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Rugen N, Senkler M, Braun HP. Deep proteomics reveals incorporation of unedited proteins into mitochondrial protein complexes in Arabidopsis. PLANT PHYSIOLOGY 2024; 195:1180-1199. [PMID: 38060994 PMCID: PMC11142381 DOI: 10.1093/plphys/kiad655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/12/2023] [Indexed: 06/02/2024]
Abstract
The mitochondrial proteome consists of numerous types of proteins which either are encoded and synthesized in the mitochondria, or encoded in the cell nucleus, synthesized in the cytoplasm and imported into the mitochondria. Their synthesis in the mitochondria, but not in the nucleus, relies on the editing of the primary transcripts of their genes at defined sites. Here, we present an in-depth investigation of the mitochondrial proteome of Arabidopsis (Arabidopsis thaliana) and a public online platform for the exploration of the data. For the analysis of our shotgun proteomic data, an Arabidopsis sequence database was created comprising all available protein sequences from the TAIR10 and Araport11 databases, supplemented with sequences of proteins translated from edited and nonedited transcripts of mitochondria. Amino acid sequences derived from partially edited transcripts were also added to analyze proteins encoded by the mitochondrial genome. Proteins were digested in parallel with six different endoproteases to obtain maximum proteome coverage. The resulting peptide fractions were finally analyzed using liquid chromatography coupled to ion mobility spectrometry and tandem mass spectrometry. We generated a "deep mitochondrial proteome" of 4,692 proteins. 1,339 proteins assigned to mitochondria by the SUBA5 database (https://suba.live) accounted for >80% of the total protein mass of our fractions. The coverage of proteins by identified peptides was particularly high compared to single-protease digests, allowing the exploration of differential splicing and RNA editing events at the protein level. We show that proteins translated from nonedited transcripts can be incorporated into native mitoribosomes and the ATP synthase complex. We present a portal for the use of our data, based on "proteomaps" with directly linked protein data. The portal is available at www.proteomeexplorer.de.
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Affiliation(s)
- Nils Rugen
- Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Michael Senkler
- Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Hans-Peter Braun
- Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
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2
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Zhao HM, Huang HB, Zhan ZX, Ye YY, Cheng JL, Xiang L, Li YW, Cai QY, Xie Y, Mo CH. Insights into the molecular network underlying phytotoxicity and phytoaccumulation of ciprofloxacin. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169392. [PMID: 38104812 DOI: 10.1016/j.scitotenv.2023.169392] [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: 11/10/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023]
Abstract
Ciprofloxacin (CIP) is frequently detected in agricultural soils and can be accumulated by crops, causing phytotoxicities and food safety concerns. However, the molecular basis of its phytotoxicity and phytoaccumulation is hardly known. Here, we analyzed physiological and molecular responses of choysum (Brassica parachinensis) to CIP stress by comparing low CIP accumulation variety (LAV) and high accumulation variety (HAV). Results showed that the LAV suffered more severe inhibition of growth and photosynthesis than the HAV, exhibiting a lower tolerance to CIP toxicity. Integrated transcriptome and proteome analyses suggested that more differentially expressed genes/proteins (DEGs/DEPs) involved in basic metabolic processes were downregulated to a larger extent in the LAV, explaining its lower CIP tolerance at molecular level. By contrast, more DEGs/DEPs involved in defense responses were upregulated to a larger extent in the HAV, showing the molecular basis of its stronger CIP tolerance. Further, a CIP phytotoxicity-responsive molecular network was constructed for the two varieties to better understand the molecular mechanisms underlying the variety-specific CIP tolerance and accumulation. The results present the first comprehensive molecular profile of plant response to CIP stress for molecular-assisted breeding to improve CIP tolerance and minimize CIP accumulation in crops.
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Affiliation(s)
- Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - He-Biao Huang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zhen-Xuan Zhan
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yao-Yao Ye
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Ji-Liang Cheng
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Lei Xiang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Quan-Ying Cai
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yunchang Xie
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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Knoch D, Meyer RC, Heuermann MC, Riewe D, Peleke FF, Szymański J, Abbadi A, Snowdon RJ, Altmann T. Integrated multi-omics analyses and genome-wide association studies reveal prime candidate genes of metabolic and vegetative growth variation in canola. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:713-728. [PMID: 37964699 DOI: 10.1111/tpj.16524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/16/2023]
Abstract
Genome-wide association studies (GWAS) identified thousands of genetic loci associated with complex plant traits, including many traits of agronomical importance. However, functional interpretation of GWAS results remains challenging because of large candidate regions due to linkage disequilibrium. High-throughput omics technologies, such as genomics, transcriptomics, proteomics and metabolomics open new avenues for integrative systems biological analyses and help to nominate systems information supported (prime) candidate genes. In the present study, we capitalise on a diverse canola population with 477 spring-type lines which was previously analysed by high-throughput phenotyping of growth-related traits and by RNA sequencing and metabolite profiling for multi-omics-based hybrid performance prediction. We deepened the phenotypic data analysis, now providing 123 time-resolved image-based traits, to gain insight into the complex relations during early vegetative growth and reanalysed the transcriptome data based on the latest Darmor-bzh v10 genome assembly. Genome-wide association testing revealed 61 298 robust quantitative trait loci (QTL) including 187 metabolite QTL, 56814 expression QTL and 4297 phenotypic QTL, many clustered in pronounced hotspots. Combining information about QTL colocalisation across omics layers and correlations between omics features allowed us to discover prime candidate genes for metabolic and vegetative growth variation. Prioritised candidate genes for early biomass accumulation include A06p05760.1_BnaDAR (PIAL1), A10p16280.1_BnaDAR, C07p48260.1_BnaDAR (PRL1) and C07p48510.1_BnaDAR (CLPR4). Moreover, we observed unequal effects of the Brassica A and C subgenomes on early biomass production.
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Affiliation(s)
- Dominic Knoch
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Corrensstrasse 3, Seeland OT, Gatersleben, Germany
| | - Rhonda C Meyer
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Corrensstrasse 3, Seeland OT, Gatersleben, Germany
| | - Marc C Heuermann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Corrensstrasse 3, Seeland OT, Gatersleben, Germany
| | - David Riewe
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Corrensstrasse 3, Seeland OT, Gatersleben, Germany
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, 14195, Berlin, Germany
| | - Fritz F Peleke
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Corrensstrasse 3, Seeland OT, Gatersleben, Germany
| | - Jędrzej Szymański
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Corrensstrasse 3, Seeland OT, Gatersleben, Germany
- Institute of Bio- and Geosciences IBG-4: Bioinformatics, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Amine Abbadi
- NPZ Innovation GmbH, Hohenlieth, 24363, Holtsee, Germany
- Norddeutsche Pflanzenzucht Hans-Georg Lembke KG, Hohenlieth, 24363, Holtsee, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, Research Centre for Biosystems, Land Use and Nutrition (iFZ), Justus-Liebig-University Giessen, 35392, Giessen, Germany
| | - Thomas Altmann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Corrensstrasse 3, Seeland OT, Gatersleben, Germany
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Devendrakumar KT, Copeland C, Adamchek C, Zhong X, Huang X, Gendron JM, Li X. Arabidopsis Tubby domain-containing F-box proteins positively regulate immunity by modulating PI4Kβ protein levels. THE NEW PHYTOLOGIST 2023; 240:354-371. [PMID: 37571862 PMCID: PMC11114105 DOI: 10.1111/nph.19187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 06/30/2023] [Indexed: 08/13/2023]
Abstract
The Tubby domain, named after the TUBBY protein in mice, binds to phosphatidylinositol 4,5-bisphosphate. Arabidopsis has 11 Tubby domain-containing proteins referred to as Tubby-Like Proteins (TLPs). Of the 11 TLPs, 10 possess the N-terminal F-box domain, which can interact with SKP-like proteins and form SKP1-Cullin-F-box E3 ligase complexes. Although mice TUBBY has been extensively studied, plant TLPs' functions are scarcely detailed. In this study, we show that the Arabidopsis Tubby-like protein 6 (TLP6) and its redundant homologs, TLP1, TLP2, TLP5, and TLP10, positively regulate Arabidopsis immune responses. Furthermore, in an immunoprecipitation mass spectrometry analysis to search for ubiquitination substrates of the TLPs, we identified two redundant phosphoinositide biosynthesis enzymes, phosphatidylinositol 4-kinase β proteins (PI4Kβs), PI4Kβ1 and PI4Kβ2, as TLP interactors. Importantly, TLP6 overexpression lines fully phenocopy the phenotypes of the pi4kβ1,2 mutant, while TLP6 overexpression also leads to increased PI4Kβ2 ubiquitination and reduction in its protein level in a proteasome-dependent manner. Most significantly, TLP6 overexpression does not further enhance the autoimmunity of the pi4kβ1,2 double mutant, supporting the hypothesis that TLP6 targets the PI4Kβs for ubiquitination and degradation. Thus, our study reveals a novel mechanism where TLPs promote plant immune responses by modulating the PI4Kβs protein levels.
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Affiliation(s)
- Karen Thulasi Devendrakumar
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Charles Copeland
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Christopher Adamchek
- Yale Science Building, Yale University, 260 Whitney Ave, New Haven, CT 06511, USA
| | - Xionghui Zhong
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Xingchuan Huang
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Joshua M. Gendron
- Yale Science Building, Yale University, 260 Whitney Ave, New Haven, CT 06511, USA
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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5
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Zhou Y, Lu X, Hao J, Li S. Quantitative Acetylome Analysis of Differentially Modified Proteins in Virulence-Differentiated Fusarium oxysporum f. sp. cucumerinum Isolates during Cucumber Colonization. J Fungi (Basel) 2023; 9:920. [PMID: 37755028 PMCID: PMC10532600 DOI: 10.3390/jof9090920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023] Open
Abstract
Fusarium oxysporum f. sp. cucumerinum (Foc) is a prominent pathogen that adversely affects cucumber (Cucumis sativus) production. In the pathogen's parasitic lifestyle, the pathogenesis and virulence evolution may be regulated by lysine acetylation, as demonstrated in many living organisms. However, its specific function in Foc remains poorly understood. In this study, the acetylome profiles of a mild virulence strain (foc-3b) and its derived virulence-enhanced strain (Ra-4) were analyzed before and post-inoculation on cucumber plants. In total, 10,664 acetylation sites were identified corresponding to 3874 proteins, and 45 conserved acetylation motifs were detected. Through comparison of the acetylomes, numerous differentially lysine-acetylated proteins were enriched in energy metabolism and protein processing processes, indicating the critical role of lysine acetylation during the transition from the saprotrophic lifestyle to the parasitic lifestyle. Comparative acetylome analyses on the two virulence-differentiated strains revealed that several differentially lysine-acetylated proteins were involved in pathways of defense response and energy metabolism. Ra-4 showed enhanced energy metabolism compared to foc-3b. This indicates that robust metabolic activity is required to achieve high virulence and facilitating adaptive evolution. Additionally, faster host responses are supported by an ample energy supply enhancing virulence. Thus, lysine acetylation plays a crucial role in the pathogenesis and virulence evolution of Foc.
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Affiliation(s)
- Ying Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaohong Lu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jianjun Hao
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
| | - Shidong Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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6
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Huang D, Jing G, Zhu S. Regulation of Mitochondrial Respiration by Hydrogen Sulfide. Antioxidants (Basel) 2023; 12:1644. [PMID: 37627639 PMCID: PMC10451548 DOI: 10.3390/antiox12081644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Hydrogen sulfide (H2S), the third gasotransmitter, has positive roles in animals and plants. Mitochondria are the source and the target of H2S and the regulatory hub in metabolism, stress, and disease. Mitochondrial bioenergetics is a vital process that produces ATP and provides energy to support the physiological and biochemical processes. H2S regulates mitochondrial bioenergetic functions and mitochondrial oxidative phosphorylation. The article summarizes the recent knowledge of the chemical and biological characteristics, the mitochondrial biosynthesis of H2S, and the regulatory effects of H2S on the tricarboxylic acid cycle and the mitochondrial respiratory chain complexes. The roles of H2S on the tricarboxylic acid cycle and mitochondrial respiratory complexes in mammals have been widely studied. The biological function of H2S is now a hot topic in plants. Mitochondria are also vital organelles regulating plant processes. The regulation of H2S in plant mitochondrial functions is gaining more and more attention. This paper mainly summarizes the current knowledge on the regulatory effects of H2S on the tricarboxylic acid cycle (TCA) and the mitochondrial respiratory chain. A study of the roles of H2S in mitochondrial respiration in plants to elucidate the botanical function of H2S in plants would be highly desirable.
