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Yang J, Ouyang L, Chen S, Zhang C, Zheng J, He S. Amendments affect the community assembly and co-occurrence network of microorganisms in Cd and Pb tailings of the Eucalyptus camaldulensis rhizosphere. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172365. [PMID: 38641118 DOI: 10.1016/j.scitotenv.2024.172365] [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: 12/03/2023] [Revised: 04/08/2024] [Accepted: 04/08/2024] [Indexed: 04/21/2024]
Abstract
Mining tailings containing large amounts of Pb and Cd cause severe regional ecosystem pollution. Soil microorganisms play a regulatory role in the restoration of degraded ecosystems. The remediation of heavy metal-contaminated tailings with amendments and economically valuable Eucalyptus camaldulensis is a research hotspot due to its cost-effectiveness and sustainability. However, the succession and co-occurrence patterns of these microbial communities in this context remain unclear. Tailing samples of five kinds of Cd and Pb were collected in E. camaldulensis restoration models. Physicochemical properties, the proportions of different Cd and Pb forms, microbial community structure, and the co-occurrence network of rhizosphere tailings during different restoration process (organic bacterial manure, organic manure, inorganic fertilizer, bacterial agent) were considered. Organic and organic bacterial manures significantly increased pH, cation exchange capacity, and the proportion of residual Pb. Still, there was a significant decrease in the proportion of reducible Pb. The changes in microbial communities were related to physicochemical properties and the types of amendments. Organic and organic bacterium manures decreased the relative abundance of oligotrophic groups and increased the relative abundance of syntrophic groups. Inorganic fertilizers and bacterial agents decreased the relative abundance of saprophytic fungi. B. subtilis would play a better role in the environment improved by organic manure, increasing the relative abundance of beneficial microorganism and reducing the relative abundance of pathogenic microorganism. pH, cation exchange capacity, and the proportion of different forms of Pb were the main factors affecting the bacterial and fungi variation. All four amendments transformed the main critical groups of the microbial network structure from acidophilus and pathogenic microorganisms to beneficial microorganisms. Heavy metal-resistant microorganisms, stress-resistant microorganisms, beneficial microorganisms that promote nutrient cycling, and copiotrophic groups have become critical to building stable rhizosphere microbial communities. The topological properties and stability of the rhizosphere co-occurrence network were also enhanced. Adding organic and organic bacterium manures combined with E. camaldulensis to repair Cd and Pb tailings improved (1) pH and cation exchange capacity, (2) reduced the biological toxicity of Pb, (3) enhanced the stability of microbial networks, and (4) improved ecological network relationships. These positive changes are conducive to the restoration of the ecological functions of tailings.
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Affiliation(s)
- Jiaqi Yang
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, State Key Laboratory of Efficient Production of Forest Resources, Zhanjiang 524022, China
| | - Linnan Ouyang
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, State Key Laboratory of Efficient Production of Forest Resources, Zhanjiang 524022, China.
| | - Shaoxiong Chen
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, State Key Laboratory of Efficient Production of Forest Resources, Zhanjiang 524022, China
| | - Cheng Zhang
- Experimental Forest Farm of Qingyuan County,Qingyuan 323800, China
| | - Jiaqi Zheng
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, State Key Laboratory of Efficient Production of Forest Resources, Zhanjiang 524022, China
| | - Shae He
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, State Key Laboratory of Efficient Production of Forest Resources, Zhanjiang 524022, China
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Mohan I, Joshi B, Pathania D, Dhar S, Bhau BS. Phytobial remediation advances and application of omics and artificial intelligence: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:37988-38021. [PMID: 38780844 DOI: 10.1007/s11356-024-33690-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 05/11/2024] [Indexed: 05/25/2024]
Abstract
Industrialization and urbanization increased the use of chemicals in agriculture, vehicular emissions, etc., and spoiled all environmental sectors. It causes various problems among living beings at multiple levels and concentrations. Phytoremediation and microbial association are emerging as a potential method for removing heavy metals and other contaminants from soil. The treatment uses plant physiology and metabolism to remove or clean up various soil contaminants efficiently. In recent years, omics and artificial intelligence have been seen as powerful techniques for phytobial remediation. Recently, AI and modeling are used to analyze large data generated by omics technologies. Machine learning algorithms can be used to develop predictive models that can help guide the selection of the most appropriate plant and plant growth-promoting rhizobacteria combination that is most effective at remediation. In this review, emphasis is given to the phytoremediation techniques being explored worldwide in soil contamination.
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Affiliation(s)
- Indica Mohan
- Department of Environmental Sciences, Central University of Jammu, Rahya-Suchani, Bagla, District Samba, Jammu and Kashmir, 181143, India
- Department of Botany, Central University of Jammu, Rahya-Suchani, Bagla, District Samba, Jammu and Kashmir, 181143, India
| | - Babita Joshi
- Plant Molecular Genetics Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, U.P., 226001, India
| | - Deepak Pathania
- Department of Environmental Sciences, Central University of Jammu, Rahya-Suchani, Bagla, District Samba, Jammu and Kashmir, 181143, India
- Department of Botany, Central University of Jammu, Rahya-Suchani, Bagla, District Samba, Jammu and Kashmir, 181143, India
| | - Sunil Dhar
- Department of Environmental Sciences, Central University of Jammu, Rahya-Suchani, Bagla, District Samba, Jammu and Kashmir, 181143, India
- Department of Botany, Central University of Jammu, Rahya-Suchani, Bagla, District Samba, Jammu and Kashmir, 181143, India
| | - Brijmohan Singh Bhau
- Department of Botany, Central University of Jammu, Rahya-Suchani, Bagla, District Samba, Jammu and Kashmir, 181143, India.
