1
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Sharma I, Talakayala A, Tiwari M, Asinti S, Kirti PB. A synchronized symphony: Intersecting roles of ubiquitin proteasome system and autophagy in cellular degradation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108700. [PMID: 38781635 DOI: 10.1016/j.plaphy.2024.108700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/01/2024] [Indexed: 05/25/2024]
Abstract
Eukaryotic cells have evolved dynamic quality control pathways and recycling mechanisms for cellular homeostasis. We discuss here, the two major systems for quality control, the ubiquitin-proteasome system (UPS) and autophagy that regulate cellular protein and organelle turnover and ensure efficient nutrient management, cellular integrity and long-term wellbeing of the plant. Both the pathways rely on ubiquitination signal to identify the targets for proteasomal and autophagic degradation, yet they use distinct degradation machinery to process these cargoes. Nonetheless, both UPS and autophagy operate together as an interrelated quality control mechanism where they communicate with each other at multiple nodes to coordinate and/or compensate the recycling mechanism particularly under development and environmental cues. Here, we provide an update on the cellular machinery of autophagy and UPS, unravel the nodes of their crosstalk and particularly highlight the factors responsible for their differential deployment towards protein, macromolecular complexes and organelles.
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Affiliation(s)
- Isha Sharma
- International Crop Research Institute for Semi-Arid Tropics, Patancheru, Hyderabad, India, 502324.
| | - Ashwini Talakayala
- International Crop Research Institute for Semi-Arid Tropics, Patancheru, Hyderabad, India, 502324
| | - Manish Tiwari
- CSIR-National Botanical Research Institute, 435, Rana Pratap Marg, Lucknow, 226001, Uttar Pradesh, India
| | - Sarath Asinti
- Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, Uttar Pradesh, 211007, India
| | - P B Kirti
- Agri Biotech Foundation, Rajendranagar, 500030, Hyderabad, India
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2
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Lv X, Deng J, Zhou C, Abdullah A, Yang Z, Wang Z, Yang L, Zhao B, Li Y, Ma Z. Comparative transcriptomic insights into molecular mechanisms of the susceptibility wheat variety MX169 response to Puccinia striiformis f. sp. tritici ( Pst) infection. Microbiol Spectr 2024:e0377423. [PMID: 38916358 DOI: 10.1128/spectrum.03774-23] [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: 10/27/2023] [Accepted: 06/02/2024] [Indexed: 06/26/2024] Open
Abstract
Stripe rust of wheat is caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst). Breeding durably resistant wheat varieties by disrupting the susceptibility (S) gene has an important impact on the control of wheat stripe rust. Mingxian169 (MX169) showed strong stripe rust susceptibility to all the races of Pst. However, molecular mechanisms and responsive genes underlying susceptibility of the wheat variety MX169 to Pst have not been elucidated. Here, we utilized next-generation sequencing technology to analyze transcriptomics data of "MX169" and high-resistance wheat "Zhong4" at 24, 48, and 120 h post-inoculation (hpi) with Pst. Comparative transcriptome analysis revealed 3,494, 2,831, and 2,700 differentially expressed genes (DEGs) at different time points. We observed an upregulation of DEGs involved in photosynthesis, flavonoid biosynthesis, pyruvate metabolism, thiamine metabolism, and other biological processes, suggesting their involvement in MX169's response to Pst. DEGs encoding transcription factors were also identified. Our study suggested the potential susceptibility gene resources in MX169 related to stripe rust response could be valuable for understanding the mechanisms involved in stripe rust susceptibility and for improving wheat resistance to Pst. IMPORTANCE Our study suggests the potential susceptibility gene resources in MX169 related to stripe rust response could be valuable for understanding the mechanisms involved in stripe rust susceptibility and for improving wheat resistance to Pst.
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Affiliation(s)
- Xuan Lv
- Department of Plant Pathology, Ministry of Agriculture and Rural Affairs (MOA) Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jie Deng
- Department of Plant Pathology, Ministry of Agriculture and Rural Affairs (MOA) Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Congying Zhou
- Department of Plant Pathology, Ministry of Agriculture and Rural Affairs (MOA) Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Ahsan Abdullah
- Department of Plant Pathology, Ministry of Agriculture and Rural Affairs (MOA) Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Ziqian Yang
- Department of Plant Pathology, Ministry of Agriculture and Rural Affairs (MOA) Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhifang Wang
- Department of Plant Pathology, Ministry of Agriculture and Rural Affairs (MOA) Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Lujia Yang
- Department of Plant Pathology, Ministry of Agriculture and Rural Affairs (MOA) Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Baoqiang Zhao
- Department of Plant Pathology, Ministry of Agriculture and Rural Affairs (MOA) Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Yuchen Li
- Department of Plant Pathology, Ministry of Agriculture and Rural Affairs (MOA) Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhanhong Ma
- Department of Plant Pathology, Ministry of Agriculture and Rural Affairs (MOA) Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
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3
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Ganapathy J, Hand KA, Shabek N. Analysis of 26S Proteasome Activity across Arabidopsis Tissues. PLANTS (BASEL, SWITZERLAND) 2024; 13:1696. [PMID: 38931128 DOI: 10.3390/plants13121696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/18/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024]
Abstract
Plants utilize the ubiquitin proteasome system (UPS) to orchestrate numerous essential cellular processes, including the rapid responses required to cope with abiotic and biotic stresses. The 26S proteasome serves as the central catalytic component of the UPS that allows for the proteolytic degradation of ubiquitin-conjugated proteins in a highly specific manner. Despite the increasing number of studies employing cell-free degradation assays to dissect the pathways and target substrates of the UPS, the precise extraction methods of highly potent tissues remain unexplored. Here, we utilize a fluorogenic reporting assay using two extraction methods to survey proteasomal activity in different Arabidopsis thaliana tissues. This study provides new insights into the enrichment of activity and varied presence of proteasomes in specific plant tissues.
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Affiliation(s)
- Jagadeesan Ganapathy
- Department of Plant Biology, College of Biological Sciences, University of California-Davis, Davis, CA 95616, USA
| | - Katherine A Hand
- Department of Plant Biology, College of Biological Sciences, University of California-Davis, Davis, CA 95616, USA
| | - Nitzan Shabek
- Department of Plant Biology, College of Biological Sciences, University of California-Davis, Davis, CA 95616, USA
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4
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Li HL, Xu RR, Guo XL, Liu YJ, You CX, Han Y, An JP. The MdNAC72-MdABI5 module acts as an interface integrating jasmonic acid and gibberellin signals and undergoes ubiquitination-dependent degradation regulated by MdSINA2 in apple. THE NEW PHYTOLOGIST 2024. [PMID: 38849319 DOI: 10.1111/nph.19888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 05/20/2024] [Indexed: 06/09/2024]
Abstract
Jasmonic acid (JA) and gibberellin (GA) coordinately regulate plant developmental programs and environmental cue responses. However, the fine regulatory network of the cross-interaction between JA and GA remains largely elusive. In this study, we demonstrate that MdNAC72 together with MdABI5 positively regulates anthocyanin biosynthesis through an exquisite MdNAC72-MdABI5-MdbHLH3 transcriptional cascade in apple. MdNAC72 interacts with MdABI5 to promote the transcriptional activation of MdABI5 on its target gene MdbHLH3 and directly activates the transcription of MdABI5. The MdNAC72-MdABI5 module regulates the integration of JA and GA signals in anthocyanin biosynthesis by combining with JA repressor MdJAZ2 and GA repressor MdRGL2a. MdJAZ2 disrupts the MdNAC72-MdABI5 interaction and attenuates the transcriptional activation of MdABI5 by MdNAC72. MdRGL2a sequesters MdJAZ2 from the MdJAZ2-MdNAC72 protein complex, leading to the release of MdNAC72. The E3 ubiquitin ligase MdSINA2 is responsive to JA and GA signals and promotes ubiquitination-dependent degradation of MdNAC72. The MdNAC72-MdABI5 interface fine-regulates the integration of JA and GA signals at the transcriptional and posttranslational levels by combining MdJAZ2, MdRGL2a, and MdSINA2. In summary, our findings elucidate the fine regulatory network connecting JA and GA signals with MdNAC72-MdABI5 as the core in apple.
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Affiliation(s)
- Hong-Liang Li
- State Key Laboratory of Plant Diversity and Specialty Crops, CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan, 430074, China
- Apple technology innovation center of Shandong Province, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Rui-Rui Xu
- College of Biology and Oceanography, Weifang University, Weifang, 261061, Shandong, China
| | - Xin-Long Guo
- Apple technology innovation center of Shandong Province, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Ya-Jing Liu
- School of Horticulture, Anhui Agricultural University, He-Fei, 230036, Anhui, China
| | - Chun-Xiang You
- Apple technology innovation center of Shandong Province, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Yuepeng Han
- State Key Laboratory of Plant Diversity and Specialty Crops, CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Jian-Ping An
- State Key Laboratory of Plant Diversity and Specialty Crops, CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan, 430074, China
- Apple technology innovation center of Shandong Province, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
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5
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Feng K, Walker JF, Marx HE, Yang Y, Brockington SF, Moore MJ, Rabeler RK, Smith SA. The link between ancient whole-genome duplications and cold adaptations in the Caryophyllaceae. AMERICAN JOURNAL OF BOTANY 2024:e16350. [PMID: 38825760 DOI: 10.1002/ajb2.16350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 06/04/2024]
Abstract
PREMISE The Caryophyllaceae (the carnation family) have undergone multiple transitions into colder climates and convergence on cushion plant adaptation, indicating that they may provide a natural system for cold adaptation research. Previous research has suggested that putative ancient whole-genome duplications (WGDs) are correlated with niche shifts into colder climates across the Caryophyllales. Here, we explored the genomic changes potentially involved in one of these discovered shifts in the Caryophyllaceae. METHODS We constructed a data set combining 26 newly generated transcriptomes with 45 published transcriptomes, including 11 cushion plant species across seven genera. With this data set, we inferred a dated phylogeny for the Caryophyllaceae and mapped ancient WGDs and gene duplications onto the phylogeny. We also examined functional groups enriched for gene duplications related to the climatic shift. RESULTS The ASTRAL topology was mostly congruent with the current consensus of relationships within the family. We inferred 15 putative ancient WGDs in the family, including eight that have not been previously published. The oldest ancient WGD (ca. 64.4-56.7 million years ago), WGD1, was found to be associated with a shift into colder climates by previous research. Gene regions associated with ubiquitination were overrepresented in gene duplications retained after WGD1 and those convergently retained by cushion plants in Colobanthus and Eremogone, along with other functional annotations. CONCLUSIONS Gene family expansions induced by ancient WGDs may have contributed to the shifts to cold climatic niches in the Caryophyllaceae. Transcriptomic data are crucial resources that help unravel heterogeneity in deep-time evolutionary patterns in plants.
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Affiliation(s)
- Keyi Feng
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Joseph F Walker
- Department of Biological Sciences, University of Illinois Chicago, Chicago, 60607, IL, USA
| | - Hannah E Marx
- Department of Biology, University of New Mexico, Albuquerque, 87131, NM, USA
| | - Ya Yang
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, 55108, MN, USA
| | | | - Michael J Moore
- Department of Biology, Oberlin College, Oberlin, 44074, OH, USA
| | - Richard K Rabeler
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
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6
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Yang Z, Lu X, Wang N, Mei Z, Fan Y, Zhang M, Wang L, Sun Y, Chen X, Huang H, Meng Y, Liu M, Han M, Chen W, Zhang X, Yu X, Chen X, Wang S, Wang J, Zhao L, Guo L, Peng F, Feng K, Gao W, Ye W. GhVIM28, a negative regulator identified from VIM family genes, positively responds to salt stress in cotton. BMC PLANT BIOLOGY 2024; 24:432. [PMID: 38773389 PMCID: PMC11107009 DOI: 10.1186/s12870-024-05156-8] [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: 04/06/2024] [Accepted: 05/16/2024] [Indexed: 05/23/2024]
Abstract
The VIM (belonged to E3 ubiquitin ligase) gene family is crucial for plant growth, development, and stress responses, yet their role in salt stress remains unclear. We analyzed phylogenetic relationships, chromosomal localization, conserved motifs, gene structure, cis-acting elements, and gene expression patterns of the VIM gene family in four cotton varieties. Our findings reveal 29, 29, 17, and 14 members in Gossypium hirsutum (G.hirsutum), Gossypium barbadense (G.barbadense), Gossypium arboreum (G.arboreum), and Gossypium raimondii (G. raimondii), respectively, indicating the maturity and evolution of this gene family. motifs among GhVIMs genes were observed, along with the presence of stress-responsive, hormone-responsive, and growth-related elements in their promoter regions. Gene expression analysis showed varying patterns and tissue specificity of GhVIMs genes under abiotic stress. Silencing GhVIM28 via virus-induced gene silencing revealed its role as a salt-tolerant negative regulator. This work reveals a mechanism by which the VIM gene family in response to salt stress in cotton, identifying a potential negative regulator, GhVIM28, which could be targeted for enhancing salt tolerance in cotton. The objective of this study was to explore the evolutionary relationship of the VIM gene family and its potential function in salt stress tolerance, and provide important genetic resources for salt tolerance breeding of cotton.
