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Khalil MI, Hassan MM, Samanta SC, Chowdhury AK, Hassan MZ, Ahmed NU, Somaddar U, Ghosal S, Robin AHK, Nath UK, Mostofa MG, Burritt DJ, Ha CV, Gupta A, Tran LSP, Saha G. Unraveling the genetic enigma of rice submergence tolerance: Shedding light on the role of ethylene response factor-encoding gene SUB1A-1. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108224. [PMID: 38091930 DOI: 10.1016/j.plaphy.2023.108224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 11/07/2023] [Accepted: 11/21/2023] [Indexed: 02/15/2024]
Abstract
The world's low-lying rice (Oryza sativa) cultivation areas are under threat of submergence or flash flooding due to global warming. Rice plants manifest a variety of physiological and morphological changes to cope with submergence and hypoxia, including lowering carbohydrate consumption, inhibiting shoot elongation, and forming a thicker leaf gas film during submergence. Functional studies have revealed that submergence tolerance in rice is mainly determined by an ethylene response factor (ERF) transcription factor-encoding gene, namely SUBMERGENCE 1A-1 (SUB1A-1) located in the SUB1 quantitative trait locus. The SUB1A-1-dependent submergence tolerance is manifested through hormonal signaling involving ethylene, gibberellic acid, brassinosteroid, auxin and jasmonic acid. Considerable progress has been made toward the introduction of SUB1A-1 into rice varieties through a conventional marker-assisted backcrossing approach. Here, we review the recent advances in the physiological, biochemical and molecular dynamics of rice submergence tolerance mediated by the 'quiescence strategy'. Thus, the present review aims to provide researchers with insights into the genetics of rice submergence tolerance and future perspectives for designing submergence-resilient plants for sustainable agriculture under the uncertainties of climate change.
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Affiliation(s)
- Md Ibrahim Khalil
- Department of Agronomy, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh; Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh.
| | - Md Mahmudul Hassan
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh.
| | - Swadesh Chandra Samanta
- Department of Agronomy, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh.
| | - Abul Kashem Chowdhury
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh.
| | - Md Zahid Hassan
- Department of Agronomy, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh.
| | - Nasar Uddin Ahmed
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh.
| | - Uzzal Somaddar
- Department of Agronomy, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh.
| | - Sharmistha Ghosal
- Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, 1701, Bangladesh.
| | - Arif Hasan Khan Robin
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh.
| | - Ujjal Kumar Nath
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh.
| | - Mohammad Golam Mostofa
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA.
| | - David J Burritt
- Department of Botany, University of Otago, Dunedin, 9054, New Zealand.
| | - Chien Van Ha
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA.
| | - Aarti Gupta
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA.
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA.
| | - Gopal Saha
- Department of Agronomy, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh.
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Lavilla-Puerta M, Latter R, Bellè F, Cervelli T, Galli A, Perata P, Chini A, Flashman E, Giuntoli B. Identification of novel plant cysteine oxidase inhibitors from a yeast chemical genetic screen. J Biol Chem 2023; 299:105366. [PMID: 37863264 PMCID: PMC10692734 DOI: 10.1016/j.jbc.2023.105366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/28/2023] [Accepted: 10/11/2023] [Indexed: 10/22/2023] Open
Abstract
Hypoxic responses in plants involve Plant Cysteine Oxidases (PCOs). They catalyze the N-terminal cysteine oxidation of Ethylene Response Factors VII (ERF-VII) in an oxygen-dependent manner, leading to their degradation via the cysteine N-degron pathway (Cys-NDP) in normoxia. In hypoxia, PCO activity drops, leading to the stabilization of ERF-VIIs and subsequent hypoxic gene upregulation. Thus far, no chemicals have been described to specifically inhibit PCO enzymes. In this work, we devised an in vivo pipeline to discover Cys-NDP effector molecules. Budding yeast expressing AtPCO4 and plant-based ERF-VII reporters was deployed to screen a library of natural-like chemical scaffolds and was further combined with an Arabidopsis Cys-NDP reporter line. This strategy allowed us to identify three PCO inhibitors, two of which were shown to affect PCO activity in vitro. Application of these molecules to Arabidopsis seedlings led to an increase in ERF-VII stability, induction of anaerobic gene expression, and improvement of tolerance to anoxia. By combining a high-throughput heterologous platform and the plant model Arabidopsis, our synthetic pipeline provides a versatile system to study how the Cys-NDP is modulated. Its first application here led to the discovery of at least two hypoxia-mimicking molecules with the potential to impact plant tolerance to low oxygen stress.
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Affiliation(s)
| | - Rebecca Latter
- Department of Chemistry, University of Oxford, Oxford, UK
| | | | | | | | | | - Andrea Chini
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | | | - Beatrice Giuntoli
- Plantlab, Center of Plant Sciences, Scuola Superiore Sant'Anna, Pisa, Italy; Biology Department, University of Pisa, Pisa, Italy.
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3
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Langin G, González-Fuente M, Üstün S. The Plant Ubiquitin-Proteasome System as a Target for Microbial Manipulation. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:351-375. [PMID: 37253695 DOI: 10.1146/annurev-phyto-021622-110443] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The plant immune system perceives pathogens to trigger defense responses. In turn, pathogens secrete effector molecules to subvert these defense responses. The initiation and maintenance of defense responses involve not only de novo synthesis of regulatory proteins and enzymes but also their regulated degradation. The latter is achieved through protein degradation pathways such as the ubiquitin-proteasome system (UPS). The UPS regulates all stages of immunity, from the perception of the pathogen to the execution of the response, and, therefore, constitutes an ideal candidate for microbial manipulation of the host. Pathogen effector molecules interfere with the plant UPS through several mechanisms. This includes hijacking general UPS functions or perturbing its ability to degrade specific targets. In this review, we describe how the UPS regulates different immunity-related processes and how pathogens subvert this to promote disease.
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Affiliation(s)
- Gautier Langin
- Centre for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany;
- Faculty of Biology and Biotechnology, Ruhr-University Bochum, Bochum, Germany
| | | | - Suayib Üstün
- Faculty of Biology and Biotechnology, Ruhr-University Bochum, Bochum, Germany
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4
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Heo AJ, Kim SB, Kwon YT, Ji CH. The N-degron pathway: From basic science to therapeutic applications. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194934. [PMID: 36990317 DOI: 10.1016/j.bbagrm.2023.194934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023]
Abstract
The N-degron pathway is a degradative system in which single N-terminal (Nt) amino acids regulate the half-lives of proteins and other biological materials. These determinants, called N-degrons, are recognized by N-recognins that link them to the ubiquitin (Ub)-proteasome system (UPS) or autophagy-lysosome system (ALS). In the UPS, the Arg/N-degron pathway targets the Nt-arginine (Nt-Arg) and other N-degrons to assemble Lys48 (K48)-linked Ub chains by UBR box N-recognins for proteasomal proteolysis. In the ALS, Arg/N-degrons are recognized by the N-recognin p62/SQSTSM-1/Sequestosome-1 to induce cis-degradation of substrates and trans-degradation of various cargoes such as protein aggregates and subcellular organelles. This crosstalk between the UPS and ALP involves reprogramming of the Ub code. Eukaryotic cells developed diverse ways to target all 20 principal amino acids for degradation. Here we discuss the components, regulation, and functions of the N-degron pathways, with an emphasis on the basic mechanisms and therapeutic applications of Arg/N-degrons and N-recognins.
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Affiliation(s)
- Ah Jung Heo
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Su Bin Kim
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Yong Tae Kwon
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; AUTOTAC Bio Inc., Changkyunggung-ro 254, Jongno-gu, Seoul 03077, Republic of Korea; Ischemic/Hypoxic Disease Institute, College of Medicine, Seoul National University, Seoul 110-799, Republic of Korea; SNU Dementia Research Center, College of Medicine, Seoul National University, Seoul 110-799, Republic of Korea.
| | - Chang Hoon Ji
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; AUTOTAC Bio Inc., Changkyunggung-ro 254, Jongno-gu, Seoul 03077, Republic of Korea.
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Winckler LI, Dissmeyer N. Molecular determinants of protein half-life in chloroplasts with focus on the Clp protease system. Biol Chem 2023; 404:499-511. [PMID: 36972025 DOI: 10.1515/hsz-2022-0320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/09/2023] [Indexed: 03/29/2023]
Abstract
Abstract
Proteolysis is an essential process to maintain cellular homeostasis. One pathway that mediates selective protein degradation and which is in principle conserved throughout the kingdoms of life is the N-degron pathway, formerly called the ‘N-end rule’. In the cytosol of eukaryotes and prokaryotes, N-terminal residues can be major determinants of protein stability. While the eukaryotic N-degron pathway depends on the ubiquitin proteasome system, the prokaryotic counterpart is driven by the Clp protease system. Plant chloroplasts also contain such a protease network, which suggests that they might harbor an organelle specific N-degron pathway similar to the prokaryotic one. Recent discoveries indicate that the N-terminal region of proteins affects their stability in chloroplasts and provides support for a Clp-mediated entry point in an N-degron pathway in plastids. This review discusses structure, function and specificity of the chloroplast Clp system, outlines experimental approaches to test for an N-degron pathway in chloroplasts, relates these aspects into general plastid proteostasis and highlights the importance of an understanding of plastid protein turnover.
