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Kaur H, Kaur G, Sirhindi G, Bhardwaj R, Alsahli AA, Ahmad P. Exploring the role of 28-homobrassinolide in regulation of temperature induced clastogenic aberrations and sugar metabolism of Brassica juncea L. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108893. [PMID: 39018776 DOI: 10.1016/j.plaphy.2024.108893] [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: 03/04/2024] [Revised: 06/08/2024] [Accepted: 06/27/2024] [Indexed: 07/19/2024]
Abstract
The present research primarily focuses on Brassica juncea's physiological and cytological responses to low and high temperature stress at 4 °C and 44 °C respectively, along with elucidating the protective role of 28-Homobrassinolide (28-homoBL). Cytological investigations performed in floral buds of Brassica juncea L. under temperature (24, 4, 44 °C) stress conditions depict the presence of some abnormalities associated with cytomixis such as chromosome stickiness or agglutination, pycnotic nature of chromatin, irregularities in spindle formation, disoriented chromatins, and non-synchronous chromatin material condensation in Brassicaceae family that subsisted at diploid level (2n = 36). Spindle abnormalities produce various size pollen grains such as sporads micronuclei at some stages of microsporogenesis, polyads, triads, dyads that irrupted the productiveness of pollen grains. Furthermore, sugars play an imperative role in protecting plants under stress besides being energy sources. Therefore, the present study revealed accumulation of total soluble sugars (TSS), with 28-homoBL treatment which pinpoints protective role of 28-homoBL under temperature stress. Sugar profiling was done by using high-performance liquid chromatography (HPLC) which helped in analyzing different sugars both quantitatively and qualitatively under 28-homoBL and temperature stress conditions. The results indicate that the 28-homoBL treatment substantially enhances plant tolerance to heat stress, as evident by higher mitotic indices, fewer chromosomal abnormalities, and significantly more sugar accumulation. The findings of the study acknowledge the potential of 28-homoBL in inducing temperature stress tolerance in B. juncea along with improving the metabolic stability thereby implying application of 28-homoBL in crop strengthening under variable temperature conditions.
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Affiliation(s)
- Harpreet Kaur
- P.G. Department of Botany, Khalsa College, Amritsar, 143001, Punjab, India; Department of Botany, Punjabi University, Patiala, 147002, Punjab, India.
| | - Gurvarinder Kaur
- Department of Botany, Punjabi University, Patiala, 147002, Punjab, India
| | - Geetika Sirhindi
- Department of Botany, Punjabi University, Patiala, 147002, Punjab, India
| | - Renu Bhardwaj
- Department of Botanical & Environmental Sciences, GNDU, Amritsar, India
| | - Abdulaziz Abdullah Alsahli
- Botany and Microbiology Department, Faculty of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Parvaiz Ahmad
- Department of Botany, GDC Pulwama, 192301, Jammu and Kashmir, India.
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Fendiyanto MH, Anshori MF, Pratami MP, Wasonga DO, Seleiman MF. Metabolite comparative variation related lipid metabolisms among fruit, leaf, and stem of Jatropha curcas. Heliyon 2024; 10:e35861. [PMID: 39170246 PMCID: PMC11337045 DOI: 10.1016/j.heliyon.2024.e35861] [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: 05/01/2024] [Revised: 07/23/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024] Open
Abstract
The issue of non-renewable energy scarcity has persisted over an extended period, primarily due to the depletion of fossil fuel reserves and the adverse effects of their utilization. This scarcity stems from the finite nature of fossil energy resources. The development of oil energy or biofuels aims to utilize oil-producing plants such as Jatropha curcas to develop alternative energy resources. However, metabolomic studies in Jatropha curcas are limited and need more investigations. Therefore, this research was essential to find biomarkers of metabolites among the fruit, leaf, and stem of Jatropha curcas using the GC-MS technique. We tested the metabolite profile with the R program, especially the metaboanalystR package, to determine fold change metabolite and pathway analysis. We found that 54 metabolites were detected in both fruit, leaf, and stem tissues of Jatropha curcas L, of which 19 metabolites were upregulated in the fruit, 20 metabolites in the leaf, and 15 up-regulated metabolites in the stem. The metabolites found formed three clusters based on correlation and networking metabolites analysis. The three clusters showed a relationship with the lipid biosynthesis pathway. In this study, provisional information was obtained that there was a different pattern of expression of metabolites between fruit, leaf, and stem tissues in Jatropha curcas, which was thought to be related to the critical metabolites of oleic acid and methylcyclohexane carboxylate in the biosynthetic pathway of fatty acids and unsaturated fatty acids. This information is essential as an initial reference for genetic engineering Jatropha curcas so that it can be used to transform plants, especially lipid-producing plants, as a source of oil.
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Affiliation(s)
- Miftahul Huda Fendiyanto
- Department of Biology, The Republic of Indonesia Defense University, Universitas Pertahanan-RI. Kampus Unhan Sentul Bogor, Kawasan IPSC, 16810, West Java, Indonesia
| | | | - Mentari Putri Pratami
- Department of Biology, The Republic of Indonesia Defense University, Universitas Pertahanan-RI. Kampus Unhan Sentul Bogor, Kawasan IPSC, 16810, West Java, Indonesia
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta-Bogor km 46 Cibinong, KST Soekarno, 16911
| | - Daniel O. Wasonga
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Mahmoud F. Seleiman
- Department of Plant Production, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
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Zhang H, Wu J, Fu D, Zhang M, Wang L, Gong M. Prokaryotic expression, purification, and the in vitro and in vivo protection study of dehydrin WDHN2 from Triticum aestivum. PROTOPLASMA 2024; 261:771-781. [PMID: 38342804 DOI: 10.1007/s00709-024-01933-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 01/28/2024] [Indexed: 02/13/2024]
Abstract
Dehydrins proteins accumulate and play important protective roles in most plants during abiotic stresses. The objective of this study was to characterize a YSK2-type dehydrin gene, WDHN2, isolated from Triticum aestivum previously. In this work, wheat dehydrin WDHN2 was expressed in Escherichia coli and purified by immobilized metal affinity chromatography, which exhibited as a single band by sodium dodecyl sulfonate polyacrylamide gel electrophoresis and western blotting. We show that WDHN2 is capable of alleviating lactate dehydrogenase inactivation from heat and desiccation in vitro enzyme activity protection assay. In vivo assay of Escherichia coli viability demonstrates the enhancement of cell survival by the overexpression of WDHN2. The protein aggregation prevention assay explores that WDHN2 has a broad protective effect on the cellular proteome. The results show that WDHN2 is mainly accumulated in the nucleus and cytosol, suggesting that this dehydrin may exert its function in both cellular compartments. Our data suggest that WDHN2 acts as a chaperone molecular in vivo.
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Affiliation(s)
- Hongmei Zhang
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, Henan, China
- Key Laboratory of Microbial Resources Exploitation and Utilization, Henan University of Science and Technology, Luoyang, 471023, Henan, China
| | - Jiafa Wu
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, Henan, China
- Key Laboratory of Microbial Resources Exploitation and Utilization, Henan University of Science and Technology, Luoyang, 471023, Henan, China
| | - Dandan Fu
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, Henan, China
| | - Min Zhang
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, Henan, China
| | - Lunji Wang
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, Henan, China
| | - Minggui Gong
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, Henan, China.
- Key Laboratory of Microbial Resources Exploitation and Utilization, Henan University of Science and Technology, Luoyang, 471023, Henan, China.
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Li X, Wen K, Zhu L, Chen C, Yin T, Yang X, Zhao K, Zi Y, Zhang H, Luo X, Zhang H. Genome-wide identification and expression analysis of the Eriobotrya japonica TIFY gene family reveals its functional diversity under abiotic stress conditions. BMC Genomics 2024; 25:468. [PMID: 38745142 PMCID: PMC11092017 DOI: 10.1186/s12864-024-10375-2] [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: 02/06/2024] [Accepted: 05/03/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Plant-specific TIFY proteins are widely found in terrestrial plants and play important roles in plant adversity responses. Although the genome of loquat at the chromosome level has been published, studies on the TIFY family in loquat are lacking. Therefore, the EjTIFY gene family was bioinformatically analyzed by constructing a phylogenetic tree, chromosomal localization, gene structure, and adversity expression profiling in this study. RESULTS Twenty-six EjTIFY genes were identified and categorized into four subfamilies (ZML, JAZ, PPD, and TIFY) based on their structural domains. Twenty-four EjTIFY genes were irregularly distributed on 11 of the 17 chromosomes, and the remaining two genes were distributed in fragments. We identified 15 covariate TIFY gene pairs in the loquat genome, 13 of which were involved in large-scale interchromosomal segmental duplication events, and two of which were involved in tandem duplication events. Many abiotic stress cis-elements were widely present in the promoter region. Analysis of the Ka/Ks ratio showed that the paralogous homologs of the EjTIFY family were mainly subjected to purifying selection. Analysis of the RNA-seq data revealed that a total of five differentially expressed genes (DEGs) were expressed in the shoots under gibberellin treatment, whereas only one gene was significantly differentially expressed in the leaves; under both low-temperature and high-temperature stresses, there were significantly differentially expressed genes, and the EjJAZ15 gene was significantly upregulated under both low- and high-temperature stress. RNA-seq and qRT-PCR expression analysis under salt stress conditions revealed that EjJAZ2, EjJAZ4, and EjJAZ9 responded to salt stress in loquat plants, which promoted resistance to salt stress through the JA pathway. The response model of the TIFY genes in the jasmonic acid pathway under salt stress in loquat was systematically summarized. CONCLUSIONS These results provide a theoretical basis for exploring the characteristics and functions of additional EjTIFY genes in the future. This study also provides a theoretical basis for further research on breeding for salt stress resistance in loquat. RT-qPCR analysis revealed that the expression of one of the three EjTIFY genes increased and the expression of two decreased under salt stress conditions, suggesting that EjTIFY exhibited different expression patterns under salt stress conditions.
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Affiliation(s)
- Xulin Li
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Ke Wen
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, China
| | - Ling Zhu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Chaoying Chen
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Tuo Yin
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, China
| | - Xiuyao Yang
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, China
| | - Ke Zhao
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, China
| | - Yinqiang Zi
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Huiyun Zhang
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agriculture Sciences, Baoshan, 678000, China.
| | - Xinping Luo
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agriculture Sciences, Baoshan, 678000, China.
| | - Hanyao Zhang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China.
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Li G, Manzoor MA, Chen R, Zhang Y, Song C. Genome-wide identification and expression analysis of TIFY genes under MeJA, cold and PEG-induced drought stress treatment in Dendrobium huoshanense. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:527-542. [PMID: 38737319 PMCID: PMC11087441 DOI: 10.1007/s12298-024-01442-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 03/17/2024] [Accepted: 03/19/2024] [Indexed: 05/14/2024]
Abstract
The TIFY family consists of plant-specific genes that regulates multiple plant functions, including developmental and defense responses. Here, we performed a comprehensive genomic analysis of TIFY genes in Dendrobium huoshanense. Our analysis encompassed their phylogenetic relationships, gene structures, chromosomal distributions, promoter regions, and patterns of collinearity. A total of 16 DhTIFY genes were identified, and classified into distinct clusters named JAZ, PPD, ZIM, and TIFY based on their phylogenetic relationship. These DhTIFYs exhibited an uneven distribution across 7 chromosomes. The expansion of the DhTIFY gene family appears to have been significantly influenced by whole-genome and segmental duplication events. The ratio of non-synonymous to synonymous substitutions (Ka/Ks) implies that the purifying selection has been predominant, maintaining a constrained functional diversification after duplication events. Gene structure analysis indicated that DhTIFYs exhibited significant structural variation, particularly in terms of gene organization and intron numbers. Moreover, numerous cis-acting elements related to hormone signaling, developmental processes, and stress responses were identified within the promoter regions. Subsequently, qRT-PCR experiments demonstrated that the expression of DhTIFYs is modulated in response to MeJA (Methyl jasmonate), cold, and drought treatment. Collectively, these results enhance our understanding of the functional dynamics of TIFY genes in D. huoshanense and may pinpoint potential candidates for detailed examination of the biological roles of TIFY genes. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01442-9.