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Affiliation(s)
| | | | - Shuhua Zhu
- College of Chemistry and Material Science, Shandong Agricultural University, Taian 271018, China; (D.H.); (G.J.)
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7
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Ghifari AS, Saha S, Murcha MW. The biogenesis and regulation of the plant oxidative phosphorylation system. PLANT PHYSIOLOGY 2023; 192:728-747. [PMID: 36806687 DOI: 10.1093/plphys/kiad108] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/19/2023] [Accepted: 01/22/2023] [Indexed: 06/01/2023]
Abstract
Mitochondria are central organelles for respiration in plants. At the heart of this process is oxidative phosphorylation (OXPHOS) system, which generates ATP required for cellular energetic needs. OXPHOS complexes comprise of multiple subunits that originated from both mitochondrial and nuclear genome, which requires careful orchestration of expression, translation, import, and assembly. Constant exposure to reactive oxygen species due to redox activity also renders OXPHOS subunits to be more prone to oxidative damage, which requires coordination of disassembly and degradation. In this review, we highlight the composition, assembly, and activity of OXPHOS complexes in plants based on recent biochemical and structural studies. We also discuss how plants regulate the biogenesis and turnover of OXPHOS subunits and the importance of OXPHOS in overall plant respiration. Further studies in determining the regulation of biogenesis and activity of OXPHOS will advances the field, especially in understanding plant respiration and its role to plant growth and development.
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Affiliation(s)
- Abi S Ghifari
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia
| | - Saurabh Saha
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia
| | - Monika W Murcha
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia
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8
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Liu YT, Senkler J, Herrfurth C, Braun HP, Feussner I. Defining the lipidome of Arabidopsis leaf mitochondria: Specific lipid complement and biosynthesis capacity. PLANT PHYSIOLOGY 2023; 191:2185-2203. [PMID: 36691154 PMCID: PMC10069894 DOI: 10.1093/plphys/kiad035] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/08/2023] [Indexed: 06/17/2023]
Abstract
Mitochondria are often considered as the power stations of the cell, playing critical roles in various biological processes such as cellular respiration, photosynthesis, stress responses, and programmed cell death. To maintain the structural and functional integrities of mitochondria, it is crucial to achieve a defined membrane lipid composition between different lipid classes wherein specific proportions of individual lipid species are present. Although mitochondria are capable of self-synthesizing a few lipid classes, many phospholipids are synthesized in the endoplasmic reticulum and transferred to mitochondria via membrane contact sites, as mitochondria are excluded from the vesicular transportation pathway. However, knowledge on the capability of lipid biosynthesis in mitochondria and the precise mechanism of maintaining the homeostasis of mitochondrial lipids is still scarce. Here we describe the lipidome of mitochondria isolated from Arabidopsis (Arabidopsis thaliana) leaves, including the molecular species of glycerolipids, sphingolipids, and sterols, to depict the lipid landscape of mitochondrial membranes. In addition, we define proteins involved in lipid metabolism by proteomic analysis and compare our data with mitochondria from cell cultures since they still serve as model systems. Proteins putatively localized to the membrane contact sites are proposed based on the proteomic results and online databases. Collectively, our results suggest that leaf mitochondria are capable-with the assistance of membrane contact site-localized proteins-of generating several lipid classes including phosphatidylethanolamines, cardiolipins, diacylgalactosylglycerols, and free sterols. We anticipate our work to be a foundation to further investigate the functional roles of lipids and their involvement in biochemical reactions in plant mitochondria.
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Affiliation(s)
| | | | - Cornelia Herrfurth
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, University of Goettingen, 37077 Goettingen, Germany
- Goettingen Center for Molecular Biosciences (GZMB), Service Unit for Metabolomics and Lipidomics, University of Goettingen, 37077 Goettingen, Germany
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9
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Yang T, Tian M, Gao T, Wang C, Wang X, Chen C, Yang W. Genome-wide transcriptomic analysis identifies candidate genes involved in jasmonic acid-mediated salt tolerance of alfalfa. PeerJ 2023; 11:e15324. [PMID: 37168537 PMCID: PMC10166079 DOI: 10.7717/peerj.15324] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/10/2023] [Indexed: 05/13/2023] Open
Abstract
Soil salinity imposes a major threat to plant growth and agricultural productivity. Despite being one of the most common fodder crops in saline locations, alfalfa is vulnerable to salt stress. Jasmonic acid (JA) is a phytohormone that influences plant response to abiotic stimuli such as salt stress. However, key genes and pathways by which JA-mediated salt tolerance of alfalfa are little known. A comprehensive transcriptome analysis was performed to elucidate the underlying molecular mechanisms of JA-mediated salt tolerance. The transcripts regulated by salt (S) compared to control (C) and JA+salt (JS) compared to C were investigated. Venn diagram and expression pattern of DEGs indicated that JS further altered a series of genes expression regulated by salt treatment, implying the roles of JA in priming salt tolerance. Enrichment analysis revealed that DEGs exclusively regulated by JS treatment belonged to primary or secondary metabolism, respiratory electron transport chain, and oxidative stress resistance. Alternatively, splicing (AS) was induced by salt alone or JA combined treatment, with skipped exon (SE) events predominately. DEGs undergo exon skipping involving some enriched items mentioned above and transcription factors. Finally, the gene expressions were validated using quantitative polymerase chain reaction (qPCR), which produced results that agreed with the sequencing results. Taken together, these findings suggest that JA modulates the expression of genes related to energy supply and antioxidant capacity at both the transcriptional and post-transcriptional levels, possibly through the involvement of transcription factors and AS events.
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Affiliation(s)
- Tianhui Yang
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Mei Tian
- Institute of Horticultural Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Ting Gao
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Chuan Wang
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Xiaochun Wang
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Caijin Chen
- Branch Institute of Guyuan, Ningxia Academy of Agriculture and Forestry Sciences, Guyuan, Ningxia, China
| | - Weidi Yang
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
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10
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Hou Q, Zhang H, Zhu J, Liu F. Transcriptome Analysis to Identify Responsive Genes under Sublethal Concentration of Bifenazate in the Diamondback Moth, Plutella xylostella (Linnaeus, 1758) (Lepidoptera: Plutellidae). Int J Mol Sci 2022; 23:ijms232113173. [PMID: 36361960 PMCID: PMC9656211 DOI: 10.3390/ijms232113173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/28/2022] [Accepted: 10/25/2022] [Indexed: 11/25/2022] Open
Abstract
Bifenazate is a novel acaricide that has been widely used to control spider mites. Interestingly, we found bifenazate had a biological activity against the diamondback moth (Plutella xylostella), one of the most economically important pests on crucifer crops around the world. However, the molecular mechanisms underlying the response of P. xylostella to bifenazate treatment are not clear. In this study, we first estimated the LC30 dose of bifenazate for third-instar P. xylostella larvae. Then, in order to identify genes that respond to the treatment of this insecticide, the comparative transcriptome profiles were used to analyze the gene expression changes in P. xylostella larvae after exposure to LC30 of bifenazate. In total, 757 differentially expressed genes (DEGs) between bifenazate-treated and control P. xylostella larvae were identified, in which 526 and 231 genes were up-regulated and down-regulated, respectively. The further Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the xenobiotics metabolisms pathway was significantly enriched, with ten detoxifying enzyme genes (four P450s, five glutathione S-transferases (GSTs), and one UDP-Glucuronosyltransferase (UGT)) were up-regulated, and their expression patterns were validated by qRT-PCR as well. Interestingly, the present results showed that 17 cuticular protein (CP) genes were also remarkably up-regulated, including 15 CPR family genes. Additionally, the oxidative phosphorylation pathway was found to be activated with eight mitochondrial genes up-regulated in bifenazate-treated larvae. In contrast, we found some genes that were involved in tyrosine metabolism and purine pathways were down-regulated, indicating these two pathways of bifenazate-exposed larvae were significantly inhibited. In conclusion, the present study would help us to better understand the molecular mechanisms of sublethal doses of bifenazate detoxification and action in P. xylostella.
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11
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Wang C, Blondel L, Quadrado M, Dargel-Graffin C, Mireau H. Pentatricopeptide repeat protein MITOCHONDRIAL STABILITY FACTOR 3 ensures mitochondrial RNA stability and embryogenesis. PLANT PHYSIOLOGY 2022; 190:669-681. [PMID: 35751603 PMCID: PMC9434245 DOI: 10.1093/plphys/kiac309] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/09/2022] [Indexed: 05/29/2023]
Abstract
Gene expression in plant mitochondria is predominantly governed at the post-transcriptional level and relies mostly on nuclear-encoded proteins. However, the protein factors involved and the underlying molecular mechanisms are still not well understood. Here, we report on the function of the MITOCHONDRIAL STABILITY FACTOR 3 (MTSF3) protein, previously named EMBRYO DEFECTIVE 2794 (EMB2794), and show that it is essential for accumulation of the mitochondrial NADH dehydrogenase subunit 2 (nad2) transcript in Arabidopsis (Arabidopsis thaliana) but not for splicing of nad2 intron 2 as previously proposed. The MTSF3 gene encodes a pentatricopeptide repeat protein that localizes in the mitochondrion. An MTSF3 null mutation induces embryonic lethality, but viable mtsf3 mutant plants can be generated through partial complementation with the developmentally regulated ABSCISIC ACID INSENSITIVE3 promoter. Genetic analyses revealed growth retardation in rescued mtsf3 plants owing to the specific destabilization of mature nad2 mRNA and a nad2 precursor transcript bearing exons 3 to 5. Biochemical data demonstrate that MTSF3 protein specifically binds to the 3' terminus of nad2. Destabilization of nad2 mRNA induces a substantial decrease in complex I assembly and activity and overexpression of the alternative respiratory pathway. Our results support a role for MTSF3 protein in protecting two nad2 transcripts from degradation by mitochondrial exoribonucleases by binding to their 3' extremities.
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Affiliation(s)
- Chuande Wang
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Lisa Blondel
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Martine Quadrado
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Céline Dargel-Graffin
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
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12
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Xiao L, Liang H, Jiang G, Ding X, Liu X, Sun J, Jiang Y, Song L, Duan X. Proteome-wide identification of non-histone lysine methylation in tomato during fruit ripening. J Adv Res 2022; 42:177-188. [PMID: 36513412 PMCID: PMC9788949 DOI: 10.1016/j.jare.2022.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/20/2022] [Accepted: 02/22/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Histone and non-histone methylations are important post-translational modifications in plants. Histone methylation plays a crucial role in regulating chromatin structure and gene expression. However, the involvement of non-histone methylation in plant biological processes remains largely unknown. METHODS The methylated substrates and methylation sites during tomato fruit ripening were identified by LC-MS/MS. Bioinformatics of lysine methylated proteins was conducted to analyze the possible role of methylated proteins. The effects of methylation modification on protein functions were preliminarily investigated by site-directed mutation simulation. RESULTS A total of 241 lysine methylation (mono-, di- and trimethylation) sites in 176 proteins were identified with two conserved methylation motifs: xxxxxxExxx_K_xxxExxxxxx and xxxxxxExxx_K_xxxxxxxxxx. These methylated proteins were mainly related to fruit ripening and senescence, oxidation reduction process, signal transduction, stimulus and stress responses, and energy metabolism. Three representative proteins, thioredoxin (Trx), glutathione S-transferase T1 (GST T1), and NADH dehydrogenase (NOX), were selected to investigate the effect of methylation modifications on protein activity. Mimicking demethylation led to decreased Trx activity but increased GST T1 and NOX activities. In addition, RT-qPCR exhibited that the expression of many genes that encode proteins subjected to methylation was upregulated during fruit ripening. CONCLUSION Our study suggests that tomato fruit ripening undergo non-histone lysine methylation, which may participate in the regulation of fruit ripening. It is the first report of methyl proteome profiling of non-histone lysine in horticultural crops.
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Affiliation(s)
- Lu Xiao
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China,Institute of Quality Standard and Monitoring Technology for Agro-products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China,Key Laboratory of Testing and Evaluation for Agro-product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
| | - Hanzhi Liang
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoxiang Jiang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xiaochun Ding
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xuncheng Liu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Jian Sun
- Agro-food Science and Technology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Yueming Jiang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Lili Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an 311300, Zhejiang Province, China,Corresponding authors at: Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China (X. Duan).
| | - Xuewu Duan
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China,Agro-food Science and Technology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China,Corresponding authors at: Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China (X. Duan).
