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Li T, Jia W, Peng S, Guo Y, Liu J, Zhang X, Li P, Zhang H, Xu R. Endogenous cAMP elevation in Brassica napus causes changes in phytohormone levels. PLANT SIGNALING & BEHAVIOR 2024; 19:2310963. [PMID: 38314783 PMCID: PMC10854363 DOI: 10.1080/15592324.2024.2310963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/22/2024] [Indexed: 02/07/2024]
Abstract
In higher plants, the regulatory roles of cAMP (cyclic adenosine 3',5'-monophosphate) signaling remain elusive until now. Cellular cAMP levels are generally much lower in higher plants than in animals and transiently elevated for triggering downstream signaling events. Moreover, plant adenylate cyclase (AC) activities are found in different moonlighting multifunctional proteins, which may pose additional complications in distinguishing a specific signaling role for cAMP. Here, we have developed rapeseed (Brassica napus L.) transgenic plants that overexpress an inducible plant-origin AC activity for generating high AC levels much like that in animal cells, which served the genetic model disturbing native cAMP signaling as a whole in plants. We found that overexpression of the soluble AC activity had significant impacts on the contents of indole-3-acetic acid (IAA) and stress phytohormones, i.e. jasmonic acid (JA), abscisic acid (ABA), and salicylic acid (SA) in the transgenic plants. Acute induction of the AC activity caused IAA overaccumulation, and upregulation of TAA1 and CYP83B1 in the IAA biosynthesis pathways, but also simultaneously the hyper-induction of PR4 and KIN2 expression indicating activation of JA and ABA signaling pathways. We observed typical overgrowth phenotypes related to IAA excess in the transgenic plants, including significant increases in plant height, internode length, width of leaf blade, petiole length, root length, and fresh shoot biomass, as well as the precocious seed development, as compared to wild-type plants. In addition, we identified a set of 1465 cAMP-responsive genes (CRGs), which are most significantly enriched in plant hormone signal transduction pathway, and function mainly in relevance to hormonal, abiotic and biotic stress responses, as well as growth and development. Collectively, our results support that cAMP elevation impacts phytohormone homeostasis and signaling, and modulates plant growth and development. We proposed that cAMP signaling may be critical in configuring the coordinated regulation of growth and development in higher plants.
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Affiliation(s)
- Tianming Li
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wenjing Jia
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Song Peng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Yanhui Guo
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Jinrui Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Xue Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Panyu Li
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Hanfeng Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Ruqiang Xu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
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Kwiatkowski M, Wong A, Fiderewicz A, Gehring C, Jaworski K. A SNF1-related protein kinase regulatory subunit functions as a molecular tuner. PHYTOCHEMISTRY 2024; 224:114146. [PMID: 38763313 DOI: 10.1016/j.phytochem.2024.114146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/21/2024]
Abstract
Metabolic processes in prokaryotic and eukaryotic organisms are often modulated by kinases which are in turn, dependent on Ca2+ and the cyclic mononucleotides cAMP and cGMP. It has been established that some proteins have both kinase and cyclase activities and that active cyclases can be embedded within the kinase domains. Here, we identified phosphodiesterase (PDE) sites, enzymes that hydrolyse cAMP and cGMP, to AMP and GMP, respectively, in some of these proteins in addition to their kinase/cyclase twin-architecture. As an example, we tested the Arabidopsis thaliana KINγ, a subunit of the SnRK2 kinase, to demonstrate that all three enzymatic centres, adenylate cyclase (AC), guanylate cyclase (GC) and PDE, are catalytically active, capable of generating and hydrolysing cAMP and cGMP. These data imply that the signal output of the KINγ subunit modulates SnRK2, consequently affecting the downstream kinome. Finally, we propose a model where a single protein subunit, KINγ, is capable of regulating cyclic mononucleotide homeostasis, thereby tuning stimulus specific signal output.
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Affiliation(s)
- Mateusz Kwiatkowski
- Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University in Toruń, Lwowska St. 1, 87-100, Toruń, Poland.
| | - Aloysius Wong
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Wenzhou, 325060, Zhejiang Province, China; Research Center for Integrative Plant Sciences, Wenzhou-Kean University, 88 Daxue Road, Wenzhou, 325060, Zhejiang Province, China.
| | - Adam Fiderewicz
- Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University in Toruń, Lwowska St. 1, 87-100, Toruń, Poland
| | - Chris Gehring
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Borgo XX Giugno, 74, 06121, Perugia, Italy.
| | - Krzysztof Jaworski
- Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University in Toruń, Lwowska St. 1, 87-100, Toruń, Poland.
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Kwiatkowski M, Zhang J, Zhou W, Gehring C, Wong A. Cyclic nucleotides - the rise of a family. TRENDS IN PLANT SCIENCE 2024; 29:915-924. [PMID: 38480090 DOI: 10.1016/j.tplants.2024.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 01/30/2024] [Accepted: 02/19/2024] [Indexed: 08/10/2024]
Abstract
Cyclic nucleotides 3',5'-cAMP and 3',5'-cGMP are now established signaling components of the plant cell while their 2',3' positional isomers are increasingly recognized as such. 3',5'-cAMP/cGMP is generated by adenylate cyclases (ACs) or guanylate cyclases (GCs) from ATP or GTP, respectively, whereas 2',3'-cAMP/cGMP is produced through the hydrolysis of double-stranded DNA or RNA by synthetases. Recent evidence suggests that the cyclic nucleotide generating and inactivating enzymes moonlight in proteins with diverse domain architecture operating as molecular tuners to enable dynamic and compartmentalized regulation of cellular signals. Further characterization of such moonlighting enzymes and extending the studies to noncanonical cyclic nucleotides promises new insights into the complex regulatory networks that underlie plant development and responses, thus offering exciting opportunities for crop improvement.
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Affiliation(s)
- Mateusz Kwiatkowski
- Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University in Toruń, Lwowska St. 1, 87-100 Toruń, Poland
| | - Jinwen Zhang
- Department of Biology, College of Science, Mathematics, and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou 325060, Zhejiang Province, China
| | - Wei Zhou
- Department of Biology, College of Science, Mathematics, and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou 325060, Zhejiang Province, China
| | - Chris Gehring
- Department of Chemistry, Biology, and Biotechnology, University of Perugia, Perugia 06121, Italy.
| | - Aloysius Wong
- Department of Biology, College of Science, Mathematics, and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou 325060, Zhejiang Province, China; Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Ouhai, Wenzhou 325060, Zhejiang Province, China; Zhejiang Bioinformatics International Science and Technology Cooperation Center, Ouhai, Wenzhou 325060, Zhejiang Province, China.
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Yamamoto C, Takahashi F, Suetsugu N, Yamada K, Yoshikawa S, Kohchi T, Kasahara M. The cAMP signaling module regulates sperm motility in the liverwort Marchantia polymorpha. Proc Natl Acad Sci U S A 2024; 121:e2322211121. [PMID: 38593080 PMCID: PMC11032487 DOI: 10.1073/pnas.2322211121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/14/2024] [Indexed: 04/11/2024] Open
Abstract
Adenosine 3',5'-cyclic monophosphate (cAMP) is a universal signaling molecule that acts as a second messenger in various organisms. It is well established that cAMP plays essential roles across the tree of life, although the function of cAMP in land plants has long been debated. We previously identified the enzyme with both adenylyl cyclase (AC) and cAMP phosphodiesterase (PDE) activity as the cAMP-synthesis/hydrolysis enzyme COMBINED AC with PDE (CAPE) in the liverwort Marchantia polymorpha. CAPE is conserved in streptophytes that reproduce with motile sperm; however, the precise function of CAPE is not yet known. In this study, we demonstrate that the loss of function of CAPE in M. polymorpha led to male infertility due to impaired sperm flagellar motility. We also found that two genes encoding the regulatory subunits of cAMP-dependent protein kinase (PKA-R) were also involved in sperm motility. Based on these findings, it is evident that CAPE and PKA-Rs act as a cAMP signaling module that regulates sperm motility in M. polymorpha. Therefore, our results have shed light on the function of cAMP signaling and sperm motility regulators in land plants. This study suggests that cAMP signaling plays a common role in plant and animal sperm motility.
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Affiliation(s)
- Chiaki Yamamoto
- Department of Biotechnology, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu525-8577, Japan
| | - Fumio Takahashi
- Department of Biotechnology, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu525-8577, Japan
| | - Noriyuki Suetsugu
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo153-8902, Japan
| | - Kazumasa Yamada
- Department of Marine Science and Technology, Faculty of Marine Science and Technology, Fukui Prefectural University, Obama917-0003, Japan
| | - Shinya Yoshikawa
- Department of Marine Science and Technology, Faculty of Marine Science and Technology, Fukui Prefectural University, Obama917-0003, Japan
| | - Takayuki Kohchi
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto606-8502, Japan
| | - Masahiro Kasahara
- Department of Biotechnology, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu525-8577, Japan
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Habte N, Girma G, Xu X, Liao CJ, Adeyanju A, Hailemariam S, Lee S, Okoye P, Ejeta G, Mengiste T. Haplotypes at the sorghum ARG4 and ARG5 NLR loci confer resistance to anthracnose. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:106-123. [PMID: 38111157 DOI: 10.1111/tpj.16594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023]
Abstract
Sorghum anthracnose caused by the fungus Colletotrichum sublineola (Cs) is a damaging disease of the crop. Here, we describe the identification of ANTHRACNOSE RESISTANCE GENES (ARG4 and ARG5) encoding canonical nucleotide-binding leucine-rich repeat (NLR) receptors. ARG4 and ARG5 are dominant resistance genes identified in the sorghum lines SAP135 and P9830, respectively, that show broad-spectrum resistance to Cs. Independent genetic studies using populations generated by crossing SAP135 and P9830 with TAM428, fine mapping using molecular markers, comparative genomics and gene expression studies determined that ARG4 and ARG5 are resistance genes against Cs strains. Interestingly, ARG4 and ARG5 are both located within clusters of duplicate NLR genes at linked loci separated by ~1 Mb genomic region. SAP135 and P9830 each carry only one of the ARG genes while having the recessive allele at the second locus. Only two copies of the ARG5 candidate genes were present in the resistant P9830 line while five non-functional copies were identified in the susceptible line. The resistant parents and their recombinant inbred lines carrying either ARG4 or ARG5 are resistant to strains Csgl1 and Csgrg suggesting that these genes have overlapping specificities. The role of ARG4 and ARG5 in resistance was validated through sorghum lines carrying independent recessive alleles that show increased susceptibility. ARG4 and ARG5 are located within complex loci displaying interesting haplotype structures and copy number variation that may have resulted from duplication. Overall, the identification of anthracnose resistance genes with unique haplotype stucture provides a foundation for genetic studies and resistance breeding.
