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Caubrière D, Moseler A, Rouhier N, Couturier J. Diversity and roles of cysteine desulfurases in photosynthetic organisms. J Exp Bot 2023; 74:3345-3360. [PMID: 36861318 DOI: 10.1093/jxb/erad065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/22/2023] [Indexed: 06/08/2023]
Abstract
As sulfur is part of many essential protein cofactors such as iron-sulfur clusters, molybdenum cofactors, or lipoic acid, its mobilization from cysteine represents a fundamental process. The abstraction of the sulfur atom from cysteine is catalysed by highly conserved pyridoxal 5'-phosphate-dependent enzymes called cysteine desulfurases. The desulfuration of cysteine leads to the formation of a persulfide group on a conserved catalytic cysteine and the concomitant release of alanine. Sulfur is then transferred from cysteine desulfurases to different targets. Numerous studies have focused on cysteine desulfurases as sulfur-extracting enzymes for iron-sulfur cluster synthesis in mitochondria and chloroplasts but also for molybdenum cofactor sulfuration in the cytosol. Despite this, knowledge about the involvement of cysteine desulfurases in other pathways is quite rudimentary, particularly in photosynthetic organisms. In this review, we summarize current understanding of the different groups of cysteine desulfurases and their characteristics in terms of primary sequence, protein domain architecture, and subcellular localization. In addition, we review the roles of cysteine desulfurases in different fundamental pathways and highlight the gaps in our knowledge to encourage future work on unresolved issues especially in photosynthetic organisms.
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Affiliation(s)
| | - Anna Moseler
- Institute of Crop Science and Resource Conservation (INRES) - Chemical Signalling, University of Bonn, 53113 Bonn, Germany
| | | | - Jérémy Couturier
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France
- Institut Universitaire de France, F-75000, Paris, France
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2
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Wang R, Wang Z, Lu H. Separation methods for system-wide profiling of protein terminome. Proteomics 2023; 23:e2100374. [PMID: 35997653 DOI: 10.1002/pmic.202100374] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 11/10/2022]
Abstract
Protein N- and C-termini have specific biochemical properties and functions. They play vital roles in various biological processes, such as protein stability and localization. In addition, post-translational modifications and proteolytic processing generate different proteoforms at protein termini. In recent years, terminomics has attracted significant attention, and numerous strategies have been developed to achieve high-throughput and global terminomics analysis. This review summarizes the recent protein N-termini and C-termini enrichment methods and their application in different samples. We also look ahead further application of terminomics in profiling protease substrates and discovery of disease biomarkers and therapeutic targets.
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Affiliation(s)
- Rui Wang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Zhongjie Wang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Haojie Lu
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China.,Department of Chemistry and Key Laboratory of Glycoconjugates Research Ministry of Public Health, Fudan University, Shanghai, People's Republic of China
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3
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Meinnel T, Giglione C. N-terminal modifications, the associated processing machinery, and their evolution in plastid-containing organisms. J Exp Bot 2022; 73:6013-6033. [PMID: 35768189 DOI: 10.1093/jxb/erac290] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
The N-terminus is a frequent site of protein modifications. Referring primarily to knowledge gained from land plants, here we review the modifications that change protein N-terminal residues and provide updated information about the associated machinery, including that in Archaeplastida. These N-terminal modifications include many proteolytic events as well as small group additions such as acylation or arginylation and oxidation. Compared with that of the mitochondrion, the plastid-dedicated N-terminal modification landscape is far more complex. In parallel, we extend this review to plastid-containing Chromalveolata including Stramenopiles, Apicomplexa, and Rhizaria. We report a well-conserved machinery, especially in the plastid. Consideration of the two most abundant proteins on Earth-Rubisco and actin-reveals the complexity of N-terminal modification processes. The progressive gene transfer from the plastid to the nuclear genome during evolution is exemplified by the N-terminus modification machinery, which appears to be one of the latest to have been transferred to the nuclear genome together with crucial major photosynthetic landmarks. This is evidenced by the greater number of plastid genes in Paulinellidae and red algae, the most recent and fossil recipients of primary endosymbiosis.
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Affiliation(s)
- Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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4
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Liu Z, Hartman S, van Veen H, Zhang H, Leeggangers HACF, Martopawiro S, Bosman F, de Deugd F, Su P, Hummel M, Rankenberg T, Hassall KL, Bailey-Serres J, Theodoulou FL, Voesenek LACJ, Sasidharan R. Ethylene augments root hypoxia tolerance via growth cessation and reactive oxygen species amelioration. Plant Physiol 2022; 190:1365-1383. [PMID: 35640551 PMCID: PMC9516759 DOI: 10.1093/plphys/kiac245] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/29/2022] [Indexed: 05/20/2023]
Abstract
Flooded plants experience impaired gas diffusion underwater, leading to oxygen deprivation (hypoxia). The volatile plant hormone ethylene is rapidly trapped in submerged plant cells and is instrumental for enhanced hypoxia acclimation. However, the precise mechanisms underpinning ethylene-enhanced hypoxia survival remain unclear. We studied the effect of ethylene pretreatment on hypoxia survival of Arabidopsis (Arabidopsis thaliana) primary root tips. Both hypoxia itself and re-oxygenation following hypoxia are highly damaging to root tip cells, and ethylene pretreatments reduced this damage. Ethylene pretreatment alone altered the abundance of transcripts and proteins involved in hypoxia responses, root growth, translation, and reactive oxygen species (ROS) homeostasis. Through imaging and manipulating ROS abundance in planta, we demonstrated that ethylene limited excessive ROS formation during hypoxia and subsequent re-oxygenation and improved oxidative stress survival in a PHYTOGLOBIN1-dependent manner. In addition, we showed that root growth cessation via ethylene and auxin occurred rapidly and that this quiescence behavior contributed to enhanced hypoxia tolerance. Collectively, our results show that the early flooding signal ethylene modulates a variety of processes that all contribute to hypoxia survival.