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Affiliation(s)
- Lioba Inken Winckler
- Department of Plant Physiology and Protein Metabolism Laboratory, University of Osnabruck, Barbarastrasse 11, D-49076 Osnabruck, Germany
- Center of Cellular Nanoanalytics (CellNanOs), Barbarastrasse 11, D-49076 Osnabruck, Germany
- Faculty of Biology, University of Osnabruck, Barbarastrasse 11, D-49076 Osnabruck, Germany
| | - Nico Dissmeyer
- Department of Plant Physiology and Protein Metabolism Laboratory, University of Osnabruck, Barbarastrasse 11, D-49076 Osnabruck, Germany
- Center of Cellular Nanoanalytics (CellNanOs), Barbarastrasse 11, D-49076 Osnabruck, Germany
- Faculty of Biology, University of Osnabruck, Barbarastrasse 11, D-49076 Osnabruck, Germany
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6
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Heo AJ, Ji CH, Kwon YT. The Cys/N-degron pathway in the ubiquitin-proteasome system and autophagy. Trends Cell Biol 2023; 33:247-259. [PMID: 35945077 DOI: 10.1016/j.tcb.2022.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 10/15/2022]
Abstract
The N-degron pathway is a degradative system in which the N-terminal residues of proteins modulate the half-lives of proteins and other cellular materials. The majority of amino acids in the genetic code have the potential to induce cis or trans degradation in diverse processes, which requires selective recognition between N-degrons and cognate N-recognins. Of particular interest is the Cys/N-degron branch, in which the N-terminal cysteine (Nt-Cys) induces proteolysis via either the ubiquitin (Ub)-proteasome system (UPS) or the autophagy-lysosome pathway (ALP), depending on physiological conditions. Recent studies provided new insights into the central role of Nt-Cys in sensing the fluctuating levels of oxygen and reactive oxygen species (ROS). Here, we discuss the components, regulations, and functions of the Cys/N-degron pathway.
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Affiliation(s)
- Ah Jung Heo
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Korea
| | - Chang Hoon Ji
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Korea; AUTOTAC Bio Inc., Changkyunggung-ro 254, Jongno-gu, Seoul 03077, Korea
| | - Yong Tae Kwon
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Korea; AUTOTAC Bio Inc., Changkyunggung-ro 254, Jongno-gu, Seoul 03077, Korea; Ischemic/Hypoxic Disease Institute, College of Medicine, Seoul National University, Seoul 110-799, Korea.
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7
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Winckler LI, Dissmeyer N. TEV protease cleavage in generation of artificial substrate proteins bearing neo-N-termini. Methods Enzymol 2023. [PMID: 37532397 DOI: 10.1016/bs.mie.2023.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
Abstract
The tobacco etch virus (TEV) protease is widely used in in vitro and in vivo approaches for the removal of affinity tags from fusion proteins or the generation of proteins with a desired N-terminal amino acid. Processing of fusion proteins by the TEV protease can either be achieved by encoding the TEV protease and its recognition site on one construct (self-cleavage) or on two different constructs (co-expression). Here, we compare the efficiency of the self-splitting approach to the co-expression approach.
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8
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Sandmann A, Dissmeyer N. In vitro autoubiquitination activity of E3 ubiquitin ligases of the N-degron pathway. Methods Enzymol 2023. [PMID: 37532400 DOI: 10.1016/bs.mie.2023.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
As a part of the ubiquitin-proteasome system, E3 ubiquitin ligases play an important role in the regulation of the proteome in eukaryotic cells. These enzymes are extensively studied because of their crucial function, however it can be challenging to observe E3 ubiquitin ligases in action. Here, we outline a method for determining whether a known or potential E3 ubiquitin ligase exhibits autoubiquitination activity in vitro using PROTEOLYSIS1 (PRT1, AT3G24800), the first identified N-degron pathway E3 ubiquitin ligase from plants as an example. The approach provided here makes it possible to analyze mutations that could reduce or eliminate activity, to test for interaction with E2 ubiquitin conjugating enzymes, as well as to check for in vitro substrate ubiquitination.
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9
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Lavilla-Puerta M, Giuntoli B. Assessing In Vivo Oxygen Dynamics Using Plant N-Terminal Degrons in Saccharomyces cerevisiae. Methods Mol Biol 2023; 2564:269-286. [PMID: 36107348 DOI: 10.1007/978-1-0716-2667-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The expression of plant cysteine oxidase (PCO) enzyme in Saccharomyces cerevisiae enables the Arg/Cys N-degron pathway (Cys-NDP) for selective protein degradation that, in plants, functions as direct oxygen perception mechanism. A synthetic construct based on the plant Cys-NDP substrate related to apetala 2.12 (RAP2.12), the dual luciferase oxygen reporter (DLOR), exploits the N-terminal Cys of RAP2.12, and its oxygen-dependent degradation through the Cys-NDP. The luminescent output of DLOR can be used as a proxy for intracellular oxygen dynamics in budding yeast. Replacement of the luciferase reporter of the DLOR with fluorescent proteins would furthermore facilitate the imaging of reporter dynamics in living cells. In this chapter, we describe the methods for delivering the DLOR synthetic construct to yeast and calibrating its output by means of oxygen quantification in the culture with a physical oxygen sensor. We explain the setup needed to carry out hypoxic treatments with several colonies as replicates. We also describe the method to measure oxygen concentration in the culture, the closest indication of intracellular oxygen levels, as a way that would serve to calibrate the DLOR output. Finally, we propose a strategy to replace the luminescent reporters in the DLOR with fluorescent proteins to visualize oxygen dynamics in vivo.
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Affiliation(s)
| | - Beatrice Giuntoli
- Biology Department, University of Pisa, Pisa, Italy.
- Sant'Anna School of Advanced Studies, Plantlab, Pisa, Italy.
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Al‐Saharin R, Mooney S, Dissmeyer N, Hellmann H. Using CRL3 BPM E3 ligase substrate recognition sites as tools to impact plant development and stress tolerance in Arabidopsis thaliana. PLANT DIRECT 2022; 6:e474. [PMID: 36545004 PMCID: PMC9763634 DOI: 10.1002/pld3.474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Cullin-based RING E3 ligases that use BTB/POZ-MATH (BPM) proteins as substrate receptors have been established over the last decade as critical regulators in plant development and abiotic stress tolerance. As such they affect general aspects of shoot and root development, flowering time, embryo development, and different abiotic stress responses, such as heat, drought and salt stress. To generate tools that can help to understand the role of CRL3BPM E3 ligases in plants, we developed a novel system using two conserved protein-binding motifs from BPM substrates to transiently block CRL3BPM activity. The work investigates in vitro and in planta this novel approach, and shows that it can affect stress tolerance in plants as well as developmental aspects. It thereby can serve as a new tool for studying this E3 ligase in plants.
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Affiliation(s)
- Raed Al‐Saharin
- Washington State UniversityPullmanWashingtonUSA
- Tafila Technical UniversityTafilaJordan
| | | | - Nico Dissmeyer
- Department of Plant Physiology and Protein Metabolism LabUniversity of OsnabruckOsnabruckGermany
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11
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Meinnel T, Giglione C. N-terminal modifications, the associated processing machinery, and their evolution in plastid-containing organisms. JOURNAL OF EXPERIMENTAL BOTANY 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] [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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12
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Ugalde JM, Aller I, Kudrjasova L, Schmidt RR, Schlößer M, Homagk M, Fuchs P, Lichtenauer S, Schwarzländer M, Müller-Schüssele SJ, Meyer AJ. Endoplasmic reticulum oxidoreductin provides resilience against reductive stress and hypoxic conditions by mediating luminal redox dynamics. THE PLANT CELL 2022; 34:4007-4027. [PMID: 35818121 PMCID: PMC9516139 DOI: 10.1093/plcell/koac202] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 07/05/2022] [Indexed: 05/28/2023]
Abstract
Oxidative protein folding in the endoplasmic reticulum (ER) depends on the coordinated action of protein disulfide isomerases and ER oxidoreductins (EROs). Strict dependence of ERO activity on molecular oxygen as the final electron acceptor implies that oxidative protein folding and other ER processes are severely compromised under hypoxia. Here, we isolated viable Arabidopsis thaliana ero1 ero2 double mutants that are highly sensitive to reductive stress and hypoxia. To elucidate the specific redox dynamics in the ER in vivo, we expressed the glutathione redox potential (EGSH) sensor Grx1-roGFP2iL-HDEL with a midpoint potential of -240 mV in the ER of Arabidopsis plants. We found EGSH values of -241 mV in wild-type plants, which is less oxidizing than previously estimated. In the ero1 ero2 mutants, luminal EGSH was reduced further to -253 mV. Recovery to reductive ER stress induced by dithiothreitol was delayed in ero1 ero2. The characteristic signature of EGSH dynamics in the ER lumen triggered by hypoxia was affected in ero1 ero2 reflecting a disrupted balance of reductive and oxidizing inputs, including nascent polypeptides and glutathione entry. The ER redox dynamics can now be dissected in vivo, revealing a central role of EROs as major redox integrators to promote luminal redox homeostasis.