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Affiliation(s)
- Nida Habte
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Gezahegn Girma
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Xiaochen Xu
- Department of Agronomy, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Chao-Jan Liao
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Adedayo Adeyanju
- Department of Agronomy, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Sara Hailemariam
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Sanghun Lee
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Pascal Okoye
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Gebisa Ejeta
- Department of Agronomy, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
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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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7
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Turek I, Gehring C. Peptide-Mediated Cyclic Nucleotide Signaling in Plants: Identification and Characterization of Interactor Proteins with Nucleotide Cyclase Activity. Methods Mol Biol 2024; 2731:179-204. [PMID: 38019435 DOI: 10.1007/978-1-0716-3511-7_14] [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] [Indexed: 11/30/2023]
Abstract
During the last decades, an increasing number of plant signaling peptides have been discovered and it appears that many of them are specific ligands for interacting receptor molecules. These receptors can enable the formation of second messengers which in turn transmit the ligand-induced stimuli into complex and tunable downstream responses. In order to perform such complex tasks, receptor proteins often contain several distinct domains such as a kinase and/or adenylate cyclase (AC) or guanylate cyclase (GC) domains. ACs catalyze the conversion of ATP to 3',5'-cyclic adenosine monophosphate (cAMP) while GCs catalyze the reaction of GTP to 3',5'-cyclic guanosine monophosphate (cGMP). Both cAMP and cGMP are now recognized as essential components of many plant responses, including responses to peptidic hormones. Here we describe the approach that led to the discovery of the Plant Natriuretic Peptide Receptor (PNP receptor), including a protocol for the identification of currently undiscovered peptidic interactions, and the subsequent application of computational methods for the identification of AC and/or GC domains in such interacting receptor candidates.
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Affiliation(s)
- Ilona Turek
- Department of Rural Clinical Sciences, La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC, Australia.
| | - Chris Gehring
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
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8
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Ma M, Yang W, Chen H, Ke W, Gong Y, Hu Q. Transcriptional profile reveals the physiological responses to prey availability in the mixotrophic chrysophyte Poterioochromonas malhamensis. Front Microbiol 2023; 14:1173541. [PMID: 37860135 PMCID: PMC10582637 DOI: 10.3389/fmicb.2023.1173541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023] Open
Abstract
Mixotrophic flagellates, which have diverse nutritional modes and play important roles in connecting the microbial loop with the classical food chain, are ideal models to study the mechanisms of adaptation between different nutritional modes in protists. In their natural ecosystems, mixotrophic flagellates may encounter microalgal prey of different digestibility, which may affect the carbon flow. To date, a molecular biological view of the metabolic processes in the mixotrophic flagellate Poterioochromonas malhamensis during nutritional adaptation and feeding on microalgal prey of different digestibility is still lacking. Accordingly, this study focused on the gene expression differences in P. malhamensis under autotrophy, being fed by the digestible microalga Chlorella sorokiniana GT-1, and being fed by the indigestible microalga C. sorokiniana CMBB-146. Results showed that the growth rate of P. malhamensis under autotrophy was much lower than that when fed by digestible microalgae. Addition of C. sorokiniana CMBB-146 could only increase the growth rate of P. malhamensis in the first 3 days, but the cell concentration of P. malhamensis started to decrease gradually after 4 days. Compared to autotrophic P. malhamensis, total 6,583 and 3,510 genes were significantly and differentially expressed in P. malhamensis fed by digestible microalgae and indigestible microalgae, respectively. Compared to autotrophic cells, genes related to the ribosome, lysosome, glycolysis, gluconeogenesis, TCA cycle, β-oxidation, duplication, and β-1,3-glucan in P. malhamensis grazing on digestible prey were up-regulated, while genes related to light harvesting and key enzymes referring to chlorophyll were down-regulated. Genes related to apoptosis and necrosis in P. malhamensis were up-regulated after grazing on indigestible microalgae compared to the autotrophic group, which we suggest is associated with the up-regulation of genes related to lysosome enzymes. This study provides abundant information on the potential intracellular physiological responses of P. malhamensis during the process of nutritional adaptation.
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Affiliation(s)
- Mingyang Ma
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Wentao Yang
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Hong Chen
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Wanwan Ke
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yingchun Gong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Qiang Hu
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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9
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Qi L, Friml J. Tale of cAMP as a second messenger in auxin signaling and beyond. THE NEW PHYTOLOGIST 2023; 240:489-495. [PMID: 37434303 PMCID: PMC10952583 DOI: 10.1111/nph.19123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/12/2023] [Indexed: 07/13/2023]
Abstract
The 3',5'-cyclic adenosine monophosphate (cAMP) is a versatile second messenger in many mammalian signaling pathways. However, its role in plants remains not well-recognized. Recent discovery of adenylate cyclase (AC) activity for transport inhibitor response 1/auxin-signaling F-box proteins (TIR1/AFB) auxin receptors and the demonstration of its importance for canonical auxin signaling put plant cAMP research back into spotlight. This insight briefly summarizes the well-established cAMP signaling pathways in mammalian cells and describes the turbulent and controversial history of plant cAMP research highlighting the major progress and the unresolved points. We also briefly review the current paradigm of auxin signaling to provide a background for the discussion on the AC activity of TIR1/AFB auxin receptors and its potential role in transcriptional auxin signaling as well as impact of these discoveries on plant cAMP research in general.
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Affiliation(s)
- Linlin Qi
- Institute of Science and Technology Austria (ISTA)Klosterneuburg3400Austria
| | - Jiří Friml
- Institute of Science and Technology Austria (ISTA)Klosterneuburg3400Austria
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10
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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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11
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Liu Z, Yuan Y, Wang L, Cao H, Wang C, Zhao X, Wang L, Liu M. Establishment and characterization of a new class of adenylate cyclases (class VII ACs) in plants. Heliyon 2023; 9:e18612. [PMID: 37593644 PMCID: PMC10427991 DOI: 10.1016/j.heliyon.2023.e18612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/14/2023] [Accepted: 07/24/2023] [Indexed: 08/19/2023] Open
Abstract
Adenylate cyclase is the key enzyme in the synthesis of cAMP. Now, more and more plant genes which possessing AC function are being identified, but the classification of plant ACs has not yet been systematically studied and the relationship of plant ACs with other existing six classes ACs in animals and microorganisms is still unclear. In this study, we found that 7 of the 15 reported plant ACs with conserved CYTH-like_AC_Ⅳ-like domain were clustered into a group with high confidence (Group Ⅳ), while the other plant ACs were clustered into other three groups with no common domain. In addition, we also found that the Group Ⅳ plant ACs were grouped into an independent and specific class (Class VII), separated from the existing six classes of ACs. The Group Ⅳ plant ACs, compared to the existing six classes of ACs, own unique CYTH-like_AC_Ⅳ-like conserved domain and EXEXK signature motif, characteristic protein tertiary structures, specific subcellular localization and catalytic conditions. In view of the above, we regarded the Group Ⅳ plant ACs as the seventh class of AC (VII AC). This study does the systematic classification of plant ACs which could lay a foundation for further identification and study of the biological functions of the plant-specific VII ACs.
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Affiliation(s)
- Zhiguo Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei, 071001, China
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071001, China
- Jujube Industry Technology Research Institute of Hebei, Baoding, Hebei, 071001, China
| | - Ye Yuan
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071001, China
| | - Lixin Wang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071001, China
| | - Haonan Cao
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071001, China
| | - Chenyu Wang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071001, China
| | - Xuan Zhao
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei, 071001, China
| | - Lili Wang
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei, 071001, China
| | - Mengjun Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei, 071001, China
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071001, China
- Jujube Industry Technology Research Institute of Hebei, Baoding, Hebei, 071001, China
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12
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Caumon H, Vernoux T. A matter of time: auxin signaling dynamics and the regulation of auxin responses during plant development. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad132. [PMID: 37042516 DOI: 10.1093/jxb/erad132] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Indexed: 06/19/2023]
Abstract
As auxin is a major regulator of plant development, studying the signaling mechanisms by which auxin influences cellular activities is of primary importance. In this review, we describe the current knowledge on the different modalities of signaling, from the well-characterized canonical nuclear auxin pathway, to the more recently discovered or re-discovered non-canonical modes of auxin signaling. In particular, we discuss how both the modularity of the nuclear auxin pathway and the dynamic regulation of its core components allow to trigger specific transcriptomic responses. We highlight the fact that the diversity of modes of auxin signaling allows for a wide range of timescales of auxin responses, from second-scale cytoplasmic responses to minute/hour-scale modifications of gene expression. Finally, we question the extent to which the temporality of auxin signaling and responses contributes to development in both the shoot and the root meristems. We conclude by stressing the fact that future investigations should allow to build an integrative view not only of the spatial control, but also of the temporality of auxin-mediated regulation of plant development, from the cell to the whole organism.
