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Turek I, Wong A, Domingo G, Vannini C, Bracale M, Irving H, Gehring C. Moonlighting Crypto-Enzymes and Domains as Ancient and Versatile Signaling Devices. Int J Mol Sci 2024; 25:9535. [PMID: 39273482 PMCID: PMC11394779 DOI: 10.3390/ijms25179535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/27/2024] [Accepted: 08/27/2024] [Indexed: 09/15/2024] Open
Abstract
Increasing numbers of reports have revealed novel catalytically active cryptic guanylate cyclases (GCs) and adenylate cyclases (ACs) operating within complex proteins in prokaryotes and eukaryotes. Here we review the structural and functional aspects of some of these cyclases and provide examples that illustrate their roles in the regulation of the intramolecular functions of complex proteins, such as the phytosulfokine receptor (PSKR), and reassess their contribution to signal generation and tuning. Another multidomain protein, Arabidopsis thaliana K+ uptake permease (AtKUP5), also harbors multiple catalytically active sites including an N-terminal AC and C-terminal phosphodiesterase (PDE) with an abscisic acid-binding site. We argue that this architecture may enable the fine-tuning and/or sensing of K+ flux and integrate hormone responses to cAMP homeostasis. We also discuss how searches with motifs based on conserved amino acids in catalytic centers led to the discovery of GCs and ACs and propose how this approach can be applied to discover hitherto masked active sites in bacterial, fungal, and animal proteomes. Finally, we show that motif searches are a promising approach to discover ancient biological functions such as hormone or gas binding.
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Affiliation(s)
- Ilona Turek
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, East Geelong, VIC 3220, Australia
| | - Aloysius Wong
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou 325060, China
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou-Kean University, Wenzhou 325060, China
| | - Guido Domingo
- Biotechnology and Life Science Department, University of Insubria, 21100 Varese, Italy
| | - Candida Vannini
- Biotechnology and Life Science Department, University of Insubria, 21100 Varese, Italy
| | - Marcella Bracale
- Biotechnology and Life Science Department, University of Insubria, 21100 Varese, Italy
| | - Helen Irving
- La Trobe Institute of Molecular Sciences, La Trobe University, Bendigo, VIC 3552, Australia
- Holsworth Initiative for Medical Research, Rural People, Department of Rural Clinical Sciences, La Trobe Rural Health School, La Trobe University, Bendigo, VIC 3552, Australia
| | - Chris Gehring
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06121 Perugia, Italy
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2
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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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3
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Kwiatkowski M, Wong A, Bi C, Gehring C, Jaworski K. Twin cyclic mononucleotide cyclase and phosphodiesterase domain architecture as a common feature in complex plant proteins. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111493. [PMID: 36216295 DOI: 10.1016/j.plantsci.2022.111493] [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: 08/01/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
The majority of proteins in both prokaryote and eukaryote proteomes consist of two or more functional centers, which allows for intramolecular tuning of protein functions. Such architecture, as opposed to animal orthologs, applies to the plant cyclases (CNC) and phosphodiesterases (PDEs), the vast majority of which are part of larger multifunctional proteins. In plants, until recently, only two cases of combinations of CNC-PDE in one protein were reported. Here we propose that in plants, multifunctional proteins in which the PDE motif has been identified, the presence of the additional CNC center is common. Searching the Arabidopsis thaliana proteome with a combined PDE-CNC motif allowed the creation of a database of proteins with both activities. One such example is methylenetetrahydrofolate dehydrogenase, in which we determined the activities of adenylate cyclase (AC) and PDE. Based on biochemical and mutagenesis analyses we assessed the impact of the AC and PDE catalytic centers on the dehydrogenase activity. This allowed us to propose additional regulatory mechanism that govern folate metabolism by cAMP. It is therefore conceivable that the combined CNC-PDE architecture is a common regulatory configuration, where control of the level of cyclic nucleotides (cNMP) influences other catalytic activities of the protein.
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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 and Technology, Wenzhou-Kean University, 88 Daxue Road, Wenzhou 325060, Zhejiang Province, China; Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou 325060, Zhejiang Province, China; Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou 325060, Zhejiang Province, China.