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Affiliation(s)
| | | | | | - Hongtao Zhang
- Plant Sciences and the Bioeconomy, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Hendrika A C F Leeggangers
- Plant-Environment Signaling, Institute of Environmental Biology, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - Shanice Martopawiro
- Plant-Environment Signaling, Institute of Environmental Biology, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - Femke Bosman
- Plant-Environment Signaling, Institute of Environmental Biology, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - Florian de Deugd
- Plant-Environment Signaling, Institute of Environmental Biology, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - Peng Su
- Plant-Environment Signaling, Institute of Environmental Biology, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - Maureen Hummel
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California 92521, USA
| | - Tom Rankenberg
- Plant-Environment Signaling, Institute of Environmental Biology, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - Kirsty L Hassall
- Intelligent Data Ecosystems, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Julia Bailey-Serres
- Plant-Environment Signaling, Institute of Environmental Biology, Utrecht University, Utrecht, 3584 CH, The Netherlands
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California 92521, USA
| | | | - Laurentius A C J Voesenek
- Plant-Environment Signaling, Institute of Environmental Biology, Utrecht University, Utrecht, 3584 CH, The Netherlands
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Wang X, Davanture M, Zivy M, Bailly C, Nambara E, Corbineau F. Label-Free Quantitative Proteomics Reveal the Involvement of PRT6 in Arabidopsis thaliana Seed Responsiveness to Ethylene. Int J Mol Sci 2022; 23:9352. [PMID: 36012613 DOI: 10.3390/ijms23169352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
In Arabidopsis thaliana, the breaking of seed dormancy in wild type (Col-0) by ethylene at 100 μL L-1 required at least 30 h application. A mutant of the proteolytic N-degron pathway, lacking the E3 ligase PROTEOLYSIS 6 (PRT6), was investigated for its role in ethylene-triggered changes in proteomes during seed germination. Label-free quantitative proteomics was carried out on dormant wild type Col-0 and prt6 seeds treated with (+) or without (-) ethylene. After 16 h, 1737 proteins were identified, but none was significantly different in protein levels in response to ethylene. After longer ethylene treatment (30 h), 2552 proteins were identified, and 619 Differentially Expressed Proteins (DEPs) had significant differences in protein abundances between ethylene treatments and genotypes. In Col, 587 DEPs were enriched for those involved in signal perception and transduction, reserve mobilization and new material generation, which potentially contributed to seed germination. DEPs up-regulated by ethylene in Col included S-adenosylmethionine synthase 1, methionine adenosyltransferase 3 and ACC oxidase involved in ethylene synthesis and of Pyrabactin Resistance1 acting as an ABA receptor, while DEPs down-regulated by ethylene in Col included aldehyde oxidase 4 involved in ABA synthesis. In contrast, in prt6 seeds, ethylene did not result in strong proteomic changes with only 30 DEPs. Taken together, the present work demonstrates that the proteolytic N-degron pathway is essential for ethylene-mediated reprogramming of seed proteomes during germination.
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Theodoulou FL, Orosa-Puente B, Trujillo M, Rubio V. Plant proteostasis: a proven and promising target for crop improvement. Essays Biochem 2022; 66:75-85. [PMID: 35929615 DOI: 10.1042/EBC20210078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 11/17/2022]
Abstract
The Green Revolution of the 1960s accomplished dramatic increases in crop yields through genetic improvement, chemical fertilisers, irrigation, and mechanisation. However, the current trajectory of population growth, against a backdrop of climate change and geopolitical unrest, predicts that agricultural production will be insufficient to ensure global food security in the next three decades. Improvements to crops that go beyond incremental gains are urgently needed. Plant biology has also undergone a revolution in recent years, through the development and application of powerful technologies including genome sequencing, a pantheon of 'omics techniques, precise genome editing, and step changes in structural biology and microscopy. Proteostasis - the collective processes that control the protein complement of the cell, comprising synthesis, modification, localisation, and degradation - is a field that has benefitted from these advances. This special issue presents a selection of the latest research in this vibrant field, with a particular focus on protein degradation. In the current article, we highlight the diverse and widespread contributions of plant proteostasis to agronomic traits, suggest opportunities and strategies to manipulate different elements of proteostatic mechanisms for crop improvement, and discuss the challenges involved in bringing these ideas into practice.
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Willems P, Ndah E, Jonckheere V, Van Breusegem F, Van Damme P. To New Beginnings: Riboproteogenomics Discovery of N-Terminal Proteoforms in Arabidopsis Thaliana. Front Plant Sci 2022; 12:778804. [PMID: 35069635 PMCID: PMC8770321 DOI: 10.3389/fpls.2021.778804] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/18/2021] [Indexed: 06/14/2023]
Abstract
Alternative translation initiation is a widespread event in biology that can shape multiple protein forms or proteoforms from a single gene. However, the respective contribution of alternative translation to protein complexity remains largely enigmatic. By complementary ribosome profiling and N-terminal proteomics (i.e., riboproteogenomics), we provide clear-cut evidence for ~90 N-terminal proteoform pairs shaped by (alternative) translation initiation in Arabidopsis thaliana. Next to several cases additionally confirmed by directed mutagenesis, identified alternative protein N-termini follow the enzymatic rules of co-translational N-terminal protein acetylation and initiator methionine removal. In contrast to other eukaryotic models, N-terminal acetylation in plants cannot generally be considered as a proxy of translation initiation because of its posttranslational occurrence on mature proteolytic neo-termini (N-termini) localized in the chloroplast stroma. Quantification of N-terminal acetylation revealed differing co- vs. posttranslational N-terminal acetylation patterns. Intriguingly, our data additionally hints to alternative translation initiation serving as a common mechanism to supply protein copies in multiple cellular compartments, as alternative translation sites are often in close proximity to cleavage sites of N-terminal transit sequences of nuclear-encoded chloroplastic and mitochondrial proteins. Overall, riboproteogenomics screening enables the identification of (differential localized) N-terminal proteoforms raised upon alternative translation.
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Affiliation(s)
- Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Vlaams Instituut voor Biotechnologie (VIB)-Center for Plant Systems Biology, Ghent, Belgium
| | - Elvis Ndah
- integrative Riboproteogenomics, Interactomics and Proteomics Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Veronique Jonckheere
- integrative Riboproteogenomics, Interactomics and Proteomics Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Vlaams Instituut voor Biotechnologie (VIB)-Center for Plant Systems Biology, Ghent, Belgium
| | - Petra Van Damme
- integrative Riboproteogenomics, Interactomics and Proteomics Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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8
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Heidorn-Czarna M, Maziak A, Janska H. Protein Processing in Plant Mitochondria Compared to Yeast and Mammals. Front Plant Sci 2022; 13:824080. [PMID: 35185991 PMCID: PMC8847149 DOI: 10.3389/fpls.2022.824080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/12/2022] [Indexed: 05/02/2023]
Abstract
Limited proteolysis, called protein processing, is an essential post-translational mechanism that controls protein localization, activity, and in consequence, function. This process is prevalent for mitochondrial proteins, mainly synthesized as precursor proteins with N-terminal sequences (presequences) that act as targeting signals and are removed upon import into the organelle. Mitochondria have a distinct and highly conserved proteolytic system that includes proteases with sole function in presequence processing and proteases, which show diverse mitochondrial functions with limited proteolysis as an additional one. In virtually all mitochondria, the primary processing of N-terminal signals is catalyzed by the well-characterized mitochondrial processing peptidase (MPP). Subsequently, a second proteolytic cleavage occurs, leading to more stabilized residues at the newly formed N-terminus. Lately, mitochondrial proteases, intermediate cleavage peptidase 55 (ICP55) and octapeptidyl protease 1 (OCT1), involved in proteolytic cleavage after MPP and their substrates have been described in the plant, yeast, and mammalian mitochondria. Mitochondrial proteins can also be processed by removing a peptide from their N- or C-terminus as a maturation step during insertion into the membrane or as a regulatory mechanism in maintaining their function. This type of limited proteolysis is characteristic for processing proteases, such as IMP and rhomboid proteases, or the general mitochondrial quality control proteases ATP23, m-AAA, i-AAA, and OMA1. Identification of processing protease substrates and defining their consensus cleavage motifs is now possible with the help of large-scale quantitative mass spectrometry-based N-terminomics, such as combined fractional diagonal chromatography (COFRADIC), charge-based fractional diagonal chromatography (ChaFRADIC), or terminal amine isotopic labeling of substrates (TAILS). This review summarizes the current knowledge on the characterization of mitochondrial processing peptidases and selected N-terminomics techniques used to uncover protease substrates in the plant, yeast, and mammalian mitochondria.