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Affiliation(s)
- Zhining Yang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University / National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Anyang, Henan, 455000, China
- Engineering Research Centre of Cotton, Ministry of Education / College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Xuke Lu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University / National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Anyang, Henan, 455000, China
| | - Ning Wang
- Institute of Crop Sciences, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, 730070, China
| | - Zhengding Mei
- Hunan Institute of Cotton Science, Changde, Hunan, 415101, China
| | - Yapeng Fan
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University / National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Anyang, Henan, 455000, China
| | - Menghao Zhang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University / National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Anyang, Henan, 455000, China
| | - Lidong Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University / National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Anyang, Henan, 455000, China
| | - Yuping Sun
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University / National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Anyang, Henan, 455000, China
| | - Xiao Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University / National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Anyang, Henan, 455000, China
| | - Hui Huang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University / National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Anyang, Henan, 455000, China
| | - Yuan Meng
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University / National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Anyang, Henan, 455000, China
| | - Mengyue Liu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University / National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Anyang, Henan, 455000, China
| | - Mingge Han
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University / National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Anyang, Henan, 455000, China
| | - Wenhua Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University / National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Anyang, Henan, 455000, China
| | - Xinrui Zhang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University / National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Anyang, Henan, 455000, China
| | - Xin Yu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University / National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Anyang, Henan, 455000, China
| | - Xiugui Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University / National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Anyang, Henan, 455000, China
| | - Shuai Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University / National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Anyang, Henan, 455000, China
| | - Junjuan Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University / National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Anyang, Henan, 455000, China
| | - Lanjie Zhao
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University / National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Anyang, Henan, 455000, China
| | - Lixue Guo
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University / National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Anyang, Henan, 455000, China
| | - Fanjia Peng
- Hunan Institute of Cotton Science, Changde, Hunan, 415101, China
| | - Keyun Feng
- Institute of Crop Sciences, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, 730070, China
| | - Wenwei Gao
- Engineering Research Centre of Cotton, Ministry of Education / College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China.
| | - Wuwei Ye
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University / National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Anyang, Henan, 455000, China.
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7
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Zhu L, Sun Y, Ullah N, Zhang G, Liu H, Xu L. UBC Gene Family Analysis in Salvia castanea and Roles of ScUBC2/5 Genes under Abiotic Stress. PLANTS (BASEL, SWITZERLAND) 2024; 13:1353. [PMID: 38794424 PMCID: PMC11125094 DOI: 10.3390/plants13101353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024]
Abstract
Salvia castanea Diels, a relative of the medicinal plant Salvia miltiorrhiza Bunge, belongs to the genus Salvia and family Lamiaceae. Ubiquitin-conjugating enzyme E2 (UBC) is an important ubiquitin-binding enzyme in protein ubiquitination. This study aimed to analyze the regulatory role of UBC genes, particularly ScUBC2/5, on the growth and adaptation of S. castanea to extreme environments including cold or drought stress. We identified nine UBC genes in S. castanea and found that these genes were extremely stable and more highly expressed in the roots than other tissues. This suggested that UBC genes might play a role in promoting root adaptation to cold and dry environments. Further analysis of UBC gene expression in hairy roots under cold (4 °C) and UV stress also confirmed their importance under stress. The contents of tanshinone and salvianolic acid in hairy roots with the overexpression of ScUBC2/5 were increased compared to non-transgenic wild type, and the cold and UV resistance of hairy roots was increased compared with that of wild type. Together, these findings highlighted the role of ScUBC2/5 in enhancing secondary metabolite accumulation and regulation in response to cold and ultraviolet stress in S. castanea, providing a new perspective for genetic improvement in its phytochemistry.
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Affiliation(s)
- Longyi Zhu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; (L.Z.); (Y.S.); (G.Z.)
| | - Yuee Sun
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; (L.Z.); (Y.S.); (G.Z.)
| | - Najeeb Ullah
- Agricultural Research Station, Office of VP for Research & Graduate Studies, Qatar University, Doha 2713, Qatar;
| | - Guilian Zhang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; (L.Z.); (Y.S.); (G.Z.)
| | - Hui Liu
- Faculty of Science, UWA Institute of Agriculture, UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia;
| | - Ling Xu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; (L.Z.); (Y.S.); (G.Z.)
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8
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Sun Y, Tian Z, Zuo D, Wang Q, Song G. GhUBC10-2 mediates GhGSTU17 degradation to regulate salt tolerance in cotton (Gossypium hirsutum). PLANT, CELL & ENVIRONMENT 2024; 47:1606-1624. [PMID: 38282268 DOI: 10.1111/pce.14839] [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: 06/27/2023] [Revised: 01/13/2024] [Accepted: 01/17/2024] [Indexed: 01/30/2024]
Abstract
Ubiquitin-conjugating enzyme (UBC) is a crucial component of the ubiquitin-proteasome system, which contributes to plant growth and development. While some UBCs have been identified as potential regulators of abiotic stress responses, the underlying mechanisms of this regulation remain poorly understood. Here, we report a cotton (Gossypium hirsutum) UBC gene, GhUBC10-2, which negatively regulates the salt stress response. We found that the gain of function of GhUBC10-2 in both Arabidopsis (Arabidopsis thaliana) and cotton leads to reduced salinity tolerance. Additionally, GhUBC10-2 interacts with glutathione S-transferase (GST) U17 (GhGSTU17), forming a heterodimeric complex that promotes GhGSTU17 degradation. Intriguingly, GhUBC10-2 can be self-polyubiquitinated, suggesting that it possesses E3-independent activity. Our findings provide new insights into the PTM of plant GST-mediated salt response pathways. Furthermore, we found that the WRKY transcription factor GhWRKY13 binds to the GhUBC10-2 promoter and suppresses its expression under salt conditions. Collectively, our study unveils a regulatory module encompassing GhWRKY13-GhUBC10-2-GhGSTU17, which orchestrates the modulation of reactive oxygen species homeostasis to enhance salt tolerance.
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Affiliation(s)
- Yaru Sun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zailong Tian
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Dongyun Zuo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qiaolian Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Guoli Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
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9
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Daldoul S, Hanzouli F, Boubakri H, Nick P, Mliki A, Gargouri M. Deciphering the regulatory networks involved in mild and severe salt stress responses in the roots of wild grapevine Vitis vinifera spp. sylvestris. PROTOPLASMA 2024; 261:447-462. [PMID: 37963978 DOI: 10.1007/s00709-023-01908-9] [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: 09/26/2023] [Accepted: 11/06/2023] [Indexed: 11/16/2023]
Abstract
Transcriptional regulatory networks are pivotal components of plant's response to salt stress. However, plant adaptation strategies varied as a function of stress intensity, which is mainly modulated by climate change. Here, we determined the gene regulatory networks based on transcription factor (TF) TF_gene co-expression, using two transcriptomic data sets generated from the salt-tolerant "Tebaba" roots either treated with 50 mM NaCl (mild stress) or 150 mM NaCl (severe stress). The analysis of these regulatory networks identified specific TFs as key regulatory hubs as evidenced by their multiple interactions with different target genes related to stress response. Indeed, under mild stress, NAC and bHLH TFs were identified as central hubs regulating nitrogen storage process. Moreover, HSF TFs were revealed as a regulatory hub regulating various aspects of cellular metabolism including flavonoid biosynthesis, protein processing, phenylpropanoid metabolism, galactose metabolism, and heat shock proteins. These processes are essentially linked to short-term acclimatization under mild salt stress. This was further consolidated by the protein-protein interaction (PPI) network analysis showing structural and plant growth adjustment. Conversely, under severe salt stress, dramatic metabolic changes were observed leading to novel TF members including MYB family as regulatory hubs controlling isoflavonoid biosynthesis, oxidative stress response, abscisic acid signaling pathway, and proteolysis. The PPI network analysis also revealed deeper stress defense changes aiming to restore plant metabolic homeostasis when facing severe salt stress. Overall, both the gene co-expression and PPI network provided valuable insights on key transcription factor hubs that can be employed as candidates for future genetic crop engineering programs.
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Affiliation(s)
- Samia Daldoul
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, BP. 901, Hammam-Lif, Tunisia.
| | - Faouzia Hanzouli
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, BP. 901, Hammam-Lif, Tunisia
- Faculty of Sciences of Tunis, University Tunis El-Manar, El Manar II, 2092, Tunis, Tunisia
| | - Hatem Boubakri
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, B.P 901, 2050, Hammam-Lif, Tunisia
| | - Peter Nick
- Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Ahmed Mliki
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, BP. 901, Hammam-Lif, Tunisia
| | - Mahmoud Gargouri
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, BP. 901, Hammam-Lif, Tunisia.
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10
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Yu P, Song X, Zhang W, Yao Y, Ren J, Wang L, Liu W, Meng Z, Meng X. Analysis of ginseng rusty root symptoms transcriptome and its pathogenesis directed by reactive oxygen species theory. PLANT DIRECT 2024; 8:e586. [PMID: 38766510 PMCID: PMC11099884 DOI: 10.1002/pld3.586] [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: 12/12/2023] [Revised: 04/07/2024] [Accepted: 04/12/2024] [Indexed: 05/22/2024]
Abstract
Ginseng rusty root symptoms (GRS) is a primary disease of ginseng, which seriously decreases the yield and quality of ginseng and causes enormous losses to ginseng production. GRS prevention and control is still challenging due to its unclear etiology. In this study, the phloem tissue of healthy Panax ginseng (AG), the nonred tissue of the phloem epidermis around the lesion (BG), and the red lesion site tissue of GRS (CG) were extracted for mRNA transcriptomic analysis; 35,958 differentially expressed genes (DEGs) were identified and were associated with multiple stress resistance pathways, reactive oxygen species (ROS), and iron ion binding. Further study showed that the contents of O2 •-, H2O2, and malondialdehyde (MDA) were significantly increased in BG and CG tissues. Under anaerobic conditions caused by excessive soil moisture, the overproduction of ROS destroys cell membranes, simultaneously converting Fe2+ to Fe3+ and depositing it in the cell wall, which results in GRS, as evidenced by the success of the GRS induction test.
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Affiliation(s)
- Pengcheng Yu
- Country College of PharmacyHeilongjiang University of Chinese MedicineHarbinChina
| | - Xiaowen Song
- Country College of PharmacyHeilongjiang University of Chinese MedicineHarbinChina
| | - Wei Zhang
- Country College of PharmacyHeilongjiang University of Chinese MedicineHarbinChina
| | - Yao Yao
- Country College of PharmacyHeilongjiang University of Chinese MedicineHarbinChina
| | - Junling Ren
- Country College of PharmacyHeilongjiang University of Chinese MedicineHarbinChina
| | - Liyang Wang
- Country College of PharmacyHeilongjiang University of Chinese MedicineHarbinChina
| | - Wenfei Liu
- Country College of PharmacyHeilongjiang University of Chinese MedicineHarbinChina
| | - Zhaoping Meng
- Country College of PharmacyHeilongjiang University of Chinese MedicineHarbinChina
| | - Xiangcai Meng
- Country College of PharmacyHeilongjiang University of Chinese MedicineHarbinChina
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11
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Regon P, Saha B, Jyoti SY, Gupta D, Kundu B, Tanti B, Panda SK. Transcriptional networks revealed late embryogenesis abundant genes regulating drought mitigation in aromatic Keteki Joha rice. PHYSIOLOGIA PLANTARUM 2024; 176:e14348. [PMID: 38769068 DOI: 10.1111/ppl.14348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 04/18/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
Climate change has become increasingly intertwined with the occurrence and severity of droughts. As global temperatures rise due to greenhouse gas emissions, weather patterns are altered, leading to shifts in precipitation levels and distribution. These exacerbate the risk of drought in many regions, with potentially devastating consequences. A comprehensive transcriptome analysis was performed on Keteki Joha, an aromatic rice from North East India, with the aim of elucidating molecular responses to drought. Numerous genes linked to drought were activated, with both ABA-dependent and ABA-independent pathways playing crucial roles. Upregulated genes were enriched with gene ontology terms with response to abscisic acid and abscisic acid-activated signalling pathway, suggesting the existence of an ABA-dependent pathway for drought mitigation. The upregulated genes were also enriched with responses to stress, water, heat, jasmonic acid, and hydrogen peroxide, indicating the presence of an ABA-independent pathway alongside the ABA-dependent mechanism. Weighted Correlation Network Analysis (WGCNA) identified 267 genes that specifically govern drought mitigation in Keteki Joha. The late embryogenesis abundant (LEA) gene family emerges as the most overrepresented in both RNA sequencing data and WGCNA analysis, suggesting their dominant role in mitigating drought. Notably, 31 LEA genes were induced in seedlings and 32 in mature stages under drought stress. The LEA3-1, LEA14/WSI18, RAB16A, RAB16B, DHN1, DHN6, LEA1, LEA3, LEA17, and LEA33 exhibited and established co-expression with numerous other drought stress-related genes, indicating their inseparable role in alleviating drought. Consequently, LEA genes have been proposed to be primary and crucial responders to drought in Keteki Joha.
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Affiliation(s)
- Preetom Regon
- Plant Molecular Biology Laboratory, Department of Botany, Gauhati University, Guwahati, Assam, India
- Department of Entomology, Agricultural Research Organization, The Volcani Institute, Rishon LeZion, Israel
| | - Bedabrata Saha
- Plant Pathology and Weed Research Department, Newe Ya'ar Research Centre, Agricultural Research Organization, Israel
| | - Sabnoor Yeasrin Jyoti
- Plant Molecular Biology Laboratory, Department of Botany, Gauhati University, Guwahati, Assam, India
| | - Divya Gupta
- Plant Functional Genomics and Molecular Biology Laboratory, Department of Biochemistry, Central University of Rajasthan, Ajmer, Bandarsindri, Rajasthan, India
| | - Bikash Kundu
- Plant Molecular Biology Laboratory, Department of Botany, Gauhati University, Guwahati, Assam, India
| | - Bhaben Tanti
- Plant Molecular Biology Laboratory, Department of Botany, Gauhati University, Guwahati, Assam, India
| | - Sanjib Kumar Panda
- Plant Functional Genomics and Molecular Biology Laboratory, Department of Biochemistry, Central University of Rajasthan, Ajmer, Bandarsindri, Rajasthan, India
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12
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Xu J, Liu H, Zhou C, Wang J, Wang J, Han Y, Zheng N, Zhang M, Li X. The ubiquitin-proteasome system in the plant response to abiotic stress: Potential role in crop resilience improvement. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 342:112035. [PMID: 38367822 DOI: 10.1016/j.plantsci.2024.112035] [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: 11/29/2023] [Revised: 02/09/2024] [Accepted: 02/11/2024] [Indexed: 02/19/2024]
Abstract
The post-translational modification (PTM) of proteins by ubiquitination modulates many physiological processes in plants. As the major protein degradation pathway in plants, the ubiquitin-proteasome system (UPS) is considered a promising target for improving crop tolerance drought, high salinity, extreme temperatures, and other abiotic stressors. The UPS also participates in abiotic stress-related abscisic acid (ABA) signaling. E3 ligases are core components of the UPS-mediated modification process due to their substrate specificity. In this review, we focus on the abiotic stress-associated regulatory mechanisms and functions of different UPS components, emphasizing the participation of E3 ubiquitin ligases. We also summarize and discuss UPS-mediated modulation of ABA signaling. In particular, we focus our review on recent research into the UPS-mediated modulation of the abiotic stress response in major crop plants. We propose that altering the ubiquitination site of the substrate or the substrate-specificity of E3 ligase using genome editing technology such as CRISPR/Cas9 may improve the resistance of crop plants to adverse environmental conditions. Such a strategy will require continued research into the role of the UPS in mediating the abiotic stress response in plants.