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Affiliation(s)
| | - Isabel Aller
- INRES-Chemical Signalling, University of Bonn, D-53113 Bonn, Germany
| | - Lika Kudrjasova
- INRES-Chemical Signalling, University of Bonn, D-53113 Bonn, Germany
| | - Romy R Schmidt
- Plant Biotechnology, Bielefeld University, D-33615 Bielefeld, Germany
| | - Michelle Schlößer
- INRES-Chemical Signalling, University of Bonn, D-53113 Bonn, Germany
| | - Maria Homagk
- INRES-Chemical Signalling, University of Bonn, D-53113 Bonn, Germany
| | | | - Sophie Lichtenauer
- Institute for Biology and Biotechnology of Plants, University of Münster, D-48143 Münster, Germany
| | - Markus Schwarzländer
- Institute for Biology and Biotechnology of Plants, University of Münster, D-48143 Münster, Germany
| | - Stefanie J Müller-Schüssele
- INRES-Chemical Signalling, University of Bonn, D-53113 Bonn, Germany
- Molecular Botany, Department of Biology, TU Kaiserslautern, D-67663, Kaiserslautern, Germany
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13
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You X, Nasrullah, Wang D, Mei Y, Bi J, Liu S, Xu W, Wang NN. N 7 -SSPP fusion gene improves salt stress tolerance in transgenic Arabidopsis and soybean through ROS scavenging. PLANT, CELL & ENVIRONMENT 2022; 45:2794-2809. [PMID: 35815549 DOI: 10.1111/pce.14392] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/30/2022] [Accepted: 07/02/2022] [Indexed: 06/15/2023]
Abstract
Considerable signal crosstalk exists in the regulatory network of senescence and stress response. Numerous senescence-associated genes are also involved in plant stress tolerance. However, the underlying mechanisms and application potential of these genes in stress-tolerant crop breeding remain poorly explored. We found that overexpression of SENESCENCE-SUPPRESSED PROTEIN PHOSPHATASE (SSPP), a negative regulator of leaf senescence, significantly improved plant salt tolerance by increasing reactive oxygen species (ROS) scavenging in both Arabidopsis and soybean. However, overexpression of SSPP severely suppressed normal plant growth, limiting its direct use in agriculture. We previously revealed that the N-terminal 1-14 residues of ACS7 (termed 'N7 ') negatively regulated its protein stability through the ubiquitin/proteasome pathway, and the N7 -mediated protein degradation was suppressed by environmental and senescence signals. To avoid the adverse effects of SSPP, the N7 element was fused to the N-terminus of SSPP. We demonstrated that N7 -SSPP fusion gene effectively rescued SSPP-induced growth suppression but maintained enhanced salt tolerance in Arabidopsis and soybean. Particularly, N7 -SSPP enhanced tolerance to long-term salt stress and increased seed yield in soybean. These results suggest that N7 -SSPP overcomes the disadvantages of SSPP on plant growth inhibition and effectively improves salt tolerance through enhanced ROS scavenging, providing an effective strategy of using posttranslational regulatory element for salt-tolerant crop breeding.
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Affiliation(s)
- Xiang You
- College of Life Sciences, College of Agricultural Sciences, Tianjin Key Laboratory of Protein Sciences, Nankai University, Tianjin, China
| | - Nasrullah
- College of Life Sciences, College of Agricultural Sciences, Tianjin Key Laboratory of Protein Sciences, Nankai University, Tianjin, China
| | - Dan Wang
- College of Life Sciences, College of Agricultural Sciences, Tianjin Key Laboratory of Protein Sciences, Nankai University, Tianjin, China
| | - Yuanyuan Mei
- College of Life Sciences, College of Agricultural Sciences, Tianjin Key Laboratory of Protein Sciences, Nankai University, Tianjin, China
| | - Juanjuan Bi
- College of Life Sciences, College of Agricultural Sciences, Tianjin Key Laboratory of Protein Sciences, Nankai University, Tianjin, China
| | - Sheng Liu
- College of Life Sciences, College of Agricultural Sciences, Tianjin Key Laboratory of Protein Sciences, Nankai University, Tianjin, China
| | - Wei Xu
- College of Life Sciences, College of Agricultural Sciences, Tianjin Key Laboratory of Protein Sciences, Nankai University, Tianjin, China
| | - Ning Ning Wang
- College of Life Sciences, College of Agricultural Sciences, Tianjin Key Laboratory of Protein Sciences, Nankai University, Tianjin, China
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Smalley S, Hellmann H. Review: Exploring possible approaches using ubiquitylation and sumoylation pathways in modifying plant stress tolerance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 319:111275. [PMID: 35487671 DOI: 10.1016/j.plantsci.2022.111275] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Ubiquitin and similar proteins, such as SUMO, are utilized by plants to modify target proteins to rapidly change their stability and activity in cells. This review will provide an overview of these crucial protein interactions with a focus on ubiquitylation and sumoylation in plants and how they contribute to stress tolerance. The work will also explore possibilities to use these highly conserved pathways for novel approaches to generate more robust crop plants better fit to cope with abiotic and biotic stress situations.
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Affiliation(s)
- Samuel Smalley
- Washington State University, Pullman, WA 99164, United States
| | - Hanjo Hellmann
- Washington State University, Pullman, WA 99164, United States.
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15
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Dissmeyer N. Oxygen sensing: Protein degradation meets retrograde signaling. Curr Biol 2022; 32:R281-R284. [PMID: 35349816 DOI: 10.1016/j.cub.2022.02.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A new study shows that mitochondrial retrograde signaling relies on strongly compartmentalized individual pathways previously not taken into account. This involves a link between mitochondrial oxygen consumption and cytosolic oxygen sensing via the N-degron pathway.
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Affiliation(s)
- Nico Dissmeyer
- Department of Plant Physiology and Protein Metabolism Lab, University of Osnabruck, Osnabruck, Germany; CellNanOs - Center of Cellular Nanoanalytics, University of Osnabruck, Osnabruck, Germany.
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16
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Pande A, Mun BG, Khan M, Rahim W, Lee DS, Lee GM, Al Azawi TNI, Hussain A, Yun BW. Nitric Oxide Signaling and Its Association with Ubiquitin-Mediated Proteasomal Degradation in Plants. Int J Mol Sci 2022; 23:ijms23031657. [PMID: 35163578 PMCID: PMC8835921 DOI: 10.3390/ijms23031657] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 01/28/2022] [Accepted: 01/29/2022] [Indexed: 02/05/2023] Open
Abstract
Nitric oxide (NO) is a versatile signaling molecule with diverse roles in plant biology. The NO-mediated signaling mechanism includes post-translational modifications (PTMs) of target proteins. There exists a close link between NO-mediated PTMs and the proteasomal degradation of proteins via ubiquitylation. In some cases, ubiquitin-mediated proteasomal degradation of target proteins is followed by an NO-mediated post-translational modification on them, while in other cases NO-mediated PTMs can regulate the ubiquitylation of the components of ubiquitin-mediated proteasomal machinery for promoting their activity. Another pathway that links NO signaling with the ubiquitin-mediated degradation of proteins is the N-degron pathway. Overall, these mechanisms reflect an important mechanism of NO signal perception and transduction that reflect a close association of NO signaling with proteasomal degradation via ubiquitylation. Therefore, this review provides insight into those pathways that link NO-PTMs with ubiquitylation.
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Affiliation(s)
- Anjali Pande
- Laboratory of Plant Molecular Pathology and Functional Genomics, Department of Plant Biosciences, School of Applied Biosciences, College of Agriculture & Life Science, Kyungpook National University, Daegu 41944, Korea; (B.-G.M.); (M.K.); (W.R.); (D.-S.L.); (G.-M.L.); (T.N.I.A.A.)