| | - Chuyun Bi
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Wenzhou 325060, Zhejiang Province, China; Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou 325060, Zhejiang Province, China; Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou 325060, Zhejiang Province, China
| | - 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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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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Liu X, Shen Y, Zhang Y, Liu F, Ma Z, Yue Z, Yue Y. IdentPMP: identification of moonlighting proteins in plants using sequence-based learning models. PeerJ 2021; 9:e11900. [PMID: 34434652 PMCID: PMC8351581 DOI: 10.7717/peerj.11900] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 07/13/2021] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND A moonlighting protein refers to a protein that can perform two or more functions. Since the current moonlighting protein prediction tools mainly focus on the proteins in animals and microorganisms, and there are differences in the cells and proteins between animals and plants, these may cause the existing tools to predict plant moonlighting proteins inaccurately. Hence, the availability of a benchmark data set and a prediction tool specific for plant moonlighting protein are necessary. METHODS This study used some protein feature classes from the data set constructed in house to develop a web-based prediction tool. In the beginning, we built a data set about plant protein and reduced redundant sequences. We then performed feature selection, feature normalization and feature dimensionality reduction on the training data. Next, machine learning methods for preliminary modeling were used to select feature classes that performed best in plant moonlighting protein prediction. This selected feature was incorporated into the final plant protein prediction tool. After that, we compared five machine learning methods and used grid searching to optimize parameters, and the most suitable method was chosen as the final model. RESULTS The prediction results indicated that the eXtreme Gradient Boosting (XGBoost) performed best, which was used as the algorithm to construct the prediction tool, called IdentPMP (Identification of Plant Moonlighting Proteins). The results of the independent test set shows that the area under the precision-recall curve (AUPRC) and the area under the receiver operating characteristic curve (AUC) of IdentPMP is 0.43 and 0.68, which are 19.44% (0.43 vs. 0.36) and 13.33% (0.68 vs. 0.60) higher than state-of-the-art non-plant specific methods, respectively. This further demonstrated that a benchmark data set and a plant-specific prediction tool was required for plant moonlighting protein studies. Finally, we implemented the tool into a web version, and users can use it freely through the URL: http://identpmp.aielab.net/.
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Affiliation(s)
- Xinyi Liu
- School of Information and Computer, Anhui Provincial Engineering Laboratory for Beidou Precision Agriculture Information, Anhui Agricultural University, Hefei, Anhui, China
| | - Yueyue Shen
- School of Information and Computer, Anhui Provincial Engineering Laboratory for Beidou Precision Agriculture Information, Anhui Agricultural University, Hefei, Anhui, China
| | - Youhua Zhang
- School of Information and Computer, Anhui Provincial Engineering Laboratory for Beidou Precision Agriculture Information, Anhui Agricultural University, Hefei, Anhui, China
| | - Fei Liu
- School of Information and Computer, Anhui Provincial Engineering Laboratory for Beidou Precision Agriculture Information, Anhui Agricultural University, Hefei, Anhui, China
| | - Zhiyu Ma
- School of Information and Computer, Anhui Provincial Engineering Laboratory for Beidou Precision Agriculture Information, Anhui Agricultural University, Hefei, Anhui, China
| | - Zhenyu Yue
- School of Information and Computer, Anhui Provincial Engineering Laboratory for Beidou Precision Agriculture Information, Anhui Agricultural University, Hefei, Anhui, China
| | - Yi Yue
- School of Information and Computer, Anhui Provincial Engineering Laboratory for Beidou Precision Agriculture Information, Anhui Agricultural University, Hefei, Anhui, China
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Kaufmann C, Stührwohldt N, Sauter M. Tyrosylprotein sulfotransferase-dependent and -independent regulation of root development and signaling by PSK LRR receptor kinases in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5508-5521. [PMID: 34028532 PMCID: PMC8318253 DOI: 10.1093/jxb/erab233] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/20/2021] [Indexed: 05/13/2023]
Abstract
Tyrosine-sulfated peptides are key regulators of plant growth and development. The disulfated pentapeptide phytosulfokine (PSK) mediates growth via leucine-rich repeat receptor-like kinases, PSKR1 and PSKR2. PSK receptors (PSKRs) are part of a response module at the plasma membrane that mediates short-term growth responses, but downstream signaling of transcriptional regulation remains unexplored. In Arabidopsis, tyrosine sulfation is catalyzed by a single-copy gene (TPST; encoding tyrosylprotein sulfotransferase). We performed a microarray-based transcriptome analysis in the tpst-1 mutant background that lacks sulfated peptides to identify PSK-regulated genes and genes that are regulated by other sulfated peptides. Of the 169 PSK-regulated genes, several had functions in root growth and development, in agreement with shorter roots and a higher lateral root density in tpst-1. Further, tpst-1 roots developed higher numbers of root hairs, and PSK induced expression of WEREWOLF (WER), its paralog MYB DOMAIN PROTEIN 23 (MYB23), and At1g66800 that maintain non-hair cell fate. The tpst-1 pskr1-3 pskr2-1 mutant showed even shorter roots, and higher lateral root and root hair density than tpst-1, revealing unexpected synergistic effects of ligand and PSKR deficiencies. While residual activities may exist, overexpression of PSKR1 in the tpst-1 background induced root growth, suggesting that PSKR1 may be active in the absence of sulfated ligands.