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Al-Obaidi JR, Jamaludin AA, Rahman NA, Ahmad-Kamil EI. How plants respond to heavy metal contamination: a narrative review of proteomic studies and phytoremediation applications. PLANTA 2024; 259:103. [PMID: 38551683 DOI: 10.1007/s00425-024-04378-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 03/07/2024] [Indexed: 04/02/2024]
Abstract
MAIN CONCLUSION Heavy metal pollution caused by human activities is a serious threat to the environment and human health. Plants have evolved sophisticated defence systems to deal with heavy metal stress, with proteins and enzymes serving as critical intercepting agents for heavy metal toxicity reduction. Proteomics continues to be effective in identifying markers associated with stress response and metabolic processes. This review explores the complex interactions between heavy metal pollution and plant physiology, with an emphasis on proteomic and biotechnological perspectives. Over the last century, accelerated industrialization, agriculture activities, energy production, and urbanization have established a constant need for natural resources, resulting in environmental degradation. The widespread buildup of heavy metals in ecosystems as a result of human activity is especially concerning. Although some heavy metals are required by organisms in trace amounts, high concentrations pose serious risks to the ecosystem and human health. As immobile organisms, plants are directly exposed to heavy metal contamination, prompting the development of robust defence mechanisms. Proteomics has been used to understand how plants react to heavy metal stress. The development of proteomic techniques offers promising opportunities to improve plant tolerance to toxicity from heavy metals. Additionally, there is substantial scope for phytoremediation, a sustainable method that uses plants to extract, sequester, or eliminate contaminants in the context of changes in protein expression and total protein behaviour. Changes in proteins and enzymatic activities have been highlighted to illuminate the complex effects of heavy metal pollution on plant metabolism, and how proteomic research has revealed the plant's ability to mitigate heavy metal toxicity by intercepting vital nutrients, organic substances, and/or microorganisms.
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Affiliation(s)
- Jameel R Al-Obaidi
- Department of Biology, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, 35900, Tanjong Malim, Perak, Malaysia.
- Applied Science Research Center, Applied Science Private University, Amman, Jordan.
| | - Azi Azeyanty Jamaludin
- Department of Biology, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, 35900, Tanjong Malim, Perak, Malaysia
- Center of Biodiversity and Conservation, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, 35900, Tanjong Malim, Perak, Malaysia
| | - Norafizah Abdul Rahman
- Gene Marker Laboratory, Faculty of Agriculture and Life Sciences (AGLS), Science South Building, Lincoln University, Lincoln, 7608, Canterbury, New Zealand
| | - E I Ahmad-Kamil
- Malaysian Nature Society (MNS), JKR 641, Jalan Kelantan, Bukit Persekutuan, 50480, Kuala Lumpur, Malaysia.
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Raza A, Salehi H, Bashir S, Tabassum J, Jamla M, Charagh S, Barmukh R, Mir RA, Bhat BA, Javed MA, Guan DX, Mir RR, Siddique KHM, Varshney RK. Transcriptomics, proteomics, and metabolomics interventions prompt crop improvement against metal(loid) toxicity. PLANT CELL REPORTS 2024; 43:80. [PMID: 38411713 PMCID: PMC10899315 DOI: 10.1007/s00299-024-03153-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/05/2024] [Indexed: 02/28/2024]
Abstract
The escalating challenges posed by metal(loid) toxicity in agricultural ecosystems, exacerbated by rapid climate change and anthropogenic pressures, demand urgent attention. Soil contamination is a critical issue because it significantly impacts crop productivity. The widespread threat of metal(loid) toxicity can jeopardize global food security due to contaminated food supplies and pose environmental risks, contributing to soil and water pollution and thus impacting the whole ecosystem. In this context, plants have evolved complex mechanisms to combat metal(loid) stress. Amid the array of innovative approaches, omics, notably transcriptomics, proteomics, and metabolomics, have emerged as transformative tools, shedding light on the genes, proteins, and key metabolites involved in metal(loid) stress responses and tolerance mechanisms. These identified candidates hold promise for developing high-yielding crops with desirable agronomic traits. Computational biology tools like bioinformatics, biological databases, and analytical pipelines support these omics approaches by harnessing diverse information and facilitating the mapping of genotype-to-phenotype relationships under stress conditions. This review explores: (1) the multifaceted strategies that plants use to adapt to metal(loid) toxicity in their environment; (2) the latest findings in metal(loid)-mediated transcriptomics, proteomics, and metabolomics studies across various plant species; (3) the integration of omics data with artificial intelligence and high-throughput phenotyping; (4) the latest bioinformatics databases, tools and pipelines for single and/or multi-omics data integration; (5) the latest insights into stress adaptations and tolerance mechanisms for future outlooks; and (6) the capacity of omics advances for creating sustainable and resilient crop plants that can thrive in metal(loid)-contaminated environments.