- Correspondence: (A.P.); (B.-W.Y.)
| | - Bong-Gyu Mun
- Laboratory of Plant Molecular Pathology and Functional Genomics, Department of Plant Biosciences, School of Applied Biosciences, College of Agriculture & Life Science, Kyungpook National University, Daegu 41944, Korea; (B.-G.M.); (M.K.); (W.R.); (D.-S.L.); (G.-M.L.); (T.N.I.A.A.)
| | - Murtaza Khan
- Laboratory of Plant Molecular Pathology and Functional Genomics, Department of Plant Biosciences, School of Applied Biosciences, College of Agriculture & Life Science, Kyungpook National University, Daegu 41944, Korea; (B.-G.M.); (M.K.); (W.R.); (D.-S.L.); (G.-M.L.); (T.N.I.A.A.)
| | - Waqas Rahim
- Laboratory of Plant Molecular Pathology and Functional Genomics, Department of Plant Biosciences, School of Applied Biosciences, College of Agriculture & Life Science, Kyungpook National University, Daegu 41944, Korea; (B.-G.M.); (M.K.); (W.R.); (D.-S.L.); (G.-M.L.); (T.N.I.A.A.)
| | - Da-Sol Lee
- Laboratory of Plant Molecular Pathology and Functional Genomics, Department of Plant Biosciences, School of Applied Biosciences, College of Agriculture & Life Science, Kyungpook National University, Daegu 41944, Korea; (B.-G.M.); (M.K.); (W.R.); (D.-S.L.); (G.-M.L.); (T.N.I.A.A.)
| | - Geun-Mo Lee
- Laboratory of Plant Molecular Pathology and Functional Genomics, Department of Plant Biosciences, School of Applied Biosciences, College of Agriculture & Life Science, Kyungpook National University, Daegu 41944, Korea; (B.-G.M.); (M.K.); (W.R.); (D.-S.L.); (G.-M.L.); (T.N.I.A.A.)
| | - Tiba Nazar Ibrahim Al Azawi
- Laboratory of Plant Molecular Pathology and Functional Genomics, Department of Plant Biosciences, School of Applied Biosciences, College of Agriculture & Life Science, Kyungpook National University, Daegu 41944, Korea; (B.-G.M.); (M.K.); (W.R.); (D.-S.L.); (G.-M.L.); (T.N.I.A.A.)
| | - Adil Hussain
- Laboratory of Cell Biology, Department of Entomology, Abdul Wali Khan University, Mardan 23200, Khyber Pakhtunkhwa, Pakistan;
| | - Byung-Wook Yun
- Laboratory of Plant Molecular Pathology and Functional Genomics, Department of Plant Biosciences, School of Applied Biosciences, College of Agriculture & Life Science, Kyungpook National University, Daegu 41944, Korea; (B.-G.M.); (M.K.); (W.R.); (D.-S.L.); (G.-M.L.); (T.N.I.A.A.)
- Correspondence: (A.P.); (B.-W.Y.)
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17
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Kozlic A, Winter N, Telser T, Reimann J, Rose K, Nehlin L, Berckhan S, Sharma G, Dambire C, Boeckx T, Holdsworth MJ, Bachmair A. A Yeast-Based Functional Assay to Study Plant N-Degron - N-Recognin Interactions. FRONTIERS IN PLANT SCIENCE 2022; 12:806129. [PMID: 35069663 PMCID: PMC8777003 DOI: 10.3389/fpls.2021.806129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
The N-degron pathway is a branch of the ubiquitin-proteasome system where amino-terminal residues serve as degradation signals. In a synthetic biology approach, we expressed ubiquitin ligase PRT6 and ubiquitin conjugating enzyme 2 (AtUBC2) from Arabidopsis thaliana in a Saccharomyces cerevisiae strain with mutation in its endogenous N-degron pathway. The two enzymes re-constitute part of the plant N-degron pathway and were probed by monitoring the stability of co-expressed GFP-linked plant proteins starting with Arginine N-degrons. The novel assay allows for straightforward analysis, whereas in vitro interaction assays often do not allow detection of the weak binding of N-degron recognizing ubiquitin ligases to their substrates, and in planta testing is usually complex and time-consuming.
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Affiliation(s)
- Aida Kozlic
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
| | - Nikola Winter
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
| | - Theresia Telser
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
| | - Jakob Reimann
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
| | - Katrin Rose
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
| | - Lilian Nehlin
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
| | - Sophie Berckhan
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Gunjan Sharma
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Charlene Dambire
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Tinne Boeckx
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | | | - Andreas Bachmair
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
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18
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Becker R, Görner C, Reichman P, Dissmeyer N. Trichome Transcripts as Efficiency Control for Synthetic Biology and Molecular Farming. Methods Mol Biol 2022; 2379:265-276. [PMID: 35188667 DOI: 10.1007/978-1-0716-1791-5_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A variety of methods for studying glandular leaf hairs (trichomes) as multicellular micro-organs are well established for synthetic biology platforms like tobacco or tomato but rather rare for nonglandular and usually single-celled trichomes of the model plant Arabidopsis thaliana. A thorough isolation of-ideally intact-trichomes is decisive for further biochemical and genomic analyses of primary and secondary metabolic compounds, enzymes, and especially transcripts to monitor initial success of an engineering approach. While isolation of tomato or tobacco trichomes is rather easy, by simply freezing whole plants in liquid nitrogen and brushing off trichomes, this approach does not work for Arabidopsis. This is mainly due to damage of trichome cells during the collection procedure and very low yield. Here, we provide a robust method for a virtually epithelial cell-free isolation of Arabidopsis trichomes. This method is then joined with an RNA isolation protocol to perform mRNA analysis on extracts of the isolated trichomes using a semi-quantitative RT-PCR setup.
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Affiliation(s)
- Richard Becker
- Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany
- ScienceCampus Halle - Plant-Based Bioeconomy, Halle (Saale), Germany
| | - Christian Görner
- Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany
- Department of Plant Physiology and Protein Metabolism Lab, University of Osnabrück, Osnabrück, Germany
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
| | - Pavel Reichman
- Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany
- ScienceCampus Halle - Plant-Based Bioeconomy, Halle (Saale), Germany
- Department of Plant Physiology and Protein Metabolism Lab, University of Osnabrück, Osnabrück, Germany
| | - Nico Dissmeyer
- Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany.
- ScienceCampus Halle - Plant-Based Bioeconomy, Halle (Saale), Germany.
- Department of Plant Physiology and Protein Metabolism Lab, University of Osnabrück, Osnabrück, Germany.
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19
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Abstract
Studying the stability of a protein dependent on its N-terminal residue requires a mechanism, which selectively exposes the amino acid at the N-terminus. Here, we describe the use of the tobacco etch virus (TEV) protease to generate a specific N-terminal amino acid in the stroma of the chloroplast. The established molecular reporter system further allows the quantification of the reporter protein half-life dependent on the identity of the N-terminal residue.
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Affiliation(s)
- Lioba Inken Winckler
- Protein Metabolism Lab, Department of Plant Physiology, University of Osnabruck, Osnabruck, Germany
- CellNanOs-Center of Cellular Nanoanalytics, University of Osnabruck, Osnabruck, Germany
- Faculty of Biology, University of Osnabruck, Osnabruck, Germany
| | - Nico Dissmeyer
- Protein Metabolism Lab, Department of Plant Physiology, University of Osnabruck, Osnabruck, Germany.
- CellNanOs-Center of Cellular Nanoanalytics, University of Osnabruck, Osnabruck, Germany.
- Faculty of Biology, University of Osnabruck, Osnabruck, Germany.
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20
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Heidorn-Czarna M, Maziak A, Janska H. Protein Processing in Plant Mitochondria Compared to Yeast and Mammals. FRONTIERS IN PLANT SCIENCE 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] [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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21
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The N-terminal cysteine is a dual sensor of oxygen and oxidative stress. Proc Natl Acad Sci U S A 2021; 118:2107993118. [PMID: 34893540 DOI: 10.1073/pnas.2107993118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2021] [Indexed: 01/01/2023] Open
Abstract
Cellular homeostasis requires the sensing of and adaptation to intracellular oxygen (O2) and reactive oxygen species (ROS). The Arg/N-degron pathway targets proteins that bear destabilizing N-terminal residues for degradation by the proteasome or via autophagy. Under normoxic conditions, the N-terminal Cys (Nt-Cys) residues of specific substrates can be oxidized by dioxygenases such as plant cysteine oxidases and cysteamine (2-aminoethanethiol) dioxygenases and arginylated by ATE1 R-transferases to generate Arg-CysO2(H) (R-CO2). Proteins bearing the R-CO2 N-degron are targeted via Lys48 (K48)-linked ubiquitylation by UBR1/UBR2 N-recognins for proteasomal degradation. During acute hypoxia, such proteins are partially stabilized, owing to decreased Nt-Cys oxidation. Here, we show that if hypoxia is prolonged, the Nt-Cys of regulatory proteins can be chemically oxidized by ROS to generate Arg-CysO3(H) (R-CO3), a lysosomal N-degron. The resulting R-CO3 is bound by KCMF1, a N-recognin that induces K63-linked ubiquitylation, followed by K27-linked ubiquitylation by the noncanonical N-recognin UBR4. Autophagic targeting of Cys/N-degron substrates is mediated by the autophagic N-recognin p62/SQTSM-1/Sequestosome-1 through recognition of K27/K63-linked ubiquitin (Ub) chains. This Cys/N-degron-dependent reprogramming in the proteolytic flux is important for cellular homeostasis under both chronic hypoxia and oxidative stress. A small-compound ligand of p62 is cytoprotective under oxidative stress through its ability to accelerate proteolytic flux of K27/K63-ubiquitylated Cys/N-degron substrates. Our results suggest that the Nt-Cys of conditional Cys/N-degron substrates acts as an acceptor of O2 to maintain both O2 and ROS homeostasis and modulates half-lives of substrates through either the proteasome or lysosome by reprogramming of their Ub codes.