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Affiliation(s)
- Christine Kaufmann
- Plant Developmental Biology and Physiology, University of Kiel, Kiel, Germany
| | - Nils Stührwohldt
- Plant Developmental Biology and Physiology, University of Kiel, Kiel, Germany
| | - Margret Sauter
- Plant Developmental Biology and Physiology, University of Kiel, Kiel, Germany
- Correspondence:
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7
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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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Świeżawska-Boniecka B, Duszyn M, Kwiatkowski M, Szmidt-Jaworska A, Jaworski K. Cross Talk Between Cyclic Nucleotides and Calcium Signaling Pathways in Plants-Achievements and Prospects. FRONTIERS IN PLANT SCIENCE 2021; 12:643560. [PMID: 33664763 PMCID: PMC7921789 DOI: 10.3389/fpls.2021.643560] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 01/26/2021] [Indexed: 06/12/2023]
Abstract
A variety of plant cellular activities are regulated through mechanisms controlling the level of signal molecules, such as cyclic nucleotides (cNMPs, e.g., cyclic adenosine 3':5'-monophosphate, cAMP, and cyclic guanosine 3':5'- monophosphate, cGMP) and calcium ions (Ca2+). The mechanism regulating cNMP levels affects their synthesis, degradation, efflux and cellular distribution. Many transporters and the spatiotemporal pattern of calcium signals, which are transduced by multiple, tunable and often strategically positioned Ca2+-sensing elements, play roles in calcium homeostasis. Earlier studies have demonstrated that while cNMPs and Ca2+ can act separately in independent transduction pathways, they can interact and function together. Regardless of the context, the balance between Ca2+ and cNMP is the most important consideration. This balance seems to be crucial for effectors, such as phosphodiesterases, cyclic nucleotide gated channels and cyclase activity. Currently, a wide range of molecular biology techniques enable thorough analyses of cellular cross talk. In recent years, data have indicated relationships between calcium ions and cyclic nucleotides in mechanisms regulating specific signaling pathways. The purpose of this study is to summarize the current knowledge on nucleotide-calcium cross talk in plants.
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Turek I, Irving H. Moonlighting Proteins Shine New Light on Molecular Signaling Niches. Int J Mol Sci 2021; 22:1367. [PMID: 33573037 PMCID: PMC7866414 DOI: 10.3390/ijms22031367] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 02/06/2023] Open
Abstract
Plants as sessile organisms face daily environmental challenges and have developed highly nuanced signaling systems to enable suitable growth, development, defense, or stalling responses. Moonlighting proteins have multiple tasks and contribute to cellular signaling cascades where they produce additional variables adding to the complexity or fuzziness of biological systems. Here we examine roles of moonlighting kinases that also generate 3',5'-cyclic guanosine monophosphate (cGMP) in plants. These proteins include receptor like kinases and lipid kinases. Their guanylate cyclase activity potentiates the development of localized cGMP-enriched nanodomains or niches surrounding the kinase and its interactome. These nanodomains contribute to allosteric regulation of kinase and other molecules in the immediate complex directly or indirectly modulating signal cascades. Effects include downregulation of kinase activity, modulation of other members of the protein complexes such as cyclic nucleotide gated channels and potential triggering of cGMP-dependent degradation cascades terminating signaling. The additional layers of information provided by the moonlighting kinases are discussed in terms of how they may be used to provide a layer of fuzziness to effectively modulate cellular signaling cascades.
