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Omar SA, Feng Y, Yu M, Eldin SAG, Eldenary ME, Shabala S, Allakhverdiev SI, Abdelfattah MH. Exogenous application of 5-azacitidin, royal jelly and folic acid regulate plant redox state, expression level of DNA methyltransferases and alleviate adverse effects of salinity stress on Vicia faba L. plants. Heliyon 2024; 10:e30934. [PMID: 38784551 PMCID: PMC11112330 DOI: 10.1016/j.heliyon.2024.e30934] [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: 01/12/2024] [Revised: 05/05/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
DNA methylation is one of induced changes under salinity stress causing reduction in the expression of several crucial genes required for normal plant's operation. Potential use of royal jelly (RJ), folic acid (FA) and 5-azacitidine (5-AZA) on two Egyptian faba bean varieties (Sakha-3 and Giza-716) grown under saline conditions was investigated. Salinity stress affects negatively on seeds germination (G %), mitotic index, membrane stability and induced a significant increase in chromosomal abnormalities (CAs). DNA methyltransferases genes (MT1 and MT2) were highly up-regulated (∼23 and 8 folds for MT1 and MT2 in shoots of Giza-716 stressed plants). On the other hand, down regulation of other studied stress related genes: superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR), heat shock protein (HSP-17.9) and proline-rich protein (GPRP) were detected in stressed plants of both studied varieties. Treating plants with RJ and FA increase G%, chlorophyll content, improves membrane properties and reduces CAs compared to non-treated stressed plants. Exogenous application of 5-AZA, RJ and FA on salinity stressed plants was associated with a significant reduction in the transcription of MT1 and MT2 which was associated with significant up regulation in the expression of Cu/Zn-SOD, CAT, GR, GPRP and HSP-17.9 encoding genes. The Lowest expression of MT1 and MT2 were induced with 5-AZA treatment in both studied varieties. Exogenous application of the FA, RJ and 5-AZA modified the methylation state of stressed plants by regulation the expression of DNA methyltransferases, subsequently, modulated the expression of studied genes and could be proposed as a promising treatment to ameliorate hazardous effects of salt stress on different plants.
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Affiliation(s)
| | - Yingming Feng
- International Research Centre for Environmental Membrane Biology & Department of Horticulture, Foshan University, Foshan, China
| | - Min Yu
- International Research Centre for Environmental Membrane Biology & Department of Horticulture, Foshan University, Foshan, China
| | | | | | - Sergey Shabala
- International Research Centre for Environmental Membrane Biology & Department of Horticulture, Foshan University, Foshan, China
- School of Biological Science, University of Western Australia, Crawley, Australia
| | - Suleyman I. Allakhverdiev
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow, 127276, Russia
- Bahcesehir University, Istanbul, 34353, Turkey
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Du SX, Wang LL, Yu WP, Xu SX, Chen L, Huang W. Appropriate induction of TOC1 ensures optimal MYB44 expression in ABA signaling and stress response in Arabidopsis. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38654596 DOI: 10.1111/pce.14922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 03/19/2024] [Accepted: 04/09/2024] [Indexed: 04/26/2024]
Abstract
Plants possess the remarkable ability to integrate the circadian clock with various signalling pathways, enabling them to quickly detect and react to both external and internal stress signals. However, the interplay between the circadian clock and biological processes in orchestrating responses to environmental stresses remains poorly understood. TOC1, a core component of the plant circadian clock, plays a vital role in maintaining circadian rhythmicity and participating in plant defences. Here, our study reveals a direct interaction between TOC1 and the promoter region of MYB44, a key gene involved in plant defence. TOC1 rhythmically represses MYB44 expression, thereby ensuring elevated MYB44 expression at dawn to help the plant in coping with lowest temperatures during diurnal cycles. Additionally, both TOC1 and MYB44 can be induced by cold stress in an Abscisic acid (ABA)-dependent and independent manner. TOC1 demonstrates a rapid induction in response to lower temperatures compared to ABA treatment, suggesting timely flexible regulation of TOC1-MYB44 regulatory module by the circadian clock in ensuring a proper response to diverse stresses and maintaining a balance between normal physiological processes and energy-consuming stress responses. Our study elucidates the role of TOC1 in effectively modulating expression of MYB44, providing insights into the regulatory network connecting the circadian clock, ABA signalling, and stress-responsive genes.
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Affiliation(s)
- Shen-Xiu Du
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Lu-Lu Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Wei-Peng Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Shu-Xuan Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Liang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Wei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
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Xue R, Guo R, Li Q, Lin T, Wu Z, Gao N, Wu F, Tong L, Zeng R, Song Y, Wang J. Rice responds to Spodoptera frugiperda infestation via epigenetic regulation of H3K9ac in the jasmonic acid signaling and phenylpropanoid biosynthesis pathways. PLANT CELL REPORTS 2024; 43:78. [PMID: 38393406 DOI: 10.1007/s00299-024-03160-8] [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: 11/01/2023] [Accepted: 01/16/2024] [Indexed: 02/25/2024]
Abstract
KEY MESSAGE This study provided important insights into the complex epigenetic regulatory of H3K9ac-modified genes involved in the jasmonic acid signaling and phenylpropanoid biosynthesis pathways of rice in response to Spodoptera frugiperda infestation. Physiological and molecular mechanisms underlying plant responses to insect herbivores have been well studied, while epigenetic modifications such as histone acetylation and their potential regulation at the genomic level of hidden genes remain largely unknown. Histone 3 lysine 9 acetylation (H3K9ac) is an epigenetic marker widely distributed in plants that can activate gene transcription. In this study, we provided the genome-wide profiles of H3K9ac in rice (Oryza sativa) infested by fall armyworm (Spodoptera frugiperda, FAW) using CUT&Tag-seq and RNA-seq. There were 3269 and 4609 up-regulated genes identified in plants infested by FAW larvae for 3 h and 12 h, respectively, which were mainly enriched in alpha-linolenic acid and phenylpropanoid pathways according to transcriptomic analysis. In addition, CUT&Tag-seq analysis revealed increased H3K9ac in FAW-infested plants, and there were 422 and 543 up-regulated genes enriched with H3K9ac observed at 3 h and 12 h after FAW feeding, respectively. Genes with increased H3K9ac were mainly enriched in the transcription start site (TSS), suggesting that H3K9ac is related to gene transcription. Integrative analysis of both RNA-seq and CUT&Tag-seq data showed that up-expressed genes with H3K9ac enrichment were mainly involved in the jasmonic acid (JA) and phenylpropanoid pathways. Particularly, two spermidine hydroxycinnamoyl transferase genes SHT1 and SHT2 involved in phenolamide biosynthesis were highly modified by H3K9ac in FAW-infested plants. Furthermore, the Ossht1 and Ossht2 transgenic lines exhibited decreased resistance against FAW larvae. Our findings suggest that rice responds to insect herbivory via H3K9ac epigenetic regulation in the JA signaling and phenolamide biosynthesis pathways.
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Affiliation(s)
- Rongrong Xue
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Ruiqing Guo
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Qing Li
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Tianhuang Lin
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Zicha Wu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Ning Gao
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Fei Wu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Lu Tong
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Rensen Zeng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
- Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuanyuan Song
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China.
- Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Jie Wang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China.
- Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Zhang MJ, Xue YY, Xu S, Jin XR, Man XC. Identification of ARF genes in Cucurbita pepo L and analysis of expression patterns, and functional analysis of CpARF22 under drought, salt stress. BMC Genomics 2024; 25:112. [PMID: 38273235 PMCID: PMC10809590 DOI: 10.1186/s12864-024-09992-8] [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: 09/04/2023] [Accepted: 01/08/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Auxin transcription factor (ARF) is an important transcription factor that transmits auxin signals and is involved in plant growth and development as well as stress response. However, genome-wide identification and responses to abiotic and pathogen stresses of the ARF gene family in Cucurbita pepo L, especially pathogen stresses, have not been reported. RESULTS Finally, 33 ARF genes (CpARF01 to CpARF33) were identified in C.pepo from the Cucurbitaceae genome database using bioinformatics methods. The putative protein contains 438 to 1071 amino acids, the isoelectric point is 4.99 to 8.54, and the molecular weight is 47759.36 to 117813.27 Da, the instability index ranged from 40.74 to 68.94, and the liposoluble index ranged from 62.56 to 76.18. The 33 genes were mainly localized in the nucleus and cytoplasm, and distributed on 16 chromosomes unevenly. Phylogenetic analysis showed that 33 CpARF proteins were divided into 6 groups. According to the amino acid sequence of CpARF proteins, 10 motifs were identified, and 1,3,6,8,10 motifs were highly conserved in most of the CpARF proteins. At the same time, it was found that genes in the same subfamily have similar gene structures. Cis-elements and protein interaction networks predicted that CpARF may be involved in abiotic factors related to the stress response. QRT-PCR analysis showed that most of the CpARF genes were upregulated under NaCl, PEG, and pathogen treatment compared to the control. Subcellular localization showed that CpARF22 was localized in the nucleus. The transgenic Arabidopsis thaliana lines with the CpARF22 gene enhanced their tolerance to salt and drought stress. CONCLUSION In this study, we systematically analyzed the CpARF gene family and its expression patterns under drought, salt, and pathogen stress, which improved our understanding of the ARF protein of zucchini, and laid a solid foundation for functional analysis of the CpARF gene.
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Affiliation(s)
- Ming-Jun Zhang
- College of Plant Protection, Gansu Agricultural University, Lanzhou, 730070, China
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, Gansu Agricultural University, Lanzhou, 730070, China
| | - Ying-Yu Xue
- College of Plant Protection, Gansu Agricultural University, Lanzhou, 730070, China.
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Shuang Xu
- College of Plant Protection, Gansu Agricultural University, Lanzhou, 730070, China
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xuan-Ru Jin
- College of Plant Protection, Gansu Agricultural University, Lanzhou, 730070, China
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xing-Chu Man
- College of Plant Protection, Gansu Agricultural University, Lanzhou, 730070, China
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, Gansu Agricultural University, Lanzhou, 730070, China
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Kovalchuk I. Role of Epigenetic Factors in Response to Stress and Establishment of Somatic Memory of Stress Exposure in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:3667. [PMID: 37960024 PMCID: PMC10648063 DOI: 10.3390/plants12213667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/18/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023]
Abstract
All species are well adapted to their environment. Stress causes a magnitude of biochemical and molecular responses in plants, leading to physiological or pathological changes. The response to various stresses is genetically predetermined, but is also controlled on the epigenetic level. Most plants are adapted to their environments through generations of exposure to all elements. Many plant species have the capacity to acclimate or adapt to certain stresses using the mechanism of priming. In most cases, priming is a somatic response allowing plants to deal with the same or similar stress more efficiently, with fewer resources diverted from growth and development. Priming likely relies on multiple mechanisms, but the differential expression of non-coding RNAs, changes in DNA methylation, histone modifications, and nucleosome repositioning play a crucial role. Specifically, we emphasize the role of BRM/CHR17, BRU1, FGT1, HFSA2, and H2A.Z proteins as positive regulators, and CAF-1, MOM1, DDM1, and SGS3 as potential negative regulators of somatic stress memory. In this review, we will discuss the role of epigenetic factors in response to stress, priming, and the somatic memory of stress exposures.
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Affiliation(s)
- Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
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Liu J, Shi K, Wang S, Zhu J, Wang X, Hong J, Wang Z. MsCYP71 is a positive regulator for drought resistance in alfalfa. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:107999. [PMID: 37678089 DOI: 10.1016/j.plaphy.2023.107999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/03/2023] [Accepted: 09/01/2023] [Indexed: 09/09/2023]
Abstract
Cytochrome P450 (CYP450) family proteins play key roles in plant growth, development, stress responses, and other physiological processes. Here, we cloned the cytochrome P450 gene MsCYP71 in alfalfa and found that the expression of MsCYP71 was induced by drought stress. Silencing the MsCYP71 gene using virus-induced gene silencing technology significantly decreased the drought resistance of alfalfa, as indicated by their lower relative water content, net photosynthetic rate, and chlorophyll fluorescence maximum (Fm); further, the heterologous overexpression of MsCYP71 in tobacco significantly enhanced the drought resistance and Fm of transgenic tobacco. Furthermore, the expression of MsCYP71 across 45 alfalfa accessions under drought stress was investigated. A significant positive correlation between drought resistance and MsCYP71 expression was observed. The 45 alfalfa accessions were clustered into four groups, and drought resistance, Fm, and MsCYP71 were higher in group I than in the other groups, indicating that group I accessions can be used as candidate germplasm resources for the breeding of drought-resistant alfalfa varieties. Overall, our findings indicated that MsCYP71 is a positive regulator of drought resistance in alfalfa, and its expression can be used to evaluate the drought resistance of alfalfa.
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Affiliation(s)
- Jia Liu
- College of Grass Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Kun Shi
- College of Grass Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Shaopeng Wang
- College of Grass Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jiahao Zhu
- College of Grass Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xijuan Wang
- College of Grass Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jun Hong
- National Animal Husbandry Services, Beijing, 100125, China
| | - Zan Wang
- College of Grass Science and Technology, China Agricultural University, Beijing, 100193, China.