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22
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Castillo MC, Costa-Broseta Á, Gayubas B, León J. NIN-like protein7 and PROTEOLYSIS6 functional interaction enhances tolerance to sucrose, ABA, and submergence. PLANT PHYSIOLOGY 2021; 187:2731-2748. [PMID: 34618055 PMCID: PMC8644111 DOI: 10.1093/plphys/kiab382] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/16/2021] [Indexed: 05/05/2023]
Abstract
Nitrate (NO3) assimilation and signaling regulate plant growth through the relevant function of the transcription factor NIN-like Protein7 (NLP7). NO3 is also the main source for plants to produce nitric oxide (NO), which regulates growth and stress responses. NO-mediated regulation requires efficient sensing via the PROTEOLYSIS6 (PRT6)-mediated proteasome-triggered degradation of group VII of ethylene response transcription factors through the Cys/Arg N-degron pathway. The convergence of NO3 signaling and N-degron proteolysis on NO-mediated regulation remains largely unknown. Here, we investigated the functional interaction between NLP7 and PRT6 using Arabidopsis (Arabidopsis thaliana) double prt6 nlp7 mutant plants as well as complementation lines overexpressing NLP7 in different mutant genetic backgrounds. prt6 nlp7 mutant plants displayed several potentiated prt6 characteristic phenotypes, including slower vegetative growth, increased NO content, and diminished tolerance to abiotic stresses such as high-sucrose concentration, abscisic acid, and hypoxia-reoxygenation. Although NLP7 has an N-terminus that could be targeted by the N-degron proteolytic pathway, it was not a PRT6 substrate. The potential PRT6- and NO-regulated nucleocytoplasmic translocation of NLP7, which is likely modulated by posttranslational modifications, is proposed to act as a regulatory loop to control NO homeostasis and action.
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Affiliation(s)
- Mari-Cruz Castillo
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas–Universidad Politécnica de Valencia), Valencia 46022, Spain
| | - Álvaro Costa-Broseta
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas–Universidad Politécnica de Valencia), Valencia 46022, Spain
| | - Beatriz Gayubas
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas–Universidad Politécnica de Valencia), Valencia 46022, Spain
| | - José León
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas–Universidad Politécnica de Valencia), Valencia 46022, Spain
- Author for communication:
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23
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Lim R, Chae J, Somers DE, Ghim CM, Kim PJ. Cost-effective circadian mechanism: rhythmic degradation of circadian proteins spontaneously emerges without rhythmic post-translational regulation. iScience 2021; 24:102726. [PMID: 34355141 PMCID: PMC8324817 DOI: 10.1016/j.isci.2021.102726] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/10/2021] [Accepted: 06/11/2021] [Indexed: 12/20/2022] Open
Abstract
Circadian protein oscillations are maintained by the lifelong repetition of protein production and degradation in daily balance. It comes at the cost of ever-replayed, futile protein synthesis each day. This biosynthetic cost with a given oscillatory protein profile is relievable by a rhythmic, not constant, degradation rate that selectively peaks at the right time of day but remains low elsewhere, saving much of the gross protein loss and of the replenishing protein synthesis. Here, our mathematical modeling reveals that the rhythmic degradation rate of proteins with circadian production spontaneously emerges under steady and limited activity of proteolytic mediators and does not necessarily require rhythmic post-translational regulation of previous focus. Additional (yet steady) post-translational modifications in a proteolytic pathway can further facilitate the degradation's rhythmicity in favor of the biosynthetic cost saving. Our work is supported by animal and plant circadian data, offering a generic mechanism for potentially widespread, time-dependent protein turnover. Rhythmic degradation of circadian proteins lowers the cost of protein synthesis This rhythmic degradation emerges without rhythmic post-translational regulation Extra, yet steady post-translational modifications enhance degradation rhythmicity This mechanism hints at how organisms afford the price of daily biological rhythms
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Affiliation(s)
- Roktaek Lim
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
| | - Junghun Chae
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - David E Somers
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.,Center for Applied Plant Sciences, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.,Arabidopsis Biological Resource Center, The Ohio State University, Columbus, OH 43210, USA
| | - Cheol-Min Ghim
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.,Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Pan-Jun Kim
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong.,Center for Quantitative Systems Biology & Institute of Computational and Theoretical Studies, Hong Kong Baptist University, Kowloon, Hong Kong.,State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon, Hong Kong.,Abdus Salam International Centre for Theoretical Physics, 34151 Trieste, Italy
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24
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Zhang J, Liu B, Song Y, Chen Y, Fu J, Liu J, Ma T, Xi Z, Liu H. Genome-wide (ChIP-seq) identification of target genes regulated by WRKY33 during submergence stress in Arabidopsis. BMC Genom Data 2021; 22:16. [PMID: 34030628 PMCID: PMC8142642 DOI: 10.1186/s12863-021-00972-5] [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: 11/27/2020] [Accepted: 05/17/2021] [Indexed: 11/30/2022] Open
Abstract
Background Hypoxia induced by flooding causes significant losses to crop production almost every year. However, the molecular network of submergence signaling pathway is still poorly understood. According to previous studies, transgenic plants overexpressing the WRKY33 gene showed enhanced resistance to submergence stress. Thus, this transcription factor may regulate a series of target genes in response to submergence. Here, to determine putative downstream targets of WRKY33 at a genome-wide scale in Arabidopsis thaliana, we performed the chromatin immunoprecipitation sequencing (ChIP-seq) using 35S:FLAG-WRKY33 overexpression transgenic lines (WRKY33-OE) after 24 h of submergence treatment. Results Using ChIP-seq data, we identified a total of 104 WRKY33-binding genes under submergence stress (WRKY33BGSs). Most WRKY33BGSs are involved in the oxidation-reduction process, programmed cell death in response to reactive oxygen species, lipid biosynthesis process, and other processes related to stress responses. Moreover, the major motif identified in the WRKY33BGSs promoters is a new cis-element, TCTCTC (named here as “TC box”). This cis-element differs from the previously known W box for WRKY33. Further qPCR experiments verified that genes carrying this motif in their promoters could be regulated by WRKY33 upon submergence treatment. Conclusions Our study has identified a new putative binding motif of WRKY33 and recovered numerous previously unknown target genes of WRKY33 during submergence stress. The WRKY33 gene positively participates in flooding response probably by transcriptional regulation of the downstream submergence-related target genes via a “TC box”. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00972-5.
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Affiliation(s)
- Junlin Zhang
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Bao Liu
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Yan Song
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Yang Chen
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Jiao Fu
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Jianquan Liu
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Tao Ma
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Zhenxiang Xi
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Huanhuan Liu
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610065, China.
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25
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Lessons from Comparison of Hypoxia Signaling in Plants and Mammals. PLANTS 2021; 10:plants10050993. [PMID: 34067566 PMCID: PMC8157222 DOI: 10.3390/plants10050993] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/12/2021] [Accepted: 05/12/2021] [Indexed: 12/12/2022]
Abstract
Hypoxia is an important stress for organisms, including plants and mammals. In plants, hypoxia can be the consequence of flooding and causes important crop losses worldwide. In mammals, hypoxia stress may be the result of pathological conditions. Understanding the regulation of responses to hypoxia offers insights into novel approaches for crop improvement, particularly for the development of flooding-tolerant crops and for producing better therapeutics for hypoxia-related diseases such as inflammation and cancer. Despite their evolutionary distance, plants and mammals deploy strikingly similar mechanisms to sense and respond to the different aspects of hypoxia-related stress, including low oxygen levels and the resulting energy crisis, nutrient depletion, and oxidative stress. Over the last two decades, the ubiquitin/proteasome system and the ubiquitin-like protein SUMO have been identified as key regulators that act in concert to regulate core aspects of responses to hypoxia in plants and mammals. Here, we review ubiquitin and SUMO-dependent mechanisms underlying the regulation of hypoxia response in plants and mammals. By comparing and contrasting these mechanisms in plants and mammals, this review seeks to pinpoint conceptually similar mechanisms but also highlight future avenues of research at the junction between different fields of research.
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26
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Aguilar Lucero D, Cantoia A, Sánchez-López C, Binolfi A, Mogk A, Ceccarelli EA, Rosano GL. Structural features of the plant N-recognin ClpS1 and sequence determinants in its targets that govern substrate selection. FEBS Lett 2021; 595:1525-1541. [PMID: 33792910 DOI: 10.1002/1873-3468.14081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/13/2022]
Abstract
In the N-degron pathway of protein degradation of Escherichia coli, the N-recognin ClpS identifies substrates bearing N-terminal phenylalanine, tyrosine, tryptophan, or leucine and delivers them to the caseinolytic protease (Clp). Chloroplasts contain the Clp system, but whether chloroplastic ClpS1 adheres to the same constraints is unknown. Moreover, the structural underpinnings of substrate recognition are not completely defined. We show that ClpS1 recognizes canonical residues of the E. coli N-degron pathway. The residue in second position influences recognition (especially in N-terminal ends starting with leucine). N-terminal acetylation abrogates recognition. ClpF, a ClpS1-interacting partner, does not alter its specificity. Substrate binding provokes local remodeling of residues in the substrate-binding cavity of ClpS1. Our work strongly supports the existence of a chloroplastic N-degron pathway.