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Affiliation(s)
- Guohui Li
- Anhui Engineering Research Center for Eco-Agriculture of Traditional Chinese Medicine, Anhui Provincial Key Laboratory for Quality Evaluation and Improvement of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, 237012 China
| | - Muhammad Aamir Manzoor
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Rui Chen
- Anhui Engineering Research Center for Eco-Agriculture of Traditional Chinese Medicine, Anhui Provincial Key Laboratory for Quality Evaluation and Improvement of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, 237012 China
| | - Yingyu Zhang
- Henan Key Laboratory of Rare Diseases, Endocrinology and Metabolism Center, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471003 China
| | - Cheng Song
- Anhui Engineering Research Center for Eco-Agriculture of Traditional Chinese Medicine, Anhui Provincial Key Laboratory for Quality Evaluation and Improvement of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, 237012 China
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Wu B, Shi S, Zhang H, Lu B, Nan P, A Y. Anabolic metabolism of autotoxic substance coumarins in plants. PeerJ 2023; 11:e16508. [PMID: 38077428 PMCID: PMC10710134 DOI: 10.7717/peerj.16508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/01/2023] [Indexed: 12/18/2023] Open
Abstract
Background Autotoxicity is an intraspecific manifestation of allelopathy in plant species. The specialized metabolites and their derivatives that cause intraspecific allelopathic inhibition in the plant are known as autotoxic substances. Consequently, autotoxic substances production seriously affects the renewal and stability of ecological communities. Methods This article systematically summarizes the types of autotoxic substances present in different plants. They mainly include phenolic compounds, terpenoids, and nitrogenous organic compounds. Phenolic coumarins are the main autotoxic substances in many plants. Therefore, we also discuss differences in coumarin types and content among plant varieties, developmental stages, and tissue parts, as well as their mechanisms of autotoxicity. In addition, we review the metabolic pathways involved in coumarin biosynthesis, the key enzymes, genes, and transcription factors, as well as factors affecting coumarin biosynthesis. Results Coumarin biosynthesis involves three stages: (1) the formation of the coumarin nucleus; (2) acylation, hydroxylation, and cyclization; (3) structural modification. The key enzymes involved in the coumarin nuclear formation stage include PAL, C4H, 4CL, HCT, CAOMT, COSY, F6'H, and CCoAOMT1, and the key genes involved include BGA, CYP450 and MDR, among others. Ortho-hydroxylation is a key step in coumarin biosynthesis and PS, COSY and S8H are the key enzymes involved in this process. Finally, UGTs are responsible for the glycosylation modification of coumarins, and the MaUGT gene may therefore be involved in coumarin biosynthesis. Conclusion It is important to elucidate the autotoxicity and anabolic mechanisms of coumarins to create new germplasms that produce fewer autotoxic substances.
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Affiliation(s)
- Bei Wu
- Key Laboratory of Grassland Ecosystem of Ministry of Education, College of Pratacultural Science, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Shangli Shi
- Key Laboratory of Grassland Ecosystem of Ministry of Education, College of Pratacultural Science, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Huihui Zhang
- Key Laboratory of Grassland Ecosystem of Ministry of Education, College of Pratacultural Science, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Baofu Lu
- Key Laboratory of Grassland Ecosystem of Ministry of Education, College of Pratacultural Science, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Pan Nan
- Key Laboratory of Grassland Ecosystem of Ministry of Education, College of Pratacultural Science, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yun A
- Key Laboratory of Grassland Ecosystem of Ministry of Education, College of Pratacultural Science, Gansu Agricultural University, Lanzhou, Gansu, China
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Unel NM, Baloglu MC, Altunoglu YÇ. Comprehensive investigation of cucumber heat shock proteins under abiotic stress conditions: A multi-omics survey. J Biotechnol 2023; 374:49-69. [PMID: 37517677 DOI: 10.1016/j.jbiotec.2023.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 08/01/2023]
Abstract
Heat-shock proteins (Hsps) are a family of proteins essential in preserving the vitality and functionality of proteins under stress conditions. Cucumber (Cucumis sativus) is a widely grown plant with high nutritional value and is used as a model organism in many studies. This study employed a genomics, transcriptomics, and metabolomics approach to investigate cucumbers' Hsps against abiotic stress conditions. Bioinformatics methods were used to identify six Hsp families in the cucumber genome and to characterize family members. Transcriptomics data from the Sequence Read Archive (SRA) database was also conducted to select CsHsp genes for further study. Real-time PCR was used to evaluate gene expression levels under different stress conditions, revealing that CssHsp-08 was a vital gene for resistance to stress conditions; including drought, salinity, cold, heat stresses, and ABA application. Gas Chromatography-Mass Spectrometry (GC-MS) analysis of plant extracts revealed that amino acids accumulate in leaves under high temperatures and roots under drought, while sucrose accumulates in both tissues under applied most stress factors. The study provides valuable insights into the structure, organization, evolution, and expression profiles of the Hsp family and contributes to a better understanding of plant stress mechanisms. These findings have important implications for developing crops that can withstand environmental stress conditions better.
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Affiliation(s)
- Necdet Mehmet Unel
- Research and Application Center, Kastamonu University, Kastamonu, Turkey; Plantomics Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
| | - Mehmet Cengiz Baloglu
- Plantomics Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey; Sabancı University Nanotechnology Research and Application Center (SUNUM), Sabancı University, Turkey.
| | - Yasemin Çelik Altunoglu
- Plantomics Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
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Azimzadeh Z, Hassani A, Mandoulakani BA, Sepehr E, Morshedloo MR. Intraspecific divergence in essential oil content, composition and genes expression patterns of monoterpene synthesis in Origanum vulgare subsp. vulgare and subsp. gracile under salinity stress. BMC PLANT BIOLOGY 2023; 23:380. [PMID: 37550621 PMCID: PMC10405414 DOI: 10.1186/s12870-023-04387-5] [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: 03/03/2023] [Accepted: 07/21/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND Oregano (Origanum vulgare L.), one of the important medicinal plants in the world, has valuable pharmacological compounds with antimicrobial, antiviral, antioxidant, anti-inflammatory, antispasmodic, antiurolithic, antiproliferative and neuroprotective activities. Phenolic monoterpenes such as thymol and carvacrol with many medical importance are found in Oregano essential oil. The biosynthesis of these compounds is carried out through the methyl erythritol-4 phosphate (MEP) pathway. Environmental stresses such as salinity might improve the secondary metabolites in medicinal plants. The influence of salinity stress (0 (control), 25, 50 and 100 mM NaCl) on the essential oil content, composition and expression of 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR), γ-terpinene synthase (Ovtps2) and cytochrome P450 monooxygenases (CYP71D180) genes involved in thymol and carvacrol biosynthesis, was investigated in two oregano subspecies (vulgare and gracile). RESULTS Essential oil content was increased at low NaCl concentration (25 mM) compared with non-stress conditions, whereas it was decreased as salinity stress intensified (50 and 100 mM). Essential oil content was significantly higher in subsp. gracile than subsp. vulgare. The highest (0.20 mL pot-1) and lowest (0.06 mL pot-1) amount of essential oil yield was obtained in subsp. gracile at 25 and 100 mM NaCl, respectively. The content of carvacrol, as the main component of essential oil, decreased with increasing salinity level in subsp. gracile, but increased in subsp. vulgare. The highest expression of DXR, Ovtps2 and CYP71D180 genes was observed at 50 mM NaCl in subsp. vulgare. While, in subsp. gracile, the expression of the mentioned genes decreased with increasing salinity levels. A positive correlation was obtained between the expression of DXR, Ovtps2 and CYP71D180 genes with carvacrol content in both subspecies. On the other hand, a negative correlation was found between the expression of CYP71D180 and carvacrol content in subsp. gracile. CONCLUSIONS The findings of this study demonstrated that both oregano subspecies can tolerate NaCl salinity up to 50 mM without significant reduction in essential oil yield. Also, moderate salinity stress (50 mM NaCl) in subsp. vulgare might increase the carvacrol content partly via increment the expression levels of DXR, Ovtps2 and CYP71D180 genes.
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Affiliation(s)
- Zahra Azimzadeh
- Department of Horticultural Science, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Abbas Hassani
- Department of Horticultural Science, Faculty of Agriculture, Urmia University, Urmia, Iran.
| | | | - Ebrahim Sepehr
- Department of Soil Science, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Mohammad Reza Morshedloo
- Department of Horticultural Science, Faculty of Agriculture, University of Maragheh, Maragheh, Iran
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Shaffique S, Hussain S, Kang SM, Imran M, Kwon EH, Khan MA, Lee IJ. Recent progress on the microbial mitigation of heavy metal stress in soybean: overview and implications. FRONTIERS IN PLANT SCIENCE 2023; 14:1188856. [PMID: 37377805 PMCID: PMC10291193 DOI: 10.3389/fpls.2023.1188856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/11/2023] [Indexed: 06/29/2023]
Abstract
Plants are adapted to defend themselves through programming, reprogramming, and stress tolerance against numerous environmental stresses, including heavy metal toxicity. Heavy metal stress is a kind of abiotic stress that continuously reduces various crops' productivity, including soybeans. Beneficial microbes play an essential role in improving plant productivity as well as mitigating abiotic stress. The simultaneous effect of abiotic stress from heavy metals on soybeans is rarely explored. Moreover, reducing metal contamination in soybean seeds through a sustainable approach is extremely needed. The present article describes the initiation of heavy metal tolerance mediated by plant inoculation with endophytes and plant growth-promoting rhizobacteria, the identification of plant transduction pathways via sensing annotation, and contemporary changes from molecular to genomics. The results suggest that the inoculation of beneficial microbes plays a significant role in rescuing soybeans under heavy metal stress. They create a dynamic, complex interaction with plants via a cascade called plant-microbial interaction. It enhances stress metal tolerance via the production of phytohormones, gene expression, and secondary metabolites. Overall, microbial inoculation is essential in mediating plant protection responses to heavy metal stress produced by a fluctuating climate.
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Affiliation(s)
- Shifa Shaffique
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Saddam Hussain
- Department of Agronomy, The University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Sang-Mo Kang
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Muhammad Imran
- National Institute of Agriculture Science, Rural Development Administration, Biosafety Division, Jeonju, Republic of Korea
| | - Eun-Hae Kwon
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Muhammad Aaqil Khan
- Department of Chemical and Life Sciences, Qurtuba University of Science and Information Technology, Peshawar, Pakistan
| | - In-Jung Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
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Li H, Tahir ul Qamar M, Yang L, Liang J, You J, Wang L. Current Progress, Applications and Challenges of Multi-Omics Approaches in Sesame Genetic Improvement. Int J Mol Sci 2023; 24:3105. [PMID: 36834516 PMCID: PMC9965044 DOI: 10.3390/ijms24043105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 02/09/2023] Open
Abstract
Sesame is one of the important traditional oil crops in the world, and has high economic and nutritional value. Recently, due to the novel high throughput sequencing techniques and bioinformatical methods, the study of the genomics, methylomics, transcriptomics, proteomics and metabonomics of sesame has developed rapidly. Thus far, the genomes of five sesame accessions have been released, including white and black seed sesame. The genome studies reveal the function and structure of the sesame genome, and facilitate the exploitation of molecular markers, the construction of genetic maps and the study of pan-genomes. Methylomics focus on the study of the molecular level changes under different environmental conditions. Transcriptomics provide a powerful tool to study abiotic/biotic stress, organ development, and noncoding RNAs, and proteomics and metabonomics also provide some support in studying abiotic stress and important traits. In addition, the opportunities and challenges of multi-omics in sesame genetics breeding were also described. This review summarizes the current research status of sesame from the perspectives of multi-omics and hopes to provide help for further in-depth research on sesame.