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Affiliation(s)
| | - Helen Irving
- Department of Pharmacy and Biomedical Sciences, La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC 3550, Australia;
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10
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Rahman H, Wang XY, Xu YP, He YH, Cai XZ. Characterization of tomato protein kinases embedding guanylate cyclase catalytic center motif. Sci Rep 2020; 10:4078. [PMID: 32139792 PMCID: PMC7057975 DOI: 10.1038/s41598-020-61000-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 02/19/2020] [Indexed: 11/09/2022] Open
Abstract
Guanylate cyclases (GCs) are enzymes that catalyze the reaction to produce cyclic GMP (cGMP), a key signaling molecule in eukaryotes. Nevertheless, systemic identification and functional analysis of GCs in crop plant species have not yet been conducted. In this study, we systematically identified GC genes in the economically important crop tomato (Solanum lycopersicum L.) and analyzed function of two putative tomato GC genes in disease resistance. Ninety-nine candidate GCs containing GC catalytic center (GC-CC) motif were identified in tomato genome. Intriguingly, all of them were putative protein kinases embedding a GC-CC motif within the protein kinase domain, which was thus tentatively named as GC-kinases here. Two homologs of Arabidopsis PEPRs, SlGC17 and SlGC18 exhibited in vitro GC activity. Co-silencing of SlGC17 and SlGC18 genes significantly reduced resistance to tobacco rattle virus, fungus Sclerotinia sclerotiorum, and bacterium Pseudomonas syringae pv. tomato (Pst) DC3000. Moreover, co-silencing of these two genes attenuated PAMP and DAMP-triggered immunity as shown by obvious decrease of flg22, chitin and AtPep1-elicited Ca2+ and H2O2 burst in SlGC-silenced plants. Additionally, silencing of these genes altered the expression of a set of Ca2+ signaling genes. Furthermore, co-silencing of these GC-kinase genes exhibited stronger effects on all above regulations in comparison with individual silencing. Collectively, our results suggest that GC-kinases might widely exist in tomato and the two SlPEPR-GC genes redundantly play a positive role in resistance to diverse pathogens and PAMP/DAMP-triggered immunity in tomato. Our results provide insights into composition and functions of GC-kinases in tomato.
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Affiliation(s)
- Hafizur Rahman
- Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xin-Yao Wang
- Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - You-Ping Xu
- Center of Analysis and Measurement, Zhejiang University, Hangzhou, 310058, China
| | - Yu-Han He
- Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xin-Zhong Cai
- Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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11
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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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12
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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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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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Kwezi L, Wheeler JI, Marondedze C, Gehring C, Irving HR. Intramolecular crosstalk between catalytic activities of receptor kinases. PLANT SIGNALING & BEHAVIOR 2018; 13:e1430544. [PMID: 29355445 PMCID: PMC5846547 DOI: 10.1080/15592324.2018.1430544] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 01/12/2018] [Indexed: 05/21/2023]
Abstract
Signal modulation is important for the growth and development of plants and this process is mediated by a number of factors including physiological growth regulators and their associated signal transduction pathways. Protein kinases play a central role in signaling, including those involving pathogen response mechanisms. We previously demonstrated an active guanylate cyclase (GC) catalytic center in the brassinosteroid insensitive receptor (AtBRI1) within an active intracellular kinase domain resulting in dual enzymatic activity. Here we propose a novel type of receptor architecture that is characterized by a functional GC catalytic center nested in the cytosolic kinase domain enabling intramolecular crosstalk. This may be through a cGMP-AtBRI1 complex forming that may induce a negative feedback mechanism leading to desensitisation of the receptor, regulated through the cGMP production pathway. We further argue that the comparatively low but highly localized cGMP generated by the GC in response to a ligand is sufficient to modulate the kinase activity. This type of receptor therefore provides a molecular switch that directly and/or indirectly affects ligand dependent phosphorylation of downstream signaling cascades and suggests that subsequent signal transduction and modulation works in conjunction with the kinase in downstream signaling.
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Affiliation(s)
- Lusisizwe Kwezi
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia
- Biosciences, Council For Scientific and Industrial Research, Brummeria, Pretoria, South Africa
| | - Janet I. Wheeler
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia
- AgriBio, La Trobe University, Bundoora, VIC, Australia
| | - Claudius Marondedze
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CEA/DRF/BIG, INRA UMR1417, CNRS UMR5168, Grenoble Cedex 9, France
| | - Chris Gehring
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- Department of Chemistry, Biology & Biotechnology, University of Perugia, Perugia, Umbria, Italy
| | - Helen R. Irving
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia
- Pharmacy & Applied Sciences, La Trobe Institute for Molecular Science, La Trobe University, Bendigo VIC, Australia
- CONTACT Helen R. Irving La Trobe Institute for Molecular Science, La Trobe University, PO Box 199, Bendigo VIC 3552,Australia
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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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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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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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Świeżawska B, Jaworski K, Duszyn M, Pawełek A, Szmidt-Jaworska A. The Hippeastrum hybridum PepR1 gene (HpPepR1) encodes a functional guanylyl cyclase and is involved in early response to fungal infection. JOURNAL OF PLANT PHYSIOLOGY 2017; 216:100-107. [PMID: 28609666 DOI: 10.1016/j.jplph.2017.05.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/21/2017] [Accepted: 05/15/2017] [Indexed: 06/07/2023]
Abstract
It is generally known that cyclic GMP widespread in prokaryotic and eukaryotic cells, is involved in essential cellular processes and stress signal transduction. However, in contrast to animals the knowledge about plant guanylyl cyclases (GCs) which catalyze the formation of cGMP from GTP is still quite obscure. Recent studies of plant GCs are focused on identification and functional analysis of a new family of membrane proteins called "moonlighting kinases with GC activity" with guanylyl cyclase catalytic center encapsulated within intracellular kinase domain. Here we report identification and characterization of plasma membrane receptor of peptide signaling molecules - HpPepR1 in Hippeastrum hybridum. Both bioinformatic analysis of amimo acid sequence and in vitro studies revealed that the protein can act as guanylyl cyclase. The predicted amino acid sequence contains highly conserved 14 aa-long search motif in the catalytic center of GCs from lower and higher eukaryotes. Here, we provide experimental evidence to show that the intracellular domain of HpPepR1 can generate cGMP in vitro. Moreover, it was shown that the accumulation of HpPepR1 transcript was sharply increased after Peyronellaea curtisii (=Phoma narcissi) fungal infection, whereas mechanical wounding has no influence on expression profile of studied gene. These results may indicate the participation of cGMP-dependent pathway in rapid, alarm plant reactions induced by pathogen infection.