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Kim TL, Lim H, Denison MIJ, Oh C. Transcriptomic and Physiological Analysis Reveals Genes Associated with Drought Stress Responses in Populus alba × Populus glandulosa. PLANTS (BASEL, SWITZERLAND) 2023; 12:3238. [PMID: 37765403 PMCID: PMC10535988 DOI: 10.3390/plants12183238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/07/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023]
Abstract
Drought stress affects plant productivity by altering plant responses at the morphological, physiological, and molecular levels. In this study, we identified physiological and genetic responses in Populus alba × Populus glandulosa hybrid clones 72-30 and 72-31 after 12 days of exposure to drought treatment. After 12 days of drought treatment, glucose, fructose, and sucrose levels were significantly increased in clone 72-30 under drought stress. The Fv/Fo and Fv/Fm values in both clones also decreased under drought stress. The changes in proline, malondialdehyde, and H2O2 levels were significant and more pronounced in clone 72-30 than in clone 72-31. The activities of antioxidant-related enzymes, such as catalase and ascorbate peroxidase, were significantly higher in the 72-31 clone. To identify drought-related genes, we conducted a transcriptomic analysis in P. alba × P. glandulosa leaves exposed to drought stress. We found 883 up-regulated and 305 down-regulated genes in the 72-30 clone and 279 and 303 in the 72-31 clone, respectively. These differentially expressed genes were mainly in synthetic pathways related to proline, abscisic acid, and antioxidants. Overall, clone 72-31 showed better drought tolerance than clone 72-30 under drought stress, and genetic changes also showed different patterns.
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Affiliation(s)
- Tae-Lim Kim
- Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Republic of Korea; (T.-L.K.); (C.O.)
| | - Hyemin Lim
- Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Republic of Korea; (T.-L.K.); (C.O.)
| | | | - Changyoung Oh
- Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Republic of Korea; (T.-L.K.); (C.O.)
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Subramanian S, Mitkus E, Souleimanov A, Smith DL. Lipo-chitooligosaccharide and thuricin 17 act as plant growth promoters and alleviate drought stress in Arabidopsis thaliana. Front Microbiol 2023; 14:1184158. [PMID: 37601342 PMCID: PMC10436337 DOI: 10.3389/fmicb.2023.1184158] [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: 03/11/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023] Open
Abstract
Lipo-chito-oligosaccharide (LCO-from Bradyrhizobium japonicum) and thuricin 17 (Th17-from Bacillus thuringiensis) are bacterial signal compounds from the rhizosphere of soybean that have been shown to enhance plant growth in a range of legumes and non-legumes. In this study, an attempt to quantify phytohormones involved in the initial hours after exposure of Arabidopsis thaliana to these compounds was conducted using UPLC-ESI-MS/MS. A petri-plate assay was conducted to screen for drought stress tolerance to PEG 8000 infusion and plant growth was studied 21-days post-stress. Arabidopsis thaliana plants grown in trays with drought stress imposed by water withhold were used for free proline determination, elemental analysis, and untargeted proteomics using LC-MS/MS studies. At 24 h post-exposure to the signal compounds under optimal growth conditions, Arabidopsis thaliana rosettes varied in their responses to the two signals. While LCO-treated rosettes showed a decrease in total IAA, cytokinins, gibberellins, and jasmonic acid, increases in ABA and SA was very clear. Th17-treated rosettes, on the other hand, showed an increase in IAA and SA. Both treatments resulted in decreased JA levels. Under severe drought stress imposed by PEG 8000 infusion, LCO and Th17 treatments were found to significantly increase fresh and dry weight over drought-stressed control plates, indicating that the presence of the signaling compounds decreased the negative effects experienced by the plants. Free proline content increased in LCO- and Th17-treated plants after water-withhold drought stress. Elemental analysis showed a significant increase in carbon percentage at the lower concentration of Th17. Untargeted proteomics revealed changes in the levels of drought-specific ribosomal proteins, glutathione S-transferase, late embryogenesis proteins, vegetative storage proteins 1 and 2, thaumatin-like proteins, and those related to chloroplast and carbon metabolism. The roles of some of these significantly affected proteins detected under drought stress are discussed.
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Affiliation(s)
| | - Erika Mitkus
- Department of Biology, McGill University, Montreal, QC, Canada
| | - Alfred Souleimanov
- Department of Plant Sciences, MacDonald Campus, McGill University, Montreal, QC, Canada
| | - Donald L. Smith
- Department of Plant Sciences, MacDonald Campus, McGill University, Montreal, QC, Canada
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Palos K, Yu L, Railey CE, Nelson Dittrich AC, Nelson ADL. Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs. THE PLANT CELL 2023; 35:1762-1786. [PMID: 36738093 PMCID: PMC10226578 DOI: 10.1093/plcell/koad027] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 05/30/2023]
Abstract
Long noncoding RNAs (lncRNAs) are a large and diverse class of genes in eukaryotic genomes that contribute to a variety of regulatory processes. Functionally characterized lncRNAs play critical roles in plants, ranging from regulating flowering to controlling lateral root formation. However, findings from the past decade have revealed that thousands of lncRNAs are present in plant transcriptomes, and characterization has lagged far behind identification. In this setting, distinguishing function from noise is challenging. However, the plant community has been at the forefront of discovery in lncRNA biology, providing many functional and mechanistic insights that have increased our understanding of this gene class. In this review, we examine the key discoveries and insights made in plant lncRNA biology over the past two and a half decades. We describe how discoveries made in the pregenomics era have informed efforts to identify and functionally characterize lncRNAs in the subsequent decades. We provide an overview of the functional archetypes into which characterized plant lncRNAs fit and speculate on new avenues of research that may uncover yet more archetypes. Finally, this review discusses the challenges facing the field and some exciting new molecular and computational approaches that may help inform lncRNA comparative and functional analyses.
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Affiliation(s)
- Kyle Palos
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Li’ang Yu
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Caylyn E Railey
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- Plant Biology Graduate Field, Cornell University, Ithaca, NY 14853, USA
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Samarina L, Wang S, Malyukova L, Bobrovskikh A, Doroshkov A, Koninskaya N, Shkhalakhova R, Matskiv A, Fedorina J, Fizikova A, Manakhova K, Loshkaryova S, Tutberidze T, Ryndin A, Khlestkina E. Long-term cold, freezing and drought: overlapping and specific regulatory mechanisms and signal transduction in tea plant ( Camellia sinensis (L.) Kuntze). FRONTIERS IN PLANT SCIENCE 2023; 14:1145793. [PMID: 37235017 PMCID: PMC10206121 DOI: 10.3389/fpls.2023.1145793] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/11/2023] [Indexed: 05/28/2023]
Abstract
Introduction Low temperatures and drought are two main environmental constraints reducing the yield and geographical distribution of horticultural crops worldwide. Understanding the genetic crosstalk between stress responses has potential importance for crop improvement. Methods In this study, Illumina RNA-seq and Pac-Bio genome resequencing were used to annotate genes and analyze transcriptome dynamics in tea plants under long-term cold, freezing, and drought. Results The highest number of differentially expressed genes (DEGs) was identified under long-term cold (7,896) and freezing (7,915), with 3,532 and 3,780 upregulated genes, respectively. The lowest number of DEGs was observed under 3-day drought (47) and 9-day drought (220), with five and 112 genes upregulated, respectively. The recovery after the cold had 6.5 times greater DEG numbers as compared to the drought recovery. Only 17.9% of cold-induced genes were upregulated by drought. In total, 1,492 transcription factor genes related to 57 families were identified. However, only 20 transcription factor genes were commonly upregulated by cold, freezing, and drought. Among the 232 common upregulated DEGs, most were related to signal transduction, cell wall remodeling, and lipid metabolism. Co-expression analysis and network reconstruction showed 19 genes with the highest co-expression connectivity: seven genes are related to cell wall remodeling (GATL7, UXS4, PRP-F1, 4CL, UEL-1, UDP-Arap, and TBL32), four genes are related to calcium-signaling (PXL1, Strap, CRT, and CIPK6), three genes are related to photo-perception (GIL1, CHUP1, and DnaJ11), two genes are related to hormone signaling (TTL3 and GID1C-like), two genes are involved in ROS signaling (ERO1 and CXE11), and one gene is related to the phenylpropanoid pathway (GALT6). Discussion Based on our results, several important overlapping mechanisms of long-term stress responses include cell wall remodeling through lignin biosynthesis, o-acetylation of polysaccharides, pectin biosynthesis and branching, and xyloglucan and arabinogalactan biosynthesis. This study provides new insight into long-term stress responses in woody crops, and a set of new target candidate genes were identified for molecular breeding aimed at tolerance to abiotic stresses.
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Affiliation(s)
- Lidiia Samarina
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia
| | - Songbo Wang
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Lyudmila Malyukova
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Alexandr Bobrovskikh
- Institute of Cytology and Genetics Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexey Doroshkov
- Institute of Cytology and Genetics Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Natalia Koninskaya
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Ruset Shkhalakhova
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Alexandra Matskiv
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Jaroslava Fedorina
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia
| | - Anastasia Fizikova
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia
| | - Karina Manakhova
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia
| | - Svetlana Loshkaryova
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Tsiala Tutberidze
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Alexey Ryndin
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Elena Khlestkina
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia
- Federal Research Center, N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), Saint Petersburg, Russia
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11
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Shen QQ, Wang TJ, Wang JG, He LL, Zhao TT, Zhao XT, Xie LY, Qian ZF, Wang XH, Liu LF, Chen SY, Zhang SZ, Li FS. The SsWRKY1 transcription factor of Saccharum spontaneum enhances drought tolerance in transgenic Arabidopsis thaliana and interacts with 21 potential proteins to regulate drought tolerance in S. spontaneum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 199:107706. [PMID: 37119548 DOI: 10.1016/j.plaphy.2023.107706] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/28/2023] [Accepted: 04/13/2023] [Indexed: 05/01/2023]
Abstract
In this study, we characterized a WRKY family member gene, SsWRKY1, which is located in the nucleus and contains multiple stress-related cis-acting elements. In addition, constructed SsWRKY1-overexpressing Arabidopsis thaliana had higher antioxidant enzyme activity and proline content under drought stress conditions, with lower malondialdehyde content and reactive oxygen species (ROS) accumulation, and the expression levels of six stress-related genes were significantly upregulated. This indicates that the overexpression of SsWRKY1 in Arabidopsis thaliana improves resistance to drought stress. SsWRKY1 does not have transcriptional autoactivation activity in yeast cells. The yeast two-hybrid (Y2H) system and the S. spontaneum cDNA library were used to screen 21 potential proteins that interact with SsWRKY1, and the interaction between SsWRKY1 and ATAF2 was verified by GST pull-down assay. In summary, our results indicate that SsWRKY1 plays an important role in the response to drought stress and provide initial insights into the molecular mechanism of SsWRKY1 in response to drought stress.
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Affiliation(s)
- Qing-Qing Shen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, 650201, People's Republic of China
| | - Tian-Ju Wang
- Institute for Bio-resources Research and Development of Central Yunnan Plateau, Chuxiong Normal University, Chuxiong, Yunnan, 675000, People's Republic of China
| | - Jun-Gang Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, People's Republic of China
| | - Li-Lian He
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, 650201, People's Republic of China
| | - Ting-Ting Zhao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, People's Republic of China
| | - Xue-Ting Zhao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, 650201, People's Republic of China
| | - Lin-Yan Xie
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, 650201, People's Republic of China
| | - Zhen-Feng Qian
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, 650201, People's Republic of China
| | - Xian-Hong Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, 650201, People's Republic of China
| | - Lu-Feng Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, 650201, People's Republic of China
| | - Shu-Ying Chen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, 650201, People's Republic of China
| | - Shu-Zhen Zhang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, People's Republic of China.
| | - Fu-Sheng Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, 650201, People's Republic of China; Key Laboratory for Crop Production and Smart Agriculture of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, People's Republic of China.
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12
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Shim JS, Jeong HI, Bang SW, Jung SE, Kim G, Kim YS, Redillas MCFR, Oh SJ, Seo JS, Kim JK. DROUGHT-INDUCED BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE enhances drought tolerance in rice. PLANT PHYSIOLOGY 2023; 191:1435-1447. [PMID: 36493384 PMCID: PMC9922417 DOI: 10.1093/plphys/kiac560] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/13/2022] [Indexed: 06/17/2023]
Abstract
Plants accumulate several metabolites in response to drought stress, including branched-chain amino acids (BCAAs). However, the roles of BCAAs in plant drought responses and the underlying molecular mechanisms for BCAA accumulation remain elusive. Here, we demonstrate that rice (Oryza sativa) DROUGHT-INDUCED BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE (OsDIAT) mediates the accumulation of BCAAs in rice in response to drought stress. An in vitro enzyme activity assay indicated that OsDIAT is a branched-chain amino acid aminotransferase, and subcellular localization analysis revealed that OsDIAT localizes to the cytoplasm. The expression of OsDIAT was induced in plants upon exposure to abiotic stress. OsDIAT-overexpressing (OsDIATOX) plants were more tolerant to drought stress, whereas osdiat plants were more susceptible to drought stress compared with nontransgenic (NT) plants. Amino acid analysis revealed that BCAA levels were higher in OsDIATOX but lower in osdiat compared with in NT plants. Finally, the exogenous application of BCAAs improved plant tolerance to osmotic stress compared with that in control plants. Collectively, these findings suggest that OsDIAT mediates drought tolerance by promoting the accumulation of BCAAs.
