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Ayadi I, Nebli S, Ben Marzoug R, Rebai A. Charge cluster occurrence in land plants' mitochondrial proteomes with functional and structural insights. J Biomol Struct Dyn 2024:1-11. [PMID: 38345014 DOI: 10.1080/07391102.2024.2313154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 01/25/2024] [Indexed: 03/22/2024]
Abstract
The Charge Clusters (CCs) are involved in key functions and are distributed according to the organism, the protein's type, and the charge of amino acids. In the present study, we have explored the occurrence, position, and annotation as a first large-scale study of the CCs in land plants mitochondrial proteomes. A new python script was used for data curation. The Finding Clusters Charge in Protein Sequences Program was performed after adjusting the reading window size. A 44316 protein sequences belonging to 52 species of land plants were analysed. The occurrence of Negative Charge Clusters (NCCs) (1.2%) is two times more frequent than the Positive Charge Clusters (PCCs) (0.64%). Moreover, 39 and 30 NCCs were conserved in 88 and 41 proteins in intra and in inter proteomes respectively, while 14 and 21 PCCs were conserved in 53 and 85 protein sequences in intra and inter proteomes consecutively. Sequences carrying mixed CCs are rare (0.12%). Despite this low abundance, CCs play a crucial role in protein function. The CCs tend to be located mainly in the terminal regions of proteins which guarantees specific protein targeting and import into the mitochondria. In addition, the functional annotation of CCs according to Gene Ontology shows that CCs are involved in binding functions of either proteins or macromolecules which are deployed in different metabolic and cellular processes such as RNA editing and transcription. This study may provide valuable information while considering the CCs in understanding the environmental adaptation of plants.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Imen Ayadi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Syrine Nebli
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Riadh Ben Marzoug
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Ahmed Rebai
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
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Wrobel TJ, Brilhaus D, Stefanski A, Stühler K, Weber APM, Linka N. Mapping the castor bean endosperm proteome revealed a metabolic interaction between plastid, mitochondria, and peroxisomes to optimize seedling growth. FRONTIERS IN PLANT SCIENCE 2023; 14:1182105. [PMID: 37868318 PMCID: PMC10588648 DOI: 10.3389/fpls.2023.1182105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 08/07/2023] [Indexed: 10/24/2023]
Abstract
In this work, we studied castor-oil plant Ricinus communis as a classical system for endosperm reserve breakdown. The seeds of castor beans consist of a centrally located embryo with the two thin cotyledons surrounded by the endosperm. The endosperm functions as major storage tissue and is packed with nutritional reserves, such as oil, proteins, and starch. Upon germination, mobilization of the storage reserves requires inter-organellar interplay of plastids, mitochondria, and peroxisomes to optimize growth for the developing seedling. To understand their metabolic interactions, we performed a large-scale organellar proteomic study on castor bean endosperm. Organelles from endosperm of etiolated seedlings were isolated and subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS). Computer-assisted deconvolution algorithms were applied to reliably assign the identified proteins to their correct subcellular localization and to determine the abundance of the different organelles in the heterogeneous protein samples. The data obtained were used to build a comprehensive metabolic model for plastids, mitochondria, and peroxisomes during storage reserve mobilization in castor bean endosperm.