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Affiliation(s)
- Jian Xu
- Qiqihar Branch of the Heilongjiang Academy of Agricultural Sciences, Qiqihar, China; Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Hongjie Liu
- State Key Laboratory of Plant Diversity and Specialty Crops, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Zhou
- Qiqihar Branch of the Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Jinxing Wang
- Suihua Branch of the Heilongjiang Academy of Agricultural Sciences, Suihua, China
| | - Junqiang Wang
- Qiqihar Branch of the Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Yehui Han
- Qiqihar Branch of the Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Nan Zheng
- Industrial Crop Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Ming Zhang
- Industrial Crop Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xiaoming Li
- State Key Laboratory of Plant Diversity and Specialty Crops, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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13
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Gao W, Zhang L, Zhang Y, Zhang P, Shahinnia F, Chen T, Yang D. Genome‑wide identification and expression analysis of the UBC gene family in wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2024; 24:341. [PMID: 38671351 PMCID: PMC11047035 DOI: 10.1186/s12870-024-05042-3] [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: 10/09/2023] [Accepted: 04/18/2024] [Indexed: 04/28/2024]
Abstract
BACKGROUND Ubiquitination is an important regulatory step of selective protein degradation in the plant UPS (ubiquitin-proteasome system), which is involved in various biological processes in eukaryotes. Ubiquitin-conjugating enzymes play an intermediate role in the process of protein ubiquitination reactions and thus play an essential role in regulating plant growth and response to adverse environmental conditions. However, a genome-wide analysis of the UBC gene family in wheat (Triticum aestivum L.) has not yet been performed. RESULTS In this study, the number, physiochemical properties, gene structure, collinearity, and phylogenetic relationships of TaUBC family members in wheat were analyzed using bioinformatics methods. The expression pattern of TaUBC genes in different tissues/organs and developmental periods, as well as the transcript levels under abiotic stress treatment, were analyzed using RNA-Seq data and qRT-PCR. Meanwhile, favorable haplotypes of TaUBC25 were investigated based on wheat resequencing data of 681 wheat cultivars from the Wheat Union Database. The analyses identified a total of 93 TaUBC family members containing a UBC domain in wheat genome. These genes were unevenly distributed across 21 chromosomes, and numerous duplication events were observed between gene members. Based on phylogenetic analysis, the TaUBC family was divided into 13 E2 groups and a separate UEV group. We investigated the expression of TaUBC family genes under different tissue/organ and stress conditions by quantitative real-time PCR (qRT-PCR) analysis. The results showed that some TaUBC genes were specifically expressed in certain tissues/organs and that most TaUBC genes responded to NaCl, PEG6000, and ABA treatment with different levels of expression. In addition, we performed association analysis for the two haplotypes based on key agronomic traits such as thousand-kernel weight (TKW), kernel length (KL), kernel weight (KW), and kernel thickness (KT), examining 122 wheat accessions at three environmental sites. The results showed that TaUBC25-Hap II had significantly higher TKW, KL, KW, and KT than TaUBC25-Hap I. The distribution analysis of haplotypes showed that TaUBC25-Hap II was preferred in the natural population of wheat. CONCLUSION Our results identified 93 members of the TaUBC family in wheat, and several genes involved in grain development and abiotic stress response. Based on the SNPs detected in the TaUBC sequence, two haplotypes, TaUBC25-Hap I and TaUBC25-Hap II, were identified among wheat cultivars, and their potential value for wheat breeding was validated by association analysis. The above results provide a theoretical basis for elucidating the evolutionary relationships of the TaUBC gene family and lay the foundation for studying the functions of family members in the future.
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Affiliation(s)
- Weidong Gao
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Long Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yanyan Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Peipei Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Fahimeh Shahinnia
- Bioanalytics Gatersleben, Am Schwabenplan 1b, Seeland, 06466, Germany
| | - Tao Chen
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Delong Yang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
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14
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Song J, Liu Y, Guo R, Pacheco A, Muñoz-Zavala C, Song W, Wang H, Cao S, Hu G, Zheng H, Dhliwayo T, San Vicente F, Prasanna BM, Wang C, Zhang X. Exploiting genomic tools for genetic dissection and improving the resistance to Fusarium stalk rot in tropical maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:109. [PMID: 38649662 DOI: 10.1007/s00122-024-04597-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/07/2024] [Indexed: 04/25/2024]
Abstract
KEY MESSAGE A stable genomic region conferring FSR resistance at ~250 Mb on chromosome 1 was identified by GWAS. Genomic prediction has the potential to improve FSR resistance. Fusarium stalk rot (FSR) is a global destructive disease in maize; the efficiency of phenotypic selection for improving FSR resistance was low. Novel genomic tools of genome-wide association study (GWAS) and genomic prediction (GP) provide an opportunity for genetic dissection and improving FSR resistance. In this study, GWAS and GP analyses were performed on 562 tropical maize inbred lines consisting of two populations. In total, 15 SNPs significantly associated with FSR resistance were identified across two populations and the combinedPOP consisting of all 562 inbred lines, with the P-values ranging from 1.99 × 10-7 to 8.27 × 10-13, and the phenotypic variance explained (PVE) values ranging from 0.94 to 8.30%. The genetic effects of the 15 favorable alleles ranged from -4.29 to -14.21% of the FSR severity. One stable genomic region at ~ 250 Mb on chromosome 1 was detected across all populations, and the PVE values of the SNPs detected in this region ranged from 2.16 to 5.18%. Prediction accuracies of FSR severity estimated with the genome-wide SNPs were moderate and ranged from 0.29 to 0.51. By incorporating genotype-by-environment interaction, prediction accuracies were improved between 0.36 and 0.55 in different breeding scenarios. Considering both the genome coverage and the threshold of the P-value of SNPs to select a subset of molecular markers further improved the prediction accuracies. These findings extend the knowledge of exploiting genomic tools for genetic dissection and improving FSR resistance in tropical maize.
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Affiliation(s)
- Junqiao Song
- Henan University of Science and Technology, Luoyang, 471000, Henan, China
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
- Anyang Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Yubo Liu
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
- CIMMYT-China Specialty Maize Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 200063, China
| | - Rui Guo
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Angela Pacheco
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
| | - Carlos Muñoz-Zavala
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
| | - Wei Song
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Hui Wang
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
- CIMMYT-China Specialty Maize Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 200063, China
| | - Shiliang Cao
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
- Institute of Maize Research, Heilongjiang Academy of Agricultural Sciences, Harbin, 150070, Heilongjiang, China
| | - Guanghui Hu
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
- Institute of Maize Research, Heilongjiang Academy of Agricultural Sciences, Harbin, 150070, Heilongjiang, China
| | - Hongjian Zheng
- CIMMYT-China Specialty Maize Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 200063, China
| | - Thanda Dhliwayo
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
| | - Felix San Vicente
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
| | - Boddupalli M Prasanna
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, Nairobi, 00621, Kenya
| | - Chunping Wang
- Henan University of Science and Technology, Luoyang, 471000, Henan, China.
| | - Xuecai Zhang
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico.
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), CIMMYT-China Office, 12 Zhongguancun South Street, Beijing, 100081, China.
- Nanfan Research Institute, CAAS, Sanya, 572024, Hainan, China.
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15
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Gracia-Rodriguez C, Lopez-Ortiz C, Flores-Iga G, Ibarra-Muñoz L, Nimmakayala P, Reddy UK, Balagurusamy N. From genes to ecosystems: Decoding plant tolerance mechanisms to arsenic stress. Heliyon 2024; 10:e29140. [PMID: 38601600 PMCID: PMC11004893 DOI: 10.1016/j.heliyon.2024.e29140] [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: 11/15/2023] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 04/12/2024] Open
Abstract
Arsenic (As), a metalloid of considerable toxicity, has become increasingly bioavailable through anthropogenic activities, raising As contamination levels in groundwater and agricultural soils worldwide. This bioavailability has profound implications for plant biology and farming systems. As can detrimentally affect crop yield and pose risks of bioaccumulation and subsequent entry into the food chain. Upon exposure to As, plants initiate a multifaceted molecular response involving crucial signaling pathways, such as those mediated by calcium, mitogen-activated protein kinases, and various phytohormones (e.g., auxin, methyl jasmonate, cytokinin). These pathways, in turn, activate enzymes within the antioxidant system, which combat the reactive oxygen/nitrogen species (ROS and RNS) generated by As-induced stress. Plants exhibit a sophisticated genomic response to As, involving the upregulation of genes associated with uptake, chelation, and sequestration. Specific gene families, such as those coding for aquaglyceroporins and ABC transporters, are key in mediating As uptake and translocation within plant tissues. Moreover, we explore the gene regulatory networks that orchestrate the synthesis of phytochelatins and metallothioneins, which are crucial for As chelation and detoxification. Transcription factors, particularly those belonging to the MYB, NAC, and WRKY families, emerge as central regulators in activating As-responsive genes. On a post-translational level, we examine how ubiquitination pathways modulate the stability and function of proteins involved in As metabolism. By integrating omics findings, this review provides a comprehensive overview of the complex genomic landscape that defines plant responses to As. Knowledge gained from these genomic and epigenetic insights is pivotal for developing biotechnological strategies to enhance crop As tolerance.
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Affiliation(s)
- Celeste Gracia-Rodriguez
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Torreón, Mexico
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, Dunbar, WV 25112-1000, USA
| | - Carlos Lopez-Ortiz
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, Dunbar, WV 25112-1000, USA
| | - Gerardo Flores-Iga
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Torreón, Mexico
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, Dunbar, WV 25112-1000, USA
| | - Lizbeth Ibarra-Muñoz
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Torreón, Mexico
| | - Padma Nimmakayala
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, Dunbar, WV 25112-1000, USA
| | - Umesh K. Reddy
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, Dunbar, WV 25112-1000, USA
| | - Nagamani Balagurusamy
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Torreón, Mexico
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16
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Wei W, Luo Q, Yang YY, Wu CJ, Kuang JF, Chen JY, Lu WJ, Shan W. E3 ubiquitin ligase MaRZF1 modulates high temperature-induced green ripening of banana by degrading MaSGR1. PLANT, CELL & ENVIRONMENT 2024; 47:1128-1140. [PMID: 38093692 DOI: 10.1111/pce.14782] [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: 10/21/2022] [Accepted: 11/29/2023] [Indexed: 03/05/2024]
Abstract
High temperatures (>24°C) prevent the development of a yellow peel on bananas called green ripening, owing to the inhibition of chlorophyll degradation. This phenomenon greatly reduces the marketability of banana fruit, but the mechanisms underlining high temperature-repressed chlorophyll catabolism need to be elucidated. Herein, we found that the protein accumulation of chlorophyll catabolic enzyme MaSGR1 (STAY-GREEN 1) was reduced when bananas ripened at high temperature. Transiently expressing MaSGR1 in banana peel showed its positive involvement in promoting chlorophyll degradation under high temperature, thereby weakening green ripening phenotype. Using yeast two-hybrid screening, we identified a RING-type E3 ubiquitin ligase, MaRZF1 (RING Zinc Finger 1), as a putative MaSGR1-interacting protein. MaRZF1 interacts with and targets MaSGR1 for ubiquitination and degradation via the proteasome pathway. Moreover, upregulating MaRZF1 inhibited chlorophyll degradation, and attenuated MaSGR1-promoted chlorophyll degradation in bananas during green ripening, indicating that MaRZF1 negatively regulates chlorophyll catabolism via the degradation of MaSGR1. Taken together, MaRZF1 and MaSGR1 form a regulatory module to mediate chlorophyll degradation associated with high temperature-induced green ripening in bananas. Therefore, our findings expand the understanding of posttranslational regulatory mechanisms of temperature stress-caused fruit quality deterioration.
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Affiliation(s)
- Wei Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables, Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Qi Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables, Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Ying-Ying Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables, Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Chao-Jie Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables, Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jian-Fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables, Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jian-Ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables, Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Wang-Jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables, Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables, Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, China
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17
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Meng Y, Lv Q, Li L, Wang B, Chen L, Yang W, Lei Y, Xie Y, Li X. E3 ubiquitin ligase TaSDIR1-4A activates membrane-bound transcription factor TaWRKY29 to positively regulate drought resistance. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:987-1000. [PMID: 38018512 PMCID: PMC10955488 DOI: 10.1111/pbi.14240] [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: 09/07/2023] [Revised: 10/30/2023] [Accepted: 11/04/2023] [Indexed: 11/30/2023]
Abstract
Drought is a deleterious abiotic stress factor that constrains crop growth and development. Post-translational modification of proteins mediated by the ubiquitin-proteasome system is an effective strategy for directing plant responses to stress, but the regulatory mechanisms in wheat remain unclear. In this study, we showed that TaSDIR1-4A is a positive modulator of the drought response. Overexpression of TaSDIR1-4A increased the hypersensitivity of stomata, root length and endogenous abscisic acid (ABA) content under drought conditions. TaSDIR1-4A encodes a C3H2C3-type RING finger protein with E3 ligase activity. Amino acid mutation in its conserved domain led to loss of activity and altered the subcellular localization. The membrane-bound transcription factor TaWRKY29 was identified by yeast two-hybrid screening, and it was confirmed as interacting with TaSDIR1-4A both in vivo and in vitro. TaSDIR1-4A mediated the polyubiquitination and proteolysis of the C-terminal amino acid of TaWRKY29, and its translocation from the plasma membrane to the nucleus. Activated TaWRKY29 bound to the TaABI5 promoter to stimulate its expression, thereby positively regulating the ABA signalling pathway and drought response. Our findings demonstrate the positive role of TaSDIR1-4A in drought tolerance and provide new insights into the involvement of UPS in the wheat stress response.