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Affiliation(s)
| | | | - Seung Woon Bang
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Se Eun Jung
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Goeun Kim
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Youn Shic Kim
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Mark Christian Felipe R Redillas
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Korea
- Department of Biology, De La Salle University, Manila 1004, Philippines
| | - Se-Jun Oh
- LaSemilla Co. Ltd., Pyeongchang 25354, Korea
| | - Jun Sung Seo
- Author for correspondence: (J. S. S.); (J.-K. K.)
| | - Ju-Kon Kim
- Author for correspondence: (J. S. S.); (J.-K. K.)
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13
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Ji W, Yu H, Shangguan Y, Cao J, Chen X, Zhao L, Guo Q, Xu P, Shen X, Xu Z. Transcriptome Profiling of Gossypium anomalum Seedlings Reveals Key Regulators and Metabolic Pathways in Response to Drought Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:312. [PMID: 36679025 PMCID: PMC9865944 DOI: 10.3390/plants12020312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/26/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Drought stress is a key limiting factor for cotton (Gossypium spp.) growth, production, development, and production worldwide. Some wild diploid cotton species are remarkably tolerant of water deficit and constitute an important reservoir for understanding the molecular mechanisms of Gossypium spp. drought tolerance and improving cultivated upland cotton. Here, we utilized RNA-Seq technology to characterize the leaf transcriptomes of a wild African diploid cotton species, Gossypium anomalum, under drought stress. A total of 12,322 differentially expressed genes (DEGs) were identified after mapping valid clean reads to the reference genome of G. anomalum, of which 1243 were commonly differentially expressed at all stages of drought stress. These genes were significantly enriched for molecular functions Gene Ontology terms related to cytoskeleton, hydrolase activity, cellular redox, and binding. Additionally, a substantial proportion of enriched biological process terms concerned cell or subcellular processes, while most in the cellular components category concerned membrane function and photosynthesis. An enrichment analysis against the Kyoto Encyclopedia of Genes and Genomes showed the top significantly enriched pathways to be photosynthesis-antenna proteins, amino sugar and nucleotide sugar metabolism, starch and sucrose metabolism, MAPK signaling pathway, glutathione metabolism, and plant hormone signal transduction. The DEGs also exhibited interestingly significant enrichments for drought stress-induced tandemly repeated genes involved in iron ion binding, oxidoreductase activity, heme binding, and other biological processes. A large number of genes encoding transcription factors, such as MYB, bHLH, ERF, NAC, WRKY, and bZIP, were identified as playing key roles in acclimatizing to drought stress. These results will provide deeper insights into the molecular mechanisms of drought stress adaptation in Gossypium spp.
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14
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Wang L, Jian Z, Wang P, Zhao L, Chen K. Combined physiological responses and differential expression of drought-responsive genes preliminarily explain the drought resistance mechanism of Lotus corniculatus. FUNCTIONAL PLANT BIOLOGY : FPB 2023; 50:46-57. [PMID: 36031596 DOI: 10.1071/fp22051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Lotus corniculatus L. is a perennial high-quality legume forage species but is vulnerable to drought, and water deficit reduces productivity. To understand the drought response mechanism of L. corniculatus , we investigated physiological responses under drought stress and constructed suppression subtractive hybridisation (SSH) cDNA libraries to isolate drought-inducible genes and quantitatively study the expression levels of candidate drought- responsive genes. Genes encoding calmodulin-like protein, mitogen-activated protein kinase, indole-3-acetic acid-induced protein, ser/thr-protein phosphatase homolog-related proteins, and β -galactosidase-related protein with hydrolysis activity were isolated and considered the main factors that explained the resistance of L. corniculatus to drought. Approximately 632 expressed sequence tags (ESTs) were identified and confirmed in the constructed SSH library. The Gene Ontology (GO) analysis revealed that these genes were involved mainly in transcription processes, protein synthesis, material metabolism, catalytic reactions, sugar metabolism, and photosynthesis. The interaction between the functions of these drought-related genes and the physiological responses preliminarily explains the drought resistance mechanisms of L. corniculatus .
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Affiliation(s)
- Leiting Wang
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Zhongling Jian
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Puchang Wang
- Guizhou Institute of Prataculture, Guiyang 550006, China
| | - Lili Zhao
- College of Animal Science, Guizhou University, Guiyang 550025, China; and State Engineering Technology Institute for Karst Rocky Desertification Control, Guiyang 550025, China
| | - Keke Chen
- College of Animal Science, Guizhou University, Guiyang 550025, China
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15
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Rauschendorfer J, Rooney R, Külheim C. Strategies to mitigate shifts in red oak (Quercus sect. Lobatae) distribution under a changing climate. TREE PHYSIOLOGY 2022; 42:2383-2400. [PMID: 35867476 DOI: 10.1093/treephys/tpac090] [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: 11/24/2021] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Red oaks (Quercus sect. Lobatae) are a taxonomic group of hardwood trees, which occur in swamp forests, subtropical chaparral and savannahs from Columbia to Canada. They cover a wide range of ecological niches, and many species are thought to be able to cope with current trends in climate change. Genus Quercus encompasses ca. 500 species, of which ca. 80 make up sect. Lobatae. Species diversity is greatest within the southeastern USA and within the northern and eastern regions of Mexico. This review discusses the weak reproductive barriers between species of red oaks and the effects this has on speciation and niche range. Distribution and diversity have been shaped by drought adaptations common to the species of sect. Lobatae, which enable them to fill various xeric niches across the continent. Drought adaptive traits of this taxonomic group include deciduousness, deep tap roots, ring-porous xylem, regenerative stump sprouting, greater leaf thickness and smaller stomata. The complex interplay between these anatomical and morphological traits has given red oaks features of drought tolerance and avoidance. Here, we discuss physiological and genetic components of these adaptations to address how many species of sect. Lobatae reside within xeric sites and/or sustain normal metabolic function during drought. Although extensive drought adaptation appears to give sect. Lobatae a resilience to climate change, aging tree stands, oak life history traits and the current genetic structures place many red oak species at risk. Furthermore, oak decline, a complex interaction between abiotic and biotic agents, has severe effects on red oaks and is likely to accelerate species decline and fragmentation. We suggest that assisted migration can be used to avoid species fragmentation and increase climate change resilience of sect. Lobatae.
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Affiliation(s)
- James Rauschendorfer
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Rebecca Rooney
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
- Department of Biology, University of Minnesota Duluth, Duluth, MN 55812, USA
| | - Carsten Külheim
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
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16
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Baoxiang W, Bo X, Yan L, Jingfang L, Zhiguang S, Ming C, Yungao X, Bo Y, Jian L, Jinbo L, Tingmu C, Zhaowei F, Baiguan L, Dayong X, Bello BK. A Novel mechanisms of the signaling cascade associated with the SAPK10-bZIP20-NHX1 synergistic interaction to enhance tolerance of plant to abiotic stress in rice (Oryza sativa L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111393. [PMID: 35878697 DOI: 10.1016/j.plantsci.2022.111393] [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: 04/13/2022] [Revised: 07/11/2022] [Accepted: 07/17/2022] [Indexed: 06/15/2023]
Abstract
The bzip transcription factors can modulate the transcriptional expressions of target genes by binding specifically to cis-regulatory elements in the promoter region of stress-related genes, hence regulating plant stress resistance. Here, we investigated a stress-responsive transcription factor Osbzip20 under abiotic stresses. The OsbZIP20-GFP fusion protein predominantly aggregated in the nucleus, in accordance with our subcellular localization. OsbZIP20 transcript was observed in all vegetative tissues with highest levels being detected in the seed. Transcription of Osbzip20 was induced by salinity, exsiccation, and abscisic acid. Overexpression of OsbZIP20 in transgenic rice considerably improved tolerance to salt and drought stresses, as well as increased sensitivity to ABA. Furthermore, abiotic stress responsive genes transcript were found to be remarkably elevated in transgenic rice overexpressing OsbZIP20 than in wild-type plants. SAPK10 was discovered to directly interact with and phosphorylate OsbZIP20. Yeast one-hybrid and luciferase assay revealed that OsbZIP20 acted as a transcriptional stimulator. Interestingly, gel shift assay showed that phosphorylated bZIP20 augmented its DNA-binding affinity to the ABRE element of the NHX1 promoter and induced its transcription. In sum, our findings establish a novel signaling pathway associated with the SAPK10-bZIP20-NHX1 synergistic interaction, as well as a new strategy for enhancing rice drought and salt tolerance.
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Affiliation(s)
- Wang Baoxiang
- Lianyungang Institute of Agricultural Sciences, Collaborative Innovation Center for Modern Crop Production, Lianyungang, Jiangsu province 222006, China
| | - Xu Bo
- Lianyungang Institute of Agricultural Sciences, Collaborative Innovation Center for Modern Crop Production, Lianyungang, Jiangsu province 222006, China
| | - Liu Yan
- Lianyungang Institute of Agricultural Sciences, Collaborative Innovation Center for Modern Crop Production, Lianyungang, Jiangsu province 222006, China
| | - Li Jingfang
- Lianyungang Institute of Agricultural Sciences, Collaborative Innovation Center for Modern Crop Production, Lianyungang, Jiangsu province 222006, China
| | - Sun Zhiguang
- Lianyungang Institute of Agricultural Sciences, Collaborative Innovation Center for Modern Crop Production, Lianyungang, Jiangsu province 222006, China
| | - Chi Ming
- Lianyungang Institute of Agricultural Sciences, Collaborative Innovation Center for Modern Crop Production, Lianyungang, Jiangsu province 222006, China
| | - Xing Yungao
- Lianyungang Institute of Agricultural Sciences, Collaborative Innovation Center for Modern Crop Production, Lianyungang, Jiangsu province 222006, China
| | - Yang Bo
- Lianyungang Institute of Agricultural Sciences, Collaborative Innovation Center for Modern Crop Production, Lianyungang, Jiangsu province 222006, China
| | - Li Jian
- Lianyungang Institute of Agricultural Sciences, Collaborative Innovation Center for Modern Crop Production, Lianyungang, Jiangsu province 222006, China
| | - Liu Jinbo
- Lianyungang Institute of Agricultural Sciences, Collaborative Innovation Center for Modern Crop Production, Lianyungang, Jiangsu province 222006, China
| | - Chen Tingmu
- Lianyungang Institute of Agricultural Sciences, Collaborative Innovation Center for Modern Crop Production, Lianyungang, Jiangsu province 222006, China
| | - Fang Zhaowei
- Lianyungang Institute of Agricultural Sciences, Collaborative Innovation Center for Modern Crop Production, Lianyungang, Jiangsu province 222006, China
| | - Lu Baiguan
- Lianyungang Institute of Agricultural Sciences, Collaborative Innovation Center for Modern Crop Production, Lianyungang, Jiangsu province 222006, China
| | - Xu Dayong
- Lianyungang Institute of Agricultural Sciences, Collaborative Innovation Center for Modern Crop Production, Lianyungang, Jiangsu province 222006, China.
| | - Babatunde Kazeem Bello
- Lianyungang Institute of Agricultural Sciences, Collaborative Innovation Center for Modern Crop Production, Lianyungang, Jiangsu province 222006, China.
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17
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Antisense Transcription in Plants: A Systematic Review and an Update on cis-NATs of Sugarcane. Int J Mol Sci 2022; 23:ijms231911603. [PMID: 36232906 PMCID: PMC9569758 DOI: 10.3390/ijms231911603] [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: 07/19/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 11/09/2022] Open
Abstract
Initially, natural antisense transcripts (NATs, natRNAs, or asRNAs) were considered repressors; however, their functions in gene regulation are diverse. Positive, negative, or neutral correlations to the cognate gene expression have been noted. Although the first studies were published about 50 years ago, there is still much to be investigated regarding antisense transcripts in plants. A systematic review of scientific publications available in the Web of Science databases was conducted to contextualize how the studying of antisense transcripts has been addressed. Studies were classified considering three categories: “Natural antisense” (208), artificial antisense used in “Genetic Engineering” (797), or “Natural antisense and Genetic Engineering”-related publications (96). A similar string was used for a systematic search in the NCBI Gene database. Of the 1132 antisense sequences found for plants, only 0.8% were cited in PubMed and had antisense information confirmed. This value was the lowest when compared to fungi (2.9%), bacteria (2.3%), and mice (54.1%). Finally, we present an update for the cis-NATs identified in Saccharum spp. Of the 1413 antisense transcripts found in different experiments, 25 showed concordant expressions, 22 were discordant, 1264 did not correlate with the cognate genes, and 102 presented variable results depending on the experiment.