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Karuthadurai T, Das DN, Kumaresan A, Sinha MK, Kamaraj E, Nag P, Ebenezer Samuel King JP, Datta TK, Manimaran A, Jeyakumar S, Ramesha K. Sperm Transcripts Associated With Odorant Binding and Olfactory Transduction Pathways Are Altered in Breeding Bulls Producing Poor-Quality Semen. Front Vet Sci 2022; 9:799386. [PMID: 35274020 PMCID: PMC8902071 DOI: 10.3389/fvets.2022.799386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/03/2022] [Indexed: 12/28/2022] Open
Abstract
Spermatozoa carries a reservoir of mRNAs regulating sperm functions and fertilizing potential. Although it is well recognized that a considerable proportion of high genetic merit breeding bulls produce poor-quality semen, the transcriptomic alterations in spermatozoa from such bulls are not understood. In the present study, comparative high-throughput transcriptomic profiling of spermatozoa from good and poor-quality semen-producing bulls was carried out to identify the transcripts associated with semen quality. Using next-generation sequencing (NGS), we identified 11,632 transcripts in Holstein Friesian bull spermatozoa; after total hit normalization, a total of 544 transcripts were detected, of which 185 transcripts were common to both good and poor-quality semen, while 181 sperm transcripts were unique to good quality semen, and 178 transcripts were unique to poor-quality semen. Among the co-expressed transcripts, 31 were upregulated, while 108 were downregulated, and 46 were neutrally expressed in poor-quality semen. Bioinformatics analysis revealed that the dysregulated transcripts were predominantly involved in molecular function, such as olfactory receptor activity and odor binding, and in biological process, such as detection of chemical stimulus involved in sensory perception, sensory perception of smell, signal transduction, and signal synaptic transmission. Since a majority of the dysregulated transcripts were involved in the olfactory pathway (85% of enriched dysregulated genes were involved in this pathway), the expression of selected five transcripts associated with this pathway (OR2T11, OR10S1, ORIL3, OR5M11, and PRRX1) were validated using real-time qPCR, and it was found that their transcriptional abundance followed the same trend as observed in NGS; the sperm transcriptional abundance of OR2T11 and OR10S1 differed significantly (p < 0.05) between good and poor-quality semen. It is concluded that poor-quality semen showed altered expression of transcripts associated with olfactory receptors and pathways indicating the relationship between olfactory pathway and semen quality in bulls.
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Affiliation(s)
- Thirumalaisamy Karuthadurai
- Theriogenology Laboratory, Veterinary Gynaecology and Obstetrics, Southern Regional Station of ICAR-National Dairy Research Institute, Bengaluru, India
| | - Dayal Nitai Das
- Dairy Production Section, Southern Regional Station of ICAR-National Dairy Research Institute, Bengaluru, India
| | - Arumugam Kumaresan
- Theriogenology Laboratory, Veterinary Gynaecology and Obstetrics, Southern Regional Station of ICAR-National Dairy Research Institute, Bengaluru, India
- *Correspondence: Arumugam Kumaresan ;
| | - Manish Kumar Sinha
- Theriogenology Laboratory, Veterinary Gynaecology and Obstetrics, Southern Regional Station of ICAR-National Dairy Research Institute, Bengaluru, India
| | - Elango Kamaraj
- Theriogenology Laboratory, Veterinary Gynaecology and Obstetrics, Southern Regional Station of ICAR-National Dairy Research Institute, Bengaluru, India
| | - Pradeep Nag
- Theriogenology Laboratory, Veterinary Gynaecology and Obstetrics, Southern Regional Station of ICAR-National Dairy Research Institute, Bengaluru, India
| | - John Peter Ebenezer Samuel King
- Theriogenology Laboratory, Veterinary Gynaecology and Obstetrics, Southern Regional Station of ICAR-National Dairy Research Institute, Bengaluru, India
| | - Tirtha Kumar Datta
- Animal Genomics Laboratory, ICAR-National Dairy Research Institute, Karnal, India
| | - Ayyasamy Manimaran
- Dairy Production Section, Southern Regional Station of ICAR-National Dairy Research Institute, Bengaluru, India
| | - Sakthivel Jeyakumar
- Dairy Production Section, Southern Regional Station of ICAR-National Dairy Research Institute, Bengaluru, India
| | - Kerekoppa Ramesha
- Dairy Production Section, Southern Regional Station of ICAR-National Dairy Research Institute, Bengaluru, India
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Mellon M, Storti M, Vera-Vives AM, Kramer DM, Alboresi A, Morosinotto T. Inactivation of mitochondrial complex I stimulates chloroplast ATPase in Physcomitrium patens. PLANT PHYSIOLOGY 2021; 187:931-946. [PMID: 34608952 PMCID: PMC8491079 DOI: 10.1093/plphys/kiab276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/18/2021] [Indexed: 06/11/2023]
Abstract
Light is the ultimate source of energy for photosynthetic organisms, but respiration is fundamental for supporting metabolism during the night or in heterotrophic tissues. In this work, we isolated Physcomitrella (Physcomitrium patens) plants with altered respiration by inactivating Complex I (CI) of the mitochondrial electron transport chain by independently targeting on two essential subunits. Inactivation of CI caused a strong growth impairment even in fully autotrophic conditions in tissues where all cells are photosynthetically active, demonstrating that respiration is essential for photosynthesis. CI mutants showed alterations in the stoichiometry of respiratory complexes while the composition of photosynthetic apparatus was substantially unaffected. CI mutants showed altered photosynthesis with high activity of both Photosystems I and II, likely the result of high chloroplast ATPase activity that led to smaller ΔpH formation across thylakoid membranes, decreasing photosynthetic control on cytochrome b6f in CI mutants. These results demonstrate that alteration of respiratory activity directly impacts photosynthesis in P. patens and that metabolic interaction between organelles is essential in their ability to use light energy for growth.
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Affiliation(s)
- Marco Mellon
- Department of Biology, University of Padova, 35121 Padova, Italy
| | - Mattia Storti
- Department of Biology, University of Padova, 35121 Padova, Italy
| | | | - David M. Kramer
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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Zhang D, Chen C, Wang H, Niu E, Zhao P, Fang S, Zhu G, Shang X, Guo W. Cotton Fiber Development Requires the Pentatricopeptide Repeat Protein GhIm for Splicing of Mitochondrial nad7 mRNA. Genetics 2021; 217:1-17. [PMID: 33683356 DOI: 10.1093/genetics/iyaa017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/18/2020] [Indexed: 12/27/2022] Open
Abstract
Pentatricopeptide repeat (PPR) proteins encoded by nuclear genomes can bind to organellar RNA and are involved in the regulation of RNA metabolism. However, the functions of many PPR proteins remain unknown in plants, especially in polyploidy crops. Here, through a map-based cloning strategy and Clustered regularly interspaced short palindromic repeats/cas9 (CRISPR/cas9) gene editing technology, we cloned and verified an allotetraploid cotton immature fiber (im) mutant gene (GhImA) encoding a PPR protein in chromosome A03, that is associated with the non-fluffy fiber phenotype. GhImA protein targeted mitochondrion and could bind to mitochondrial nad7 mRNA, which encodes the NAD7 subunit of Complex I. GhImA and its homolog GhImD had the same function and were dosage-dependent. GhImA in the im mutant was a null allele with a 22 bp deletion in the coding region. Null GhImA resulted in the insufficient GhIm dosage, affected mitochondrial nad7 pre-mRNA splicing, produced less mature nad7 transcripts, and eventually reduced Complex I activities, up-regulated alternative oxidase metabolism, caused reactive oxygen species (ROS) burst and activation of stress or hormone response processes. This study indicates that the GhIm protein participates in mitochondrial nad7 splicing, affects respiratory metabolism, and further regulates cotton fiber development via ATP supply and ROS balance.
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Affiliation(s)
- Dayong Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Chuan Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Haitang Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Erli Niu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Peiyue Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuai Fang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Guozhong Zhu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoguang Shang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
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Klusch N, Senkler J, Yildiz Ö, Kühlbrandt W, Braun HP. A ferredoxin bridge connects the two arms of plant mitochondrial complex I. THE PLANT CELL 2021; 33:2072-2091. [PMID: 33768254 PMCID: PMC8290278 DOI: 10.1093/plcell/koab092] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/19/2021] [Indexed: 05/23/2023]
Abstract
Mitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. Complex I is composed of two arms, which form a conserved L-shape. We report the structures of the intact, 47-subunit mitochondrial complex I from Arabidopsis thaliana and the 51-subunit complex I from the green alga Polytomella sp., both at around 2.9 Å resolution. In both complexes, a heterotrimeric γ-carbonic anhydrase domain is attached to the membrane arm on the matrix side. Two states are resolved in A. thaliana complex I, with different angles between the two arms and different conformations of the ND1 (NADH dehydrogenase subunit 1) loop near the quinol binding site. The angle appears to depend on a bridge domain, which links the peripheral arm to the membrane arm and includes an unusual ferredoxin. We propose that the bridge domain participates in regulating the activity of plant complex I.
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Affiliation(s)
- Niklas Klusch
- Department of Structural Biology, Max-Planck-Institute of Biophysics, Frankfurt 60438, Germany
| | - Jennifer Senkler
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Özkan Yildiz
- Department of Structural Biology, Max-Planck-Institute of Biophysics, Frankfurt 60438, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max-Planck-Institute of Biophysics, Frankfurt 60438, Germany
| | - Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover 30419, Germany
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17
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Alber NA, Vanlerberghe GC. The flexibility of metabolic interactions between chloroplasts and mitochondria in Nicotiana tabacum leaf. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1625-1646. [PMID: 33811402 DOI: 10.1111/tpj.15259] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/24/2021] [Accepted: 03/26/2021] [Indexed: 05/02/2023]
Abstract
To examine the effect of mitochondrial function on photosynthesis, wild-type and transgenic Nicotiana tabacum with varying amounts of alternative oxidase (AOX) were treated with different respiratory inhibitors. Initially, each inhibitor increased the reduction state of the chloroplast electron transport chain, most severely in AOX knockdowns and least severely in AOX overexpressors. This indicated that the mitochondrion was a necessary sink for photo-generated reductant, contributing to the 'P700 oxidation capacity' of photosystem I. Initially, the Complex III inhibitor myxothiazol and the mitochondrial ATP synthase inhibitor oligomycin caused an increase in photosystem II regulated non-photochemical quenching not evident with the Complex III inhibitor antimycin A (AA). This indicated that the increased quenching depended upon AA-sensitive cyclic electron transport (CET). Following 12 h with oligomycin, the reduction state of the chloroplast electron transport chain recovered in all plant lines. Recovery was associated with large increases in the protein amount of chloroplast ATP synthase and mitochondrial uncoupling protein. This increased the capacity for photophosphorylation in the absence of oxidative phosphorylation and enabled the mitochondrion to act again as a sink for photo-generated reductant. Comparing the AA and myxothiazol treatments at 12 h showed that CET optimized photosystem I quantum yield, depending upon the P700 oxidation capacity. When this capacity was too high, CET drew electrons away from other sinks, moderating the P700+ amount. When P700 oxidation capacity was too low, CET acted as an electron overflow, moderating the amount of reduced P700. This study reveals flexible chloroplast-mitochondrion interactions able to overcome lesions in energy metabolism.
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Affiliation(s)
- Nicole A Alber
- Department of Biological Sciences, Department of Cell and Systems Biology, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C1A4, Canada
| | - Greg C Vanlerberghe
- Department of Biological Sciences, Department of Cell and Systems Biology, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C1A4, Canada
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18
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Ivanova A, Ghifari AS, Berkowitz O, Whelan J, Murcha MW. The mitochondrial AAA protease FTSH3 regulates Complex I abundance by promoting its disassembly. PLANT PHYSIOLOGY 2021; 186:599-610. [PMID: 33616659 PMCID: PMC8154063 DOI: 10.1093/plphys/kiab074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/28/2021] [Indexed: 06/02/2023]
Abstract
ATP is generated in mitochondria by oxidative phosphorylation. Complex I (NADH:ubiquinone oxidoreductase or NADH dehydrogenase) is the first multisubunit protein complex of this pathway, oxidizing NADH and transferring electrons to the ubiquinone pool. Typically, Complex I mutants display a slow growth rate compared to wild-type plants. Here, using a forward genetic screen approach for restored growth of a Complex I mutant, we have identified the mitochondrial ATP-dependent metalloprotease, Filamentous Temperature Sensitive H 3 (FTSH3), as a factor that is required for the disassembly of Complex I. An ethyl methanesulfonate-induced mutation in FTSH3, named as rmb1 (restoration of mitochondrial biogenesis 1), restored Complex I abundance and plant growth. Complementation could be achieved with FTSH3 lacking proteolytic activity, suggesting the unfoldase function of FTSH3 has a role in Complex I disassembly. The introduction of the rmb1 to an additional, independent, and extensively characterized Complex I mutant, ndufs4, resulted in similar increases to Complex I abundance and a partial restoration of growth. These results show that disassembly or degradation of Complex I plays a role in determining its steady-state abundance and thus turnover may vary under different conditions.