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Wang Y, Cheng X, Yang T, Su Y, Lin S, Zhang S, Zhang Z. Nitrogen-Regulated Theanine and Flavonoid Biosynthesis in Tea Plant Roots: Protein-Level Regulation Revealed by Multiomics Analyses. J Agric Food Chem 2021; 69:10002-10016. [PMID: 34406741 DOI: 10.1021/acs.jafc.1c02589] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Theanine and flavonoids (especially proanthocyanidins) are the most important and abundant secondary metabolites synthesized in the roots of tea plants. Nitrogen promotes theanine and represses flavonoid biosynthesis in tea plant roots, but the underlying mechanism is still elusive. Here, we analyzed theanine and flavonoid metabolism in tea plant roots under nitrogen deficiency and explored the regulatory mechanism using proteome and ubiquitylome profiling together with transcriptome data. Differentially expressed proteins responsive to nitrogen deficiency were identified and found to be enriched in flavonoid, nitrogen, and amino acid metabolism pathways. The proteins responding to nitrogen deficiency at the transcriptional level, translational level, and both transcriptional and translational levels were classified. Nitrogen-deficiency-responsive and ubiquitinated proteins were further identified. Our results showed that most genes encoding enzymes in the theanine synthesis pathway, such as CsAlaDC, CsGDH, and CsGOGATs, were repressed by nitrogen deficiency at transcriptional and/or protein level(s). While a large number of enzymes in flavonoid metabolism were upregulated at the transcriptional and/or translational level(s). Importantly, the ubiquitylomic analysis identified important proteins, especially the hub enzymes in theanine and flavonoid biosynthesis, such as CsAlaDC, CsTSI, CsGS, CsPAL, and CsCHS, modified by ubiquitination. This study provided novel insights into the regulation of theanine and flavonoid biosynthesis and will contribute to future studies on the post-translational regulation of secondary metabolism in tea plants.
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Affiliation(s)
- Yan Wang
- State Key Laboratory of Tea Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, People's Republic of China
| | - Xunmin Cheng
- State Key Laboratory of Tea Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, People's Republic of China
| | - Tianyuan Yang
- State Key Laboratory of Tea Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, People's Republic of China
| | - Yanlei Su
- State Key Laboratory of Tea Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, People's Republic of China
| | - Shijia Lin
- State Key Laboratory of Tea Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, People's Republic of China
| | - Shupei Zhang
- State Key Laboratory of Tea Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, People's Republic of China
| | - Zhaoliang Zhang
- State Key Laboratory of Tea Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, People's Republic of China
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Chen Y, Inzé D, Vanhaeren H. Post-translational modifications regulate the activity of the growth-restricting protease DA1. J Exp Bot 2021; 72:3352-3366. [PMID: 33587751 DOI: 10.1093/jxb/erab062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/06/2021] [Indexed: 06/12/2023]
Abstract
Plants are a primary food source and can form the basis for renewable energy resources. The final size of their organs is by far the most important trait to consider when seeking increased plant productivity. Being multicellular organisms, plant organ size is mainly determined by the coordination between cell proliferation and cell expansion. The protease DA1 limits the duration of cell proliferation and thereby restricts final organ size. Since its initial identification as a negative regulator of organ growth, various transcriptional regulators of DA1, but also interacting proteins, have been identified. These interactors include cleavage substrates of DA1, and also proteins that modulate the activity of DA1 through post-translational modifications, such as ubiquitination, deubiquitination, and phosphorylation. In addition, many players in the DA1 pathway display conserved phenotypes in other dicot and even monocot species. In this review, we provide a timely overview of the complex, but intriguing, molecular mechanisms that fine-tune the activity of DA1 and therefore final organ size. Moreover, we lay out a roadmap to identify and characterize substrates of proteases and frame the substrate cleavage events in their biological context.
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Affiliation(s)
- Ying Chen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Hannes Vanhaeren
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
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Giglione C, Meinnel T. Evolution-Driven Versatility of N Terminal Acetylation in Photoautotrophs. Trends Plant Sci 2021; 26:375-391. [PMID: 33384262 DOI: 10.1016/j.tplants.2020.11.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 10/27/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
N terminal protein α-acetylation (NTA) is a pervasive protein modification that has recently attracted renewed interest. Early studies on NTA were mostly conducted in yeast and metazoans, providing a detailed portrait of the modification, which was indirectly applied to all eukaryotes. However, new findings originating from photosynthetic organisms have expanded our knowledge of this modification, revealing strong similarities as well as idiosyncratic features. Here, we review the most recent advances on NTA and its dedicated machinery in photosynthetic organisms. We discuss the cytosolic and unique plastid NTA machineries and their critical biological roles in development, stress responses, protein translocation, and stability. These new findings suggest that the multitasking plastid and cytosolic machineries evolved to support the specific needs of photoautotrophs.
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Affiliation(s)
- Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
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Manrique-Gil I, Sánchez-Vicente I, Torres-Quezada I, Lorenzo O. Nitric oxide function during oxygen deprivation in physiological and stress processes. J Exp Bot 2021; 72:904-916. [PMID: 32976588 PMCID: PMC7876777 DOI: 10.1093/jxb/eraa442] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/16/2020] [Indexed: 05/07/2023]
Abstract
Plants are aerobic organisms that have evolved to maintain specific requirements for oxygen (O2), leading to a correct respiratory energy supply during growth and development. There are certain plant developmental cues and biotic or abiotic stress responses where O2 is scarce. This O2 deprivation known as hypoxia may occur in hypoxic niches of plant-specific tissues and during adverse environmental cues such as pathogen attack and flooding. In general, plants respond to hypoxia through a complex reprogramming of their molecular activities with the aim of reducing the impact of stress on their physiological and cellular homeostasis. This review focuses on the fine-tuned regulation of hypoxia triggered by a network of gaseous compounds that includes O2, ethylene, and nitric oxide. In view of recent scientific advances, we summarize the molecular mechanisms mediated by phytoglobins and by the N-degron proteolytic pathway, focusing on embryogenesis, seed imbibition, and germination, and also specific structures, most notably root apical and shoot apical meristems. In addition, those biotic and abiotic stresses that comprise hypoxia are also highlighted.