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Affiliation(s)
- Ying Meng
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of AgronomyNorthwest A&F UniversityYanglingChina
| | - Qian Lv
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of AgronomyNorthwest A&F UniversityYanglingChina
| | - Liqun Li
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of AgronomyNorthwest A&F UniversityYanglingChina
| | - Bingxin Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of AgronomyNorthwest A&F UniversityYanglingChina
| | - Liuping Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of AgronomyNorthwest A&F UniversityYanglingChina
| | - Weibing Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of AgronomyNorthwest A&F UniversityYanglingChina
| | - Yanhong Lei
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of AgronomyNorthwest A&F UniversityYanglingChina
| | - Yanzhou Xie
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of AgronomyNorthwest A&F UniversityYanglingChina
| | - Xuejun Li
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of AgronomyNorthwest A&F UniversityYanglingChina
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18
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Niu L, Wang W, Li Y, Wu X, Wang W. Maize multi-omics reveal leaf water status controlling of differential transcriptomes, proteomes and hormones as mechanisms of age-dependent osmotic stress response in leaves. STRESS BIOLOGY 2024; 4:19. [PMID: 38498254 PMCID: PMC10948690 DOI: 10.1007/s44154-024-00159-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/06/2024] [Indexed: 03/20/2024]
Abstract
Drought-induced osmotic stress severely affects the growth and yield of maize. However, the mechanisms underlying the different responses of young and old maize leaves to osmotic stress remain unclear. To gain a systematic understanding of age-related stress responses, we compared osmotic-stress-induced changes in maize leaves of different ages using multi-omics approaches. After short-term osmotic stress, old leaves suffered more severe water deficits than young leaves. The adjustments of transcriptomes, proteomes, and hormones in response to osmotic stress were more dynamic in old leaves. Metabolic activities, stress signaling pathways, and hormones (especially abscisic acid) responded to osmotic stress in an age-dependent manner. We identified multiple functional clusters of genes and proteins with potential roles in stress adaptation. Old leaves significantly accumulated stress proteins such as dehydrin, aquaporin, and chaperones to cope with osmotic stress, accompanied by senescence-like cellular events, whereas young leaves exhibited an effective water conservation strategy mainly by hydrolyzing transitory starch and increasing proline production. The stress responses of individual leaves are primarily determined by their intracellular water status, resulting in differential transcriptomes, proteomes, and hormones. This study extends our understanding of the mechanisms underlying plant responses to osmotic stress.
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Affiliation(s)
- Liangjie Niu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450046, China
| | - Wenkang Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yingxue Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xiaolin Wu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Wei Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450046, China.
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19
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Panahi B, Shahi A. Trancriptome data mining in combination with co-expression network analysis identifies the functional modules and critical regulators in Hordeum vulgare L. in response to cold stress. Biochem Biophys Rep 2024; 37:101620. [PMID: 38155945 PMCID: PMC10753052 DOI: 10.1016/j.bbrep.2023.101620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/13/2023] [Accepted: 12/13/2023] [Indexed: 12/30/2023] Open
Abstract
Cold stress, as an abiotic stress, is one of the most limiting factors which pose a great threat to the plant's productivity. To understand the transcriptional regulation and connectivity pattern of genes involved in barley cold stress responses, co-expression network analysis was performed based on the global transcriptome profiling. The microarray datasets related to cold stress treatments were retrieved from the Gene Expression Omnibus (GEO) and Array express databases. Four microarray datasets related to cold stress-responsive transcriptome in barley were included in our study. Gene co-expression analysis was constructed using WGCNA method. Module-Trait Relationships (MTR) analysis and hub genes determination and validation were carried out. Finally, transcription factor and kinase regulatory networks were Inferred using machine learning algorithm. The co-expression modules were determined using beta index = 10. In total 13 co-expressed modules were identified with an average size of 153 genes. Functional enrichment based on gene ontology (GO) showed that each of the stress related significant modules were enriched in different biological processes. Annotation of significant modules identifies some TFs and Kinases such as ethylene-responsive transcription factor 1-like, transcription factor PCL1-like, transcription factor MYC2, WRKY, serine/threonine-protein kinase PBL7, and receptor-like protein kinase At2g42960 were contributed in barley cold stress response. Our analysis highlighted the functional importance of ABA signaling pathway, ROS signaling, defensive and protective proteins, degrading protein, Ca2+ related signaling, ribosome-mediated translation and etc. in responding of barley to cold stress condition. The current findings add substantially to our understanding of the cold responsive underlying mechanism of barley which can serve in future studies and breeding programs.
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Affiliation(s)
- Bahman Panahi
- Department of Genomics, Branch for Northwest & West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran
| | - Ali Shahi
- Faculty of Agriculture (Meshgin-Shahr Campus), University of Mohaghegh Ardabili, Ardabil, Iran
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20
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Inès D, Courty PE, Wendehenne D, Rosnoblet C. CDC48 in plants and its emerging function in plant immunity. TRENDS IN PLANT SCIENCE 2024:S1360-1385(23)00398-9. [PMID: 38218650 DOI: 10.1016/j.tplants.2023.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/14/2023] [Accepted: 12/14/2023] [Indexed: 01/15/2024]
Abstract
Protein homeostasis, namely the balance between protein synthesis and degradation, must be finely controlled to ensure cell survival, notably through the ubiquitin-proteasome system (UPS). In all species, including plants, homeostasis is disrupted by biotic and abiotic stresses. A key player in the maintenance of protein balance, the protein CDC48, shows emerging functions in plants, particularly in response to biotic stress. In this review on CDC48 in plants, we detail its highly conserved structure, describe a gene expansion that is only present in Viridiplantae, discuss its various functions and regulations, and finally highlight its recruitment, still not clear, during the plant immune response.
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Affiliation(s)
- Damien Inès
- Agroécologie, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Institut Agro, Université de Bourgogne, Université Bourgogne-Franche-Comté, Dijon, France
| | - Pierre-Emmanuel Courty
- Agroécologie, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Institut Agro, Université de Bourgogne, Université Bourgogne-Franche-Comté, Dijon, France
| | - David Wendehenne
- Agroécologie, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Institut Agro, Université de Bourgogne, Université Bourgogne-Franche-Comté, Dijon, France
| | - Claire Rosnoblet
- Agroécologie, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Institut Agro, Université de Bourgogne, Université Bourgogne-Franche-Comté, Dijon, France.
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21
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Wei W, Yang YY, Wu CJ, Kuang JF, Lu WJ, Chen JY, Shan W. MaNAC19-MaXB3 regulatory module mediates sucrose synthesis in banana fruit during ripening. Int J Biol Macromol 2023; 253:127144. [PMID: 37802454 DOI: 10.1016/j.ijbiomac.2023.127144] [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: 07/25/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/10/2023]
Abstract
Sucrose, a predominant sweetener in banana (Musa acuminata) fruit, determines sweetness and consumer preferences. Although sucrose phosphate synthase (SPS) is known to catalyze starch conversion into sucrose in banana fruit during the ripening process, the SPS regulatory mechanism during ripening still demands investigation. Hence, this study discovered that the MaSPS1 expression was promoted during ethylene-mediated ripening in banana fruit. MaNAC19, recognized as the MaSPS1 putative binding protein using yeast one-hybrid screening, directly binds to the MaSPS1 promoter, thereby transcriptionally activating its expression, which was verified by transient overexpression experiments, where the sucrose synthesis was accelerated through MaNAC19-induced transcription of MaSPS1. Interestingly, MaXB3, an ethylene-inhibited E3 ligase, was found to ubiquitinate MaNAC19, making it prone to proteasomal degradation, inhibiting transactivation of MaNAC19 to MaSPS1, thereby attenuating MaNAC19-promoted sucrose accumulation. This study's findings collectively illustrated the mechanistic basis of a MaXB3-MaNAC19-MaSPS1 regulatory module controlling sucrose synthesis during banana fruit ripening. These outcomes have broadened our understanding of the regulation mechanisms that contributed to sucrose metabolism occurring in transcriptional and post-transcriptional stages, which might help develop molecular approaches for controlling ripening and improving fruit quality.
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Affiliation(s)
- Wei Wei
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Ying-Ying Yang
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Chao-Jie Wu
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jian-Fei Kuang
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wang-Jin Lu
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jian-Ye Chen
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wei Shan
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China.
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22
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Muthego D, Moloi SJ, Brown AP, Goche T, Chivasa S, Ngara R. Exogenous abscisic acid treatment regulates protein secretion in sorghum cell suspension cultures. PLANT SIGNALING & BEHAVIOR 2023; 18:2291618. [PMID: 38100609 PMCID: PMC10730228 DOI: 10.1080/15592324.2023.2291618] [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: 08/17/2023] [Accepted: 11/28/2023] [Indexed: 12/17/2023]
Abstract
Drought stress adversely affects plant growth, often leading to total crop failure. Upon sensing soil water deficits, plants switch on biosynthesis of abscisic acid (ABA), a stress hormone for drought adaptation. Here, we used exogenous ABA application to dark-grown sorghum cell suspension cultures as an experimental system to understand how a drought-tolerant crop responds to ABA. We evaluated intracellular and secreted proteins using isobaric tags for relative and absolute quantification. While the abundance of only ~ 7% (46 proteins) intracellular proteins changed in response to ABA, ~32% (82 proteins) of secreted proteins identified in this study were ABA responsive. This shows that the extracellular matrix is disproportionately targeted and suggests it plays a vital role in sorghum adaptation to drought. Extracellular proteins responsive to ABA were predominantly defense/detoxification and cell wall-modifying enzymes. We confirmed that sorghum plants exposed to drought stress activate genes encoding the same proteins identified in the in vitro cell culture system with ABA. Our results suggest that ABA activates defense and cell wall remodeling systems during stress response. This could underpin the success of sorghum adaptation to drought stress.
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Affiliation(s)
- Dakalo Muthego
- Department of Plant Sciences, University of the Free State, Phuthaditjhaba, South Africa
| | - Sellwane J. Moloi
- Department of Plant Sciences, University of the Free State, Phuthaditjhaba, South Africa
| | | | - Tatenda Goche
- Department of Biosciences, Durham University, Durham, UK
- Department of Crop Science, Bindura University of Science Education, Bindura, Zimbabwe
| | | | - Rudo Ngara
- Department of Plant Sciences, University of the Free State, Phuthaditjhaba, South Africa
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23
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Liu Q, Maqbool A, Mirkin FG, Singh Y, Stevenson CEM, Lawson DM, Kamoun S, Huang W, Hogenhout SA. Bimodular architecture of bacterial effector SAP05 that drives ubiquitin-independent targeted protein degradation. Proc Natl Acad Sci U S A 2023; 120:e2310664120. [PMID: 38039272 DOI: 10.1073/pnas.2310664120] [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: 06/26/2023] [Accepted: 10/19/2023] [Indexed: 12/03/2023] Open
Abstract
In eukaryotes, targeted protein degradation (TPD) typically depends on a series of interactions among ubiquitin ligases that transfer ubiquitin molecules to substrates leading to degradation by the 26S proteasome. We previously identified that the bacterial effector protein SAP05 mediates ubiquitin-independent TPD. SAP05 forms a ternary complex via interactions with the von Willebrand Factor Type A (vWA) domain of the proteasomal ubiquitin receptor Rpn10 and the zinc-finger (ZnF) domains of the SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) and GATA BINDING FACTOR (GATA) transcription factors (TFs). This leads to direct TPD of the TFs by the 26S proteasome. Here, we report the crystal structures of the SAP05-Rpn10vWA complex at 2.17 Å resolution and of the SAP05-SPL5ZnF complex at 2.20 Å resolution. Structural analyses revealed that SAP05 displays a remarkable bimodular architecture with two distinct nonoverlapping surfaces, a "loop surface" with three protruding loops that form electrostatic interactions with ZnF, and a "sheet surface" featuring two β-sheets, loops, and α-helices that establish polar interactions with vWA. SAP05 binding to ZnF TFs involves single amino acids responsible for multiple contacts, while SAP05 binding to vWA is more stable due to the necessity of multiple mutations to break the interaction. In addition, positioning of the SAP05 complex on the 26S proteasome points to a mechanism of protein degradation. Collectively, our findings demonstrate how a small bacterial bimodular protein can bypass the canonical ubiquitin-proteasome proteolysis pathway, enabling ubiquitin-independent TPD in eukaryotic cells. This knowledge holds significant potential for the creation of TPD technologies.
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Affiliation(s)
- Qun Liu
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Abbas Maqbool
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Federico G Mirkin
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Yeshveer Singh
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Clare E M Stevenson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - David M Lawson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Weijie Huang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Centre for Plant Stress Biology, Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 20032, China
| | - Saskia A Hogenhout
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
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24
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Li HL, Liu ZY, Wang XN, Han Y, You CX, An JP. E3 ubiquitin ligases SINA4 and SINA11 regulate anthocyanin biosynthesis by targeting the IAA29-ARF5-1-ERF3 module in apple. PLANT, CELL & ENVIRONMENT 2023; 46:3902-3918. [PMID: 37658649 DOI: 10.1111/pce.14709] [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: 04/08/2023] [Revised: 07/13/2023] [Accepted: 08/22/2023] [Indexed: 09/03/2023]
Abstract
Auxin/indole-3-acetic acid (AUX/IAA) and auxin response factor (ARF) proteins are important components of the auxin signalling pathway, but their ubiquitination modification and the mechanism of auxin-mediated anthocyanin biosynthesis remain elusive. Here, the ARF MdARF5-1 was identified as a negative regulator of anthocyanin biosynthesis in apple, and it integrates auxin and ethylene signals by inhibiting the expression of the ethylene response factor MdERF3. The auxin repressor MdIAA29 decreased the inhibitory effect of MdARF5-1 on anthocyanin biosynthesis by attenuating the transcriptional inhibition of MdERF3 by MdARF5-1. In addition, the E3 ubiquitin ligases MdSINA4 and MdSINA11 played negative and positive regulatory roles in anthocyanin biosynthesis by targeting MdIAA29 and MdARF5-1 for ubiquitination degradation, respectively. MdSINA4 destabilized MdSINA11 to regulate anthocyanin accumulation in response to auxin signalling. In sum, our data revealed the crosstalk between auxin and ethylene signals mediated by the IAA29-ARF5-1-ERF3 module and provide new insights into the ubiquitination modification of the auxin signalling pathway.