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Affiliation(s)
- Huan Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Muhammad Tahir ul Qamar
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Li Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Junchao Liang
- Jiangxi Province Key Laboratory of Oil Crops Biology, Crop Research Institute, Nanchang Branch of National Center of Oil Crops Improvement, Jiangxi Academy of Agricultural Sciences, Nanchang 330000, China
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
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Naik B, Kumar V, Rizwanuddin S, Chauhan M, Choudhary M, Gupta AK, Kumar P, Kumar V, Saris PEJ, Rather MA, Bhuyan S, Neog PR, Mishra S, Rustagi S. Genomics, Proteomics, and Metabolomics Approaches to Improve Abiotic Stress Tolerance in Tomato Plant. Int J Mol Sci 2023; 24:3025. [PMID: 36769343 PMCID: PMC9918255 DOI: 10.3390/ijms24033025] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
To explore changes in proteins and metabolites under stress circumstances, genomics, proteomics, and metabolomics methods are used. In-depth research over the previous ten years has gradually revealed the fundamental processes of plants' responses to environmental stress. Abiotic stresses, which include temperature extremes, water scarcity, and metal toxicity brought on by human activity and urbanization, are a major cause for concern, since they can result in unsustainable warming trends and drastically lower crop yields. Furthermore, there is an emerging reliance on agrochemicals. Stress is responsible for physiological transformations such as the formation of reactive oxygen, stomatal opening and closure, cytosolic calcium ion concentrations, metabolite profiles and their dynamic changes, expression of stress-responsive genes, activation of potassium channels, etc. Research regarding abiotic stresses is lacking because defense feedbacks to abiotic factors necessitate regulating the changes that activate multiple genes and pathways that are not properly explored. It is clear from the involvement of these genes that plant stress response and adaptation are complicated processes. Targeting the multigenicity of plant abiotic stress responses caused by genomic sequences, transcripts, protein organization and interactions, stress-specific and cellular transcriptome collections, and mutant screens can be the first step in an integrative approach. Therefore, in this review, we focused on the genomes, proteomics, and metabolomics of tomatoes under abiotic stress.
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Affiliation(s)
- Bindu Naik
- Department of Food Science and Technology, Graphic Era (Deemed to Be) University, Bell Road, Clement Town, Dehradun 248002, Uttarakhand, India
| | - Vijay Kumar
- Himalayan School of Biosciences, Swami Rama Himalayan University, Swami Rama Nagar, Jolly Grant, Dehradun 248014, Uttarakhand, India
| | - Sheikh Rizwanuddin
- Department of Life Sciences, Graphic Era (Deemed to Be) University, Bell Road, Clement Town, Dehradun 248002, Uttarakhand, India
| | - Mansi Chauhan
- Department of Life Sciences, Graphic Era (Deemed to Be) University, Bell Road, Clement Town, Dehradun 248002, Uttarakhand, India
| | - Megha Choudhary
- Himalayan School of Biosciences, Swami Rama Himalayan University, Swami Rama Nagar, Jolly Grant, Dehradun 248014, Uttarakhand, India
| | - Arun Kumar Gupta
- Department of Food Science and Technology, Graphic Era (Deemed to Be) University, Bell Road, Clement Town, Dehradun 248002, Uttarakhand, India
| | - Pankaj Kumar
- Department of Microbiology, Dolphin (PG) Institute of Biomedical and Natural Sciences, Dehradun 248007, Uttarakhand, India
| | - Vivek Kumar
- Himalayan School of Biosciences, Swami Rama Himalayan University, Swami Rama Nagar, Jolly Grant, Dehradun 248014, Uttarakhand, India
| | - Per Erik Joakim Saris
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, FI-00014 Helsinki, Finland
| | - Muzamil Ahmad Rather
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Shuvam Bhuyan
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Panchi Rani Neog
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Sadhna Mishra
- Faculty of Agricultural Sciences, GLA University, Mathura 281406, Uttar Pradesh, India
| | - Sarvesh Rustagi
- Department of Food Technology, Uttaranchal University, Dehradun 248007, Uttarakhand, India
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Kaur N, Prashanth KH, Bhatti MS, Pati PK. OsSalT gene cloned from rice provides evidence of its role in salinity and drought stress tolerance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 320:111306. [PMID: 35643601 DOI: 10.1016/j.plantsci.2022.111306] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/31/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
Abiotic stresses impose a huge threat to agricultural productivity and global food security. To counter this challenge, the precise identification of the right candidate gene (s) for conferring abiotic stress tolerance without compromising the growth and yield is crucial. OsSalT is identified as a salt stress responsive gene located on SalTol QTL of chromosome 1 of rice, however, there is no genetic evidence of its function and probable pathway of its regulation. To get better insights into its functioning, earlier we elucidated the structure of SALT protein at atomic scale {PDB ID (5GVY)} and solution state that provided key clues on the probable mode of its action. Herein, we report the modulation of OsSalT gene in response to various factors and its functional characterization. Results indicate that OsSalT operates through both abscisic acid and gibberellic acid-dependent pathways and is linked to the adaptive stress mechanisms of plants. Its overexpression in a model plant resulted in improved salinity and drought stress tolerance. The OsSalT transformed plants also showed vigorous root growth, early flowering, and better seed germination. The triggering of multiple responses by OsSalT suggested that modulation of such mannose-binding lectin could be a potential game-changer for the improvement of many crops in future.
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Affiliation(s)
- Navdeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab 143005, India.
| | | | - Manpreet Singh Bhatti
- Department of Botanical & Environmental Sciences, Guru Nanak Dev University, Amritsar, Punjab 143005, India.
| | - Pratap Kumar Pati
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab 143005, India.
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Singh CM, Kumar M, Pratap A, Tripathi A, Singh S, Mishra A, Kumar H, Nair RM, Singh NP. Genome-Wide Analysis of Late Embryogenesis Abundant Protein Gene Family in Vigna Species and Expression of VrLEA Encoding Genes in Vigna glabrescens Reveal Its Role in Heat Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:843107. [PMID: 35392521 PMCID: PMC8981728 DOI: 10.3389/fpls.2022.843107] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/02/2022] [Indexed: 06/12/2023]
Abstract
Late embryogenesis abundant (LEA) proteins are identified in many crops for their response and role in adaptation to various abiotic stresses, such as drought, salinity, and temperature. The LEA genes have been studied systematically in several crops but not in Vigna crops. In this study, we reported the first comprehensive analysis of the LEA gene family in three legume species, namely, mung bean (Vigna radiata), adzuki bean (Vigna angularis), and cowpea (Vigna unguiculata), and the cross-species expression of VrLEA genes in a wild tetraploid species, Vigna glabrescens. A total of 201 LEA genes from three Vigna crops were identified harboring the LEA conserved motif. Among these 55, 64, and 82 LEA genes were identified in mung bean, adzuki bean, and cowpea genomes, respectively. These LEA genes were grouped into eight different classes. Our analysis revealed that the cowpea genome comprised all eight classes of LEA genes, whereas the LEA-6 class was absent in the mung bean genome. Similarly, LEA-5 and LEA-6 were absent in the adzuki bean genome. The analysis of LEA genes provides an insight into their structural and functional diversity in the Vigna genome. The genes, such as VrLEA-2, VrLEA-40, VrLEA-47, and VrLEA-55, were significantly upregulated in the heat-tolerant genotype under stress conditions indicating the basis of heat tolerance. The successful amplification and expression of VrLEA genes in V. glabrescens indicated the utility of the developed markers in mung bean improvement. The results of this study increase our understanding of LEA genes and provide robust candidate genes for future functional investigations and a basis for improving heat stress tolerance in Vigna crops.
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Affiliation(s)
- Chandra Mohan Singh
- Department of Genetics and Plant Breeding, Banda University of Agriculture and Technology, Banda, India
| | - Mukul Kumar
- Department of Genetics and Plant Breeding, Banda University of Agriculture and Technology, Banda, India
| | - Aditya Pratap
- ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Anupam Tripathi
- Department of Genetics and Plant Breeding, Banda University of Agriculture and Technology, Banda, India
| | - Smita Singh
- Department of Genetics and Plant Breeding, Banda University of Agriculture and Technology, Banda, India
| | - Anuj Mishra
- Department of Genetics and Plant Breeding, Banda University of Agriculture and Technology, Banda, India
| | - Hitesh Kumar
- Department of Genetics and Plant Breeding, Banda University of Agriculture and Technology, Banda, India
| | | | - Narendra Pratap Singh
- Department of Genetics and Plant Breeding, Banda University of Agriculture and Technology, Banda, India
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Erythrina velutina Willd. alkaloids: Piecing biosynthesis together from transcriptome analysis and metabolite profiling of seeds and leaves. J Adv Res 2022; 34:123-136. [PMID: 35024185 PMCID: PMC8655131 DOI: 10.1016/j.jare.2021.01.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/01/2021] [Accepted: 01/30/2021] [Indexed: 12/27/2022] Open
Abstract
Introduction Natural products of pharmaceutical interest often do not reach the drug market due to the associated low yields and difficult extraction. Knowledge of biosynthetic pathways is a key element in the development of biotechnological strategies for plant specialized metabolite production. Erythrina species are mainly used as central nervous system depressants in folk medicine and are important sources of bioactive tetracyclic benzylisoquinoline alkaloids (BIAs), which can act on several pathology-related biological targets. Objectives In this sense, in an unprecedented approach used with a non-model Fabaceae species grown in its unique arid natural habitat, a combined transcriptome and metabolome analyses (seeds and leaves) is presented. Methods The Next Generation Sequencing-based transcriptome (de novo RNA sequencing) was carried out in a NextSeq 500 platform. Regarding metabolite profiling, the High-resolution Liquid Chromatography was coupled to DAD and a micrOTOF-QII mass spectrometer by using electrospray ionization (ESI) and Time of Flight (TOF) analyzer. The tandem MS/MS data were processed and analyzed through Molecular Networking approach. Results This detailed macro and micromolecular approach applied to seeds and leaves of E. velutina revealed 42 alkaloids, several of them unique. Based on the combined evidence, 24 gene candidates were put together in a putative pathway leading to the singular alkaloid diversity of this species. Conclusion Overall, these results could contribute by indicating potential biotechnological targets for modulation of erythrina alkaloids biosynthesis as well as improve molecular databases with omic data from a non-model medicinal plant, and reveal an interesting chemical diversity of Erythrina BIA harvested in Caatinga.
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Yang Z, Mu Y, Wang Y, He F, Shi L, Fang Z, Zhang J, Zhang Q, Geng G, Zhang S. Characterization of a Novel TtLEA2 Gene From Tritipyrum and Its Transformation in Wheat to Enhance Salt Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:830848. [PMID: 35444677 PMCID: PMC9014267 DOI: 10.3389/fpls.2022.830848] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/11/2022] [Indexed: 05/12/2023]
Abstract
Late embryogenesis-abundant (LEA) proteins are critical in helping plants cope with salt stress. "Y1805" is a salt-tolerant Tritipyrum. We identified a "Y1805"-specific LEA gene that was expressed highly and sensitively under salt stress using transcriptome analysis. The novel group 2 LEA gene (TtLEA2-1) was cloned from "Y1805." TtLEA2-1 contained a 453 bp open reading frame encoding an 151-amino-acid protein that showed maximum sequence identity (77.00%) with Thinopyrum elongatum by phylogenetic analysis. It was mainly found to be expressed highly in the roots by qRT-PCR analysis and was located in the whole cell. Forty-eight candidate proteins believed to interact with TtLEA2-1 were confirmed by yeast two-hybrid analysis. These interacting proteins were mainly enriched in "environmental information processing," "glycan biosynthesis and metabolism," and "carbohydrate metabolism." Protein-protein interaction analysis indicated that the translation-related 40S ribosomal protein SA was the central node. An efficient wheat transformation system has been established. A coleoptile length of 2 cm, an Agrobacteria cell density of 0.55-0.60 OD600, and 15 KPa vacuum pressure were ideal for common wheat transformation, with an efficiency of up to 43.15%. Overexpression of TaLEA2-1 in wheat "1718" led to greater height, stronger roots, and higher catalase activity than in wild type seedlings. TaLEA2-1 conferred enhanced salt tolerance in transgenic wheat and may be a valuable gene for genetic modification in crops.