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Affiliation(s)
- Ali Raza
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Hajar Salehi
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
| | - Shanza Bashir
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology, Islamabad, Pakistan
| | - Javaria Tabassum
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Monica Jamla
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Sidra Charagh
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Hangzhou, China
| | - Rutwik Barmukh
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
| | - Rakeeb Ahmad Mir
- Department of Biotechnology, School of Life Sciences, Central University of Kashmir, Ganderbal, India
| | - Basharat Ahmad Bhat
- Department of Bio-Resources, Amar Singh College Campus, Cluster University Srinagar, Srinagar, JK, India
| | - Muhammad Arshad Javed
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Dong-Xing Guan
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST), Srinagar, Kashmir, India
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia.
| | - Rajeev K Varshney
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
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Sanjana S, Jazeel K, Janeeshma E, Nair SG, Shackira AM. Synergistic interactions of assorted ameliorating agents to enhance the potential of heavy metal phytoremediation. STRESS BIOLOGY 2024; 4:13. [PMID: 38363436 PMCID: PMC10873264 DOI: 10.1007/s44154-024-00153-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/29/2024] [Indexed: 02/17/2024]
Abstract
Pollution by toxic heavy metals creates a significant impact on the biotic community of the ecosystem. Nowadays, a solution to this problem is an eco-friendly approach like phytoremediation, in which plants are used to ameliorate heavy metals. In addition, various amendments are used to enhance the potential of heavy metal phytoremediation. Symbiotic microorganisms such as phosphate-solubilizing bacteria (PSB), endophytes, mycorrhiza and plant growth-promoting rhizobacteria (PGPR) play a significant role in the improvement of heavy metal phytoremediation potential along with promoting the growth of plants that are grown in contaminated environments. Various chemical chelators (Indole 3-acetic acid, ethylene diamine tetra acetic acid, ethylene glycol tetra acetic acid, ethylenediamine-N, N-disuccinic acid and nitrilotri-acetic acid) and their combined action with other agents also contribute to heavy metal phytoremediation enhancement. With modern techniques, transgenic plants and microorganisms are developed to open up an alternative strategy for phytoremediation. Genomics, proteomics, transcriptomics and metabolomics are widely used novel approaches to develop competent phytoremediators. This review accounts for the synergistic interactions of the ameliorating agent's role in enhancing heavy metal phytoremediation, intending to highlight the importance of these various approaches in reducing heavy metal pollution.
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Affiliation(s)
- S Sanjana
- Department of Botany, Sir Syed College, Kannur University, Kerala, 670142, India
| | - K Jazeel
- Department of Botany, Sir Syed College, Kannur University, Kerala, 670142, India
| | - E Janeeshma
- Department of Botany, MES KEVEEYAM College, Valanchery, Malappuram, Kerala, India
| | - Sarath G Nair
- Department of Botany, Mar Athanasius College, Mahatma Gandhi University, Kottayam, Kerala, India
| | - A M Shackira
- Department of Botany, Sir Syed College, Kannur University, Kerala, 670142, India.
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Zhu FY, Chen X, Song YC, Lam LPY, Tobimatsu Y, Gao B, Chen MX, Cao FL. SWATH-MS-based proteogenomic analysis reveals the involvement of alternative splicing in poplar upon lead stress. Genome Res 2023; 33:371-385. [PMID: 36963844 PMCID: PMC10078296 DOI: 10.1101/gr.277473.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/22/2023] [Indexed: 03/26/2023]
Abstract
Alternative splicing (AS) regulates gene expression and increases proteomic diversity for the fine tuning of stress responses in plants, but the exact mechanism through which AS functions in plant stress responses is not thoroughly understood. Here, we investigated how AS functions in poplar (Populus trichocarpa), a popular plant for bioremediation, in response to lead (Pb) stress. Using a proteogenomic analysis, we determine that Pb stress induced alterations in AS patterns that are characterized by an increased use of nonconventional splice sites and a higher abundance of Pb-responsive splicing factors (SFs) associated with Pb-responsive transcription factors. A strong Pb(II)-inducible chaperone protein, PtHSP70, that undergoes AS was further characterized. Overexpression of its two spliced isoforms, PtHSP70-AS1 and PtHSP70-AS2, in poplar and Arabidopsis significantly enhances the tolerance to Pb. Further characterization shows that both isoforms can directly bind to Pb(II), and PtHSP70-AS2 exhibits 10-fold higher binding capacities and a greater increase in expression under Pb stress, thereby reducing cellular toxicity through Pb(II) extrusion and conferring Pb tolerance. AS of PtHSP70 is found to be regulated by PtU1-70K, a Pb(II)-inducible core SF involved in 5'-splice site recognition. Because the same splicing pattern is also found in HSP70 orthologs in other plant species, AS of HSP70 may be a common regulatory mechanism to cope with Pb(II) toxicity. Overall, we have revealed a novel post-transcriptional machinery that mediates heavy metal tolerance in diverse plant species. Our findings offer new molecular targets and bioengineering strategies for phytoremediation and provide new insight for future directions in AS research.