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Affiliation(s)
- Isabel Manrique-Gil
- Departamento de Botánica y Fisiología Vegetal, Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Facultad de Biología, Universidad de Salamanca. C/ Río Duero 12, Salamanca, Spain
| | - Inmaculada Sánchez-Vicente
- Departamento de Botánica y Fisiología Vegetal, Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Facultad de Biología, Universidad de Salamanca. C/ Río Duero 12, Salamanca, Spain
| | - Isabel Torres-Quezada
- Departamento de Botánica y Fisiología Vegetal, Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Facultad de Biología, Universidad de Salamanca. C/ Río Duero 12, Salamanca, Spain
| | - Oscar Lorenzo
- Departamento de Botánica y Fisiología Vegetal, Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Facultad de Biología, Universidad de Salamanca. C/ Río Duero 12, Salamanca, Spain
- Correspondence:
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Abstract
INTRODUCTION The N-terminus of a protein can encode several protein features, including its half-live and its localization. As the proteomics field remains dominated by bottom-up approaches and as N-terminal peptides only account for a fraction of all analyzable peptides, there is a need for their enrichment prior to analysis. COFRADIC, TAILS, and the subtiligase method were among the first N-terminomics methods developed, and several variants and novel methods were introduced that often reduce processing time and/or the amount of material required. AREAS COVERED We present an overview of how the field of N-terminomics developed, including a discussion of the founding methods, several updates made to these and introduce newer methods such as TMPP-labeling, biotin-based methods besides some necessary improvements in data analysis. EXPERT OPINION N-terminomic methods remain being used and improved methods are published however, more efficient use of contemporary mass spectrometers, promising data-independent approaches, and mass spectrometry-free single peptide or protein sequences may threat the N-terminomics field.
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Affiliation(s)
- Annelies Bogaert
- VIB Center for Medical Biotechnology , Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University , Ghent, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology , Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University , Ghent, Belgium
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Mooney BC, Graciet E. A simple and efficient Agrobacterium-mediated transient expression system to dissect molecular processes in Brassica rapa and Brassica napus. Plant Direct 2020; 4:e00237. [PMID: 32775949 PMCID: PMC7403836 DOI: 10.1002/pld3.237] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/05/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
The family Brassicaceae is a source of important crop species, including Brassica napus (oilseed rape), Brassica oleracea, and B. rapa, that is used globally for oil production or as a food source (e.g., pak choi or turnip). However, despite advances in recent years, including genome sequencing, a lack of established tools tailored to the study of Brassica crop species has impeded efforts to understand their molecular processes in greater detail. Here, we describe the use of a simple Agrobacterium-mediated transient expression system adapted to B. rapa and B. napus that could facilitate study of molecular and biochemical events in these species. We also demonstrate the use of this method to characterize the N-degron pathway of protein degradation in B. rapa. The N-degron pathway is a subset of the ubiquitin-proteasome system and represents a mechanism through which proteins may be targeted for degradation based on the identity of their N-terminal amino acid residue. Interestingly, N-degron-mediated processes in plants have been implicated in the regulation of traits with potential agronomic importance, including the responses to pathogens and to abiotic stresses such as flooding tolerance. The stability of transiently expressed N-degron reporter proteins in B. rapa indicates that its N-degron pathway is highly conserved with that of Arabidopsis thaliana. These findings highlight the utility of Agrobacterium-mediated transient expression in B. rapa and B. napus and establish a framework to investigate the N-degron pathway and its roles in regulating agronomical traits in these species. SIGNIFICANCE STATEMENT We describe an Agrobacterium-mediated transient expression system applicable to Brassica crops and demonstrate its utility by identifying the destabilizing residues of the N-degron pathway in B. rapa. As the N-degron pathway functions as an integrator of environmental signals, this study could facilitate efforts to improve the robustness of Brassica crops.
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Affiliation(s)
| | - Emmanuelle Graciet
- Department of BiologyMaynooth UniversityMaynoothIreland
- Kathleen Lonsdale Institute for Human Health ResearchMaynooth UniversityMaynoothIreland
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15
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Ju S, Kwon Y, Kim JM, Park D, Lee S, Lee JW, Hwang CS, Lee C. iNrich, Rapid and Robust Method to Enrich N-Terminal Proteome in a Highly Multiplexed Platform. Anal Chem 2020; 92:6462-6469. [DOI: 10.1021/acs.analchem.9b05653] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Shinyeong Ju
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Yumi Kwon
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Jeong-Mok Kim
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Daechan Park
- Department of Biological Sciences, Ajou University, Suwon, Gyeonggi 16499, Republic of Korea
| | - Seonjeong Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
| | - Jin-Won Lee
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Cheol-Sang Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
- Department of Converging Science and Technology, KHU-KIST, Kyung Hee University, Seoul 02447, Republic of Korea
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16
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Thouly C, Le Masson M, Lai X, Carles CC, Vachon G. Unwinding BRAHMA Functions in Plants. Genes (Basel) 2020; 11:genes11010090. [PMID: 31941094 PMCID: PMC7017052 DOI: 10.3390/genes11010090] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/02/2020] [Accepted: 01/07/2020] [Indexed: 02/07/2023] Open
Abstract
The ATP-dependent Switch/Sucrose non-fermenting (SWI/SNF) chromatin remodeling complex (CRC) regulates the transcription of many genes by destabilizing interactions between DNA and histones. In plants, BRAHMA (BRM), one of the two catalytic ATPase subunits of the complex, is the closest homolog of the yeast and animal SWI2/SNF2 ATPases. We summarize here the advances describing the roles of BRM in plant development as well as its recently reported chromatin-independent role in pri-miRNA processing in vitro and in vivo. We also enlighten the roles of plant-specific partners that physically interact with BRM. Three main types of partners can be distinguished: (i) DNA-binding proteins such as transcription factors which mostly cooperate with BRM in developmental processes, (ii) enzymes such as kinases or proteasome-related proteins that use BRM as substrate and are often involved in response to abiotic stress, and (iii) an RNA-binding protein which is involved with BRM in chromatin-independent pri-miRNA processing. This overview contributes to the understanding of the central position occupied by BRM within regulatory networks controlling fundamental biological processes in plants.
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17
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Holdsworth MJ, Vicente J, Sharma G, Abbas M, Zubrycka A. The plant N-degron pathways of ubiquitin-mediated proteolysis. J Integr Plant Biol 2020; 62:70-89. [PMID: 31638740 DOI: 10.1111/jipb.12882] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 10/20/2019] [Indexed: 05/29/2023]
Abstract
The amino-terminal residue of a protein (or amino-terminus of a peptide following protease cleavage) can be an important determinant of its stability, through the Ubiquitin Proteasome System associated N-degron pathways. Plants contain a unique combination of N-degron pathways (previously called the N-end rule pathways) E3 ligases, PROTEOLYSIS (PRT)6 and PRT1, recognizing non-overlapping sets of amino-terminal residues, and others remain to be identified. Although only very few substrates of PRT1 or PRT6 have been identified, substrates of the oxygen and nitric oxide sensing branch of the PRT6 N-degron pathway include key nuclear-located transcription factors (ETHYLENE RESPONSE FACTOR VIIs and LITTLE ZIPPER 2) and the histone-modifying Polycomb Repressive Complex 2 component VERNALIZATION 2. In response to reduced oxygen or nitric oxide levels (and other mechanisms that reduce pathway activity) these stabilized substrates regulate diverse aspects of growth and development, including response to flooding, salinity, vernalization (cold-induced flowering) and shoot apical meristem function. The N-degron pathways show great promise for use in the improvement of crop performance and for biotechnological applications. Upstream proteases, components of the different pathways and associated substrates still remain to be identified and characterized to fully appreciate how regulation of protein stability through the amino-terminal residue impacts plant biology.
