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Jobby R, Sarkar M, Bose R, Srivastava S, Suprasanna P. Chromiomics: Chromium detoxification and approaches for engineering tolerance in plants. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 350:123991. [PMID: 38631449 DOI: 10.1016/j.envpol.2024.123991] [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: 01/17/2024] [Revised: 04/03/2024] [Accepted: 04/14/2024] [Indexed: 04/19/2024]
Abstract
Chromium (Cr) is a heavy metal that poses a grave threat to the ecosystem including plants. Chromium is very harmful to plants due to its effects on many physiological and metabolic pathways culminating in a negative impact on plant's growth, development, and ability to take up nutrients. Plants have developed physiological, biochemical, and molecular ways of defense against Cr, such as by augmenting antioxidant potential to reduce reactive oxygen species (ROS). A number of genes have been discovered to play a significant role in the defense mechanisms of plants against Cr, for example, genes associated with the activation of phytochelatins, metallothioneins, and those of enzymes like glutathione-S-transferases. Along with this, a few miRNAs have been found to be associated in alleviating Cr stress and, to augment plant tolerance by controlling transcription factors, HSPs, and the expression of a few proteins and hormones. Defense pathway genes and miRNAs have been used for the generation of transgenic phytoremediator plants. Not only do the transgenic plants have a higher tolerance to Cr, but they also act as hyperaccumulators for Cr and have the potential to remediate other heavy metals. This article describes about environmental Cr contamination, Cr effects on plants, different genes and miRNAs involved in Cr stress mitigation and use of candidate genes, microRNAs for creating transgenic plant systems for phytoremediation, and the applications of CRISPR technology. It is expected that the integration of omics approach and advanced genomics will offer scope for more effective phytoremediation of Chromium in the coming years.
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Affiliation(s)
- Renitta Jobby
- Amity Institute of Biotechnology, Amity University, Maharashtra - Pune Expressway, Bhatan, Panvel, Maharashtra 410206, India; Amity Centre of Excellence in Astrobiology, Amity University Maharashtra - Pune Expressway, Bhatan, Panvel, Mumbai, Maharashtra 410206, India
| | - Mrittika Sarkar
- Amity Institute of Biotechnology, Amity University, Maharashtra - Pune Expressway, Bhatan, Panvel, Maharashtra 410206, India
| | - Roshnee Bose
- Amity Institute of Biotechnology, Amity University, Maharashtra - Pune Expressway, Bhatan, Panvel, Maharashtra 410206, India
| | - Sudhakar Srivastava
- Institute of Environment & Sustainable Development, Banaras Hindu University, Varanasi-221005, India
| | - Penna Suprasanna
- Amity Institute of Biotechnology, Amity University, Maharashtra - Pune Expressway, Bhatan, Panvel, Maharashtra 410206, India; Amity Centre for Nuclear Biotechnology, Amity University, Maharashtra - Pune Expressway, Bhatan, Panvel, Maharashtra 410206, India.
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Zaynab M, Sharif Y, Xu Z, Fiaz S, Al-Yahyai R, Yadikar HA, Al Kashgry NAT, Qari SH, Sadder M, Li S. Genome-Wide Analysis and Expression Profiling of DUF668 Genes in Glycine max under Salt Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:2923. [PMID: 37631135 PMCID: PMC10459691 DOI: 10.3390/plants12162923] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023]
Abstract
The DUF668 gene performs a critical role in mitigating the impact of abiotic stress factors. In this study, we identified 30 DUF668 genes in a soybean genome, distributed across fifteen chromosomes. The phylogenetic analysis classified the DUF668 genes into three groups (group I, group II, and group III). Interestingly, gene structure analysis illustrated that several GmDUF668 genes were without introns. Furthermore, the subcellular localization results suggested that GmDUF668 proteins were present in the nucleus, mitochondria, cytoplasm, and plasma membrane. GmDUF668 promoters were analyzed in silico to gain insight into the presence of regulatory sequences for TFs binding. The expression profiling illustrated that GmDUF668 genes showed expression in leaves, roots, nodules, and flowers. To investigate their response to salt stress, we utilized the RNA sequencing data of GmDUF668 genes. The results unveiled that GmDUF668-8, GmDUF668-20, and GmDUF668-30 genes were upregulated against salt stress treatment. We further validated these findings using qRT-PCR analysis. These findings provide a scientific basis to explore the functions of GmDUF668 genes against different stress conditions.