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Affiliation(s)
- Zhifen Yang
- College of Agriculture, Guizhou University, Guiyang, China
| | - Yuanhang Mu
- College of Agriculture, Guizhou University, Guiyang, China
| | - Yiqin Wang
- College of Agriculture, Guizhou University, Guiyang, China
| | - Fang He
- College of Agriculture, Guizhou University, Guiyang, China
- Guizhou Subcenter of National Wheat Improvement Center, Guiyang, China
| | - Luxi Shi
- College of Agriculture, Guizhou University, Guiyang, China
| | - Zhongming Fang
- College of Agriculture, Guizhou University, Guiyang, China
| | - Jun Zhang
- College of Agriculture, Guizhou University, Guiyang, China
| | - Qingqin Zhang
- College of Agriculture, Guizhou University, Guiyang, China
| | - Guangdong Geng
- College of Agriculture, Guizhou University, Guiyang, China
- *Correspondence: Guangdong Geng,
| | - Suqin Zhang
- College of Agriculture, Guizhou University, Guiyang, China
- Guizhou Subcenter of National Wheat Improvement Center, Guiyang, China
- Suqin Zhang,
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Yue J, Wang Y, Jiao J, Wang H. Comparative transcriptomic and metabolic profiling provides insight into the mechanism by which the autophagy inhibitor 3-MA enhances salt stress sensitivity in wheat seedlings. BMC PLANT BIOLOGY 2021; 21:577. [PMID: 34872497 PMCID: PMC8647401 DOI: 10.1186/s12870-021-03351-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Salt stress hinders plant growth and production around the world. Autophagy induced by salt stress helps plants improve their adaptability to salt stress. However, the underlying mechanism behind this adaptability remains unclear. To obtain deeper insight into this phenomenon, combined metabolomics and transcriptomics analyses were used to explore the coexpression of differentially expressed-metabolite (DEM) and gene (DEG) between control and salt-stressed wheat roots and leaves in the presence or absence of the added autophagy inhibitor 3-methyladenine (3-MA). RESULTS The results indicated that 3-MA addition inhibited autophagy, increased ROS accumulation, damaged photosynthesis apparatus and impaired the tolerance of wheat seedlings to NaCl stress. A total of 14,759 DEGs and 554 DEMs in roots and leaves of wheat seedlings were induced by salt stress. DEGs were predominantly enriched in cellular amino acid catabolic process, response to external biotic stimulus, regulation of the response to salt stress, reactive oxygen species (ROS) biosynthetic process, regulation of response to osmotic stress, ect. The DEMs were mostly associated with amino acid metabolism, carbohydrate metabolism, phenylalanine metabolism, carbapenem biosynthesis, and pantothenate and CoA biosynthesis. Further analysis identified some critical genes (gene involved in the oxidative stress response, gene encoding transcription factor (TF) and gene involved in the synthesis of metabolite such as alanine, asparagine, aspartate, glutamate, glutamine, 4-aminobutyric acid, abscisic acid, jasmonic acid, ect.) that potentially participated in a complex regulatory network in the wheat response to NaCl stress. The expression of the upregulated DEGs and DEMs were higher, and the expression of the down-regulated DEGs and DEMs was lower in 3-MA-treated plants under NaCl treatment. CONCLUSION 3-MA enhanced the salt stress sensitivity of wheat seedlings by inhibiting the activity of the roots and leaves, inhibiting autophagy in the roots and leaves, increasing the content of both H2O2 and O2•-, damaged photosynthesis apparatus and changing the transcriptome and metabolome of salt-stressed wheat seedlings.
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Affiliation(s)
- Jieyu Yue
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, 300387, China.
| | - Yingjie Wang
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, 300387, China
| | - Jinlan Jiao
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, 300387, China
| | - Huazhong Wang
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, 300387, China.
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El Boukhari MEM, Barakate M, Choumani N, Bouhia Y, Lyamlouli K. Ulva lactuca Extract and Fractions as Seed Priming Agents Mitigate Salinity Stress in Tomato Seedlings. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10061104. [PMID: 34070914 PMCID: PMC8230233 DOI: 10.3390/plants10061104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 05/02/2023]
Abstract
The present study investigates the effect of Ulva lactuca extract as seed-priming agent for tomato plants under optimal and salinity stress conditions. The aims of this experiment were to assess the effect of seed priming using Ulva lactuca extract in alleviating the salinity stress tomato plants were subjected to, and to find out the possible mechanism of actions behind such a positive effect via means of fractionation of the crude extract and characterization. Salinity application decreased the plant biomass and altered different physiological traits of tomato. However, the application of Ulva lactuca methanol extract (ME) and its fractions (residual fraction (RF), chloroform fraction (CF), butanol fraction (BF), and hexane fraction (HF)) at 1 mg·mL-1 as seed priming substances attenuated the negative effects of salinity on tomato seedlings. Under salinity stress conditions, RF application increased the tomato fresh weight; while ME, RF, and HF treatments significantly decreased the hydrogen peroxide (H2O2) concentration and antioxidant activity in tomato plants. The biochemical analyses of Ulva lactuca extract and fractions showed that the RF recorded the highest concentration of glycine betaine, while the ME was the part with the highest concentrations of total phenols and soluble sugars. This suggests that these compounds might play a key role in the mechanism by which seaweed extracts mitigate salinity stress on plants.
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Affiliation(s)
- Mohammed El Mehdi El Boukhari
- Biodiversity and Plant Sciences Program, Mohammed 6 Polytechnic University (UM6P), AgroBioScience, Benguerir 43150, Morocco; (M.E.M.E.B.); (M.B.); (Y.B.)
- Laboratory of Microbial Biotechnology, AgroSciences and Environment, Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco
| | - Mustapha Barakate
- Biodiversity and Plant Sciences Program, Mohammed 6 Polytechnic University (UM6P), AgroBioScience, Benguerir 43150, Morocco; (M.E.M.E.B.); (M.B.); (Y.B.)
- Laboratory of Microbial Biotechnology, AgroSciences and Environment, Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco
| | - Nadia Choumani
- Department of Chemical and Biochemical Sciences-Green Process Engineering (CBS-GPE), Mohammed VI Polytechnic University (UM6P), Benguerir 43150, Morocco;
| | - Youness Bouhia
- Biodiversity and Plant Sciences Program, Mohammed 6 Polytechnic University (UM6P), AgroBioScience, Benguerir 43150, Morocco; (M.E.M.E.B.); (M.B.); (Y.B.)
- Laboratory of Microbial Biotechnology, AgroSciences and Environment, Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco
| | - Karim Lyamlouli
- Biodiversity and Plant Sciences Program, Mohammed 6 Polytechnic University (UM6P), AgroBioScience, Benguerir 43150, Morocco; (M.E.M.E.B.); (M.B.); (Y.B.)
- Correspondence:
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Shehzad M, Zhou Z, Ditta A, Khan M, Cai X, Xu Y, Maqbool A, Khalofah A, Shaban M, Naeem M, Ansari MJ, Wang K, Liu F. Identification and characterization of genes related to salt stress tolerance within segregation distortion regions of genetic map in F2 population of upland cotton. PLoS One 2021; 16:e0247593. [PMID: 33770112 PMCID: PMC7997035 DOI: 10.1371/journal.pone.0247593] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/09/2021] [Indexed: 12/12/2022] Open
Abstract
Segregation distortion (SD) is a genetic mechanism commonly found in segregating or stable populations. The principle behind this puzzles many researchers. The F2 generation developed from wild Gossypium darwinii and G. hirsutum CCRI12 species was used to investigate the possible transcription factors within the segregation distortion regions (SDRs). The 384 out of 2763 markers were distorted in 29 SDRs on 18 chromosomes. Good collinearity was observed among genetic and physical maps of G. hirsutum and G. barbadense syntenic blocks. Total 568 genes were identified from SDRs of 18 chromosomes. Out of these genes, 128 belonged to three top-ranked salt-tolerant gene families. The DUF597 contained 8 uncharacterized genes linked to Pkinase (PF00069) gene family in the phylogenetic tree, while 15 uncharacterized genes clustered with the zinc finger gene family. Two hundred thirty four miRNAs targeted numerous genes, including ghr-miR156, ghr-miR399 and ghr-miR482, while others targeted top-ranked stress-responsive transcription factors. Moreover, these genes were involved in the regulation of numerous stress-responsive cis-regulatory elements. The RNA sequence data of fifteen upregulated genes were verified through the RT-qPCR. The expression profiles of two highly upregulated genes (Gh_D01G2015 and Gh_A01G1773) in salt-tolerant G. darwinii showed antagonistic expression in G. hirsutum. The results indicated that salt-tolerant genes have been possibly transferred from the wild G. darwinii species. A detailed functional analysis of these genes can be carried out which might be helpful in the future for gene cloning, transformation, gene editing and the development of salt-resistant cotton varieties.
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Affiliation(s)
- Muhammad Shehzad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
| | - Allah Ditta
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
- Plant Breeding, and Genetics Division, Cotton Group, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Punjab, Pakistan
| | - Majid Khan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
| | - Amir Maqbool
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Ahlam Khalofah
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Muhammad Shaban
- Department of Plant Breeding and Genetics, Faculty of Agricultural Science & Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Naeem
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Mohammad Javed Ansari
- Department of Botany, Hindu College Moradabad (Mahatma Jyotiba Phule Rohilkhand University Bareilly), Bareilly, India
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
- * E-mail: (KW); (FL)
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- * E-mail: (KW); (FL)
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Wang H, Leng X, Yang J, Zhang M, Zeng M, Xu X, Wang F, Li C. Comprehensive analysis of AHL gene family and their expression under drought stress and ABA treatment in Populus trichocarpa. PeerJ 2021; 9:e10932. [PMID: 33643717 PMCID: PMC7896510 DOI: 10.7717/peerj.10932] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 01/21/2021] [Indexed: 12/13/2022] Open
Abstract
The AT-hook motif nuclear-localized (AHL) family is a plant transcription factor family, which plays an important role in growth and development and stress responses. We identified and analyzed 37 AHL genes in poplar (Populus trichocarpa). Phylogenetic analysis classified the PtrAHL members into three subfamilies based on their conserved domain. All PtrAHL paralogous pairs evolved under purifying selection. The promoter analysis revealed the presence of stress-related and phytohormone-related cis-elements of the PtrAHL genes. Our analysis of the tissue-specific expression pattern of PtrAHL genes indicated their significance in tissue and organ development. Network-based prediction suggested that PtrAHL genes may interact with histone deacetylases (HDAC) and participate in the development of organs, such as roots. Drought negatively impacts plant growth and development. ABA is produced under osmotic stress condition, and it takes an important part in the stress response and tolerance of plants. Real-time quantitative PCR (qRT-PCR) showed that PtrAHL genes were induced by drought stress and ABA treatment. These insights into the expression of PtrAHL genes under stress provide a basis for PtrAHL gene functional analysis. Our study will help develop new breeding strategies to improve drought tolerance in poplar.
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Affiliation(s)
- Hanzeng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xue Leng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Jia Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Mengqiu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Minzhen Zeng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xuemei Xu
- Library of Northeast Forestry University, Harbin, China
| | - Fude Wang
- Institute of Forestry Science, Harbin, China
| | - Chenghao Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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20
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Comprehensive Analysis of the TIFY Gene Family and Its Expression Profiles under Phytohormone Treatment and Abiotic Stresses in Roots of Populus trichocarpa. FORESTS 2020. [DOI: 10.3390/f11030315] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The TIFY gene family is specific to land plants, exerting immense influence on plant growth and development as well as responses to biotic and abiotic stresses. Here, we identify 25 TIFY genes in the poplar (Populus trichocarpa) genome. Phylogenetic tree analysis revealed these PtrTIFY genes were divided into four subfamilies within two groups. Promoter cis-element analysis indicated most PtrTIFY genes possess stress- and phytohormone-related cis-elements. Quantitative real-time reverse transcription polymerase chain reaction (qRT–PCR) analysis showed that PtrTIFY genes displayed different expression patterns in roots under abscisic acid, methyl jasmonate, and salicylic acid treatments, and drought, heat, and cold stresses. The protein interaction network indicated that members of the PtrTIFY family may interact with COI1, MYC2/3, and NINJA. Our results provide important information and new insights into the evolution and functions of TIFY genes in P. trichocarpa.