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Affiliation(s)
- Aneta Ivanova
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - Abi S Ghifari
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Science, School of Life Science, The ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora 3086, Vic, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Science, School of Life Science, The ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora 3086, Vic, Australia
| | - Monika W Murcha
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
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Pacheco JM, Canal MV, Pereyra CM, Welchen E, Martínez-Noël GMA, Estevez JM. The tip of the iceberg: emerging roles of TORC1, and its regulatory functions in plant cells. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4085-4101. [PMID: 33462577 DOI: 10.1093/jxb/eraa603] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
Target of Rapamycin (TOR) is an evolutionarily conserved protein kinase that plays a central role in coordinating cell growth with light availability, the diurnal cycle, energy availability, and hormonal pathways. TOR Complex 1 (TORC1) controls cell proliferation, growth, metabolism, and defense in plants. Sugar availability is the main signal for activation of TOR in plants, as it also is in mammals and yeast. Specific regulators of the TOR kinase pathway in plants are inorganic compounds in the form of major nutrients in the soils, and light inputs via their impact on autotrophic metabolism. The lack of TOR is embryo-lethal in plants, whilst dysregulation of TOR signaling causes major alterations in growth and development. TOR exerts control as a regulator of protein translation via the action of proteins such as S6K, RPS6, and TAP46. Phytohormones are central players in the downstream systemic physiological TOR effects. TOR has recently been attributed to have roles in the control of DNA methylation, in the abundance of mRNA splicing variants, and in the variety of regulatory lncRNAs and miRNAs. In this review, we summarize recent discoveries in the plant TOR signaling pathway in the context of our current knowledge of mammalian and yeast cells, and highlight the most important gaps in our understanding of plants that need to be addressed in the future.
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Affiliation(s)
| | - María Victoria Canal
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas,, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Cintia M Pereyra
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET) and Fundación para Investigaciones Biológicas Aplicadas (FIBA), Vieytes, Mar Del Plata, Argentina
| | - Elina Welchen
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas,, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Giselle M A Martínez-Noël
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET) and Fundación para Investigaciones Biológicas Aplicadas (FIBA), Vieytes, Mar Del Plata, Argentina
| | - José M Estevez
- Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires CP, Argentina
- Centro de Biotecnología Vegetal (CBV), Facultad de Ciencias de la Vida (FCsV), Universidad Andres Bello, Santiago, Chile and Millennium Institute for Integrative Biology (iBio), Santiago, Chile
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Shevtsov-Tal S, Best C, Matan R, Chandran SA, Brown GG, Ostersetzer-Biran O. nMAT3 is an essential maturase splicing factor required for holo-complex I biogenesis and embryo development in Arabidopsis thaliana plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1128-1147. [PMID: 33683754 DOI: 10.1111/tpj.15225] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 05/21/2023]
Abstract
Group-II introns are self-splicing mobile genetic elements consisting of catalytic intron-RNA and its related intron-encoded splicing maturase protein cofactor. Group-II sequences are particularly plentiful within the mitochondria of land plants, where they reside within many critical gene loci. During evolution, the plant organellar introns have degenerated, such as they lack regions that are are required for splicing, and also lost their evolutionary related maturase proteins. Instead, for their splicing the organellar introns in plants rely on different host-acting protein cofactors, which may also provide a means to link cellular signals with respiratory functions. The nuclear genome of Arabidopsis thaliana encodes four maturase-related factors. Previously, we showed that three of the maturases, nMAT1, nMAT2 and nMAT4, function in the excision of different group-II introns in Arabidopsis mitochondria. The function of nMAT3 (encoded by the At5g04050 gene locus) was found to be essential during early embryogenesis. Using a modified embryo-rescue method, we show that nMAT3-knockout plants are strongly affected in the splicing of nad1 introns 1, 3 and 4 in Arabidopsis mitochondria, resulting in complex-I biogenesis defects and altered respiratory activities. Functional complementation of nMAT3 restored the organellar defects and embryo-arrested phenotypes associated with the nmat3 mutant line. Notably, nMAT3 and nMA4 were found to act on the same RNA targets but have no redundant functions in the splicing of nad1 transcripts. The two maturases, nMAT3 and nMAT4 are likely to cooperate together in the maturation of nad1 pre-RNAs. Our results provide important insights into the roles of maturases in mitochondria gene expression and the biogenesis of the respiratory system during early plant life.
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Affiliation(s)
- Sofia Shevtsov-Tal
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem, 91904, Israel
| | - Corinne Best
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem, 91904, Israel
| | - Roei Matan
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem, 91904, Israel
| | - Sam A Chandran
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, 613 401, India
| | - Gregory G Brown
- Department of Biology, McGill University, Montreal, Quebec, H3A 1B1, Canada
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem, 91904, Israel
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21
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ROS Homeostasis and Plant Salt Tolerance: Plant Nanobiotechnology Updates. SUSTAINABILITY 2021. [DOI: 10.3390/su13063552] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Salinity is an issue impairing crop production across the globe. Under salinity stress, besides the osmotic stress and Na+ toxicity, ROS (reactive oxygen species) overaccumulation is a secondary stress which further impairs plant performance. Chloroplasts, mitochondria, the apoplast, and peroxisomes are the main ROS generation sites in salt-stressed plants. In this review, we summarize ROS generation, enzymatic and non-enzymatic antioxidant systems in salt-stressed plants, and the potential for plant biotechnology to maintain ROS homeostasis. Overall, this review summarizes the current understanding of ROS homeostasis of salt-stressed plants and highlights potential applications of plant nanobiotechnology to enhance plant tolerance to stresses.
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Popov VN, Syromyatnikov MY, Fernie AR, Chakraborty S, Gupta KJ, Igamberdiev AU. The uncoupling of respiration in plant mitochondria: keeping reactive oxygen and nitrogen species under control. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:793-807. [PMID: 33245770 DOI: 10.1093/jxb/eraa510] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/26/2020] [Indexed: 06/11/2023]
Abstract
Plant mitochondrial respiration involves the operation of various alternative pathways. These pathways participate, both directly and indirectly, in the maintenance of mitochondrial functions though they do not contribute to energy production, being uncoupled from the generation of an electrochemical gradient across the mitochondrial membrane and thus from ATP production. Recent findings suggest that uncoupled respiration is involved in reactive oxygen species (ROS) and nitric oxide (NO) scavenging, regulation, and homeostasis. Here we discuss specific roles and possible functions of uncoupled mitochondrial respiration in ROS and NO metabolism. The mechanisms of expression and regulation of the NDA-, NDB- and NDC-type non-coupled NADH and NADPH dehydrogenases, the alternative oxidase (AOX), and the uncoupling protein (UCP) are examined in relation to their involvement in the establishment of the stable far-from-equilibrium state of plant metabolism. The role of uncoupled respiration in controlling the levels of ROS and NO as well as inducing signaling events is considered. Secondary functions of uncoupled respiration include its role in protection from stress factors and roles in biosynthesis and catabolism. It is concluded that uncoupled mitochondrial respiration plays an important role in providing rapid adaptation of plants to changing environmental factors via regulation of ROS and NO.
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Affiliation(s)
- Vasily N Popov
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia
- Voronezh State University of Engineering Technologies, Voronezh, Russia
| | - Mikhail Y Syromyatnikov
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia
- Voronezh State University of Engineering Technologies, Voronezh, Russia
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Subhra Chakraborty
- National Institute for Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | | | - Abir U Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
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Chen EH, Duan JY, Song W, Wang DX, Tang PA. RNA-seq Analysis Reveals Mitochondrial and Cuticular Protein Genes Are Associated with Phosphine Resistance in the Rusty Grain Beetle (Coleoptera:Laemophloeidae). JOURNAL OF ECONOMIC ENTOMOLOGY 2021; 114:440-453. [PMID: 33346362 DOI: 10.1093/jee/toaa273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Indexed: 06/12/2023]
Abstract
The rusty grain beetle, Cryptolestes ferrugineus (Stephens), is a serious pest of stored grain, which has developed high levels of resistance to phosphine. In this study, five geographically distant populations of C. ferrugineus had been collected in China, specifically in granaries where phosphine fumigant is used for pest control, and they showed a high resistance ratio up to 1,907 (LC50 = 21.0 mg/liter). Then, a reference transcriptome was constructed to use as a basis for investigating the molecular mechanisms of phosphine resistance in this species, which consisted of 47,006 unigenes with a mean length of 1,090. Subsequently, the RNA-Seq analysis of individuals from the most susceptible and resistant populations led to the identification of 54 genes that are differentially expressed. GO and KEGG analysis demonstrated that genes associated with mitochondrial and respiration functions were significantly enriched. Also, the 'structural constituent of cuticle' term was annotated in the GO enrichment analysis and further qRT-PCR confirmed that the expression levels of nine cuticular protein genes were significantly increased in the resistant population. In conclusion, we present here a transcriptome-wide overview of gene expression changes between resistant and susceptible populations of C. ferrugineus, and this in turn documents that mitochondria and cuticular protein genes may play together a crucial role in phosphine resistance. Further gene function analysis should enable the provision of advice to expedite resistance management decisions.
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Affiliation(s)
- Er-Hu Chen
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, Jiangsu, China
| | - Jin-Yan Duan
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, Jiangsu, China
| | - Wei Song
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, Jiangsu, China
| | - Dian-Xuan Wang
- Collaborative Innovation Center of Grain Storage Security, Zhengzhou, Henan, China
| | - Pei-An Tang
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, Jiangsu, China
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Jurdak R, Launay-Avon A, Paysant-Le Roux C, Bailly C. Retrograde signalling from the mitochondria to the nucleus translates the positive effect of ethylene on dormancy breaking of Arabidopsis thaliana seeds. THE NEW PHYTOLOGIST 2021; 229:2192-2205. [PMID: 33020928 DOI: 10.1111/nph.16985] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/21/2020] [Indexed: 05/22/2023]
Abstract
Ethylene and reactive oxygen species (ROS) regulate seed dormancy alleviation, but the molecular basis of their action and crosstalk remains largely unknown. Here we studied the mechanism of Arabidopsis seed dormancy release by ethylene using cell imaging, and genetic and transcriptomics approaches, in order to tackle its possible interaction with ROS homeostasis. We found that the effect of ethylene on seed germination required ROS production by the mitochondrial electron transport chain. Seed response to ethylene involved a mitochondrial retrograde response (MRR) through nuclear ROS production and upregulation of the MRR components AOX1a and ANAC013, but also required the activation of the ethylene canonical pathway. Together our data allowed deciphering of the mode of action of ethylene on seed germination and the associated dynamics of ROS production. Our findings highlight the occurrence of retrograde signalling in seed germination.
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Affiliation(s)
- Rana Jurdak
- IBPS, CNRS, UMR 7622 Biologie du Développement, Sorbonne Université, Paris, F-75005, France
- Biodiversity and Functional Genomics Laboratory, Université Saint-Joseph de Beyrouth, Beyrouth, 1107 2050, Lebanon
| | - Alexandra Launay-Avon
- CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, Orsay, 91405, France
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, Orsay, 91405, France
| | - Christine Paysant-Le Roux
- CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, Orsay, 91405, France
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, Orsay, 91405, France
| | - Christophe Bailly
- IBPS, CNRS, UMR 7622 Biologie du Développement, Sorbonne Université, Paris, F-75005, France
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25
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Liu H, Chen H, Ding G, Li K, Ren Q. Identification of candidate genes conferring tolerance to aluminum stress in Pinus massoniana inoculated with ectomycorrhizal fungus. BMC PLANT BIOLOGY 2020; 20:521. [PMID: 33198640 PMCID: PMC7667757 DOI: 10.1186/s12870-020-02719-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/25/2020] [Indexed: 05/17/2023]
Abstract
BACKGROUND Pinus massoniana Lamb. is an important afforestation tree species with high economic, ecological and medicinal values. Aluminum (Al) toxicity driven by soil acidification causes dieback of P. massoniana plantations. Previous studies showed that ectomycorrhizal fungi alleviate Al stress damages in Pinus, but the underlying molecular mechanisms and key genes induced by ectomycorrhizal fungi inoculation under Al stress in Pinus have not been explored. Herein, we applied Al stress for 60 days to P. massoniana seedlings inoculated with Suillus luteus (SL) and those non-inoculated. Then, we compared their growth parameters and transcriptome in order to detect candidate genes induced by SL conferring Al tolerance in P. massoniana. RESULT Our results showed that SL inoculation confers Al stress tolerance in P. massoniana through improved growth performance, strong antioxidant enzyme activities and reduced malondialdehyde accumulation as compared to non-inoculated seedlings. Transcriptome sequencing further supported these findings as very few genes (51 genes) were transcriptionally altered by Al in SL inoculated plants as compared to non-inoculated plants (2140 genes). We identified three core genes (cox1, cox3 and Nd1) that were strongly up-regulated by Al in the SL inoculated plants but were down-regulated in the non-inoculated plants. We also identified 42 genes specifically regulated by SL inoculated plants under Al stress, which are involved in a wide range of biological processes such as antioxidative response, transporters, hormone signaling and plant pathogen infection responses. CONCLUSIONS Altogether, our data suggest that SL inoculation induces priming of key stress response pathways and triggers specific genes that efficiently alleviate Al stress effects in P. massoniana. The candidate genes resources generated in this study are of utmost importance for functional characterization and molecular studies aiming at improving Al tolerance in plants.
