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Yang Y, Ahmed W, Wang G, Ye C, Li S, Zhao M, Zhang J, Wang J, Salmen SH, Wu L, Zhao Z. Transcriptome profiling reveals the impact of various levels of biochar application on the growth of flue-cured tobacco plants. BMC PLANT BIOLOGY 2024; 24:655. [PMID: 38987695 PMCID: PMC11234667 DOI: 10.1186/s12870-024-05321-z] [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: 05/16/2024] [Accepted: 06/21/2024] [Indexed: 07/12/2024]
Abstract
BACKGROUND Biochar, a carbon-rich source and natural growth stimulant, is usually produced by the pyrolysis of agricultural biomass. It is widely used to enhance plant growth, enzyme activity, and crop productivity. However, there are no conclusive studies on how different levels of biochar application influence these systems. METHODS AND RESULTS The present study elucidated the dose-dependent effects of biochar application on the physiological performance, enzyme activity, and dry matter accumulation of tobacco plants via field experiments. In addition, transcriptome analysis was performed on 60-day-old (early growth stage) and 100-day-old (late growth stage) tobacco leaves to determine the changes in transcript levels at the molecular level under various biochar application levels (0, 600, and 1800 kg/ha). The results demonstrated that optimum biochar application enhances plant growth, regulates enzymatic activity, and promotes biomass accumulation in tobacco plants, while higher biochar doses had adverse effects. Furthermore, transcriptome analysis revealed a total of 6561 differentially expressed genes (DEGs) that were up- or down-regulated in the groupwise comparison under different treatments. KEGG pathways analysis demonstrated that carbon fixation in photosynthetic organisms (ko00710), photosynthesis (ko00195), and starch and sucrose metabolism (ko00500) pathways were significantly up-regulated under the optimal biochar dosage (600 kg/ha) and down-regulated under the higher biochar dosage (1800 kg/ha). CONCLUSION Collectively, these results indicate that biochar application at an optimal rate (600 kg/ha) could positively affect photosynthesis and carbon fixation, which in turn increased the synthesis and accumulation of sucrose and starch, thus promoting the growth and dry matter accumulation of tobacco plants. However, a higher biochar dosage (1800 kg/ha) disturbs the crucial source-sink balance of organic compounds and inhibits the growth of tobacco plants.
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Affiliation(s)
- Yingfen Yang
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Waqar Ahmed
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Gang Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Yancheng Teachers University, Yancheng, 224007, China
| | - Chenghu Ye
- Yunnan Revert Medical and Biotechnology Co., Ltd, Kunming, Yunnan, 65021, China
| | - Shichen Li
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Meiwei Zhao
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Jinhao Zhang
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Junjie Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Yancheng Teachers University, Yancheng, 224007, China
| | - Saleh H Salmen
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Lianzhang Wu
- Nujiang Green Spice Industry Research Institute, Lushui, Yunnan, 673200, China
| | - Zhengxiong Zhao
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
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Gao N, Wen H, Shang Z, Zou Y, Zhao W, He Y, Yang S, Zhang H, Qin J, Zhu S, Wang W. Macrogenomics reveal the effects of inter-cropping perilla on kiwifruit: impact on inter-root soil microbiota and gene expression of carbon, nitrogen, and phosphorus cycles in kiwifruit. Front Microbiol 2024; 15:1349305. [PMID: 38887707 PMCID: PMC11180754 DOI: 10.3389/fmicb.2024.1349305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 05/13/2024] [Indexed: 06/20/2024] Open
Abstract
Intercropping systems can improve soil fertility and health, however, soil microbial communities and functional genes related to carbon, nitrogen and phosphorus cycling under the intercropping system of mesquite and perilla have not been studied. Therefore, in the present study, different planting densities and varieties of Perilla frutescens (L.) Britt and kiwifruit were used for intercropping, and changes in soil microbial communities and carbon, nitrogen, and phosphorus cycling genes in kiwifruit inter-roots under inter-cropping conditions were investigated by macro-genome sequencing technology. The results showed that intercropping with Perill caused a decrease in most soil nutrients, soil enzyme activities, and had a significant impact on the microbial (bacteria and fungi) diversity. Inter-cropping increased the relative abundance of the dominant bacterial phylum "Proteobacteria" and "Actinobacteria" by 47 and 57%, respectively, but decreased the relative abundance of the dominant fungal phylum "Chordata" and "Streptophyta" by 11 and 20%, respectively, in the inter-root soil of kiwifruit, and had a significant impact on the microbial (bacteria and fungi) diversity. In addition, inter-cropping could greatly increase the inter-root soil carbon sequestration (PccA, korA/B/C/D, fhs, and rbcl/s), carbon degradation (abfD), organic nitrogen mineralization (GDH2), denitrification (napA/B, nirB, norB), organic phosphorus mineralization (phop, phn), and inorganic phosphorus solubilization (gcd, ppk) gene abundance. The gene co-occurrence network indicated that soil korB, nirB, and gnd key functional genes for carbon, nitrogen, and phosphorus cycling in kiwifruit inter-root soils and their expression was up-regulated in the inter-cropping group. Structural equation (SEM) further showed that soil total nitrogen, organic matter, total carbon and acid phosphatase had significant effects on microbial diversity (p < 0.05) and soil carbon cycling gene korB and phosphorus cycling gene purH (p < 0.001), while korB and purH had positive effects on kiwifruit quality. In conclusion, intercropping perilla in kiwifruit orchards changed the structure of bacterial and fungal communities in the inter-root soil of kiwifruit, but I believe that intercropping perilla stimulates carbon degradation, leading to carbon emission and serious loss of soil nutrients, and that prolonged intercropping may adversely affect the quality of kiwifruit, and thus its limitations should be noted in future studies.