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Affiliation(s)
- Thomas J. Wrobel
- Institute of Plant Biochemistry and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
| | - Dominik Brilhaus
- Institute of Plant Biochemistry and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
| | - Anja Stefanski
- Molecular Proteomics Laboratory, Biologisch-Medizinisches Forschungszentrum (BMFZ), Universitätsklinikum, Düsseldorf, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory, Biologisch-Medizinisches Forschungszentrum (BMFZ), Universitätsklinikum, Düsseldorf, Germany
| | - Andreas P. M. Weber
- Institute of Plant Biochemistry and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
| | - Nicole Linka
- Institute of Plant Biochemistry and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
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Sági-Kazár M, Sárvári É, Cseh B, Illés L, May Z, Hegedűs C, Barócsi A, Lenk S, Solymosi K, Solti Á. Iron uptake of etioplasts is independent from photosynthesis but applies the reduction-based strategy. FRONTIERS IN PLANT SCIENCE 2023; 14:1227811. [PMID: 37636109 PMCID: PMC10457162 DOI: 10.3389/fpls.2023.1227811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/21/2023] [Indexed: 08/29/2023]
Abstract
Introduction Iron (Fe) is one of themost important cofactors in the photosynthetic apparatus, and its uptake by chloroplasts has also been associated with the operation of the photosynthetic electron transport chain during reduction-based plastidial Fe uptake. Therefore, plastidial Fe uptake was considered not to be operational in the absence of the photosynthetic activity. Nevertheless, Fe is also required for enzymatic functions unrelated to photosynthesis, highlighting the importance of Fe acquisition by non-photosynthetic plastids. Yet, it remains unclear how these plastids acquire Fe in the absence of photosynthetic function. Furthermore, plastids of etiolated tissues should already possess the ability to acquire Fe, since the biosynthesis of thylakoid membrane complexes requires a massive amount of readily available Fe. Thus, we aimed to investigate whether the reduction-based plastidial Fe uptake solely relies on the functioning photosynthetic apparatus. Methods In our combined structure, iron content and transcript amount analysis studies, we used Savoy cabbage plant as a model, which develops natural etiolation in the inner leaves of the heads due to the shading of the outer leaf layers. Results Foliar and plastidial Fe content of Savoy cabbage leaves decreased towards the inner leaf layers. The leaves of the innermost leaf layers proved to be etiolated, containing etioplasts that lacked the photosynthetic machinery and thus were photosynthetically inactive. However, we discovered that these etioplasts contained, and were able to take up, Fe. Although the relative transcript abundance of genes associated with plastidial Fe uptake and homeostasis decreased towards the inner leaf layers, both ferric chelate reductase FRO7 transcripts and activity were detected in the innermost leaf layer. Additionally, a significant NADP(H) pool and NAD(P)H dehydrogenase activity was detected in the etioplasts of the innermost leaf layer, indicating the presence of the reducing capacity that likely supports the reduction-based Fe uptake of etioplasts. Discussion Based on these findings, the reduction-based plastidial Fe acquisition should not be considered exclusively dependent on the photosynthetic functions.
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Affiliation(s)
- Máté Sági-Kazár
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Éva Sárvári
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Barnabás Cseh
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Levente Illés
- Department of Atomic Physics, Budapest University of Technology and Economics, Budapest, Hungary
| | - Zoltán May
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Budapest, Hungary
| | - Csaba Hegedűs
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Attila Barócsi
- Department of Atomic Physics, Budapest University of Technology and Economics, Budapest, Hungary
| | - Sándor Lenk
- Department of Atomic Physics, Budapest University of Technology and Economics, Budapest, Hungary
| | - Katalin Solymosi
- Department of Plant Anatomy, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Ádám Solti
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
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Boussardon C, Carrie C, Keech O. Comparing plastid proteomes points towards a higher plastidial redox turnover in vascular tissues than in mesophyll cells. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad133. [PMID: 37026385 PMCID: PMC10400147 DOI: 10.1093/jxb/erad133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Indexed: 06/19/2023]
Abstract
Plastids are complex organelles that vary in size and function depending on the cell type. Accordingly, they can be referred to as amyloplasts, chloroplasts, chromoplasts, etioplasts, proplasts to only cite a few denominations. Over the past decades, methods based on density gradients and differential centrifugations have been extensively used for the purification of plastids. However, these methods need large amounts of starting material, and hardly provide a tissue-specific resolution. Here, we applied our IPTACT (Isolation of Plastids TAgged in specific Cell Types) method, which involves the biotinylation of plastids in vivo using one-shot transgenic lines expressing the TOC64 gene coupled with a biotin ligase receptor particle and the BirA biotin ligase, to isolate plastids from mesophyll and companion cells of Arabidopsis thaliana using tissue specific pCAB3 and pSUC2 promoters, respectively. Subsequently, a proteome profiling was performed, and allowed the identification of 1672 proteins, among which 1342 were predicted plastidial, and 705 were fully confirmed according to SUBA5. Interestingly, although 92% of plastidial proteins were equally distributed between the two tissues, we observed an accumulation of proteins associated with jasmonic acid biosynthesis, plastoglobuli (e.g. NDC1, VTE1, PGL34, ABC1K1) and cyclic electron flow in plastids originating from vascular tissues. Besides demonstrating the technical feasibility of isolating plastids in a tissue-specific manner, our work provides strong evidence that plastids from vascular tissue have a higher redox turnover to ensure optimal functioning, notably under high solute strength as encountered in vascular cells.