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Affiliation(s)
- Haiyan Liu
- College of Forestry, Guizhou University/Institute for Forest Resources & Environment of Guizhou, Guiyang, 550025, Guizhou, China
- Guizhou Botanical Garden, Guiyang, 550004, Guizhou, China
| | - Houying Chen
- College of Forestry, Guizhou University/Institute for Forest Resources & Environment of Guizhou, Guiyang, 550025, Guizhou, China
| | - Guijie Ding
- College of Forestry, Guizhou University/Institute for Forest Resources & Environment of Guizhou, Guiyang, 550025, Guizhou, China.
| | - Kuaifen Li
- College of Forestry, Guizhou University/Institute for Forest Resources & Environment of Guizhou, Guiyang, 550025, Guizhou, China
| | - Qifei Ren
- Guizhou Botanical Garden, Guiyang, 550004, Guizhou, China
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26
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Abstract
Ubiquitin C-terminal Hydrolase L1 (UCHL1) is a deubiquitinating enzyme that was originally identified in neurons. Our recent study showed that UCHL1 was expressed in C2C12 myoblast cells and mouse skeletal muscle. Here we report that in mouse skeletal muscle, UCHL1 is primarily expressed in oxidative muscle fibers. Skeletal muscle specific gene knockout (smKO) of UCHL1 in mice reduced oxidative activity in skeletal muscle measured by SDH staining. The in situ muscle contraction test revealed that gastrocnemius muscle from UCHL1 smKO mice was more prone to fatigue in response to the repetitive stimulation. This data suggests that UCHL1 plays a role in maintenance of muscle oxidative metabolism. Moreover, UCHL1 smKO caused a significant reduction in key proteins that are involved in mitochondrial oxidative phosphorylation in soleus muscles, suggesting that UCHL1 may be involved in regulation of mitochondrial content and function. Immunostaining showed the co-localization of UCHL1 and mitochondrial marker VDAC in skeletal muscle. Mitochondrial fractionation assay revealed that, although UCHL1 was primarily present in the cytosolic fraction, a low level of UCHL1 protein was present in mitochondrial fraction. The level of phosphorylation of AMPKα, a master regulator of mitochondrial biogenesis, were unchanged in UCHL1 smKO muscle. On the other hand, immunoprecipitation from soleus muscle sample indicated the interaction between UCHL1 and HSP60, a chaperon protein that is involved in mitochondrial protein transport. There was a trend of downregulation of HSP60 in UCHL1 smKO muscle. Overall, our data suggests UCHL1 is a novel regulator of mitochondrial function and oxidative activity in skeletal muscle.
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Best C, Mizrahi R, Ostersetzer-Biran O. Why so Complex? The Intricacy of Genome Structure and Gene Expression, Associated with Angiosperm Mitochondria, May Relate to the Regulation of Embryo Quiescence or Dormancy-Intrinsic Blocks to Early Plant Life. PLANTS (BASEL, SWITZERLAND) 2020; 9:E598. [PMID: 32397140 PMCID: PMC7284508 DOI: 10.3390/plants9050598] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/30/2020] [Accepted: 04/30/2020] [Indexed: 12/14/2022]
Abstract
Mitochondria play key roles in cellular-energy metabolism and are vital for plant-life, such as for successful germination and early-seedling establishment. Most mitochondria contain their own genetic system (mtDNA, mitogenome), with an intrinsic protein-synthesis machinery. Although the challenges of maintaining prokaryotic-type structures and functions are common to Eukarya, land plants possess some of the most complex organelle composition of all known organisms. Angiosperms mtDNAs are characteristically the largest and least gene-dense among the eukaryotes. They often contain highly-variable intergenic regions of endogenous or foreign origins and undergo frequent recombination events, which result in different mtDNA configurations, even between closely-related species. The expression of the mitogenome in angiosperms involves extensive mtRNA processing steps, including numerous editing and splicing events. Why do land-plant's mitochondria have to be so complex? The answer to this remains a matter of speculation. We propose that this complexity may have arisen throughout the terrestrialization of plants, as a means to control embryonic mitochondrial functions -a critical adaptive trait to optimize seed germination. The unique characteristics of plant mtDNA may play pivotal roles in the nuclear-regulation of organellar biogenesis and metabolism, possibly to control embryos quiescence or dormancy, essential determinants for the establishment of viable plantlets that can survive post-germination.
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Affiliation(s)
| | | | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus—Givat Ram, Jerusalem 9190401, Israel; (C.B.); (R.M.)
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28
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Braun HP. The Oxidative Phosphorylation system of the mitochondria in plants. Mitochondrion 2020; 53:66-75. [PMID: 32334143 DOI: 10.1016/j.mito.2020.04.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/26/2020] [Accepted: 04/21/2020] [Indexed: 10/24/2022]
Abstract
Mitochondrial Oxidative Phosphorylation (OXPHOS) provides ATP for driving cellular functions. In plants, OXPHOS takes place in the context of photosynthesis. Indeed, metabolism of mitochondria and chloroplasts is tightly linked. OXPHOS has several extra functions in plants. This review takes a view on the OXPHOS system of plants, the electron transfer chain (ETC), the ATP synthase complex and the numerous supplementary enzymes involved. Electron transport pathways are especially branched in plants. Furthermore, the "classical" OXPHOS complexes include extra subunits, some of which introduce side activities into these complexes. Consequently, and to a remarkable degree, OXPHOS is a multi-functional system in plants that needs to be efficiently regulated with respect to all its physiological tasks in the mitochondria, the chloroplasts, and beyond. Regulatory mechanisms based on posttranslational protein modifications and formation of supramolecular protein assemblies are summarized and discussed.
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Affiliation(s)
- Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany.
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29
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Neubert L, Borchert P, Stark H, Hoefer A, Vogel-Claussen J, Warnecke G, Eubel H, Kuenzler P, Kreipe HH, Hoeper MM, Kuehnel M, Jonigk D. Molecular Profiling of Vascular Remodeling in Chronic Pulmonary Disease. THE AMERICAN JOURNAL OF PATHOLOGY 2020; 190:1382-1396. [PMID: 32275906 DOI: 10.1016/j.ajpath.2020.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 03/10/2020] [Accepted: 03/24/2020] [Indexed: 01/06/2023]
Abstract
Pulmonary hypertension and pulmonary vascular remodeling (PVR) are common in many lung diseases leading to right ventricular dysfunction and death. Differences in PVR result in significant prognostic divergences in both the pulmonary arterial and venous compartments, as in pulmonary arterial hypertension (PAH) and pulmonary veno-occlusive disease (PVOD), respectively. Our goal was to identify compartment-specific molecular hallmarks of PVR, considering the risk of life-threatening pulmonary edema in PVOD, if treated by conventional pulmonary hypertension therapy. Formalin-fixed and paraffin-embedded tissues from fresh explanted human lungs of patients with PVOD (n = 19), PAH (n = 20), idiopathic pulmonary fibrosis (n = 13), and chronic obstructive pulmonary disease (n = 15), were analyzed for inflammation and kinome-related gene regulation. The generated neuronal network differentiated PVOD from PAH samples with a sensitivity of 100% and a specificity of 92% in a randomly chosen validation set, a level far superior to established diagnostic algorithms. Further, various alterations were identified regarding the gene expression of explanted lungs with PVR, compared with controls. Specifically, the dysregulation of microtubule-associated serine/threonine kinase 2 and protein-o-mannose kinase SGK196 in all disease groups suggests a key role in pulmonary vasculopathy for the first time. Our findings promise to help develop novel target-specific interventions and innovative approaches to facilitate clinical diagnostics in an elusive group of diseases.
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Affiliation(s)
- Lavinia Neubert
- Institute of Pathology, Hannover Medical School, Hannover, Germany; German Center for Lung Research (DZL), Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany.
| | - Paul Borchert
- Institute of Pathology, Hannover Medical School, Hannover, Germany; German Center for Lung Research (DZL), Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
| | - Helge Stark
- Institute of Pathology, Hannover Medical School, Hannover, Germany; German Center for Lung Research (DZL), Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
| | - Anne Hoefer
- Institute of Pathology, Hannover Medical School, Hannover, Germany; German Center for Lung Research (DZL), Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
| | - Jens Vogel-Claussen
- German Center for Lung Research (DZL), Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany; Institute for Radiology, Hannover Medical School, Hannover, Germany
| | - Gregor Warnecke
- German Center for Lung Research (DZL), Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany; Department of Cardiothoracic, Transplantation and Vascular Surgery, Hannover Medical School
| | - Holger Eubel
- Institute of Plant Genetics, Leibniz University Hanover, Hannover, Germany
| | - Patrick Kuenzler
- Institute of Plant Genetics, Leibniz University Hanover, Hannover, Germany
| | | | - Marius M Hoeper
- German Center for Lung Research (DZL), Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany; Clinic for Pneumology, Hannover Medical School, Hannover, Germany
| | - Mark Kuehnel
- Institute of Pathology, Hannover Medical School, Hannover, Germany; German Center for Lung Research (DZL), Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
| | - Danny Jonigk
- Institute of Pathology, Hannover Medical School, Hannover, Germany; German Center for Lung Research (DZL), Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
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30
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Lee PY, Saraygord-Afshari N, Low TY. The evolution of two-dimensional gel electrophoresis - from proteomics to emerging alternative applications. J Chromatogr A 2020; 1615:460763. [DOI: 10.1016/j.chroma.2019.460763] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/28/2019] [Accepted: 11/30/2019] [Indexed: 01/05/2023]
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31
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Liu ZJ, Zhang YH, Ma XF, Ye P, Gao F, Li XF, Zhou YJ, Shi ZH, Cheng HM, Zheng CX, Li HJ, Zhang GF. Biological functions of Arabidopsis thaliana MBP-1-like protein encoded by ENO2 in the response to drought and salt stresses. PHYSIOLOGIA PLANTARUM 2020; 168:660-674. [PMID: 31343741 DOI: 10.1111/ppl.13013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 06/21/2019] [Accepted: 07/16/2019] [Indexed: 06/10/2023]
Abstract
Arabidopsis thaliana ENO2 (AtENO2) plays an important role in plant growth and development. It encodes two proteins, a full-length AtENO2 and a truncated version, AtMBP-1, alternatively translated from the second start codon of the mRNA. The AtENO2 mutant (eno2- ) exhibited reduced leaf size, shortened siliques, a dwarf phenotype and higher sensitivity to abiotic stress. The objectives of this study were to analyze the regulatory network of the ENO2 gene in plant growth development and understand the function of AtENO2/AtMBP-1 to abiotic stresses. An eno2- /35S:AtENO2-GFP line and an eno2- /35S:AtMBP-1-GFP line of Arabidopsis were obtained. Results of sequencing by 454 GS FLX identified 578 upregulated and 720 downregulated differential expressed genes (DEGs) in a pairwise comparison (WT-VS-eno2- ). All the high-quality reads were annotated using the Gene Ontology (GO) terms. The DEGs with KEGG pathway annotations occurred in 110 pathways. The metabolic pathways and biosynthesis of secondary metabolites contained more DEGs. Moreover, the eno2- /35S:AtENO2-GFP line returned to the wild-type (WT) phenotype and was tolerant to drought and salt stresses. However, the eno2- /35S:AtMBP-1-GFP line was not able to recover the WT phenotype but it has a higher tolerance to drought and salt stresses. Results from this study demonstrate that AtENO2 is critical for the growth and development, and the AtMBP-1 coded by AtENO2 is important in tolerance of Arabidopsis to abiotic stresses.