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Affiliation(s)
- Ning Gao
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
- Guizhou Minzu University, Guizhou, China
| | - He Wen
- Guizhou Minzu University, Guizhou, China
| | | | - Yifei Zou
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Wei Zhao
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Yun He
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Sen Yang
- Guizhou Minzu University, Guizhou, China
| | - Heng Zhang
- Guizhou Minzu University, Guizhou, China
| | - Jiahao Qin
- Guizhou Minzu University, Guizhou, China
| | - Sixi Zhu
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
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3
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Parra M, Coppola M, Hellmann H. PDX proteins from Arabidopsis thaliana as novel substrates of cathepsin B: implications for vitamin B 6 biosynthesis regulation. FEBS J 2024; 291:2372-2387. [PMID: 38431778 DOI: 10.1111/febs.17110] [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: 05/29/2023] [Revised: 12/18/2023] [Accepted: 02/21/2024] [Indexed: 03/05/2024]
Abstract
Vitamin B6 is a critical molecule for metabolism, development, and stress sensitivity in plants. It is a cofactor for numerous biochemical reactions, can serve as an antioxidant, and has the potential to increase tolerance against both biotic and abiotic stressors. Due to the importance of vitamin B6, its biosynthesis is likely tightly regulated. Plants can synthesize vitamin B6 de novo via the concerted activity of Pyridoxine Biosynthesis Protein 1 (PDX1) and PDX2. Previously, PDX proteins have been identified as targets for ubiquitination, indicating they could be marked for degradation by two highly conserved pathways: the Ubiquitin Proteasome Pathway (UPP) and the autophagy pathway. Initial experiments show that PDXs are in fact degraded, but surprisingly, in a ubiquitin-independent manner. Inhibitor studies pointed toward cathepsin B, a conserved lysosomal cysteine protease, which is implicated in both programed cell death and autophagy in humans and plants. In plants, cathepsin Bs are poorly described, and no confirmed substrates have been identified. Here, we present PDX proteins from Arabidopsis thaliana as interactors and substrates of a plant Cathepsin B. These findings not only describe a novel cathepsin B substrate in plants, but also provide new insights into how plants regulate de novo biosynthesis of vitamin B6.
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Affiliation(s)
- Marcelina Parra
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | | | - Hanjo Hellmann
- School of Biological Sciences, Washington State University, Pullman, WA, USA
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Lodovici A, Buoso S, Miras-Moreno B, Lucini L, Garcia-Perez P, Tomasi N, Pinton R, Zanin L. Peculiarity of the early metabolomic response in tomato after urea, ammonium or nitrate supply. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108666. [PMID: 38723490 DOI: 10.1016/j.plaphy.2024.108666] [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: 02/16/2024] [Revised: 04/18/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024]
Abstract
Nitrogen (N) is the nutrient most applied in agriculture as fertilizer (as nitrate, Nit; ammonium, A; and/or urea, U, forms) and its availability strongly constrains the crop growth and yield. To investigate the early response (24 h) of N-deficient tomato plants to these three N forms, a physiological and molecular study was performed. In comparison to N-deficient plants, significant changes in the transcriptional, metabolomic and ionomic profiles were observed. As a probable consequence of N mobility in plants, a wide metabolic modulation occurred in old leaves rather than in young leaves. The metabolic profile of U and A-treated plants was more similar than Nit-treated plant profile, which in turn presented the lowest metabolic modulation with respect to N-deficient condition. Urea and A forms induced some changes at the biosynthesis of secondary metabolites, amino acids and phytohormones. Interestingly, a specific up-regulation by U and down-regulation by A of carbon synthesis occurred in roots. Along with the gene expression, data suggest that the specific N form influences the activation of metabolic pathways for its assimilation (cytosolic GS/AS and/or plastidial GS/GOGAT cycle). Urea induced an up-concentration of Cu and Mn in leaves and Zn in whole plant. This study highlights a metabolic reprogramming depending on the N form applied, and it also provide evidence of a direct relationship between urea nutrition and Zn concentration. The understanding of the metabolic pathways activated by the different N forms represents a milestone in improving the efficiency of urea fertilization in crops.
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Affiliation(s)
- Arianna Lodovici
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206 - 33100, Udine, Italy.
| | - Sara Buoso
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206 - 33100, Udine, Italy.
| | - Begoña Miras-Moreno
- Department for Sustainable Food Process, Research Centre for Nutrigenomics and Proteomics, Università Cattolica del Sacro Cuore, Piacenza, Italy.
| | - Luigi Lucini
- Department for Sustainable Food Process, Research Centre for Nutrigenomics and Proteomics, Università Cattolica del Sacro Cuore, Piacenza, Italy.
| | - Pascual Garcia-Perez
- Department for Sustainable Food Process, Research Centre for Nutrigenomics and Proteomics, Università Cattolica del Sacro Cuore, Piacenza, Italy.
| | - Nicola Tomasi
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206 - 33100, Udine, Italy.
| | - Roberto Pinton
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206 - 33100, Udine, Italy.
| | - Laura Zanin
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206 - 33100, Udine, Italy.
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Grover K, Koblova A, Pezacki AT, Chang CJ, New EJ. Small-Molecule Fluorescent Probes for Binding- and Activity-Based Sensing of Redox-Active Biological Metals. Chem Rev 2024; 124:5846-5929. [PMID: 38657175 DOI: 10.1021/acs.chemrev.3c00819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Although transition metals constitute less than 0.1% of the total mass within a human body, they have a substantial impact on fundamental biological processes across all kingdoms of life. Indeed, these nutrients play crucial roles in the physiological functions of enzymes, with the redox properties of many of these metals being essential to their activity. At the same time, imbalances in transition metal pools can be detrimental to health. Modern analytical techniques are helping to illuminate the workings of metal homeostasis at a molecular and atomic level, their spatial localization in real time, and the implications of metal dysregulation in disease pathogenesis. Fluorescence microscopy has proven to be one of the most promising non-invasive methods for studying metal pools in biological samples. The accuracy and sensitivity of bioimaging experiments are predominantly determined by the fluorescent metal-responsive sensor, highlighting the importance of rational probe design for such measurements. This review covers activity- and binding-based fluorescent metal sensors that have been applied to cellular studies. We focus on the essential redox-active metals: iron, copper, manganese, cobalt, chromium, and nickel. We aim to encourage further targeted efforts in developing innovative approaches to understanding the biological chemistry of redox-active metals.