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Affiliation(s)
- Brygida Świeżawska
- Nicolaus Copernicus University, Chair of Plant Physiology and Biotechnology, Lwowska St. 1, PL 87-100, Torun, Poland.
| | - Krzysztof Jaworski
- Nicolaus Copernicus University, Chair of Plant Physiology and Biotechnology, Lwowska St. 1, PL 87-100, Torun, Poland.
| | - Maria Duszyn
- Nicolaus Copernicus University, Chair of Plant Physiology and Biotechnology, Lwowska St. 1, PL 87-100, Torun, Poland.
| | - Agnieszka Pawełek
- Nicolaus Copernicus University, Chair of Plant Physiology and Biotechnology, Lwowska St. 1, PL 87-100, Torun, Poland.
| | - Adriana Szmidt-Jaworska
- Nicolaus Copernicus University, Chair of Plant Physiology and Biotechnology, Lwowska St. 1, PL 87-100, Torun, Poland.
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Wheeler JI, Wong A, Marondedze C, Groen AJ, Kwezi L, Freihat L, Vyas J, Raji MA, Irving HR, Gehring C. The brassinosteroid receptor BRI1 can generate cGMP enabling cGMP-dependent downstream signaling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:590-600. [PMID: 28482142 DOI: 10.1111/tpj.13589] [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: 01/24/2017] [Revised: 04/20/2017] [Accepted: 04/21/2017] [Indexed: 05/24/2023]
Abstract
The brassinosteroid receptor brassinosteroid insensitive 1 (BRI1) is a member of the leucine-rich repeat receptor-like kinase family. The intracellular kinase domain of BRI1 is an active kinase and also encapsulates a guanylate cyclase catalytic centre. Using liquid chromatography tandem mass spectrometry, we confirmed that the recombinant cytoplasmic domain of BRI1 generates pmol amounts of cGMP per μg protein with a preference for magnesium over manganese as a co-factor. Importantly, a functional BRI1 kinase is essential for optimal cGMP generation. Therefore, the guanylate cyclase activity of BRI1 is modulated by the kinase while cGMP, the product of the guanylate cyclase, in turn inhibits BRI1 kinase activity. Furthermore, we show using Arabidopsis root cell cultures that cGMP rapidly potentiates phosphorylation of the downstream substrate brassinosteroid signaling kinase 1 (BSK1). Taken together, our results suggest that cGMP acts as a modulator that enhances downstream signaling while dampening signal generation from the receptor.