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Affiliation(s)
| | - Jorge Vicente
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Gunjan Sharma
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Mohamad Abbas
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Agata Zubrycka
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
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18
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Till CJ, Vicente J, Zhang H, Oszvald M, Deery MJ, Pastor V, Lilley KS, Ray RV, Theodoulou FL, Holdsworth MJ. The Arabidopsis thaliana N-recognin E3 ligase PROTEOLYSIS1 influences the immune response. Plant Direct 2019; 3:e00194. [PMID: 31891113 PMCID: PMC6933115 DOI: 10.1002/pld3.194] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 11/22/2019] [Accepted: 12/02/2019] [Indexed: 05/11/2023]
Abstract
N-degron pathways of ubiquitin-mediated proteolysis (formerly known as the N-end rule pathway) control the stability of substrate proteins dependent on the amino-terminal (Nt) residue. Unlike yeast or mammalian N-recognin E3 ligases, which each recognize several different classes of Nt residues, in Arabidopsis thaliana, N-recognin functions of different N-degron pathways are carried out independently by PROTEOLYSIS (PRT)1, PRT6, and other unknown proteins. PRT1 recognizes type 2 aromatic Nt-destabilizing residues and PRT6 recognizes type 1 basic residues. These two N-recognin functions diverged as separate proteins early in the evolution of plants, before the conquest of the land. We demonstrate that loss of PRT1 function promotes the plant immune system, as mutant prt1-1 plants showed greater apoplastic resistance than WT to infection by the bacterial hemi-biotroph Pseudomonas syringae pv tomato (Pst) DC3000. Quantitative proteomics revealed increased accumulation of proteins associated with specific components of plant defense in the prt1-1 mutant, concomitant with increased accumulation of salicylic acid. The effects of the prt1 mutation were additional to known effects of prt6 in influencing the immune system, in particular, an observed over-accumulation of pipecolic acid (Pip) in the double-mutant prt1-1 prt6-1. These results demonstrate a potential role for PRT1 in controlling aspects of the plant immune system and suggest that PRT1 limits the onset of the defense response via degradation of substrates with type 2 Nt-destabilizing residues.
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Affiliation(s)
- Christopher J. Till
- School of BiosciencesUniversity of NottinghamLoughboroughUK
- Plant Sciences DepartmentRothamsted ResearchHarpendenUK
| | - Jorge Vicente
- School of BiosciencesUniversity of NottinghamLoughboroughUK
| | - Hongtao Zhang
- Plant Sciences DepartmentRothamsted ResearchHarpendenUK
- Cambridge Centre for ProteomicsDepartment of BiochemistryUniversity of CambridgeCambridgeUK
| | - Maria Oszvald
- Plant Sciences DepartmentRothamsted ResearchHarpendenUK
| | - Michael J. Deery
- Cambridge Centre for ProteomicsDepartment of BiochemistryUniversity of CambridgeCambridgeUK
| | - Victoria Pastor
- Área de Fisiología VegetalDepartamento de Ciencias Agrarias y del Medio NaturalUniversitat Jaume ICastellónSpain
| | - Kathryn S. Lilley
- Cambridge Centre for ProteomicsDepartment of BiochemistryUniversity of CambridgeCambridgeUK
| | - Rumiana V. Ray
- School of BiosciencesUniversity of NottinghamLoughboroughUK
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19
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Abstract
Protein amino (N) termini are major determinants of protein stability in the cytosol of eukaryotes and prokaryotes, conceptualized in the N-end rule pathway, lately referred to as N-degron pathways. Here we argue for the existence of N-degron pathways in plastids of apicomplexa, algae, and plants. The prokaryotic N-degron pathway depends on a caseinolytic protease (CLP) S recognin (adaptor) for the recognition and delivery of N-degron-bearing substrates to CLP chaperone-protease systems. Diversified CLP systems are found in chloroplasts and nonphotosynthetic plastids, including CLPS homologs that specifically interact with a subset of N-terminal residues and stromal proteins. Chloroplast N-terminome data show enrichment of classic stabilizing residues [Ala (A), Ser (S), Val (V), Thr (T)] and avoidance of charged and large hydrophobic residues. We outline experimental test strategies for plastid N-degron pathways.
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Affiliation(s)
- Imen Bouchnak
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY 14850, USA
| | - Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY 14850, USA.
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20
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Hartman S, Liu Z, van Veen H, Vicente J, Reinen E, Martopawiro S, Zhang H, van Dongen N, Bosman F, Bassel GW, Visser EJW, Bailey-Serres J, Theodoulou FL, Hebelstrup KH, Gibbs DJ, Holdsworth MJ, Sasidharan R, Voesenek LACJ. Ethylene-mediated nitric oxide depletion pre-adapts plants to hypoxia stress. Nat Commun 2019; 10:4020. [PMID: 31488841 DOI: 10.1038/s41467-019-12045-4] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/16/2019] [Indexed: 11/09/2022] Open
Abstract
Timely perception of adverse environmental changes is critical for survival. Dynamic changes in gases are important cues for plants to sense environmental perturbations, such as submergence. In Arabidopsis thaliana, changes in oxygen and nitric oxide (NO) control the stability of ERFVII transcription factors. ERFVII proteolysis is regulated by the N-degron pathway and mediates adaptation to flooding-induced hypoxia. However, how plants detect and transduce early submergence signals remains elusive. Here we show that plants can rapidly detect submergence through passive ethylene entrapment and use this signal to pre-adapt to impending hypoxia. Ethylene can enhance ERFVII stability prior to hypoxia by increasing the NO-scavenger PHYTOGLOBIN1. This ethylene-mediated NO depletion and consequent ERFVII accumulation pre-adapts plants to survive subsequent hypoxia. Our results reveal the biological link between three gaseous signals for the regulation of flooding survival and identifies key regulatory targets for early stress perception that could be pivotal for developing flood-tolerant crops.
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21
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Sánchez-Vicente I, Fernández-Espinosa MG, Lorenzo O. Nitric oxide molecular targets: reprogramming plant development upon stress. J Exp Bot 2019; 70:4441-4460. [PMID: 31327004 PMCID: PMC6736187 DOI: 10.1093/jxb/erz339] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 07/18/2019] [Indexed: 05/09/2023]
Abstract
Plants are sessile organisms that need to complete their life cycle by the integration of different abiotic and biotic environmental signals, tailoring developmental cues and defense concomitantly. Commonly, stress responses are detrimental to plant growth and, despite the fact that intensive efforts have been made to understand both plant development and defense separately, most of the molecular basis of this trade-off remains elusive. To cope with such a diverse range of processes, plants have developed several strategies including the precise balance of key plant growth and stress regulators [i.e. phytohormones, reactive nitrogen species (RNS), and reactive oxygen species (ROS)]. Among RNS, nitric oxide (NO) is a ubiquitous gasotransmitter involved in redox homeostasis that regulates specific checkpoints to control the switch between development and stress, mainly by post-translational protein modifications comprising S-nitrosation of cysteine residues and metals, and nitration of tyrosine residues. In this review, we have sought to compile those known NO molecular targets able to balance the crossroads between plant development and stress, with special emphasis on the metabolism, perception, and signaling of the phytohormones abscisic acid and salicylic acid during abiotic and biotic stress responses.