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Affiliation(s)
- Karandeep Grover
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Alla Koblova
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Aidan T Pezacki
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Christopher J Chang
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Elizabeth J New
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
- Sydney Nano Institute, The University of Sydney, Sydney, New South Wales 2006, Australia
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She Z, Wang J, Pan X, Ma D, Gao Y, Wang S, Chuai X, Mu Y, Yue Z. Multi-omics insights into biogeochemical responses to organic matter addition in an acidic pit lake: Implications for bioremediation. WATER RESEARCH 2024; 254:121404. [PMID: 38442608 DOI: 10.1016/j.watres.2024.121404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 01/30/2024] [Accepted: 02/29/2024] [Indexed: 03/07/2024]
Abstract
Acidic pit lakes (APLs) emerge as reservoirs of acid mine drainage in flooded open-pit mines, representing extreme ecosystems and environmental challenges worldwide. The bioremediation of these oligotrophic waters necessitates the addition of organic matter, but the biogeochemical response of APLs to exogenous organic matter remains inadequately comprehended. This study delves into the biogeochemical impacts and remediation effects of digestate-derived organic matter within an APL, employing a multi-omics approach encompassing geochemical analyses, amplicon and metagenome sequencing, and ultra-high resolution mass spectrometry. The results indicated that digestate addition first stimulated fungal proliferation, particularly Ascomycetes and Basidiomycetes, which generated organic acids through lignocellulosic hydrolysis and fermentation. These simple compounds further supported heterotrophic growth, including Acidiphilium, Acidithrix, and Clostridium, thereby facilitating nitrate, iron, and sulfate reduction linked with acidity consumption. Nutrients derived from digestate also promoted the macroscopic development of acidophilic algae. Notably, the increased sulfate reduction-related genes primarily originated from assimilatory metabolism, thus connecting sulfate decrease to organosulfur increase. Assimilatory and dissimilatory sulfate reduction collectively contributed to sulfate removal and metal fixation. These findings yield multi-omics insights into APL biogeochemical responses to organic matter addition, enhancing the understanding of carbon-centered biogeochemical cycling in extreme ecosystems and guiding organic amendment-based bioremediation in oligotrophic polluted environments.
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Affiliation(s)
- Zhixiang She
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, Anhui 230009, China; Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Jin Wang
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, Anhui 230009, China; Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui 230009, China.
| | - Xin Pan
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, Anhui 230009, China; Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Ding Ma
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, Anhui 230009, China; Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Yijun Gao
- Luohe Mining Company Ltd, Anhui Maanshan Iron and Steel Mining Resources Group, Hefei, Anhui 230009, China
| | - Shaoping Wang
- Nanshan Mining Company Ltd, Anhui Maanshan Iron and Steel Mining Resources Group, Ma'anshan, Anhui 243000, China
| | - Xin Chuai
- Nanshan Mining Company Ltd, Anhui Maanshan Iron and Steel Mining Resources Group, Ma'anshan, Anhui 243000, China
| | - Yang Mu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Zhengbo Yue
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, Anhui 230009, China; Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui 230009, China.
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Moreira E, Ferreira J, Coimbra S, Melo P. The significance of the two cytosolic glutamine synthetase enzymes, GLN1;3 and GLN1;5, in the context of seed development and germination in Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108631. [PMID: 38657550 DOI: 10.1016/j.plaphy.2024.108631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/21/2024] [Accepted: 04/14/2024] [Indexed: 04/26/2024]
Abstract
Glutamine synthetase (GS), an initial enzyme in nitrogen (N) plant metabolism, exists as a group of isoenzymes found in both cytosolic (GS1) and plastids (GS2) and has gathered significant attention for enhancing N use efficiency and crop yield. This work focuses on the A. thaliana GLN1;3 and GLN1;5 genes, the two predicted most expressed genes in seeds, among the five isogenes encoding GS1 in this species. The expression patterns were studied using transgenic marker line plants and qPCR during seed development and germination. The observed patterns highlight distinct functions for the two genes and confirm GLN1;5 as the most highly expressed GS1 gene in seeds. The GLN1;5, expression, oriented towards hypocotyl and cotyledons, suggests a role in protein turnover during germination, while the radicle-oriented expression of GLN1;3 supports a function in early external N uptake. While the single mutants exhibited a normal phenotype, except for a decrease in seed parameters, the double gln1;3/gln1;5 mutant displayed a germination delay, substantial impairment in growth, nitrogen metabolism, and number and quality of the seeds, as well as a diminishing in flowering. Although seed and pollen-specific, GLN1;5 expression is upregulated in the meristems of the gln1;3 mutants, filling the lack of GLN1;3 and ensuring the normal functioning of the gln1;3 mutants. These findings validate earlier in silico data on the expression patterns of GLN1;3 and GL1;5 genes in seeds, explore their different functions, and underscore their essential role in plant growth, seed production, germination, and early stages of plant development.
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Affiliation(s)
- Emanuel Moreira
- Department of Biology, Faculty of Sciences of the University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal; INOV4Agro - GreenUPorto - Research Centre on Sustainable Agri-Food Production, Department of Biology, Faculty of Sciences of the University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.
| | - João Ferreira
- Department of Biology, Faculty of Sciences of the University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.
| | - Sílvia Coimbra
- Department of Biology, Faculty of Sciences of the University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal; LAQV/REQUIMTE, Department of Biology, Faculty of Sciences of the University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.
| | - Paula Melo
- Department of Biology, Faculty of Sciences of the University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal; INOV4Agro - GreenUPorto - Research Centre on Sustainable Agri-Food Production, Department of Biology, Faculty of Sciences of the University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.
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Li D, Wang J, Chen R, Chen J, Zong J, Li L, Hao D, Guo H. Review: Nitrogen acquisition, assimilation, and seasonal cycling in perennial grasses. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 342:112054. [PMID: 38423392 DOI: 10.1016/j.plantsci.2024.112054] [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: 12/06/2023] [Revised: 01/19/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
Perennial grasses seasonal nitrogen (N) cycle extends the residence and reuse time of N within the plant system, thereby enhancing N use efficiency. Currently, the mechanism of N metabolism has been extensively examined in model plants and annual grasses, and although perennial grasses exhibit similarities, they also possess distinct characteristics. Apart from assimilating and utilizing N throughout the growing season, perennial grasses also translocate N from aerial parts to perennial tissues, such as rhizomes, after autumn senescence. Subsequently, they remobilize the N from these perennial tissues to support new growth in the subsequent year, thereby ensuring their persistence. Previous studies indicate that the seasonal storage and remobilization of N in perennial grasses are not significantly associated with winter survival despite some amino acids and proteins associated with low temperature tolerance accumulating, but primarily with regrowth during the subsequent spring green-up stage. Further investigation can be conducted in perennial grasses to explore the correlation between stored N and dormant bud outgrowth in perennial tissues, such as rhizomes, during the spring green-up stage, building upon previous research on the relationship between N and axillary bud outgrowth in annual grasses. This exploration on seasonal N cycling in perennial grasses can offer valuable theoretical insights for new perennial grasses varieties with high N use efficiency through the application of gene editing and other advanced technologies.
