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Das Laha S, Kundu A, Podder S. Impact of biotic stresses on the Brassicaceae family and opportunities for crop improvement by exploiting genotyping traits. PLANTA 2024; 259:97. [PMID: 38520529 DOI: 10.1007/s00425-024-04379-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/07/2024] [Indexed: 03/25/2024]
Abstract
MAIN CONCLUSION Utilizing RNAi, miRNA, siRNA, lncRNA and exploiting genotyping traits can help safeguard the food supply from illnesses and pest damage to Brassicas, as well as reduce yield losses caused by plant pathogens and insect pests. In the natural environment, plants face significant challenges in the form of biotic stress, due to various living organisms, leading to biological stress and a sharp decline in crop yields. To cope with these effects, plants have evolved specialized mechanisms to mitigate these challenges. Plant stress tolerance and resistance are influenced by genes associated with stress-responsive pathogens that interact with various stress-related signaling pathway components. Plants employ diverse strategies and mechanisms to combat biological stress, involving a complex network of transcription factors that interact with specific cis-elements to regulate gene expression. Understanding both plant developmental and pathogenic disease resistance mechanisms can allow us to develop stress-tolerant and -resistant crops. Brassica genus includes commercially important crops, e.g., broccoli, cabbage, cauliflower, kale, and rapeseed, cultivated worldwide, with several applications, e.g., oil production, consumption, condiments, fodder, as well as medicinal ones. Indeed, in 2020, global production of vegetable Brassica reached 96.4 million tones, a 10.6% rise from the previous decade. Taking into account their commercial importance, coupled to the impact that pathogens can have in Brassica productivity, yield losses up to 60%, this work complies the major diseases caused due to fungal, bacterial, viral, and insects in Brassica species. The review is structured into three parts. In the first part, an overview is provided of the various pathogens affecting Brassica species, including fungi, bacteria, viruses, and insects. The second part delves into the exploration of defense mechanisms that Brassica plants encounter against these pathogens including secondary metabolites, duplicated genes, RNA interference (RNAi), miRNA (micro-RNA), siRNA (small interfering RNA), and lncRNA (long non-coding RNA). The final part comprehensively outlines the current applications of CRISPR/Cas9 technology aimed at enhancing crop quality. Taken collectively, this review will contribute to our enhanced understanding of these mechanisms and their role in the development of resistance in Brassica plants, thus supporting strategies to protect this crucial crop.
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Affiliation(s)
- Shayani Das Laha
- Computational and Systems Biology Laboratory, Department of Microbiology, Raiganj University, Raiganj, West Bengal, India
- Department of Genetics and Plant Breeding, Uttar Banga Krishi Viswavidyalaya, Coochbehar, West Bengal, India
| | - Avijit Kundu
- Department of Genetics and Plant Breeding, Uttar Banga Krishi Viswavidyalaya, Coochbehar, West Bengal, India
| | - Soumita Podder
- Computational and Systems Biology Laboratory, Department of Microbiology, Raiganj University, Raiganj, West Bengal, India.
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Corbridge E, MacGregor A, Al-Saharin R, Garneau MG, Smalley S, Mooney S, Roje S, Bates PD, Hellmann H. Brassica napus Plants Gain Improved Salt-Stress Tolerance and Increased Storage Oil Biosynthesis by Interfering with CRL3 BPM Activities. PLANTS (BASEL, SWITZERLAND) 2023; 12:1085. [PMID: 36903945 PMCID: PMC10005049 DOI: 10.3390/plants12051085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/20/2023] [Accepted: 02/25/2023] [Indexed: 06/18/2023]
Abstract
Generating new strategies to improve plant performance and yield in crop plants becomes increasingly relevant with ongoing and predicted global climate changes. E3 ligases that function as key regulators within the ubiquitin proteasome pathway often are involved in abiotic stress responses, development, and metabolism in plants. The aim of this research was to transiently downregulate an E3 ligase that uses BTB/POZ-MATH proteins as substrate adaptors in a tissue-specific manner. Interfering with the E3 ligase at the seedling stage and in developing seeds results in increased salt-stress tolerance and elevated fatty acid levels, respectively. This novel approach can help to improve specific traits in crop plants to maintain sustainable agriculture.