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18
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Phour M, Sindhu SS. Mitigating abiotic stress: microbiome engineering for improving agricultural production and environmental sustainability. PLANTA 2022; 256:85. [PMID: 36125564 DOI: 10.1007/s00425-022-03997-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 09/11/2022] [Indexed: 06/15/2023]
Abstract
The responses of plants to different abiotic stresses and mechanisms involved in their mitigation are discussed. Production of osmoprotectants, antioxidants, enzymes and other metabolites by beneficial microorganisms and their bioengineering ameliorates environmental stresses to improve food production. Progressive intensification of global agriculture, injudicious use of agrochemicals and change in climate conditions have deteriorated soil health, diminished the microbial biodiversity and resulted in environment pollution along with increase in biotic and abiotic stresses. Extreme weather conditions and erratic rains have further imposed additional stress for the growth and development of plants. Dominant abiotic stresses comprise drought, temperature, increased salinity, acidity, metal toxicity and nutrient starvation in soil, which severely limit crop production. For promoting sustainable crop production in environmentally challenging environments, use of beneficial microbes has emerged as a safer and sustainable means for mitigation of abiotic stresses resulting in improved crop productivity. These stress-tolerant microorganisms play an effective role against abiotic stresses by enhancing the antioxidant potential, improving nutrient acquisition, regulating the production of plant hormones, ACC deaminase, siderophore and exopolysaccharides and accumulating osmoprotectants and, thus, stimulating plant biomass and crop yield. In addition, bioengineering of beneficial microorganisms provides an innovative approach to enhance stress tolerance in plants. The use of genetically engineered stress-tolerant microbes as inoculants of crop plants may facilitate their use for enhanced nutrient cycling along with amelioration of abiotic stresses to improve food production for the ever-increasing population. In this chapter, an overview is provided about the current understanding of plant-bacterial interactions that help in alleviating abiotic stress in different crop systems in the face of climate change. This review largely focuses on the importance and need of sustainable and environmentally friendly approaches using beneficial microbes for ameliorating the environmental stresses in our agricultural systems.
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Affiliation(s)
- Manisha Phour
- Department of Microbiology, CCS Haryana Agricultural University, Hisar, 125004, India
- University Institute of Biotechnology, Chandigarh University, Mohali, India
| | - Satyavir S Sindhu
- Department of Microbiology, CCS Haryana Agricultural University, Hisar, 125004, India.
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19
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Yu Y, Portolés S, Ren Y, Sun G, Wang XF, Zhang H, Guo S. The key clock component ZEITLUPE (ZTL) negatively regulates ABA signaling by degradation of CHLH in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:995907. [PMID: 36176682 PMCID: PMC9513469 DOI: 10.3389/fpls.2022.995907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
Ubiquitination-mediated protein degradation plays important roles in ABA signal transduction and delivering responses to chloroplast stress signals in plants, but additional E3 ligases of protein ubiquitination remain to be identified to understand the complex signaling network. Here we reported that ZEITLUPE (ZTL), an F-box protein, negatively regulates abscisic acid (ABA) signaling during ABA-inhibited early seedling growth and ABA-induced stomatal closure in Arabidopsis thaliana. Using molecular biology and biochemistry approaches, we demonstrated that ZTL interacts with and ubiquitinates its substrate, CHLH/ABAR (Mg-chelatase H subunit/putative ABA receptor), to modulate CHLH stability via the 26S proteasome pathway. CHLH acts genetically downstream of ZTL in ABA and drought stress signaling. Interestingly, ABA conversely induces ZTL phosphorylation, and high levels of ABA also induce CHLH proteasomal degradation, implying that phosphorylated ZTL protein may enhance the affinity to CHLH, leading to the increased degradation of CHLH after ABA treatment. Taken together, our results revealed a possible mechanism of reciprocal regulation between ABA signaling and the circadian clock, which is thought to be essential for plant fitness and survival.
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Affiliation(s)
- Yongtao Yu
- National Watermelon and Melon Improvement Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Sergi Portolés
- MOE Key Lab of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yi Ren
- National Watermelon and Melon Improvement Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Guangyu Sun
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Xiao-Fang Wang
- MOE Key Lab of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Huihui Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Shaogui Guo
- National Watermelon and Melon Improvement Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
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20
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Zhang C, Zhang J, Liu H, Qu X, Wang J, He Q, Zou J, Yang K, Le J. Transcriptomic analysis reveals the role of FOUR LIPS in response to salt stress in rice. PLANT MOLECULAR BIOLOGY 2022; 110:37-52. [PMID: 35583702 DOI: 10.1007/s11103-022-01282-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
An R2R3-MYB transcription factor FOUR LIPS associated with B-type Cyclin-Dependent Kinase 1;1 confers salt tolerance in rice. The Arabidopsis FOUR LIPS (AtFLP), an R2R3 MYB transcription factor, acts as an important stomatal development regulator. Only one orthologue protein of AtFLP, Oryza sativa FLP (OsFLP), was identified in rice. However, the function of OsFLP is largely unknown. In this study, we conducted RNA-seq and ChIP-seq to investigate the potential role of OsFLP in rice. Our results reveal that OsFLP is probably a multiple functional regulator involved in many biological processes in growth development and stress responses in rice. However, we mainly focus on the role of OsFLP in salt stress response. Consistently, phenotypic analysis under salt stress conditions showed that osflp exhibited significant sensitivity to salt stress, while OsFLP over-expression lines displayed obvious salt tolerance. Additionally, Yeast one-hybrid assay and electrophoretic mobility shift assay (EMSA) showed that OsFLP directly bound to the promoter region of Oryza sativa B-type Cyclin-Dependent Kinase 1;1 (OsCDKB1;1), and the expression of OsCDKB1;1 was repressed in osflp. Disturbing the expression of OsCDKB1;1 remarkably enhanced the tolerance to salt stress. Taken together, our findings reveal a crucial function of OsFLP regulating OsCDKB1;1 in salt tolerance and largely extend the knowledge about the role of OsFLP in rice.
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Affiliation(s)
- Chunxia Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jie Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huichao Liu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxiao Qu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junxue Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Wenbo School, Jinan, 250100, China
| | - Qixiumei He
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junjie Zou
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Kezhen Yang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jie Le
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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21
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Ferrari RC, Kawabata AB, Ferreira SS, Hartwell J, Freschi L. A matter of time: regulatory events behind the synchronization of C4 and crassulacean acid metabolism in Portulaca oleracea. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4867-4885. [PMID: 35439821 DOI: 10.1093/jxb/erac163] [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: 11/30/2021] [Accepted: 04/14/2022] [Indexed: 06/14/2023]
Abstract
Portulaca species can switch between C4 and crassulacean acid metabolism (CAM) depending on environmental conditions. However, the regulatory mechanisms behind this rare photosynthetic adaptation remain elusive. Using Portulaca oleracea as a model system, here we investigated the involvement of the circadian clock, plant hormones, and transcription factors in coordinating C4 and CAM gene expression. Free-running experiments in constant conditions suggested that C4 and CAM gene expression are intrinsically connected to the circadian clock. Detailed time-course, drought, and rewatering experiments revealed distinct time frames for CAM induction and reversion (days versus hours, respectively), which were accompanied by changes in abscisic acid (ABA) and cytokinin metabolism and signaling. Exogenous ABA and cytokinins were shown to promote and repress CAM expression in P. oleracea, respectively. Moreover, the drought-induced decline in C4 transcript levels was completely recovered upon cytokinin treatment. The ABA-regulated transcription factor genes HB7, NFYA7, NFYC9, TT8, and ARR12 were identified as likely candidate regulators of CAM induction following this approach, whereas NFYC4 and ARR9 were connected to C4 expression patterns. Therefore, we provide insights into the signaling events controlling C4-CAM transitions in response to water availability and over the day/night cycle, highlighting candidate genes for future functional studies in the context of facultative C4-CAM photosynthesis.
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Affiliation(s)
- Renata Callegari Ferrari
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brasil
| | - Aline Bastos Kawabata
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brasil
| | - Sávio Siqueira Ferreira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brasil
| | - James Hartwell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Luciano Freschi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brasil
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22
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Zhang H, Hu Y, Gu B, Cui X, Zhang J. VaMYB44 transcription factor from Chinese wild Vitis amurensis negatively regulates cold tolerance in transgenic Arabidopsis thaliana and V. vinifera. PLANT CELL REPORTS 2022; 41:1673-1691. [PMID: 35666271 DOI: 10.1007/s00299-022-02883-w] [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: 03/04/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Heterologous expression of VaMYB44 gene in Arabidopsis and V. vinifera cv. 'Thompson Seedless' increases cold sensitivity, which is mediated by the interaction of VaMYC2 and VaTIFY5A with VaMYB44 MYB transcription factors play critical roles in plant stress response. However, the function of MYB44 under low temperature stress is largely unknown in grapes. Here, we isolated a VaMYB44 gene from Chinese wild Vitis amurensis acc. 'Shuangyou' (cold-resistant). The VaMYB44 is expressed in various organs and has lower expression levels in stems and young leaves. Exposure of the cold-sensitive V. vinifera cv. 'Thompson Seedless' and cold-resistant 'Shuangyou' grapevines to cold stress (-1 °C) resulted in differential expression of MYB44 in leaves with the former reaching 14 folds of the latter after 3 h of cold stress. Moreover, the expression of VaMYB44 was induced by exogenous ethylene, abscisic acid, and methyl jasmonate in the leaves of 'Shuangyou'. Notably, the subcellular localization assay identified VaMYB44 in the nucleus. Interestingly, heterologous expression of VaMYB44 in Arabidopsis and 'Thompson Seedless' grape increased freezing-induced damage compared to their wild-type counterparts. Accordingly, the transgenic lines had higher malondialdehyde content and electrolyte permeability, and lower activities of superoxide dismutase, peroxidase, and catalase. Moreover, the expression levels of some cold resistance-related genes decreased in transgenic lines. Protein interaction assays identified VaMYC2 and VaTIFY5A as VaMYB44 interacting proteins, and VaMYC2 could bind to the VaMYB44 promoter and promote its transcription. In conclusion, the study reveals VaMYB44 as the negative regulator of cold tolerance in transgenic Arabidopsis and transgenic grapes, and VaMYC2 and VaTIFY5A are involved in the cold sensitivity of plants by interacting with VaMYB44.
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Affiliation(s)
- Hongjuan Zhang
- College of Horticulture, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Xianyang, 712100, Shaanxi, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China
| | - Yafan Hu
- College of Horticulture, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Xianyang, 712100, Shaanxi, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China
| | - Bao Gu
- College of Horticulture, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Xianyang, 712100, Shaanxi, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China
| | - Xiaoyue Cui
- College of Horticulture, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Xianyang, 712100, Shaanxi, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China
| | - Jianxia Zhang
- College of Horticulture, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China.
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Xianyang, 712100, Shaanxi, China.
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China.
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23
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Vergata C, Yousefi S, Buti M, Vestrucci F, Gholami M, Sarikhani H, Salami SA, Martinelli F. Meta-analysis of transcriptomic responses to cold stress in plants. FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:704-724. [PMID: 35379384 DOI: 10.1071/fp21230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Transcriptomic analyses are needful tools to gain insight into the molecular mechanisms underlying plant responses to abiotic stresses. The aim of this study was to identify key genes differentially regulated in response to chilling stress in various plant species with different levels of tolerance to low temperatures. A meta-analysis was performed using the RNA-Seq data of published studies whose experimental conditions were comparable. The results confirmed the importance of ethylene in the hormonal cross-talk modulating the defensive responses against chilling stress, especially in sensitive species. The transcriptomic activity of five Ethylene Response Factors genes and a REDOX Responsive Transcription Factor 1 involved in hormone-related pathways belonging to ethylene metabolism and signal transduction were induced. Transcription activity of two genes encoding for heat shock factors was enhanced, together with various genes associated with developmental processes. Several transcription factor families showed to be commonly induced between different plant species. Protein-protein interaction networks highlighted the role of the photosystems I and II, as well as genes encoding for HSF and WRKY transcription factors. A model of gene regulatory network underlying plant responses to chilling stress was developed, allowing the delivery of new candidate genes for genetic improvement of crops towards low temperatures tolerance.