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Affiliation(s)
- Dandan Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem, Sun Yat-Sen), Nanjing, Jiangsu 210014, China
| | - Jingjing Wang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem, Sun Yat-Sen), Nanjing, Jiangsu 210014, China
| | - Rongrong Chen
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem, Sun Yat-Sen), Nanjing, Jiangsu 210014, China
| | - Jingbo Chen
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem, Sun Yat-Sen), Nanjing, Jiangsu 210014, China
| | - Junqin Zong
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem, Sun Yat-Sen), Nanjing, Jiangsu 210014, China
| | - Ling Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem, Sun Yat-Sen), Nanjing, Jiangsu 210014, China
| | - Dongli Hao
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem, Sun Yat-Sen), Nanjing, Jiangsu 210014, China
| | - Hailin Guo
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem, Sun Yat-Sen), Nanjing, Jiangsu 210014, China.
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Wu Y, Yang Y, Wan M, Chen L, Yuan Y, He J, Zhang B. Paenibacillus glufosinatiresistens sp. nov., a glufosinate-resistant bacterium isolated from sludge. Int J Syst Evol Microbiol 2024; 74. [PMID: 38305710 DOI: 10.1099/ijsem.0.006259] [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] [Indexed: 02/03/2024] Open
Abstract
A Gram-stain-positive bacterium capable of resisting 5.0 mM glufosinate, designated strain YX-27T, was isolated from a sludge sample collected from a factory in Wuxi, Jiangsu, PR China. Cells were rod-shaped, facultatively anaerobic, endospore-forming, and motile by peritrichous flagella. Growth was observed at 15-42 °C (optimum at 30 °C), pH 4.0-8.0 (optimum pH 7.0-7.5) and with 0-2.5% NaCl (w/v; optimum, 0.5 %). Strain YX-27T could tolerate up to 6.0 mM glufosinate. Strain YX-27T showed the highest 16S rRNA gene sequence similarity to Paenibacillus tianjinensis TB2019T (96.17 %), followed by Paenibacillus odorifer DSM 1539T (96.15 %), Paenibacillus sophorae S27T (96.04 %), Paenibacillus apii 7124T (96.02 %) and Paenibacillus stellifer DSM 14472T (95.87 %). The phylogenetic tree based on genome and 16S rRNA gene sequences indicated that strain YX-27T was clustered in the genus Paenibacillus but formed a separate clade. The genome size of YX-27T was 5.22 Mb with a G+C content of 57.5 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between the genomes of strain YX-27T and 12 closely related type strains ranged from 70.8 to 74.8% and 19.8 to 23.0 %, respectively. The major cellular fatty acids were C16 : 0, anteiso-C15 : 0 and iso-C16 : 0. The major polar lipids were one diphosphatidylglycerol, one phosphatidylethanolamine, one phosphatidylglycerol, one phospholipid, four aminophospholipids and four unidentified lipids. The predominant respiratory quinone was MK-7. Based on phylogenetic, genomic, chemotaxonomic and phenotypic data, strain YX-27T was considered to represent a novel species for which the name Paenibacillus glufosinatiresistens sp. nov. is proposed, with YX-27T (=MCCC 1K08803T= KCTC 43611T) as the type strain.
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Affiliation(s)
- Yan Wu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Yuwen Yang
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, PR China
| | - Minglai Wan
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, PR China
| | - Le Chen
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, PR China
| | - Ye Yuan
- Cuiying Honors College, Lanzhou University, Lanzhou 730000, Gansu, PR China
| | - Jian He
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
| | - Baolong Zhang
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, PR China
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10
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Li S, Yan L, Zhang W, Yi C, Haider S, Wang C, Liu Y, Shi L, Xu F, Ding G. Nitrate alleviates ammonium toxicity in Brassica napus by coordinating rhizosphere and cell pH and ammonium assimilation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:786-804. [PMID: 37955989 DOI: 10.1111/tpj.16529] [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: 07/07/2022] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023]
Abstract
In natural and agricultural situations, ammonium (NH 4 + ) is a preferred nitrogen (N) source for plants, but excessive amounts can be hazardous to them, known asNH 4 + toxicity. Nitrate (NO 3 - ) has long been recognized to reduceNH 4 + toxicity. However, little is known about Brassica napus, a major oil crop that is sensitive to highNH 4 + . Here, we found thatNO 3 - can mitigateNH 4 + toxicity by balancing rhizosphere and intracellular pH and accelerating ammonium assimilation in B. napus.NO 3 - increased the uptake ofNO 3 - andNH 4 + under highNH 4 + circumstances by triggering the expression ofNO 3 - andNH 4 + transporters, whileNO 3 - and H+ efflux from the cytoplasm to the apoplast was enhanced by promoting the expression ofNO 3 - efflux transporters and genes encoding plasma membrane H+ -ATPase. In addition,NO 3 - increased pH in the cytosol, vacuole, and rhizosphere, and down-regulated genes induced by acid stress. Root glutamine synthetase (GS) activity was elevated byNO 3 - under highNH 4 + conditions to enhance the assimilation ofNH 4 + into amino acids, thereby reducingNH 4 + accumulation and translocation to shoot in rapeseed. In addition, root GS activity was highly dependent on the environmental pH.NO 3 - might induce metabolites involved in amino acid biosynthesis and malate metabolism in the tricarboxylic acid cycle, and inhibit phenylpropanoid metabolism to mitigateNH 4 + toxicity. Collectively, our results indicate thatNO 3 - balances both rhizosphere and intracellular pH via effectiveNO 3 - transmembrane cycling, acceleratesNH 4 + assimilation, and up-regulates malate metabolism to mitigateNH 4 + toxicity in oilseed rape.