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Affiliation(s)
- Janet I Wheeler
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, 3052, Australia
- AgriBio, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Aloysius Wong
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- College of Natural, Applied and Health Sciences, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, China, 325060
| | - Claudius Marondedze
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Arnoud J Groen
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Lusisizwe Kwezi
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, 3052, Australia
- Council for Scientific and Industrial Research, Biosciences, Brummeria, Pretoria, 0001, South Africa
| | - Lubna Freihat
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, 3052, Australia
| | - Jignesh Vyas
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, 3052, Australia
| | - Misjudeen A Raji
- Analytical Chemistry Core Laboratory, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Helen R Irving
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, 3052, Australia
| | - Chris Gehring
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Świeżawska B, Jaworski K, Szewczuk P, Pawełek A, Szmidt-Jaworska A. Identification of a Hippeastrum hybridum guanylyl cyclase responsive to wounding and pathogen infection. JOURNAL OF PLANT PHYSIOLOGY 2015; 189:77-86. [PMID: 26523507 DOI: 10.1016/j.jplph.2015.09.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 09/08/2015] [Accepted: 09/09/2015] [Indexed: 05/21/2023]
Abstract
Guanosine 3',5'-cyclic monophosphate (cGMP) is a critical component of many (patho)physiological processes in plants whilst guanylyl cyclases (GCs) which catalyse the formation of cGMP from GTP have remained somewhat elusive. Consequently, the two major aims are the discovery of novel guanylyl cyclases and the identification of GC/cGMP mediated processes. To identify a novel GC from Hippeastrum hybridum plant and facilitate the preparation of guanylyl cyclase in an amount sufficient for further crystallographic studies, we have constructed an overproduction system for this enzyme. This gene encodes a protein of 256 amino acids, with a calculated molecular mass of 28kD. The predicted amino acid sequence contains all the typical features and shows a high identity to other plant GCs. The GST-HpGC1 was catalytically active in Escherichia coli cells and the purified, recombinant HpGC1 was able to convert GTP to cGMP in the presence of divalent cations. The used overexpression system yields a guanylyl cyclase as 6% of the bacterial cytosolic protein. Besides the identification of HpGC1 as a guanylyl cyclase, the study has shown that the level of HpCG1 mRNA changed during stress conditions. Both mechanical damage and a Peyronellaea curtisii (=Phoma narcissi) fungi infection led to an initial decrease in the HpGC1 transcript level, followed by a substantial increase during the remainder of the 48-h test cycle. Moreover, significant changes in cyclic GMP level were observed, taking the form of oscillations. In conclusion, our data unequivocally identified the product of the HpGC1 gene as a guanylyl cyclase and demonstrates that such an overproduction system can be successfully used in enzyme synthesis. Furthermore, they indicate a link between the causing stimulus (wounding, infection) and guanylyl cyclase expression and the increase in cGMP amplitude. Therefore, it is concluded that appearance of cyclic GMP as a mediator in defense and wound-healing mechanisms provides a clue to the regulation of these processes.
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Abstract
Over 30 receptor-like kinases contain a guanylate cyclase (GC) catalytic centre embedded within the C-terminal region of their kinase domain in the model plant Arabidopsis. A number of the kinase GCs contain both functional kinase and GC activity in vitro and the natural ligands of these receptors stimulate increases in cGMP within isolated protoplasts. The GC activity could be described as a minor or moonlighting activity. We have also identified mammalian proteins that contain the novel GC centre embedded within kinase domains. One example is the interleukin 1 receptor-associated kinase 3 (IRAK3). We compare the GC functionality of the mammalian protein IRAK3 with the cytoplasmic domain of the plant prototype molecule, the phytosulfokine receptor 1 (PSKR1). We have developed homology models of these molecules and have undertaken in vitro experiments to compare their functionality and structural features. Recombinant IRAK3 produces cGMP at levels comparable to those produced by PSKR1, suggesting that IRAK3 contains GC activity. Our findings raise the possibility that kinase-GCs may switch between downstream kinase-mediated or cGMP-mediated signalling cascades to elicit desired outputs to particular stimuli. The challenge now lies in understanding the interaction between the GC and kinase domains and how these molecules utilize their dual functionality within cells.
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Wong A, Gehring C, Irving HR. Conserved Functional Motifs and Homology Modeling to Predict Hidden Moonlighting Functional Sites. Front Bioeng Biotechnol 2015; 3:82. [PMID: 26106597 PMCID: PMC4460814 DOI: 10.3389/fbioe.2015.00082] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/18/2015] [Indexed: 12/11/2022] Open
Abstract
Moonlighting functional centers within proteins can provide them with hitherto unrecognized functions. Here, we review how hidden moonlighting functional centers, which we define as binding sites that have catalytic activity or regulate protein function in a novel manner, can be identified using targeted bioinformatic searches. Functional motifs used in such searches include amino acid residues that are conserved across species and many of which have been assigned functional roles based on experimental evidence. Molecules that were identified in this manner seeking cyclic mononucleotide cyclases in plants are used as examples. The strength of this computational approach is enhanced when good homology models can be developed to test the functionality of the predicted centers in silico, which, in turn, increases confidence in the ability of the identified candidates to perform the predicted functions. Computational characterization of moonlighting functional centers is not diagnostic for catalysis but serves as a rapid screening method, and highlights testable targets from a potentially large pool of candidates for subsequent in vitro and in vivo experiments required to confirm the functionality of the predicted moonlighting centers.