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Affiliation(s)
- Fu-Yuan Zhu
- The Southern Modern Forestry Collaborative Innovation Center, State Key Laboratory of Tree Genetics and Breeding, the Key Lab of Tree Genetics and Biotechnology of Educational Department of China and the Key Lab of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Xin Chen
- The Southern Modern Forestry Collaborative Innovation Center, State Key Laboratory of Tree Genetics and Breeding, the Key Lab of Tree Genetics and Biotechnology of Educational Department of China and the Key Lab of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Yu-Chen Song
- The Southern Modern Forestry Collaborative Innovation Center, State Key Laboratory of Tree Genetics and Breeding, the Key Lab of Tree Genetics and Biotechnology of Educational Department of China and the Key Lab of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Lydia Pui Ying Lam
- Center for Crossover Education, Graduate School of Engineering Science, Akita University, Akita City 010-8502, Akita, Japan
| | - Yuki Tobimatsu
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Bei Gao
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi, Xinjiang 830054, China
| | - Mo-Xian Chen
- The Southern Modern Forestry Collaborative Innovation Center, State Key Laboratory of Tree Genetics and Breeding, the Key Lab of Tree Genetics and Biotechnology of Educational Department of China and the Key Lab of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China;
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Fu-Liang Cao
- The Southern Modern Forestry Collaborative Innovation Center, State Key Laboratory of Tree Genetics and Breeding, the Key Lab of Tree Genetics and Biotechnology of Educational Department of China and the Key Lab of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China;
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
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Yao X, Liang X, Chen Q, Liu Y, Wu C, Wu M, Shui J, Qiao Y, Zhang Y, Geng Y. MePAL6 regulates lignin accumulation to shape cassava resistance against two-spotted spider mite. FRONTIERS IN PLANT SCIENCE 2023; 13:1067695. [PMID: 36684737 PMCID: PMC9853075 DOI: 10.3389/fpls.2022.1067695] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION The two-spotted spider mite (TSSM) is a devastating pest of cassava production in China. Lignin is considered as an important defensive barrier against pests and diseases, several genes participate in lignin biosynthesis, however, how these genes modulate lignin accumulation in cassava and shape TSSM-resistance is largely unknown. METHODS To fill this knowledge gap, while under TSSM infestation, the cassava lignin biosynthesis related genes were subjected to expression pattern analysis followed by family identification, and genes with significant induction were used for further function exploration. RESULTS Most genes involved in lignin biosynthesis were up-regulated when the mite-resistant cassava cultivars were infested by TSSM, noticeably, the MePAL gene presented the most vigorous induction among these genes. Therefore, we paid more attention to dissect the function of MePAL gene during cassava-TSSM interaction. Gene family identification showed that there are 6 MePAL members identified in cassava genome, further phylogenetic analysis, gene duplication, cis-elements and conserved motif prediction speculated that these genes may probably contribute to biotic stress responses in cassava. The transcription profile of the 6 MePAL genes in TSSM-resistant cassava cultivar SC9 indicated a universal up-regulation pattern. To further elucidate the potential correlation between MePAL expression and TSSM-resistance, the most strongly induced gene MePAL6 were silenced using virus-induced gene silencing (VIGS) assay, we found that silencing of MePAL6 in SC9 not only simultaneously suppressed the expression of other lignin biosynthesis genes such as 4-coumarate--CoA ligase (4CL), hydroxycinnamoyltransferase (HCT) and cinnamoyl-CoA reductase (CCR), but also resulted in decrease of lignin content. Ultimately, the suppression of MePAL6 in SC9 can lead to significant deterioration of TSSM-resistance. DISCUSSION This study accurately identified MePAL6 as critical genes in conferring cassava resistance to TSSM, which could be considered as promising marker gene for evaluating cassava resistance to insect pest.
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Affiliation(s)
- Xiaowen Yao
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, China
- Sanya Research Academy, Chinese Academy of Tropical Agriculture Science/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Xiao Liang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, China
- Sanya Research Academy, Chinese Academy of Tropical Agriculture Science/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Qing Chen
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, China
- Sanya Research Academy, Chinese Academy of Tropical Agriculture Science/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Ying Liu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, China
- Sanya Research Academy, Chinese Academy of Tropical Agriculture Science/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Chunling Wu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, China
- Sanya Research Academy, Chinese Academy of Tropical Agriculture Science/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Mufeng Wu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, China
- Sanya Research Academy, Chinese Academy of Tropical Agriculture Science/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Jun Shui
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, China
- Sanya Research Academy, Chinese Academy of Tropical Agriculture Science/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Yang Qiao
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, China
- Sanya Research Academy, Chinese Academy of Tropical Agriculture Science/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Yao Zhang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, China
- Sanya Research Academy, Chinese Academy of Tropical Agriculture Science/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Yue Geng
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, China
- Sanya Research Academy, Chinese Academy of Tropical Agriculture Science/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
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Shi W, Li J, Kan D, Yu W, Chen X, Zhang Y, Ma C, Deng S, Zhou J, Fayyaz P, Luo ZB. Sulfur metabolism, organic acid accumulation and phytohormone regulation are crucial physiological processes modulating the different tolerance to Pb stress of two contrasting poplars. TREE PHYSIOLOGY 2022; 42:1799-1811. [PMID: 35313352 DOI: 10.1093/treephys/tpac033] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
To investigate the pivotal physiological processes modulating lead (Pb) tolerance capacities of poplars, the saplings of two contrasting poplar species, Populus × canescens with high Pb sensitivity and Populus nigra with relatively low Pb sensitivity, were treated with either 0 or 8 mM Pb for 6 weeks. Lead was absorbed by the roots and accumulated massively in the roots and leaves, leading to overproduction of reactive oxygen species, reduced photosynthesis and biomass in both poplar species. Particularly, the tolerance index of P. × canescens was significantly lower than that of P. nigra. Moreover, the physiological responses including the concentrations of nutrient elements, thiols, organic acids, phytohormones and nonenzymatic antioxidants, and the activities of antioxidative enzymes in the roots and leaves were different between the two poplar species. Notably, the differences in concentrations of nutrient elements, organic acids and phytohormones were remarkable between the two poplar species. A further evaluation of the Pb tolerance-related physiological processes showed that the change of 'sulfur (S) metabolism' in the roots was greater, and that of 'organic acid accumulation' in the roots and 'phytohormone regulation' in the leaves were markedly smaller in P. × canescens than those in P. nigra. These results suggest that there are differences in Pb tolerance capacities between P. × canescens and P. nigra, which is probably associated with their contrasting physiological responses to Pb stress, and that S metabolism, organic acid accumulation and phytohormone regulation are probably the key physiological processes modulating the different Pb tolerance capacities between the two poplar species.
