1
|
Zhang H, Rundle C, Winter N, Miricescu A, Mooney BC, Bachmair A, Graciet E, Theodoulou FL. BIG enhances Arg/N-degron pathway-mediated protein degradation to regulate Arabidopsis hypoxia responses and suberin deposition. THE PLANT CELL 2024; 36:3177-3200. [PMID: 38608155 PMCID: PMC11371152 DOI: 10.1093/plcell/koae117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 03/15/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024]
Abstract
BIG/DARK OVEREXPRESSION OF CAB1/TRANSPORT INHIBITOR RESPONSE3 is a 0.5 MDa protein associated with multiple functions in Arabidopsis (Arabidopsis thaliana) signaling and development. However, the biochemical functions of BIG are unknown. We investigated a role for BIG in the Arg/N-degron pathways, in which substrate protein fate is influenced by the N-terminal residue. We crossed a big loss-of-function allele to 2 N-degron pathway E3 ligase mutants, proteolysis6 (prt6) and prt1, and examined the stability of protein substrates. Stability of model substrates was enhanced in prt6-1 big-2 and prt1-1 big-2 relative to the respective single mutants, and the abundance of the PRT6 physiological substrates, HYPOXIA-RESPONSIVE ERF2 (HRE2) and VERNALIZATION2 (VRN2), was similarly increased in prt6 big double mutants. Hypoxia marker expression was enhanced in prt6 big double mutants; this constitutive response required arginyl transferase activity and RAP-type Group VII ethylene response factor (ERFVII) transcription factors. Transcriptomic analysis of roots not only demonstrated increased expression of multiple hypoxia-responsive genes in the double mutant relative to prt6, but also revealed other roles for PRT6 and BIG, including regulation of suberin deposition through both ERFVII-dependent and independent mechanisms, respectively. Our results show that BIG acts together with PRT6 to regulate the hypoxia-response and broader processes in Arabidopsis.
Collapse
Affiliation(s)
- Hongtao Zhang
- Plant Sciences and the Bioeconomy, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Chelsea Rundle
- Plant Sciences and the Bioeconomy, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Nikola Winter
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | | | - Brian C Mooney
- Department of Biology, Maynooth University, Maynooth, Ireland
| | - Andreas Bachmair
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | | | | |
Collapse
|
2
|
Isono E, Li J, Pulido P, Siao W, Spoel SH, Wang Z, Zhuang X, Trujillo M. Protein degrons and degradation: Exploring substrate recognition and pathway selection in plants. THE PLANT CELL 2024; 36:3074-3098. [PMID: 38701343 PMCID: PMC11371205 DOI: 10.1093/plcell/koae141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/27/2024] [Accepted: 04/07/2024] [Indexed: 05/05/2024]
Abstract
Proteome composition is dynamic and influenced by many internal and external cues, including developmental signals, light availability, or environmental stresses. Protein degradation, in synergy with protein biosynthesis, allows cells to respond to various stimuli and adapt by reshaping the proteome. Protein degradation mediates the final and irreversible disassembly of proteins, which is important for protein quality control and to eliminate misfolded or damaged proteins, as well as entire organelles. Consequently, it contributes to cell resilience by buffering against protein or organellar damage caused by stresses. Moreover, protein degradation plays important roles in cell signaling, as well as transcriptional and translational events. The intricate task of recognizing specific proteins for degradation is achieved by specialized systems that are tailored to the substrate's physicochemical properties and subcellular localization. These systems recognize diverse substrate cues collectively referred to as "degrons," which can assume a range of configurations. They are molecular surfaces recognized by E3 ligases of the ubiquitin-proteasome system but can also be considered as general features recognized by other degradation systems, including autophagy or even organellar proteases. Here we provide an overview of the newest developments in the field, delving into the intricate processes of protein recognition and elucidating the pathways through which they are recruited for degradation.