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Affiliation(s)
- Hugo Caumon
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, CNRS, INRAE, F-69342, Lyon, France
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, CNRS, INRAE, F-69342, Lyon, France
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13
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Wong A, Bi C, Chi W, Hu N, Gehring C. Amino acid motifs for the identification of novel protein interactants. Comput Struct Biotechnol J 2022; 21:326-334. [PMID: 36582434 PMCID: PMC9791077 DOI: 10.1016/j.csbj.2022.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Biological systems consist of multiple components of different physical and chemical properties that require complex and dynamic regulatory loops to function efficiently. The discovery of ever more novel interacting sites in complex proteins suggests that we are only beginning to understand how cellular and biological functions are integrated and tuned at the molecular and systems levels. Here we review recently discovered interacting sites which have been identified through rationally designed amino acid motifs diagnostic for specific molecular functions, including enzymatic activities and ligand-binding properties. We specifically discuss the nature of the latter using as examples, novel hormone recognition and gas sensing sites that occur in moonlighting protein complexes. Drawing evidence from the current literature, we discuss the potential implications at the cellular, tissue, and/or organismal levels of such non-catalytic interacting sites and provide several promising avenues for the expansion of amino acid motif searches to discover hitherto unknown protein interactants and interaction networks. We believe this knowledge will unearth unexpected functions in both new and well-characterized proteins, thus filling existing conceptual gaps or opening new avenues for applications either as drug targets or tools in pharmacology, cell biology and bio-catalysis. Beyond this, motif searches may also support the design of novel, effective and sustainable approaches to crop improvements and the development of new therapeutics.
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Affiliation(s)
- Aloysius Wong
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China,Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Ouhai, Wenzhou, Zhejiang Province 325060, China,Zhejiang Bioinformatics International Science and Technology Cooperation Center, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Chuyun Bi
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China,Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Ouhai, Wenzhou, Zhejiang Province 325060, China,Zhejiang Bioinformatics International Science and Technology Cooperation Center, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Wei Chi
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Ningxin Hu
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Chris Gehring
- Department of Chemistry, Biology & Biotechnology, University of Perugia, Perugia 06121, Italy,Corresponding author.
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14
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Wong A, Tian X, Yang Y, Gehring C. Adenylate cyclase activity of TIR1/AFB links cAMP to auxin-dependent responses. MOLECULAR PLANT 2022; 15:1838-1840. [PMID: 36419358 DOI: 10.1016/j.molp.2022.11.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/21/2022] [Accepted: 11/21/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Aloysius Wong
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou 325060, Zhejiang Province, China; Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Ouhai, Wenzhou 325060, Zhejiang Province, China; Zhejiang Bioinformatics International Science and Technology Cooperation Center, Ouhai, Wenzhou 325060, Zhejiang Province, China
| | - Xuechen Tian
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou 325060, Zhejiang Province, China; Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Ouhai, Wenzhou 325060, Zhejiang Province, China; Zhejiang Bioinformatics International Science and Technology Cooperation Center, Ouhai, Wenzhou 325060, Zhejiang Province, China
| | - Yixin Yang
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou 325060, Zhejiang Province, China; Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Ouhai, Wenzhou 325060, Zhejiang Province, China; Zhejiang Bioinformatics International Science and Technology Cooperation Center, Ouhai, Wenzhou 325060, Zhejiang Province, China
| | - Chris Gehring
- Department of Chemistry, Biology & Biotechnology, University of Perugia, Perugia 06121, Italy.
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15
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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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16
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Shahoha M, Cohen R, Ben-Simon Y, Ashery U. cAMP-Dependent Synaptic Plasticity at the Hippocampal Mossy Fiber Terminal. Front Synaptic Neurosci 2022; 14:861215. [PMID: 35444523 PMCID: PMC9013808 DOI: 10.3389/fnsyn.2022.861215] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/23/2022] [Indexed: 11/24/2022] Open
Abstract
Cyclic adenosine monophosphate (cAMP) is a crucial second messenger involved in both pre- and postsynaptic plasticity in many neuronal types across species. In the hippocampal mossy fiber (MF) synapse, cAMP mediates presynaptic long-term potentiation and depression. The main cAMP-dependent signaling pathway linked to MF synaptic plasticity acts via the activation of the protein kinase A (PKA) molecular cascade. Accordingly, various downstream putative synaptic PKA target proteins have been linked to cAMP-dependent MF synaptic plasticity, such as synapsin, rabphilin, synaptotagmin-12, RIM1a, tomosyn, and P/Q-type calcium channels. Regulating the expression of some of these proteins alters synaptic release probability and calcium channel clustering, resulting in short- and long-term changes to synaptic efficacy. However, despite decades of research, the exact molecular mechanisms by which cAMP and PKA exert their influences in MF terminals remain largely unknown. Here, we review current knowledge of different cAMP catalysts and potential downstream PKA-dependent molecular cascades, in addition to non-canonical cAMP-dependent but PKA-independent cascades, which might serve as alternative, compensatory or competing pathways to the canonical PKA cascade. Since several other central synapses share a similar form of presynaptic plasticity with the MF, a better description of the molecular mechanisms governing MF plasticity could be key to understanding the relationship between the transcriptional and computational levels across brain regions.
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Affiliation(s)
- Meishar Shahoha
- Faculty of Life Sciences, School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Ronni Cohen
- Faculty of Life Sciences, School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Yoav Ben-Simon
- Department of Neurophysiology, Vienna Medical University, Vienna, Austria
- *Correspondence: Yoav Ben-Simon,
| | - Uri Ashery
- Faculty of Life Sciences, School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Uri Ashery,
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17
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Hayashida Y, Yamamoto C, Takahashi F, Shibata A, Kasahara M. Characterization of the cAMP phosphodiesterase domain in plant adenylyl cyclase/cAMP phosphodiesterase CAPE from the liverwort Marchantia polymorpha. JOURNAL OF PLANT RESEARCH 2022; 135:137-144. [PMID: 34779957 DOI: 10.1007/s10265-021-01359-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/07/2021] [Indexed: 06/13/2023]
Abstract
Cyclic AMP (cAMP) acts as a second messenger and is involved in the regulation of various physiological responses. Recently, we identified the cAMP-synthesis/hydrolysis enzyme CAPE, which contains the two catalytic domains adenylyl cyclase (AC) and cAMP phosphodiesterase (PDE) from the liverwort Marchantia polymorpha. Here we characterize the PDE domain of M. polymorpha CAPE (MpCAPE-PDE) using the purified protein expressed in E. coli. The Km and Vmax of MpCAPE-PDE were 30 µM and 5.8 nmol min-1 mg-1, respectively. Further, we investigated the effect of divalent cations on PDE activity and found that Ca2+ enhanced PDE activity, suggesting that Ca2+ may be involved in cAMP signaling through the regulation of PDE activity of CAPE. Among the PDE inhibitors tested, only dipyridamole moderately inhibited PDE activity by approximately 40% at high concentrations. Conversely, 3-isobutyl-1-methylxanthine (IBMX) did not inhibit PDE activity.
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Affiliation(s)
- Yuta Hayashida
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Chiaki Yamamoto
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Fumio Takahashi
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Aika Shibata
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Masahiro Kasahara
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan.
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18
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Kwiatkowski M, Wong A, Kozakiewicz-Piekarz A, Gehring C, Jaworski K. In Search of Monocot Phosphodiesterases: Identification of a Calmodulin Stimulated Phosphodiesterase from Brachypodium distachyon. Int J Mol Sci 2021; 22:ijms22179654. [PMID: 34502563 PMCID: PMC8431786 DOI: 10.3390/ijms22179654] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 12/18/2022] Open
Abstract
In plants, rapid and reversible biological responses to environmental cues may require complex cellular reprograming. This is enabled by signaling molecules such as the cyclic nucleotide monophosphates (cNMPs) cAMP and cGMP, as well as Ca2+. While the roles and synthesis of cAMP and cGMP in plants are increasingly well-characterized, the “off signal” afforded by cNMP-degrading enzymes, the phosphodiesterases (PDEs), is, however, poorly understood, particularly so in monocots. Here, we identified a candidate PDE from the monocot Brachypodium distachyon (BDPDE1) and showed that it can hydrolyze cNMPs to 5′NMPs but with a preference for cAMP over cGMP in vitro. Notably, the PDE activity was significantly enhanced by Ca2+ only in the presence of calmodulin (CaM), which interacts with BDPDE1, most likely at a predicted CaM-binding site. Finally, based on our biochemical, mutagenesis and structural analyses, we constructed a comprehensive amino acid consensus sequence extracted from the catalytic centers of annotated and/or experimentally validated PDEs across species to enable a broad application of this search motif for the identification of similar active sites in eukaryotes and prokaryotes.
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Affiliation(s)
- Mateusz Kwiatkowski
- Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University, Lwowska St. 1, 87-100 Torun, Poland;
- Correspondence: ; Tel.: +48-56-611-44-56; Fax: +48-56-61-14-772
| | - Aloysius Wong
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou 325060, China;
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou-Kean University, Wenzhou 325060, China
| | - Anna Kozakiewicz-Piekarz
- Department of Biomedical and Polymer Chemistry, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina St. 7, 87-100 Torun, Poland;
| | - Christoph Gehring
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Borgo XX giugno, 74, 06121 Perugia, Italy;
| | - Krzysztof Jaworski
- Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University, Lwowska St. 1, 87-100 Torun, Poland;
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19
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Al-Younis I, Moosa B, Kwiatkowski M, Jaworski K, Wong A, Gehring C. Functional Crypto-Adenylate Cyclases Operate in Complex Plant Proteins. FRONTIERS IN PLANT SCIENCE 2021; 12:711749. [PMID: 34456950 PMCID: PMC8387589 DOI: 10.3389/fpls.2021.711749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/21/2021] [Indexed: 05/08/2023]
Abstract
Adenylyl cyclases (ACs) and their catalytic product cAMP are regulatory components of many plant responses. Here, we show that an amino acid search motif based on annotated adenylate cyclases (ACs) identifies 12 unique Arabidopsis thaliana candidate ACs, four of which have a role in the biosynthesis of the stress hormone abscisic acid (ABA). One of these, the 9-cis-epoxycarotenoid dioxygenase (NCED3 and At3g14440), was identified by sequence and structural analysis as a putative AC and then tested experimentally with two different methods. Given that the in vitro activity is low (fmoles cAMP pmol-1 protein min-1), but highly reproducible, we term the enzyme a crypto-AC. Our results are consistent with a role for ACs with low activities in multi-domain moonlighting proteins that have at least one other distinct molecular function, such as catalysis or ion channel activation. We propose that crypto-ACs be examined from the perspective that considers their low activities as an innate feature of regulatory ACs embedded within multi-domain moonlighting proteins. It is therefore conceivable that crypto-ACs form integral components of complex plant proteins participating in intra-molecular regulatory mechanisms, and in this case, potentially linking cAMP to ABA synthesis.