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Affiliation(s)
- Hong-Liang Li
- Apple Technology Innovation Center of Shandong Province, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Zhi-Ying Liu
- Apple Technology Innovation Center of Shandong Province, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Xiao-Na Wang
- Apple Technology Innovation Center of Shandong Province, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Yuepeng Han
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, China
| | - Chun-Xiang You
- Apple Technology Innovation Center of Shandong Province, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Jian-Ping An
- Apple Technology Innovation Center of Shandong Province, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, China
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25
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Gasparis S, Miłoszewski MM. Genetic Basis of Grain Size and Weight in Rice, Wheat, and Barley. Int J Mol Sci 2023; 24:16921. [PMID: 38069243 PMCID: PMC10706642 DOI: 10.3390/ijms242316921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Grain size is a key component of grain yield in cereals. It is a complex quantitative trait controlled by multiple genes. Grain size is determined via several factors in different plant development stages, beginning with early tillering, spikelet formation, and assimilates accumulation during the pre-anthesis phase, up to grain filling and maturation. Understanding the genetic and molecular mechanisms that control grain size is a prerequisite for improving grain yield potential. The last decade has brought significant progress in genomic studies of grain size control. Several genes underlying grain size and weight were identified and characterized in rice, which is a model plant for cereal crops. A molecular function analysis revealed most genes are involved in different cell signaling pathways, including phytohormone signaling, transcriptional regulation, ubiquitin-proteasome pathway, and other physiological processes. Compared to rice, the genetic background of grain size in other important cereal crops, such as wheat and barley, remains largely unexplored. However, the high level of conservation of genomic structure and sequences between closely related cereal crops should facilitate the identification of functional orthologs in other species. This review provides a comprehensive overview of the genetic and molecular bases of grain size and weight in wheat, barley, and rice, focusing on the latest discoveries in the field. We also present possibly the most updated list of experimentally validated genes that have a strong effect on grain size and discuss their molecular function.
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Affiliation(s)
- Sebastian Gasparis
- Plant Breeding and Acclimatization Institute—National Research Institute in Radzików, 05-870 Błonie, Poland;
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26
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Gätjens-Boniche O, Jiménez-Madrigal JP, Whetten RW, Valenzuela-Diaz S, Alemán-Gutiérrez A, Hanson PE, Pinto-Tomás AA. Microbiome and plant cell transformation trigger insect gall induction in cassava. FRONTIERS IN PLANT SCIENCE 2023; 14:1237966. [PMID: 38126017 PMCID: PMC10731979 DOI: 10.3389/fpls.2023.1237966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 10/18/2023] [Indexed: 12/23/2023]
Abstract
Several specialised insects can manipulate normal plant development to induce a highly organised structure known as a gall, which represents one of the most complex interactions between insects and plants. Thus far, the mechanism for insect-induced plant galls has remained elusive. To study the induction mechanism of insect galls, we selected the gall induced by Iatrophobia brasiliensis (Diptera: Cecidomyiidae) in cassava (Euphorbiaceae: Manihot esculenta Crantz) as our model. PCR-based molecular markers and deep metagenomic sequencing data were employed to analyse the gall microbiome and to test the hypothesis that gall cells are genetically transformed by insect vectored bacteria. A shotgun sequencing discrimination approach was implemented to selectively discriminate between foreign DNA and the reference host plant genome. Several known candidate insertion sequences were identified, the most significant being DNA sequences found in bacterial genes related to the transcription regulatory factor CadR, cadmium-transporting ATPase encoded by the cadA gene, nitrate transport permease protein (nrtB gene), and arsenical pump ATPase (arsA gene). In addition, a DNA fragment associated with ubiquitin-like gene E2 was identified as a potential accessory genetic element involved in gall induction mechanism. Furthermore, our results suggest that the increased quality and rapid development of gall tissue are mostly driven by microbiome enrichment and the acquisition of critical endophytes. An initial gall-like structure was experimentally obtained in M. esculenta cultured tissues through inoculation assays using a Rhodococcus bacterial strain that originated from the inducing insect, which we related to the gall induction process. We provide evidence that the modification of the endophytic microbiome and the genetic transformation of plant cells in M. esculenta are two essential requirements for insect-induced gall formation. Based on these findings and having observed the same potential DNA marker in galls from other plant species (ubiquitin-like gene E2), we speculate that bacterially mediated genetic transformation of plant cells may represent a more widespread gall induction mechanism found in nature.
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Affiliation(s)
- Omar Gätjens-Boniche
- Laboratorio de Biología Molecular, Escuela de Ciencias Naturales y Exactas, Campus Tecnológico Local San Carlos, Instituto Tecnológico de Costa Rica, Alajuela, Costa Rica
| | - Jose Pablo Jiménez-Madrigal
- Laboratorio de Biología Molecular, Escuela de Ciencias Naturales y Exactas, Campus Tecnológico Local San Carlos, Instituto Tecnológico de Costa Rica, Alajuela, Costa Rica
| | - Ross W. Whetten
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Sandro Valenzuela-Diaz
- Human Microbiome Research Program, Faculty of Medicine, The Helsinki University, Helsinki, Finland
| | - Alvaro Alemán-Gutiérrez
- Laboratorio de Biología Molecular, Escuela de Ciencias Naturales y Exactas, Campus Tecnológico Local San Carlos, Instituto Tecnológico de Costa Rica, Alajuela, Costa Rica
- Laboratorio de Genómica y Biodiversidad, Facultad de Ciencias, Universidad del Bío-Bío, Chillán, Chile
| | - Paul E. Hanson
- Escuela de Biología, Universidad de Costa Rica, San Pedro, San José, Costa Rica
| | - Adrián A. Pinto-Tomás
- Center for Research in Microscopic Structures and Department of Biochemistry, School of Medicine, University of Costa Rica, San José, Costa Rica
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27
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Piatkowski B, Weston DJ, Aguero B, Duffy A, Imwattana K, Healey AL, Schmutz J, Shaw AJ. Divergent selection and climate adaptation fuel genomic differentiation between sister species of Sphagnum (peat moss). ANNALS OF BOTANY 2023; 132:499-512. [PMID: 37478307 PMCID: PMC10666999 DOI: 10.1093/aob/mcad104] [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: 05/12/2023] [Accepted: 07/24/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND AND AIMS New plant species can evolve through the reinforcement of reproductive isolation via local adaptation along habitat gradients. Peat mosses (Sphagnaceae) are an emerging model system for the study of evolutionary genomics and have well-documented niche differentiation among species. Recent molecular studies have demonstrated that the globally distributed species Sphagnum magellanicum is a complex of morphologically cryptic lineages that are phylogenetically and ecologically distinct. Here, we describe the architecture of genomic differentiation between two sister species in this complex known from eastern North America: the northern S. diabolicum and the largely southern S. magniae. METHODS We sampled plant populations from across a latitudinal gradient in eastern North America and performed whole genome and restriction-site associated DNA sequencing. These sequencing data were then analyzed computationally. KEY RESULTS Using sliding-window population genetic analyses we find that differentiation is concentrated within 'islands' of the genome spanning up to 400 kb that are characterized by elevated genetic divergence, suppressed recombination, reduced nucleotide diversity and increased rates of non-synonymous substitution. Sequence variants that are significantly associated with genetic structure and bioclimatic variables occur within genes that have functional enrichment for biological processes including abiotic stress response, photoperiodism and hormone-mediated signalling. Demographic modelling demonstrates that these two species diverged no more than 225 000 generations ago with secondary contact occurring where their ranges overlap. CONCLUSIONS We suggest that this heterogeneity of genomic differentiation is a result of linked selection and reflects the role of local adaptation to contrasting climatic zones in driving speciation. This research provides insight into the process of speciation in a group of ecologically important plants and strengthens our predictive understanding of how plant populations will respond as Earth's climate rapidly changes.
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Affiliation(s)
- Bryan Piatkowski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Blanka Aguero
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Aaron Duffy
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Karn Imwattana
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Adam L Healey
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - A Jonathan Shaw
- Department of Biology, Duke University, Durham, NC 27708, USA
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Wei W, Yang YY, Chen JY, Lakshmanan P, Kuang JF, Lu WJ, Shan W. MaNAC029 modulates ethylene biosynthesis and fruit quality and undergoes MaXB3-mediated proteasomal degradation during banana ripening. J Adv Res 2023; 53:33-47. [PMID: 36529351 PMCID: PMC10658243 DOI: 10.1016/j.jare.2022.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 10/12/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTIONS Ethylene regulates ripening by activating various metabolic pathways that controlcolor, aroma, flavor, texture, and consequently, the quality of fruits. However, the modulation of ethylene biosynthesis and quality formation during banana fruit ripening remains unclear. OBJECTIVES The present study aimed to identify the regulatory module that regulates ethylene and fruit quality-related metabolisms during banana fruit ripening. METHODS We used RNA-seq to compare unripe and ripe banana fruits and identified a ripening-induced NAC transcription factor, MaNAC029. We further performed DNA affinity purification sequencing to identify the MaNAC029's target genes involved in ethylene biosynthesis and fruit quality formation, and electrophoretic mobility shift assay, chromatin immunoprecipitation with real-time polymerase chain reaction and dual luciferase assays to explore the underlying regulatory mechanisms. Immunoprecipitation combined with mass spectrometry, yeast two-hybrid assay, and bimolecular fluorescence complementation assay were used to screen and verify the proteins interacting with MaNAC029. Finally, the function of MaNAC029 and its interacting protein associated with ethylene biosynthesis and quality formation was verified through transient overexpression experiments in banana fruits. RESULTS The study identified a nucleus-localized, ripening-induced NAC transcription factor MaNAC029. It transcriptionally activated genes associated with ethylene biosynthesis and a variety of cellular metabolisms related to fruit quality formation (cell wall degradation, starch degradation, aroma compound synthesis, and chlorophyll catabolism) by directly modulating their promoter activity during ripening. Overexpression of MaNAC029 in banana fruits activated ethylene biosynthesis and accelerated fruit ripening and quality formation. Notably, the E3 ligase MaXB3 interacted with and ubiquitinated MaNAC029 protein, facilitating MaNAC029 proteasomal degradation. Consistent with this finding, MaXB3 overexpression attenuated MaNAC029-enhanced ethylene biosynthesis and quality formation. CONCLUSION Our findings demonstrate that a MaXB3-MaNAC029 module regulates ethylene biosynthesis and a series of cellular metabolisms related to fruit quality formation during banana ripening. These results expand the understanding of the transcriptional and post-translational mechanisms of fruit ripening and quality formation.
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Affiliation(s)
- Wei Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Ying-Ying Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jian-Ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Prakash Lakshmanan
- Sugarcane Research Institute, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing 400716, China; Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia 4067, QLD, Australia
| | - Jian-Fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wang-Jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China.
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Liao G, Luo S, Li X, Li A, Mo Y, Wang A, Xiao D, He LF, Zhan J. Identification and functional characterization of REGULATORY PARTICLE NON-ATPASE 1a-like (AhRPN1a-like) in peanuts during aluminum-induced programmed cell death. JOURNAL OF PLANT PHYSIOLOGY 2023; 289:154079. [PMID: 37703767 DOI: 10.1016/j.jplph.2023.154079] [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: 04/29/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/15/2023]
Abstract
The toxicity of aluminum (Al) in acidic soil is a prevalent problem and causes reduced crop yields. In the plant response to Al toxicity, programmed cell death (PCD) appears to be one of the important mechanisms. However, the regulation of Al-induced PCD remains poorly understood. Here, we found that an uncharacterized protein REGULATORY PARTICLE NON-ATPASE 1a-like in peanut (AhRPN1a-like), located in the nucleus and cytoplasm, directly interacted with type I metacaspase in peanut (AhMC1). The overexpression of AhRPN1a-like in Arabidopsis strongly enhanced Al inhibition of root growth with a loss of root tip cell viability. Furthermore, in response to Al treatment, the VIGS knockdown line of AhRPN1a-like in peanut displayed decreased transcription of AhMC1, increased root growth, reduced Al-induced PCD and decreased 26S proteasomal activity. Taken together, these findings demonstrated that AhRPN1a-like interacted directly with AhMC1, and promotes the occurrence of Al-induced PCD via the 26S proteasome pathway, thereby reducing Al-resistance.
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Affiliation(s)
- Guoting Liao
- College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Shuzhen Luo
- College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Xinyue Li
- College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Ailing Li
- College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Yunchuan Mo
- College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Aiqin Wang
- College of Agriculture, Guangxi University, Nanning, Guangxi, China; Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China; Guangxi Key Laboratory of Agro-environment and Agric-products Safety, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Dong Xiao
- College of Agriculture, Guangxi University, Nanning, Guangxi, China; Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China; Guangxi Key Laboratory of Agro-environment and Agric-products Safety, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Long-Fei He
- College of Agriculture, Guangxi University, Nanning, Guangxi, China; Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China; Guangxi Key Laboratory of Agro-environment and Agric-products Safety, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Jie Zhan
- College of Agriculture, Guangxi University, Nanning, Guangxi, China; Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China; Guangxi Key Laboratory of Agro-environment and Agric-products Safety, College of Agriculture, Guangxi University, Nanning, Guangxi, China.