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Affiliation(s)
- Inmaculada Sánchez-Vicente
- Departamento de Botánica y Fisiología Vegetal, Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Facultad de Biología, Universidad de Salamanca, C/ Río Duero 12, 37185 Salamanca, Spain
| | - María Guadalupe Fernández-Espinosa
- Departamento de Botánica y Fisiología Vegetal, Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Facultad de Biología, Universidad de Salamanca, C/ Río Duero 12, 37185 Salamanca, Spain
| | - Oscar Lorenzo
- Departamento de Botánica y Fisiología Vegetal, Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Facultad de Biología, Universidad de Salamanca, C/ Río Duero 12, 37185 Salamanca, Spain
- Correspondence:
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22
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Hander T, Fernández-Fernández ÁD, Kumpf RP, Willems P, Schatowitz H, Rombaut D, Staes A, Nolf J, Pottie R, Yao P, Gonçalves A, Pavie B, Boller T, Gevaert K, Van Breusegem F, Bartels S, Stael S. Damage on plants activates Ca 2+-dependent metacaspases for release of immunomodulatory peptides. Science 2019; 363:363/6433/eaar7486. [PMID: 30898901 DOI: 10.1126/science.aar7486] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 12/06/2018] [Accepted: 02/13/2019] [Indexed: 12/14/2022]
Abstract
Physical damage to cells leads to the release of immunomodulatory peptides to elicit a wound defense response in the surrounding tissue. In Arabidopsis thaliana, the plant elicitor peptide 1 (Pep1) is processed from its protein precursor, PRECURSOR OF PEP1 (PROPEP1). We demonstrate that upon damage, both at the tissue and single-cell levels, the cysteine protease METACASPASE4 (MC4) is instantly and spatiotemporally activated by binding high levels of Ca2+ and is necessary and sufficient for Pep1 maturation. Cytosol-localized PROPEP1 and MC4 react only after loss of plasma membrane integrity and prolonged extracellular Ca2+ entry. Our results reveal that a robust mechanism consisting of conserved molecular components links the intracellular and Ca2+-dependent activation of a specific cysteine protease with the maturation of damage-induced wound defense signals.
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Affiliation(s)
- Tim Hander
- Zürich-Basel Plant Science Center, Department of Environmental Sciences, Botany, University of Basel, 4056 Basel, Switzerland
| | - Álvaro D Fernández-Fernández
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB-UGent Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Robert P Kumpf
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB-UGent Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB-UGent Center for Plant Systems Biology, 9052 Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, 9000 Ghent, Belgium
| | - Hendrik Schatowitz
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB-UGent Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Debbie Rombaut
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB-UGent Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - An Staes
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, 9000 Ghent, Belgium
| | - Jonah Nolf
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB-UGent Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Robin Pottie
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB-UGent Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Panfeng Yao
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB-UGent Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Amanda Gonçalves
- VIB BioImaging Core Gent, VIB-UGent Center for Inflammation Research (IRC), 9052 Ghent, Belgium
| | - Benjamin Pavie
- VIB BioImaging Core Gent, VIB-UGent Center for Inflammation Research (IRC), 9052 Ghent, Belgium
| | - Thomas Boller
- Zürich-Basel Plant Science Center, Department of Environmental Sciences, Botany, University of Basel, 4056 Basel, Switzerland
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, 9000 Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB-UGent Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Sebastian Bartels
- Zürich-Basel Plant Science Center, Department of Environmental Sciences, Botany, University of Basel, 4056 Basel, Switzerland.,Department of Medicine II, University Hospital Freiburg-Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Simon Stael
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium. .,VIB-UGent Center for Plant Systems Biology, 9052 Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, 9000 Ghent, Belgium
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23
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Goslin K, Eschen-Lippold L, Naumann C, Linster E, Sorel M, Klecker M, de Marchi R, Kind A, Wirtz M, Lee J, Dissmeyer N, Graciet E. Differential N-end Rule Degradation of RIN4/NOI Fragments Generated by the AvrRpt2 Effector Protease. Plant Physiol 2019; 180:2272-2289. [PMID: 31227619 PMCID: PMC6670102 DOI: 10.1104/pp.19.00251] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/13/2019] [Indexed: 05/29/2023]
Abstract
In plants, the protein RPM1-INTERACTING PROTEIN4 (RIN4) is a central regulator of both pattern-triggered immunity and effector-triggered immunity. RIN4 is targeted by several effectors, including the Pseudomonas syringae protease effector AvrRpt2. Cleavage of RIN4 by AvrRpt2 generates potentially unstable RIN4 fragments, whose degradation leads to the activation of the resistance protein RESISTANT TO P. SYRINGAE2. Hence, identifying the determinants of RIN4 degradation is key to understanding RESISTANT TO P. SYRINGAE2-mediated effector-triggered immunity, as well as virulence functions of AvrRpt2. In addition to RIN4, AvrRpt2 cleaves host proteins from the nitrate-induced (NOI) domain family. Although cleavage of NOI domain proteins by AvrRpt2 may contribute to pattern-triggered immunity regulation, the (in)stability of these proteolytic fragments and the determinants regulating their stability remain unexamined. Notably, a common feature of RIN4, and of many NOI domain protein fragments generated by AvrRpt2 cleavage, is the exposure of a new N-terminal residue that is destabilizing according to the N-end rule. Using antibodies raised against endogenous RIN4, we show that the destabilization of AvrRpt2-cleaved RIN4 fragments is independent of the N-end rule pathway (recently renamed the N-degron pathway). By contrast, several NOI domain protein fragments are genuine substrates of the N-degron pathway. The discovery of this set of substrates considerably expands the number of known proteins targeted for degradation by this ubiquitin-dependent pathway in plants. These results advance our current understanding of the role of AvrRpt2 in promoting bacterial virulence.