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Affiliation(s)
- Wenguang Shi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Xiangshan road, Haidian district, Beijing 100091, China
| | - Jing Li
- Department of Food Science and Technology, College of Light Industry and Food Engineering, Nanjing Forestry University, Longpan road, Xuanwu district, Nanjing 210037, China
| | - Donxu Kan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Xiangshan road, Haidian district, Beijing 100091, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Hexing road, Xiangfang district, Harbin 150040, China
| | - Wenjian Yu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Xiangshan road, Haidian district, Beijing 100091, China
| | - Xin Chen
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Xiangshan road, Haidian district, Beijing 100091, China
| | - Yuhong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Xiangshan road, Haidian district, Beijing 100091, China
| | - Chaofeng Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Xiangshan road, Haidian district, Beijing 100091, China
| | - Shurong Deng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Xiangshan road, Haidian district, Beijing 100091, China
| | - Jing Zhou
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Xiangshan road, Haidian district, Beijing 100091, China
| | - Payam Fayyaz
- Forest, Range and Watershed Management Department, Agriculture and Natural Resources Faculty, Yasouj University, Daneshjoo St, Yasuj 75919-63179, Iran
| | - Zhi-Bin Luo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Xiangshan road, Haidian district, Beijing 100091, China
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Huang BX, Jia ZC, Yang X, Cheng CL, Liu XR, Zhang J, Chen MX, Yang JF, Chen YS. Genome-wide comparison and in silico analysis of splicing factor SYF2/NTC31/p29 in eukaryotes: Special focus on vertebrates. Front Genet 2022; 13:873869. [PMID: 36118875 PMCID: PMC9479762 DOI: 10.3389/fgene.2022.873869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/18/2022] [Indexed: 11/20/2022] Open
Abstract
The gene SYF2—an RNA splicing factor—can interact with Cyclin D-type binding protein 1 (GICP) in many biological processes, including splicing regulation, cell cycle regulation, and DNA damage repair. In our previous study we performed genome-wide identification and functional analysis of SYF2 in plant species. The phylogenetic relationships and expression profiles of SYF2 have not been systematically studied in animals, however. To this end, the gene structure, genes, and protein conserved motifs of 102 SYF2 homologous genes from 91 different animal species were systematically analyzed, along with conserved splicing sites in 45 representative vertebrate species. A differential comparative analysis of expression patterns in humans and mice was made. Molecular bioinformatics analysis of SYF2 showed the gene was conserved and functional in different animal species. In addition, expression pattern analysis found that SYF2 was highly expressed in hematopoietic stem cells, T cells, and lymphoid progenitor cells; in ovary, lung, and spleen; and in other cells and organs. This suggests that changes in SYF2 expression may be associated with disease development in these cells, tissues, or organs. In conclusion, our study analyzes the SYF2 disease resistance genes of different animal species through bioinformatics, reveals the relationship between the SYF2 genotype and the occurrence of certain diseases, and provides a theoretical basis for follow-up study of the relationship between the SYF2 gene and animal diseases.
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Affiliation(s)
- Bao-Xing Huang
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, China
| | - Zi-Chang Jia
- Co-Innovation Center for Sustainable Forestry in Southern China and Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Xue Yang
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Chao-Lin Cheng
- Department of Biology, Hong Kong Baptist University, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Xiao-Rong Liu
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Mo-Xian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China and Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Jing-Fang Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Jing-Fang Yang, ; Yun-Sheng Chen,
| | - Yun-Sheng Chen
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, China
- *Correspondence: Jing-Fang Yang, ; Yun-Sheng Chen,
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10
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Ye M, Jiang Z, Wang Z, Wang Y, Fang S, Sun Y, Guan H, Sun D, Ma X, Zhang C, Ge Y. Physiological and proteomic responses of Chlamydomonas reinhardtii to arsenate and lead mixtures. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 242:113856. [PMID: 35809392 DOI: 10.1016/j.ecoenv.2022.113856] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/22/2022] [Accepted: 07/02/2022] [Indexed: 06/15/2023]
Abstract
Arsenic (As) and lead (Pb) are frequently emitted from various sources into environment, but microbial responses to their combined toxicity have not been systematically investigated. In this study, Chlamydomonas reinhardtii was exposed to two levels of arsenate (As (V), 50, 500 μg/L), Pb (II) (500, 5000 μg/L) and their mixture (50 μg/L As (V) + 500 μg/L Pb (II); 500 μg/L As (V) + 5000 μg/L Pb (II)). The growth of C. reinhardtii was inhibited more remarkably by As (V) than by Pb (II). The As stress was alleviated by Pb in the 50 μg/L As (V) + 500 μg/L Pb (II) treatment, but was enhanced upon the 500 μg/L As (V) + 5000 μg/L Pb (II) exposure, with more pronounced changes in a number of physiological parameters of the algal cells. Proteomic results showed that 71 differently expressed proteins (DEPs) in the treatment of 50 μg/L As (V) + 500 μg/L Pb (II), and 167 DEPs were identified in that of 500 μg/L As (V) + 5000 μg/L Pb (II). These proteins were involved in energy metabolism, photosynthetic carbon fixation, reactive oxygen scavenging and defense, and amino acid synthesis. Taken together, these physiological and proteomic data demonstrated that C. reinhardtii could resist the As (V) and Pb (II) combined treatments through extracellular complexation and intracellular pathways.