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An JP, Liu ZY, Zhang XW, Wang DR, Zeng F, You CX, Han Y. Brassinosteroid signaling regulator BIM1 integrates brassinolide and jasmonic acid signaling during cold tolerance in apple. PLANT PHYSIOLOGY 2023; 193:1652-1674. [PMID: 37392474 DOI: 10.1093/plphys/kiad371] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/25/2023] [Accepted: 06/05/2023] [Indexed: 07/03/2023]
Abstract
Although brassinolide (BR) and jasmonic acid (JA) play essential roles in the regulation of cold stress responses, the molecular basis of their crosstalk remains elusive. Here, we show a key component of BR signaling in apple (Malus × domestica), BR INSENSITIVE1 (BRI1)-EMS-SUPPRESSOR1 (BES1)-INTERACTING MYC-LIKE PROTEIN1 (MdBIM1), increases cold tolerance by directly activating expression of C-REPEAT BINDING FACTOR1 (MdCBF1) and forming a complex with C-REPEAT BINDING FACTOR2 (MdCBF2) to enhance MdCBF2-activated transcription of cold-responsive genes. Two repressors of JA signaling, JAZMONATE ZIM-DOMAIN1 (MdJAZ1) and JAZMONATE ZIM-DOMAIN2 (MdJAZ2), interact with MdBIM1 to integrate BR and JA signaling under cold stress. MdJAZ1 and MdJAZ2 reduce MdBIM1-promoted cold stress tolerance by attenuating transcriptional activation of MdCBF1 expression by MdBIM1 and interfering with the formation of the MdBIM1-MdCBF2 complex. Furthermore, the E3 ubiquitin ligase ARABIDOPSIS TÓXICOS en LEVADURA73 (MdATL73) decreases MdBIM1-promoted cold tolerance by targeting MdBIM1 for ubiquitination and degradation. Our results not only reveal crosstalk between BR and JA signaling mediated by a JAZ-BIM1-CBF module but also provide insights into the posttranslational regulatory mechanism of BR signaling.
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Affiliation(s)
- Jian-Ping An
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, Shandong, China
| | - Zhi-Ying Liu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, Shandong, China
| | - Xiao-Wei Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, Shandong, China
| | - Da-Ru Wang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, Shandong, China
| | - Fanchang Zeng
- College of Agriculture, Shandong Agricultural University, Tai-An 271018, Shandong, China
| | - Chun-Xiang You
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, Shandong, China
| | - Yuepeng Han
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
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Akbar MA, Mohd Yusof NY, Usup G, Ahmad A, Baharum SN, Bunawan H. Nutrient Deficiencies Impact on the Cellular and Metabolic Responses of Saxitoxin Producing Alexandrium minutum: A Transcriptomic Perspective. Mar Drugs 2023; 21:497. [PMID: 37755110 PMCID: PMC10532982 DOI: 10.3390/md21090497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 09/28/2023] Open
Abstract
Dinoflagellate Alexandrium minutum Halim is commonly associated with harmful algal blooms (HABs) in tropical marine waters due to its saxitoxin production. However, limited information is available regarding the cellular and metabolic changes of A. minutum in nutrient-deficient environments. To fill this gap, our study aimed to investigate the transcriptomic responses of A. minutum under nitrogen and phosphorus deficiency. The induction of nitrogen and phosphorus deficiency resulted in the identification of 1049 and 763 differently expressed genes (DEGs), respectively. Further analysis using gene set enrichment analysis (GSEA) revealed 702 and 1251 enriched gene ontology (GO) terms associated with nitrogen and phosphorus deficiency, respectively. Our results indicate that in laboratory cultures, nitrogen deficiency primarily affects meiosis, carbohydrate catabolism, ammonium assimilation, ion homeostasis, and protein kinase activity. On the other hand, phosphorus deficiency primarily affects the carbon metabolic response, cellular ion transfer, actin-dependent cell movement, signalling pathways, and protein recycling. Our study provides valuable insights into biological processes and genes regulating A. minutum's response to nutrient deficiencies, furthering our understanding of the ecophysiological response of HABs to environmental change.
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Affiliation(s)
- Muhamad Afiq Akbar
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Aquatic Animal Health and Therapeutics Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Institute of System Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia;
| | - Nurul Yuziana Mohd Yusof
- Department of Earth Science and Environment, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (N.Y.M.Y.); (G.U.)
| | - Gires Usup
- Department of Earth Science and Environment, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (N.Y.M.Y.); (G.U.)
| | - Asmat Ahmad
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia;
| | - Syarul Nataqain Baharum
- Institute of System Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia;
| | - Hamidun Bunawan
- Institute of System Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia;
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32
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Zhao K, Nan S, Li Y, Yu C, Zhou L, Hu J, Jin X, Han Y, Wang S. Comprehensive Analysis and Characterization of the GATA Gene Family, with Emphasis on the GATA6 Transcription Factor in Poplar. Int J Mol Sci 2023; 24:14118. [PMID: 37762421 PMCID: PMC10532138 DOI: 10.3390/ijms241814118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
GATA transcription factors are ubiquitously present in eukaryotic organisms and play a crucial role in multiple biological processes, such as plant growth, stress response, and hormone signaling. However, the study of GATA factors in poplar is currently limited to a small number of proteins, despite their evident functional importance. In this investigation, we utilized the most recent genome annotation and stringent criteria to identify 38 GATA transcription factor genes in poplar. Subsequently, we conducted a comprehensive analysis of this gene family, encompassing phylogenetic classification, protein characterization, analysis of promoter cis-acting elements, and determination of chromosomal location. Our examination of gene duplication events indicated that both tandem and segmental duplications have contributed to the expansion of the GATA gene family in poplar, with segmental duplication potentially being a major driving force. By performing collinearity analysis of genes across six different species, we identified 74 pairs of co-linear genes, which provide valuable insights for predicting gene functions from a comparative genomics perspective. Furthermore, through the analysis of gene expression patterns, we identified five GATA genes that exhibited differential expression in leaf-stem-root tissues and eight genes that were responsive to salt stress. Of particular interest was GATA6, which displayed strong induction by salt stress and overlapped between the two gene sets. We discovered that GATA6 encodes a nuclear-localized protein with transcription activation activity, which is continuously induced by salt stress in leaf and root tissues. Moreover, we constructed a co-expression network centered around GATA6, suggesting the potential involvement of these genes in the growth, development, and response to abiotic stress processes in poplar through cell transport systems and protein modification mechanisms, such as vesicle-mediated transport, intracellular transport, ubiquitination, and deubiquitination. This research provides a foundation for further exploration of the functions and mechanisms of GATA transcription factors in poplar.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Shengji Wang
- College of Forestry, Shanxi Agricultural University, Jinzhong 030801, China
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Tang X, Sun F, Zhang N, Rana BB, Kharel R, Luo P, Si H. RNA-seq provides insights into potato deubiquitinase responses to drought stress in seedling stage. FRONTIERS IN PLANT SCIENCE 2023; 14:1268448. [PMID: 37780518 PMCID: PMC10539648 DOI: 10.3389/fpls.2023.1268448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023]
Abstract
Ubiquitination is a specific protein degradation and reversible post-translational modification process that can be reversed by deubiquitinase (DUBs). DUBs can hydrolyze and release ubiquitin in the substrate protein so that the substrate can avoid degradation or change its activity, and it has an impact on plant growth and development, cell cycle, abiotic stress response, and other biological processes. Transcript sequences of potato varieties "DM1-3", "Atlantic" and "Cooperation-88" downloaded from Potato Genome Resources were used for genome-wide identification of the DUB gene family using Hidden Markov Models and verified in the NCBI CD-Search tool. The characteristics of DUB genes from different potato varieties were analyzed including subcellular localization, gene structural motifs, phylogenetic tree, and sequence homology. Polyethylene glycol 6000 (PEG6000) induced drought stress transcriptome analysis was performed on the "Atlantic", and differentially expressed genes were screened, with emphasis on the characterization of deubiquitinase. DUB genes have a complex gene structure, often with a large number of exons and alternative splicing. Their promoters contain abundant abiotic stress-responsive elements, such as 425 MYC, 325 ABRE, and 320 MYB. There are also a large number of orthologous genes in the DUBs of the three potato varieties, and these genes are often clustered in similar regions on the genome. We performed transcriptome sequencing of the potato under PEG-induced drought stress and analyzed it for the first time using the Atlantic as a reference genome. We identified a total of 6067 down-regulated differentially expressed genes (DEGs) and 4950 up-regulated DEGs under PEG-induced drought stress. We screened the expression of DUBs and observed that 120 DUBs were up-regulated where most of them functioned in the nucleus, and the interacting proteins of DUBs were also localized in the nucleus. We have comprehensively identified and analyzed potato DUBs, and the accurately aligned transcriptome data which will further deepen the understanding of DUBs involved in the regulation of osmotic stress.
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Affiliation(s)
- Xun Tang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fujun Sun
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Ning Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Birendra Bahadur Rana
- Nepal Agricultural Research Council, National Potato Research Program, Lalitpur, Nepal
| | - Raju Kharel
- Department of Genetics and Plant Breeding, Agricultural and Forestry University, Chitwan, Nepal
| | - Pan Luo
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
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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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35
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An JP, Li HL, Liu ZY, Wang DR, You CX, Han Y. The E3 ubiquitin ligase SINA1 and the protein kinase BIN2 cooperatively regulate PHR1 in apple anthocyanin biosynthesis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2175-2193. [PMID: 37272713 DOI: 10.1111/jipb.13538] [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: 01/19/2023] [Accepted: 06/02/2023] [Indexed: 06/06/2023]
Abstract
PHR1 (PHOSPHATE STARVATION RESPONSE1) plays key roles in the inorganic phosphate (Pi) starvation response and in Pi deficiency-induced anthocyanin biosynthesis in plants. However, the post-translational regulation of PHR1 is unclear, and the molecular basis of PHR1-mediated anthocyanin biosynthesis remains elusive. In this study, we determined that MdPHR1 was essential for Pi deficiency-induced anthocyanin accumulation in apple (Malus × domestica). MdPHR1 interacted with MdWRKY75, a positive regulator of anthocyanin biosynthesis, to enhance the MdWRKY75-activated transcription of MdMYB1, leading to anthocyanin accumulation. In addition, the E3 ubiquitin ligase SEVEN IN ABSENTIA1 (MdSINA1) negatively regulated MdPHR1-promoted anthocyanin biosynthesis via the ubiquitination-mediated degradation of MdPHR1. Moreover, the protein kinase apple BRASSINOSTEROID INSENSITIVE2 (MdBIN2) phosphorylated MdPHR1 and positively regulated MdPHR1-mediated anthocyanin accumulation by attenuating the MdSINA1-mediated ubiquitination degradation of MdPHR1. Taken together, these findings not only demonstrate the regulatory role of MdPHR1 in Pi starvation induced anthocyanin accumulation, but also provide an insight into the post-translational regulation of PHR1.
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Affiliation(s)
- Jian-Ping An
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China
| | - Hong-Liang Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China
| | - Zhi-Ying Liu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China
| | - Da-Ru Wang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China
| | - Chun-Xiang You
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China
| | - Yuepeng Han
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
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Xu X, Fonseca de Lima CF, Vu LD, De Smet I. When drought meets heat - a plant omics perspective. FRONTIERS IN PLANT SCIENCE 2023; 14:1250878. [PMID: 37674736 PMCID: PMC10478009 DOI: 10.3389/fpls.2023.1250878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023]
Abstract
Changes in weather patterns with emerging drought risks and rising global temperature are widespread and negatively affect crop growth and productivity. In nature, plants are simultaneously exposed to multiple biotic and abiotic stresses, but most studies focus on individual stress conditions. However, the simultaneous occurrence of different stresses impacts plant growth and development differently than a single stress. Plants sense the different stress combinations in the same or in different tissues, which could induce specific systemic signalling and acclimation responses; impacting different stress-responsive transcripts, protein abundance and modifications, and metabolites. This mini-review focuses on the combination of drought and heat, two abiotic stress conditions that often occur together. Recent omics studies indicate common or independent regulators involved in heat or drought stress responses. Here, we summarize the current research results, highlight gaps in our knowledge, and flag potential future focus areas.
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Affiliation(s)
- Xiangyu Xu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Cassio Flavio Fonseca de Lima
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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Zhang J, Wysocki R, Li F, Yu M, Martinoia E, Song WY. Role of ubiquitination in arsenic tolerance in plants. TRENDS IN PLANT SCIENCE 2023; 28:880-892. [PMID: 37002000 DOI: 10.1016/j.tplants.2023.03.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/18/2023] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
Arsenic (As) is harmful to all living organisms, including humans and plants. To limit As uptake and avoid its toxicity, plants employ systems that regulate the uptake of As from the soil and its translocation from roots to grains. Ubiquitination, a highly conserved post-translational modification (PTM) in all eukaryotes, plays crucial roles in modulating As detoxification mechanisms in budding yeast (Saccharomyces cerevisiae), but little is known about its roles in As tolerance and transport in plants. In this opinion article we review recent findings and suggest that ubiquitination plays a crucial role in regulating As transport in plants. We also propose ideas for future research to explore the importance of ubiquitination for enhancing As tolerance in crops.
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Affiliation(s)
- Jie Zhang
- Research Center for Environmental Membrane Biology and Department of Horticulture, Foshan University, Foshan, Guangdong 528000, China
| | - Robert Wysocki
- Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Fangbai Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Min Yu
- Research Center for Environmental Membrane Biology and Department of Horticulture, Foshan University, Foshan, Guangdong 528000, China.
| | - Enrico Martinoia
- Research Center for Environmental Membrane Biology and Department of Horticulture, Foshan University, Foshan, Guangdong 528000, China; Institute of Plant Biology, University Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.
| | - Won-Yong Song
- Research Center for Environmental Membrane Biology and Department of Horticulture, Foshan University, Foshan, Guangdong 528000, China; Department of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
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Cho NH, Kim EY, Park K, Lim CJ, Seo DH, Kim WT. Cosuppression of AtGELP22 and AtGELP23, two ubiquitinated target proteins of RING E3 ligase AtAIRP5, increases tolerance to drought stress in Arabidopsis. PLANT MOLECULAR BIOLOGY 2023:10.1007/s11103-023-01368-y. [PMID: 37479835 DOI: 10.1007/s11103-023-01368-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 06/27/2023] [Indexed: 07/23/2023]
Abstract
AtAIRP5 RING E3 ubiquitin ligase was recently identified as a positive regulator of the abscisic acid (ABA)-mediated drought stress response by stimulating the degradation of serine carboxypeptidase-like 1. Here, we identified GDSL-type esterase/lipase 22 (AtGELP22) and AtGELP23 as additional interacting partners of AtAIRP5. Yeast two-hybrid, pull-down, co-immunoprecipitation, and ubiquitination analyses verified that AtGELP22 and AtGELP23 are ubiquitinated target proteins of AtAIRP5. AtGELP22 and AtGELP23 were colocalized with AtAIRP5 to punctate-like structures in the cytosolic fraction, in which PYK10 and NAI2, two ER body marker proteins, are localized. T-DNA insertion atgelp22 and atgelp23 single knockout mutant plants showed phenotypes indistinguishable from those of wild-type plants under ABA treatment. In contrast, RNAi-mediated cosuppression of AtGELP22 and AtGELP23 resulted in hypersensitive ABA-mediated stomatal movements and higher tolerance to drought stress than that of the single mutant and wild-type plants. Taken together, our results suggest that the putative GDSL-type esterases/lipases AtGELP22 and AtGELP23 act as redundant negative regulators of the ABA-mediated drought stress response in Arabidopsis.