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Affiliation(s)
- Chiara Vergata
- Department of Biology, University of Florence, Firenze, Italy
| | - Sanaz Yousefi
- Department of Horticultural Science, Bu-Ali Sina University, Hamedan, Iran
| | - Matteo Buti
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Firenze, Italy
| | | | - Mansour Gholami
- Department of Horticultural Science, Bu-Ali Sina University, Hamedan, Iran
| | - Hassan Sarikhani
- Department of Horticultural Science, Bu-Ali Sina University, Hamedan, Iran
| | - Seyed Alireza Salami
- Department of Horticultural Sciences, Faculty of Agriculture and Natural Resources, University of Tehran, Tehran, Iran
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24
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Cao P, Zhao Y, Wu F, Xin D, Liu C, Wu X, Lv J, Chen Q, Qi Z. Multi-Omics Techniques for Soybean Molecular Breeding. Int J Mol Sci 2022; 23:4994. [PMID: 35563386 PMCID: PMC9099442 DOI: 10.3390/ijms23094994] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/22/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
Soybean is a major crop that provides essential protein and oil for food and feed. Since its origin in China over 5000 years ago, soybean has spread throughout the world, becoming the second most important vegetable oil crop and the primary source of plant protein for global consumption. From early domestication and artificial selection through hybridization and ultimately molecular breeding, the history of soybean breeding parallels major advances in plant science throughout the centuries. Now, rapid progress in plant omics is ushering in a new era of precision design breeding, exemplified by the engineering of elite soybean varieties with specific oil compositions to meet various end-use targets. The assembly of soybean reference genomes, made possible by the development of genome sequencing technology and bioinformatics over the past 20 years, was a great step forward in soybean research. It facilitated advances in soybean transcriptomics, proteomics, metabolomics, and phenomics, all of which paved the way for an integrated approach to molecular breeding in soybean. In this review, we summarize the latest progress in omics research, highlight novel findings made possible by omics techniques, note current drawbacks and areas for further research, and suggest that an efficient multi-omics approach may accelerate soybean breeding in the future. This review will be of interest not only to soybean breeders but also to researchers interested in the use of cutting-edge omics technologies for crop research and improvement.
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Affiliation(s)
- Pan Cao
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Ying Zhao
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Fengjiao Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Dawei Xin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Chunyan Liu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Xiaoxia Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Jian Lv
- Department of Innovation, Syngenta Biotechnology China, Beijing 102206, China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Zhaoming Qi
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
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25
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Causier B, Hopes T, McKay M, Paling Z, Davies B. Plants utilise ancient conserved peptide upstream open reading frames in stress-responsive translational regulation. PLANT, CELL & ENVIRONMENT 2022; 45:1229-1241. [PMID: 35128674 PMCID: PMC9305500 DOI: 10.1111/pce.14277] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 05/08/2023]
Abstract
The regulation of protein synthesis plays an important role in the growth and development of all organisms. Upstream open reading frames (uORFs) are commonly found in eukaryotic messenger RNA transcripts and typically attenuate the translation of associated downstream main ORFs (mORFs). Conserved peptide uORFs (CPuORFs) are a rare subset of uORFs, some of which have been shown to conditionally regulate translation by ribosome stalling. Here, we show that Arabidopsis CPuORF19, CPuORF46 and CPuORF47, which are ancient in origin, regulate translation of any downstream ORF, in response to the agriculturally significant environmental signals, heat stress and water limitation. Consequently, these CPuORFs represent a versatile toolkit for inducible gene expression with broad applications. Finally, we note that different classes of CPuORFs may operate during distinct phases of translation, which has implications for the bioengineering of these regulatory factors.
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Affiliation(s)
- Barry Causier
- Faculty of Biological Sciences, Centre for Plant SciencesUniversity of LeedsLeedsUK
| | - Tayah Hopes
- Faculty of Biological Sciences, Centre for Plant SciencesUniversity of LeedsLeedsUK
- Faculty of Biological Sciences, School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
| | - Mary McKay
- Faculty of Biological Sciences, Centre for Plant SciencesUniversity of LeedsLeedsUK
| | - Zachary Paling
- Faculty of Biological Sciences, Centre for Plant SciencesUniversity of LeedsLeedsUK
| | - Brendan Davies
- Faculty of Biological Sciences, Centre for Plant SciencesUniversity of LeedsLeedsUK
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26
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Burks DJ, Sengupta S, De R, Mittler R, Azad RK. The Arabidopsis gene co-expression network. PLANT DIRECT 2022; 6:e396. [PMID: 35492683 PMCID: PMC9039629 DOI: 10.1002/pld3.396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/05/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Identifying genes that interact to confer a biological function to an organism is one of the main goals of functional genomics. High-throughput technologies for assessment and quantification of genome-wide gene expression patterns have enabled systems-level analyses to infer pathways or networks of genes involved in different functions under many different conditions. Here, we leveraged the publicly available, information-rich RNA-Seq datasets of the model plant Arabidopsis thaliana to construct a gene co-expression network, which was partitioned into clusters or modules that harbor genes correlated by expression. Gene ontology and pathway enrichment analyses were performed to assess functional terms and pathways that were enriched within the different gene modules. By interrogating the co-expression network for genes in different modules that associate with a gene of interest, diverse functional roles of the gene can be deciphered. By mapping genes differentially expressing under a certain condition in Arabidopsis onto the co-expression network, we demonstrate the ability of the network to uncover novel genes that are likely transcriptionally active but prone to be missed by standard statistical approaches due to their falling outside of the confidence zone of detection. To our knowledge, this is the first A. thaliana co-expression network constructed using the entire mRNA-Seq datasets (>20,000) available at the NCBI SRA database. The developed network can serve as a useful resource for the Arabidopsis research community to interrogate specific genes of interest within the network, retrieve the respective interactomes, decipher gene modules that are transcriptionally altered under certain condition or stage, and gain understanding of gene functions.
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Affiliation(s)
- David J. Burks
- Department of Biological Sciences and BioDiscovery Institute, College of ScienceUniversity of North TexasDentonTexasUSA
| | - Soham Sengupta
- Department of Biological Sciences and BioDiscovery Institute, College of ScienceUniversity of North TexasDentonTexasUSA
| | - Ronika De
- Department of Biological Sciences and BioDiscovery Institute, College of ScienceUniversity of North TexasDentonTexasUSA
| | - Ron Mittler
- The Division of Plant Sciences and Interdisciplinary Plant Group, College of Agriculture, Food and Natural ResourcesChristopher S. Bond Life Sciences Center University of MissouriColumbiaMissouriUSA
- Department of SurgeryUniversity of Missouri School of MedicineColumbiaMissouriUSA
| | - Rajeev K. Azad
- Department of Biological Sciences and BioDiscovery Institute, College of ScienceUniversity of North TexasDentonTexasUSA
- Department of MathematicsUniversity of North TexasDentonTexasUSA
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27
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Regulatory Role of Circadian Clocks on ABA Production and Signaling, Stomatal Responses, and Water-Use Efficiency under Water-Deficit Conditions. Cells 2022; 11:cells11071154. [PMID: 35406719 PMCID: PMC8997731 DOI: 10.3390/cells11071154] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/15/2022] [Accepted: 03/25/2022] [Indexed: 02/04/2023] Open
Abstract
Plants deploy molecular, physiological, and anatomical adaptations to cope with long-term water-deficit exposure, and some of these processes are controlled by circadian clocks. Circadian clocks are endogenous timekeepers that autonomously modulate biological systems over the course of the day–night cycle. Plants’ responses to water deficiency vary with the time of the day. Opening and closing of stomata, which control water loss from plants, have diurnal responses based on the humidity level in the rhizosphere and the air surrounding the leaves. Abscisic acid (ABA), the main phytohormone modulating the stomatal response to water availability, is regulated by circadian clocks. The molecular mechanism of the plant’s circadian clock for regulating stress responses is composed not only of transcriptional but also posttranscriptional regulatory networks. Despite the importance of regulatory impact of circadian clock systems on ABA production and signaling, which is reflected in stomatal responses and as a consequence influences the drought tolerance response of the plants, the interrelationship between circadian clock, ABA homeostasis, and signaling and water-deficit responses has to date not been clearly described. In this review, we hypothesized that the circadian clock through ABA directs plants to modulate their responses and feedback mechanisms to ensure survival and to enhance their fitness under drought conditions. Different regulatory pathways and challenges in circadian-based rhythms and the possible adaptive advantage through them are also discussed.
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28
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Xue Y, Ma L, Wang H, Hao P, Cheng S, Su Z, Li L, Yu S, Wei H. The MADS transcription factor GhFYF is involved in abiotic stress responses in upland cotton (Gossypium hirsutum L.). Gene 2022; 815:146138. [PMID: 34979233 DOI: 10.1016/j.gene.2021.146138] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/06/2021] [Accepted: 12/20/2021] [Indexed: 11/26/2022]
Abstract
Cotton is an important textile industry raw material crops, which plays a critical role in the development of society. MADS transcription factors (TFs) play a key role about the flowering time, flower development, and abiotic stress responses in plants, but little is known about their functions on abiotic stress in cotton. In this study, a MIKCC subfamily gene from cotton, GhFYF (FOREVER YOUNG FLOWER), was isolated and characterized. Our data showed that GhFYF localized to the nucleus. A β-glucuronidase (GUS) activity assay revealed that the promoter of GhFYF was mainly expressed in the flower and seed of ProGhFYF::GUS transgenic A. thaliana plants. The GUS staining of flowers and seeds was deepened after drought, salt treatment, and the expression level of the GUS gene and corresponding stress genes AtERD10, AtAnnexin1 are up-regulated in the inflorescence. Overexpression GhFYF in A. thaliana could promote the seed germination and growth under different salt concentrations, and determin the proline content. Yeast two-hybrid (Y2H) assays showed that GhFYF interacted with the HAD-like protein GhGPP2, which has responds to abiotic stress. Our findings indicate that GhFYF is involved in abiotic stress responses, especially for salt stress. This work establishes a solid foundation for further functional analysis of the GhFYF gene in cotton.
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Affiliation(s)
- Yujun Xue
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Liang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Pengbo Hao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Shuaishuai Cheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Zhengzheng Su
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Lin Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
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29
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Singh D, Singh CK, Taunk J, Gaikwad K, Singh V, Sanwal SK, Karwa S, Singh D, Sharma PC, Yadav RK, Pal M. Linking genome wide RNA sequencing with physio-biochemical and cytological responses to catalogue key genes and metabolic pathways for alkalinity stress tolerance in lentil (Lens culinaris Medikus). BMC PLANT BIOLOGY 2022; 22:99. [PMID: 35247970 PMCID: PMC8897830 DOI: 10.1186/s12870-022-03489-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/03/2021] [Indexed: 06/02/2023]
Abstract
BACKGROUND Alkaline soils cause low productivity in crop plants including lentil. Alkalinity adaptation strategies in lentil were revealed when morpho-anatomical and physio-biochemical observations were correlated with transcriptomics analysis in tolerant (PDL-1) and sensitive (L-4076) cultivars at seedling stage. RESULTS PDL-1 had lesser salt injury and performed better as compared to L-4076. Latter showed severe wilting symptoms and higher accumulation of Na+ and lower K+ in roots and shoots. PDL-1 performed better under high alkalinity stress which can be attributed to its higher mitotic index, more accumulation of K+ in roots and shoots and less aberrantly dividing cells. Also, antioxidant enzyme activities, osmolytes' accumulation, relative water content, membrane stability index and abscisic acid were higher in this cultivar. Differentially expressed genes (DEGs) related to these parameters were upregulated in tolerant genotypes compared to the sensitive one. Significantly up-regulated DEGs were found to be involved in abscisic acid (ABA) signalling and secondary metabolites synthesis. ABA responsive genes viz. dehydrin 1, 9-cis-epoxycarotenoid dioxygenase, ABA-responsive protein 18 and BEL1-like homeodomain protein 1 had log2fold change above 4.0. A total of 12,836 simple sequence repeats and 4,438 single nucleotide polymorphisms were identified which can be utilized in molecular studies. CONCLUSIONS Phyto-hormones biosynthesis-predominantly through ABA signalling, and secondary metabolism are the most potent pathways for alkalinity stress tolerance in lentil. Cultivar PDL-1 exhibited high tolerance towards alkalinity stress and can be used in breeding programmes for improving lentil production under alkalinity stress conditions.
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Affiliation(s)
- Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Chandan Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Jyoti Taunk
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute of Plant Biotechnology, 110012, New Delhi, India
| | - Vijayata Singh
- Division of Crop Improvement, Central Soil Salinity Research Institute, 132001, Karnal, India
| | - Satish Kumar Sanwal
- Division of Crop Improvement, Central Soil Salinity Research Institute, 132001, Karnal, India
| | - Sourabh Karwa
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Deepti Singh
- Depatment of Botany, Meerut College, 250001, Meerut, India
| | - Parbodh Chander Sharma
- Division of Crop Improvement, Central Soil Salinity Research Institute, 132001, Karnal, India
| | - Rajendra Kumar Yadav
- Department of Genetics and Plant Breeding, Chandra Shekhar Azad University of Agriculture and Technology, 208002, Kanpur, India
| | - Madan Pal
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012, India.