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Affiliation(s)
- Madiha Zaynab
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China;
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Yasir Sharif
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhaoshi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur 22620, Pakistan
| | - Rashid Al-Yahyai
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khod, P.O. Box 34, Muscat 123, Oman
| | - Hamad. A. Yadikar
- Department of Biological Sciences, Faculty of Science, Kuwait University, P.O. Box 5969, Safat 13060, Kuwait
| | - Najla Amin T. Al Kashgry
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Sameer H. Qari
- Department of Biology, Al-Jumum University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Monther Sadder
- School of Agriculture, University of Jordan, Amman 11942, Jordan
| | - Shuangfei Li
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
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Lv J, Zhang R, Li D, Liu Y. Resveratrol plays an anti-fibrotic and anti-autophagy role by stimulating miR-192-5p expression in urethral fibrosis. Funct Integr Genomics 2023; 23:241. [PMID: 37450096 DOI: 10.1007/s10142-023-01173-2] [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: 03/14/2023] [Revised: 06/25/2023] [Accepted: 07/09/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Resveratrol (RSV) exerts anti-fibrotic effects on various fibrotic diseases. Whereas the biological role of RSV on urethral fibrosis remains to be elucidated. This study aimed to determine the mechanisms by which RSV affects urethral fibrosis and autophagy. METHODS Sprague‒Dawley rats and primary fibroblasts were treated with transforming growth factor-β1 (TGFβ1) to generate in vivo and in vitro fibrosis models. Then, those were treated with RSV, and autophagy and fibrosis-related indicators were tested. RESULTS Firstly, we found that RSV reversed the upregulation of indicators related to TGFβ1-induced fibrosis (TGFβ1, α-smooth muscle actin, collagen type I, and collagen type III), autophagy (TFEB and LC3), and TGFβR1/Smad4 pathway, as well as the downregulation of p62 and miR-192-5p expression both in vivo and in vitro. Overexpression of miR-192-5p suppressed the upregulation of fibrosis-related markers expression, as well as TFEB and LC3 expression, induced by TGFβ1, while the expression trend of p62 was the opposite. Inhibiting miR-192-5p reversed the effects of RSV on the model group cells. It was also shown that RSV combined with sh-Smad4 inhibited autophagy more effectively than RSV alone. CONCLUSION These results suggest that RSV inhibits urinary fibrosis and autophagy via the miR-192-5p/TGFβR1/Smad4 pathway. RAV may be a potential drug for alleviating urethral fibrosis.
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Affiliation(s)
- Jin Lv
- Hunan Traditional Chinese Medical College, Zhuzhou, China
| | - Rui Zhang
- Hunan Traditional Chinese Medical College, Zhuzhou, China
| | - DaoYuan Li
- Department of Urology, Hainan Afliated Hospital of Hainan Medical University, Haikou, China
- Department of Urology, Hainan General Hospital, Haikou, China
| | - Yan Liu
- Department of Anesthesiology, Second Xiangya Hospital, Central South University, Changsha, China.