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Affiliation(s)
- Kevin Goslin
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
| | - Lennart Eschen-Lippold
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany
| | - Christin Naumann
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany
- Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Eric Linster
- Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Maud Sorel
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
| | - Maria Klecker
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany
- ScienceCampus Halle - Plant-Based Bioeconomy, 06120 Halle (Saale), Germany
| | - Rémi de Marchi
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
| | - Anne Kind
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
| | - Markus Wirtz
- Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Justin Lee
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany
| | - Nico Dissmeyer
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany
- ScienceCampus Halle - Plant-Based Bioeconomy, 06120 Halle (Saale), Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Emmanuelle Graciet
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
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24
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Willems P, Horne A, Van Parys T, Goormachtig S, De Smet I, Botzki A, Van Breusegem F, Gevaert K. The Plant PTM Viewer, a central resource for exploring plant protein modifications. Plant J 2019; 99:752-762. [PMID: 31004550 DOI: 10.1111/tpj.14345] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 04/01/2019] [Accepted: 04/10/2019] [Indexed: 05/15/2023]
Abstract
Post-translational modifications (PTMs) of proteins are central in any kind of cellular signaling. Modern mass spectrometry technologies enable comprehensive identification and quantification of various PTMs. Given the increased numbers and types of mapped protein modifications, a database is necessary that simultaneously integrates and compares site-specific information for different PTMs, especially in plants for which the available PTM data are poorly catalogued. Here, we present the Plant PTM Viewer (http://www.psb.ugent.be/PlantPTMViewer), an integrative PTM resource that comprises approximately 370 000 PTM sites for 19 types of protein modifications in plant proteins from five different species. The Plant PTM Viewer provides the user with a protein sequence overview in which the experimentally evidenced PTMs are highlighted together with an estimate of the confidence by which the modified peptides and, if possible, the actual modification sites were identified and with functional protein domains or active site residues. The PTM sequence search tool can query PTM combinations in specific protein sequences, whereas the PTM BLAST tool searches for modified protein sequences to detect conserved PTMs in homologous sequences. Taken together, these tools help to assume the role and potential interplay of PTMs in specific proteins or within a broader systems biology context. The Plant PTM Viewer is an open repository that allows the submission of mass spectrometry-based PTM data to remain at pace with future PTM plant studies.
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Affiliation(s)
- Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000, Ghent, Belgium
- VIB Center for Medical Biotechnology, VIB, 9000, Ghent, Belgium
| | - Alison Horne
- VIB Bioinformatics Core, VIB, 9052, Ghent, Belgium
| | | | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | | | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, 9000, Ghent, Belgium
- VIB Center for Medical Biotechnology, VIB, 9000, Ghent, Belgium
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25
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Zhang H, Linster E, Gannon L, Leemhuis W, Rundle CA, Theodoulou FL, Wirtz M. Tandem Fluorescent Protein Timers for Noninvasive Relative Protein Lifetime Measurement in Plants. Plant Physiol 2019; 180:718-731. [PMID: 30872425 PMCID: PMC6548237 DOI: 10.1104/pp.19.00051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/08/2019] [Indexed: 05/17/2023]
Abstract
Targeted protein degradation is an important and pervasive regulatory mechanism in plants, required for perception and response to the environment as well as developmental signaling. Despite the significance of this process, relatively few studies have assessed plant protein turnover in a quantitative fashion. Tandem fluorescent protein timers (tFTs) offer a powerful approach for the assessment of in vivo protein turnover in distinct subcellular compartments of single or multiple cells. A tFT is a fusion of two different fluorescent proteins with distinct fluorophore maturation kinetics, which enable protein age to be estimated from the ratio of fluorescence intensities of the two fluorescent proteins. Here, we used short-lived auxin signaling proteins and model N-end rule (N-recognin) pathway reporters to demonstrate the utility of tFTs for studying protein turnover in living plant cells of Arabidopsis (Arabidopsis thaliana) and Nicotiana benthamiana We present transient expression of tFTs as an efficient screen for relative protein lifetime, useful for testing the effects of mutations and different genetic backgrounds on protein stability. This work demonstrates the potential for using stably expressed tFTs to study native protein dynamics with high temporal resolution in response to exogenous or endogenous stimuli.
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Affiliation(s)
- Hongtao Zhang
- Plant Sciences Department, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom
| | - Eric Linster
- Centre for Organismal Studies, University of Heidelberg, Heidelberg 69120, Germany
| | - Lucy Gannon
- Plant Sciences Department, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom
| | - Wiebke Leemhuis
- Centre for Organismal Studies, University of Heidelberg, Heidelberg 69120, Germany
| | - Chelsea A Rundle
- Plant Sciences Department, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom
| | | | - Markus Wirtz
- Centre for Organismal Studies, University of Heidelberg, Heidelberg 69120, Germany
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26
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Abstract
The N-degron pathway, formerly the N-end rule pathway, regulates functions of regulatory proteins. It impacts protein half-life and therefore directs the actual presence of target proteins in the cell. The current concept holds that the N-degron pathway depends on the identity of the amino (N)-terminal amino acid and many other factors, such as the follow-up sequence at the N terminus, conformation, flexibility, and protein localization. It is evolutionarily conserved throughout the kingdoms. One possible entry point for substrates of the N-degron pathway is oxidation of N-terminal Cys residues. Oxidation of N-terminal Cys is decisive for further enzymatic modification of various neo-N termini by arginylation that generates potentially neofunctionalized or instable proteoforms. Here, I focus on the posttranslational modifications that are encompassed by protein degradation via the Cys/Arg branch of the N-degron pathway-part of the PROTEOLYSIS 6 (PRT6)/N-degron pathway-as well as the underlying physiological principles of this branch and its biological significance in stress response.
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Affiliation(s)
- Nico Dissmeyer
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry (IPB) and ScienceCampus Halle-Plant-Based Bioeconomy, D-06120 Halle (Saale), Germany; ; Twitter: @NDissmeyer
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27
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Millar AH, Heazlewood JL, Giglione C, Holdsworth MJ, Bachmair A, Schulze WX. The Scope, Functions, and Dynamics of Posttranslational Protein Modifications. Annu Rev Plant Biol 2019; 70:119-151. [PMID: 30786234 DOI: 10.1146/annurev-arplant-050718-100211] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Assessing posttranslational modification (PTM) patterns within protein molecules and reading their functional implications present grand challenges for plant biology. We combine four perspectives on PTMs and their roles by considering five classes of PTMs as examples of the broader context of PTMs. These include modifications of the N terminus, glycosylation, phosphorylation, oxidation, and N-terminal and protein modifiers linked to protein degradation. We consider the spatial distribution of PTMs, the subcellular distribution of modifying enzymes, and their targets throughout the cell, and we outline the complexity of compartmentation in understanding of PTM function. We also consider PTMs temporally in the context of the lifetime of a protein molecule and the need for different PTMs for assembly, localization, function, and degradation. Finally, we consider the combined action of PTMs on the same proteins, their interactions, and the challenge ahead of integrating PTMs into an understanding of protein function in plants.
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Affiliation(s)
- A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia;
| | - Joshua L Heazlewood
- School of BioSciences, University of Melbourne, Melbourne, Victoria 3010, Australia;
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell, CNRS UMR9198, F-91198 Gif-sur-Yvette Cedex, France;
| | - Michael J Holdsworth
- School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom;
| | - Andreas Bachmair
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria;
| | - Waltraud X Schulze
- Systembiologie der Pflanze, Universität Hohenheim, 70599 Stuttgart, Germany;
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28
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Abstract
Nitrogen (N) is a core component of fertilizers used in modern agriculture to increase yields and thus to help feed a growing global population. However, this comes at a cost to the environment, through run-off of excess N as a result of poor N-use efficiency (NUE) by crops. An obvious remedy to this problem would therefore be the improvement of NUE, which requires advancing our understanding on N homeostasis, sensing, and uptake. Proteolytic pathways are linked to N homeostasis as they recycle proteins that contain N and carbon; however, emerging data suggest that their functions extend beyond this simple recycling. Here, we highlight roles of proteolytic pathways in non-symbiotic and symbiotic N uptake and in systemic N sensing. We also offer a novel view in which we suggest that proteolytic pathways have roles in N homeostasis that differ from their accepted function in recycling.