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Affiliation(s)
- Zi-Jin Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yong-Hua Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xiao-Feng Ma
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Pan Ye
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Fei Gao
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
| | - Xiao-Feng Li
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yi-Jun Zhou
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
| | - Zi-Han Shi
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Hui-Mei Cheng
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Chao-Xing Zheng
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Hong-Jie Li
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Gen-Fa Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
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32
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Kuhnert F, Stefanski A, Overbeck N, Drews L, Reichert AS, Stühler K, Weber APM. Rapid Single-Step Affinity Purification of HA-Tagged Plant Mitochondria. PLANT PHYSIOLOGY 2020; 182:692-706. [PMID: 31818904 PMCID: PMC6997695 DOI: 10.1104/pp.19.00732] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 11/22/2019] [Indexed: 05/19/2023]
Abstract
Photosynthesis in plant cells would not be possible without the supportive role of mitochondria. However, isolating mitochondria from plant cells for physiological and biochemical analyses is a lengthy and tedious process. Established isolation protocols require multiple centrifugation steps and substantial amounts of starting material. To overcome these limitations, we tagged mitochondria in Arabidopsis (Arabidopsis thaliana) with a triple hemagglutinin tag for rapid purification via a single affinity-purification step. This protocol yields a substantial quantity of highly pure mitochondria from 1 g of Arabidopsis seedlings. The purified mitochondria were suitable for enzyme activity analyses and yielded sufficient amounts of proteins for deep proteomic profiling. We applied this method for the proteomic analysis of the Arabidopsis bou-2 mutant deficient in the mitochondrial Glu transporter À BOUT DE SOUFFLE (BOU) and identified 27 differentially expressed mitochondrial proteins compared with tagged Col-0 controls. Our work sets the stage for the development of advanced mitochondria isolation protocols for distinct cell types.
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Affiliation(s)
- Franziska Kuhnert
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Anja Stefanski
- Molecular Proteomics Laboratory, Biomedical Research Center, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Nina Overbeck
- Molecular Proteomics Laboratory, Biomedical Research Center, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Leonie Drews
- Institute of Biochemistry and Molecular Biology I, Medical Faculty, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Andreas S Reichert
- Institute of Biochemistry and Molecular Biology I, Medical Faculty, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory, Biomedical Research Center, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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Mao GH, Huang XH, Geng XJ, Li Q, Zhang Y, Dou Q. Correlation between sperm mitochondrial ND5 and ND6 gene variations and total fertilisation failure. Arch Med Sci 2020; 16:692-698. [PMID: 32399119 PMCID: PMC7212212 DOI: 10.5114/aoms.2020.94658] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 08/10/2017] [Indexed: 11/23/2022] Open
Abstract
INTRODUCTION The purpose of this study was to investigate the correlation between sperm mitochondrial NADH dehydrogenase subunit 5 (ND5) and NADH dehydrogenase subunit 6 (ND6) gene variations and total fertilisation failure (TFF). MATERIAL AND METHODS A total of 232 sperm samples at the fresh in vitro fertilisation (IVF) cycle or the half-intracytoplasmic sperm injection (ICSI) cycle were collected for this retrospective controlled study on Han Chinese people between July 2011 and April 2014. Of the 232 total samples, 45 were from the IVF-TFF group and 187 were from couples with normal fertilisation (fertilisation rate > 50%). The mitochondrial ND5 and ND6 gene variations and sperm haplotypes were confirmed using nested PCR and DNA sequencing. RESULTS Ten homozygous variations were newly discovered, namely C12417T, T12441A, C12543A, C13650A, C13765A, T13769C, C13775T, A13776G, C13785A and C13845T. The gene variation rates of six sites, C12417T, C13650A, C13765A, T13769C, C13785A and C13845T, in the TFF group were significantly higher than those in the control group (p < 0.05). There were 231 heterozygous variations discovered; however, only nine heterozygous sites (12441, 12561, 12735, 13164, 13743, 13812, 13928, 14172 and 14368) had significantly higher gene variation rates than those in the control group (p < 0.05). In addition, the results showed that haplogroup C did not affect TFF (p > 0.05), and the fertilisation failure rates of haplogroup R and haplogroup D4a were both higher than those in the control group (p < 0.05). CONCLUSIONS Our results suggested that the ND5 and ND6 gene variations are correlated with TFF. Furthermore, this study indicated that haplogroup R and haplogroup D4a might be risk factors for TFF.
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Affiliation(s)
- Gen-Hong Mao
- Reproductive Medical Center, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Xiao-Hui Huang
- Reproductive Medical Center, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Xu-Jing Geng
- Reproductive Medical Center, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Qian Li
- Reproductive Medical Center, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Yu Zhang
- Reproductive Medical Center, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Qian Dou
- Reproductive Medical Center, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
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Navazio L, Formentin E, Cendron L, Szabò I. Chloroplast Calcium Signaling in the Spotlight. FRONTIERS IN PLANT SCIENCE 2020; 11:186. [PMID: 32226434 PMCID: PMC7081724 DOI: 10.3389/fpls.2020.00186] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 02/07/2020] [Indexed: 05/22/2023]
Abstract
Calcium has long been known to regulate the metabolism of chloroplasts, concerning both light and carbon reactions of photosynthesis, as well as additional non photosynthesis-related processes. In addition to undergo Ca2+ regulation, chloroplasts can also influence the overall Ca2+ signaling pathways of the plant cell. Compelling evidence indicate that chloroplasts can generate specific stromal Ca2+ signals and contribute to the fine tuning of cytoplasmic Ca2+ signaling in response to different environmental stimuli. The recent set up of a toolkit of genetically encoded Ca2+ indicators, targeted to different chloroplast subcompartments (envelope, stroma, thylakoids) has helped to unravel the participation of chloroplasts in intracellular Ca2+ handling in resting conditions and during signal transduction. Intra-chloroplast Ca2+ signals have been demonstrated to occur in response to specific environmental stimuli, suggesting a role for these plant-unique organelles in transducing Ca2+-mediated stress signals. In this mini-review we present current knowledge of stimulus-specific intra-chloroplast Ca2+ transients, as well as recent advances in the identification and characterization of Ca2+-permeable channels/transporters localized at chloroplast membranes. In particular, the potential role played by cMCU, a chloroplast-localized member of the mitochondrial calcium uniporter (MCU) family, as component of plant environmental sensing is discussed in detail, taking into account some specific structural features of cMCU. In summary, the recent molecular identification of some players of chloroplast Ca2+ signaling has opened new avenues in this rapidly developing field and will hopefully allow a deeper understanding of the role of chloroplasts in shaping physiological responses in plants.
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Affiliation(s)
- Lorella Navazio
- Department of Biology, University of Padova, Padova, Italy
- Botanical Garden, University of Padova, Padova, Italy
| | - Elide Formentin
- Department of Biology, University of Padova, Padova, Italy
- Botanical Garden, University of Padova, Padova, Italy
| | - Laura Cendron
- Department of Biology, University of Padova, Padova, Italy
| | - Ildikò Szabò
- Department of Biology, University of Padova, Padova, Italy
- Botanical Garden, University of Padova, Padova, Italy
- *Correspondence: Ildikò Szabò,
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35
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Ivanova A, Gill-Hille M, Huang S, Branca RM, Kmiec B, Teixeira PF, Lehtiö J, Whelan J, Murcha MW. A Mitochondrial LYR Protein Is Required for Complex I Assembly. PLANT PHYSIOLOGY 2019; 181:1632-1650. [PMID: 31601645 PMCID: PMC6878026 DOI: 10.1104/pp.19.00822] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/25/2019] [Indexed: 05/04/2023]
Abstract
Complex I biogenesis requires the expression of both nuclear and mitochondrial genes, the import of proteins, cofactor biosynthesis, and the assembly of at least 49 individual subunits. Assembly factors interact with subunits of Complex I but are not part of the final holocomplex. We show that in Arabidopsis (Arabidopsis thaliana), a mitochondrial matrix protein (EMB1793, At1g76060), which we term COMPLEX I ASSEMBLY FACTOR 1 (CIAF1), contains a LYR domain and is required for Complex I assembly. T-DNA insertion mutants of CIAF1 lack Complex I and the Supercomplex I+III. Biochemical characterization shows that the assembly of Complex I is stalled at 650 and 800 kD intermediates in mitochondria isolated from ciaf1 mutant lines.I. Yeast-two-hybrid interaction and complementation assays indicate that CIAF1 specifically interacts with the 23-kD TYKY-1 matrix domain subunit of Complex I and likely plays a role in Fe-S insertion into this subunit. These data show that CIAF1 plays an essential role in assembling the peripheral matrix arm Complex I subunits into the Complex I holoenzyme.
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Affiliation(s)
- Aneta Ivanova
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Perth 6009, Australia
- The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, Australia
| | - Mabel Gill-Hille
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Perth 6009, Australia
- The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, Australia
| | - Shaobai Huang
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Perth 6009, Australia
- The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, Australia
| | - Rui M Branca
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory and Karolinska Institutet, Stockholm 171 77, Sweden
| | - Beata Kmiec
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm SE-106 91, Sweden
| | - Pedro F Teixeira
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm SE-106 91, Sweden
| | - Janne Lehtiö
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory and Karolinska Institutet, Stockholm 171 77, Sweden
| | - James Whelan
- Department of Animal, Plant and Soil Science, School of Life Science, The ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora 3086, Australia
| | - Monika W Murcha
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Perth 6009, Australia
- The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, Australia
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36
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Launay A, Cabassa-Hourton C, Eubel H, Maldiney R, Guivarc’h A, Crilat E, Planchais S, Lacoste J, Bordenave-Jacquemin M, Clément G, Richard L, Carol P, Braun HP, Lebreton S, Savouré A. Proline oxidation fuels mitochondrial respiration during dark-induced leaf senescence in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6203-6214. [PMID: 31504781 PMCID: PMC6859731 DOI: 10.1093/jxb/erz351] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/18/2019] [Indexed: 05/20/2023]
Abstract
Leaf senescence is a form of developmentally programmed cell death that allows the remobilization of nutrients and cellular materials from leaves to sink tissues and organs. Among the catabolic reactions that occur upon senescence, little is known about the role of proline catabolism. In this study, the involvement in dark-induced senescence of proline dehydrogenases (ProDHs), which catalyse the first and rate-limiting step of proline oxidation in mitochondria, was investigated using prodh single- and double-mutants with the help of biochemical, proteomic, and metabolomic approaches. The presence of ProDH2 in mitochondria was confirmed by mass spectrometry and immunogold labelling in dark-induced leaves of Arabidopsis. The prodh1 prodh2 mutant exhibited enhanced levels of most tricarboxylic acid cycle intermediates and free amino acids, demonstrating a role of ProDH in mitochondrial metabolism. We also found evidence of the involvement and the importance of ProDH in respiration, with proline as an alternative substrate, and in remobilization of proline during senescence to generate glutamate and energy that can then be exported to sink tissues and organs.
