs, where the Hill coefficient is only 1.9 for oleoyl-CoA. ACH2-6His hydrolyzes both medium and long chain fatty acyl-CoAs but has highest activity toward the long chain unsaturated fatty acyl-CoAs. Maximum rates were found with palmitoleoyl-CoA, which is hydrolyzed at 21 micromol/min/mg protein. Additionally, ACH2-6His is insensitive to feedback inhibition by free CoASH levels as high as 100 microm. ACH2 is most highly expressed in mature tissues such as young leaves and flowers rather than in germinating seedlings where beta-oxidation is rapidly proceeding. Taken together, these results suggest that ACH2 activity is not linked to fatty acid oxidation as has been suggested for its eukaryotic homologs, but rather has a unique role in the plant cell.
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Affiliation(s)
- Gregory B Tilton
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340, USA
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