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Affiliation(s)
- Inas Al-Younis
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Basem Moosa
- Physical Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Mateusz Kwiatkowski
- Chair of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Krzysztof Jaworski
- Chair of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Aloysius Wong
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center of Wenzhou-Kean University, Wenzhou, China
| | - Chris Gehring
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Department of Chemistry, Biology & Biotechnology, University of Perugia, Perugia, Italy
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20
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Distribution of adenylyl cyclase/cAMP phosphodiesterase gene, CAPE, in streptophytes reproducing via motile sperm. Sci Rep 2021; 11:10054. [PMID: 33980894 PMCID: PMC8115329 DOI: 10.1038/s41598-021-89539-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/28/2021] [Indexed: 02/03/2023] Open
Abstract
We recently isolated a novel adenylyl cyclase/cAMP phosphodiesterase gene from the liverwort, Marchantia polymorpha. The protein encoded by this gene has a class III adenylyl cyclase (AC) in the C-terminal domain and class I phosphodiesterase (PDE) in the N-terminal domain; therefore, we named it CAPE (COMBINED AC with PDE). CAPE protein is likely involved in spermatogenesis and sperm motility due to its tissue-specific expression pattern in M. polymorpha and the distribution of CAPE genes in streptophytes. However, little is known about the distribution of CAPE in gymnosperms that use motile sperm for fertilization, such as cycads and ginkgo. The present study aimed to isolate CAPE genes from the cycad, Cycas revoluta, the ginkgo, Ginkgo biloba, and the hornwort, Anthoceros agerestis. Sequences with high homology to CAPE were obtained from these species. Our analyses revealed that all plant taxonomic groups reproducing via motile sperm possessed CAPE, whereas those that do not produce motile sperm did not possess CAPE, with one exception in gymnosperm Cupressales. The phylogenic distribution of CAPE almost corresponds to the evolutionary history of motile sperm production and further suggests that CAPE may be involved in sexual reproduction process using motile sperm in streptophytes.
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21
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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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Zhou W, Chi W, Shen W, Dou W, Wang J, Tian X, Gehring C, Wong A. Computational Identification of Functional Centers in Complex Proteins: A Step-by-Step Guide With Examples. FRONTIERS IN BIOINFORMATICS 2021; 1:652286. [PMID: 36303732 PMCID: PMC9581015 DOI: 10.3389/fbinf.2021.652286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/02/2021] [Indexed: 11/13/2022] Open
Abstract
In proteins, functional centers consist of the key amino acids required to perform molecular functions such as catalysis, ligand-binding, hormone- and gas-sensing. These centers are often embedded within complex multi-domain proteins and can perform important cellular signaling functions that enable fine-tuning of temporal and spatial regulation of signaling molecules and networks. To discover hidden functional centers, we have developed a protocol that consists of the following sequential steps. The first is the assembly of a search motif based on the key amino acids in the functional center followed by querying proteomes of interest with the assembled motif. The second consists of a structural assessment of proteins that harbor the motif. This approach, that relies on the application of computational tools for the analysis of data in public repositories and the biological interpretation of the search results, has to-date uncovered several novel functional centers in complex proteins. Here, we use recent examples to describe a step-by-step guide that details the workflow of this approach and supplement with notes, recommendations and cautions to make this protocol robust and widely applicable for the discovery of hidden functional centers.
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Affiliation(s)
- Wei Zhou
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Wei Chi
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Wanting Shen
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Wanying Dou
- Department of Computer Science, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Junyi Wang
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Xuechen Tian
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Christoph Gehring
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Aloysius Wong
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center of Wenzhou-Kean University, Wenzhou, China
- *Correspondence: Aloysius Wong
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23
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James AM, Seal SE, Bailey AM, Foster GD. Viral inosine triphosphatase: A mysterious enzyme with typical activity, but an atypical function. MOLECULAR PLANT PATHOLOGY 2021; 22:382-389. [PMID: 33471956 PMCID: PMC7865087 DOI: 10.1111/mpp.13021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 05/03/2023]
Abstract
Plant viruses typically have highly condensed genomes, yet the plant-pathogenic viruses Cassava brown streak virus, Ugandan cassava brown streak virus, and Euphorbia ringspot virus are unusual in encoding an enzyme not yet found in any other virus, the "house-cleaning" enzyme inosine triphosphatase. Inosine triphosphatases (ITPases) are highly conserved enzymes that occur in all kingdoms of life and perform a house-cleaning function by hydrolysing the noncanonical nucleotide inosine triphosphate to inosine monophosphate. The ITPases encoded by cassava brown streak virus and Ugandan cassava brown streak virus have been characterized biochemically and are shown to have typical ITPase activity. However, their biological role in virus infection has yet to be elucidated. Here we review what is known of viral-encoded ITPases and speculate on potential roles in infection with the aim of generating a greater understanding of cassava brown streak viruses, a group of the world's most devastating viruses.
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Affiliation(s)
- Amy M. James
- School of Biological SciencesLife Sciences BuildingUniversity of BristolBristolUK
| | - Susan E. Seal
- Natural Resources Institute, Chatham MaritimeGillinghamUK
| | - Andy M. Bailey
- School of Biological SciencesLife Sciences BuildingUniversity of BristolBristolUK
| | - Gary D. Foster
- School of Biological SciencesLife Sciences BuildingUniversity of BristolBristolUK
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24
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Yang H, Zhao Y, Chen N, Liu Y, Yang S, Du H, Wang W, Wu J, Tai F, Chen F, Hu X. A new adenylyl cyclase, putative disease-resistance RPP13-like protein 3, participates in abscisic acid-mediated resistance to heat stress in maize. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:283-301. [PMID: 32936902 DOI: 10.1093/jxb/eraa431] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/13/2020] [Indexed: 05/24/2023]
Abstract
In plants, 3´,5´-cyclic adenosine monophosphate (cAMP) is an important second messenger with varied functions; however, only a few adenylyl cyclases (ACs) that synthesize cAMP have been identified. Moreover, the biological roles of ACs/cAMP in response to stress remain largely unclear. In this study, we used quantitative proteomics techniques to identify a maize heat-induced putative disease-resistance RPP13-like protein 3 (ZmRPP13-LK3), which has three conserved catalytic AC centres. The AC activity of ZmRPP13-LK3 was confirmed by in vitro enzyme activity analysis, in vivo RNAi experiments, and functional complementation in the E. coli cyaA mutant. ZmRPP13-LK3 is located in the mitochondria. The results of in vitro and in vivo experiments indicated that ZmRPP13-LK3 interacts with ZmABC2, a possible cAMP exporter. Under heat stress, the concentrations of ZmRPP13-LK3 and cAMP in the ABA-deficient mutant vp5 were significantly less than those in the wild-type, and treatment with ABA and an ABA inhibitor affected ZmRPP13-LK3 expression in the wild-type. Application of 8-Br-cAMP, a cAMP analogue, increased heat-induced expression of heat-shock proteins in wild-type plants and alleviated heat-activated oxidative stress. Taken together, our results indicate that ZmRPP13-LK3, a new AC, can catalyse ATP for the production of cAMP and may be involved in ABA-regulated heat resistance.
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Affiliation(s)
- Hao Yang
- State Key Laboratory of Wheat & Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Yulong Zhao
- State Key Laboratory of Wheat & Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Ning Chen
- State Key Laboratory of Wheat & Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Yanpei Liu
- State Key Laboratory of Wheat & Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Shaoyu Yang
- State Key Laboratory of Wheat & Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Hanwei Du
- State Key Laboratory of Wheat & Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Wei Wang
- State Key Laboratory of Wheat & Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Jianyu Wu
- State Key Laboratory of Wheat & Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Fuju Tai
- State Key Laboratory of Wheat & Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Feng Chen
- State Key Laboratory of Wheat & Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Xiuli Hu
- State Key Laboratory of Wheat & Maize Crop Science, Henan Agricultural University, Zhengzhou, China
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25
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Marondedze C, Elia G, Thomas L, Wong A, Gehring C. Citrullination of Proteins as a Specific Response Mechanism in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:638392. [PMID: 33897727 PMCID: PMC8060559 DOI: 10.3389/fpls.2021.638392] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 02/17/2021] [Indexed: 05/19/2023]
Abstract
Arginine deimination, also referred to as citrullination of proteins by L-arginine deiminases, is a post-translational modification affecting histone modifications, epigenetic transcriptional regulation, and proteolysis in animals but has not been reported in higher plants. Here we report, firstly, that Arabidopsis thaliana proteome contains proteins with a specific citrullination signature and that many of the citrullinated proteins have nucleotide-binding regulatory functions. Secondly, we show that changes in the citrullinome occur in response to cold stress, and thirdly, we identify an A. thaliana protein with peptidyl arginine deiminase activity that was shown to be calcium-dependent for many peptide substrates. Taken together, these findings establish this post-translational modification as a hitherto neglected component of cellular reprogramming during stress responses.
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Affiliation(s)
- Claudius Marondedze
- Division of Biological and Chemical Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Rijk Zwaan, De Lier, Netherlands
- Department of Biochemistry, Faculty of Medicine, Midlands State University, Gweru, Zimbabwe
- Claudius Marondedze,
| | - Giuliano Elia
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Ludivine Thomas
- Division of Biological and Chemical Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Aloysius Wong
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center of Wenzhou-Kean University, Wenzhou, China
| | - Chris Gehring
- Division of Biological and Chemical Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
- *Correspondence: Chris Gehring,
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26
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Crystal structure and enzymatic characterization of the putative adenylyl cyclase HpAC1 from Hippeastrum reveal dominant triphosphatase activity. J Struct Biol 2020; 212:107649. [PMID: 33075486 DOI: 10.1016/j.jsb.2020.107649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/05/2020] [Accepted: 10/11/2020] [Indexed: 11/24/2022]
Abstract
HpAC1, a protein from Hippeastrum hybrid cultivars, was previously suggested to be a plant adenylyl cyclase. We describe a structural and enzymatic characterization of HpAC1. A crystal structure of HpAC1 in complex with a non-hydrolyzable GTP analog confirms a generic CYTH architecture, comprising a β-barrel with an internal substrate site. The structure reveals significant active site differences to AC proteins with CYTH fold, however, and we find that HpAC1 lacks measurable AC activity. Instead, HpAC1 has substantial triphosphatase activity, indicating this protective activity or a related activity as the protein's physiological function.