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Affiliation(s)
- Na Hyun Cho
- Division of Life Science, Department of Systems Biology, Yonsei University, Seoul, 03722, Korea
- Institute of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Eun Yu Kim
- Division of Life Science, Department of Systems Biology, Yonsei University, Seoul, 03722, Korea
- Institute of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Korea
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, 215316, China
| | - Kiyoul Park
- Division of Life Science, Department of Systems Biology, Yonsei University, Seoul, 03722, Korea
- Institute of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Korea
- Department of Biochemistry, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Cheol Jin Lim
- Division of Life Science, Department of Systems Biology, Yonsei University, Seoul, 03722, Korea
- Institute of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Dong Hye Seo
- Division of Life Science, Department of Systems Biology, Yonsei University, Seoul, 03722, Korea
- Institute of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Woo Taek Kim
- Division of Life Science, Department of Systems Biology, Yonsei University, Seoul, 03722, Korea.
- Institute of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Korea.
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Luo Q, Wei W, Yang YY, Wu CJ, Chen JY, Lu WJ, Kuang JF, Shan W. E3 ligase MaNIP1 degradation of NON-YELLOW COLORING1 at high temperature inhibits banana degreening. PLANT PHYSIOLOGY 2023; 192:1969-1981. [PMID: 36794407 PMCID: PMC10315274 DOI: 10.1093/plphys/kiad096] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/17/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Banana (Musa acuminata) fruit ripening under high temperatures (>24 °C) undergoes green ripening due to failure of chlorophyll degradation, which greatly reduces marketability. However, the mechanism underlying high temperature-repressed chlorophyll catabolism in banana fruit is not yet well understood. Here, using quantitative proteomic analysis, 375 differentially expressed proteins were identified in normal yellow and green ripening in banana. Among these, one of the key enzymes involved in chlorophyll degradation, NON-YELLOW COLORING 1 (MaNYC1), exhibited reduced protein levels when banana fruit ripened under high temperature. Transient overexpression of MaNYC1 in banana peels resulted in chlorophyll degradation under high temperature, which weakens the green ripening phenotype. Importantly, high temperature induced MaNYC1 protein degradation via the proteasome pathway. A banana RING E3 ligase, NYC1-interacting protein 1 (MaNIP1), was found to interact with and ubiquitinate MaNYC1, leading to its proteasomal degradation. Furthermore, transient overexpression of MaNIP1 attenuated MaNYC1-induced chlorophyll degradation in banana fruits, indicating that MaNIP1 negatively regulates chlorophyll catabolism by affecting MaNYC1 degradation. Taken together, the findings establish a post-translational regulatory module of MaNIP1-MaNYC1 that mediates high temperature-induced green ripening in bananas.
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Affiliation(s)
- Qi Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wei Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Ying-ying Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Chao-jie Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jian-ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wang-jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jian-fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
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40
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Saroha A, Gomashe SS, Kaur V, Pal D, Ujjainwal S, Aravind J, Singh M, Rajkumar S, Singh K, Kumar A, Wankhede DP. Genetic dissection of thousand-seed weight in linseed ( Linum usitatissimum L.) using multi-locus genome-wide association study. FRONTIERS IN PLANT SCIENCE 2023; 14:1166728. [PMID: 37332700 PMCID: PMC10272591 DOI: 10.3389/fpls.2023.1166728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/08/2023] [Indexed: 06/20/2023]
Abstract
Flaxseed/linseed is an important oilseed crop having applications in the food, nutraceutical, and paint industry. Seed weight is one of the most crucial determinants of seed yield in linseed. Here, quantitative trait nucleotides (QTNs) associated with thousand-seed weight (TSW) have been identified using multi-locus genome-wide association study (ML-GWAS). Field evaluation was carried out in five environments in multi-year-location trials. SNP genotyping information of the AM panel of 131 accessions comprising 68,925 SNPs was employed for ML-GWAS. From the six ML-GWAS methods employed, five methods helped identify a total of 84 unique significant QTNs for TSW. QTNs identified in ≥ 2 methods/environments were designated as stable QTNs. Accordingly, 30 stable QTNs have been identified for TSW accounting up to 38.65% trait variation. Alleles with positive effect on trait were analyzed for 12 strong QTNs with r 2 ≥ 10.00%, which showed significant association of specific alleles with higher trait value in three or more environments. A total of 23 candidate genes have been identified for TSW, which included B3 domain-containing transcription factor, SUMO-activating enzyme, protein SCARECROW, shaggy-related protein kinase/BIN2, ANTIAUXIN-RESISTANT 3, RING-type E3 ubiquitin transferase E4, auxin response factors, WRKY transcription factor, and CBS domain-containing protein. In silico expression analysis of candidate genes was performed to validate their possible role in different stages of seed development process. The results from this study provide significant insight and elevate our understanding on genetic architecture of TSW trait in linseed.
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Affiliation(s)
- Ankit Saroha
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sunil S. Gomashe
- ICAR-National Bureau of Plant Genetic Resources, Regional Station Akola, Maharashtra, India
| | - Vikender Kaur
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Deepa Pal
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Shraddha Ujjainwal
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - J. Aravind
- Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Mamta Singh
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - S. Rajkumar
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Kuldeep Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ashok Kumar
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Dhammaprakash Pandhari Wankhede
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
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Wu Z, Zhang T, Li J, Chen S, Grin IR, Zharkov DO, Yu B, Li H. Genome-wide analysis of WD40 protein family and functional characterization of BvWD40-82 in sugar beet. FRONTIERS IN PLANT SCIENCE 2023; 14:1185440. [PMID: 37332716 PMCID: PMC10272600 DOI: 10.3389/fpls.2023.1185440] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/10/2023] [Indexed: 06/20/2023]
Abstract
Sugar beet is one of the most important sugar crops in the world. It contributes greatly to the global sugar production, but salt stress negatively affects the crop yield. WD40 proteins play important roles in plant growth and response to abiotic stresses through their involvement in a variety of biological processes, such as signal transduction, histone modification, ubiquitination, and RNA processing. The WD40 protein family has been well-studied in Arabidopsis thaliana, rice and other plants, but the systematic analysis of the sugar beet WD40 proteins has not been reported. In this study, a total of 177 BvWD40 proteins were identified from the sugar beet genome, and their evolutionary characteristics, protein structure, gene structure, protein interaction network and gene ontology were systematically analyzed to understand their evolution and function. Meanwhile, the expression patterns of BvWD40s under salt stress were characterized, and a BvWD40-82 gene was hypothesized as a salt-tolerant candidate gene. Its function was further characterized using molecular and genetic methods. The result showed that BvWD40-82 enhanced salt stress tolerance in transgenic Arabidopsis seedlings by increasing the contents of osmolytes and antioxidant enzyme activities, maintaining intracellular ion homeostasis and increasing the expression of genes related to SOS and ABA pathways. The result has laid a foundation for further mechanistic study of the BvWD40 genes in sugar beet tolerance to salt stress, and it may inform biotechnological applications in improving crop stress resilience.
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Affiliation(s)
- Zhirui Wu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Tingyue Zhang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Jinna Li
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Sixue Chen
- Department of Biology, University of Mississippi, Oxford, MS, United States
| | - Inga R. Grin
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Dmitry O. Zharkov
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Bing Yu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Haiying Li
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
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Raffeiner M, Zhu S, González-Fuente M, Üstün S. Interplay between autophagy and proteasome during protein turnover. TRENDS IN PLANT SCIENCE 2023; 28:698-714. [PMID: 36801193 DOI: 10.1016/j.tplants.2023.01.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 01/13/2023] [Accepted: 01/26/2023] [Indexed: 05/13/2023]
Abstract
Protein homeostasis is epitomized by an equilibrium between protein biosynthesis and degradation: the 'life and death' of proteins. Approximately one-third of newly synthesized proteins are degraded. As such, protein turnover is required to maintain cellular integrity and survival. Autophagy and the ubiquitin-proteasome system (UPS) are the two principal degradation pathways in eukaryotes. Both pathways orchestrate many cellular processes during development and upon environmental stimuli. Ubiquitination of degradation targets is used as a 'death' signal by both processes. Recent findings revealed a direct functional link between both pathways. Here, we summarize key findings in the field of protein homeostasis, with an emphasis on the newly revealed crosstalk between both degradation machineries and how it is decided which pathway facilitates target degradation.
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Affiliation(s)
- Margot Raffeiner
- Eberhard-Karls-Universität Tübingen, Zentrum für Molekular Biologie der Pflanzen, 72076 Tübingen, Germany; Faculty of Biology & Biotechnology, Ruhr-University of Bochum, 44780 Bochum, Germany
| | - Shanshuo Zhu
- Eberhard-Karls-Universität Tübingen, Zentrum für Molekular Biologie der Pflanzen, 72076 Tübingen, Germany; Faculty of Biology & Biotechnology, Ruhr-University of Bochum, 44780 Bochum, Germany
| | - Manuel González-Fuente
- Eberhard-Karls-Universität Tübingen, Zentrum für Molekular Biologie der Pflanzen, 72076 Tübingen, Germany; Faculty of Biology & Biotechnology, Ruhr-University of Bochum, 44780 Bochum, Germany
| | - Suayib Üstün
- Eberhard-Karls-Universität Tübingen, Zentrum für Molekular Biologie der Pflanzen, 72076 Tübingen, Germany; Faculty of Biology & Biotechnology, Ruhr-University of Bochum, 44780 Bochum, Germany.
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43
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Li S, Yao X, Zhang B, Tang H, Lu L. Genome-wide characterization of the U-box gene in Camellia sinensis and functional analysis in transgenic tobacco under abiotic stresses. Gene 2023; 865:147301. [PMID: 36813060 DOI: 10.1016/j.gene.2023.147301] [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: 05/11/2022] [Revised: 12/16/2022] [Accepted: 02/16/2023] [Indexed: 02/22/2023]
Abstract
Plants U-box genes are crucial for plant survival, and they extensively regulate plant growth, reproduction and development as well as coping with stress and other processes. In this study, we identified 92 CsU-box genes through genome-wide analysis in the tea plant (Camellia sinensis), all of them contained the conserved U-box domain and were divided into 5 groups, which supported by the further genes structure analysis. The expression profiles in eight tea plant tissues and under abiotic and hormone stresses were analyzed using the TPIA database. 7 CsU-box genes (CsU-box27/28/39/46/63/70/91) were selected to verify and analyze expression patterns under PEG-induced drought and heat stress in tea plant respectively, the qRT-PCR results showed consistent with transcriptome datasets; and the CsU-box39 were further heterologous expressed in tobacco to perform gene function analysis. Phenotypic analyses of overexpression transgenic tobacco seedlings and physiological experiments revealed that CsU-box39 positively regulated the plant response to drought stress. These results lay a solid foundation for studying the biological function of CsU-box, and will provide breeding strategy basis for tea plant breeders.
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Affiliation(s)
- Shiyu Li
- College of Tea Sciences, Guizhou University, Guiyang 550025, China
| | - Xinzhuan Yao
- College of Tea Sciences, Guizhou University, Guiyang 550025, China
| | - Baohui Zhang
- Institute of Agricultural Bioengineering/College of Life Sciences, Key Laboratory of Mountain Plant Resources Conservation and Germplasm Innovation, Ministry of Education, Collaborative Innovation Center for Mountain Ecology and Agricultural Bioengineering, Guiyang 550025, China
| | - Hu Tang
- College of Tea Sciences, Guizhou University, Guiyang 550025, China; Institute of Agricultural Bioengineering/College of Life Sciences, Key Laboratory of Mountain Plant Resources Conservation and Germplasm Innovation, Ministry of Education, Collaborative Innovation Center for Mountain Ecology and Agricultural Bioengineering, Guiyang 550025, China.
| | - Litang Lu
- College of Tea Sciences, Guizhou University, Guiyang 550025, China; Institute of Agricultural Bioengineering/College of Life Sciences, Key Laboratory of Mountain Plant Resources Conservation and Germplasm Innovation, Ministry of Education, Collaborative Innovation Center for Mountain Ecology and Agricultural Bioengineering, Guiyang 550025, China.
