1
|
Yoo JY, Ko KS, Vu BN, Lee YE, Choi HN, Lee YN, Fanata WID, Harmoko R, Lee SK, Chung WS, Hong JC, Lee KO. IRE1 is implicated in protein synthesis regulation under ER stress conditions in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:108963. [PMID: 39084166 DOI: 10.1016/j.plaphy.2024.108963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/14/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024]
Abstract
The unfolded protein response (UPR) is a crucial cellular mechanism for maintaining protein folding homeostasis during endoplasmic reticulum (ER) stress. In this study, the role of IRE1, a key component of the UPR, was investigated in protein translation regulation under ER stress conditions in Arabidopsis. We discovered that the loss of IRE1A and IRE1B leads to diminished protein translation, indicating a significant role for IRE1 in this process. However, this regulation was not solely dependent on the interaction with bZIP60, a key transcription factor in the UPR. Interestingly, while chemical chaperones TUDCA and PBA effectively alleviated the translation inhibition observed in ire1a ire1b mutants, this effect was more pronounced than the mitigation observed from suppressing GCN2 expression or introducing a non-phosphorylatable eIF2α variant. Additionally, the kinase and ribonuclease activities of IRE1B were demonstrated to be crucial for plant adaptation and protein synthesis regulation under ER stress conditions. Overall, this study not only highlights the complex regulatory mechanisms of IRE1 in plant ER stress responses but also provides insights into its multifaceted roles in protein translation regulation.
Collapse
Affiliation(s)
- Jae Yong Yoo
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea
| | - Ki Seong Ko
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea
| | - Bich Ngoc Vu
- Division of Life Science, Division of Applied Life Sciences (BK4 Program) Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea
| | - Young Eun Lee
- Division of Life Science, Division of Applied Life Sciences (BK4 Program) Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea
| | - Ha Na Choi
- Division of Life Science, Division of Applied Life Sciences (BK4 Program) Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea
| | - Yoo Na Lee
- Division of Life Science, Division of Applied Life Sciences (BK4 Program) Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea
| | - Wahyu Indra Duwi Fanata
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea; Department of Agrotechnology, Faculty of Agriculture, University of Jember, Jember, 68121, Indonesia
| | - Rikno Harmoko
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea; Research Center for Genetic Engineering, National Research and Innovation Agency, Jl. Raya Jakarta-Bogor, Cibinong, Bogor, 16911, Indonesia
| | - Sang-Kyu Lee
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea; Division of Life Science, Division of Applied Life Sciences (BK4 Program) Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea
| | - Woo Sik Chung
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea; Division of Life Science, Division of Applied Life Sciences (BK4 Program) Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea
| | - Jong Chan Hong
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea; Division of Life Science, Division of Applied Life Sciences (BK4 Program) Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea
| | - Kyun Oh Lee
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea; Division of Life Science, Division of Applied Life Sciences (BK4 Program) Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea.
| |
Collapse
|
2
|
Ko DK, Brandizzi F. Dynamics of ER stress-induced gene regulation in plants. Nat Rev Genet 2024; 25:513-525. [PMID: 38499769 PMCID: PMC11186725 DOI: 10.1038/s41576-024-00710-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2024] [Indexed: 03/20/2024]
Abstract
Endoplasmic reticulum (ER) stress is a potentially lethal condition that is induced by the abnormal accumulation of unfolded or misfolded secretory proteins in the ER. In eukaryotes, ER stress is managed by the unfolded protein response (UPR) through a tightly regulated, yet highly dynamic, reprogramming of gene transcription. Although the core principles of the UPR are similar across eukaryotes, unique features of the plant UPR reflect the adaptability of plants to their ever-changing environments and the need to balance the demands of growth and development with the response to environmental stressors. The past decades have seen notable progress in understanding the mechanisms underlying ER stress sensing and signalling transduction pathways, implicating the UPR in the effects of physiological and induced ER stress on plant growth and crop yield. Facilitated by sequencing technologies and advances in genetic and genomic resources, recent efforts have driven the discovery of transcriptional regulators and elucidated the mechanisms that mediate the dynamic and precise gene regulation in response to ER stress at the systems level.