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Affiliation(s)
- Shuang Li
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lei Yan
- Institute of Biomedical Engineering, College of Life Science, Qingdao University, Qingdao, 266071, China
| | - Wen Zhang
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ceng Yi
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sharjeel Haider
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chuang Wang
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yu Liu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Lei Shi
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fangsen Xu
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangda Ding
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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11
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Lu L, Wang Q, Zhang W, Gao M, Xv Y, Li S, Dong H, Chen D, Yan P, Dong Z. Urea Coated with Polyaspartic Acid-Chitosan Increases Foxtail Millet ( Setaria italica L. Beauv.) Grain Yield by Improving Nitrogen Metabolism. PLANTS (BASEL, SWITZERLAND) 2024; 13:415. [PMID: 38337948 PMCID: PMC10857690 DOI: 10.3390/plants13030415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/26/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024]
Abstract
Innovative measures of nitrogen (N) fertilization to increase season-long N availability is essential for gaining the optimal foxtail millet (Setaria italica L. Beauv.) productivity and N use efficiency. A split plot field experiment was conducted using the foxtail millet variety Huayougu 9 in 2020 and 2021 in Northeast China to clarify the physiological mechanism of a novel polyaspartic acid-chitosan (PAC)-coated urea on N assimilation and utilization from foxtail millet. Conventional N fertilizer (CN) and the urea-coated -PAC treatments were tested under six nitrogen fertilizer application levels of 0, 75, 112.5, 150, 225, and 337.5 kg N ha-1. The results showed that compared to CN, PN increased the foxtail millet yield by 5.53-15.75% and 10.43-16.17% in 2020 and 2021, respectively. PN increased the leaf area index and dry matter accumulation by 7.81-18.15% and 12.91-41.92%, respectively. PN also enhanced the activities of nitrate reductase, glutamine synthetase, glutamic oxaloacetic transaminase, and glutamic-pyruvic transaminase, thereby increasing the soluble protein in the leaf, plant, and grain N content at harvest compared to CN. Consequently, partial factor productivity from applied N, the agronomic efficiency of applied N, recovery efficiency of applied N, and physiological efficiency of applied N of foxtail millet under PN treatments compared to CN were increased. The improvement effect of the items above was more noticeable under the low-middle N application levels (75, 112.5, and 150 kg N ha-1). In conclusion, the PAC could achieve the goal of high yield and high N use efficiency in foxtail millet under the background of a one-time basic fertilizer application.
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Affiliation(s)
- Lin Lu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.L.); (W.Z.); (Y.X.); (H.D.); (D.C.)
| | - Qi Wang
- Beijing Agricultural Technology Extension, Beijing 100029, China;
| | - Wei Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.L.); (W.Z.); (Y.X.); (H.D.); (D.C.)
- College of Resources and Environment, Shanxi Agricultural University, Jinzhong 030801, China
| | - Ming Gao
- Institute of Crop Resources Sciences, Jilin Academy of Agricultural Sciences, Changchun 130033, China; (M.G.); (S.L.)
| | - Yanli Xv
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.L.); (W.Z.); (Y.X.); (H.D.); (D.C.)
| | - Shujie Li
- Institute of Crop Resources Sciences, Jilin Academy of Agricultural Sciences, Changchun 130033, China; (M.G.); (S.L.)
| | - Haosheng Dong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.L.); (W.Z.); (Y.X.); (H.D.); (D.C.)
| | - Disu Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.L.); (W.Z.); (Y.X.); (H.D.); (D.C.)
| | - Peng Yan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.L.); (W.Z.); (Y.X.); (H.D.); (D.C.)
| | - Zhiqiang Dong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.L.); (W.Z.); (Y.X.); (H.D.); (D.C.)
- College of Resources and Environment, Shanxi Agricultural University, Jinzhong 030801, China
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12
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Mei Y, Lei J, Liu W, Yue Z, Hu Q, Tao P, Li B, Zhao Y. Transcriptomic and Proteomic Analyses Unveil the Role of Nitrogen Metabolism in the Formation of Chinese Cabbage Petiole Spot. Int J Mol Sci 2024; 25:1366. [PMID: 38338646 PMCID: PMC10855159 DOI: 10.3390/ijms25031366] [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: 12/10/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 02/12/2024] Open
Abstract
Chinese cabbage is the most widely consumed vegetable crop due to its high nutritional value and rock-bottom price. Notably, the presence of the physiological disease petiole spot significantly impacts the appearance quality and marketability of Chinese cabbage. It is well known that excessive nitrogen fertilizer is a crucial factor in the occurrence of petiole spots; however, the mechanism by which excessive nitrogen triggers the formation of petiole spots is not yet clear. In this study, we found that petiole spots initially gather in the intercellular or extracellular regions, then gradually extend into intracellular regions, and finally affect adjacent cells, accompanied by cell death. Transcriptomic and proteomic as well as physiology analyses revealed that the genes/proteins involved in nitrogen metabolism exhibited different expression patterns in resistant and susceptible Chinese cabbage lines. The resistant Chinese cabbage line has high assimilation ability of NH4+, whereas the susceptible one accumulates excessive NH4+, thus inducing a burst of reactive oxygen species (ROS). These results introduce a novel perspective to the investigation of petiole spot induced by the nitrogen metabolism pathway, offering a theoretical foundation for the development of resistant strains in the control of petiole spot.
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Affiliation(s)
- Ying Mei
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China (P.T.)
| | - Juanli Lei
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China (P.T.)
| | - Wenqi Liu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China (P.T.)
- College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China
| | - Zhichen Yue
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China (P.T.)
| | - Qizan Hu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China (P.T.)
| | - Peng Tao
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China (P.T.)
| | - Biyuan Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China (P.T.)
| | - Yanting Zhao
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China (P.T.)
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13
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Shukla PS, Nivetha N, Nori SS, Kumar S, Critchley AT, Suryanarayan S. A biostimulant prepared from red seaweed Kappaphycus alvarezii induces flowering and improves the growth of Pisum sativum grown under optimum and nitrogen-limited conditions. FRONTIERS IN PLANT SCIENCE 2024; 14:1265432. [PMID: 38510831 PMCID: PMC10951999 DOI: 10.3389/fpls.2023.1265432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 12/15/2023] [Indexed: 03/22/2024]
Abstract
Nitrogen (N) is one of the critical elements required by plants and is therefore one of the important limiting factors for growth and yield. To increase agricultural productivity, farmers are using excessive N fertilizers to the soil, which poses a threat to the ecosystem, as most of the applied nitrogen fertilizer is not taken up by crops, and runoff to aquatic bodies and the environment causes eutrophication, pollution, and greenhouse gas emissions. In this study, we used LBS6, a Kappaphycus alvarezii-based biostimulant as a sustainable alternative to improve the growth of plants under different NO3 - fertigation. A root drench treatment of 1 ml/L LBS6 significantly improved the growth of Pisum sativum plants grown under optimum and deficient N conditions. No significant difference was observed in the growth of LBS6-treated plants grown with excessive N. The application of LBS6 induced flowering under optimum and deficient N conditions. The total nitrogen, nitrate and ammonia contents of tissues were found to be higher in treated plants grown under N deficient conditions. The LBS6 treatments had significantly higher chlorophyll content in those plants grown under N-deficient conditions. The root drench application of LBS6 also regulated photosynthetic efficiency by modulating electron and proton transport-related processes of leaves in the light-adapted state. The rate of linear electron flux, proton conductivity and steady-state proton flux across the thylakoid membrane were found to be higher in LBS6-treated plants. Additionally, LBS6 also reduced nitrogen starvation-induced, reactive oxygen species accumulation by reduction in lipid peroxidation in treated plants. Gene expression analysis showed differential regulation of expression of those genes involved in N uptake, transport, assimilation, and remobilization in LBS6-treated plants. Taken together, LBS6 improved growth of those treated plants under optimum and nitrogen-limited condition by positively modulating their biochemical, molecular, and physiological processes.