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Trends in Seaweed Extract Based Biostimulants: Manufacturing Process and Beneficial Effect on Soil-Plant Systems. PLANTS 2020; 9:plants9030359. [PMID: 32178418 PMCID: PMC7154814 DOI: 10.3390/plants9030359] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/08/2020] [Accepted: 02/10/2020] [Indexed: 12/31/2022]
Abstract
The time when plant biostimulants were considered as "snake oil" is erstwhile and the skepticism regarding their agricultural benefits has significantly faded, as solid scientific evidences of their positive effects are continuously provided. Currently plant biostimulants are considered as a full-fledged class of agri-inputs and highly attractive business opportunity for major actors of the agroindustry. As the dominant category of the biostimulant segment, seaweed extracts were key in this growing renown. They are widely known as substances with the function of mitigating abiotic stress and enhancing plant productivity. Seaweed extracts are derived from the extraction of several macroalgae species, which depending on the extraction methodology lead to the production of complex mixtures of biologically active compounds. Consequently, plant responses are often inconsistent, and precisely deciphering the involved mechanism of action remains highly intricate. Recently, scientists all over the world have been interested to exploring hidden mechanism of action of these resources through the employment of multidisciplinary and high-throughput approaches, combining plant physiology, molecular biology, agronomy, and multi-omics techniques. The aim of this review is to provide fresh insights into the concept of seaweed extract (SE), through addressing the subject in newfangled standpoints based on current scientific knowledge, and taking into consideration both academic and industrial claims in concomitance with market's requirements. The crucial extraction process as well as the effect of such products on nutrient uptake and their role in abiotic and biotic stress tolerance are scrutinized with emphasizing the involved mechanisms at the metabolic and genetic level. Additionally, some often overlooked and indirect effects of seaweed extracts, such as their influence on plant microbiome are discussed. Finally, the plausible impact of the recently approved plant biostimulant regulation on seaweed extract industry is addressed.
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Li Y, Kong D, Fu Y, Sussman MR, Wu H. The effect of developmental and environmental factors on secondary metabolites in medicinal plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 148:80-89. [PMID: 31951944 DOI: 10.1016/j.plaphy.2020.01.006] [Citation(s) in RCA: 357] [Impact Index Per Article: 89.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 12/12/2019] [Accepted: 01/04/2020] [Indexed: 05/25/2023]
Abstract
Secondary metabolites (SMs) of medicinal plants are the material basis of their clinically curative effects. They are also important indicators for evaluating the quality of medicinal materials. However, the synthesis and accumulation of SMs are very complex, which are affected by many factors including internal developmental genetic circuits (regulated gene, enzyme) and by external environment factors (light, temperature, water, salinity, etc.). Currently, lots of literatures focused on the effect of environmental factors on the synthesis and accumulation of SMs of medicinal plants, the effect of the developmental growth and genetic factors on the synthesis and accumulation of SMs still lack systematic classification and summary. Here, we have given the review base on our previous works on the morphological development of medicinal plants and their secondary metabolites, and systematically outlined the literature reports how different environmental factors affected the synthesis and accumulation of SMs. The results of our reviews can know how developmental and environmental factors qualitatively and quantitatively influence SMs of medicinal plants and how these can be integrated as tools to quality control, as well as on the improvement of clinical curative effects by altering their genomes, and/or growth conditions.
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Affiliation(s)
- Yanqun Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China; Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, 510642, China; Guangdong Technology Research Center for Traditional Chinese Veterinary Medicine and Natural Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Dexin Kong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Ying Fu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, 510642, China
| | - Michael R Sussman
- Biotechnology Center, University of Wisconsin, Madison, WI, 53706, USA
| | - Hong Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China; Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, 510642, China; Guangdong Technology Research Center for Traditional Chinese Veterinary Medicine and Natural Medicine, South China Agricultural University, Guangzhou, 510642, China.
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Genome-wide identification of and functional insights into the late embryogenesis abundant (LEA) gene family in bread wheat (Triticum aestivum). Sci Rep 2019; 9:13375. [PMID: 31527624 PMCID: PMC6746774 DOI: 10.1038/s41598-019-49759-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 08/29/2019] [Indexed: 12/20/2022] Open
Abstract
Late embryogenesis abundant (LEA) proteins are involved in the responses and adaptation of plants to various abiotic stresses, including dehydration, salinity, high temperature, and cold. Here, we report the first comprehensive survey of the LEA gene family in “Chinese Spring” wheat (Triticum aestivum). A total of 179 TaLEA genes were identified in T. aestivum and classified into eight groups. All TaLEA genes harbored the LEA conserved motif and had few introns. TaLEA genes belonging to the same group exhibited similar gene structures and chromosomal locations. Our results revealed that most TaLEA genes contained abscisic acid (ABA)-responsive elements (ABREs) and various cis-acting elements associated with the stress response in the promoter region and were induced under ABA and abiotic stress treatments. In addition, 8 genes representing each group were introduced into E. coli and yeast to investigate the protective function of TaLEAs under heat and salt stress. TaLEAs enhanced the tolerance of E. coli and yeast to salt and heat, indicating that these proteins have protective functions in host cells under stress conditions. These results increase our understanding of LEA genes and provide robust candidate genes for future functional investigations aimed at improving the stress tolerance of wheat.
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Shameer K, Naika MB, Shafi KM, Sowdhamini R. Decoding systems biology of plant stress for sustainable agriculture development and optimized food production. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 145:19-39. [DOI: 10.1016/j.pbiomolbio.2018.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 10/23/2018] [Accepted: 12/06/2018] [Indexed: 12/13/2022]
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Liu H, Yang Y, Zhang L. Identification of upstream transcription factors and an interacting PP2C protein of dehydrin WZY2 gene in wheat. PLANT SIGNALING & BEHAVIOR 2019; 14:1678370. [PMID: 31608778 PMCID: PMC6866685 DOI: 10.1080/15592324.2019.1678370] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
As functional proteins dehydrins are found in many maturing seeds and vegetable tissue under adverse environmental conditions. However, the regulation of dehydrin expression remains unclear.To explore regulatory mechanisms of wheat dehydrin WZY2 expression under abiotic stresses, we constructed a cDNA library from PEG- and cold-treated wheat seedlings and performed yeast one-hybrid assay and yeast two-hybrid assay to identify the upstream transcription factors and protein interacting with dehydrin WZY2 gene. Yeast one-hybrid assay illustrated that bHLH49-like (GenBank NO. XM_020296294), zinc finger A20 and AN1 domain-containing stress-associated protein 6-like (GenBank NO. XM_020341647), and bHLH47-like (GenBank NO. XM_020313116) proteins can bind and interact with the promoter of the WZY2, these sequences are Aegilops tauschii transcription factors, the diploid progenitor of the D genome of hexaploid wheat (Triticum aestivum, genomes AABBDD). Real-time PCR analyzes unraveled the stress responsive expression of XM_020296294, XM_020341647, and XM_020313116 in wheat. XM_020296294 and XM_020341647 showed a similar expression patterns with WZY2. Yeast two-hybrid assay indicated that PP2C (GenBank NO. XM_020293398) protein can interact with WZY2. These results provided evidences that WZY2 could be positively regulated by XM_020296294 and XM_020341647 transcription factors, and WZY2 may also play an important role in the ABA signaling pathway through interaction with PP2C to regulate stress-responsive genes expression in wheat. The obtained results contribute for provide a better understanding of the regulatory mechanism of dehydrin expression under abiotic stresses in wheat.
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Affiliation(s)
- Hao Liu
- College of life science/State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shannxi, China
| | - Ying Yang
- College of life science/State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shannxi, China
- College of Nursing, Weinan Vocational&Technical College, Weinan, Shannxi, China
| | - Linsheng Zhang
- College of life science/State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shannxi, China
- CONTACT Linsheng Zhang College of life science/State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shannxi, China
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Bayram M, Aşar R, Özdemir V. Is Space the New Frontier for Omics? Mars-Omics, Planetary Science, and the Next-Generation Technology Futurists. ACTA ACUST UNITED AC 2018; 22:696-699. [DOI: 10.1089/omi.2018.0167] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Mustafa Bayram
- Department of Food Engineering, Faculty of Engineering, Gaziantep University, Gaziantep, Turkey
| | - Remziye Aşar
- Department of Food Engineering, Faculty of Engineering, Gaziantep University, Gaziantep, Turkey
| | - Vural Özdemir
- Senior Advisor, Writer and Researcher, Technology, Society and Democracy, Toronto, Canada
- School of Biotechnology, Amrita Vishwa Vidyapeetham (Amrita University), Kerala, India
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Magwanga RO, Lu P, Kirungu JN, Diouf L, Dong Q, Hu Y, Cai X, Xu Y, Hou Y, Zhou Z, Wang X, Wang K, Liu F. GBS Mapping and Analysis of Genes Conserved between Gossypium tomentosum and Gossypium hirsutum Cotton Cultivars that Respond to Drought Stress at the Seedling Stage of the BC₂F₂ Generation. Int J Mol Sci 2018; 19:E1614. [PMID: 29848989 PMCID: PMC6032168 DOI: 10.3390/ijms19061614] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/21/2018] [Accepted: 05/28/2018] [Indexed: 12/13/2022] Open
Abstract
Cotton production is on the decline due to ever-changing environmental conditions. Drought and salinity stress contribute to over 30% of total loss in cotton production, the situation has worsened more due to the narrow genetic base of the cultivated upland cotton. The genetic diversity of upland cotton has been eroded over the years due to intense selection and inbreeding. To break the bottleneck, the wild cotton progenitors offer unique traits which can be introgressed into the cultivated cotton, thereby improving their performance. In this research, we developed a BC₂F₂ population between wild male parent, G. tomentosum as the donor, known for its high tolerance to drought and the elite female parent, G. hirsutum as the recurrent parent, which is high yielding but sensitive to drought stress. The population was genotyped through the genotyping by sequencing (GBS) method, in which 10,888 single-nucleotide polymorphism (SNP) s were generated and used to construct a genetic map. The map spanned 4191.3 cM, with average marker distance of 0.3849 cM. The map size of the two sub genomes had a narrow range, 2149 cM and 2042.3 cM for At and Dt_sub genomes respectively. A total of 66,434 genes were mined, with 32,032 (48.2%) and 34,402 (51.8%) genes being obtained within the At and Dt_sub genomes respectively. Pkinase (PF00069) was found to be the dominant domain, with 1069 genes. Analysis of the main sub family, serine threonine protein kinases through gene ontology (GO), cis element and miRNA targets analysis revealed that most of the genes were involved in various functions aimed at enhancing abiotic stress tolerance. Further analysis of the RNA sequence data and qRT-PCR validation revealed 16 putative genes, which were highly up regulated under drought stress condition, and were found to be targeted by ghr-miR169a and ghr-miR164, previously associated with NAC(NAM, ATAF1/2 and CUC2) and myeloblastosis (MYB), the top rank drought stress tolerance genes. These genes can be exploited further to aid in development of more drought tolerant cotton genotypes.