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Affiliation(s)
- Anna Tornkvist
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Chen Liu
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Panagiotis N Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece
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29
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Perrar A, Dissmeyer N, Huesgen PF. New beginnings and new ends: methods for large-scale characterization of protein termini and their use in plant biology. J Exp Bot 2019; 70:2021-2038. [PMID: 30838411 PMCID: PMC6460961 DOI: 10.1093/jxb/erz104] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/27/2019] [Indexed: 05/17/2023]
Abstract
Dynamic regulation of protein function and abundance plays an important role in virtually every aspect of plant life. Diversifying mechanisms at the RNA and protein level result in many protein molecules with distinct sequence and modification, termed proteoforms, arising from a single gene. Distinct protein termini define proteoforms arising from translation of alternative transcripts, use of alternative translation initiation sites, and different co- and post-translational modifications of the protein termini. Also site-specific proteolytic processing by endo- and exoproteases generates truncated proteoforms, defined by distinct protease-generated neo-N- and neo-C-termini, that may exhibit altered activity, function, and localization compared with their precursor proteins. In eukaryotes, the N-degron pathway targets cytosolic proteins, exposing destabilizing N-terminal amino acids and/or destabilizing N-terminal modifications for proteasomal degradation. This enables rapid and selective removal not only of unfolded proteins, but also of substrate proteoforms generated by proteolytic processing or changes in N-terminal modifications. Here we summarize current protocols enabling proteome-wide analysis of protein termini, which have provided important new insights into N-terminal modifications and protein stability determinants, protein maturation pathways, and protease-substrate relationships in plants.
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Affiliation(s)
- Andreas Perrar
- Forschungszentrum Jülich, Central Institute for Engineering, Electronics and Analytics, ZEA-3 Analytics, Jülich, Germany
| | - Nico Dissmeyer
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry (IPB), Weinberg, Halle (Saale), Germany
- ScienceCampus Halle – Plant-based Bioeconomy, Halle (Saale), Germany
| | - Pitter F Huesgen
- Forschungszentrum Jülich, Central Institute for Engineering, Electronics and Analytics, ZEA-3 Analytics, Jülich, Germany
- Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
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30
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Buono RA, Hudecek R, Nowack MK. Plant proteases during developmental programmed cell death. J Exp Bot 2019; 70:2097-2112. [PMID: 30793182 PMCID: PMC7612330 DOI: 10.1093/jxb/erz072] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/12/2019] [Indexed: 05/08/2023]
Abstract
Proteases are among the key regulators of most forms of programmed cell death (PCD) in animals. Many PCD processes have also been associated with protease expression or activation in plants, However, functional evidence for the roles and actual modes of action of plant proteases in PCD remains surprisingly limited. In this review, we provide an update on protease involvement in the context of developmentally regulated plant PCD. To illustrate the diversity of protease functions, we focus on several prominent developmental PCD processes, including xylem and tapetum maturation, suspensor elimination, endosperm degradation, and seed coat formation, as well as plant senescence processes. Despite the substantial advances in the field, protease functions are often only correlatively linked to developmental PCD, and the specific molecular roles of proteases in many developmental PCD processes remain to be elucidated.
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Affiliation(s)
- Rafael Andrade Buono
- Department of Plant Biotechnology and Genetics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Roman Hudecek
- Department of Plant Biotechnology and Genetics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Moritz K. Nowack
- Department of Plant Biotechnology and Genetics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
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31
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Zhang H, Gannon L, Jones PD, Rundle CA, Hassall KL, Gibbs DJ, Holdsworth MJ, Theodoulou FL. Genetic interactions between ABA signalling and the Arg/N-end rule pathway during Arabidopsis seedling establishment. Sci Rep 2018; 8:15192. [PMID: 30315202 PMCID: PMC6185960 DOI: 10.1038/s41598-018-33630-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/01/2018] [Indexed: 11/25/2022] Open
Abstract
The Arg/N-end rule pathway of ubiquitin-mediated proteolysis has multiple functions throughout plant development, notably in the transition from dormant seed to photoautotrophic seedling. PROTEOLYSIS6 (PRT6), an N-recognin E3 ligase of the Arg/N-end rule regulates the degradation of transcription factor substrates belonging to Group VII of the Ethylene Response Factor superfamily (ERFVIIs). It is not known whether ERFVIIs are associated with all known functions of the Arg/N-end rule, and the downstream pathways influenced by ERFVIIs are not fully defined. Here, we examined the relationship between PRT6 function, ERFVIIs and ABA signalling in Arabidopsis seedling establishment. Physiological analysis of seedlings revealed that N-end rule-regulated stabilisation of three of the five ERFVIIs, RAP2.12, RAP2.2 and RAP2.3, controls sugar sensitivity of seedling establishment and oil body breakdown following germination. ABA signalling components ABA INSENSITIVE (ABI)4 as well as ABI3 and ABI5 were found to enhance ABA sensitivity of germination and sugar sensitivity of establishment in a background containing stabilised ERFVIIs. However, N-end rule regulation of oil bodies was not dependent on canonical ABA signalling. We propose that the N-end rule serves to control multiple aspects of the seed to seedling transition by regulation of ERFVII activity, involving both ABA-dependent and independent signalling pathways.
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Affiliation(s)
- Hongtao Zhang
- Plant Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Lucy Gannon
- Plant Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Peter D Jones
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK.,Department of Cardiovascular Sciences, University of Leicester, Leicester, LE3 7QP, UK
| | - Chelsea A Rundle
- Plant Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Kirsty L Hassall
- Computational and Analytical Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Daniel J Gibbs
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
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32
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Miricescu A, Goslin K, Graciet E. Ubiquitylation in plants: signaling hub for the integration of environmental signals. J Exp Bot 2018; 69:4511-4527. [PMID: 29726957 DOI: 10.1093/jxb/ery165] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 04/27/2018] [Indexed: 05/20/2023]
Abstract
A fundamental question in biology is how organisms integrate the plethora of environmental cues that they perceive to trigger a co-ordinated response. The regulation of protein stability, which is largely mediated by the ubiquitin-proteasome system in eukaryotes, plays a pivotal role in these processes. Due to their sessile lifestyle and the need to respond rapidly to a multitude of environmental factors, plants are thought to be especially dependent on proteolysis to regulate cellular processes. In this review, we present the complexity of the ubiquitin system in plants, and discuss the relevance of the proteolytic and non-proteolytic roles of this system in the regulation and co-ordination of plant responses to environmental signals. We also discuss the role of the ubiquitin system as a key regulator of plant signaling pathways. We focus more specifically on the functions of E3 ligases as regulators of the jasmonic acid (JA), salicylic acid (SA), and ethylene hormone signaling pathways that play important roles to mount a co-ordinated response to multiple environmental stresses. We also provide examples of new players in this field that appear to integrate different cues and signaling pathways.
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Affiliation(s)
- Alexandra Miricescu
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland
| | - Kevin Goslin
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland
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33
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Affiliation(s)
| | - Susana Rivas
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
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