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30
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Gupta S, Singh R, Sharma A, Rather GA, Lattoo SK, Dhar MK. Comparative transcriptome mining for terpenoid biosynthetic pathway genes in wild and cultivated species of Plantago. PROTOPLASMA 2022; 259:439-452. [PMID: 34191123 DOI: 10.1007/s00709-021-01663-9] [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: 11/18/2020] [Accepted: 05/03/2021] [Indexed: 06/13/2023]
Abstract
Plantagos are important economical and medicinal plants that possess several bioactive secondary metabolites, such as phenolics, iridoids, triterpenes, and alkaloids. Triterpenoids are the ubiquitous and dynamic secondary metabolites that are deployed by plants for chemical interactions and protection under biotic/abiotic stress. Plantago ovata, a cultivated species, is the source of psyllium, while Plantago major, a wild species, has significant therapeutic potential. Wild species are considered more tolerant to stressful conditions in comparison to their cultivated allies. In view of this, the present study aimed to decipher the terpenoid biosynthetic pathway operative in P. ovata and P. major using a comparative transcriptomics approach. Majority of terpenoid biosynthetic genes were observed as upregulated in P. major including rate limiting genes of MVA (HMGR) and MEP (DXR) pathways and genes (α-AS, BAS, SM, and CYP716) involved in ursolic acid biosynthesis, an important triterpenoid prevalent in Plantago species. The HPLC output further confirmed the higher concentration of ursolic acid in P. major as compared to P. ovata leaf samples, respectively. In addition to terpenoid biosynthesis, KEGG annotation revealed the involvement of differentially expressed unigenes in several metabolic pathways, aminoacyl-tRNA biosynthesis, biosynthesis of antibiotics, and biosynthesis of secondary metabolites. MYB was found as the most abundant transcription factor family in Plantago transcriptome. We have been able to generate valuable information which can help in improving terpenoid production in Plantago. Additionally, the present study has laid a strong foundation for deciphering other important metabolic pathways in Plantago.
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Affiliation(s)
- Suruchi Gupta
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, Jammu, 180001, India
| | - Ravail Singh
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, Jammu, 180001, India
| | - Arti Sharma
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, Jammu, 180001, India
| | - Gulzar A Rather
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, Jammu, 180001, India
| | - Surrinder K Lattoo
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, Jammu, 180001, India
| | - Manoj K Dhar
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, India.
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Fernández-Parras I, Ramírez-Tejero JA, Luque F, Navarro F. Several Isoforms for Each Subunit Shared by RNA Polymerases are Differentially Expressed in the Cultivated Olive Tree ( Olea europaea L.). Front Mol Biosci 2022; 8:679292. [PMID: 34988111 PMCID: PMC8721170 DOI: 10.3389/fmolb.2021.679292] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 10/07/2021] [Indexed: 11/13/2022] Open
Abstract
Plants contain five nuclear RNA polymerases, with RNA pols IV and V in addition to conserved eukaryotic RNA pols I, II, and III. These transcriptional complexes share five common subunits, which have been extensively analyzed only in yeasts. By taking advantage of the recently published olive tree cultivar (Olea europaea L. cv. Picual) genome, we performed a genome-wide analysis of the genomic composition corresponding to subunits common to RNA pols. The cultivated olive tree genome is quite complex and contains many genes with several copies. We also investigated, for the first time, gene expression patterns for subunits common to RNA pols using RNA-Seq under different economically and biologically relevant conditions for the cultivar "Picual": tissues/organs, biotic and abiotic stresses, and early development from seeds. Our results demonstrated the existence of a multigene family of subunits common to RNA pols, and a variable number of paralogs for each subunit in the olive cultivar "Picual." Furthermore, these isoforms display specific and differentiated expression profiles depending on the isoform and growth conditions, which may be relevant for their role in olive tree biology.
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Affiliation(s)
| | | | - Francisco Luque
- Departamento de Biología Experimental-Genética, Jaén, Spain.,Centro de Estudios Avanzados en Aceite de Oliva y Olivar, Universidad de Jaén, Jaén, Spain
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Jaén, Spain.,Centro de Estudios Avanzados en Aceite de Oliva y Olivar, Universidad de Jaén, Jaén, Spain
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Alagoz Y, Mi J, Balakrishna A, Almarwaey L, Al-Babili S. Characterizing cytochrome P450 enzymes involved in plant apocarotenoid metabolism by using an engineered yeast system. Methods Enzymol 2022; 671:527-552. [DOI: 10.1016/bs.mie.2022.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Bansal J, Gupta K, Rajkumar MS, Garg R, Jain M. Draft genome and transcriptome analyses of halophyte rice Oryza coarctata provide resources for salinity and submergence stress response factors. PHYSIOLOGIA PLANTARUM 2021; 173:1309-1322. [PMID: 33215706 DOI: 10.1111/ppl.13284] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/05/2020] [Accepted: 11/17/2020] [Indexed: 05/24/2023]
Abstract
Oryza coarctata is a wild relative of rice that has adapted to diverse ecological environments, including high salinity and submergence. Thus, it can provide an important resource for discovering candidate genes/factors involved in tolerance to these stresses. Here, we report a draft genome assembly of 573 Mb comprised of 8877 scaffolds with N50 length of 205 kb. We predicted a total of 50,562 protein-coding genes, of which a significant fraction was found to be involved in secondary metabolite biosynthesis and hormone signal transduction pathways. Several salinity and submergence stress-responsive protein-coding and long noncoding RNAs involved in diverse biological processes were identified using RNA-sequencing data. Based on small RNA sequencing, we identified 168 unique miRNAs and 3219 target transcripts (coding and noncoding) involved in several biological processes, including abiotic stress responses. Further, whole genome bisulphite sequencing data analysis revealed at least 19%-48% methylcytosines in different sequence contexts and the influence of methylation status on gene expression. The genome assembly along with other datasets have been made publicly available at http://ccbb.jnu.ac.in/ory-coar. Altogether, we provide a comprehensive genomic resource for understanding the regulation of salinity and submergence stress responses and identification of candidate genes/factors involved for functional genomics studies.
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Affiliation(s)
- Juhi Bansal
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Khushboo Gupta
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Noida, India
| | - Mohan Singh Rajkumar
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rohini Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Noida, India
| | - Mukesh Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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Wang F, Chen S, Cai K, Lu Z, Yang Y, Tigabu M, Zhao X. Transcriptome sequencing and gene expression profiling of Pinus sibirica under different cold stresses. BREEDING SCIENCE 2021; 71:550-563. [PMID: 35087319 PMCID: PMC8784350 DOI: 10.1270/jsbbs.21009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 08/05/2021] [Indexed: 05/11/2023]
Abstract
Cold stress is a major abiotic factor that affects plant growth and geographical distribution. Pinus sibirica is extremely frigostable tree species. To understand the molecular mechanisms of cold tolerance by P. sibirica, physiological responses were analyzed and transcriptome profiling was conducted to the plants treated by cold stress. The physiological data showed that membrane permeability relative conductivity (REC), reactive oxygen species (ROS), malonaldehyde (MDA) content, peroxidase (POD) and catalase (CAT) activity, soluble sugar, soluble protein and proline contents were increased significantly (p < 0.05) in response to cold stress. Transcriptome analysis identified a total of 871, 1397 and 872 differentially expressed genes (DEGs) after cold treatment for 6 h, 24 h and 48 h at -20°C, respectively. The signaling pathway mediated by Ca2+ as a signaling molecule and abscisic acid pathways were the main cold signal transduction pathways in P. sibirica. The APETALA2/Ethylene-Responsive Factor (AP2/ERF) and MYB transcription factor families also play an important role in the transcriptional regulation of P. sibirica. In addition, many genes related to photosynthesis were differentially expressed under cold stress. We also validated the reliability of transcriptome data with quantitative real-time PCR. This study lays the foundation for understanding the molecular mechanisms related to cold responses in P. sibirica.
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Affiliation(s)
- Fang Wang
- College of Forestry and Grassland, Jilin Agricultural University, Changchun, China
- Jinlin Provincial Academy of Forestry Sciences, Changchun, China
| | - Song Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Kewei Cai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Zhimin Lu
- Jinlin Provincial Academy of Forestry Sciences, Changchun, China
| | - Yuchun Yang
- Jinlin Provincial Academy of Forestry Sciences, Changchun, China
| | - Mulualem Tigabu
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Xiyang Zhao
- College of Forestry and Grassland, Jilin Agricultural University, Changchun, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Corresponding author (e-mail: )
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35
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Koh E, Cohen D, Brandis A, Fluhr R. Attenuation of cytosolic translation by RNA oxidation is involved in singlet oxygen-mediated transcriptomic responses. PLANT, CELL & ENVIRONMENT 2021; 44:3597-3615. [PMID: 34370334 DOI: 10.1111/pce.14162] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 08/03/2021] [Indexed: 06/13/2023]
Abstract
Singlet oxygen (1 O2 ) production is associated with stress signalling. Here, using Arabidopsis as a model system, we study the effects of the accumulation of 8-hydroxyguanosine (8-oxoG), a major product of 1 O2 -mediated RNA oxidation. We show that 8-oxoG can accumulate in vivo when 1 O2 is produced in the cytoplasm. Conditions for such production include the application of RB in the light, dark-to-light transitions in the flu mutant, or subjecting plants to combined dehydration/light exposure. Transcriptomes of these treatments displayed a significant overlap with transcripts stimulated by the cytosolic 80S ribosomal translation inhibitors, cycloheximide and homoharringtonine. We demonstrate that 8-oxoG accumulation correlates with a decrease in RNA translatability, resulting in the rapid decrease of the levels of labile gene repressor elements such as IAA1 and JAZ1 in a proteasome-dependent manner. Indeed, genes regulated by the labile repressors of the jasmonic acid signalling pathway were induced by cycloheximide, RB or dehydration/light treatment independently of the hormone. The results suggest that 1 O2 , by oxidizing RNA, attenuated cellular translatability and caused specific genes to be released from the repression of their cognate short half-life repressors. The findings here describe a novel means of gene regulation via the direct interaction of 1 O2 with RNA.
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Affiliation(s)
- Eugene Koh
- Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Dekel Cohen
- Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Brandis
- Life Sciences Core Facility, Weizmann Institute of Science, Rehovot, Israel
| | - Robert Fluhr
- Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
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36
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Zeng J, Li X, Ge Q, Dong Z, Luo L, Tian Z, Zhao Z. Endogenous stress-related signal directs shoot stem cell fate in Arabidopsis thaliana. NATURE PLANTS 2021; 7:1276-1287. [PMID: 34354259 DOI: 10.1038/s41477-021-00985-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Stem cell populations in all multicellular organisms are situated in a niche, which is a special microenvironment that defines stem cell fate. The interplay between stem cells and their niches is crucial for stem cell maintenance. Here, we show that an endogenous stress-related signal (ESS) is overrepresented in the shoot stem cell niche under natural growth conditions, and the vast majority of known stem-cell-specific and niche-specific genes responded to stress signals. Interference with the ESS in the stem cell niche by blocking ethylene signalling impaired stem cell maintenance. Ethylene-insensitive 3 (EIN3), the key transcription factor in ethylene signalling, directly actives the expression of the stress hub transcription factor AGAMOUS-LIKE 22 (AGL22) in the stem cell niche and relays ESS signals to the WUSCHEL/CLAVATA network. Our results provide a mechanistic framework for ESS signalling control of the stem cell niche and demonstrate that plant stem cells are maintained by a native stress microenvironment in vivo.
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Affiliation(s)
- Jian Zeng
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Xiang Li
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Qiang Ge
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Zhicheng Dong
- School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Linjie Luo
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Zhaoxia Tian
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Zhong Zhao
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
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37
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Ahmad Z, Bashir K, Matsui A, Tanaka M, Sasaki R, Oikawa A, Hirai MY, Zu Y, Kawai-Yamada M, Rashid B, Husnain T, Seki M. Overexpression of nicotinamidase 3 (NIC3) gene and the exogenous application of nicotinic acid (NA) enhance drought tolerance and increase biomass in Arabidopsis. PLANT MOLECULAR BIOLOGY 2021; 107:63-84. [PMID: 34460049 DOI: 10.1007/s11103-021-01179-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/02/2021] [Indexed: 05/27/2023]
Abstract
Overexpressing Nicotinamidase 3 gene, and the exogenous application of its metabolite nicotinic acid (NA), enhance drought stress tolerance and increase biomass in Arabidopsis thaliana. With progressive global climatic changes, plant productivity is threatened severely by drought stress. Deciphering the molecular mechanisms regarding genes responsible for balancing plant growth and stress amelioration could imply multiple possibilities for future sustainable goals. Nicotinamide adenine dinucleotide (NAD) biosynthesis and recycling/ distribution is a crucial feature for plant growth. The current study focuses on the functional characterization of nicotinamidase 3 (NIC3) gene, which is involved in the biochemical conversion of nicotinamide (NAM) to nicotinic acid (NA) in the salvage pathway of NAD biosynthesis. Our data show that overexpression of NIC3 gene enhances drought stress tolerance and increases plant growth. NIC3-OX plants accumulated more NA as compared to WT plants. Moreover, the upregulation of several genes related to plant growth/stress tolerance indicates that regulating the NAD salvage pathway could significantly enhance plant growth and drought stress tolerance. The exogenous application of nicotinic acid (NA) showed a similar phenotype as the effect of overexpressing NIC3 gene. In short, we contemplated the role of NIC3 gene and NA application in drought stress tolerance and plant growth. Our results would be helpful in engineering plants with enhanced drought stress tolerance and increased growth potential.