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Affiliation(s)
- Dianela Aguilar Lucero
- CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Universidad Nacional de Rosario, Argentina
| | - Alejo Cantoia
- CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Universidad Nacional de Rosario, Argentina
| | - Carolina Sánchez-López
- CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Universidad Nacional de Rosario, Argentina
| | - Andrés Binolfi
- CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Universidad Nacional de Rosario, Argentina.,Plataforma Argentina de Biología Estructural y Metabolómica (PLABEM), Rosario, Argentina
| | - Axel Mogk
- DKFZ-ZMBH Alliance, Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Germany
| | - Eduardo A Ceccarelli
- CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Universidad Nacional de Rosario, Argentina
| | - Germán L Rosano
- CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Universidad Nacional de Rosario, Argentina
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27
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Chen Y, Inzé D, Vanhaeren H. Post-translational modifications regulate the activity of the growth-restricting protease DA1. JOURNAL OF EXPERIMENTAL BOTANY 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] [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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28
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Winter N, Novatchkova M, Bachmair A. Cellular Control of Protein Turnover via the Modification of the Amino Terminus. Int J Mol Sci 2021; 22:ijms22073545. [PMID: 33805528 PMCID: PMC8037982 DOI: 10.3390/ijms22073545] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
The first amino acid of a protein has an important influence on its metabolic stability. A number of ubiquitin ligases contain binding domains for different amino-terminal residues of their substrates, also known as N-degrons, thereby mediating turnover. This review summarizes, in an exemplary way, both older and more recent findings that unveil how destabilizing amino termini are generated. In most cases, a step of proteolytic cleavage is involved. Among the over 500 proteases encoded in the genome of higher eukaryotes, only a few are known to contribute to the generation of N-degrons. It can, therefore, be expected that many processing paths remain to be discovered.
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Affiliation(s)
- Nikola Winter
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, A-1030 Vienna, Austria;
| | - Maria Novatchkova
- Vienna BioCenter, Research Institute of Molecular Pathology, A-1030 Vienna, Austria;
- Vienna BioCenter, Institute of Molecular Biotechnology, A-1030 Vienna, Austria
| | - Andreas Bachmair
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, A-1030 Vienna, Austria;
- Correspondence:
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29
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Konkina A, Klepadlo M, Lakehal A, Zein ZE, Krokida A, Botros M, Iakovidis M, Chernobavskiy P, Elfatih Zerroumda M, Tsanakas G, Petrakis N, Dourou AM, Kalaitzis P. An Arabidopsis Prolyl 4 Hydroxylase Is Involved in the Low Oxygen Response. FRONTIERS IN PLANT SCIENCE 2021; 12:637352. [PMID: 33790927 PMCID: PMC8006943 DOI: 10.3389/fpls.2021.637352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Plant responses to flooding, submergence and waterlogging are important for adaptation to climate change environments. Therefore, the characterization of the molecular mechanisms activated under hypoxic and anoxic conditions might lead to low oxygen resilient crops. Although in mammalian systems prolyl 4 hydroxylases (P4Hs) are involved in the oxygen sensing pathway, their role in plants under low oxygen has not been extensively investigated. In this report, an Arabidopsis AtP4H3 T-DNA knock out mutant line showed higher sensitivity to anoxic treatment possibly due to lower induction of the fermentation pathway genes, ADH and PDC1, and of sucrose synthases, SUS1 and SUS4. This sensitivity to anoxia was accompanied by lower protein levels of AGPs-bound epitopes such as LM14 in the mutant line and induction of extensins-bound epitopes, while the expression levels of the majority of the AGPs genes were stable throughout a low oxygen time course. The lower AGPs content might be related to altered frequency of proline hydroxylation occurrence in the p4h3 line. These results indicate active involvement of proline hydroxylation, a post-translational modification, to low oxygen response in Arabidopsis.
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30
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Molecular basis for ubiquitin ligase CRL2 FEM1C-mediated recognition of C-degron. Nat Chem Biol 2021; 17:263-271. [PMID: 33398170 DOI: 10.1038/s41589-020-00703-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/30/2020] [Indexed: 01/28/2023]
Abstract
Proteome integrity depends on the ubiquitin-proteasome system to degrade unwanted or abnormal proteins. In addition to the N-degrons, C-terminal residues of proteins can also serve as degradation signals (C-degrons) that are recognized by specific cullin-RING ubiquitin ligases (CRLs) for proteasomal degradation. FEM1C is a CRL2 substrate receptor that targets the C-terminal arginine degron (Arg/C-degron), but the molecular mechanism of substrate recognition remains largely elusive. Here, we present crystal structures of FEM1C in complex with Arg/C-degron and show that FEM1C utilizes a semi-open binding pocket to capture the C-terminal arginine and that the extreme C-terminal arginine is the major structural determinant in recognition by FEM1C. Together with biochemical and mutagenesis studies, we provide a framework for understanding molecular recognition of the Arg/C-degron by the FEM family of proteins.
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31
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Labandera A, Tedds HM, Bailey M, Sprigg C, Etherington RD, Akintewe O, Kalleechurn G, Holdsworth MJ, Gibbs DJ. The PRT6 N-degron pathway restricts VERNALIZATION 2 to endogenous hypoxic niches to modulate plant development. THE NEW PHYTOLOGIST 2021; 229:126-139. [PMID: 32043277 PMCID: PMC7754370 DOI: 10.1111/nph.16477] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 02/04/2020] [Indexed: 05/20/2023]
Abstract
VERNALIZATION2 (VRN2), an angiosperm-specific subunit of the polycomb repressive complex 2 (PRC2), is an oxygen (O2 )-regulated target of the PCO branch of the PRT6 N-degron pathway of ubiquitin-mediated proteolysis. How this post-translational regulation coordinates VRN2 activity remains to be fully established. Here we use Arabidopsis thaliana ecotypes, mutants and transgenic lines to determine how control of VRN2 stability contributes to its functions during plant development. VRN2 localizes to endogenous hypoxic regions in aerial and root tissues. In the shoot apex, VRN2 differentially modulates flowering time dependent on photoperiod, whilst its presence in lateral root primordia and the root apical meristem negatively regulates root system architecture. Ectopic accumulation of VRN2 does not enhance its effects on flowering, but does potentiate its repressive effects on root growth. In late-flowering vernalization-dependent ecotypes, VRN2 is only active outside meristems when its proteolysis is inhibited in response to cold exposure, as its function requires concomitant cold-triggered increases in other PRC2 subunits and cofactors. We conclude that the O2 -sensitive N-degron of VRN2 has a dual function, confining VRN2 to meristems and primordia, where it has specific developmental roles, whilst also permitting broad accumulation outside of meristems in response to environmental cues, leading to other functions.
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Affiliation(s)
| | - Hannah M. Tedds
- School of BiosciencesUniversity of BirminghamEdgbastonB15 2TTUK
| | - Mark Bailey
- School of BiosciencesUniversity of BirminghamEdgbastonB15 2TTUK
| | - Colleen Sprigg
- School of BiosciencesUniversity of BirminghamEdgbastonB15 2TTUK
| | | | | | | | | | - Daniel J. Gibbs
- School of BiosciencesUniversity of BirminghamEdgbastonB15 2TTUK
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32
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Weits DA, van Dongen JT, Licausi F. Molecular oxygen as a signaling component in plant development. THE NEW PHYTOLOGIST 2021; 229:24-35. [PMID: 31943217 DOI: 10.1111/nph.16424] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 12/10/2019] [Indexed: 05/24/2023]
Abstract
While traditionally hypoxia has been studied as a detrimental component of flooding stress, the last decade has flourished with studies reporting the involvement of molecular oxygen availability in plant developmental processes. Moreover, proliferating and undifferentiated cells from different plant tissues were found to reside in endogenously generated hypoxic niches. Thus, stress-associated acute hypoxia may be distinguished from constitutively generated chronic hypoxia. The Cys/Arg branch of the N-degron pathway assumes a central role in integrating oxygen levels resulting in proteolysis of transcriptional regulators that control different aspects of plant growth and development. As a target of this pathway, group VII of the Ethylene Response Factor (ERF-VII) family has emerged as a hub for the integration of oxygen dynamics in root development and during seedling establishment. Additionally, vegetative shoot meristem activity and reproductive transition were recently associated with oxygen availability via two novel substrates of the N-degron pathways: VERNALISATION 2 (VRN2) and LITTLE ZIPPER 2 (ZPR2). Together, these observations support roles for molecular oxygen as a signalling molecule in plant development, as well as in essential metabolic reactions. Here, we review recent findings regarding oxygen-regulated development, and discuss outstanding questions that spring from these discoveries.