Collapse
Affiliation(s)
- Erika Isono
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Jianming Li
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Pablo Pulido
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain
| | - Wei Siao
- Department of Biology, Aachen RWTH University, Institute of Molecular Plant Physiology, 52074 Aachen, Germany
| | - Steven H Spoel
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Zhishuo Wang
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Xiaohong Zhuang
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Marco Trujillo
- Department of Biology, Aachen RWTH University, Institute of Molecular Plant Physiology, 52074 Aachen, Germany
| |
Collapse
|
3
|
Spoel SH, Dong X. Salicylic acid in plant immunity and beyond. THE PLANT CELL 2024; 36:1451-1464. [PMID: 38163634 PMCID: PMC11062473 DOI: 10.1093/plcell/koad329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/06/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024]
Abstract
As the most widely used herbal medicine in human history and a major defence hormone in plants against a broad spectrum of pathogens and abiotic stresses, salicylic acid (SA) has attracted major research interest. With applications of modern technologies over the past 30 years, studies of the effects of SA on plant growth, development, and defence have revealed many new research frontiers and continue to deliver surprises. In this review, we provide an update on recent advances in our understanding of SA metabolism, perception, and signal transduction mechanisms in plant immunity. An overarching theme emerges that SA executes its many functions through intricate regulation at multiple steps: SA biosynthesis is regulated both locally and systemically, while its perception occurs through multiple cellular targets, including metabolic enzymes, redox regulators, transcription cofactors, and, most recently, an RNA-binding protein. Moreover, SA orchestrates a complex series of post-translational modifications of downstream signaling components and promotes the formation of biomolecular condensates that function as cellular signalling hubs. SA also impacts wider cellular functions through crosstalk with other plant hormones. Looking into the future, we propose new areas for exploration of SA functions, which will undoubtedly uncover more surprises for many years to come.
Collapse
Affiliation(s)
- Steven H Spoel
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, The King's Buildings, Edinburgh EH9 3BF, UK
| | - Xinnian Dong
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| |
Collapse
|
4
|
Tajdel-Zielińska M, Janicki M, Marczak M, Ludwików A. Arabidopsis HECT and RING-type E3 Ligases Promote MAPKKK18 Degradation to Regulate Abscisic Acid Signaling. PLANT & CELL PHYSIOLOGY 2024; 65:390-404. [PMID: 38153765 PMCID: PMC11020294 DOI: 10.1093/pcp/pcad165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/29/2023] [Accepted: 12/20/2023] [Indexed: 12/29/2023]
Abstract
Mitogen-activated protein kinase (MAPK) cascades are conserved signaling pathways that transduce extracellular signals into diverse cellular responses. Arabidopsis MAPKKK18 is a component of the MAPKKK17/18-MKK3-MPK1/2/7/14 cascades, which play critical roles in abscisic acid (ABA) signaling, drought tolerance and senescence. A very important aspect of MAP kinase signaling is both its activation and its termination, which must be tightly controlled to achieve appropriate biological responses. Recently, the ubiquitin-proteasome system (UPS) has received increasing attention as a key mechanism for maintaining the homeostasis of MAPK cascade components and other ABA signaling effectors. Previous studies have shown that the stability of MAPKKK18 is regulated by the UPS via the ABA core pathway. Here, using multiple proteomic approaches, we found that MAPKKK17/18 turnover is tightly controlled by three E3 ligases, UPL1, UPL4 and KEG. We also identified lysines 154 and 237 as critical for MAPKKK18 stability. Taken together, this study sheds new light on the mechanism that controls MAPKKK17/18 activity and function.