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Affiliation(s)
- Zarnab Ahmad
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
- Plant Genomics Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Khurram Bashir
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
- Laboratory of Plant Biotechnology, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences (LUMS), Lahore, Pakistan
| | - Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Ryosuke Sasaki
- Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
| | - Akira Oikawa
- Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
- Faculty of Agriculture, Yamagata University, Tsuruoka, 997-8555, Japan
| | - Masami Yokota Hirai
- Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Yanhui Zu
- Graduate School of Science and Engineering, Saitama University, 225 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Maki Kawai-Yamada
- Graduate School of Science and Engineering, Saitama University, 225 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Bushra Rashid
- Plant Genomics Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Tayyab Husnain
- Plant Genomics Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan.
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, 244-0813, Japan.
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Jiménez A, Sevilla F, Martí MC. Reactive oxygen species homeostasis and circadian rhythms in plants. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5825-5840. [PMID: 34270727 DOI: 10.1093/jxb/erab318] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
Elucidation of the molecular mechanisms by which plants sense and respond to environmental stimuli that influence their growth and yield is a prerequisite for understanding the adaptation of plants to climate change. Plants are sessile organisms and one important factor for their successful acclimation is the temporal coordination of the 24 h daily cycles and the stress response. The crosstalk between second messengers, such as Ca2+, reactive oxygen species (ROS), and hormones is a fundamental aspect in plant adaptation and survival under environmental stresses. In this sense, the circadian clock, in conjunction with Ca2+- and hormone-signalling pathways, appears to act as an important mechanism controlling plant adaptation to stress. The relationship between the circadian clock and ROS-generating and ROS-scavenging mechanisms is still not fully understood, especially at the post-transcriptional level and in stress situations in which ROS levels increase and changes in cell redox state occur. In this review, we summarize the information regarding the relationship between the circadian clock and the ROS homeostasis network. We pay special attention not only to the transcriptional regulation of ROS-generating and ROS-scavenging enzymes, but also to the few studies that have been performed at the biochemical level and those conducted under stress conditions.
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Affiliation(s)
- Ana Jiménez
- Abiotic Stress, Production and Quality Laboratory, Department of Stress Biology and Plant Pathology, Centre of Edaphology and Applied Biology of Segura (CEBAS-CSIC), Murcia, Spain
| | - Francisca Sevilla
- Abiotic Stress, Production and Quality Laboratory, Department of Stress Biology and Plant Pathology, Centre of Edaphology and Applied Biology of Segura (CEBAS-CSIC), Murcia, Spain
| | - María Carmen Martí
- Abiotic Stress, Production and Quality Laboratory, Department of Stress Biology and Plant Pathology, Centre of Edaphology and Applied Biology of Segura (CEBAS-CSIC), Murcia, Spain
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Gan Z, Yuan X, Shan N, Wan C, Chen C, Xu Y, Xu Q, Chen J. AcWRKY40 mediates ethylene biosynthesis during postharvest ripening in kiwifruit. PLANT SCIENCE 2021; 309:110948. [PMID: 34134847 DOI: 10.1016/j.plantsci.2021.110948] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 02/07/2023]
Abstract
WRKY transcription factors belong to a superfamily that is involved in many important biological processes, including plant development and senescence. However, little is known about the transcriptional regulation mechanisms of WRKY genes involved in kiwifruit postharvest ripening. Here, we isolated a WRKY gene from the kiwifruit genome and named it AcWRKY40. AcWRKY40 is a nucleus-localized protein that possesses transcriptional activation activity. The expression of AcWRKY40 was detected, and the gene responded to ethylene treatment during kiwifruit postharvest ripening, indicating its involvement in this process at the transcriptional level. We found multiple cis-acting elements related to maturation and senescence in the AcWRKY40 promoter. GUS activity analysis showed that its promoter activity was induced by exogenous ethylene. Yeast one-hybrid and dual-luciferase assays demonstrated that AcWRKY40 binds to the promoters of AcSAM2, AcACS1, and AcACS2 to activate them. In addition, transient transformations showed that AcWRKY40 enhances the expression of AcSAM2, AcACS1, and AcACS2. Taken together, these results suggest that AcWRKY40 is involved in kiwifruit postharvest ripening, possibly by regulating the expression of genes related to ethylene biosynthesis, thus deepening our understanding of the regulatory mechanisms of WRKY transcription factors in fruit ripening.
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Affiliation(s)
- Zengyu Gan
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang, 330045, China; Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xin Yuan
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Nan Shan
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Chunpeng Wan
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Chuying Chen
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yunhe Xu
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Qin Xu
- Agriculture and Rural Bureau of Gongcheng Yao Autonomous County, Guilin, 542500, China
| | - Jinyin Chen
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang, 330045, China; Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, 330045, China; College of Materials and Chemical Engineering, Pingxiang University, Pingxiang, 330075, China.
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The Genetic Regulation of Secondary Metabolic Pathways in Response to Salinity and Drought as Abiotic Stresses. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11156668] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Global development has generated a plethora of unfavorable and adverse environmental factors for the living organisms in the ecosystem. Plants are sessile organisms, and they are crucial to sustain life on earth. Since plants are sessile, they face a great number of environmental challenges related to abiotic stresses, such as temperature fluctuation, drought, salinity, flood and metal contamination. Salinity and drought are considered major abiotic stresses that negatively affect the plants’ growth and production of useful content. However, plants have evolved various molecular mechanisms to increase their tolerance to these environmental stresses. There is a whole complex system of communication (cross-talk) through massive signaling cascades that are activated and modulated in response to salinity and drought. Secondary metabolites are believed to play significant roles in the plant’s response and resistance to salinity and drought stress. Until recently, attempts to unravel the biosynthetic pathways were limited mainly due to the inadequate plant genomics resources. However, recent advancements in generating high-throughput “omics” datasets, computational tools and functional genomics approach integration have aided in the elucidation of biosynthetic pathways of many plant bioactive metabolites. This review gathers comprehensive knowledge of plants’ complex system that is involved in the response and resistance to salinity and water deficit stresses as abiotic stress. Additionally, it offers clues in determining the genes involved in this complex and measures its activity. It covers basic information regarding the signaling molecules involved in salinity and drought resistance and how plant hormones regulate the cross-talking mechanism with emphasis on transcriptional activity. Moreover, it discusses many studies that illustrate the relationship between salinity and drought and secondary metabolite production. Furthermore, several transcriptome analysis research papers of medicinal plants are illustrated. The aim of this review is to be a key for any researcher that is aspiring to study the relationship between salinity and drought stresses and secondary metabolite production at the transcriptome and transcription level.
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Singh S, Koyama H, Bhati KK, Alok A. The biotechnological importance of the plant-specific NAC transcription factor family in crop improvement. JOURNAL OF PLANT RESEARCH 2021; 134:475-495. [PMID: 33616799 PMCID: PMC8106581 DOI: 10.1007/s10265-021-01270-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/13/2021] [Indexed: 05/02/2023]
Abstract
Climate change, malnutrition, and food insecurity are the inevitable challenges being faced by the agriculture sector today. Plants are susceptible to extreme temperatures during the crucial phases of flowering and seed development, and elevated carbon levels also lead to yield losses. Productivity is also affected by floods and droughts. Therefore, increasing plant yield and stress tolerance are the priorities to be met through novel biotechnological interventions. The contributions of NAC genes towards enhancing plant survivability under stress is well known. Here we focus on the potential of NAC genes in the regulation of abiotic stress tolerance, secondary cell wall synthesis, lateral root development, yield potential, seed size and biomass, ROS signaling, leaf senescence, and programmed cell death. Once naturally tolerant candidate NAC genes have been identified, and the nature of their association with growth and fitness against multi-environmental stresses has been determined, they can be exploited for building inherent tolerance in future crops via transgenic technologies. An update on the latest developments is provided in this review, which summarizes the current understanding of the roles of NAC in the establishment of various stress-adaptive mechanisms in model and food crop plants.
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Affiliation(s)
- Sadhana Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
| | - Hiroyuki Koyama
- Laboratory of Plant Cell Technology, Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan
| | - Kaushal K Bhati
- Louvain Institute of Biomolecular Sciences, Catholic University of Louvain, Louvain-la-Neuve, Belgium
| | - Anshu Alok
- Department of Biotechnology, UIET, Punjab University, Chandigarh, India
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Kumari S, Kanth BK, Ahn JY, Kim JH, Lee GJ. Genome-Wide Transcriptomic Identification and Functional Insight of Lily WRKY Genes Responding to Botrytis Fungal Disease. PLANTS (BASEL, SWITZERLAND) 2021; 10:776. [PMID: 33920859 PMCID: PMC8071302 DOI: 10.3390/plants10040776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/28/2021] [Accepted: 04/12/2021] [Indexed: 05/25/2023]
Abstract
Genome-wide transcriptome analysis using RNA-Seq of Lilium longiflorum revealed valuable genes responding to biotic stresses. WRKY transcription factors are regulatory proteins playing essential roles in defense processes under environmental stresses, causing considerable losses in flower quality and production. Thirty-eight WRKY genes were identified from the transcriptomic profile from lily genotypes, exhibiting leaf blight caused by Botrytis elliptica. Lily WRKYs have a highly conserved motif, WRKYGQK, with a common variant, WRKYGKK. Phylogeny of LlWRKYs with homologous genes from other representative plant species classified them into three groups- I, II, and III consisting of seven, 22, and nine genes, respectively. Base on functional annotation, 22 LlWRKY genes were associated with biotic stress, nine with abiotic stress, and seven with others. Sixteen unique LlWRKY were studied to investigate responses to stress conditions using gene expression under biotic and abiotic stress treatments. Five genes-LlWRKY3, LlWRKY4, LlWRKY5, LlWRKY10, and LlWRKY12-were substantially upregulated, proving to be biotic stress-responsive genes in vivo and in vitro conditions. Moreover, the expression patterns of LlWRKY genes varied in response to drought, heat, cold, and different developmental stages or tissues. Overall, our study provides structural and molecular insights into LlWRKY genes for use in the genetic engineering in Lilium against Botrytis disease.
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Affiliation(s)
- Shipra Kumari
- Department of Horticulture, Chungnam National University, Daejeon 34134, Korea; (S.K.); (B.K.K.); (J.y.A.)
| | - Bashistha Kumar Kanth
- Department of Horticulture, Chungnam National University, Daejeon 34134, Korea; (S.K.); (B.K.K.); (J.y.A.)
| | - Ju young Ahn
- Department of Horticulture, Chungnam National University, Daejeon 34134, Korea; (S.K.); (B.K.K.); (J.y.A.)
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Korea
| | - Jong Hwa Kim
- Department of Horticulture, Kangwon National University, Chuncheon 24341, Gangwon-do, Korea;
| | - Geung-Joo Lee
- Department of Horticulture, Chungnam National University, Daejeon 34134, Korea; (S.K.); (B.K.K.); (J.y.A.)
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Korea
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43
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Kumar P, Parveen A, Sharma H, Rahim MS, Mishra A, Kumar P, Shah K, Rishi V, Roy J. Understanding the regulatory relationship of abscisic acid and bZIP transcription factors towards amylose biosynthesis in wheat. Mol Biol Rep 2021; 48:2473-2483. [PMID: 33834358 DOI: 10.1007/s11033-021-06282-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 03/11/2021] [Indexed: 12/15/2022]
Abstract
Starch is biosynthesized during seed development and this process is regulated by many bZIP proteins in bread wheat. Abscisic acid (ABA), an important phyto-hormone involved in various physiological processes mediated by bZIPs in plants including seed development. The 'Group A' TabZIP transcription factors play important roles in the ABA signaling pathway in Arabidopsis, rice and other cereal crops but their role in regulation of amylose biosynthesis in wheat is limited. In this study 83 'Group A' TabZIPs were characterized by gene expression analysis in wheat amylose mutants. A set of 17 TabZIPs was selected on the basis of differential expression (> 2 fold) in low and high amylose mutants from RNA-seq data and validated by qRT PCR. Based on qRT PCR and correlation analysis out of the 17 TabZIPs six differentially expressed candidate TabZIPs were identified, involving in high amylose biosynthesis. The TabZIP175.2, identified as upregulated in all high amylose lines and TabZIP90.2, TabZIP129.1, TabZIP132.2, TabZIP143 and TabZIP159.2 were found downregulated in all low amylose lines, after exogenous supply of ABA. Proximal promoter analysis of starch pathway genes revealed the presence of ABA-responsive elements (ABREs) that are putative binding sites for bZIPs. Collectively, these findings indicated the involvement of putative six candidate TabZIPs as transcriptional regulators of amylose related genes via an ABA-dependent pathway in wheat. This study could help the investigators to make an informed decision to edit wheat genome for high/low amylose content using gene-editing technologies.