Collapse
Affiliation(s)
- Dae Kwan Ko
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA.
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA.
| |
Collapse
|
3
|
Varshney V, Singh J, Mishra V. Unlocking the plant ER stress code: IRE1-proteasome signaling cohort takes the lead. TRENDS IN PLANT SCIENCE 2024; 29:610-612. [PMID: 38102044 DOI: 10.1016/j.tplants.2023.12.003] [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: 11/17/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023]
Abstract
In the intricate landscape of cellular function, proper protein folding is pivotal for cellular processes, particularly within the endoplasmic reticulum (ER). In a recent study, Ko et al. reveal a signaling role for inositol-requiring enzyme 1 (IRE1) in ER stress and identify PHOSPHATASE TYPE 2CA (PP2CA)-INTERACTING RING FINGER PROTEIN 1 (PIR1) as a crucial plant-specific regulator, balancing the unfolded protein response (UPR) and ubiquitin-proteasome system (UPS) by modulating ABI5 stability, unveiling intricate stress response connections.
Collapse
Affiliation(s)
- Vishal Varshney
- Department of Botany, Govt. Shaheed Gend Singh College, Charama, Chhattisgarh, India.
| | - Jawahar Singh
- National Institute of Plant Genome Research (NIPGR), New Delhi, India; University of Cambridge, Sainsbury Laboratory (SLCU), Cambridge, UK
| | - Vishnu Mishra
- National Institute of Plant Genome Research (NIPGR), New Delhi, India; Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| |
Collapse
|
4
|
Thibault E, Brandizzi F. Post-translational modifications: emerging directors of cell-fate decisions during endoplasmic reticulum stress in Arabidopsis thaliana. Biochem Soc Trans 2024; 52:831-848. [PMID: 38600022 PMCID: PMC11088923 DOI: 10.1042/bst20231025] [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: 01/19/2024] [Revised: 03/23/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
Homeostasis of the endoplasmic reticulum (ER) is critical for growth, development, and stress responses. Perturbations causing an imbalance in ER proteostasis lead to a potentially lethal condition known as ER stress. In ER stress situations, cell-fate decisions either activate pro-life pathways that reestablish homeostasis or initiate pro-death pathways to prevent further damage to the organism. Understanding the mechanisms underpinning cell-fate decisions in ER stress is critical for crop development and has the potential to enable translation of conserved components to ER stress-related diseases in metazoans. Post-translational modifications (PTMs) of proteins are emerging as key players in cell-fate decisions in situations of imbalanced ER proteostasis. In this review, we address PTMs orchestrating cell-fate decisions in ER stress in plants and provide evidence-based perspectives for where future studies may focus to identify additional PTMs involved in ER stress management.
Collapse
Affiliation(s)
- Ethan Thibault
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, U.S.A
- Department of Plant Biology, Michigan State University, East Lansing, MI, U.S.A
| | - Federica Brandizzi
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, U.S.A
- Department of Plant Biology, Michigan State University, East Lansing, MI, U.S.A
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, U.S.A
| |
Collapse
|
5
|
Ducloy A, Azzopardi M, Ivsic C, Cueff G, Sourdeval D, Charif D, Cacas JL. A transcriptomic dataset for investigating the Arabidopsis Unfolded Protein Response under chronic, proteotoxic endoplasmic reticulum stress. Data Brief 2024; 53:110243. [PMID: 38533111 PMCID: PMC10964056 DOI: 10.1016/j.dib.2024.110243] [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: 11/21/2023] [Revised: 01/26/2024] [Accepted: 02/19/2024] [Indexed: 03/28/2024] Open
Abstract
The Unfolded Protein Response (UPR) is a retrograde, ER-to-nucleus, signalling pathway which is conserved across kingdoms. In plants, it contributes to development, reproduction, immunity and tolerance to abiotic stress. This RNA sequencing (RNA-seq) dataset was produced from 14-day-old Arabidopsis thaliana seedlings challenged by tunicamycin (Tm), an antibiotic inhibiting Asn-linked glycosylation in the endoplasmic reticulum (ER), causing an ER stress and eventually activating the UPR. Wild-type (WT) and a double mutant deficient for two main actors of the UPR (INOSITOL-REQUIRING ENZYME 1A and INOSITOL-REQUIRING ENZYME 1B) were used as genetic backgrounds in our experimental setup, allowing to distinguish among differentially-expressed genes (DEGs) which ones are dependent on or independent on IRE1s. Also, shoots and roots were harvested separately to determine organ-specific transcriptomic responses to Tm. Library