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Affiliation(s)
- Menglei Ye
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Zhongquan Jiang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Zhongyang Wang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yanyan Wang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Shu Fang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yutong Sun
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Huize Guan
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Danqing Sun
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xuening Ma
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Chunhua Zhang
- Demonstration Laboratory of Element and Life Science Research, Laboratory Centre of Life Science, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Ge
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
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11
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Fu CC, Xu FY, Qian YC, Koo HL, Duan YF, Weng GM, Fan TP, Chen MX, Zhu FY. Secondary Metabolites of Osmanthus fragrans: Metabolism and Medicinal Value. Front Pharmacol 2022; 13:922204. [PMID: 35924042 PMCID: PMC9340074 DOI: 10.3389/fphar.2022.922204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 06/20/2022] [Indexed: 11/19/2022] Open
Abstract
Osmanthus fragrans (scientific name: Osmanthus fragrans (Thunb.) Lour.) is a species of the Osmanthus genus in the family Oleaceae, and it has a long history of cultivation in China. O. fragrans is edible and is well known for conferring a natural fragrance to desserts. This flowering plant has long been cultivated for ornamental purposes. Most contemporary literature related to O. fragrans focuses on its edible value and new species discovery, but the functional use of O. fragrans is often neglected. O, fragrans has many properties that are beneficial to human health, and its roots, stems, leaves, flowers and fruits have medicinal value. These characteristics are recorded in the classics of traditional Chinese medicine. Studies on the metabolites and medicinal value of O. fragrans published in recent years were used in this study to evaluate the medicinal value of O. fragrans. Using keywords such as metabolites and Osmanthus fragrans, a systematic and nonexhaustive search of articles, papers and books related to the medicinal use of Osmanthus fragrans metabolites was conducted. Fifteen metabolites were identified through this literature search and classified into three categories according to their properties and structure: flavonoids, terpenes and phenolic acids. It was found that the pharmacological activities of these secondary metabolites mainly include antioxidant, anticancer, anti-inflammatory and antibacterial activities and that these metabolites can be used to treat many human diseases, such as cancer, skin diseases, cardiovascular diseases, and neurological diseases. Most of the reports that are currently available and concern the secondary metabolites of Osmanthus fragrans have limitations. Some reports introduce only the general classification of compounds in Osmanthus fragrans, and some reports introduce only a single compound. In contrast, the introduction section of this paper includes both the category and the functional value of each compound. While reviewing the data for this study, the authors found that the specific action sites of these compounds and their mechanisms of action in plants are relatively weak, and in the future, additional research should be conducted to investigate this topic further.
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Affiliation(s)
- Chen-Chen Fu
- Co-Innovation Center for Sustainable Forestry in Southern China and Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Fa-Ying Xu
- Department of Chinese Medicine, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Yu-Chen Qian
- Co-Innovation Center for Sustainable Forestry in Southern China and Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Hoi-Lun Koo
- RCI Research Institute Limited, Hong Kong, China
| | - Yi-Fan Duan
- Co-Innovation Center for Sustainable Forestry in Southern China and Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Geng-Min Weng
- Department of Chinese Medicine, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Tai-Ping Fan
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Mo-Xian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China and Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- *Correspondence: Mo-Xian Chen, ; Fu-Yuan Zhu,
| | - Fu-Yuan Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China and Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- *Correspondence: Mo-Xian Chen, ; Fu-Yuan Zhu,
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Wheat Proteomics for Abiotic Stress Tolerance and Root System Architecture: Current Status and Future Prospects. Proteomes 2022; 10:proteomes10020017. [PMID: 35645375 PMCID: PMC9150004 DOI: 10.3390/proteomes10020017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/03/2022] [Accepted: 05/11/2022] [Indexed: 02/06/2023] Open
Abstract
Wheat is an important staple cereal for global food security. However, climate change is hampering wheat production due to abiotic stresses, such as heat, salinity, and drought. Besides shoot architectural traits, improving root system architecture (RSA) traits have the potential to improve yields under normal and stressed environments. RSA growth and development and other stress responses involve the expression of proteins encoded by the trait controlling gene/genes. Hence, mining the key proteins associated with abiotic stress responses and RSA is important for improving sustainable yields in wheat. Proteomic studies in wheat started in the early 21st century using the two-dimensional (2-DE) gel technique and have extensively improved over time with advancements in mass spectrometry. The availability of the wheat reference genome has allowed the exploration of proteomics to identify differentially expressed or abundant proteins (DEPs or DAPs) for abiotic stress tolerance and RSA improvement. Proteomics contributed significantly to identifying key proteins imparting abiotic stress tolerance, primarily related to photosynthesis, protein synthesis, carbon metabolism, redox homeostasis, defense response, energy metabolism and signal transduction. However, the use of proteomics to improve RSA traits in wheat is in its infancy. Proteins related to cell wall biogenesis, carbohydrate metabolism, brassinosteroid biosynthesis, and transportation are involved in the growth and development of several RSA traits. This review covers advances in quantification techniques of proteomics, progress in identifying DEPs and/or DAPs for heat, salinity, and drought stresses, and RSA traits, and the limitations and future directions for harnessing proteomics in wheat improvement.