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Affiliation(s)
- Pushp Sheel Shukla
- Research and Development Division, Sea6 Energy Private Limited, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences-Tata Institute of Fundamental Research, Bengaluru, Karnataka, India
| | - Nagarajan Nivetha
- Research and Development Division, Sea6 Energy Private Limited, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences-Tata Institute of Fundamental Research, Bengaluru, Karnataka, India
| | - Sri Sailaja Nori
- Research and Development Division, Sea6 Energy Private Limited, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences-Tata Institute of Fundamental Research, Bengaluru, Karnataka, India
| | - Sawan Kumar
- Research and Development Division, Sea6 Energy Private Limited, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences-Tata Institute of Fundamental Research, Bengaluru, Karnataka, India
| | - Alan T. Critchley
- Verschuren Centre for Sustainability in Energy and the Environment, Sydney, NS, Canada
| | - Shrikumar Suryanarayan
- Research and Development Division, Sea6 Energy Private Limited, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences-Tata Institute of Fundamental Research, Bengaluru, Karnataka, India
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14
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Kobercová E, Melo P, Fischer L. Validating the role of glutamine synthetase GLN2 during photorespiration in Arabidopsis thaliana. PLANT PHYSIOLOGY 2023; 194:324-328. [PMID: 37787606 PMCID: PMC10756748 DOI: 10.1093/plphys/kiad521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/04/2023]
Affiliation(s)
- Eliška Kobercová
- Faculty of Science, Department of Experimental Plant Biology, Charles University, Viničná 5, Prague 2, 128 44, Czech Republic
| | - Paula Melo
- Faculty of Sciences, Department of Biology and GreenUPorto - Research Centre on Sustainable Agrifood Production, University of Porto, Rua do Campo Alegre s/n, Porto, 4169-007, Portugal
| | - Lukáš Fischer
- Faculty of Science, Department of Experimental Plant Biology, Charles University, Viničná 5, Prague 2, 128 44, Czech Republic
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15
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Lee KT, Liao HS, Hsieh MH. Glutamine Metabolism, Sensing and Signaling in Plants. PLANT & CELL PHYSIOLOGY 2023; 64:1466-1481. [PMID: 37243703 DOI: 10.1093/pcp/pcad054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/23/2023] [Accepted: 05/24/2023] [Indexed: 05/29/2023]
Abstract
Glutamine (Gln) is the first amino acid synthesized in nitrogen (N) assimilation in plants. Gln synthetase (GS), converting glutamate (Glu) and NH4+ into Gln at the expense of ATP, is one of the oldest enzymes in all life domains. Plants have multiple GS isoenzymes that work individually or cooperatively to ensure that the Gln supply is sufficient for plant growth and development under various conditions. Gln is a building block for protein synthesis and an N-donor for the biosynthesis of amino acids, nucleic acids, amino sugars and vitamin B coenzymes. Most reactions using Gln as an N-donor are catalyzed by Gln amidotransferase (GAT) that hydrolyzes Gln to Glu and transfers the amido group of Gln to an acceptor substrate. Several GAT domain-containing proteins of unknown function in the reference plant Arabidopsis thaliana suggest that some metabolic fates of Gln have yet to be identified in plants. In addition to metabolism, Gln signaling has emerged in recent years. The N regulatory protein PII senses Gln to regulate arginine biosynthesis in plants. Gln promotes somatic embryogenesis and shoot organogenesis with unknown mechanisms. Exogenous Gln has been implicated in activating stress and defense responses in plants. Likely, Gln signaling is responsible for some of the new Gln functions in plants.
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Affiliation(s)
- Kim-Teng Lee
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
- Molecular and Biological Agricultural Sciences, The Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung 40227, Taiwan
| | - Hong-Sheng Liao
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Ming-Hsiun Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
- Molecular and Biological Agricultural Sciences, The Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung 40227, Taiwan
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16
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Fortunato S, Nigro D, Lasorella C, Marcotuli I, Gadaleta A, de Pinto MC. The Role of Glutamine Synthetase (GS) and Glutamate Synthase (GOGAT) in the Improvement of Nitrogen Use Efficiency in Cereals. Biomolecules 2023; 13:1771. [PMID: 38136642 PMCID: PMC10742212 DOI: 10.3390/biom13121771] [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: 11/18/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Cereals are the most broadly produced crops and represent the primary source of food worldwide. Nitrogen (N) is a critical mineral nutrient for plant growth and high yield, and the quality of cereal crops greatly depends on a suitable N supply. In the last decades, a massive use of N fertilizers has been achieved in the desire to have high yields of cereal crops, leading to damaging effects for the environment, ecosystems, and human health. To ensure agricultural sustainability and the required food source, many attempts have been made towards developing cereal crops with a more effective nitrogen use efficiency (NUE). NUE depends on N uptake, utilization, and lastly, combining the capability to assimilate N into carbon skeletons and remobilize the N assimilated. The glutamine synthetase (GS)/glutamate synthase (GOGAT) cycle represents a crucial metabolic step of N assimilation, regulating crop yield. In this review, the physiological and genetic studies on GS and GOGAT of the main cereal crops will be examined, giving emphasis on their implications in NUE.
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Affiliation(s)
- Stefania Fortunato
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (S.F.)
| | - Domenica Nigro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.N.); (I.M.)
| | - Cecilia Lasorella
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (S.F.)
| | - Ilaria Marcotuli
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.N.); (I.M.)
| | - Agata Gadaleta
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.N.); (I.M.)
| | - Maria Concetta de Pinto
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (S.F.)