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Raza A, Sharif Y, Chen K, Wang L, Fu H, Zhuang Y, Chitikineni A, Chen H, Zhang C, Varshney RK, Zhuang W. Genome-Wide Characterization of Ascorbate Peroxidase Gene Family in Peanut ( Arachis hypogea L.) Revealed Their Crucial Role in Growth and Multiple Stress Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:962182. [PMID: 36186077 PMCID: PMC9524023 DOI: 10.3389/fpls.2022.962182] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 06/23/2022] [Indexed: 06/16/2023]
Abstract
Ascorbate peroxidase (APX), an important antioxidant enzyme, plays a significant role in ROS scavenging by catalyzing the decrease of hydrogen peroxide under various environmental stresses. Nevertheless, information about the APX gene family and their evolutionary and functional attributes in peanut (Arachis hypogea L.) was not reported. Therefore, a comprehensive genome-wide study was performed to discover the APX genes in cultivated peanut genome. This study identified 166 AhAPX genes in the peanut genome, classified into 11 main groups. The gene duplication analysis showed that AhAPX genes had experienced segmental duplications and purifying selection pressure. Gene structure and motif investigation indicated that most of the AhAPX genes exhibited a comparatively well-preserved exon-intron pattern and motif configuration contained by the identical group. We discovered five phytohormones-, six abiotic stress-, and five growth and development-related cis-elements in the promoter regions of AhAPX. Fourteen putative ah-miRNAs from 12 families were identified, targeting 33 AhAPX genes. Furthermore, we identified 3,257 transcription factors from 38 families (including AP2, ARF, B3, bHLH, bZIP, ERF, MYB, NAC, WRKY, etc.) in 162 AhAPX genes. Gene ontology and KEGG enrichment analysis confirm the role of AhAPX genes in oxidoreductase activity, catalytic activity, cell junction, cellular response to stimulus and detoxification, biosynthesis of metabolites, and phenylpropanoid metabolism. Based on transcriptome datasets, some genes such as AhAPX4/7/17/77/82/86/130/133 and AhAPX160 showed significantly higher expression in diverse tissues/organs, i.e., flower, leaf, stem, roots, peg, testa, and cotyledon. Likewise, only a few genes, including AhAPX4/17/19/55/59/82/101/102/137 and AhAPX140, were significantly upregulated under abiotic (drought and cold), and phytohormones (ethylene, abscisic acid, paclobutrazol, brassinolide, and salicylic acid) treatments. qRT-PCR-based expression profiling presented the parallel expression trends as generated from transcriptome datasets. Our discoveries gave new visions into the evolution of APX genes and provided a base for further functional examinations of the AhAPX genes in peanut breeding programs.
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Affiliation(s)
- Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Plant Genetics and Systems Biology, College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Yasir Sharif
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Kun Chen
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Lihui Wang
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Huiwen Fu
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Yuhui Zhuang
- College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Annapurna Chitikineni
- Murdoch’s Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Hua Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Plant Genetics and Systems Biology, College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Chong Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Plant Genetics and Systems Biology, College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Rajeev K. Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Plant Genetics and Systems Biology, College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- Murdoch’s Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Weijian Zhuang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Plant Genetics and Systems Biology, College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
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Yang X, Patil S, Joshi S, Jamla M, Kumar V. Exploring epitranscriptomics for crop improvement and environmental stress tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 183:56-71. [PMID: 35567875 DOI: 10.1016/j.plaphy.2022.04.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/27/2022] [Accepted: 04/30/2022] [Indexed: 06/15/2023]
Abstract
Climate change and stressful environmental conditions severely hamper crop growth, development and yield. Plants respond to environmental perturbations, through their plasticity provided by key-genes, governed at post-/transcriptional levels. Gene-regulation in plants is a multilevel process controlled by diverse cellular entities that includes transcription factors (TF), epigenetic regulators and non-coding RNAs beside others. There are successful studies confirming the role of epigenetic modifications (DNA-methylation/histone-modifications) in gene expression. Recent years have witnessed emergence of a highly specialized field the "Epitranscriptomics". Epitranscriptomics deals with investigating post-transcriptional RNA chemical-modifications present across the life forms that change structural, functional and biological characters of RNA. However, deeper insights on of epitranscriptomic modifications, with >140 types known so far, are to be understood fully. Researchers have identified epitranscriptome marks (writers, erasers and readers) and mapped the site-specific RNA modifications (m6A, m5C, 3' uridylation, etc.) responsible for fine-tuning gene expression in plants. Simultaneous advancement in sequencing platforms, upgraded bioinformatic tools and pipelines along with conventional labelled techniques have further given a statistical picture of these epitranscriptomic modifications leading to their potential applicability in crop improvement and developing climate-smart crops. We present herein the insights on epitranscriptomic machinery in plants and how epitranscriptome and epitranscriptomic modifications underlying plant growth, development and environmental stress responses/adaptations. Third-generation sequencing technology, advanced bioinformatics tools and databases being used in plant epitranscriptomics are also discussed. Emphasis is given on potential exploration of epitranscriptome engineering for crop-improvement and developing environmental stress tolerant plants covering current status, challenges and future directions.
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Affiliation(s)
- Xiangbo Yang
- College of Agriculture, Jilin Agricultural Science and Technology University, Jilin, 132101, PR China.
| | - Suraj Patil
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Shrushti Joshi
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Monica Jamla
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India.
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