and sequencing were performed using DNBseq™ technology by the Beijing Genomics Institute. Reads were mapped and quantified against the Arabidopsis genome. Differentially-expressed genes were identified using Rflomics upon filtering and normalization by the Trimmed Mean of M-value (TMM) method. While the genotype effect was weak under mock conditions (with a total of 182 DEGs in shoots and 195 DEGs in roots), the tunicamycin effect on each genotype was characterized by several hundred of DEGs in both shoots and roots. Among these genes, 872 and 563 genes were statistically up- and down-regulated in the shoot tissues of the double mutant when compared to those of WT, respectively. In roots of Tm-challenged seedlings, 425 and 439 genes were significantly up- and down-regulated in mutants with respect to WT. We believe that our dataset could be reused for investigating any biological questions linked to ER homeostasis and its role in plant physiology.
Collapse
Affiliation(s)
- Amélie Ducloy
- University Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Marianne Azzopardi
- University Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Caroline Ivsic
- University Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
- School of biological Sciences, University of Western Australia, Australia
| | - Gwendal Cueff
- University Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
- Unité de Nutrition Humaine, UM1019 - INRAE - Clermont Auvergne Rhône Alpes, France
| | - Delphine Sourdeval
- University Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Delphine Charif
- University Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Jean-Luc Cacas
- University Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| |
Collapse
|
6
|
Ko DK, Brandizzi F. Multi-omics Resources for Understanding Gene Regulation in Response to ER Stress in Plants. Methods Mol Biol 2024; 2772:261-272. [PMID: 38411820 PMCID: PMC11139047 DOI: 10.1007/978-1-0716-3710-4_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Proteotoxic stress of the endoplasmic reticulum (ER) is a potentially lethal condition that ensues when the biosynthetic capacity of the ER is overwhelmed. A sophisticated and largely conserved signaling, known as the unfolded protein response (UPR), is designed to monitor and alleviate ER stress. In plants, the emerging picture of gene regulation by the UPR now appears to be more complex than ever before, requiring multi-omics-enabled network-level approaches to be untangled. In the past decade, with an increasing access and decreasing costs of next-generation sequencing (NGS) and high-throughput protein-DNA interaction (PDI) screening technologies, multitudes of global molecular measurements, known as omics, have been generated and analyzed by the research community to investigate the complex gene regulation of plant UPR. In this chapter, we present a comprehensive catalog of omics resources at different molecular levels (transcriptomes, protein-DNA interactomes, and networks) along with the introduction of key concepts in experimental and computational tools in data generation and analyses. This chapter will serve as a starting point for both experimentalists and bioinformaticians to explore diverse omics datasets for their biological questions in the plant UPR, with likely applications also in other species for conserved mechanisms.
Collapse
Affiliation(s)
- Dae Kwan Ko
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA.
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA.
| |
Collapse
|
7
|
Duan Z, Chen K, Yang T, You R, Chen B, Li J, Liu L. Mechanisms of Endoplasmic Reticulum Protein Homeostasis in Plants. Int J Mol Sci 2023; 24:17599. [PMID: 38139432 PMCID: PMC10743519 DOI: 10.3390/ijms242417599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023] Open
Abstract
Maintenance of proteome integrity is essential for cell function and survival in changing cellular and environmental conditions. The endoplasmic reticulum (ER) is the major site for the synthesis of secretory and membrane proteins. However, the accumulation of unfolded or misfolded proteins can perturb ER protein homeostasis, leading to ER stress and compromising cellular function. Eukaryotic organisms have evolved sophisticated and conserved protein quality control systems to ensure protein folding fidelity via the unfolded protein response (UPR) and to eliminate potentially harmful proteins via ER-associated degradation (ERAD) and ER-phagy. In this review, we summarize recent advances in our understanding of the mechanisms of ER protein homeostasis in plants and discuss the crosstalk between different quality control systems. Finally, we will address unanswered questions in this field.