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Affiliation(s)
- Emily Corbridge
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Alexandra MacGregor
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Raed Al-Saharin
- Department of Applied Biology, Tafila Technical University, Tafila 66110, Jordan
| | - Matthew G. Garneau
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Samuel Smalley
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Sutton Mooney
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Sanja Roje
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Philip D. Bates
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Hanjo Hellmann
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
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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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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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5
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Al-Saharin R, Hellmann H, Mooney S. Plant E3 Ligases and Their Role in Abiotic Stress Response. Cells 2022; 11:cells11050890. [PMID: 35269512 PMCID: PMC8909703 DOI: 10.3390/cells11050890] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/24/2022] [Accepted: 03/02/2022] [Indexed: 11/16/2022] Open
Abstract
Plants, as sessile organisms, have limited means to cope with environmental changes. Consequently, they have developed complex regulatory systems to ameliorate abiotic stresses im-posed by environmental changes. One such system is the ubiquitin proteasome pathway, which utilizes E3 ligases to target proteins for proteolytic degradation via the 26S proteasome. Plants ex-press a plethora of E3 ligases that are categorized into four major groups depending on their structure. They are involved in many biological and developmental processes in plants, such as DNA repair, photomorphogenesis, phytohormones signaling, and biotic stress. Moreover, many E3 ligase targets are proteins involved in abiotic stress responses, such as salt, drought, heat, and cold. In this review, we will provide a comprehensive overview of E3 ligases and their substrates that have been connected with abiotic stress in order to illustrate the diversity and complexity of how this pathway enables plant survival under stress conditions.
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Affiliation(s)
- Raed Al-Saharin
- Department of Applied Biology, Tafila Technical University, At-Tafilah 66110, Jordan
- Correspondence:
| | - Hanjo Hellmann
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA; (H.H.); (S.M.)
| | - Sutton Mooney
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA; (H.H.); (S.M.)
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Qi H, Xia FN, Xiao S, Li J. TRAF proteins as key regulators of plant development and stress responses. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:431-448. [PMID: 34676666 DOI: 10.1111/jipb.13182] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
Tumor necrosis factor receptor-associated factor (TRAF) proteins are conserved in higher eukaryotes and play key roles in transducing cellular signals across different organelles. They are characterized by their C-terminal region (TRAF-C domain) containing seven to eight anti-parallel β-sheets, also known as the meprin and TRAF-C homology (MATH) domain. Over the past few decades, significant progress has been made toward understanding the diverse roles of TRAF proteins in mammals and plants. Compared to other eukaryotic species, the Arabidopsis thaliana and rice (Oryza sativa) genomes encode many more TRAF/MATH domain-containing proteins; these plant proteins cluster into five classes: TRAF/MATH-only, MATH-BPM, MATH-UBP (ubiquitin protease), Seven in absentia (SINA), and MATH-Filament and MATH-PEARLI-4 proteins, suggesting parallel evolution of TRAF proteins in plants. Increasing evidence now indicates that plant TRAF proteins form central signaling networks essential for multiple biological processes, such as vegetative and reproductive development, autophagosome formation, plant immunity, symbiosis, phytohormone signaling, and abiotic stress responses. Here, we summarize recent advances and highlight future prospects for understanding on the molecular mechanisms by which TRAF proteins act in plant development and stress responses.
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Affiliation(s)
- Hua Qi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Fan-Nv Xia
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shi Xiao
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Juan Li
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
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Beathard C, Mooney S, Al-Saharin R, Goyer A, Hellmann H. Characterization of Arabidopsis thaliana R2R3 S23 MYB Transcription Factors as Novel Targets of the Ubiquitin Proteasome-Pathway and Regulators of Salt Stress and Abscisic Acid Response. FRONTIERS IN PLANT SCIENCE 2021; 12:629208. [PMID: 34489986 PMCID: PMC8417012 DOI: 10.3389/fpls.2021.629208] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 07/30/2021] [Indexed: 05/27/2023]
Abstract
Rapid response to environmental changes and abiotic stress to coordinate developmental programs is critical for plants. To accomplish this, plants use the ubiquitin proteasome pathway as a flexible and efficient mechanism to control protein stability and to direct cellular reactions. Here, we show that all three members of the R2R3 S23 MYB transcription factor subfamily, MYB1, MYB25, and MYB109, are degraded by the 26S proteasome, likely facilitated by a CUL3-based E3 ligase that uses MATH-BTB/POZ proteins as substrate adaptors. A detailed description of MYB1, MYB25, and MYB109 expression shows their nuclear localization and specific tissue specific expression patterns. It further demonstrates that elevated expression of MYB25 reduces sensitivities toward abscisic acid, osmotic and salt stress in Arabidopsis, while downregulation of all S23 members results in hypersensitivities. Transcriptional profiling in root and shoot of seedlings overexpressing MYB25 shows that the transcription factor widely affects cellular stress pathways related to biotic and abiotic stress control. Overall, the work extends our knowledge on proteins targeted by CUL3-based E3 ligases that use MATH-BTB/POZ proteins as substrate adaptors and provides first information on all members of the MYB S23 subfamily.