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17
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Lebedev VG, Korobova AV, Shendel GV, Shestibratov KA. Hormonal Status of Transgenic Birch with a Pine Glutamine Synthetase Gene during Rooting In Vitro and Budburst Outdoors. Biomolecules 2023; 13:1734. [PMID: 38136605 PMCID: PMC10741575 DOI: 10.3390/biom13121734] [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: 10/17/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Improving nitrogen use efficiency (NUE) is one of the main ways of increasing plant productivity through genetic engineering. The modification of nitrogen (N) metabolism can affect the hormonal content, but in transgenic plants, this aspect has not been sufficiently studied. Transgenic birch (Betula pubescens) plants with the pine glutamine synthetase gene GS1 were evaluated for hormone levels during rooting in vitro and budburst under outdoor conditions. In the shoots of the transgenic lines, the content of indoleacetic acid (IAA) was 1.5-3 times higher than in the wild type. The addition of phosphinothricin (PPT), a glutamine synthetase (GS) inhibitor, to the medium reduced the IAA content in transgenic plants, but it did not change in the control. In the roots of birch plants, PPT had the opposite effect. PPT decreased the content of free amino acids in the leaves of nontransgenic birch, but their content increased in GS-overexpressing plants. A three-year pot experiment with different N availability showed that the productivity of the transgenic birch line was significantly higher than in the control under N deficiency, but not excess, conditions. Nitrogen availability did not affect budburst in the spring of the fourth year; however, bud breaking in transgenic plants was delayed compared to the control. The IAA and abscisic acid (ABA) contents in the buds of birch plants at dormancy and budburst depended both on N availability and the transgenic status. These results enable a better understanding of the interaction between phytohormones and nutrients in woody plants.
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Affiliation(s)
- Vadim G. Lebedev
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Alla V. Korobova
- Ufa Institute of Biology of the Ufa Federal Research Center of the Russian Academy of Sciences, 450054 Ufa, Russia; (A.V.K.); (G.V.S.)
| | - Galina V. Shendel
- Ufa Institute of Biology of the Ufa Federal Research Center of the Russian Academy of Sciences, 450054 Ufa, Russia; (A.V.K.); (G.V.S.)
| | - Konstantin A. Shestibratov
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 142290 Pushchino, Russia;
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18
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Safdar LB, Foulkes MJ, Kleiner FH, Searle IR, Bhosale RA, Fisk ID, Boden SA. Challenges facing sustainable protein production: Opportunities for cereals. PLANT COMMUNICATIONS 2023; 4:100716. [PMID: 37710958 PMCID: PMC10721536 DOI: 10.1016/j.xplc.2023.100716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/01/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
Rising demands for protein worldwide are likely to drive increases in livestock production, as meat provides ∼40% of dietary protein. This will come at a significant environmental cost, and a shift toward plant-based protein sources would therefore provide major benefits. While legumes provide substantial amounts of plant-based protein, cereals are the major constituents of global foods, with wheat alone accounting for 15-20% of the required dietary protein intake. Improvement of protein content in wheat is limited by phenotyping challenges, lack of genetic potential of modern germplasms, negative yield trade-offs, and environmental costs of nitrogen fertilizers. Presenting wheat as a case study, we discuss how increasing protein content in cereals through a revised breeding strategy combined with robust phenotyping could ensure a sustainable protein supply while minimizing the environmental impact of nitrogen fertilizer.
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Affiliation(s)
- Luqman B Safdar
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA 5064, Australia; School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - M John Foulkes
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Friedrich H Kleiner
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK; Faculty of Applied Science, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Iain R Searle
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Rahul A Bhosale
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Ian D Fisk
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA 5064, Australia; School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK.
| | - Scott A Boden
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA 5064, Australia.
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19
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Traxler C, Gaines TA, Küpper A, Luemmen P, Dayan FE. The nexus between reactive oxygen species and the mechanism of action of herbicides. J Biol Chem 2023; 299:105267. [PMID: 37734554 PMCID: PMC10591016 DOI: 10.1016/j.jbc.2023.105267] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023] Open
Abstract
Herbicides are small molecules that act by inhibiting specific molecular target sites within primary plant metabolic pathways resulting in catastrophic and lethal consequences. The stress induced by herbicides generates reactive oxygen species (ROS), but little is known about the nexus between each herbicide mode of action (MoA) and their respective ability to induce ROS formation. Indeed, some herbicides cause dramatic surges in ROS levels as part of their primary MoA, whereas other herbicides may generate some ROS as a secondary effect of the stress they imposed on plants. In this review, we discuss the types of ROS and their respective reactivity and describe their involvement for each known MoA based on the new Herbicide Resistance Action Committee classification.
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Affiliation(s)
- Catherine Traxler
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Todd A Gaines
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Anita Küpper
- Plant Biotechnology Division, Bayer CropScience, Chesterfield, Missouri, USA
| | - Peter Luemmen
- Research & Development Division, Bayer AG, Industriepark Höchst, Frankfurt am Main, Germany
| | - Franck E Dayan
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, USA.
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20
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Thangaraj S, Kim HR, Heo JM, Son S, Ryu J, Park JW, Kim JH, Kim SY, Jung HK, Kim IN. Unraveling prokaryotic diversity distribution and functional pattern on nitrogen and methane cycling in the subtropical Western North Pacific Ocean. MARINE POLLUTION BULLETIN 2023; 196:115569. [PMID: 37922593 DOI: 10.1016/j.marpolbul.2023.115569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 11/07/2023]
Abstract
Prokaryotes play an important role in marine nitrogen and methane cycles. However, their community changes and metabolic modifications to the concurrent impact of ocean warming (OW), acidification (OA), deoxygenation (OD), and anthropogenic‑nitrogen-deposition (AND) from the surface to the deep ocean remains unknown. We examined here the amplicon sequencing approach across the surface (0-200 m; SL), intermediate (200-1000 m; IL), and deep layers (1000-2200 m; DL), and characterized the simultaneous impacts of OW, OA, OD, and AND on the Western North Pacific Ocean prokaryotic changes and their functional pattern in nitrogen and methane cycles. Results showed that SL possesses higher ammonium oxidation community/metabolic composition assumably the reason for excess nitrogen input from AND and modification of their kinetic properties to OW adaptation. Expanding OD at IL showed hypoxic conditions in the oxygen minimum layer, inducing higher microbial respiration that elevates the dimerization of nitrification genes for higher nitrous oxide production. The aerobic methane-oxidation composition was dominant in SL presumably the reason for adjustment in prokaryotic optimal temperature to OW, while anaerobic oxidation composition was dominant at IL due to the evolutionary changes coupling with higher nitrification. Our findings refocus on climate-change impacts on the open ocean ecosystem from the surface to the deep-environment integrating climate-drivers as key factors for higher nitrous-oxide and methane emissions.