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Affiliation(s)
- Daan A Weits
- Plantlab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, 56010, Italy
| | | | - Francesco Licausi
- Plantlab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, 56010, Italy
- Biology Department, University of Pisa, Pisa, 56126, Italy
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33
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Hammarlund EU, Flashman E, Mohlin S, Licausi F. Oxygen-sensing mechanisms across eukaryotic kingdoms and their roles in complex multicellularity. Science 2020; 370:370/6515/eaba3512. [PMID: 33093080 DOI: 10.1126/science.aba3512] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 07/07/2020] [Indexed: 12/17/2022]
Abstract
Oxygen-sensing mechanisms of eukaryotic multicellular organisms coordinate hypoxic cellular responses in a spatiotemporal manner. Although this capacity partly allows animals and plants to acutely adapt to oxygen deprivation, its functional and historical roots in hypoxia emphasize a broader evolutionary role. For multicellular life-forms that persist in settings with variable oxygen concentrations, the capacity to perceive and modulate responses in and between cells is pivotal. Animals and higher plants represent the most complex life-forms that ever diversified on Earth, and their oxygen-sensing mechanisms demonstrate convergent evolution from a functional perspective. Exploring oxygen-sensing mechanisms across eukaryotic kingdoms can inform us on biological innovations to harness ever-changing oxygen availability at the dawn of complex life and its utilization for their organismal development.
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Affiliation(s)
- Emma U Hammarlund
- Translational Cancer Research, Department of Laboratory Medicine, Lund University, Scheelevägen 8, 223 81 Lund, Sweden. .,Nordic Center for Earth Evolution, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.,Department of Geology, Lund University, Sölvegatan 12, 223 62 Lund, Sweden
| | - Emily Flashman
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Sofie Mohlin
- Translational Cancer Research, Department of Laboratory Medicine, Lund University, Scheelevägen 8, 223 81 Lund, Sweden.,Division of Pediatrics, Department of Clinical Sciences, Lund University, 221 00 Lund, Sweden
| | - Francesco Licausi
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK. .,PlantLab, Institute of Life Sciences, Scuola Superiore, Sant'Anna, 56124 Pisa, Italy.,Department of Biology, University of Pisa, Pisa, Italy
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34
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Molecular basis for cysteine oxidation by plant cysteine oxidases from Arabidopsis thaliana. J Struct Biol 2020; 213:107663. [PMID: 33207269 DOI: 10.1016/j.jsb.2020.107663] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/30/2022]
Abstract
Plant Cysteine Oxidases (PCOs) play important roles in controlling the stability of Group VII ethylene response factors (ERF-VIIs) via Arg/N-degron pathway through catalyzing the oxidation of their N-Cys for subsequent Arginyl-tRNA--protein transferase 1 (ATE1) mediated arginine installation. Here we presented the crystal structures of PCO2, PCO4, and PCO5 from Arabidopsis thaliana (AtPCOs) and examined their in vitro activity by Mass spectrometry (MS). On the basis of Tris-bound AtPCO2, we modelled the structure of Cys-bound AtPCO2 and identified key AtPCO2 residues involved in N-Cys recognition and oxidation. Alanine substitution of potential N-Cys interaction residues impaired the activity of AtPCO5 remarkably. The structural research, complemented by mutagenesis and MS experiments, not only uncovers the substrate recognition and catalytic mode by AtPCOs, but also sheds light on the future design of potent inhibitors for plant cysteine oxidases.
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35
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Lamichhane S, Alpuerto JB, Han A, Fukao T. The Central Negative Regulator of Flooding Tolerance, the PROTEOLYSIS 6 Branch of the N-degron Pathway, Adversely Modulates Salinity Tolerance in Arabidopsis. PLANTS 2020; 9:plants9111415. [PMID: 33113884 PMCID: PMC7690746 DOI: 10.3390/plants9111415] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 10/21/2020] [Accepted: 10/21/2020] [Indexed: 11/25/2022]
Abstract
Seawater intrusion in coastal regions and waterlogging in salinized lands are serious constraints that reduce crop productivity under changing climate scenarios. Under these conditions, plants encounter flooding and salinity concurrently or sequentially. Identification and characterization of genes and pathways associated with both flooding and salinity adaptation are critical steps for the simultaneous improvement of plant tolerance to these stresses. The PROTEOLYSIS 6 (PRT6) branch of the N-degron pathway is a well-characterized process that negatively regulates flooding tolerance in plants. Here, we determined the role of the PRT6/N-degron pathway in salinity tolerance in Arabidopsis. This study demonstrates that the prt6 mutation enhances salinity tolerance at the germination, seedling, and adult plant stages. Maintenance of chlorophyll content and root growth under high salt in the prt6 mutant was linked with the restricted accumulation of sodium ions (Na+) in shoots and roots of the mutant genotype. The prt6 mutation also stimulated mRNA accumulation of key transcription factors in ABA-dependent and independent pathways of osmotic/salinity tolerance, accompanied by the prominent expression of their downstream genes. Furthermore, the prt6 mutant displayed increased sensitivity to ethylene and brassinosteroids, which can suppress Na+ uptake and promote the expression of stress-responsive genes. This study provides genetic evidence that both salinity and flooding tolerance is coordinated through a common regulatory pathway in Arabidopsis.
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Affiliation(s)
- Suman Lamichhane
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; (S.L.); (J.B.A.); (A.H.)
- Texas A & M Agrilife Research, Beaumont, TX 77713, USA
| | - Jasper B. Alpuerto
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; (S.L.); (J.B.A.); (A.H.)
- Texas A & M Agrilife Research, Beaumont, TX 77713, USA
| | - Abigail Han
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; (S.L.); (J.B.A.); (A.H.)
| | - Takeshi Fukao
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; (S.L.); (J.B.A.); (A.H.)
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Eiheiji, Fukui 910-1195, Japan
- Correspondence:
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36
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Chua NK, Coates HW, Brown AJ. Squalene monooxygenase: a journey to the heart of cholesterol synthesis. Prog Lipid Res 2020; 79:101033. [DOI: 10.1016/j.plipres.2020.101033] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 02/07/2023]
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37
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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] [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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38
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Avcilar-Kucukgoze I, Gamper H, Polte C, Ignatova Z, Kraetzner R, Shtutman M, Hou YM, Dong DW, Kashina A. tRNA Arg-Derived Fragments Can Serve as Arginine Donors for Protein Arginylation. Cell Chem Biol 2020; 27:839-849.e4. [PMID: 32553119 DOI: 10.1016/j.chembiol.2020.05.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/12/2020] [Accepted: 05/27/2020] [Indexed: 12/23/2022]
Abstract
Arginyltransferase ATE1 mediates posttranslational arginylation and plays key roles in multiple physiological processes. ATE1 utilizes arginyl (Arg)-tRNAArg as the donor of Arg, putting this reaction into a direct competition with the protein synthesis machinery. Here, we address the question of ATE1- Arg-tRNAArg specificity as a potential mechanism enabling this competition in vivo. Using in vitro arginylation assays and Ate1 knockout models, we find that, in addition to full-length tRNA, ATE1 is also able to utilize short tRNAArg fragments that bear structural resemblance to tRNA-derived fragments (tRF), a recently discovered class of small regulatory non-coding RNAs with global emerging biological role. Ate1 knockout cells show a decrease in tRFArg generation and a significant increase in the ratio of tRNAArg:tRFArg compared with wild type, suggesting a functional link between tRFArg and arginylation. We propose that generation of physiologically important tRFs can serve as a switch between translation and protein arginylation.
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Affiliation(s)
- Irem Avcilar-Kucukgoze
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Christine Polte
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20148 Hamburg, Germany
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20148 Hamburg, Germany
| | - Ralph Kraetzner
- Department of Pediatrics and Adolescent Medicine, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Michael Shtutman
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Dawei W Dong
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anna Kashina
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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39
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Elfiky AA, Ismail AM, Elshemey WM. Recognition of gluconeogenic enzymes; Icl1, Fbp1, and Mdh2 by Gid4 ligase: A molecular docking study. J Mol Recognit 2020; 33:e2831. [DOI: 10.1002/jmr.2831] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 02/03/2023]
Affiliation(s)
- Abdo A. Elfiky
- Biophysics Department, Faculty of ScienceCairo University Giza Egypt
- College of Applied Medical SciencesUniversity of Al‐Jouf Sakaka Saudi Arabia
| | - Alaa M. Ismail
- Biophysics Department, Faculty of ScienceCairo University Giza Egypt
| | - Wael M. Elshemey
- Biophysics Department, Faculty of ScienceCairo University Giza Egypt
- Department of Physics, Faculty of ScienceIslamic University in Madinah Medina Saudi Arabia
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40
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Bäumler J, Riber W, Klecker M, Müller L, Dissmeyer N, Weig AR, Mustroph A. AtERF#111/ABR1 is a transcriptional activator involved in the wounding response. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:969-990. [PMID: 31385625 DOI: 10.1111/tpj.14490] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 07/24/2019] [Accepted: 07/29/2019] [Indexed: 06/10/2023]
Abstract
AtERF#111/ABR1 belongs to the group X of the ERF/AP2 transcription factor family (GXERFs) and is shoot specifically induced under submergence and hypoxia. It was described to be an ABA-response repressor, but our data reveal a completely different function. Surprisingly, AtERF#111 expression is strongly responsive to wounding stress. Expression profiling of ERF#111-overexpressing (OE) plants, which show morphological phenotypes like increased root hair length and number, strengthens the hypothesis of AtERF#111 being involved in the wounding response, thereby acting as a transcriptional activator of gene expression. Consistent with a potential function outside of oxygen signalling, we could not assign AtERF#111 as a target of the PRT6 N-degron pathway, even though it starts with a highly conserved N-terminal Met-Cys (MC) motif. However, the protein is unstable as it is degraded in an ubiquitin-dependent manner. Finally, direct target genes of AtERF#111 were identified by microarray analyses and subsequently confirmed by protoplast transactivation assays. The special roles of diverse members of the plant-specific GXERFs in coordinating stress signalling and wound repair mechanisms have been recently hypothesized, and our data suggest that AtERF#111 is indeed involved in these processes.