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Affiliation(s)
- Aloysius Wong
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology , Thuwal , Saudi Arabia
| | - Chris Gehring
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology , Thuwal , Saudi Arabia
| | - Helen R Irving
- Monash Institute of Pharmaceutical Sciences, Monash University , Melbourne, VIC , Australia
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Pichlo M, Bungert-Plümke S, Weyand I, Seifert R, Bönigk W, Strünker T, Kashikar ND, Goodwin N, Müller A, Pelzer P, Van Q, Enderlein J, Klemm C, Krause E, Trötschel C, Poetsch A, Kremmer E, Kaupp UB, Körschen HG, Collienne U. High density and ligand affinity confer ultrasensitive signal detection by a guanylyl cyclase chemoreceptor. J Cell Biol 2014; 206:541-57. [PMID: 25135936 PMCID: PMC4137060 DOI: 10.1083/jcb.201402027] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 07/15/2014] [Indexed: 12/28/2022] Open
Abstract
Guanylyl cyclases (GCs), which synthesize the messenger cyclic guanosine 3',5'-monophosphate, control several sensory functions, such as phototransduction, chemosensation, and thermosensation, in many species from worms to mammals. The GC chemoreceptor in sea urchin sperm can decode chemoattractant concentrations with single-molecule sensitivity. The molecular and cellular underpinnings of such ultrasensitivity are not known for any eukaryotic chemoreceptor. In this paper, we show that an exquisitely high density of 3 × 10(5) GC chemoreceptors and subnanomolar ligand affinity provide a high ligand-capture efficacy and render sperm perfect absorbers. The GC activity is terminated within 150 ms by dephosphorylation steps of the receptor, which provides a means for precise control of the GC lifetime and which reduces "molecule noise." Compared with other ultrasensitive sensory systems, the 10-fold signal amplification by the GC receptor is surprisingly low. The hallmarks of this signaling mechanism provide a blueprint for chemical sensing in small compartments, such as olfactory cilia, insect antennae, or even synaptic boutons.
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Affiliation(s)
- Magdalena Pichlo
- Center of Advanced European Studies and Research, 53175 Bonn, Germany Marine Biological Laboratory, Woods Hole, MA 02543
| | - Stefanie Bungert-Plümke
- Marine Biological Laboratory, Woods Hole, MA 02543 Institute of Complex Systems (ICS-4), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Ingo Weyand
- Marine Biological Laboratory, Woods Hole, MA 02543 Institute of Complex Systems (ICS-4), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Reinhard Seifert
- Center of Advanced European Studies and Research, 53175 Bonn, Germany Marine Biological Laboratory, Woods Hole, MA 02543
| | - Wolfgang Bönigk
- Center of Advanced European Studies and Research, 53175 Bonn, Germany
| | - Timo Strünker
- Center of Advanced European Studies and Research, 53175 Bonn, Germany Marine Biological Laboratory, Woods Hole, MA 02543
| | - Nachiket Dilip Kashikar
- Center of Advanced European Studies and Research, 53175 Bonn, Germany Marine Biological Laboratory, Woods Hole, MA 02543 Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton BN1 9QG, England, UK
| | - Normann Goodwin
- Center of Advanced European Studies and Research, 53175 Bonn, Germany Marine Biological Laboratory, Woods Hole, MA 02543 Babraham Institute, Cambridge CB22 3AT, England, UK
| | - Astrid Müller
- Center of Advanced European Studies and Research, 53175 Bonn, Germany
| | - Patric Pelzer
- Marine Biological Laboratory, Woods Hole, MA 02543 Department of Functional Neuroanatomy, Institute of Anatomy and Cell Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Qui Van
- III. Physikalisches Institut, Universität Göttingen, 37077 Göttingen, Germany
| | - Jörg Enderlein
- III. Physikalisches Institut, Universität Göttingen, 37077 Göttingen, Germany
| | - Clementine Klemm
- Leibniz-Institut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Eberhard Krause
- Leibniz-Institut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | | | - Ansgar Poetsch
- Plant Biochemistry, Ruhr University Bochum. 44801 Bochum, Germany
| | - Elisabeth Kremmer
- Institut für Molekulare Immunologie, Helmholtz-Zentrum München, 81377 München, Germany
| | - U Benjamin Kaupp
- Center of Advanced European Studies and Research, 53175 Bonn, Germany Marine Biological Laboratory, Woods Hole, MA 02543
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Zhao Y, Qi Z, Berkowitz GA. Teaching an old hormone new tricks: cytosolic Ca2+ elevation involvement in plant brassinosteroid signal transduction cascades. PLANT PHYSIOLOGY 2013; 163:555-65. [PMID: 23852441 PMCID: PMC3793037 DOI: 10.1104/pp.112.213371] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Brassinosteroids (BRs) are hormones that control many aspects of plant growth and development, acting at the cell level to promote division and expansion. BR regulation of plant and plant cell function occurs through altered expression of many genes. Transcriptional reprogramming downstream from cell perception of this hormone is currently known to be mediated by a phosphorylation/dephosphorylation ("phosphorelay") cascade that alters the stability of two master transcription regulators. Here, we provide evidence that BR perception by their receptor also causes an elevation in cytosolic Ca(2+), initiating a Ca(2+) signaling cascade in Arabidopsis (Arabidopsis thaliana) cell cytosol. BR-dependent increases in the expression of some genes (INDOLE-3-ACETIC ACID-INDUCIBLE1 and PHYTOCHROME B ACTIVATION-TAGGED SUPPRESSOR1) were impaired in wild-type plants by a Ca(2+) channel blocker and also in the defense-no-death (dnd1) mutant, which lacks a functional cyclic GMP-activated cell membrane Ca(2+)-conducting channel. Alternatively, mutations that impair the BR phosphorelay cascade did not much affect the BR-dependent expression of these genes. Similar effects of the Ca(2+) channel blocker and dnd1 mutation were observed on a BR plant growth phenotype, deetiolation of the seedling hypocotyl. Further evidence presented in this report suggests that a BR-dependent elevation in cyclic GMP may be involved in the Ca(2+) signaling cascade initiated by this hormone. The work presented here leads to a new model of the molecular steps that mediate some of the cell responses to this plant hormone.