Collapse
Affiliation(s)
- Małgorzata Tajdel-Zielińska
- Laboratory Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University Poznan, Uniwersytetu Poznańskiego 6, Poznań 61-614, Poland
| | - Maciej Janicki
- Laboratory Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University Poznan, Uniwersytetu Poznańskiego 6, Poznań 61-614, Poland
| | - Małgorzata Marczak
- Laboratory Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University Poznan, Uniwersytetu Poznańskiego 6, Poznań 61-614, Poland
| | - Agnieszka Ludwików
- Laboratory Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University Poznan, Uniwersytetu Poznańskiego 6, Poznań 61-614, Poland
| |
Collapse
|
5
|
Sachdeva S, Singh R, Maurya A, Singh VK, Singh UM, Kumar A, Singh GP. New insights into QTNs and potential candidate genes governing rice yield via a multi-model genome-wide association study. BMC PLANT BIOLOGY 2024; 24:124. [PMID: 38373874 PMCID: PMC10877931 DOI: 10.1186/s12870-024-04810-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/08/2024] [Indexed: 02/21/2024]
Abstract
BACKGROUND Rice (Oryza sativa L.) is one of the globally important staple food crops, and yield-related traits are prerequisites for improved breeding efficiency in rice. Here, we used six different genome-wide association study (GWAS) models for 198 accessions, with 553,229 single nucleotide markers (SNPs) to identify the quantitative trait nucleotides (QTNs) and candidate genes (CGs) governing rice yield. RESULTS Amongst the 73 different QTNs in total, 24 were co-localized with already reported QTLs or loci in previous mapping studies. We obtained fifteen significant QTNs, pathway analysis revealed 10 potential candidates within 100kb of these QTNs that are predicted to govern plant height, days to flowering, and plot yield in rice. Based on their superior allelic information in 20 elite and 6 inferior genotypes, we found a higher percentage of superior alleles in the elite genotypes in comparison to inferior genotypes. Further, we implemented expression analysis and enrichment analysis enabling the identification of 73 candidate genes and 25 homologues of Arabidopsis, 19 of which might regulate rice yield traits. Of these candidate genes, 40 CGs were found to be enriched in 60 GO terms of the studied traits for instance, positive regulator metabolic process (GO:0010929), intracellular part (GO:0031090), and nucleic acid binding (GO:0090079). Haplotype and phenotypic variation analysis confirmed that LOC_OS09G15770, LOC_OS02G36710 and LOC_OS02G17520 are key candidates associated with rice yield. CONCLUSIONS Overall, we foresee that the QTNs, putative candidates elucidated in the study could summarize the polygenic regulatory networks controlling rice yield and be useful for breeding high-yielding varieties.
Collapse
Grants
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
Collapse
Affiliation(s)
- Supriya Sachdeva
- Division of Genomic Resources, ICAR-NBPGR, Pusa, New Delhi, India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-NBPGR, Pusa, New Delhi, India.
| | - Avantika Maurya
- Division of Genomic Resources, ICAR-NBPGR, Pusa, New Delhi, India
| | - Vikas K Singh
- International Rice Research Institute (IRRI), South Asia Hub, ICRISAT, Hyderabad, India
| | - Uma Maheshwar Singh
- International Rice Research Institute (IRRI), South Asia Regional Centre (ISARC), Varanasi, India
| | - Arvind Kumar
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | | |
Collapse
|
6
|
Xue B, Zhang C, Wang Y, Liu L, Wang W, Schiefelbein J, Yu F, An L. HECT-type ubiquitin ligase KAKTUS mediates the proteasome-dependent degradation of cyclin-dependent kinase inhibitor KRP2 during trichome morphogenesis in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:871-886. [PMID: 37565606 DOI: 10.1111/tpj.16415] [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: 09/06/2022] [Accepted: 07/19/2023] [Indexed: 08/12/2023]
Abstract
SUMMARYTrichome development is a fascinating model to elaborate the plant cell differentiation and growth processes. A wealth of information has pointed to the contributions of the components associated with cell cycle control and ubiquitin/26S proteasome system (UPS) to trichome morphogenesis, but how these two pathways are connected remains obscure. Here, we report that HECT‐type ubiquitin ligase KAKTUS (KAK) targets the cyclin‐dependent kinase (CDK) inhibitor KRP2 (for kip‐related protein 2) for proteasome‐dependent degradation during trichome branching in Arabidopsis. We show that over‐expression of KRP2 promotes trichome branching and endoreduplication which is similar to kak loss of function mutants. KAK directly interacts with KRP2 and mediates KRP2 degradation. Mutation of KAK results in the accumulation of steady‐state KRP2. Consistently, in kak pKRP2:KRP2‐GFP plants, the trichome branching is further induced compared with the single mutant. Taken together, our studies bridge the cell cycle control and UPS pathways during trichome development and underscore the importance of post‐translational control in epidermal differentiation.