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Emerging Function of Ecotype-Specific Splicing in the Recruitment of Commensal Microbiome. Int J Mol Sci 2022; 23:ijms23094860. [PMID: 35563250 PMCID: PMC9100151 DOI: 10.3390/ijms23094860] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 04/15/2022] [Accepted: 04/25/2022] [Indexed: 12/20/2022] Open
Abstract
In recent years, host-microbiome interactions in both animals and plants has emerged as a novel research area for studying the relationship between host organisms and their commensal microbial communities. The fitness advantages of this mutualistic interaction can be found in both plant hosts and their associated microbiome, however, the driving forces mediating this beneficial interaction are poorly understood. Alternative splicing (AS), a pivotal post-transcriptional mechanism, has been demonstrated to play a crucial role in plant development and stress responses among diverse plant ecotypes. This natural variation of plants also has an impact on their commensal microbiome. In this article, we review the current progress of plant natural variation on their microbiome community, and discuss knowledge gaps between AS regulation of plants in response to their intimately related microbiota. Through the impact of this article, an avenue could be established to study the biological mechanism of naturally varied splicing isoforms on plant-associated microbiome assembly.
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The Importance of a Genome-Wide Association Analysis in the Study of Alternative Splicing Mutations in Plants with a Special Focus on Maize. Int J Mol Sci 2022; 23:ijms23084201. [PMID: 35457019 PMCID: PMC9024592 DOI: 10.3390/ijms23084201] [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: 03/09/2022] [Revised: 04/03/2022] [Accepted: 04/08/2022] [Indexed: 02/01/2023] Open
Abstract
Alternative splicing is an important mechanism for regulating gene expressions at the post-transcriptional level. In eukaryotes, the genes are transcribed in the nucleus to produce pre-mRNAs and alternative splicing can splice a pre-mRNA to eventually form multiple different mature mRNAs, greatly increasing the number of genes and protein diversity. Alternative splicing is involved in the regulation of various plant life activities, especially the response of plants to abiotic stresses and is also an important process of plant growth and development. This review aims to clarify the usefulness of a genome-wide association analysis in the study of alternatively spliced variants by summarizing the application of alternative splicing, genome-wide association analyses and genome-wide association analyses in alternative splicing, as well as summarizing the related research progress.
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15
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Identifying QTLs for Grain Size in a Colossal Grain Rice ( Oryza sativa L.) Line, and Analysis of Additive Effects of QTLs. Int J Mol Sci 2022; 23:ijms23073526. [PMID: 35408887 PMCID: PMC8998697 DOI: 10.3390/ijms23073526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/21/2022] [Accepted: 03/21/2022] [Indexed: 02/01/2023] Open
Abstract
Grain size is an important component of quality and harvest traits in the field of rice breeding. Although numerous quantitative trait loci (QTLs) of grain size in rice have been reported, the molecular mechanisms of these QTLs remain poorly understood, and further research on QTL observation and candidate gene identification is warranted. In our research, we developed a suite of F2 intercross populations from a cross of 9311 and CG. These primary populations were used to map QTLs conferring grain size, evaluated across three environments, and then subjected to bulked-segregant analysis-seq (BSA-seq). In total, 4, 11, 12 and 14 QTLs for grain length (GL), grain width (GW), 1000-grain weight (TGW), and length/width ratio (LWR), respectively, were detected on the basis of a single-environment analysis. In particular, over 200 splicing-related sites were identified by whole-genome sequencing, including one splicing-site mutation with G>A at the beginning of intron 4 on Os03g0841800 (qGL3.3), producing a smaller open reading frame, without the third and fourth exons. A previous study revealed that the loss-of-function allele caused by this splicing site can negatively regulate rice grain length. Furthermore, qTGW2.1 and qGW2.3 were new QTLs for grain width. We used the near-isogenic lines (NILs) of these GW QTLs to study their genetic effects on individuals and pyramiding, and found that they have additive effects on GW. In summary, these discoveries provide a valuable genetic resource, which will facilitate further study of the genetic polymorphism of new rice varieties in rice breeding.
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Debela AS, Dawit M, Tekere M, Itanna F. Phytoremediation of soils contaminated by lead and cadmium in Ethiopia, using Endod ( Phytolacca dodecandra L). INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2022; 24:1339-1349. [PMID: 35060415 DOI: 10.1080/15226514.2021.2025336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Phytoremediation is a cost effective and environmentally sustainable green technology for remediation of metal contaminated sites. In Addis Ababa, the capital of Ethiopia, large vegetable farms are grown on contaminated sites. This study evaluates the potential of Phytolacca dodecandra L to remediate Pb and Cd from contaminated sites in Addis Ababa. Pb and Cd in soil samples and different plant parts were determined using AAS. Phytoremediation potential of P. dodecandra in different seasons was estimated by calculating the Bioconcentration factor (BCF) and translocation factor (TF). The average BCF recorded for plant shoot in dry season samples varied from 0.87 to 1.74 for Pb and 1.06 to 2.00 for Cd, while in wet season it was within the range of 1.1-1.53 for Pb and 0.93-3.89 for Cd. The TF values for P. dodecandra ranged from 0.84 to 3.49 for Pb and 1.81 to 4.11 for Cd in dry season, whereas for wet season it varied between 1.34 and 2.01 for Pb and 1.78 and 2.97 for Cd. Since the mean values of BCF and TF were >1, it was concluded that P. dodecandra has considerable potential for phytoextraction of Pb and Cd in contaminated sites.