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Affiliation(s)
- Chase Beathard
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - Sutton Mooney
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - Raed Al-Saharin
- School of Biological Sciences, Washington State University, Pullman, WA, United States
- Department of Applied Biology, Tafila Technical University, At-Tafilah, Jordan
| | - Aymeric Goyer
- Department of Botany and Plant Pathology, Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR, United States
| | - Hanjo Hellmann
- School of Biological Sciences, Washington State University, Pullman, WA, United States
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Ban Z, Estelle M. CUL3 E3 ligases in plant development and environmental response. NATURE PLANTS 2021; 7:6-16. [PMID: 33452490 PMCID: PMC8932378 DOI: 10.1038/s41477-020-00833-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/08/2020] [Indexed: 05/19/2023]
Abstract
Thirty years of research have revealed the fundamental role of the ubiquitin-proteasome system in diverse aspects of cellular regulation in eukaryotes. The ubiquitin-protein ligases or E3s are central to the ubiquitin-proteasome system since they determine the specificity of ubiquitylation. The cullin-RING ligases (CRLs) constitute one large class of E3s that can be subdivided based on the cullin isoform and the substrate adapter. SCF complexes, composed of CUL1 and the SKP1/F-box protein substrate adapter, are perhaps the best characterized in plants. More recently, accumulating evidence has demonstrated the essential roles of CRL3 E3s, consisting of a CUL3 protein and a BTB/POZ substrate adaptor. In this Review, we describe the variety of CRL3s functioning in plants and the wide range of processes that they regulate. Furthermore, we illustrate how different classes of E3s may cooperate to regulate specific pathways or processes.
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Affiliation(s)
- Zhaonan Ban
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Mark Estelle
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA.
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9
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Das Laha S, Dutta S, Schäffner AR, Das M. Gene duplication and stress genomics in Brassicas: Current understanding and future prospects. JOURNAL OF PLANT PHYSIOLOGY 2020; 255:153293. [PMID: 33181457 DOI: 10.1016/j.jplph.2020.153293] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 09/09/2020] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
Polyploidy or whole genome duplication (WGD) is an evolutionary phenomenon that happened in all angiosperms multiple times over millions of years. Extensive studies on the model plant Arabidopsis thaliana genome have revealed that it has undergone five rounds of WGDs followed, in the Brassicaceae tribe, by a characteristic whole genome triplication (WGT). In addition, small-scale events such as tandem or segmental duplications and retrotransposition also enable plants to reshape their genomes. Over the decades, extensive research efforts have been undertaken to understand the evolutionary significance of polyploidy. On the other hand, much less attention has been paid to understanding the impact of gene duplication on the diversification of important stress response genes. The main objective of this review is to discuss key aspects of gene and genome duplications with a focus on genes primarily regulated by osmotic stresses. The focal family is the Brassicaceae, since it (i) underwent multiple rounds of WGDs plus WGTs, (ii) hosts many economically important crops and wild relatives that are tolerant to a range of stresses, and (iii) comprises many species that have already been sequenced. Diverse molecular mechanisms that lead to structural and regulatory alterations of duplicated genes are discussed. Examples are drawn from recent literature to elucidate expanded, stress responsive gene families identified from different Brassica crops. A combined bioinformatic and transcriptomic method has been proposed and tested on a known stress-responsive gene pair to prove that stress-responsive duplicated allelic variants can be identified by this method. Finally, future prospects for engineering these genes into crops to enhance stress tolerance are discussed, and important resources for Brassica genome research are provided.
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Affiliation(s)
- Shayani Das Laha
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Smritikana Dutta
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Anton R Schäffner
- Institute of Biochemical Plant Pathology, Department of Environmental Sciences, Helmholtz Zentrum München, München, Germany
| | - Malay Das
- Department of Life Sciences, Presidency University, Kolkata, India.
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