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Affiliation(s)
- Richard Odongo Magwanga
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
- School of Biological and Physical Sciences (SBPS), Main Campus, Jaramogi Oginga Odinga University of Science and Technology (JOOUST), Main Campus, P.O. Box 210-40601 Bondo, Kenya.
| | - Pu Lu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Joy Nyangasi Kirungu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Latyr Diouf
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Qi Dong
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Yangguang Hu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Yuqing Hou
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Xingxing Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Fang Liu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
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Irani S, Todd CD. Exogenous allantoin increases Arabidopsis seedlings tolerance to NaCl stress and regulates expression of oxidative stress response genes. JOURNAL OF PLANT PHYSIOLOGY 2018; 221:43-50. [PMID: 29245127 DOI: 10.1016/j.jplph.2017.11.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 11/22/2017] [Accepted: 11/24/2017] [Indexed: 05/21/2023]
Abstract
Allantoin is a nitrogenous compound derived from purine catabolism that contributes to nitrogen recycling in plants. Accumulation of allantoin in plant tissues and a potential role in protection of plants from abiotic stress conditions has been identified. The present work shows that application of exogenous allantoin increased stress tolerance of Arabidopsis seedlings when germinated on, or subjected to the media containing NaCl. Allantoin-induced tolerance to NaCl stress was associated with decreased production of superoxide and hydrogen peroxide in seedlings. To understand the molecular mechanism, the effect of exogenous allantoin treatment on expression of several stress-related genes was investigated. Exogenous allantoin altered the expression of several antioxidant encoding genes and upregulated the expression of two genes involved in oxidative stress tolerance, SOS1 and RCD1, in the presence or absence of NaCl. Allantoin increased the NaCl tolerance of abscisic acid insensitive mutants, suggesting that it can function independently of abscisic acid signaling. These results provide additional evidence for the role of allantoin in enhancing plants tolerance to oxidative stress.
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Affiliation(s)
- Solmaz Irani
- University of Saskatchewan, Department of Biology, 112 Science Place, Saskatoon, SK, S7N5E2, Canada
| | - Christopher D Todd
- University of Saskatchewan, Department of Biology, 112 Science Place, Saskatoon, SK, S7N5E2, Canada.
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Gomes de Oliveira Dal'Molin C, Nielsen LK. Plant genome-scale reconstruction: from single cell to multi-tissue modelling and omics analyses. Curr Opin Biotechnol 2017; 49:42-48. [PMID: 28806583 DOI: 10.1016/j.copbio.2017.07.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 07/17/2017] [Accepted: 07/17/2017] [Indexed: 10/25/2022]
Abstract
In this review, we present the latest developments in plant systems biology with particular emphasis on plant genome-scale reconstructions and multi-omics analyses. Understanding multicellular metabolism is far from trivial and 'omics' data are difficult to interpret in the absence of a systems framework. 'Omics' data appropriately integrated with genome-scale reconstructions and modelling facilitates our understanding of how individual components interact and influence overall cell, tissue or organisms function. Here we present examples of how plant metabolic reconstructions and modelling are used as a systems-based framework for improving our understanding of the plant metabolic processes in single cells and multiple tissues.
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Affiliation(s)
| | - Lars Keld Nielsen
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland 4072, Australia.
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Li M, Yang Y, Feng F, Zhang B, Chen S, Yang C, Gu L, Wang F, Zhang J, Chen A, Lin W, Chen X, Zhang Z. Differential proteomic analysis of replanted Rehmannia glutinosa roots by iTRAQ reveals molecular mechanisms for formation of replant disease. BMC PLANT BIOLOGY 2017; 17:116. [PMID: 28693420 PMCID: PMC5504617 DOI: 10.1186/s12870-017-1060-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 06/22/2017] [Indexed: 05/07/2023]
Abstract
BACKGROUND The normal growth of Rehmannia glutinosa, a widely used medicinal plant in China, is severely disturbed by replant disease. The formation of replant disease commonly involves interactions among plants, allelochemicals and microbes; however, these relationships remain largely unclear. As a result, no effective measures are currently available to treat replant disease. RESULTS In this study, an integrated R. glutinosa transcriptome was constructed, from which an R. glutinosa protein library was obtained. iTRAQ technology was then used to investigate changes in the proteins in replanted R. glutinosa roots, and the proteins that were expressed in response to replant disease were identified. An integrated R. glutinosa transcriptome from different developmental stages of replanted and normal-growth R. glutinosa produced 65,659 transcripts, which were accurately translated into 47,818 proteins. Using this resource, a set of 189 proteins was found to be significantly differentially expressed between normal-growth and replanted R. glutinosa. Of the proteins that were significantly upregulated in replanted R. glutinosa, most were related to metabolism, immune responses, ROS generation, programmed cell death, ER stress, and lignin synthesis. CONCLUSIONS By integrating these key events and the results of previous studies on replant disease formation, a new picture of the damaging mechanisms that cause replant disease stress emerged. Replant disease altered the metabolic balance of R. glutinosa, activated immune defence systems, increased levels of ROS and antioxidant enzymes, and initiated the processes of cell death and senescence in replanted R. glutinosa. Additionally, lignin deposition in R. glutinosa roots that was caused by replanting significantly inhibited tuberous root formation. These key processes provide important insights into the underlying mechanisms leading to the formation of replant disease and also for the subsequent development of new control measures to improve production and quality of replanted plants.
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Affiliation(s)
- Mingjie Li
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanhui Yang
- College of Bioengineering, Henan University of Technology, Zhengzhou, China
| | - Fajie Feng
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bao Zhang
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuqiang Chen
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chuyun Yang
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Li Gu
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | - Junyi Zhang
- College of Chemical Engineering, Huaqiao University, Xiamen, China
| | - Aiguo Chen
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenxiong Lin
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | - Zhongyi Zhang
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
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Ahn H, Jung I, Shin SJ, Park J, Rhee S, Kim JK, Jung W, Kwon HB, Kim S. Transcriptional Network Analysis Reveals Drought Resistance Mechanisms of AP2/ERF Transgenic Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:1044. [PMID: 28663756 PMCID: PMC5471331 DOI: 10.3389/fpls.2017.01044] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/30/2017] [Indexed: 05/18/2023]
Abstract
This study was designed to investigate at the molecular level how a transgenic version of rice "Nipponbare" obtained a drought-resistant phenotype. Using multi-omics sequencing data, we compared wild-type rice (WT) and a transgenic version (erf71) that had obtained a drought-resistant phenotype by overexpressing OsERF71, a member of the AP2/ERF transcription factor (TF) family. A comprehensive bioinformatics analysis pipeline, including TF networks and a cascade tree, was developed for the analysis of multi-omics data. The results of the analysis showed that the presence of OsERF71 at the source of the network controlled global gene expression levels in a specific manner to make erf71 survive longer than WT. Our analysis of the time-series transcriptome data suggests that erf71 diverted more energy to survival-critical mechanisms related to translation, oxidative response, and DNA replication, while further suppressing energy-consuming mechanisms, such as photosynthesis. To support this hypothesis further, we measured the net photosynthesis level under physiological conditions, which confirmed the further suppression of photosynthesis in erf71. In summary, our work presents a comprehensive snapshot of transcriptional modification in transgenic rice and shows how this induced the plants to acquire a drought-resistant phenotype.
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Affiliation(s)
- Hongryul Ahn
- Department of Computer Science and Engineering, Seoul National UniversitySeoul, South Korea
| | - Inuk Jung
- Interdisciplinary Program in Bioinformatics, Seoul National UniversitySeoul, South Korea
| | - Seon-Ju Shin
- Department of Biomedical Sciences, Sunmoon UniversityAsan, South Korea
| | - Jinwoo Park
- Department of Computer Science and Engineering, Seoul National UniversitySeoul, South Korea
| | - Sungmin Rhee
- Department of Computer Science and Engineering, Seoul National UniversitySeoul, South Korea
| | - Ju-Kon Kim
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National UniversitySeoul, South Korea
| | - Woosuk Jung
- Department of Applied Bioscience, Konkuk UniversitySeoul, South Korea
| | - Hawk-Bin Kwon
- Department of Biomedical Sciences, Sunmoon UniversityAsan, South Korea
| | - Sun Kim
- Department of Computer Science and Engineering, Seoul National UniversitySeoul, South Korea
- Interdisciplinary Program in Bioinformatics, Seoul National UniversitySeoul, South Korea
- Bioinformatics Institute, Seoul National UniversitySeoul, South Korea
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Sablok G, Powell JJ, Kazan K. Emerging Roles and Landscape of Translating mRNAs in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:1443. [PMID: 28919899 PMCID: PMC5585741 DOI: 10.3389/fpls.2017.01443] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 08/03/2017] [Indexed: 05/03/2023]
Abstract
Plants use a wide range of mechanisms to adapt to different environmental stresses. One of the earliest responses displayed under stress is rapid alterations in stress responsive gene expression that has been extensively analyzed through expression profiling such as microarrays and RNA-sequencing. Recently, expression profiling has been complemented with proteome analyses to establish a link between transcriptional and the corresponding translational changes. However, proteome profiling approaches have their own technical limitations. More recently, ribosome-associated mRNA profiling has emerged as an alternative and a robust way of identifying translating mRNAs, which are a set of mRNAs associated with ribosomes and more likely to contribute to proteome abundance. In this article, we briefly review recent studies that examined the processes affecting the abundance of translating mRNAs, their regulation during plant development and tolerance to stress conditions and plant factors affecting the selection of translating mRNA pools. This review also highlights recent findings revealing differential roles of alternatively spliced mRNAs and their translational control during stress adaptation. Overall, better understanding of processes involved in the regulation of translating mRNAs has obvious implications for improvement of stress tolerance in plants.
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Affiliation(s)
- Gaurav Sablok
- Finnish Museum of Natural HistoryHelsinki, Finland
- Department of Biosciences, Viikki Plant Science Center, University of HelsinkiHelsinki, Finland
- *Correspondence: Gaurav Sablok, Kemal Kazan,
| | - Jonathan J. Powell
- Commonwealth Scientific and Industrial Research Organization Agriculture, St. LuciaQLD, Australia
| | - Kemal Kazan
- Commonwealth Scientific and Industrial Research Organization Agriculture, St. LuciaQLD, Australia
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. LuciaQLD, Australia
- *Correspondence: Gaurav Sablok, Kemal Kazan,
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Wu Z, Yin X, Bañuelos GS, Lin ZQ, Liu Y, Li M, Yuan L. Indications of Selenium Protection against Cadmium and Lead Toxicity in Oilseed Rape ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2016; 7:1875. [PMID: 28018407 PMCID: PMC5156728 DOI: 10.3389/fpls.2016.01875] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 11/28/2016] [Indexed: 05/03/2023]
Abstract
The present study investigated the beneficial role of selenium (Se) in protecting oilseed rape (Brassica napus L.) plants from cadmium (Cd+2) and lead (Pb+2) toxicity. Exogenous Se markedly reduced Cd and Pb concentration in both roots and shoots. Supplementation of the medium with Se (5, 10, and 15 mg kg-1) alleviated the negative effect of Cd and Pb on growth and led to a decrease in oxidative damages caused by Cd and Pb. Furthermore, Se-enhanced superoxide free radicals ([Formula: see text]), hydrogen peroxide (H2O2), and lipid peroxidation, as indicated by malondialdehyde accumulation, but decreased superoxide dismutase and glutathione peroxidase activities. Meanwhile, the presence of Cd and Pb in the medium affected Se speciation in shoots. The results suggest that Se could alleviate Cd and Pb toxicity by preventing oxidative stress in oilseed rape plant.