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Affiliation(s)
- Alban Launay
- Sorbonne Université, CNRS, IRD 242, INRA, PARIS 7, UPEC, Institut d’Ecologie et des Sciences de l’Environnement de Paris, iEES, Paris, France
| | - Cécile Cabassa-Hourton
- Sorbonne Université, CNRS, IRD 242, INRA, PARIS 7, UPEC, Institut d’Ecologie et des Sciences de l’Environnement de Paris, iEES, Paris, France
| | - Holger Eubel
- Institute of Plant Genetics, Plant Proteomics, Leibniz University Hannover, Hannover, Germany
| | - Régis Maldiney
- Sorbonne Université, CNRS, IRD 242, INRA, PARIS 7, UPEC, Institut d’Ecologie et des Sciences de l’Environnement de Paris, iEES, Paris, France
| | - Anne Guivarc’h
- Sorbonne Université, CNRS, IRD 242, INRA, PARIS 7, UPEC, Institut d’Ecologie et des Sciences de l’Environnement de Paris, iEES, Paris, France
| | - Emilie Crilat
- Sorbonne Université, CNRS, IRD 242, INRA, PARIS 7, UPEC, Institut d’Ecologie et des Sciences de l’Environnement de Paris, iEES, Paris, France
| | - Séverine Planchais
- Sorbonne Université, CNRS, IRD 242, INRA, PARIS 7, UPEC, Institut d’Ecologie et des Sciences de l’Environnement de Paris, iEES, Paris, France
| | - Jérôme Lacoste
- Sorbonne Université, CNRS, IRD 242, INRA, PARIS 7, UPEC, Institut d’Ecologie et des Sciences de l’Environnement de Paris, iEES, Paris, France
- Present address: Sorbonne Université, CNRS, Institut de Biologie Paris Seine, IBPS, F-75005 Paris, France
| | - Marianne Bordenave-Jacquemin
- Sorbonne Université, CNRS, IRD 242, INRA, PARIS 7, UPEC, Institut d’Ecologie et des Sciences de l’Environnement de Paris, iEES, Paris, France
| | - Gilles Clément
- Institut Jean-Pierre Bourgin, UMR 1318, INRA-AgroParisTech, Centre INRA Versailles, Versailles Cedex, France
| | - Luc Richard
- Sorbonne Université, CNRS, IRD 242, INRA, PARIS 7, UPEC, Institut d’Ecologie et des Sciences de l’Environnement de Paris, iEES, Paris, France
| | - Pierre Carol
- Sorbonne Université, CNRS, IRD 242, INRA, PARIS 7, UPEC, Institut d’Ecologie et des Sciences de l’Environnement de Paris, iEES, Paris, France
| | - Hans-Peter Braun
- Institute of Plant Genetics, Plant Proteomics, Leibniz University Hannover, Hannover, Germany
| | - Sandrine Lebreton
- Sorbonne Université, CNRS, IRD 242, INRA, PARIS 7, UPEC, Institut d’Ecologie et des Sciences de l’Environnement de Paris, iEES, Paris, France
- Correspondence: or
| | - Arnould Savouré
- Sorbonne Université, CNRS, IRD 242, INRA, PARIS 7, UPEC, Institut d’Ecologie et des Sciences de l’Environnement de Paris, iEES, Paris, France
- Correspondence: or
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37
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Emami H, Kempken F. PRECOCIOUS1 (POCO1), a mitochondrial pentatricopeptide repeat protein affects flowering time in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:265-278. [PMID: 31219634 DOI: 10.1111/tpj.14441] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 06/03/2019] [Accepted: 06/11/2019] [Indexed: 05/24/2023]
Abstract
Flowering is a vital developmental shift in plants from vegetative to reproductive phase. The timing of this shift is regulated by various linked genetic pathways including environmental cues and internal regulation. Here we report a role for an Arabidopsis gene, AT1G15480, which encodes a P-class pentatricopeptide repeat (PPR) protein, affecting flowering time. We show that AT1G15480 is localized to mitochondria. An AT1G15480 T-DNA insertion line exhibits an early-flowering phenotype, which is quite a rare phenotype among PPR mutants. The early-flowering phenotype was observed under both long and short days compared with wild type plants. Genetic complementation confirmed the observed phenotype. We therefore named the PPR protein PRECOCIOUS1 (POCO1). poco1 plants showed lower respiration, ATP content and higher accumulation of superoxide. Importantly, the quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis showed that the expression of FLOWERING LOCUS C (FLC), which is a key floral repressor, was strongly downregulated in the poco1. Likewise, the expression level of the FLC positive regulator ABSCISIC ACID-INSENSITIVE 5 (ABI5) was reduced in the poco1. Consistent with the qRT-PCR results, poco1 plants showed reduced sensitivity to abscisic acid compared with wild type with respect to primary root growth and days to flowering. Furthermore, the poco1 mutation enhances the sensitivity to drought stress. Further analysis showed that POCO1 affects mitochondrial RNA editing. Taken together, our data demonstrate a remarkable function of POCO1 in flowering time and the abscisic acid signalling pathway.
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Affiliation(s)
- Hossein Emami
- Department of Botany, Christian Albrechts University, Olshausenstr. 40, 24098, Kiel, Germany
| | - Frank Kempken
- Department of Botany, Christian Albrechts University, Olshausenstr. 40, 24098, Kiel, Germany
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38
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Abstract
Eukaryotic life has developed a fascinating and highly optimized system for energy transduction: the mitochondrial respiratory chain. Typically composed of five core protein complexes, we now learn from two studies that plant hemi-parasites of the type Viscum cope without Complex I, the entry point of the classical respiratory system.
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Affiliation(s)
- Karin B Busch
- Institute of Molecular Cell Biology, Department of Biology, Westfälische Universität Münster, D-48149 Münster, Germany.
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39
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Ren Z, Fan K, Fang T, Zhang J, Yang L, Wang J, Wang G, Liu Y. Maize Empty Pericarp602 Encodes a P-Type PPR Protein That Is Essential for Seed Development. PLANT & CELL PHYSIOLOGY 2019; 60:1734-1746. [PMID: 31076755 DOI: 10.1093/pcp/pcz083] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/22/2019] [Indexed: 05/23/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins play crucial roles in intron splicing, which is important for RNA maturation. Identification of novel PPR protein with the function of intron splicing would help to understand the RNA splicing mechanism. In this study, we identified the maize empty pericarp602 (emp602) mutants, the mature kernels of which showed empty pericarp phenotype. We cloned the Emp602 gene from emp602 mutants and revealed that Emp602 encodes a mitochondrial-localized P-type PPR protein. We further revealed that Emp602 is specific for the cis-splicing of mitochondrial Nad4 intron 1 and intron 3, and mutation of Emp602 led to the loss of mature Nad4 transcripts. The loss of function of Emp602 nearly damaged the assembly and accumulation of complex I and arrested mitochondria formation, which arrested the seed development. The failed assembly of complex I triggers significant upregulation of Aox expression in emp602 mutants. Transcriptome analysis showed that the expression of mitochondrial-related genes, e.g. the genes associated with mitochondrial inner membrane presequence translocase complex and electron carrier activity, were extensively upregulated in emp602 mutant. These results demonstrate that EMP602 functions in the splicing of Nad4 intron 1 and intron 3, and the loss of function of Emp602 arrested maize seed development by disrupting the mitochondria complex I assembly.
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Affiliation(s)
- Zhenjing Ren
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Center of Seed Science and Technology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Kaijian Fan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Center of Seed Science and Technology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Ting Fang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiaojiao Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianhua Wang
- Center of Seed Science and Technology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunjun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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40
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C�rdoba JP, Fassolari M, Marchetti F, Soto D, Pagnussat GC, Zabaleta E. Different Types Domains are Present in Complex I from Immature Seeds and of CA Adult Plants in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2019; 60:986-998. [PMID: 30668784 PMCID: PMC6498749 DOI: 10.1093/pcp/pcz011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/10/2019] [Indexed: 05/10/2023]
Abstract
Mitochondrial Nicotinamide adenine dinucleotide (NADH) dehydrogenase complex is the first complex of the mitochondrial electron transfer chain. In plants and in a variety of eukaryotes except Opisthokonta, complex I (CI) contains an extra spherical domain called carbonic anhydrase (CA) domain. This domain is thought to be composed of trimers of gamma type CA and CA-like subunits. In Arabidopsis, the CA gene family contains five members (CA1, CA2, CA3, CAL1 and CAL2). The CA domain appears to be crucial for CI assembly and is essential for normal embryogenesis. As CA and CA-like proteins are arranged in trimers to form the CA domain, it is possible for the complex to adopt different arrangements that might be tissue-specific or have specialized functions. In this work, we show that the proportion of specific CI changes in a tissue-specific manner. In immature seeds, CI assembly may be indistinctly dependent on CA1, CA2 or CA3. However, in adult plant tissues (or tissues derived from stem cells, as cell cultures), CA2-dependent CI is clearly the most abundant. This difference might account for specific physiological functions. We present evidence suggesting that CA3 does not interact with any other CA family member. As CA3 was found to interact with CI FRO1 (NDUFS4) subunit, which is located in the matrix arm, this suggests a role for CA3 in assembly and stability of CI.
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Affiliation(s)
- Juan Pablo C�rdoba
- Instituto de Investigaciones Biol�gicas (IIB)-Universidad Nacional de Mar del Plata (UNMdP)-CONICET, Funes 3250 3er nivel, Mar del Plata, Argentina
| | - Marisol Fassolari
- Instituto de Investigaciones Biol�gicas (IIB)-Universidad Nacional de Mar del Plata (UNMdP)-CONICET, Funes 3250 3er nivel, Mar del Plata, Argentina
| | - Fernanda Marchetti
- Instituto de Investigaciones Biol�gicas (IIB)-Universidad Nacional de Mar del Plata (UNMdP)-CONICET, Funes 3250 3er nivel, Mar del Plata, Argentina
| | - D�bora Soto
- Instituto de Investigaciones Biol�gicas (IIB)-Universidad Nacional de Mar del Plata (UNMdP)-CONICET, Funes 3250 3er nivel, Mar del Plata, Argentina
| | - Gabriela C Pagnussat
- Instituto de Investigaciones Biol�gicas (IIB)-Universidad Nacional de Mar del Plata (UNMdP)-CONICET, Funes 3250 3er nivel, Mar del Plata, Argentina
| | - Eduardo Zabaleta
- Instituto de Investigaciones Biol�gicas (IIB)-Universidad Nacional de Mar del Plata (UNMdP)-CONICET, Funes 3250 3er nivel, Mar del Plata, Argentina
- Corresponding author: E-mail, ; Fax, +54 223 475 30 30
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41
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Rovira AG, Smith AG. PPR proteins - orchestrators of organelle RNA metabolism. PHYSIOLOGIA PLANTARUM 2019; 166:451-459. [PMID: 30809817 DOI: 10.1111/ppl.12950] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/21/2019] [Accepted: 02/21/2019] [Indexed: 05/21/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins are important RNA regulators in chloroplasts and mitochondria, aiding in RNA editing, maturation, stabilisation or intron splicing, and in transcription and translation of organellar genes. In this review, we summarise all PPR proteins documented so far in plants and the green alga Chlamydomonas. By further analysis of the known target RNAs from Arabidopsis thaliana PPR proteins, we find that all organellar-encoded complexes are regulated by these proteins, although to differing extents. In particular, the orthologous complexes of NADH dehydrogenase (Complex I) in the mitochondria and NADH dehydrogenase-like (NDH) complex in the chloroplast were the most regulated, with respectively 60 and 28% of all characterised A. thaliana PPR proteins targeting their genes.
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Affiliation(s)
- Aleix Gorchs Rovira
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
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42
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Li H, Guan K, Li X, Ma Y, Zhou S. MFG-E8 induced differences in proteomic profiles in mouse C2C12 cells and its effect on PI3K/Akt and ERK signal pathways. Int J Biol Macromol 2019; 124:681-688. [DOI: 10.1016/j.ijbiomac.2018.11.265] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/27/2018] [Accepted: 11/27/2018] [Indexed: 12/13/2022]
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43
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Takenaka M, Jörg A, Burger M, Haag S. RNA editing mutants as surrogates for mitochondrial SNP mutants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 135:310-321. [PMID: 30599308 DOI: 10.1016/j.plaphy.2018.12.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/13/2018] [Accepted: 12/16/2018] [Indexed: 06/09/2023]
Abstract
In terrestrial plants, RNA editing converts specific cytidines to uridines in mitochondrial and plastidic transcripts. Most of these events appear to be important for proper function of organellar encoded genes, since translated proteins from edited mRNAs show higher similarity with evolutionary conserved polypeptide sequences. So far about 100 nuclear encoded proteins have been characterized as RNA editing factors in plant organelles. Respective RNA editing mutants reduce or lose editing activity at different sites and display various macroscopic phenotypes from pale or albino in the case of chloroplasts to growth retardation or even embryonic lethality. Therefore, RNA editing mutants can be a useful resource of surrogate mutants for organellar encoded genes, especially for mitochondrially encoded genes that it is so far unfeasible to manipulate. However, connections between RNA editing defects and observed phenotypes in the mutants are often hard to elucidate, since RNA editing factors often target multiple RNA sites in different genes simultaneously. In this review article, we summarize the physiological aspects of respective RNA editing mutants and discuss them as surrogate mutants for functional analysis of mitochondrially encoded genes.