Collapse
Affiliation(s)
- Zhihao Duan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Kai Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Tao Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Ronghui You
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Binzhao Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Jianming Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
| | - Linchuan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| |
Collapse
|
8
|
Yu CY, Nakamura Y. SMALLER TRICHOMES WITH VARIABLE BRANCHES (SVB) and its homolog SVBL act downstream of transcription factor NAC089 and function redundantly in Arabidopsis unfolded protein response. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5870-5880. [PMID: 37578504 DOI: 10.1093/jxb/erad296] [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: 04/05/2023] [Accepted: 08/11/2023] [Indexed: 08/15/2023]
Abstract
The unfolded protein response (UPR) is a cellular mechanism that alleviates endoplasmic reticulum stress to maintain protein homeostasis. Although SMALLER TRICHOMES WITH VARIABLE BRANCHES (SVB) is characterized as an emerging UPR factor downstream of the IRE-bZIP60 pathway, whether its homologs participate in the plant UPR remains unknown. Here, we showed that an SVB homolog, SVB-like (SVBL), functions redundantly with SVB in endoplasmic reticulum stress tolerance. The svb-1 svbl-1 double mutant showed a hypersensitivity phenotype and had higher UPR gene expression under endoplasmic reticulum stress than single mutants and the wild type. SVB responded to endoplasmic reticulum stress by accumulating in the root epidermis and phloem cells, but SVBL did not. Ectopic expression of the UPR factor NAC089 up-regulated both SVB and SVBL genes, suggesting that SVB and SVBL work downstream of NAC089. Thus, SVB and SVBL play distinct roles that are modulated by the common upstream regulator NAC089 to cope with endoplasmic reticulum stress in Arabidopsis.
Collapse
Affiliation(s)
- Chao-Yuan Yu
- RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Yuki Nakamura
- RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-8654, Japan
| |
Collapse
|
9
|
Ko DK, Kim JY, Thibault EA, Brandizzi F. An IRE1-proteasome system signalling cohort controls cell fate determination in unresolved proteotoxic stress of the plant endoplasmic reticulum. NATURE PLANTS 2023; 9:1333-1346. [PMID: 37563456 PMCID: PMC10481788 DOI: 10.1038/s41477-023-01480-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 07/04/2023] [Indexed: 08/12/2023]
Abstract
Excessive accumulation of misfolded proteins in the endoplasmic reticulum (ER) causes ER stress, which is an underlying cause of major crop losses and devastating human conditions. ER proteostasis surveillance is mediated by the conserved master regulator of the unfolded protein response (UPR), Inositol Requiring Enzyme 1 (IRE1), which determines cell fate by controlling pro-life and pro-death outcomes through as yet largely unknown mechanisms. Here we report that Arabidopsis IRE1 determines cell fate in ER stress by balancing the ubiquitin-proteasome system (UPS) and UPR through the plant-unique E3 ligase, PHOSPHATASE TYPE 2CA (PP2CA)-INTERACTING RING FINGER PROTEIN 1 (PIR1). Indeed, PIR1 loss leads to suppression of pro-death UPS and the lethal phenotype of an IRE1 loss-of-function mutant in unresolved ER stress in addition to activating pro-survival UPR. Specifically, in ER stress, PIR1 loss stabilizes ABI5, a basic leucine zipper (bZIP) transcription factor, that directly activates expression of the critical UPR regulator gene, bZIP60, triggering transcriptional cascades enhancing pro-survival UPR. Collectively, our results identify new cell fate effectors in plant ER stress by showing that IRE1's coordination of cell death and survival hinges on PIR1, a key pro-death component of the UPS, which controls ABI5, a pro-survival transcriptional activator of bZIP60.
Collapse
Affiliation(s)
- Dae Kwan Ko
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
| | - Joo Yong Kim
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA
| | - Ethan A Thibault
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA.
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA.