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27
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Blanco E, Fortunato S, Viggiano L, de Pinto MC. Cyclic AMP: A Polyhedral Signalling Molecule in Plants. Int J Mol Sci 2020; 21:E4862. [PMID: 32660128 PMCID: PMC7402341 DOI: 10.3390/ijms21144862] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 02/07/2023] Open
Abstract
The cyclic nucleotide cAMP (3',5'-cyclic adenosine monophosphate) is nowadays recognised as an important signalling molecule in plants, involved in many molecular processes, including sensing and response to biotic and abiotic environmental stresses. The validation of a functional cAMP-dependent signalling system in higher plants has spurred a great scientific interest on the polyhedral role of cAMP, as it actively participates in plant adaptation to external stimuli, in addition to the regulation of physiological processes. The complex architecture of cAMP-dependent pathways is far from being fully understood, because the actors of these pathways and their downstream target proteins remain largely unidentified. Recently, a genetic strategy was effectively used to lower cAMP cytosolic levels and hence shed light on the consequences of cAMP deficiency in plant cells. This review aims to provide an integrated overview of the current state of knowledge on cAMP's role in plant growth and response to environmental stress. Current knowledge of the molecular components and the mechanisms of cAMP signalling events is summarised.
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Affiliation(s)
- Emanuela Blanco
- Institute of Biosciences and Bioresources, National Research Council, Via G. Amendola 165/A, 70126 Bari, Italy
| | - Stefania Fortunato
- Department of Biology, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy; (S.F.); (L.V.)
| | - Luigi Viggiano
- Department of Biology, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy; (S.F.); (L.V.)
| | - Maria Concetta de Pinto
- Department of Biology, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy; (S.F.); (L.V.)
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28
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Liu H, Able AJ, Able JA. Transgenerational Effects of Water-Deficit and Heat Stress on Germination and Seedling Vigour-New Insights from Durum Wheat microRNAs. PLANTS (BASEL, SWITZERLAND) 2020; 9:E189. [PMID: 32033017 PMCID: PMC7076468 DOI: 10.3390/plants9020189] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/03/2020] [Accepted: 02/03/2020] [Indexed: 11/18/2022]
Abstract
Water deficiency and heat stress can severely limit crop production and quality. Stress imposed on the parents during reproduction could have transgenerational effects on their progeny. Seeds with different origins can vary significantly in their germination and early growth. Here, we investigated how water-deficit and heat stress on parental durum wheat plants affected seedling establishment of the subsequent generation. One stress-tolerant and one stress-sensitive Australian durum genotype were used. Seeds were collected from parents with or without exposure to stress during reproduction. Generally, stress on the previous generation negatively affected seed germination and seedling vigour, but to a lesser extent in the tolerant variety. Small RNA sequencing utilising the new durum genome assembly revealed significant differences in microRNA (miRNA) expression in the two genotypes. A bioinformatics approach was used to identify multiple miRNA targets which have critical molecular functions in stress adaptation and plant development and could therefore contribute to the phenotypic differences observed. Our data provide the first confirmation of the transgenerational effects of reproductive-stage stress on germination and seedling establishment in durum wheat. New insights gained on the epigenetic level indicate that durum miRNAs could be key factors in optimising seed vigour for breeding superior germplasm and/or varieties.
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Affiliation(s)
- Haipei Liu
- School of Agriculture, Food & Wine, Waite Research Institute, The University of Adelaide, Urrbrae SA5064, Australia; (A.J.A.); (J.A.A.)
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29
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Aznar-Fernández T, Barilli E, Cobos MJ, Kilian A, Carling J, Rubiales D. Identification of quantitative trait loci (QTL) controlling resistance to pea weevil (Bruchus pisorum) in a high-density integrated DArTseq SNP-based genetic map of pea. Sci Rep 2020; 10:33. [PMID: 31913335 PMCID: PMC6949260 DOI: 10.1038/s41598-019-56987-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 12/19/2019] [Indexed: 12/22/2022] Open
Abstract
Pea weevil (Bruchus pisorum) is a damaging insect pest affecting pea (Pisum sativum) production worldwide. No resistant cultivars are available, although some levels of incomplete resistance have been identified in Pisum germplasm. To decipher the genetic control underlying the resistance previously identify in P. sativum ssp. syriacum, a recombinant inbred line (RIL F8:9) population was developed. The RIL was genotyped through Diversity Arrays Technology PL's DArTseq platform and screened under field conditions for weevil seed infestation and larval development along 5 environments. A newly integrated genetic linkage map was generated with a subset of 6,540 markers, assembled into seven linkage groups, equivalent to the number of haploid pea chromosomes. An accumulated distance of 2,503 cM was covered with an average density of 2.61 markers cM-1. The linkage map allowed the identification of three QTLs associated to reduced seed infestation along LGs I, II and IV. In addition, a QTL for reduced larval development was also identified in LGIV. Expression of these QTLs varied with the environment, being particularly interesting QTL BpSI.III that was detected in most of the environments studied. This high-saturated pea genetic map has also allowed the identification of seven potential candidate genes co-located with QTLs for marker-assisted selection, providing an opportunity for breeders to generate effective and sustainable strategies for weevil control.
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Affiliation(s)
| | - Eleonora Barilli
- Institute for Sustainable Agriculture, CSIC, Córdoba, E-14004, Spain.
| | - María J Cobos
- Institute for Sustainable Agriculture, CSIC, Córdoba, E-14004, Spain
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, University of Canberra, Kirinari St. Bruce, ACT2617, Australia
| | - Jason Carling
- Diversity Arrays Technology Pty Ltd, University of Canberra, Kirinari St. Bruce, ACT2617, Australia
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Córdoba, E-14004, Spain
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30
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Su B, Qian Z, Li T, Zhou Y, Wong A. PlantMP: a database for moonlighting plant proteins. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5476724. [PMID: 31032837 PMCID: PMC6482322 DOI: 10.1093/database/baz050] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/13/2019] [Accepted: 03/28/2019] [Indexed: 11/15/2022]
Abstract
Moonlighting proteins are single polypeptide chains capable of executing two or more distinct biochemical and/or biological functions. Here, we describe the development of PlantMP, which is a manually curated online-based database of plant proteins that are known to `moonlight’. The database contains searchable UniProt IDs and names, canonical and moonlighting functions, gene ontology numbers, plant species as well as links to the PubMed indexed articles. Proteins homologous to experimentally confirmed moonlighting proteins from the model plant Arabidopsis thaliana are provided as a separate list of `likely moonlighters’. Additionally, we also provide a list of predicted Arabidopsis moonlighting proteins reported in the literature. Currently, PlantMP contains 110 plant moonlighting proteins, 10 `likely moonlighters’ and 27 `predicted moonlighters’. Organizing plant moonlighting proteins in one platform enables researchers to conveniently harvest plant-specific raw and processed data such as the molecular functions, biological roles and structural features essential for hypothesis formulation in basic research and for biotechnological innovations.
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Affiliation(s)
- Bo Su
- Department of Computer Science, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, China
| | - Zhuang Qian
- Department of Computer Science, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, China
| | - Tianshu Li
- Department of Computer Science, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, China
| | - Yuwei Zhou
- Department of Computer Science, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, China
| | - Aloysius Wong
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, China
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31
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Ruzvidzo O, Gehring C, Wong A. New Perspectives on Plant Adenylyl Cyclases. Front Mol Biosci 2019; 6:136. [PMID: 31850369 PMCID: PMC6901789 DOI: 10.3389/fmolb.2019.00136] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/13/2019] [Indexed: 01/01/2023] Open
Abstract
It is increasingly clear that plant genomes encode numerous complex multidomain proteins that harbor functional adenylyl cyclase (AC) centers. These AC containing proteins have well-documented roles in development and responses to the environment. However, it is only for a few of these proteins that we are beginning to understand the intramolecular mechanisms that govern their cellular and biological functions, as detailed characterizations are biochemically and structurally challenging given that these poorly conserved AC centers typically constitute only a small fraction (<10%) of complex plant proteins. Here, we offer fresh perspectives on their seemingly cryptic activities specifically showing evidence for the presence of multiple functional AC centers in a single protein and linking their catalytic strengths to the Mg2+/Mn2+-binding amino acids. We used a previously described computational approach to identify candidate multidomain proteins from Arabidopsis thaliana that contain multiple AC centers and show, using an Arabidopsis leucine-rich repeat containing protein (TAIR ID: At3g14460; AtLRRAC1) as example, biochemical evidence for multienzymatic activities. Importantly, all AC-containing fragments of this protein can complement the AC-deficient mutant cyaA in Escherichia coli, while structural modeling coupled with molecular docking simulations supports catalytic feasibility albeit to varying degrees as determined by the frequency of suitable substrate binding poses predicted for the AC sites. This statistic correlates well with the enzymatic assays, which implied that the greatly reduced AC activities is due to the absence of the negatively charged [DE] amino acids previously assigned to cation-, in particular Mg2+/Mn2+-binding roles in ACs.
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Affiliation(s)
- Oziniel Ruzvidzo
- Department of Botany, School of Biological Sciences, North-West University, Mmabatho, South Africa
| | - Chris Gehring
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Aloysius Wong
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
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32
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Luzarowski M, Skirycz A. Emerging strategies for the identification of protein-metabolite interactions. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4605-4618. [PMID: 31087097 PMCID: PMC6760282 DOI: 10.1093/jxb/erz228] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 05/10/2019] [Indexed: 05/31/2023]
Abstract
Interactions between biological molecules enable life. The significance of a cell-wide understanding of molecular complexes is thus obvious. In comparison to protein-protein interactions, protein-metabolite interactions remain under-studied. However, this has been gradually changing due to technological progress. Here, we focus on the interactions between ligands and receptors, the triggers of signalling events. While the number of small molecules with proven or proposed signalling roles is rapidly growing, most of their protein receptors remain unknown. Conversely, there are numerous signalling proteins with predicted ligand-binding domains for which the identities of the metabolite counterparts remain elusive. Here, we discuss the current biochemical strategies for identifying protein-metabolite interactions and how they can be used to characterize known metabolite regulators and identify novel ones.