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Affiliation(s)
- Clément Boussardon
- Department of Plant Physiology, Umeå Plant Science, Umeå University, S-90187 Umeå, Sweden
| | - Chris Carrie
- School of Biological Sciences, University of Auckland, 3A Symonds St, Auckland,1142, New Zealand
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science, Umeå University, S-90187 Umeå, Sweden
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Tian Y, Wang Y, Zhang N, Xiao M, Zhang J, Xing X, Zhang Y, Fan Y, Li X, Nan B, Wang Y, Liu J. Antioxidant Mechanism of Lactiplantibacillus plantarum KM1 Under H2O2 Stress by Proteomics Analysis. Front Microbiol 2022; 13:897387. [PMID: 35832808 PMCID: PMC9271951 DOI: 10.3389/fmicb.2022.897387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
Lactiplantibacillus plantarum KM1 was screened from natural fermented products, which had probiotic properties and antioxidant function. The survival rate of L. plantarum KM1 was 78.26% at 5 mM H2O2. In this study, the antioxidant mechanism of L. plantarum KM1 was deeply analyzed by using the proteomics method. The results demonstrated that a total of 112 differentially expressed proteins (DEPs) were screened, of which, 31 DEPs were upregulated and 81 were downregulated. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that DEPs participated in various metabolic pathways such as pyruvate metabolism, carbon metabolism, trichloroacetic acid cycle, amino acid metabolism, and microbial metabolism in diverse environments. These metabolic pathways were related to oxidative stress caused by H2O2 in L. plantarum KM1. Therefore, the antioxidant mechanism of L. plantarum KM1 under H2O2 stress provided a theoretical basis for its use as a potential natural antioxidant.
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Affiliation(s)
- Yuan Tian
- College of Food Science, Jilin Agricultural University, Changchun, China
- Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
| | - Yu Wang
- College of Food Science, Jilin Agricultural University, Changchun, China
- Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
| | - Nan Zhang
- College of Food Science, Jilin Agricultural University, Changchun, China
- Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
| | - Minmin Xiao
- College of Food Science, Jilin Agricultural University, Changchun, China
- Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
| | - Jing Zhang
- College of Food Science, Jilin Agricultural University, Changchun, China
- Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
| | - Xinyue Xing
- College of Food Science, Jilin Agricultural University, Changchun, China
- Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
| | - Yue Zhang
- College of Food Science, Jilin Agricultural University, Changchun, China
- Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
| | - Yuling Fan
- College of Food Science, Jilin Agricultural University, Changchun, China
- Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
| | - Xia Li
- College of Food Science, Jilin Agricultural University, Changchun, China
- Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
- Xia Li
| | - Bo Nan
- College of Food Science, Jilin Agricultural University, Changchun, China
- Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
| | - Yuhua Wang
- College of Food Science, Jilin Agricultural University, Changchun, China
- Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
- National Processing Laboratory for Soybean Industry and Technology, Changchun, China
- National Engineering Laboratory for Wheat and Corn Deep Processing, Changchun, China
- *Correspondence: Yuhua Wang
| | - Jingsheng Liu
- College of Food Science, Jilin Agricultural University, Changchun, China
- Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
- National Engineering Laboratory for Wheat and Corn Deep Processing, Changchun, China
- Jingsheng Liu
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Choudhary A, Kumar A, Kaur N, Kaur H. Molecular cues of sugar signaling in plants. PHYSIOLOGIA PLANTARUM 2022; 174:e13630. [PMID: 35049040 DOI: 10.1111/ppl.13630] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/02/2022] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
Sugars, the chemically bound form of energy, are formed by the absorption of photosynthetically active radiation and fixation in plants. During evolution, plants availed the sugar molecules as a resource, balancing molecule, and signaling molecule. The multifaceted role of sugar molecules in response to environmental stimuli makes it the central coordinator required for growth, survival, and continuity. During the course of evolution, the molecular networks have become complex to adapt or acclimate to the changing environment. Sugar molecules are sensed both intra and extracellularly by their specific sensors. The signal is transmitted by a signaling loop that involves various downstream signaling molecules, transcriptional factors and, most pertinent, the sensors TOR and SnRK1. In this review, the focus has been retained on the significance of the sugar sensors during signaling and induced modules to regulate plant growth, development, biotic and abiotic stress. It is interesting to visualize the sugar molecule as a signaling unit and not only a nutrient. Complete information on the downstream components of sugar signaling will open the gates for improving the qualitative and quantitative elements of crop plants.