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Teng L, Zhang X, Wang R, Lin K, Zeng M, Chen H, Cao F. miRNA transcriptome reveals key miRNAs and their targets contributing to the difference in Cd tolerance of two contrasting maize genotypes. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 256:114881. [PMID: 37030049 DOI: 10.1016/j.ecoenv.2023.114881] [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: 11/29/2022] [Revised: 03/06/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
Soil cadmium (Cd) contamination is a global environmental and food safety production issue. microRNAs (miRNAs) are proven to be involved in plant growth and development, and abiotic/biotic stress response, but their role in Cd tolerance is largely unknown in maize. To understand the genetic basis of Cd tolerance, two maize genotypes differing in Cd tolerance (L42, a sensitive genotype and L63, a tolerant genotype) were selected, and miRNA sequencing was carried out at nine-day-old seedlings exposed to 24 h Cd stress (5 μM CdCl2). A total of 151 differentially expressed miRNAs were identified, including 20 known miRNAs and 131 novel miRNAs. The results revealed that 90 and 22 miRNAs were up-regulated and down-regulated by Cd in Cd-tolerant genotype L63, and there were 23 and 43 miRNAs in Cd-sensitive genotype L42, respectively. Twenty-six miRNAs were up-regulated in L42 and unchanged or down-regulated in L63, or unchanged in L42 and down-regulated in L63. There were 108 miRNAs that were up-regulated in L63 and unchanged or down-regulated in L42, or unchanged in L63 and down-regulated in L42. Their target genes were enriched mainly in peroxisomes, glutathione (GSH) metabolism, ABC transporter, and ubiquitin-protease system. Among them, target genes involved in the peroxisome pathway and GSH metabolism might play key roles in Cd tolerance in L63. Besides, several ABC transporters which might involve in Cd uptake and transport were identified. The differentially expressed miRNAs or target genes could be used for breeding low grain Cd accumulation and high Cd tolerance cultivars in maize.
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Affiliation(s)
- Lidong Teng
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China
| | - Xueqing Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China
| | - Runfeng Wang
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China
| | - Kaina Lin
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China
| | - Meng Zeng
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China
| | - Hao Chen
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China; Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
| | - Fangbin Cao
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China.
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Fiorillo A, Manai M, Visconti S, Camoni L. The Salt Tolerance-Related Protein (STRP) Is a Positive Regulator of the Response to Salt Stress in Arabidopsis thaliana. PLANTS (BASEL, SWITZERLAND) 2023; 12:1704. [PMID: 37111928 PMCID: PMC10145591 DOI: 10.3390/plants12081704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/06/2023] [Accepted: 04/17/2023] [Indexed: 06/19/2023]
Abstract
Salt stress is a major abiotic stress limiting plant survival and crop productivity. Plant adaptation to salt stress involves complex responses, including changes in gene expression, regulation of hormone signaling, and production of stress-responsive proteins. The Salt Tolerance-Related Protein (STRP) has been recently characterized as a Late Embryogenesis Abundant (LEA)-like, intrinsically disordered protein involved in plant responses to cold stress. In addition, STRP has been proposed as a mediator of salt stress response in Arabidopsis thaliana, but its role has still to be fully clarified. Here, we investigated the role of STRP in salt stress responses in A. thaliana. The protein rapidly accumulates under salt stress due to a reduction of proteasome-mediated degradation. Physiological and biochemical responses of the strp mutant and STRP-overexpressing (STRP OE) plants demonstrate that salt stress impairs seed germination and seedling development more markedly in the strp mutant than in A. thaliana wild type (wt). At the same time, the inhibitory effect is significantly reduced in STRP OE plants. Moreover, the strp mutant has a lower ability to counteract oxidative stress, cannot accumulate the osmocompatible solute proline, and does not increase abscisic acid (ABA) levels in response to salinity stress. Accordingly, the opposite effect was observed in STRP OE plants. Overall, obtained results suggest that STRP performs its protective functions by reducing the oxidative burst induced by salt stress, and plays a role in the osmotic adjustment mechanisms required to preserve cellular homeostasis. These findings propose STRP as a critical component of the response mechanisms to saline stress in A. thaliana.
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Affiliation(s)
- Anna Fiorillo
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; (A.F.); (M.M.)
| | - Michela Manai
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; (A.F.); (M.M.)
- Ph.D. Program in Cellular and Molecular Biology, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Sabina Visconti
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; (A.F.); (M.M.)
| | - Lorenzo Camoni
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; (A.F.); (M.M.)
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Castro JC, Castro CG, Cobos M. Genetic and biochemical strategies for regulation of L-ascorbic acid biosynthesis in plants through the L-galactose pathway. FRONTIERS IN PLANT SCIENCE 2023; 14:1099829. [PMID: 37021310 PMCID: PMC10069634 DOI: 10.3389/fpls.2023.1099829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
Vitamin C (L-ascorbic acid, AsA) is an essential compound with pleiotropic functions in many organisms. Since its isolation in the last century, AsA has attracted the attention of the scientific community, allowing the discovery of the L-galactose pathway, which is the main pathway for AsA biosynthesis in plants. Thus, the aim of this review is to analyze the genetic and biochemical strategies employed by plant cells for regulating AsA biosynthesis through the L-galactose pathway. In this pathway, participates eight enzymes encoded by the genes PMI, PMM, GMP, GME, GGP, GPP, GDH, and GLDH. All these genes and their encoded enzymes have been well characterized, demonstrating their participation in AsA biosynthesis. Also, have described some genetic and biochemical strategies that allow its regulation. The genetic strategy includes regulation at transcriptional and post-transcriptional levels. In the first one, it was demonstrated that the expression levels of the genes correlate directly with AsA content in the tissues/organs of the plants. Also, it was proved that these genes are light-induced because they have light-responsive promoter motifs (e.g., ATC, I-box, GT1 motif, etc.). In addition, were identified some transcription factors that function as activators (e.g., SlICE1, AtERF98, SlHZ24, etc.) or inactivators (e.g., SlL1L4, ABI4, SlNYYA10) regulate the transcription of these genes. In the second one, it was proved that some genes have alternative splicing events and could be a mechanism to control AsA biosynthesis. Also, it was demonstrated that a conserved cis-acting upstream open reading frame (5'-uORF) located in the 5'-untranslated region of the GGP gene induces its post-transcriptional repression. Among the biochemical strategies discovered is the control of the enzyme levels (usually by decreasing their quantities), control of the enzyme catalytic activity (by increasing or decreasing its activity), feedback inhibition of some enzymes (GME and GGP), subcellular compartmentation of AsA, the metabolon assembly of the enzymes, and control of AsA biosynthesis by electron flow. Together, the construction of this basic knowledge has been establishing the foundations for generating genetically improved varieties of fruits and vegetables enriched with AsA, commonly used in animal and human feed.
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Affiliation(s)
- Juan C. Castro
- Unidad Especializada del Laboratorio de Investigación en Biotecnología (UELIB), Centro de Investigaciones de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru
- Departamento Académico de Ciencias Biomédicas y Biotecnología (DACBB), Facultad de Ciencias Biológicas (FCB), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru
| | - Carlos G. Castro
- Unidad Especializada del Laboratorio de Investigación en Biotecnología (UELIB), Centro de Investigaciones de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru
| | - Marianela Cobos
- Unidad Especializada del Laboratorio de Investigación en Biotecnología (UELIB), Centro de Investigaciones de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru
- Departamento Académico de Ciencias Biomédicas y Biotecnología (DACBB), Facultad de Ciencias Biológicas (FCB), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru
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UPL5 modulates WHY2 protein distribution in a Kub-site dependent ubiquitination in response to [Ca2+]cyt-induced leaf senescence. iScience 2023; 26:106216. [PMID: 36994183 PMCID: PMC10040967 DOI: 10.1016/j.isci.2023.106216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/08/2023] [Accepted: 02/13/2023] [Indexed: 03/08/2023] Open
Abstract
The translocation of proteins between various compartments of cells is the simplest and most direct way of an/retrograde communication. However, the mechanism of protein trafficking is far understood. In this study, we showed that the alteration of WHY2 protein abundance in various compartments of cells was dependent on a HECT-type ubiquitin E3 ligase UPL5 interacting with WHY2 in the cytoplasm, plastid, and nucleus, as well as mitochondrion to selectively ubiquitinate various Kub-sites (Kub 45 and Kub 227) of WHY2. Plastid genome stability can be maintained by the UPL5-WHY2 module, accompany by the alteration of photosystem activity and senescence-associated gene expression. In addition, the specificity of UPL5 ubiquitinating various Kub-sites of WHY2 was responded to cold or CaCl2 stress, in a dose [Ca2+]cyt-dependent manner. This demonstrates the integration of the UPL5 ubiquitination with the regulation of WHY2 distribution and retrograde communication between organelle and nuclear events of leaf senescence.
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Xiong E, Qu X, Li J, Liu H, Ma H, Zhang D, Chu S, Jiao Y. The soybean ubiquitin-proteasome system: Current knowledge and future perspective. THE PLANT GENOME 2023; 16:e20281. [PMID: 36345561 DOI: 10.1002/tpg2.20281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Increasing soybean [Glycine max (L.) Merr.] yield has become a worldwide scientific problem in the world. Many studies have shown that ubiquitination plays a key role in stress response and yield formation. In the UniProtKB database, 2,429 ubiquitin-related proteins were predicted in soybean, however, <20 were studied. One key way to address this lack of progress in increasing soybean yield will be a deeper understanding of the ubiquitin-proteasome system (UPS) in soybean. In this review, we summarized the current knowledge about soybean ubiquitin-related proteins and discussed the method of combining phenotype, mutant library, transgenic system, genomics, and proteomics approaches to facilitate the exploration of the soybean UPS. We also proposed the strategy of applying the UPS in soybean improvement based on related studies in model plants. Our review will be helpful for soybean scientists to learn current research progress of the soybean UPS and further lay a theoretical reference for the molecular improvement of soybean in future research by use of this knowledge.
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Affiliation(s)
- Erhui Xiong
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, Henan, 450002, China
| | - Xuelian Qu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, Henan, 450002, China
| | - Junfeng Li
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, Henan, 450002, China
| | - Hongli Liu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, Henan, 450002, China
| | - Hui Ma
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, Henan, 450002, China
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, Henan, 450002, China
| | - Shanshan Chu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, Henan, 450002, China
| | - Yongqing Jiao
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, Henan, 450002, China
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Bojórquez-Orozco AM, Arce-Leal ÁP, Montes RAC, Santos-Cervantes ME, Cruz-Mendívil A, Méndez-Lozano J, Castillo AG, Rodríguez-Negrete EA, Leyva-López NE. Differential Expression of miRNAs Involved in Response to Candidatus Liberibacter asiaticus Infection in Mexican Lime at Early and Late Stages of Huanglongbing Disease. PLANTS (BASEL, SWITZERLAND) 2023; 12:1039. [PMID: 36903899 PMCID: PMC10005081 DOI: 10.3390/plants12051039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/13/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Huanglongbing (HLB) is one of the most destructive diseases threatening citriculture worldwide. This disease has been associated with α-proteobacteria species, namely Candidatus Liberibacter. Due to the unculturable nature of the causal agent, it has been difficult to mitigate the disease, and nowadays a cure is not available. MicroRNAs (miRNAs) are key regulators of gene expression, playing an essential role in abiotic and biotic stress in plants including antibacterial responses. However, knowledge derived from non-model systems including Candidatus Liberibacter asiaticus (CLas)-citrus pathosystem remains largely unknown. In this study, small RNA profiles from Mexican lime (Citrus aurantifolia) plants infected with CLas at asymptomatic and symptomatic stages were generated by sRNA-Seq, and miRNAs were obtained with ShortStack software. A total of 46 miRNAs, including 29 known miRNAs and 17 novel miRNAs, were identified in Mexican lime. Among them, six miRNAs were deregulated in the asymptomatic stage, highlighting the up regulation of two new miRNAs. Meanwhile, eight miRNAs were differentially expressed in the symptomatic stage of the disease. The target genes of miRNAs were related to protein modification, transcription factors, and enzyme-coding genes. Our results provide new insights into miRNA-mediated regulation in C. aurantifolia in response to CLas infection. This information will be useful to understand molecular mechanisms behind the defense and pathogenesis of HLB.
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Affiliation(s)
- Ana Marlenne Bojórquez-Orozco
- Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave 81101, Sinaloa, Mexico
| | - Ángela Paulina Arce-Leal
- Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave 81101, Sinaloa, Mexico
| | - Ricardo A. Chávez Montes
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX 79409, USA
| | - María Elena Santos-Cervantes
- Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave 81101, Sinaloa, Mexico
| | - Abraham Cruz-Mendívil
- CONACYT—Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave 81101, Sinaloa, Mexico
| | - Jesús Méndez-Lozano
- Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave 81101, Sinaloa, Mexico
| | - Araceli G. Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM), Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Área de Genética, Facultad de Ciencias, E-29071 Málaga, Spain
| | - Edgar A. Rodríguez-Negrete
- Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave 81101, Sinaloa, Mexico
| | - Norma Elena Leyva-López
- Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave 81101, Sinaloa, Mexico
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Proteomics Provide Insight into the Interaction between Selenite and the Microalgae Dunaliella salina. Processes (Basel) 2023. [DOI: 10.3390/pr11020563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
Dunaliella salina is currently one of the most commercially valuable microalgae species in the world. In reponse to selenite, D. salina is a microalgae with a high selenium content, thereby increasing its value, which is crucial for increasing its economic value as a nutrional supplement. However, the effects of selenite on D. salina are still unclear, and its molecular mechanism of the response to selenite stress is also elusive. Here, in order to study the effects of selenite on D. salina and the corresponding regulatory mechanism, we characterized the physiological phenotypes of D. salina under different selenite concentrations and carried out a quantitative proteomic study. The results showed that the effective concentration for 50% growth inhibition (EC50) of the algae was 192.7 mg/L after 11 days of cultivation. When selenite concentration was lower than 100 mg/L, selenite did not hinder the growth of D. salina in the early stage, but shortened the cell growth cycle, although cell growth was significantly inhibited when the concentration of selenium was higher than 250 mg/L. Bioaccumulation experiments showed that the content of intracellular selenium in D. salina cells reached the highest level under the treatment with 50 mg/L selenite, and the contents of total selenium and organic selenium in D. salina cells were 499.77 μg/g and 303.01 μg/g (dry weight), respectively. Proteomic analysis revealed that a series of proteins related to stress responses, amino acid metabolism and energy production pathways were profoundly altered by the selenite treatment. Glutathione peroxidase (GPX7), a selenium-containing protein, was identified in the group given the selenium treatment. Moreover, proteins involved in photoreactions and oxidative phosphorylation were significantly upregulated, indicating that D. salina effectively balanced the energy demand and energy production under selenite stress. This study provides novel insights into the responses to selenite of D. salina, a microalgae candidate as a biological carrier of selenium and would be helpful for the development of industrial strains rich in selenium.
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