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Affiliation(s)
- Judith Bäumler
- Plant Physiology, University Bayreuth, Universitaetsstr. 30, 95440, Bayreuth, Germany
| | - Willi Riber
- Plant Physiology, University Bayreuth, Universitaetsstr. 30, 95440, Bayreuth, Germany
| | - Maria Klecker
- Plant Physiology, University Bayreuth, Universitaetsstr. 30, 95440, Bayreuth, Germany
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
- Science Campus Halle - Plant-Based Bioeconomy, Betty-Heimann-Str. 3, 06120, Halle (Saale), Germany
| | - Leon Müller
- Plant Physiology, University Bayreuth, Universitaetsstr. 30, 95440, Bayreuth, Germany
| | - Nico Dissmeyer
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
- Science Campus Halle - Plant-Based Bioeconomy, Betty-Heimann-Str. 3, 06120, Halle (Saale), Germany
| | - Alfons R Weig
- Genomics & Bioinformatics, University Bayreuth, Universitaetsstr. 30, 95440, Bayreuth, Germany
| | - Angelika Mustroph
- Plant Physiology, University Bayreuth, Universitaetsstr. 30, 95440, Bayreuth, Germany
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41
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Bouchnak I, van Wijk KJ. N-Degron Pathways in Plastids. TRENDS IN PLANT SCIENCE 2019; 24:917-926. [PMID: 31300194 DOI: 10.1016/j.tplants.2019.06.013] [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: 04/26/2019] [Revised: 06/12/2019] [Accepted: 06/19/2019] [Indexed: 06/10/2023]
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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42
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Eldeeb MA, Siva-Piragasam R, Ragheb MA, Esmaili M, Salla M, Fahlman RP. A molecular toolbox for studying protein degradation in mammalian cells. J Neurochem 2019; 151:520-533. [PMID: 31357232 DOI: 10.1111/jnc.14838] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/03/2019] [Accepted: 07/24/2019] [Indexed: 12/14/2022]
Abstract
Protein degradation is a crucial regulatory process in maintaining cellular proteostasis. The selective degradation of intracellular proteins controls diverse cellular and biochemical processes in all kingdoms of life. Targeted protein degradation is implicated in controlling the levels of regulatory proteins as well as eliminating misfolded and any otherwise abnormal proteins. Deregulation of protein degradation is concomitant with the progression of various neurodegenerative disorders such as Parkinson's and Alzheimer's diseases. Thus, methods of measuring metabolic half-lives of proteins greatly influence our understanding of the diverse functions of proteins in mammalian cells including neuronal cells. Historically, protein degradation rates have been studied via exploiting methods that estimate overall protein degradation or focus on few individual proteins. Notably, with the recent technical advances and developments in proteomic and imaging techniques, it is now possible to measure degradation rates of a large repertoire of defined proteins and analyze the degradation profile in a detailed spatio-temporal manner, with the aim of determining proteome-wide protein stabilities upon different physiological conditions. Herein, we discuss some of the classical and novel methods for determining protein degradation rates highlighting the crucial role of some state of art approaches in deciphering the global impact of dynamic nature of targeted degradation of cellular proteins. This article is part of the Special Issue "Proteomics".
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Affiliation(s)
- Mohamed A Eldeeb
- Department of Chemistry (Biochemistry Division), Faculty of Science, Cairo University, Giza, Egypt.,Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | | | - Mohamed A Ragheb
- Department of Chemistry (Biochemistry Division), Faculty of Science, Cairo University, Giza, Egypt
| | - Mansoore Esmaili
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Mohamed Salla
- Department of Biological Sciences, Lebanese International University, Bekaa, Lebanon
| | - Richard P Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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43
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Abstract
Protein arginylation-enzymatic addition of the amino acid arginine (Arg) to proteins, mediated by arginyltransferase ATE1, has been discovered in 1963, but is still relatively poorly understood. Studies of arginylation present many technical challenges, which arise from the fact that Arg is a regular amino acid that also incorporates into proteins during translation. Thus, in vitro arginylation needs to be conducted in a strictly ribosome-free system, in highly controlled conditions. Identification of arginylated proteins is currently only possible by high precision mass spectrometry, which relies on very high mass accuracy of the instruments, specific ionization patterns during mass fragmentation, as well as multiple stringent steps of automated and manual validation. Below we describe the methods of in vitro arginylation and mass spectrometry analysis of arginylated proteins, developed by our groups during the last 15 years.
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Affiliation(s)
- Junling Wang
- University of Pennsylvania, Philadelphia, PA, United States
| | - John R Yates
- The Scripps Research Institute, LaJolla, CA, United States
| | - Anna Kashina
- University of Pennsylvania, Philadelphia, PA, United States.
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44
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Montandon C, Dougan DA, van Wijk KJ. N-degron specificity of chloroplast ClpS1 in plants. FEBS Lett 2019; 593:962-970. [PMID: 30953344 DOI: 10.1002/1873-3468.13378] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 12/29/2022]
Abstract
The prokaryotic N-degron pathway depends on the Clp chaperone-protease system and the ClpS adaptor for recognition of N-degron bearing substrates. Plant chloroplasts contain a diversified Clp protease, including the ClpS homolog ClpS1. Several candidate ClpS1 substrates have been identified, but the N-degron specificity is unclear. Here, we employed in vitro ClpS1 affinity assays using eight N-degron green fluorescence protein reporters containing either F, Y, L, W, I, or R in the N-terminal position. This demonstrated that ClpS1 has a restricted N-degron specificity, recognizing proteins bearing an N-terminal F or W, only weakly recognizing L, but not recognizing Y or I. This affinity is dependent on two conserved residues in the ClpS1 binding pocket and is sensitive to FR dipeptide competition, suggesting a unique chloroplast N-degron pathway.
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Affiliation(s)
- Cyrille Montandon
- Plant Biology Section, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY, USA
| | - David A Dougan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Klaas J van Wijk
- Plant Biology Section, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY, USA
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45
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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. JOURNAL OF EXPERIMENTAL BOTANY 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] [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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46
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Faden F, Mielke S, Dissmeyer N. Modulating Protein Stability to Switch Toxic Protein Function On and Off in Living Cells. PLANT PHYSIOLOGY 2019; 179:929-942. [PMID: 30679267 PMCID: PMC6393803 DOI: 10.1104/pp.18.01215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/10/2019] [Indexed: 05/02/2023]
Abstract
Toxic proteins are prime targets for molecular farming (the generation of pharmacologically active or biotechnologically usable compounds in plants) and are also efficient tools for targeted cell ablation in genetics, developmental biology, and biotechnology. However, achieving conditional activity of cytotoxins and maintaining the toxin-expressing plants as stably transformed lines remain challenging. Here, we produce a switchable version of the highly cytotoxic bacterial RNase barnase by fusing the protein to a portable protein degradation cassette, the low-temperature degron cassette. This method allows conditional genetics based on conditional protein degradation via the N-end rule or N-degron pathway and has been used to vice versa accumulate and/or deplete a diverse variety of highly active, unstable or stable target proteins in different living multicellular organisms and cell systems. Moreover, we expressed the barnase fusion under control of the trichome-specific TRIPTYCHON promoter. This enabled efficient temperature-dependent control of protein accumulation in Arabidopsis (Arabidopsis thaliana) leaf hairs (trichomes). By tuning the levels of the protein, we were able to control the fate of trichomes in vivo. The on-demand formation of trichomes through manipulating the balance between stabilization and destabilization of barnase provides proof of concept for a robust and powerful tool for conditional switchable cell arrest. We present this tool as a potential strategy for the manufacture and accumulation of cytotoxic proteins and toxic high-value products in plants or for conditional genetic cell ablation.
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Affiliation(s)
- Frederik Faden
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany
- ScienceCampus Halle, Plant-Based Bioeconomy, D-06120 Halle (Saale), Germany
| | - Stefan Mielke
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany
- ScienceCampus Halle, Plant-Based Bioeconomy, D-06120 Halle (Saale), Germany
| | - Nico Dissmeyer
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany
- ScienceCampus Halle, Plant-Based Bioeconomy, D-06120 Halle (Saale), Germany
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