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Affiliation(s)
- Marcin Luzarowski
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
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33
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Discovery of a Nitric Oxide-Responsive Protein in Arabidopsis thaliana. Molecules 2019; 24:molecules24152691. [PMID: 31344907 PMCID: PMC6696476 DOI: 10.3390/molecules24152691] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 07/20/2019] [Accepted: 07/22/2019] [Indexed: 11/17/2022] Open
Abstract
In plants, much like in animals, nitric oxide (NO) has been established as an important gaseous signaling molecule. However, contrary to animal systems, NO-sensitive or NO-responsive proteins that bind NO in the form of a sensor or participating in redox reactions have remained elusive. Here, we applied a search term constructed based on conserved and functionally annotated amino acids at the centers of Heme Nitric Oxide/Oxygen (H-NOX) domains in annotated and experimentally-tested gas-binding proteins from lower and higher eukaryotes, in order to identify candidate NO-binding proteins in Arabidopsis thaliana. The selection of candidate NO-binding proteins identified from the motif search was supported by structural modeling. This approach identified AtLRB3 (At4g01160), a member of the Light Response Bric-a-Brac/Tramtrack/Broad Complex (BTB) family, as a candidate NO-binding protein. AtLRB3 was heterologously expressed and purified, and then tested for NO-response. Spectroscopic data confirmed that AtLRB3 contains a histidine-ligated heme cofactor and importantly, the addition of NO to AtLRB3 yielded absorption characteristics reminiscent of canonical H-NOX proteins. Furthermore, substitution of the heme iron-coordinating histidine at the H-NOX center with a leucine strongly impaired the NO-response. Our finding therefore established AtLRB3 as a NO-interacting protein and future characterizations will focus on resolving the nature of this response.
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34
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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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The repertoire of effector candidates in Colletotrichum lindemuthianum reveals important information about Colletotrichum genus lifestyle. Appl Microbiol Biotechnol 2019; 103:2295-2309. [DOI: 10.1007/s00253-019-09639-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/04/2019] [Accepted: 01/08/2019] [Indexed: 01/04/2023]
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36
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Bianchet C, Wong A, Quaglia M, Alqurashi M, Gehring C, Ntoukakis V, Pasqualini S. An Arabidopsis thaliana leucine-rich repeat protein harbors an adenylyl cyclase catalytic center and affects responses to pathogens. JOURNAL OF PLANT PHYSIOLOGY 2019; 232:12-22. [PMID: 30530199 DOI: 10.1016/j.jplph.2018.10.025] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/29/2018] [Accepted: 10/30/2018] [Indexed: 05/21/2023]
Abstract
Adenylyl cyclases (ACs) catalyze the formation of the second messenger cAMP from ATP. Here we report the characterization of an Arabidopsis thaliana leucine-rich repeat (LRR) protein (At3g14460; AtLRRAC1) as an adenylyl cyclase. Using an AC-specific search motif supported by computational assessments of protein models we identify an AC catalytic center within the N-terminus and demonstrate that AtLRRAC1 can generate cAMP in vitro. Knock-out mutants of AtLRRAC1 have compromised immune responses to the biotrophic fungus Golovinomyces orontii and the hemibiotrophic bacteria Pseudomonas syringae, but not against the necrotrophic fungus Botrytis cinerea. These findings are consistent with a role of cAMP-dependent pathways in the defense against biotrophic and hemibiotrophic plant pathogens.
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Affiliation(s)
- Chantal Bianchet
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Borgo XX giugno, 74, 06121 Perugia, Italy
| | - Aloysius Wong
- College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, 325060, China
| | - Mara Quaglia
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX giugno, 74, 06121 Perugia, Italy
| | - May Alqurashi
- Biological and Environmental Sciences and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Chris Gehring
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Borgo XX giugno, 74, 06121 Perugia, Italy; Biological and Environmental Sciences and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Vardis Ntoukakis
- School of Life Sciences, University of Warwick, CV4 7AL, Coventry, UK; Warwick Integrative Synthetic Biology Centre, The University of Warwick, Coventry, CV4 7AL, UK
| | - Stefania Pasqualini
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Borgo XX giugno, 74, 06121 Perugia, Italy.
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Al-Younis I, Wong A, Lemtiri-Chlieh F, Schmöckel S, Tester M, Gehring C, Donaldson L. The Arabidopsis thaliana K +-Uptake Permease 5 (AtKUP5) Contains a Functional Cytosolic Adenylate Cyclase Essential for K + Transport. FRONTIERS IN PLANT SCIENCE 2018; 9:1645. [PMID: 30483296 PMCID: PMC6243130 DOI: 10.3389/fpls.2018.01645] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/23/2018] [Indexed: 05/24/2023]
Abstract
Potassium (K+) is the most abundant cation in plants, and its uptake and transport are key to growth, development and responses to the environment. Here, we report that Arabidopsis thaliana K+ uptake permease 5 (AtKUP5) contains an adenylate cyclase (AC) catalytic center embedded in its N-terminal cytosolic domain. The purified recombinant AC domain generates cAMP in vitro; and when expressed in Escherichia coli, increases cAMP levels in vivo. Both the AC domain and full length AtKUP5 rescue an AC-deficient E. coli mutant, cyaA, and together these data provide evidence that AtKUP5 functions as an AC. Furthermore, full length AtKUP5 complements the Saccharomyces cerevisiae K+ transport impaired mutant, trk1 trk2, demonstrating its function as a K+ transporter. Surprisingly, a point mutation in the AC center that impairs AC activity, also abolishes complementation of trk1 trk2, suggesting that a functional catalytic AC domain is essential for K+ uptake. AtKUP5-mediated K+ uptake is not affected by cAMP, the catalytic product of the AC, but, interestingly, causes cytosolic cAMP accumulation. These findings are consistent with a role for AtKUP5 as K+ flux sensor, where the flux-dependent cAMP increases modulate downstream components essential for K+ homeostasis, such as cyclic nucleotide gated channels.
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Affiliation(s)
- Inas Al-Younis
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Aloysius Wong
- College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Fouad Lemtiri-Chlieh
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Department of Neuroscience, University of Connecticut School of Medicine, Farmington, CT, United States
| | - Sandra Schmöckel
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Mark Tester
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Chris Gehring
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Lara Donaldson
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
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Irving HR, Cahill DM, Gehring C. Moonlighting Proteins and Their Role in the Control of Signaling Microenvironments, as Exemplified by cGMP and Phytosulfokine Receptor 1 (PSKR1). FRONTIERS IN PLANT SCIENCE 2018; 9:415. [PMID: 29643865 PMCID: PMC5883070 DOI: 10.3389/fpls.2018.00415] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 03/14/2018] [Indexed: 05/24/2023]
Abstract
Signal generating and processing complexes and changes in concentrations of messenger molecules such as calcium ions and cyclic nucleotides develop gradients that have critical roles in relaying messages within cells. Cytoplasmic contents are densely packed, and in plant cells this is compounded by the restricted cytoplasmic space. To function in such crowded spaces, scaffold proteins have evolved to keep key enzymes in the correct place to ensure ordered spatial and temporal and stimulus-specific message generation. Hence, throughout the cytoplasm there are gradients of messenger molecules that influence signaling processes. However, it is only recently becoming apparent that specific complexes involving receptor molecules can generate multiple signal gradients and enriched microenvironments around the cytoplasmic domains of the receptor that regulate downstream signaling. Such gradients or signal circuits can involve moonlighting proteins, so called because they can enable fine-tune signal cascades via cryptic additional functions that are just being defined. This perspective focuses on how enigmatic activity of moonlighting proteins potentially contributes to regional intracellular microenvironments. For instance, the proteins associated with moonlighting proteins that generate cyclic nucleotides may be regulated by cyclic nucleotide binding directly or indirectly. In this perspective, we discuss how generation of cyclic nucleotide-enriched microenvironments can promote and regulate signaling events. As an example, we use the phytosulfokine receptor (PSKR1), discuss the function of its domains and their mutual interactions and argue that this complex architecture and function enhances tuning of signals in microenvironments.
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Affiliation(s)
- Helen R. Irving
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC, Australia
| | - David M. Cahill
- Faculty of Science Engineering and Built Environment, Deakin University, Geelong, VIC, Australia
| | - Chris Gehring
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
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39
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Chatukuta P, Dikobe TB, Kawadza DT, Sehlabane KS, Takundwa MM, Wong A, Gehring C, Ruzvidzo O. An Arabidopsis Clathrin Assembly Protein with a Predicted Role in Plant Defense Can Function as an Adenylate Cyclase. Biomolecules 2018; 8:biom8020015. [PMID: 29570675 PMCID: PMC6022867 DOI: 10.3390/biom8020015] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 11/29/2022] Open
Abstract
Adenylate cyclases (ACs), much like guanylate cyclases (GCs), are increasingly recognized as essential parts of many plant processes including biotic and abiotic stress responses. In order to identify novel ACs, we have applied a search motif derived from experimentally tested GCs and identified a number of Arabidopsis thaliana candidates including a clathrin assembly protein (AT1G68110; AtClAP). AtClAP contains a catalytic centre that can complement the AC-deficient mutant cyaA in E. coli, and a recombinant AtClAP fragment (AtClAP261–379) can produce cyclic adenosine 3′,5′ monophosphate (cAMP) from adenosine triphosphate (ATP) in vitro. Furthermore, an integrated analysis of gene expression and expression correlation implicate cAMP in pathogen defense and in actin cytoskeletal remodeling during endocytic internalization.