Collapse
Affiliation(s)
- Baoyong Xue
- State Key Laboratory of Crop Stress Biology for Arid Area and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chi Zhang
- State Key Laboratory of Crop Stress Biology for Arid Area and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yali Wang
- State Key Laboratory of Crop Stress Biology for Arid Area and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lu Liu
- State Key Laboratory of Crop Stress Biology for Arid Area and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Wenjia Wang
- CAS Center for Excellence in Molecular Plant Science, Chinese Academy of Sciences, Shanghai, 200032, China
| | - John Schiefelbein
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Fei Yu
- State Key Laboratory of Crop Stress Biology for Arid Area and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lijun An
- State Key Laboratory of Crop Stress Biology for Arid Area and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| |
Collapse
|
7
|
Plant proteostasis: a proven and promising target for crop improvement. Essays Biochem 2022; 66:75-85. [PMID: 35929615 DOI: 10.1042/ebc20210078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 11/17/2022]
Abstract
The Green Revolution of the 1960s accomplished dramatic increases in crop yields through genetic improvement, chemical fertilisers, irrigation, and mechanisation. However, the current trajectory of population growth, against a backdrop of climate change and geopolitical unrest, predicts that agricultural production will be insufficient to ensure global food security in the next three decades. Improvements to crops that go beyond incremental gains are urgently needed. Plant biology has also undergone a revolution in recent years, through the development and application of powerful technologies including genome sequencing, a pantheon of 'omics techniques, precise genome editing, and step changes in structural biology and microscopy. Proteostasis - the collective processes that control the protein complement of the cell, comprising synthesis, modification, localisation, and degradation - is a field that has benefitted from these advances. This special issue presents a selection of the latest research in this vibrant field, with a particular focus on protein degradation. In the current article, we highlight the diverse and widespread contributions of plant proteostasis to agronomic traits, suggest opportunities and strategies to manipulate different elements of proteostatic mechanisms for crop improvement, and discuss the challenges involved in bringing these ideas into practice.
Collapse
|
8
|
Lan W, Ma W, Zheng S, Qiu Y, Zhang H, Lu H, Zhang Y, Miao Y. Ubiquitome profiling reveals a regulatory pattern of UPL3 with UBP12 on metabolic-leaf senescence. Life Sci Alliance 2022; 5:e202201492. [PMID: 35926874 PMCID: PMC9354775 DOI: 10.26508/lsa.202201492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 12/03/2022] Open
Abstract
The HECT-type UPL3 ligase plays critical roles in plant development and stress protection, but understanding of its regulation remains limited. Here, the multi-omics analyses of ubiquitinated proteins in <i>upl3</i> mutants were performed. A landscape of UPL3-dependent ubiquitinated proteins is constructed: Preferential ubiquitination of proteins related to carbon fixation represented the largest set of proteins with increased ubiquitination in the <i>upl3</i> plant, including most of carbohydrate metabolic enzymes, BRM, and variant histone, whereas a small set of proteins with reduced ubiquitination caused by the <i>upl3</i> mutation were linked to cysteine/methionine synthesis, as well as hexokinase 1 (HXK1) and phosphoenolpyruvate carboxylase 2 (PPC2). Notably, ubiquitin hydrolase 12 (UBP12), BRM, HXK1, and PPC2 were identified as the UPL3-interacting partners in vivo and in vitro. Characterization of <i>brm</i>, <i>upl3</i>, <i>ppc2</i>, <i>gin2</i>, and <i>ubp12</i> mutant plants and proteomic and transcriptomic analysis suggested that UPL3 fine-tunes carbohydrate metabolism, mediating cellular senescence by interacting with UBP12, BRM, HXK1, and PPC2. Our results highlight a regulatory pattern of UPL3 with UBP12 as a hub of regulator on proteolysis-independent regulation and proteolysis-dependent degradation.
Collapse
Affiliation(s)
- Wei Lan
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weibo Ma
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuai Zheng
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuhao Qiu
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Han Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Haisen Lu
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|