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Affiliation(s)
- Zhilin Wu
- Key Laboratory of Agri-Food Safety of Anhui Province, Scientific Observing and Experimental Station of Agricultural Environment of the Ministry of Agriculture – Laboratory of Quality and Safty Risk Assessment for Agricultural Products on Storage and Preservation of the Ministry of Agriculture, School of Plant Protection – School of Resources and Environment, Anhui Agricultural UniversityHefei, China
- School of Earth and Space Sciences, University of Science and Technology of ChinaHefei, China
- Jiangsu Bio-Engineering Research Centre of Selenium, Suzhou Institute for Advanced Study, University of Science and Technology of ChinaSuzhou, China
| | - Xuebin Yin
- School of Earth and Space Sciences, University of Science and Technology of ChinaHefei, China
- Jiangsu Bio-Engineering Research Centre of Selenium, Suzhou Institute for Advanced Study, University of Science and Technology of ChinaSuzhou, China
- Institute of Advanced Technology, University of Science and Technology of ChinaHefei, China
| | - Gary S. Bañuelos
- San Joaquin Valley Agricultural Sciences Center, United States Department of Agriculture – Agricultural Research Service, ParlierCA, USA
| | - Zhi-Qing Lin
- Environmental Sciences Program and Department of Biological Sciences, Southern Illinois University Edwardsville, EdwardsvilleIL, USA
| | - Ying Liu
- School of Earth and Space Sciences, University of Science and Technology of ChinaHefei, China
- Jiangsu Bio-Engineering Research Centre of Selenium, Suzhou Institute for Advanced Study, University of Science and Technology of ChinaSuzhou, China
- Institute of Advanced Technology, University of Science and Technology of ChinaHefei, China
| | - Miao Li
- Key Laboratory of Agri-Food Safety of Anhui Province, Scientific Observing and Experimental Station of Agricultural Environment of the Ministry of Agriculture – Laboratory of Quality and Safty Risk Assessment for Agricultural Products on Storage and Preservation of the Ministry of Agriculture, School of Plant Protection – School of Resources and Environment, Anhui Agricultural UniversityHefei, China
- Institute of Advanced Technology, University of Science and Technology of ChinaHefei, China
- The Northwest of Anhui Province Station for Integrative Agriculture, Research Institute for New Rural Development, Anhui Agricultural UniversityHefei, China
| | - Linxi Yuan
- School of Earth and Space Sciences, University of Science and Technology of ChinaHefei, China
- Jiangsu Bio-Engineering Research Centre of Selenium, Suzhou Institute for Advanced Study, University of Science and Technology of ChinaSuzhou, China
- Institute of Advanced Technology, University of Science and Technology of ChinaHefei, China
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Rasheed R, Wahid A, Hussain I, Mahmood S, Parveen A. Partial repair of salinity-induced damage to sprouting sugarcane buds by proline and glycinebetaine pretreatment. PROTOPLASMA 2016; 253:803-813. [PMID: 26043840 DOI: 10.1007/s00709-015-0841-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 05/26/2015] [Indexed: 06/04/2023]
Abstract
Sugarcane shows reduced crop stand under relatively suboptimal conditions; the main reason for this is its sensitivity to ionic stress in the soil solution. This research was performed to explore some physiological and developmental changes in the immature sugarcane buds submitted to salt stress and possible role of glycinebetaine (GB) and proline (Pro) in mitigating the ion toxicity in a time course manner. Salinity stress reduced fresh and dry weight, induced the generation of hydrogen peroxide, increased tissue levels of Na(+) sand Cl(-), reduced K(+) and Ca(2+), and K(+):Na(+) and Ca(2+):Na(+) ratios, while increasing the osmolyte synthesis in expanding sugarcane buds. Salinity stress reduced and delayed the formation of new bud leaves and their expansion, which was mainly because of reduction in the number and area of mesophyll cells and poor development of vascular bundles. The pretreatment of bud chips with 20 mM each of GB and Pro decreased tissue levels of Na(+) and Cl(-), reduced the generation of H2O2, improved K(+) and Ca(2+), K(+):Na(+) and Ca(2+):Na(+) ratios, and further increased the levels of GB, free proline (FP), and soluble sugars in the buds. The pretreatment increased mesophyll cell number and expansion of bud leaves and formation of elaborated vascular tissues, which apparently enabled the sprouting buds to adapt to salinity stress. Of the two osmolytes, GB was a relatively better inducer of salinity tolerance than Pro. In short, salinity-induced oxidative stress was the main cause for altered tissue development, the production of which was offset by pretreatment of bud tissues with Pro and GB.
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Affiliation(s)
- Rizwan Rasheed
- Department of Botany, Government College University, Faisalabad, 38000, Pakistan
| | - Abdul Wahid
- Department of Botany, University of Agriculture, Faisalabad, 38040, Pakistan.
| | - Iqbal Hussain
- Department of Botany, Government College University, Faisalabad, 38000, Pakistan
| | - Saqib Mahmood
- Department of Botany, Government College University, Faisalabad, 38000, Pakistan
| | - Abida Parveen
- Department of Botany, Government College University, Faisalabad, 38000, Pakistan
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Sircar S, Parekh N. Functional characterization of drought-responsive modules and genes in Oryza sativa: a network-based approach. Front Genet 2015; 6:256. [PMID: 26284112 PMCID: PMC4519691 DOI: 10.3389/fgene.2015.00256] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 07/16/2015] [Indexed: 01/18/2023] Open
Abstract
Drought is one of the major environmental stress conditions affecting the yield of rice across the globe. Unraveling the functional roles of the drought-responsive genes and their underlying molecular mechanisms will provide important leads to improve the yield of rice. Co-expression relationships derived from condition-dependent gene expression data is an effective way to identify the functional associations between genes that are part of the same biological process and may be under similar transcriptional control. For this purpose, vast amount of freely available transcriptomic data may be used. In this study, we consider gene expression data for different tissues and developmental stages in response to drought stress. We analyze the network of co-expressed genes to identify drought-responsive genes modules in a tissue and stage-specific manner based on differential expression and gene enrichment analysis. Taking cues from the systems-level behavior of these modules, we propose two approaches to identify clusters of tightly co-expressed/co-regulated genes. Using graph-centrality measures and differential gene expression, we identify biologically informative genes that lack any functional annotation. We show that using orthologous information from other plant species, the conserved co-expression patterns of the uncharacterized genes can be identified. Presence of a conserved neighborhood enables us to extrapolate functional annotation. Alternatively, we show that single 'guide-gene' approach can help in understanding tissue-specific transcriptional regulation of uncharacterized genes. Finally, we confirm the predicted roles of uncharacterized genes by the analysis of conserved cis-elements and explain the possible roles of these genes toward drought tolerance.
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Affiliation(s)
- Sanchari Sircar
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology Hyderabad, India
| | - Nita Parekh
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology Hyderabad, India
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Dawkar VV, Dholakia BB, Gupta VS. Agriproteomics of Bread Wheat: Comparative Proteomics and Network Analyses of Grain Size Variation. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:372-82. [PMID: 26134253 DOI: 10.1089/omi.2015.0040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Agriproteomics signifies the merging of agriculture research and proteomics systems science and is impacting plant research and societal development. Wheat is a frequently consumed foodstuff, has highly variable grain size that in effect contributes to wheat grain yield and the end-product quality. Very limited information is available on molecular basis of grain size due to complex multifactorial nature of this trait. Here, using liquid chromatography-mass spectrometry, we investigated the proteomics profiles from grains of wheat genotypes, Rye selection 111 (RS111) and Chinese spring (CS), which differ in their size. Significant differences in protein expression were found, including 33 proteins uniquely present in RS111 and 32 only in CS, while 54 proteins were expressed from both genotypes. Among differentially expressed proteins, 22 were upregulated, while 21 proteins were downregulated in RS111 compared to CS. Functional classification revealed their role in energy metabolism, seed storage, stress tolerance and transcription. Further, protein interactive network analysis was performed to predict the targets of identified proteins. Significantly different interactions patterns were observed between these genotypes with detection of proteins such as Cyp450, Sus2, and WRKY that could potentially affect seed size. The present study illustrates the potentials of agriproteomics as a veritable new frontier of plant omics research.
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Affiliation(s)
- Vishal V Dawkar
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune, India
| | - Bhushan B Dholakia
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune, India
| | - Vidya S Gupta
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune, India
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Jain A, Sinilal B, Starnes DL, Sanagala R, Krishnamurthy S, Sahi SV. Role of Fe-responsive genes in bioreduction and transport of ionic gold to roots of Arabidopsis thaliana during synthesis of gold nanoparticles. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 84:189-196. [PMID: 25289518 DOI: 10.1016/j.plaphy.2014.09.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 09/24/2014] [Indexed: 06/03/2023]
Abstract
Several studies have shown potassium chloroaurate (KAuCl4)-mediated synthesis of gold nanoparticles (AuNPs) by using extracts of different parts of diverse plant species. However, the mechanism underlying the formation of AuNPs in planta has far from being elucidated. Here, we report the molecular evidence towards the role of genes involved in iron (Fe) homeostasis during in planta synthesis of AuNPs in roots of Arabidopsis thaliana. Firstly, we examined the dosage-dependent effects of KAuCl4 treatment on primary root length (PRL), and meristematic activity of roots in transgenic CycB1;1::uidA. Compared to control seedling (0 ppm KAuCl4), PRL and meristematic activity of primary and lateral roots showed progressive attenuation in seedlings treated with higher concentrations of KAuCl4 (25 ppm or above). Therefore, subsequent studies on in planta synthesis of AuNPs, and molecular responses were carried out in roots of the seedlings treated with 10 ppm KAuCl4 for 7 d. TEM of KAuCl4-treated seedlings showed the presence of monodisperse AuNPs of different shapes and sizes in root biomatrix. There was a significant induction of FRO2 in KAuCl4-treated roots, and therefore its likely involvement in bioreduction of Au(3)(+) could be assumed. Elevated expression levels of Fe transporters IRT1 and IRT2 further suggested their potential role in transport of bioreduced Au(3+) across root membrane. Expression levels of other genes involved in Fe homeostasis, and also different members of zinc (Zn), phosphate (Pi), and potassium (K) transporter families remained unaffected by KAuCl4 treatment. An increased Au content in Fe-deprived roots further provided evidence towards the specific role of a subset of Fe-responsive genes during in planta synthesis of AuNPs.
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Affiliation(s)
- Ajay Jain
- Department of Biology, Western Kentucky University, Bowling Green, KY 42101-1080, USA; National Research Centre on Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Campus, New Delhi 110012, India
| | - Bhaskaran Sinilal
- Department of Biology, Western Kentucky University, Bowling Green, KY 42101-1080, USA
| | - Daniel L Starnes
- Department of Biology, Western Kentucky University, Bowling Green, KY 42101-1080, USA
| | - Raghavendrarao Sanagala
- National Research Centre on Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Campus, New Delhi 110012, India
| | - Sneha Krishnamurthy
- Department of Biology, Western Kentucky University, Bowling Green, KY 42101-1080, USA
| | - Shivendra V Sahi
- Department of Biology, Western Kentucky University, Bowling Green, KY 42101-1080, USA.
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Expression and molecular evolution of two DREB1 genes in black poplar (Populus nigra). PLoS One 2014; 9:e98334. [PMID: 24887081 PMCID: PMC4041773 DOI: 10.1371/journal.pone.0098334] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 05/01/2014] [Indexed: 11/19/2022] Open
Abstract
Environmental stresses such as low temperature, drought, and high salinity significantly affect plant growth and yield. As selective forces, these adverse factors play essential roles in shaping phenotypic variation in plant populations. Black poplar (Populus nigra) is an economically and ecologically important forest tree species with widely distributed populations and is thus suitable for experiments detecting evolutionary footprints left by stress. Here, we performed expression and evolutionary analysis of two duplicated DREB A1-subgroup (DREB1) genes, PnDREB68 and PnDREB69, encoding transcription factors that are involved in stress responses. The two genes showed partially overlapping but distinct expression patterns in response to stresses. These genes were strongly and rapidly induced by cold stress in leaves, stems, and roots. In leaf tissue, dehydration stress induced the expression of PnDREB68 but not PnDREB69. PnDREB69 displayed more rapid responses and longer expression durations than PnDREB68 under salt and ABA stress, respectively. Based on single nucleotide polymorphism (SNP) analysis, we found significant population genetic differentiation, with a greater FST value (0.09189) for PnDREB69 than for PnDREB68 (0.07743). Nucleotide diversity analysis revealed a two-fold higher πT for PnDREB68 than for PnDREB69 (0.00563 vs. 0.00243), reflecting strong purifying selection acting on the former. The results suggest that positive selection acted on PnDREB69, as evidenced by neutral testing using Tajima’s D statistic. The distinct selective forces to which each of the genes was subjected may be associated with expression divergence. Linkage disequilibrium (LD) was low for the sequenced region, with a higher level for PnDREB68 than for PnDREB69. Additionally, analysis of the relationship among carbon isotope ratios, SNP classes and gene expression, together with motif and domain analysis, suggested that 14 polymorphisms within the two genes may be candidates for an association study of important traits such as water use efficiency/drought tolerance in black poplar.