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
| |
Collapse
|
10
|
Ko DK, Brandizzi F. Coexpression Network Construction and Visualization from Transcriptomes Underlying ER Stress Responses. Methods Mol Biol 2023; 2581:385-401. [PMID: 36413332 PMCID: PMC10500560 DOI: 10.1007/978-1-0716-2784-6_27] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Dynamic gene expression changes are primary cellular reactions in response to most stresses and developmental cues in all organisms, including plants. With the ever-decreasing cost and increasing access, high-throughput transcriptome analyses have become a significant research tool to understand a wide spectrum of complex gene regulatory mechanisms. However, it is still challenging to understand the complete picture of gene responses because of the interactive and dynamic nature of gene expression in biological networks. Coexpression network analyses followed by network mapping are being increasingly applied to overcome this challenge. In this chapter, we will introduce detailed instructions for performing a weighted coexpression network analysis (WGCNA) and network visualization using a transcriptome dataset obtained during recovery from endoplasmic reticulum (ER) stress in Arabidopsis thaliana. The streamlined workflow described here allows biologists to identify and visualize coexpression interactions among genes, accessing a comprehensive landscape of dynamic gene expression changes for further downstream analyses using their datasets.
Collapse
Affiliation(s)
- Dae Kwan Ko
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA.
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA.
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
| |
Collapse
|
11
|
Liu Y, Lv Y, Wei A, Guo M, Li Y, Wang J, Wang X, Bao Y. Unfolded protein response in balancing plant growth and stress tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:1019414. [PMID: 36275569 PMCID: PMC9585285 DOI: 10.3389/fpls.2022.1019414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
The ER (endoplasmic reticulum) is the largest membrane-bound multifunctional organelle in eukaryotic cells, serving particularly important in protein synthesis, modification, folding and transport. UPR (unfolded protein response) is one of the systematized strategies that eukaryotic cells employ for responding to ER stress, a condition represents the processing capability of ER is overwhelmed and stressed. UPR is usually triggered when the protein folding capacity of ER is overloaded, and indeed, mounting studies were focused on the stress responding side of UPR. In plants, beyond stress response, accumulating evidence suggests that UPR is essential for growth and development, and more importantly, the necessity of UPR in this regard requires its endogenous basal activation even without stress. Then plants must have to fine tune the activation level of UPR pathway for balancing growth and stress response. In this review, we summarized the recent progresses in plant UPR, centering on its role in controlling plant reproduction and root growth, and lay out some outstanding questions to be addressed in the future.
Collapse
Affiliation(s)
- Yao Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yonglun Lv
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - An Wei
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Mujin Guo
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yanjie Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiaojiao Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinhua Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Bao
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
12
|
Ko DK, Brandizzi F. Transcriptional competition shapes proteotoxic ER stress resolution. NATURE PLANTS 2022; 8:481-490. [PMID: 35577961 PMCID: PMC9187302 DOI: 10.1038/s41477-022-01150-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
Through dynamic activities of conserved master transcription factors (mTFs), the unfolded protein response (UPR) relieves proteostasis imbalance of the endoplasmic reticulum (ER), a condition known as ER stress1,2. Because dysregulated UPR is lethal, the competence for fate changes of the UPR mTFs must be tightly controlled3,4. However, the molecular mechanisms underlying regulatory dynamics of mTFs remain largely elusive. Here, we identified the abscisic acid-related regulator G-class bZIP TF2 (GBF2) and the cis-regulatory element G-box as regulatory components of the plant UPR led by the mTFs, bZIP28 and bZIP60. We demonstrate that, by competing with the mTFs at G-box, GBF2 represses UPR gene expression. Conversely, a gbf2 null mutation enhances UPR gene expression and suppresses the lethality of a bzip28 bzip60 mutant in unresolved ER stress. By demonstrating that GBF2 functions as a transcriptional repressor of the UPR, we address the long-standing challenge of identifying shared signalling components for a better understanding of the dynamic nature and complexity of stress biology. Furthermore, our results identify a new layer of UPR gene regulation hinged upon an antagonistic mTFs-GFB2 competition for proteostasis and cell fate determination.
Collapse
Affiliation(s)
- Dae Kwan Ko
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA.
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA.
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
| |
Collapse
|