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Affiliation(s)
- Pankaj Kumar
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India
| | - Afsana Parveen
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India.,Department of Biotechnology, Panjab University, Chandigarh, 160014, India
| | - Himanshu Sharma
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India
| | - Mohammed Saba Rahim
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India
| | - Ankita Mishra
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India
| | - Prashant Kumar
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India
| | - Koushik Shah
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India
| | - Vikas Rishi
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India
| | - Joy Roy
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India.
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Yong X, Zheng T, Zhuo X, Ahmad S, Li L, Li P, Yu J, Wang J, Cheng T, Zhang Q. Genome-wide identification, characterisation, and evolution of ABF/AREB subfamily in nine Rosaceae species and expression analysis in mei ( Prunus mume). PeerJ 2021; 9:e10785. [PMID: 33604183 PMCID: PMC7868070 DOI: 10.7717/peerj.10785] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/23/2020] [Indexed: 01/15/2023] Open
Abstract
Rosaceae is an important family containing some of the highly evolved fruit and ornamental plants. Abiotic stress responses play key roles in the seasonal growth and development of plants. However, the molecular basis of stress responses remains largely unknown in Rosaceae. Abscisic acid (ABA) is a stress hormone involving abiotic stress response pathways. The ABRE-binding factor/ABA-responsive element-binding protein (ABF/AREB) is a subfamily of the basic domain/leucine zipper (bZIP) transcription factor family. It plays an important role in the ABA-mediated signaling pathway. Here, we analyzed the ABF/AREB subfamily genes in nine Rosaceae species. A total of 64 ABF/AREB genes were identified, including 18, 28, and 18 genes in the Rosoideae, Amygdaloideae, and Maloideae traditional subfamilies, respectively. The evolutionary relationship of the ABF/AREB subfamily genes was studied through the phylogenetic analysis, the gene structure and conserved motif composition, Ka/Ks values, and interspecies colinearity. These gene sets were clustered into four groups. In the Prunus ABF/AREB (PmABF) promoters, several cis-elements related to light, hormone, and abiotic stress response were predicted. PmABFs expressed in five different tissues, except PmABF5, which expressed only in buds. In the dormancy stages, PmABF1, 2, 5 and 7 showed differential expression. The expression of PmABF3, 4 and 6 was positively correlated with the ABA concentration. Except for PmABF5, all the PmABFs were sensitive to ABA. Several ABRE elements were contained in the promoters of PmABF1, 3, 6, 7. Based on the findings of our study, we speculate that PmABFs may play a role in flower bud dormancy in P. mume.
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Affiliation(s)
- Xue Yong
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Tangchun Zheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Xiaokang Zhuo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Sagheer Ahmad
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Lulu Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Ping Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Jiayao Yu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
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45
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CRISPR/Cas9-Mediated Knockout of HOS1 Reveals Its Role in the Regulation of Secondary Metabolism in Arabidopsis thaliana. PLANTS 2021; 10:plants10010104. [PMID: 33419060 PMCID: PMC7825447 DOI: 10.3390/plants10010104] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/31/2020] [Accepted: 01/03/2021] [Indexed: 11/17/2022]
Abstract
In Arabidopsis, the RING finger-containing E3 ubiquitin ligase HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 1 (HOS1) functions as a main regulator of the cold signaling. In this study, CRISPR/Cas9-mediated targeted mutagenesis of the HOS1 gene in the first exon was performed. DNA sequencing showed that frameshift indels introduced by genome editing of HOS1 resulted in the appearance of premature stop codons, disrupting the open reading frame. Obtained hos1Cas9 mutant plants were compared with the SALK T-DNA insertion mutant, line hos1-3, in terms of their tolerance to abiotic stresses, accumulation of secondary metabolites and expression levels of genes participating in these processes. Upon exposure to cold stress, enhanced tolerance and expression of cold-responsive genes were observed in both hos1-3 and hos1Cas9 plants. The hos1 mutation caused changes in the synthesis of phytoalexins in transformed cells. The content of glucosinolates (GSLs) was down-regulated by 1.5-times, while flavonol glycosides were up-regulated by 1.2 to 4.2 times in transgenic plants. The transcript abundance of the corresponding MYB and bHLH transcription factors, which are responsible for the regulation of secondary metabolism in Arabidopsis, were also altered. Our data suggest a relationship between HOS1-regulated downstream signaling and phytoalexin biosynthesis.
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Yang Y, Saand MA, Huang L, Abdelaal WB, Zhang J, Wu Y, Li J, Sirohi MH, Wang F. Applications of Multi-Omics Technologies for Crop Improvement. FRONTIERS IN PLANT SCIENCE 2021; 12:563953. [PMID: 34539683 PMCID: PMC8446515 DOI: 10.3389/fpls.2021.563953] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/06/2021] [Indexed: 05/19/2023]
Abstract
Multiple "omics" approaches have emerged as successful technologies for plant systems over the last few decades. Advances in next-generation sequencing (NGS) have paved a way for a new generation of different omics, such as genomics, transcriptomics, and proteomics. However, metabolomics, ionomics, and phenomics have also been well-documented in crop science. Multi-omics approaches with high throughput techniques have played an important role in elucidating growth, senescence, yield, and the responses to biotic and abiotic stress in numerous crops. These omics approaches have been implemented in some important crops including wheat (Triticum aestivum L.), soybean (Glycine max), tomato (Solanum lycopersicum), barley (Hordeum vulgare L.), maize (Zea mays L.), millet (Setaria italica L.), cotton (Gossypium hirsutum L.), Medicago truncatula, and rice (Oryza sativa L.). The integration of functional genomics with other omics highlights the relationships between crop genomes and phenotypes under specific physiological and environmental conditions. The purpose of this review is to dissect the role and integration of multi-omics technologies for crop breeding science. We highlight the applications of various omics approaches, such as genomics, transcriptomics, proteomics, metabolomics, phenomics, and ionomics, and the implementation of robust methods to improve crop genetics and breeding science. Potential challenges that confront the integration of multi-omics with regard to the functional analysis of genes and their networks as well as the development of potential traits for crop improvement are discussed. The panomics platform allows for the integration of complex omics to construct models that can be used to predict complex traits. Systems biology integration with multi-omics datasets can enhance our understanding of molecular regulator networks for crop improvement. In this context, we suggest the integration of entire omics by employing the "phenotype to genotype" and "genotype to phenotype" concept. Hence, top-down (phenotype to genotype) and bottom-up (genotype to phenotype) model through integration of multi-omics with systems biology may be beneficial for crop breeding improvement under conditions of environmental stresses.
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Affiliation(s)
- Yaodong Yang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- *Correspondence: Yaodong Yang
| | - Mumtaz Ali Saand
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Department of Botany, Shah Abdul Latif University, Khairpur, Pakistan
| | - Liyun Huang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Walid Badawy Abdelaal
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Jun Zhang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Yi Wu
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Jing Li
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | | | - Fuyou Wang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
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Global Profiling of lncRNAs Expression Responsive to Allopolyploidization in Cucumis. Genes (Basel) 2020; 11:genes11121500. [PMID: 33322817 PMCID: PMC7763881 DOI: 10.3390/genes11121500] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/02/2020] [Accepted: 12/10/2020] [Indexed: 12/18/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play critical regulatory roles in various biological processes. However, the presence of lncRNAs and how they function in plant polyploidy are still largely unknown. Hence, we examined the profile of lncRNAs in a nascent allotetraploid Cucumis hytivus (S14), its diploid parents, and the F1 hybrid, to reveal the function of lncRNAs in plant-interspecific hybridization and whole genome duplication. Results showed that 2206 lncRNAs evenly transcribed from all 19 chromosomes were identified in C. hytivus, 44.6% of which were from intergenic regions. Based on the expression trend in allopolyploidization, we found that a high proportion of lncRNAs (94.6%) showed up-regulated expression to varying degrees following hybridization. However, few lncRNAs (33, 2.1%) were non-additively expressed after genome duplication, suggesting the significant effect of hybridization on lncRNAs, rather than genome duplication. Furthermore, 253 cis-regulated target genes were predicted for these differentially expressed lncRNAs in S14, which mainly participated in chloroplast biological regulation (e.g., chlorophyll synthesis and light harvesting system). Overall, this study provides new insight into the function of lncRNAs during the processes of hybridization and polyploidization in plant evolution.
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48
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Wang J, Nan N, Shi L, Li N, Huang S, Zhang A, Liu Y, Guo P, Liu B, Xu ZY. Arabidopsis BRCA1 represses RRTF1-mediated ROS production and ROS-responsive gene expression under dehydration stress. THE NEW PHYTOLOGIST 2020; 228:1591-1610. [PMID: 32621388 DOI: 10.1111/nph.16786] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
Reactive oxygen species (ROS) act as important secondary messengers in abscisic acid (ABA) signaling and induce stomatal closure under dehydration stress. The breast cancer susceptibility gene 1 (BRCA1), an important tumor suppressor in animals, functions primarily in the maintenance of genome integrity in animals and plants. However, whether and how the plant BRCA1 regulates intracellular ROS homeostasis in guard cells under dehydration stress remains unknown. Here, we found that Arabidopsis atbrca1 loss-of-function mutants showed dehydration stress tolerance. This stress tolerant phenotype of atbrca1 was a result of ABA- and ROS-induced stomatal closure, which was enhanced in atbrca1 mutants compared with the wild-type. AtBRCA1 downregulated the expression of ROS-responsive and marker genes. Notably, these genes were also the targets of the AP2/ERF transcriptional activator RRTF1/ERF109. Under normal conditions, AtBRCA1 physically interacted with RRTF1 and inhibited its binding to the GCC-box-like sequence in target gene promoters. Under dehydration stress, the expression of AtBRCA1 was dramatically reduced and that of RRTF1 was activated, thus inducing the expression of ROS-responsive genes. Overall, our study reveals a novel molecular function of AtBRCA1 in the transcriptional regulation of intracellular ROS homeostasis under dehydration stress.
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Affiliation(s)
- Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Nan Nan
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Lulu Shi
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Shuangzhan Huang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Peng Guo
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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Phour M, Sehrawat A, Sindhu SS, Glick BR. Interkingdom signaling in plant-rhizomicrobiome interactions for sustainable agriculture. Microbiol Res 2020; 241:126589. [DOI: 10.1016/j.micres.2020.126589] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/19/2020] [Accepted: 08/21/2020] [Indexed: 12/24/2022]
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50
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Meng X, Cai J, Deng L, Li G, Sun J, Han Y, Dong T, Liu Y, Xu T, Liu S, Li Z, Zhu M. SlSTE1 promotes abscisic acid-dependent salt stress-responsive pathways via improving ion homeostasis and reactive oxygen species scavenging in tomato. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:1942-1966. [PMID: 32618097 DOI: 10.1111/jipb.12987] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 06/29/2020] [Indexed: 06/11/2023]
Abstract
High salinity is one of the major limiting factors that reduces crop productivity and quality. Herein, we report that small SALT TOLERANCE ENHANCER1 (STE1) protein without any known conserved domains is required for tomato salt tolerance. Overexpression (OE) of SlSTE1 enhanced the tolerance to multiple chloride salts (NaCl, KCl, and LiCl) and oxidative stress, along with elevated antioxidant enzyme activities, increased abscisic acid (ABA) and chlorophyll contents, and reduced malondialdehyde (MDA) and reactive oxygen species (ROS) accumulations compared to that of wild-type (WT) plants. Moreover, decreased K+ efflux and increased H+ efflux were detected in the OE plants, which induced a higher K+ /Na+ ratio. In contrast, SlSTE1-RNAi plants displayed decreased tolerance to salt stress. RNA-seq data revealed 1 330 differentially expressed genes in the OE plants versus WT plants under salt stress, and the transcription of numerous and diverse genes encoding transcription factors, stress-related proteins, secondary metabolisms, kinases, and hormone synthesis/signaling-related proteins (notably ABA and 1-aminocyclopropane-1-carboxylate) was greatly elevated. Furthermore, SlSTE1-OE plants showed increased sensitivity to ABA, and the results suggest that SlSTE1 promotes ABA-dependent salt stress-responsive pathways by interacting with SlPYLs and SlSnRK2s. Collectively, our findings reveal that the small SlSTE1 protein confers salt tolerance via ABA signaling and ROS scavenging and improves ion homeostasis in tomato.
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Affiliation(s)
- Xiaoqing Meng
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
- Jiangsu Key laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Jing Cai
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
- Jiangsu Key laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Lei Deng
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Ge Li
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
- Jiangsu Key laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Jian Sun
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
- Jiangsu Key laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Yonghua Han
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
- Jiangsu Key laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Tingting Dong
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
- Jiangsu Key laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Yang Liu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
- Jiangsu Key laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Tao Xu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
- Jiangsu Key laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Siyuan Liu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
- Jiangsu Key laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Zongyun Li
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
- Jiangsu Key laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Mingku Zhu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
- Jiangsu Key laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
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