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The Arabidopsis thaliana proteome harbors undiscovered multi-domain molecules with functional guanylyl cyclase catalytic centers. Cell Commun Signal 2013; 11:48. [PMID: 23835195 PMCID: PMC3726316 DOI: 10.1186/1478-811x-11-48] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Accepted: 07/05/2013] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Second messengers link external cues to complex physiological responses. One such messenger, 3',5'-cyclic guanosine monophosphate (cGMP), has been shown to play a key role in many physiological responses in plants. However, in higher plants, guanylyl cyclases (GCs), enzymes that generate cGMP from guanosine-5'-triphosphate (GTP) have remained elusive until recently. GC search motifs constructed from the alignment of known GCs catalytic centers form vertebrates and lower eukaryotes have led to the identification of a number of plant GCs that have been characterized in vitro and in vivo.Presentation of the hypothesis. Recently characterized GCs in Arabidopsis thaliana contributed to the development of search parameters that can identify novel candidate GCs in plants. We hypothesize that there are still a substantial number (> 40) of multi-domain molecules with potentially functional GC catalytic centers in plants that remain to be discovered and characterized. TESTING THE HYPOTHESIS The hypothesis can be tested, firstly, by computational methods constructing 3D models of selected GC candidates using available crystal structures as templates. Homology modeling must include substrate docking that can provide support for the structural feasibility of the GC catalytic centers in those candidates. Secondly, recombinant peptides containing the GC domain need to be tested in in vitro GC assays such as the enzyme-linked immune-sorbent assay (ELISA) and/or in mass spectrometry based cGMP assays. In addition, quantification of in vivo cGMP transients with fluorescent cGMP-reporter assays in wild-type or selected mutants will help to elucidate the biological role of novel GCs. Implications of the hypothesis. If it turns out that plants do harbor a large number of functional GC domains as part of multi-domain enzymes, then major new insights will be gained into the complex signal transduction pathways that link cGMP to fundamental processes such as ion transport and homeostasis, biotic and abiotic stress responses as well as cGMP-dependent responses to hormones.
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Irving HR, Gehring C. Molecular methods for the study of signal transduction in plants. Methods Mol Biol 2013; 1016:1-11. [PMID: 23681568 DOI: 10.1007/978-1-62703-441-8_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Novel and improved analytical methods have led to a rapid increase in our understanding of the molecular mechanism underlying plant signal transduction. Progress has been made both at the level of single-component analysis and in vivo imaging as well as at the systems level where transcriptomics and particularly phosphoproteomics afford a window into complex biological responses. Here we review the role of the cyclic nucleotides cAMP and cGMP in plant signal transduction as well as the discovery and biochemical and biological characterization of an increasing number of complex multi-domain nucleotide cyclases that catalyze the synthesis of cAMP and cGMP from ATP and GTP, respectively.
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Affiliation(s)
- Helen R Irving
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
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Muleya V, Wheeler JI, Irving HR. Structural and functional characterization of receptor kinases with nucleotide cyclase activity. Methods Mol Biol 2013; 1016:175-94. [PMID: 23681579 DOI: 10.1007/978-1-62703-441-8_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
There has been an increase in the identification and characterization of plant receptor kinases possessing nucleotide cyclase activity. This has necessitated the development of robust methodologies for the structural and functional characterization of this biologically important family of proteins. Here we outline some of the techniques that can be effectively used in the characterization of this bifunctional family of proteins.
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Affiliation(s)
- Victor Muleya
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
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