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Affiliation(s)
- Mizuki Takenaka
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan.
| | - Anja Jörg
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069, Ulm, Germany
| | - Matthias Burger
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069, Ulm, Germany
| | - Sascha Haag
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069, Ulm, Germany
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44
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Ligas J, Pineau E, Bock R, Huynen MA, Meyer EH. The assembly pathway of complex I in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:447-459. [PMID: 30347487 DOI: 10.1111/tpj.14133] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/09/2018] [Accepted: 10/16/2018] [Indexed: 05/23/2023]
Abstract
All present-day mitochondria originate from a single endosymbiotic event that gave rise to the last eukaryotic common ancestor more than a billion years ago. However, to date, many aspects of mitochondrial evolution have remained unresolved. Comparative genomics and proteomics have revealed a complex evolutionary origin for many mitochondrial components. To understand the evolution of the respiratory chain, we have examined both the components and the mechanisms of the assembly pathway of complex I. Complex I represents the first enzyme in the respiratory chain, and complex I deficiencies have dramatic consequences in both animals and plants. The complex is located in the mitochondrial inner membrane and possesses two arms: one embedded in the inner membrane and one protruding in the matrix. Here, we describe the assembly pathway of complex I in the model plant Arabidopsis thaliana. Using a proteomics approach called complexome profiling, we have resolved the different steps in the assembly process in plants. We propose a model for the stepwise assembly of complex I, including every subunit. We then compare this pathway with the corresponding pathway in humans and find that complex I assembly in plants follows a different, and likely ancestral, pathway compared with the one in humans. We show that the main evolutionary changes in complex I structure and assembly in humans occurred at the level of the membrane arm, whereas the matrix arm remained rather conserved.
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Affiliation(s)
- Joanna Ligas
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Emmanuelle Pineau
- Institut de Biologie Moléculaire des Plantes du CNRS, 12 Rue du Général Zimmer, 67084, Strasbourg, France
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud Centre for Mitochondrial Medicine, Radboud University, Nijmegen, The Netherlands
| | - Etienne H Meyer
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Institut de Biologie Moléculaire des Plantes du CNRS, 12 Rue du Général Zimmer, 67084, Strasbourg, France
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45
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Larosa V, Remacle C. Insights into the respiratory chain and oxidative stress. Biosci Rep 2018; 38:BSR20171492. [PMID: 30201689 PMCID: PMC6167499 DOI: 10.1042/bsr20171492] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 08/15/2018] [Accepted: 09/05/2018] [Indexed: 01/13/2023] Open
Abstract
Reactive oxygen species (ROS) are highly reactive reduced oxygen molecules that result from aerobic metabolism. The common forms are the superoxide anion (O2∙-) and hydrogen peroxide (H2O2) and their derived forms, hydroxyl radical (HO∙) and hydroperoxyl radical (HOO∙). Their production sites in mitochondria are reviewed. Even though being highly toxic products, ROS seem important in transducing information from dysfunctional mitochondria. Evidences of signal transduction mediated by ROS in mitochondrial deficiency contexts are then presented in different organisms such as yeast, mammals or photosynthetic organisms.
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Affiliation(s)
- Véronique Larosa
- Genetics and Physiology of Microalgae, UR InBios/Phytosystems, Chemin de la Vallée, 4, University of Liège, Liège 4000, Belgium
| | - Claire Remacle
- Genetics and Physiology of Microalgae, UR InBios/Phytosystems, Chemin de la Vallée, 4, University of Liège, Liège 4000, Belgium
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46
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da Fonseca-Pereira P, Silva WB, Araújo WL, Nunes-Nesi A. How Does European Mistletoe Survive Without Complex I? TRENDS IN PLANT SCIENCE 2018; 23:847-850. [PMID: 30097375 DOI: 10.1016/j.tplants.2018.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/23/2018] [Accepted: 07/26/2018] [Indexed: 06/08/2023]
Abstract
Two independent but complementary studies recently provided the first biochemical proof of the complete absence of mitochondrial Complex I in a multicellular eukaryote. The mitochondrial electron transport chain (mETC) of the hemiparasitic European mistletoe (Viscum album) displays dramatic rearrangements of its components, most likely reflecting its parasitic lifestyle.
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Affiliation(s)
- Paula da Fonseca-Pereira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil; Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Willian Batista Silva
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil; Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil; Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.
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Lorenz C, Brandt S, Borisjuk L, Rolletschek H, Heinzel N, Tohge T, Fernie AR, Braun HP, Hildebrandt TM. The Role of Persulfide Metabolism During Arabidopsis Seed Development Under Light and Dark Conditions. FRONTIERS IN PLANT SCIENCE 2018; 9:1381. [PMID: 30283487 PMCID: PMC6156424 DOI: 10.3389/fpls.2018.01381] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/30/2018] [Indexed: 05/25/2023]
Abstract
The sulfur dioxygenase ETHE1 oxidizes persulfides in the mitochondrial matrix and is involved in the degradation of L-cysteine and hydrogen sulfide. ETHE1 has an essential but as yet undefined function in early embryo development of Arabidopsis thaliana. In leaves, ETHE1 is strongly induced by extended darkness and participates in the use of amino acids as alternative respiratory substrates during carbohydrate starvation. Thus, we tested the effect of darkness on seed development in an ETHE1 deficient mutant in comparison to the wild type. Since ETHE1 knock-out is embryo lethal, the knock-down line ethe1-1 with about 1% residual sulfur dioxygenase activity was used for this study. We performed phenotypic analysis, metabolite profiling and comparative proteomics in order to investigate the general effect of extended darkness on seed metabolism and further define the specific function of the mitochondrial sulfur dioxygenase ETHE1 in seeds. Shading of the siliques had no morphological effect on embryogenesis in wild type plants. However, the developmental delay that was already visible in ethe1-1 seeds under control conditions was further enhanced in the darkness. Dark conditions strongly affected seed quality parameters of both wild type and mutant plants. The effect of ETHE1 knock-down on amino acid profiles was clearly different from that found in leaves indicating that in seeds persulfide oxidation interacts with alanine and glycine rather than branched-chain amino acid metabolism. Sulfur dioxygenase deficiency led to defects in endosperm development possibly due to alterations in the cellularization process. In addition, we provide evidence for a potential role of persulfide metabolism in abscisic acid (ABA) signal transduction in seeds. We conclude that the knock-down of ETHE1 causes metabolic re-arrangements in seeds that differ from those in leaves. Putative mechanisms that cause the aberrant endosperm and embryo development are discussed.
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Affiliation(s)
- Christin Lorenz
- Department of Plant Proteomics, Institute of Plant Genetics, Leibniz University Hannover, Hanover, Germany
| | - Saskia Brandt
- Department of Plant Proteomics, Institute of Plant Genetics, Leibniz University Hannover, Hanover, Germany
| | - Ljudmilla Borisjuk
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Hardy Rolletschek
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Nicolas Heinzel
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | | | - Hans-Peter Braun
- Department of Plant Proteomics, Institute of Plant Genetics, Leibniz University Hannover, Hanover, Germany
| | - Tatjana M. Hildebrandt
- Department of Plant Proteomics, Institute of Plant Genetics, Leibniz University Hannover, Hanover, Germany
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Podgórska A, Ostaszewska-Bugajska M, Tarnowska A, Burian M, Borysiuk K, Gardeström P, Szal B. Nitrogen Source Dependent Changes in Central Sugar Metabolism Maintain Cell Wall Assembly in Mitochondrial Complex I-Defective frostbite1 and Secondarily Affect Programmed Cell Death. Int J Mol Sci 2018; 19:ijms19082206. [PMID: 30060552 PMCID: PMC6121878 DOI: 10.3390/ijms19082206] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/20/2018] [Accepted: 07/24/2018] [Indexed: 12/13/2022] Open
Abstract
For optimal plant growth, carbon and nitrogen availability needs to be tightly coordinated. Mitochondrial perturbations related to a defect in complex I in the Arabidopsis thalianafrostbite1 (fro1) mutant, carrying a point mutation in the 8-kD Fe-S subunit of NDUFS4 protein, alter aspects of fundamental carbon metabolism, which is manifested as stunted growth. During nitrate nutrition, fro1 plants showed a dominant sugar flux toward nitrogen assimilation and energy production, whereas cellulose integration in the cell wall was restricted. However, when cultured on NH4+ as the sole nitrogen source, which typically induces developmental disorders in plants (i.e., the ammonium toxicity syndrome), fro1 showed improved growth as compared to NO3− nourishing. Higher energy availability in fro1 plants was correlated with restored cell wall assembly during NH4+ growth. To determine the relationship between mitochondrial complex I disassembly and cell wall-related processes, aspects of cell wall integrity and sugar and reactive oxygen species signaling were analyzed in fro1 plants. The responses of fro1 plants to NH4+ treatment were consistent with the inhibition of a form of programmed cell death. Resistance of fro1 plants to NH4+ toxicity coincided with an absence of necrotic lesion in plant leaves.
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Affiliation(s)
- Anna Podgórska
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Monika Ostaszewska-Bugajska
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Agata Tarnowska
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Maria Burian
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Klaudia Borysiuk
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Per Gardeström
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-90187 Umeå, Sweden, .
| | - Bożena Szal
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096 Warsaw, Poland.
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Thal B, Braun HP, Eubel H. Proteomic analysis dissects the impact of nodulation and biological nitrogen fixation on Vicia faba root nodule physiology. PLANT MOLECULAR BIOLOGY 2018; 97:233-251. [PMID: 29779088 DOI: 10.1007/s11103-018-0736-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 05/08/2018] [Indexed: 05/25/2023]
Abstract
Symbiotic nitrogen fixation in root nodules of legumes is a highly important biological process which is only poorly understood. Root nodule metabolism differs from that of roots. Differences in root and nodule metabolism are expressed by altered protein abundances and amenable to quantitative proteome analyses. Differences in the proteomes may either be tissue specific and related to the presence of temporary endosymbionts (the bacteroids) or related to nitrogen fixation activity. An experimental setup including WT bacterial strains and strains not able to conduct symbiotic nitrogen fixation as well as root controls enables identification of tissue and nitrogen fixation specific proteins. Root nodules are specialized plant organs housing and regulating the mutual symbiosis of legumes with nitrogen fixing rhizobia. As such, these organs fulfill unique functions in plant metabolism. Identifying the proteins required for the metabolic reactions of nitrogen fixation and those merely involved in sustaining the rhizobia:plant symbiosis, is a challenging task and requires an experimental setup which allows to differentiate between these two physiological processes. Here, quantitative proteome analyses of nitrogen fixing and non-nitrogen fixing nodules as well as fertilized and non-fertilized roots were performed using Vicia faba and Rhizobium leguminosarum. Pairwise comparisons revealed altered enzyme abundance between active and inactive nodules. Similarly, general differences between nodules and root tissue were observed. Together, these results allow distinguishing the proteins directly involved in nitrogen fixation from those related to nodulation. Further observations relate to the control of nodulation by hormones and provide supportive evidence for the previously reported correlation of nitrogen and sulfur fixation in these plant organs. Additionally, data on altered protein abundance relating to alanine metabolism imply that this amino acid may be exported from the symbiosomes of V. faba root nodules in addition to ammonia. Data are available via ProteomeXchange with identifier PXD008548.
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Affiliation(s)
- Beate Thal
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hanover, Germany
| | - Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hanover, Germany
| | - Holger Eubel
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hanover, Germany.
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Senkler J, Rugen N, Eubel H, Hegermann J, Braun HP. Absence of Complex I Implicates Rearrangement of the Respiratory Chain in European Mistletoe. Curr Biol 2018; 28:1606-1613.e4. [PMID: 29731306 DOI: 10.1016/j.cub.2018.03.050] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/31/2018] [Accepted: 03/21/2018] [Indexed: 01/06/2023]
Abstract
The mitochondrial oxidative phosphorylation (OXPHOS) system, which is based on the presence of five protein complexes, is in the very center of cellular ATP production. Complexes I to IV are components of the respiratory electron transport chain that drives proton translocation across the inner mitochondrial membrane. The resulting proton gradient is used by complex V (the ATP synthase complex) for the phosphorylation of ADP. Occurrence of complexes I to V is highly conserved in eukaryotes, with exceptions being restricted to unicellular parasites that take up energy-rich compounds from their hosts. Here we present biochemical evidence that the European mistletoe (Viscum album), an obligate semi-parasite living on branches of trees, has a highly unusual OXPHOS system. V. album mitochondria completely lack complex I and have greatly reduced amounts of complexes II and V. At the same time, the complexes III and IV form remarkably stable respiratory supercomplexes. Furthermore, complexome profiling revealed the presence of 150 kDa complexes that include type II NAD(P)H dehydrogenases and an alternative oxidase. Although the absence of complex I genes in mitochondrial genomes of mistletoe species has recently been reported, this is the first biochemical proof that these genes have not been transferred to the nuclear genome and that this respiratory complex indeed is not assembled. As a consequence, the whole respiratory chain is remodeled. Our results demonstrate that, in the context of parasitism, multicellular life can cope with lack of one of the OXPHOS complexes and give new insights into the life strategy of mistletoe species.
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Affiliation(s)
- Jennifer Senkler
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
| | - Nils Rugen
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
| | - Holger Eubel
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
| | - Jan Hegermann
- Institut für Funktionelle und Angewandte Anatomie, Medizinische Hochschule Hannover, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany.
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