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Affiliation(s)
- Patience Chatukuta
- Department of Botany, School of Biological Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa.
| | - Tshegofatso B Dikobe
- Department of Botany, School of Biological Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa.
| | - David T Kawadza
- Department of Botany, School of Biological Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa.
| | - Katlego S Sehlabane
- Department of Botany, School of Biological Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa.
| | - Mutsa M Takundwa
- Department of Botany, School of Biological Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa.
| | - Aloysius Wong
- College of Natural, Applied and Health Sciences, Wenzhou-Kean University, 88 Daxue Road, Wenzhou 325060, Zhejiang Province, China.
| | - Chris Gehring
- Department of Chemistry, Biology & Biotechnology, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy.
| | - Oziniel Ruzvidzo
- Department of Botany, School of Biological Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa.
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40
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Abstract
Cyclic nucleotides such as 3',5'-cyclic adenosine monophosphate (cAMP) and 3',5'-cyclic guanosine monophosphate (cGMP) are increasingly recognized as key signaling molecules in plants, and a growing number of plant mononucleotide cyclases, both adenylate cyclases (ACs) and guanylate cyclases (GCs), have been reported. Catalytically active cytosolic GC domains have been shown to be part of many plant receptor kinases and hence directly linked to plant signaling and downstream cellular responses. Here we detail, firstly, methods to identify and express essential functional GC domains of receptor kinases, and secondly, we describe mass spectrometric methods to quantify cGMP generated by recombinant GCs from receptor kinases in vitro.
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41
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Kännaste A, Laanisto L, Pazouki L, Copolovici L, Suhorutšenko M, Azeem M, Toom L, Borg-Karlson AK, Niinemets Ü. Diterpenoid fingerprints in pine foliage across an environmental and chemotypic matrix: Isoabienol content is a key trait differentiating chemotypes. PHYTOCHEMISTRY 2018; 147:80-88. [PMID: 29304384 PMCID: PMC6020065 DOI: 10.1016/j.phytochem.2017.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 12/12/2017] [Accepted: 12/14/2017] [Indexed: 06/07/2023]
Abstract
Diterpenoids constitute an important part of oleoresin in conifer needles, but the environmental and genetic controls on diterpenoid composition are poorly known. We studied the presence of diterpenoids in four pine populations spanning an extensive range of nitrogen (N) availability. In most samples, isoabienol was the main diterpenoid. Additionally, low contents of (Z)-biformene, abietadiene isomers, manoyl oxide isomers, labda-7,13,14-triene and labda-7,14-dien-13-ol were quantified in pine needles. According to the occurrence and content of diterpenoids it was possible to distinguish 'non diterpenoid pines', 'high isoabienol pines', 'manoyl oxide - isoabienol pines' and 'other diterpenoid pines'. 'Non diterpenoid pines', 'high isoabienol pines' and 'other diterpenoid pines' were characteristic to the dry forest, yet the majority of pines (>80%) of the bog Laeva represented 'high isoabienol pines'. 'Manoyl oxide - isoabienol pines' were present only in the wet sites. Additionally, orthogonal partial least-squares analysis showed, that in the bogs foliar nitrogen content per dry mass (NM) correlated to diterpenoids. Significant correlations existed between abietadienes, isoabienol and foliar NM in 'manoyl oxide - isoabienol pines', and chemotypic variation was also associated by population genetic distance estimated by nuclear microsatellite markers. Previously, the presence of low and high Δ-3-carene pines has been demonstrated, but the results of the current study indicate that also diterpenoids form an independent axis of chemotypic differentiation. Further studies are needed to understand whether the enhanced abundance of diterpenoids in wetter sites reflects a phenotypic or genotypic response.
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Affiliation(s)
- Astrid Kännaste
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51014, Estonia.
| | - Lauri Laanisto
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51014, Estonia.
| | - Leila Pazouki
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51014, Estonia; Department of Biology, University of Louisville, Louisville, KY 40292, USA.
| | - Lucian Copolovici
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51014, Estonia; Institute of Technical and Natural Sciences Research-Development of "Aurel Vlaicu" University, 2 Elena Dragoi St., Arad 310330, Romania.
| | - Marina Suhorutšenko
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51014, Estonia.
| | - Muhammad Azeem
- Department of Chemistry, COMSATS Institute of Information Technology, Abbottabad 22060, Pakistan; Ecological Chemistry Group, Department of Chemistry, KTH, Royal Institute of Technology, 100 44 Stockholm, Sweden.
| | - Lauri Toom
- Institute of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia.
| | - Anna-Karin Borg-Karlson
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51014, Estonia; Ecological Chemistry Group, Department of Chemistry, KTH, Royal Institute of Technology, 100 44 Stockholm, Sweden; Institute of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia.
| | - Ülo Niinemets
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51014, Estonia; Estonian Academy of Sciences, Kohtu 6, 10130 Tallinn, Estonia.
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42
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Wong A, Tian X, Gehring C, Marondedze C. Discovery of Novel Functional Centers With Rationally Designed Amino Acid Motifs. Comput Struct Biotechnol J 2018; 16:70-76. [PMID: 29977479 PMCID: PMC6026216 DOI: 10.1016/j.csbj.2018.02.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 01/23/2018] [Accepted: 02/25/2018] [Indexed: 12/14/2022] Open
Abstract
Plants are constantly exposed to environmental stresses and in part due to their sessile nature, they have evolved signal perception and adaptive strategies that are distinct from those of other eukaryotes. This is reflected at the cellular level where receptors and signalling molecules cannot be identified using standard homology-based searches querying with proteins from prokaryotes and other eukaryotes. One of the reasons for this is the complex domain architecture of receptor molecules. In order to discover hidden plant signalling molecules, we have developed a motif-based approach designed specifically for the identification of functional centers in plant molecules. This has made possible the discovery of novel components involved in signalling and stimulus-response pathways; the molecules include cyclic nucleotide cyclases, a nitric oxide sensor and a novel target for the hormone abscisic acid. Here, we describe the major steps of the method and illustrate it with recent and experimentally confirmed molecules as examples. We foresee that carefully curated search motifs supported by structural and bioinformatic assessments will uncover many more structural and functional aspects, particularly of signalling molecules.
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Affiliation(s)
- Aloysius Wong
- Department of Biology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Xuechen Tian
- Department of Biology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Chris Gehring
- Department of Chemistry, Biology & Biotechnology, University of Perugia, Borgo XX giugno, 74, 06121 Perugia, Italy
| | - Claudius Marondedze
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CEA/DRF/BIG, INRA UMR1417, CNRS UMR5168, 38054 Grenoble Cedex 9, France
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43
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Świeżawska B, Duszyn M, Jaworski K, Szmidt-Jaworska A. Downstream Targets of Cyclic Nucleotides in Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:1428. [PMID: 30327660 PMCID: PMC6174285 DOI: 10.3389/fpls.2018.01428] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/07/2018] [Indexed: 05/04/2023]
Abstract
Efficient integration of various external and internal signals is required to maintain adaptive cellular function. Numerous distinct signal transduction systems have evolved to allow cells to receive these inputs, to translate their codes and, subsequently, to expand and integrate their meanings. Two of these, cyclic AMP and cyclic GMP, together referred to as the cyclic nucleotide signaling system, are between them. The cyclic nucleotides regulate a vast number of processes in almost all living organisms. Once synthesized by adenylyl or guanylyl cyclases, cyclic nucleotides transduce signals by acting through a number of cellular effectors. Because the activities of several of these effectors are altered simultaneously in response to temporal changes in cyclic nucleotide levels, agents that increase cAMP/cGMP levels can trigger multiple signaling events that markedly affect numerous cellular functions. In this mini review, we summarize recent evidence supporting the existence of cNMP effectors in plant cells. Specifically, we highlight cAMP-dependent protein kinase A (PKA), cGMP-dependent kinase G (PKG), and cyclic nucleotide phosphodiesterases (PDEs). Essentially this manuscript documents the progress that has been achieved in recent decades in improving our understanding of the regulation and function of cNMPs in plants and emphasizes the current gaps and unanswered questions in this field of plant signaling research.
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44
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Wu H, Kwaaitaal M, Strugala R, Schaffrath U, Bednarek P, Panstruga R. Chemical suppressors of mlo-mediated powdery mildew resistance. Biosci Rep 2017; 37:BSR20171389. [PMID: 29127104 PMCID: PMC5725617 DOI: 10.1042/bsr20171389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/27/2017] [Accepted: 11/07/2017] [Indexed: 01/19/2023] Open
Abstract
Loss-of-function of barley mildew locus o (Mlo) confers durable broad-spectrum penetration resistance to the barley powdery mildew pathogen, Blumeria graminis f. sp. hordei (Bgh). Given the importance of mlo mutants in agriculture, surprisingly few molecular components have been identified to be required for this type of resistance in barley. With the aim to identify novel cellular factors contributing to mlo-based resistance, we devised a pharmacological inhibitor screen. Of the 41 rationally chosen compounds tested, five caused a partial suppression of mlo resistance in barley, indicated by increased levels of Bgh host cell entry. These chemicals comprise brefeldin A (BFA), 2',3'-dideoxyadenosine (DDA), 2-deoxy-d-glucose, spermidine, and 1-aminobenzotriazole. Further inhibitor analysis corroborated a key role for both anterograde and retrograde endomembrane trafficking in mlo resistance. In addition, all four ribonucleosides, some ribonucleoside derivatives, two of the five nucleobases (guanine and uracil), some guanine derivatives as well as various polyamines partially suppress mlo resistance in barley via yet unknown mechanisms. Most of the chemicals identified to be effective in partially relieving mlo resistance in barley also to some extent compromised powdery mildew resistance in an Arabidopsis mlo2 mlo6 double mutant. In summary, our study identified novel suppressors of mlo resistance that may serve as valuable probes to unravel further the molecular processes underlying this unusual type of disease resistance.