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Affiliation(s)
- Anuj Choudhary
- Department of Botany, College of Basic Sciences and Humanities, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Antul Kumar
- Department of Botany, College of Basic Sciences and Humanities, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Nirmaljit Kaur
- Department of Botany, College of Basic Sciences and Humanities, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Harmanjot Kaur
- Department of Botany, College of Basic Sciences and Humanities, Punjab Agricultural University, Ludhiana, Punjab, India
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Grabsztunowicz M, Rantala M, Ivanauskaite A, Blomster T, Koskela MM, Vuorinen K, Tyystjärvi E, Burow M, Overmyer K, Mähönen AP, Mulo P. Root-type ferredoxin-NADP + oxidoreductase isoforms in Arabidopsis thaliana: Expression patterns, location and stress responses. PLANT, CELL & ENVIRONMENT 2021; 44:548-558. [PMID: 33131061 DOI: 10.1111/pce.13932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/23/2020] [Accepted: 10/24/2020] [Indexed: 06/11/2023]
Abstract
In Arabidopsis, two leaf-type ferredoxin-NADP+ oxidoreductase (LFNR) isoforms function in photosynthetic electron flow in reduction of NADP+ , while two root-type FNR (RFNR) isoforms catalyse reduction of ferredoxin in non-photosynthetic plastids. As the key to understanding, the function of RFNRs might lie in their spatial and temporal distribution in different plant tissues and cell types, we examined expression of RFNR1 and RFNR2 genes using β-glucuronidase (GUS) reporter lines and investigated accumulation of distinct RFNR isoforms using a GFP approach and Western blotting upon various stresses. We show that while RFNR1 promoter is active in leaf veins, root tips and in the stele of roots, RFNR2 promoter activity is present in leaf tips and root stele, epidermis and cortex. RFNR1 protein accumulates as a soluble protein within the plastids of root stele cells, while RFNR2 is mainly present in the outer root layers. Ozone treatment of plants enhanced accumulation of RFNR1, whereas low temperature treatment specifically affected RFNR2 accumulation in roots. We further discuss the physiological roles of RFNR1 and RFNR2 based on characterization of rfnr1 and rfnr2 knock-out plants and show that although the function of these proteins is partly redundant, the RFNR proteins are essential for plant development and survival.
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Affiliation(s)
- Magda Grabsztunowicz
- Department of Biochemistry, Molecular Plant Biology, University of Turku, Turku, Finland
| | - Marjaana Rantala
- Department of Biochemistry, Molecular Plant Biology, University of Turku, Turku, Finland
| | - Aiste Ivanauskaite
- Department of Biochemistry, Molecular Plant Biology, University of Turku, Turku, Finland
| | - Tiina Blomster
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Minna M Koskela
- Department of Biochemistry, Molecular Plant Biology, University of Turku, Turku, Finland
| | - Katariina Vuorinen
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Esa Tyystjärvi
- Department of Biochemistry, Molecular Plant Biology, University of Turku, Turku, Finland
| | - Meike Burow
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Kirk Overmyer
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Ari P Mähönen
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Paula Mulo
- Department of Biochemistry, Molecular Plant Biology, University of Turku, Turku, Finland
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