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Murillo-Amador B, Córdoba-Matson MV, Villegas-Espinoza JA, Hernández-Montiel LG, Troyo-Diéguez E, García-Hernández JL. Mineral content and biochemical variables of Aloe vera L. under salt stress. PLoS One 2014; 9:e94870. [PMID: 24736276 PMCID: PMC3988083 DOI: 10.1371/journal.pone.0094870] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 03/20/2014] [Indexed: 12/02/2022] Open
Abstract
Despite the proven economic importance of Aloe vera, studies of saline stress and its effects on the biochemistry and mineral content in tissues of this plant are scarce. The objective of this study was to grow Aloe under NaCl stress of 0, 30, 60, 90 and 120 mM and compare: (1) proline, total protein, and enzyme phosphoenolpyruvate carboxylase (PEP-case) in chlorenchyma and parenchyma tissues, and (2) ion content (Na, K, Ca, Mg, Cl, Fe, P. N, Zn, B, Mn, and Cu) in roots, stems, leaves and sprouts. Proline and PEP-case increased as salinity increased in both parenchyma and chlorenchyma, while total protein increased in parenchyma and decreased in chlorenchyma, although at similar salt concentrations total protein was always higher in chlorenchyma. As salinity increased Na and Cl ions increased in roots, stems, leaves, while K decreased only significantly in sprouts. Salinity increases typically caused mineral content in tissue to decrease, or not change significantly. In roots, as salinity increased Mg decreased, while all other minerals failed to show a specific trend. In stems, the mineral concentrations that changed were Fe and P which increased with salinity while Cu decreased. In leaves, Mg, Mn, N, and B decreased with salinity, while Cu increased. In sprouts, the minerals that decreased with increasing salinity were Mg, Mn, and Cu. Zinc did not exhibit a trend in any of the tissues. The increase in protein, proline and PEP-case activity, as well as the absorption and accumulation of cations under moderate NaCl stress caused osmotic adjustment which kept the plant healthy. These results suggest that Aloe may be a viable crop for soil irrigated with hard water or affected by salinity at least at concentrations used in the present study.
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Affiliation(s)
| | | | | | | | - Enrique Troyo-Diéguez
- Centro de Investigaciones Biológicas del Noroeste, S.C. La Paz, Baja California Sur, México
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Delorge I, Janiak M, Carpentier S, Van Dijck P. Fine tuning of trehalose biosynthesis and hydrolysis as novel tools for the generation of abiotic stress tolerant plants. FRONTIERS IN PLANT SCIENCE 2014; 5:147. [PMID: 24782885 PMCID: PMC3995065 DOI: 10.3389/fpls.2014.00147] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 03/27/2014] [Indexed: 05/18/2023]
Abstract
The impact of abiotic stress on plant growth and development has been and still is a major research topic. An important pathway that has been linked to abiotic stress tolerance is the trehalose biosynthetic pathway. Recent findings showed that trehalose metabolism is also important for normal plant growth and development. The intermediate compound - trehalose-6-phosphate (T6P) - is now confirmed to act as a sensor for available sucrose, hereby directly influencing the type of response to the changing environmental conditions. This is possible because T6P and/or trehalose or their biosynthetic enzymes are part of complex interaction networks with other crucial hormone and sugar-induced signaling pathways, which may function at different developmental stages. Because of its effect on plant growth and development, modification of trehalose biosynthesis, either at the level of T6P synthesis, T6P hydrolysis, or trehalose hydrolysis, has been utilized to try to improve crop yield and biomass. It was shown that alteration of the amounts of either T6P and/or trehalose did result in increased stress tolerance, but also resulted in many unexpected phenotypic alterations. A main challenge is to characterize the part of the signaling pathway resulting in improved stress tolerance, without affecting the pathways resulting in the unwanted phenotypes. One such specific pathway where modification of trehalose metabolism improved stress tolerance, without any side effects, was recently obtained by overexpression of trehalase, which results in a more sensitive reaction of the stomatal guard cells and closing of the stomata under drought stress conditions. We have used the data that have been obtained from different studies to generate the optimal plant that can be constructed based on modifications of trehalose metabolism.
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Affiliation(s)
- Ines Delorge
- Department of Molecular Microbiology, VIBLeuven, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and MicrobiologyKU Leuven, Leuven, Belgium
| | - Michal Janiak
- Department of Molecular Microbiology, VIBLeuven, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and MicrobiologyKU Leuven, Leuven, Belgium
- Division of Crop Biotechnics, Department of BiosystemsKU Leuven, Leuven, Belgium
| | - Sebastien Carpentier
- Division of Crop Biotechnics, Department of BiosystemsKU Leuven, Leuven, Belgium
| | - Patrick Van Dijck
- Department of Molecular Microbiology, VIBLeuven, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and MicrobiologyKU Leuven, Leuven, Belgium
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O’Brien JA, Benková E. Cytokinin cross-talking during biotic and abiotic stress responses. FRONTIERS IN PLANT SCIENCE 2013; 4:451. [PMID: 24312105 PMCID: PMC3833016 DOI: 10.3389/fpls.2013.00451] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 10/22/2013] [Indexed: 05/18/2023]
Abstract
As sessile organisms, plants have to be able to adapt to a continuously changing environment. Plants that perceive some of these changes as stress signals activate signaling pathways to modulate their development and to enable them to survive. The complex responses to environmental cues are to a large extent mediated by plant hormones that together orchestrate the final plant response. The phytohormone cytokinin is involved in many plant developmental processes. Recently, it has been established that cytokinin plays an important role in stress responses, but does not act alone. Indeed, the hormonal control of plant development and stress adaptation is the outcome of a complex network of multiple synergistic and antagonistic interactions between various hormones. Here, we review the recent findings on the cytokinin function as part of this hormonal network. We focus on the importance of the crosstalk between cytokinin and other hormones, such as abscisic acid, jasmonate, salicylic acid, ethylene, and auxin in the modulation of plant development and stress adaptation. Finally, the impact of the current research in the biotechnological industry will be discussed.
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Affiliation(s)
- José A. O’Brien
- Department of Plant Systems Biology, VIB, GentBelgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University GentBelgium
| | - Eva Benková
- Department of Plant Systems Biology, VIB, GentBelgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University GentBelgium
- Institute of Science and Technology AustriaKlosterneuburg, Austria
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42
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Naika M, Shameer K, Sowdhamini R. Comparative analyses of stress-responsive genes in Arabidopsis thaliana: insight from genomic data mining, functional enrichment, pathway analysis and phenomics. MOLECULAR BIOSYSTEMS 2013; 9:1888-908. [PMID: 23645342 DOI: 10.1039/c3mb70072k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Biotic and abiotic stresses adversely affect agriculture by reducing crop growth and productivity worldwide. To investigate the abiotic stress-responsive genes in Arabidopsis thaliana, we compiled a dataset of stress signals and differentially upregulated genes (>= 2.5 fold change) from Stress-responsive transcription Factors DataBase (STIFDB) with additional set of stress signals and genes curated from PubMed and Gene Expression Omnibus. A dataset of 3091 genes differentially upregulated due to 14 different stress signals (abscisic acid, aluminum, cold, cold-drought-salt, dehydration, drought, heat, iron, light, NaCl, osmotic stress, oxidative stress, UV-B and wounding) were curated and used for the analysis. Details about stress-responsive enriched genes and their association with stress signals can be obtained from STIFDB2 database . The gene-stress-signal data were analyzed using an enrichment-based meta-analysis framework consisting of two different ontologies (Gene Ontology and Plant Ontology), biological pathway and functional domain annotations. We found several shared and distinct biological processes, cellular components and molecular functions associated with stress-responsive genes. Pathway analysis revealed that stress-responsive genes perturbed the pathways under the "Metabolic pathways" category. We also found several shared and stress-signal specific protein domains, suggesting functional mechanisms regulating stress-response. Phenomic characteristics of abiotic stress-responsive genes were ascertained for several stresses and found to be shared by multiple stresses in both anatomy and temporal categories of Plant Ontology. We found several constitutive stress-responsive genes that are differentially upregulated due to perturbation of different stress signals, for example a gene (AT1G68440) involved in phenylpropanoid metabolism and polyamine catabolism as responsive to seven different stress signals. We also performed structure-function prediction of five genes associated responsive to multiple abiotic stress signals. We envisage that results from our analysis that provide insight into functional repertoire, metabolic pathways and phenomic characteristics common and specifically associated with stress signals would help to understand abiotic stress regulome in Arabidopsis thaliana and may also help to develop an improved plant variety using molecular breeding and genetic engineering techniques that are rapidly stress-responsive and tolerant.
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Affiliation(s)
- Mahantesha Naika
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, 560065, India.
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Fuoco R, Bogani P, Capodaglio G, Del Bubba M, Abollino O, Giannarelli S, Spiriti MM, Muscatello B, Doumett S, Turetta C, Zangrando R, Zelano V, Buiatti M. Response to metal stress of Nicotiana langsdorffii plants wild-type and transgenic for the rat glucocorticoid receptor gene. JOURNAL OF PLANT PHYSIOLOGY 2013; 170:668-75. [PMID: 23395537 DOI: 10.1016/j.jplph.2012.12.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 12/15/2012] [Accepted: 12/17/2012] [Indexed: 06/01/2023]
Abstract
Recently our findings have shown that the integration of the gene coding for the rat gluco-corticoid receptor (GR receptor) in Nicotiana langsdorffii plants induced morphophysiological effects in transgenic plants through the modification of their hormonal pattern. Phytohormones play a key role in plant responses to many different biotic and abiotic stresses since a modified hormonal profile up-regulates the activation of secondary metabolites involved in the response to stress. In this work transgenic GR plants and isogenic wild type genotypes were exposed to metal stress by treating them with 30ppm cadmium(II) or 50ppm chromium(VI). Hormonal patterns along with changes in key response related metabolites were then monitored and compared. Heavy metal up-take was found to be lower in the GR plants. The transgenic plants exhibited higher values of S-abscisic acid (S-ABA) and 3-indole acetic acid (IAA), salicylic acid and total polyphenols, chlorogenic acid and antiradical activity, compared to the untransformed wild type plants. Both Cd and Cr treatments led to an increase in hormone concentrations and secondary metabolites only in wild type plants. Analysis of the results suggests that the stress responses due to changes in the plant's hormonal system may derive from the interaction between the GR receptor and phytosteroids, which are known to play a key role in plant physiology and development.
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Affiliation(s)
- Roger Fuoco
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Risorgimento 35, 56126 Pisa, Italy.
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du Preez I, Loots DT. Altered Fatty Acid Metabolism Due to Rifampicin-Resistance Conferring Mutations in therpoBGene ofMycobacterium tuberculosis: Mapping the Potential of Pharmaco-metabolomics for Global Health and Personalized Medicine. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2012; 16:596-603. [PMID: 22966781 DOI: 10.1089/omi.2012.0028] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Ilse du Preez
- Centre for Human Metabonomics, School for Physical and Chemical Sciences, North-West University (Potchefstroom Campus), Potchefstroom, South Africa
- Department of Biochemistry, School of Environmental and Health Sciences, North-West University (Mafikeng Campus), Mmabatho, South Africa
| | - Du Toit Loots
- Centre for Human Metabonomics, School for Physical and Chemical Sciences, North-West University (Potchefstroom Campus), Potchefstroom, South Africa
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Hakeem KR, Chandna R, Ahmad P, Iqbal M, Ozturk M. Relevance of Proteomic Investigations in Plant Abiotic Stress Physiology. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2012; 16:621-35. [DOI: 10.1089/omi.2012.0041] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Khalid Rehman Hakeem
- Molecular Ecology Laboratory, Department of Botany, Jamia Hamdard, New Delhi, India
| | - Ruby Chandna
- Molecular Ecology Laboratory, Department of Botany, Jamia Hamdard, New Delhi, India
| | - Parvaiz Ahmad
- Department of Botany, Amar Singh College, University of Kashmir, Srinagar, India
| | - Muhammad Iqbal
- Molecular Ecology Laboratory, Department of Botany, Jamia Hamdard, New Delhi, India
| | - Munir Ozturk
- Department of Botany, Ege University, Bornova, Izmir, Turkey
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