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Affiliation(s)
- Hongpo Wu
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056 Aachen, Germany
| | - Mark Kwaaitaal
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056 Aachen, Germany
| | - Roxana Strugala
- Institute for Biology III, RWTH Aachen University, Worringerweg 1, 52056 Aachen, Germany
| | - Ulrich Schaffrath
- Institute for Biology III, RWTH Aachen University, Worringerweg 1, 52056 Aachen, Germany
| | - Paweł Bednarek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznán, Poland
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056 Aachen, Germany
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45
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Marondedze C, Wong A, Thomas L, Irving H, Gehring C. Cyclic Nucleotide Monophosphates in Plants and Plant Signaling. Handb Exp Pharmacol 2017; 238:87-103. [PMID: 26721677 DOI: 10.1007/164_2015_35] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cyclic nucleotide monophosphates (cNMPs) and the enzymes that can generate them are of increasing interest in the plant sciences. Arguably, the major recent advance came with the release of the complete Arabidopsis thaliana genome that has enabled the systematic search for adenylate (ACs) or guanylate cyclases (GCs) and did eventually lead to the discovery of a number of GCs in higher plants. Many of these proteins have complex domain architectures with AC or GC centers moonlighting within cytosolic kinase domains. Recent reports indicated the presence of not just the canonical cNMPs (i.e., cAMP and cGMP), but also the noncanonical cCMP, cUMP, cIMP, and cdTMP in plant tissues, and this raises several questions. Firstly, what are the functions of these cNMPs, and, secondly, which enzymes can convert the substrate triphosphates into the respective noncanonical cNMPs? The first question is addressed here by comparing the reactive oxygen species (ROS) response of cAMP and cGMP to that elicited by the noncanonical cCMP or cIMP. The results show that particularly cIMP can induce significant ROS production. To answer, at least in part, the second question, we have evaluated homology models of experimentally confirmed plant GCs probing the substrate specificity by molecular docking simulations to determine if they can conceivably catalytically convert substrates other than ATP or GTP. In summary, molecular modeling and substrate docking simulations can contribute to the evaluation of cyclases for noncanonical cyclic mononucleotides and thereby further our understanding of the molecular mechanism that underlie cNMP-dependent signaling in planta.
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Affiliation(s)
- Claudius Marondedze
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
| | - Aloysius Wong
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Ludivine Thomas
- Proteomics Core Laboratory, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Helen Irving
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Chris Gehring
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.
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46
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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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47
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Luzarowski M, Kosmacz M, Sokolowska E, Jasińska W, Willmitzer L, Veyel D, Skirycz A. Affinity purification with metabolomic and proteomic analysis unravels diverse roles of nucleoside diphosphate kinases. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3487-3499. [PMID: 28586477 PMCID: PMC5853561 DOI: 10.1093/jxb/erx183] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/04/2017] [Indexed: 05/22/2023]
Abstract
Interactions between metabolites and proteins play an integral role in all cellular functions. Here we describe an affinity purification (AP) approach in combination with LC/MS-based metabolomics and proteomics that allows, to our knowledge for the first time, analysis of protein-metabolite and protein-protein interactions simultaneously in plant systems. More specifically, we examined protein and small-molecule partners of the three (of five) nucleoside diphosphate kinases present in the Arabidopsis genome (NDPK1-NDPK3). The bona fide role of NDPKs is the exchange of terminal phosphate groups between nucleoside diphosphates (NDPs) and triphosphates (NTPs). However, other functions have been reported, which probably depend on both the proteins and small molecules specifically interacting with the NDPK. Using our approach we identified 23, 17, and 8 novel protein partners of NDPK1, NDPK2, and NDPK3, respectively, with nucleotide-dependent proteins such as actin and adenosine kinase 2 being enriched. Particularly interesting, however, was the co-elution of glutathione S-transferases (GSTs) and reduced glutathione (GSH) with the affinity-purified NDPK1 complexes. Following up on this finding, we could demonstrate that NDPK1 undergoes glutathionylation, opening a new paradigm of NDPK regulation in plants. The described results extend our knowledge of NDPKs, the key enzymes regulating NDP/NTP homeostasis.
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Affiliation(s)
- Marcin Luzarowski
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
| | - Monika Kosmacz
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
| | - Ewelina Sokolowska
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
| | - Weronika Jasińska
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
| | - Lothar Willmitzer
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
| | - Daniel Veyel
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
| | - Aleksandra Skirycz
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
- Correspondence:
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48
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Luzarowski M, Kosmacz M, Sokolowska E, Jasinska W, Willmitzer L, Veyel D, Skirycz A. Affinity purification with metabolomic and proteomic analysis unravels diverse roles of nucleoside diphosphate kinases. JOURNAL OF EXPERIMENTAL BOTANY 2017. [PMID: 28586477 DOI: 10.93/jxb/erx183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Interactions between metabolites and proteins play an integral role in all cellular functions. Here we describe an affinity purification (AP) approach in combination with LC/MS-based metabolomics and proteomics that allows, to our knowledge for the first time, analysis of protein-metabolite and protein-protein interactions simultaneously in plant systems. More specifically, we examined protein and small-molecule partners of the three (of five) nucleoside diphosphate kinases present in the Arabidopsis genome (NDPK1-NDPK3). The bona fide role of NDPKs is the exchange of terminal phosphate groups between nucleoside diphosphates (NDPs) and triphosphates (NTPs). However, other functions have been reported, which probably depend on both the proteins and small molecules specifically interacting with the NDPK. Using our approach we identified 23, 17, and 8 novel protein partners of NDPK1, NDPK2, and NDPK3, respectively, with nucleotide-dependent proteins such as actin and adenosine kinase 2 being enriched. Particularly interesting, however, was the co-elution of glutathione S-transferases (GSTs) and reduced glutathione (GSH) with the affinity-purified NDPK1 complexes. Following up on this finding, we could demonstrate that NDPK1 undergoes glutathionylation, opening a new paradigm of NDPK regulation in plants. The described results extend our knowledge of NDPKs, the key enzymes regulating NDP/NTP homeostasis.
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Affiliation(s)
- Marcin Luzarowski
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Monika Kosmacz
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ewelina Sokolowska
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Weronika Jasinska
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Lothar Willmitzer
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Daniel Veyel
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Aleksandra Skirycz
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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Yang YC, Wang YT, Tseng WL. Amplified Peroxidase-Like Activity in Iron Oxide Nanoparticles Using Adenosine Monophosphate: Application to Urinary Protein Sensing. ACS APPLIED MATERIALS & INTERFACES 2017; 9:10069-10077. [PMID: 28233488 DOI: 10.1021/acsami.6b15654] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Numerous compounds such as protein and double-stranded DNA have been shown to efficiently inhibit intrinsic peroxidase-mimic activity in Fe3O4 nanoparticles (NP) and other related nanomaterials. However, only a few studies have focused on finding new compounds for enhancing the catalytic activity of Fe3O4 NP-related nanomaterials. Herein, phosphate containing adenosine analogs are reported to enhance the oxidation reaction of hydrogen peroxide (H2O2) and amplex ultrared (AU) for improving the peroxidase-like activity in Fe3O4 NPs. This enhancement is suggested to be a result of the binding of adenosine analogs to Fe2+/Fe3+ sites on the NP surface and from adenosine 5'-monophosphate (AMP) acting as the distal histidine residue of horseradish peroxidase for activating H2O2. Phosphate containing adenosine analogs revealed the following trend for the enhanced activity of Fe3O4 NPs: AMP > adenosine 5'-diphosphate > adenosine 5'-triphosphate. The peroxidase-like activity in the Fe3O4 NPs progressively increased with increasing AMP concentration and polyadenosine length. The Michaelis constant for AMP attached Fe3O4 NPs is 5.3-fold lower and the maximum velocity is 2.7-fold higher than those of the bare Fe3O4 NPs. Furthermore, on the basis of AMP promoted peroxidase mimicking activity in the Fe3O4 NPs and the adsorption of protein on the NP surface, a selective fluorescent turn-off system for the detection of urinary protein is developed.
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Affiliation(s)
- Ya-Chun Yang
- Department of Chemistry, National Sun Yat-sen University , Taiwan
| | - Yen-Ting Wang
- Department of Chemistry, National Sun Yat-sen University , Taiwan
| | - Wei-Lung Tseng
- Department of Chemistry, National Sun Yat-sen University , Taiwan
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University , Taiwan
- Center for Nanoscience and Nanotechnology, National Sun Yat-sen University , Taiwan
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Kasahara M, Suetsugu N, Urano Y, Yamamoto C, Ohmori M, Takada Y, Okuda S, Nishiyama T, Sakayama H, Kohchi T, Takahashi F. An adenylyl cyclase with a phosphodiesterase domain in basal plants with a motile sperm system. Sci Rep 2016; 6:39232. [PMID: 27982074 PMCID: PMC5159850 DOI: 10.1038/srep39232] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/18/2016] [Indexed: 01/03/2023] Open
Abstract
Adenylyl cyclase (AC), which produces the signalling molecule cAMP, has numerous important cellular functions in diverse organisms from prokaryotes to eukaryotes. Here we report the identification and characterization of an AC gene from the liverwort Marchantia polymorpha. The encoded protein has both a C-terminal AC catalytic domain similar to those of class III ACs and an N-terminal cyclic nucleotide phosphodiesterase (PDE) domain that degrades cyclic nucleotides, thus we designated the gene MpCAPE (COMBINED AC with PDE). Biochemical analyses of recombinant proteins showed that MpCAPE has both AC and PDE activities. In MpCAPE-promoter-GUS lines, GUS activity was specifically detected in the male sexual organ, the antheridium, suggesting MpCAPE and thus cAMP signalling may be involved in the male reproductive process. CAPE orthologues are distributed only in basal land plants and charophytes that use motile sperm as the male gamete. CAPE is a subclass of class III AC and may be important in male organ and cell development in basal plants.
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Affiliation(s)
- Masahiro Kasahara
- Graduate School of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
- College of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Noriyuki Suetsugu
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Yuki Urano
- Graduate School of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Chiaki Yamamoto
- College of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Mikiya Ohmori
- College of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Yuki Takada
- College of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Shujiro Okuda
- Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
| | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, Ishikawa 920-0934, Japan
| | - Hidetoshi Sakayama
- Department of Biology, Graduate School of Science, Kobe University, Hyogo 657-8501, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Fumio Takahashi
- Graduate School of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
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