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Affiliation(s)
- Alemu Shiferaw Debela
- Department of Environmental Management, Kotebe Metropolitan University, Addis Ababa, Ethiopia
| | - Mekibib Dawit
- Department of Environmental Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Pretoria, South Africa
| | - Memory Tekere
- Department of Environmental Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Pretoria, South Africa
| | - Fisseha Itanna
- Department of Soil Science and Resource Conservation, National University of Lesotho, Maseru, Lesotho
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17
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Lu S, Gao C, Wang Y, He Y, Du J, Chen M, Zhao H, Fang H, Wang B, Cao Y. Phylogenetic Analysis of the Plant U2 snRNP Auxiliary Factor Large Subunit A Gene Family in Response to Developmental Cues and Environmental Stimuli. FRONTIERS IN PLANT SCIENCE 2021; 12:739671. [PMID: 34868124 PMCID: PMC8635922 DOI: 10.3389/fpls.2021.739671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
In all organisms, splicing occurs through the formation of spliceosome complexes, and splicing auxiliary factors are essential during splicing. U2AF65 is a crucial splicing cofactor, and the two typical RNA-recognition motifs at its center recognize and bind the polypyrimidine sequence located between the intron branch site and the 3'-splice site. U2AF65A is a member of the U2AF65 gene family, with pivotal roles in diseases in mammals, specifically humans; however, few studies have investigated plant U2AF65A, and its specific functions are poorly understood. Therefore, in the present study, we systematically identified U2AF65A in plant species from algae to angiosperms. Based on 113 putative U2AF65A sequences from 33 plant species, phylogenetic analyses were performed, followed by basic bioinformatics, including the comparisons of gene structure, protein domains, promoter motifs, and gene expression levels. In addition, using rice as the model crop, we demonstrated that the OsU2AF65A protein is localized to the nucleus and cytoplasm, and it is involved in responses to various stresses, such as drought, high salinity, low temperature, and heavy metal exposure (e.g., cadmium). Using Arabidopsis thaliana and rice mutants, we demonstrated that U2AF65A is involved in the accumulation of plant biomass, growth of hypocotyl upon thermal stimulation, and reduction of tolerance of high temperature stress. These findings offer an overview of the U2AF65 gene family and its stress response functions, serving as the reference for further comprehensive functional studies of the essential specific splicing cofactor U2AF65A in the plant kingdom.
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Affiliation(s)
- Shuai Lu
- School of Life Sciences, Nantong University, Nantong, China
| | - Cong Gao
- School of Life Sciences, Nantong University, Nantong, China
| | - Yongzhou Wang
- School of Life Sciences, Nantong University, Nantong, China
| | - Yingying He
- School of Life Sciences, Nantong University, Nantong, China
| | - Junrong Du
- School of Life Sciences, Nantong University, Nantong, China
| | - Moxian Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hua Zhao
- School of Life Sciences, Nantong University, Nantong, China
| | - Hui Fang
- School of Life Sciences, Nantong University, Nantong, China
| | - Baohua Wang
- School of Life Sciences, Nantong University, Nantong, China
| | - Yunying Cao
- School of Life Sciences, Nantong University, Nantong, China
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Wang L, Wang N, Ji G. Pb contaminated soil influence on aboveground biomass and bioactive compounds in leaves of mulberry. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2021; 24:1100-1106. [PMID: 34787032 DOI: 10.1080/15226514.2021.2002808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
This study investigated the effects of soil lead (Pb), biochar, and partial root zone drought (PRD) on mulberry (Morus alba L.) branches and leaves biomass, Pb accumulation, and bioactive compounds including 1-deoxynojirimycin (DNJ) and flavonoids. Three-factor pot experiments were conducted with biochar, PRD, and soil Pb at four concentration levels (0, 50, 200, and 800 mg kg-1). Results revealed that mulberry aboveground biomass did not decrease significantly across the soil Pb levels. Pb concentration of mulberry leaves do not increase significantly when soil Pb was 200 mg kg-1; however, it significantly accumulated under 800 mg kg-1. There was a dose-effect between the Pb concentration in branches and the soil Pb levels. Mulberry leaf flavonoids were affected by the interaction of soil Pb and biochar. The interaction between two of the three factors significantly affected leaves DNJ concentration. The combination of biochar and PRD maintained the biomass of mulberry and did not significantly increase Pb in leaves under 200 mg kg-1 soil Pb concentration. In summary, mulberry has a higher resistance to soil Pb stress, and it can be planted in moderate Pb-contaminated soils for no loss of biomass and can safely harvest the branches and leaves.Novelty statementAn economic benefit is a key to the practical application and sustainability of phytoremediation. Based on this, we studied the effects of soil Pb on biomass, Pb accumulation, and bioactive substance concentration of harvesting organs in mulberry.Phytoremediation is not isolated, and techniques, such as soil amendments and water management also play a role. In this study, we found that biochar and partial root-zone irrigation had a synergistic effect on the response of mulberry to soil Pb, which could be co-applied in the phytoremediation of lead-contaminated soil.The concentration of heavy metals is the key to ensuring product safety in heavy metal contaminated soil. We found that Pb concentration in leaf and stem of mulberry did not significantly increase under 200 mg kg-1 soil Pb, while increased at 800 mg kg-1 soil Pb. Therefore, planting mulberry on 200 mg kg-1 Pb contaminated soil can safely harvest branches and leaves.
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Affiliation(s)
- Lei Wang
- College of Biotechnology, Jiangsu University of Science and Technology, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Na Wang
- College of Biotechnology, Jiangsu University of Science and Technology, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Gengsheng Ji
- College of Biotechnology, Jiangsu University of Science and Technology, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
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