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Affiliation(s)
- Satheeswaran Thangaraj
- Department of Marine Science, Incheon National University, Incheon, South Korea; Freddy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of Jerusalem, Jerusalem, Israel; Interuniversity Institute for Marine Sciences, Eilat, Israel; Department of Physiology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Hyo-Ryeon Kim
- Department of Marine Science, Incheon National University, Incheon, South Korea
| | - Jang-Mu Heo
- Department of Marine Science, Incheon National University, Incheon, South Korea
| | - Seunghyun Son
- Cooperative Institute for Satellite Earth System Studies (CISESS) / Earth System Science Interdisciplinary Center (ESSIC), University of Maryland, USA
| | - Jongseong Ryu
- Department of Marine Biotechnology, Anyang University, Incheon, South Korea
| | - Jong-Woo Park
- Tidal Flat Research Center, National Institute of Fisheries Science, Gunsan, South Korea
| | - Ju-Hyoung Kim
- Department of Aquaculture and Aquatic Science, Kunsan National University, Gunsan, South Korea
| | - Seo-Young Kim
- Department of Marine Science, Incheon National University, Incheon, South Korea
| | - Hae-Kun Jung
- Environment and Fisheries Resources Research Division, East Sea Fisheries Institute, National Institute of Fisheries Science, Gangneung, South Korea
| | - Il-Nam Kim
- Department of Marine Science, Incheon National University, Incheon, South Korea.
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21
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Yin ML, Zhao SP, Lai JL, Yang X, Dong B, Zhu YB, Zhang Y. Oxygen-insensitive nitroreductase bacteria-mediated degradation of TNT and proteomic analysis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:116227-116238. [PMID: 37907824 DOI: 10.1007/s11356-023-30568-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/16/2023] [Indexed: 11/02/2023]
Abstract
2,4,6-trinitrotoluene (TNT) is a nitroaromatic compound that causes soil and groundwater pollution during manufacture, transportation, and use, posing significant environmental and safety hazards. In this study, a TNT-degrading strain, Bacillus cereus strain T4, was screened and isolated from TNT-contaminated soil to explore its degradation characteristics and proteomic response to TNT. The results showed that after inoculation with the bacteria for 4 h, the TNT degradation rate reached 100% and was transformed into 2-amino-4,6-dinitrotoluene (2-ADNT), 4-amino-2,6-dinitrotoluene (4-ADNT), 2,4-diamino-6-nitrotoluene (2,4-DANT), and 2,6-diamino-4-nitrotoluene (2,6-DANT), accompanied by the accumulation of nitrite and ammonium ions. Through proteomic sequencing, we identified 999 differentially expressed proteins (482 upregulated, 517 downregulated), mainly enriched in the pentose phosphate, glycolysis/gluconeogenesis, and amino acid metabolism pathways. In addition, the significant upregulation of nitroreductase and N-ethylmaleimide reductase was closely related to TNT denitration and confirmed that the strain T4 converted TNT into intermediate metabolites such as 2-ADNT and 4-ADNT. Therefore, Bacillus cereus strain T4 has the potential to degrade TNT and has a high tolerance to intermediate products, which may effectively degrade nitroaromatic pollutants such as TNT in situ remediation in combination with other bacterial communities.
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Affiliation(s)
- Mao-Ling Yin
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - San-Ping Zhao
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China.
| | - Jin-Long Lai
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Xu Yang
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Bin Dong
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Yong-Bing Zhu
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Yu Zhang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
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22
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Prabhakaran P, Nazir MYM, Thananusak R, Hamid AA, Vongsangnak W, Song Y. Uncovering global lipid accumulation routes towards docosahexaenoic acid (DHA) production in Aurantiochytrium sp. SW1 using integrative proteomic analysis. Biochim Biophys Acta Mol Cell Biol Lipids 2023; 1868:159381. [PMID: 37625782 DOI: 10.1016/j.bbalip.2023.159381] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/15/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023]
Abstract
Aurantiochytrium sp., a marine thraustochytrid possesses a remarkable ability to produce lipid rich in polyunsaturated fatty acids (PUFAs), such as docosahexaenoic acid (DHA). Although gene regulation underlying lipid biosynthesis has been previously reported, proteomic analysis is still limited. In this study, high DHA accumulating strain Aurantiochytrium sp. SW1 has been used as a study model to elucidate the alteration in proteome profile under different cultivation phases i.e. growth, nitrogen-limitation and lipid accumulation. Of the total of 5146 identified proteins, 852 proteins were differentially expressed proteins (DEPs). The largest number of DEPs (488 proteins) was found to be uniquely expressed between lipid accumulating phase and growth phase. Interestingly, there were up-regulated proteins involved in glycolysis, glycerolipid, carotenoid and glutathione metabolism which were preferable metabolic routes towards lipid accumulation and DHA production as well as cellular oxidative defence. Integrated proteomic and transcriptomic data were also conducted to comprehend the gene and protein regulation underlying the lipid and DHA biosynthesis. A significant up-regulation of acetyl-CoA synthetase was observed which suggests alternative route of acetate metabolism for acetyl-CoA producer. This study presents the holistic routes underlying lipid accumulation and DHA production in Aurantiochytrium sp. SW1 and other relevant thraustochytrid.
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Affiliation(s)
- Pranesha Prabhakaran
- Colin Ratledge Centre for Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, China; Interdisciplinary Graduate Programs in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Mohamed Yusuf Mohamed Nazir
- Colin Ratledge Centre for Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, China; Department of Food Sciences, Faculty of Science and Technology, University Kebangsaan Malaysia, UKM, Bangi, Malaysia
| | - Roypim Thananusak
- Duckweed Holobiont Resource & Research Center (DHbRC), Faculty of Science, Kasetsart University, Bangkok, Thailand; Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, Thailand
| | - Aidil Abdul Hamid
- Department of Biological Science and Biotechnology, Faculty of Science and Technology, National University of Malaysia, Bangi, Malaysia.
| | - Wanwipa Vongsangnak
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, Thailand; Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand.
| | - Yuanda Song
- Colin Ratledge Centre for Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, China.
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23
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He S, Liu M, Chen W, Bai D, Liao Y, Bai L, Pan L. Eleusine indica Cytochrome P450 and Glutathione S-Transferase Are Linked to High-Level Resistance to Glufosinate. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:14243-14250. [PMID: 37749769 DOI: 10.1021/acs.jafc.3c04325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Eleusine indica has become a global nuisance weed and has evolved resistance to glufosinate. The involvement of target-site resistance (TSR) in glufosinate resistance in E. indica has been elucidated, while the role of nontarget-site resistance (NTSR) remains unclear. Here, we identified a glufosinate-resistant (R) population that is highly resistant to glufosinate, with a resistance index of 13.5-fold. Molecular analysis indicated that the resistance mechanism of this R population does not involve TSR. In addition, pretreatment with two known metabolic enzyme inhibitors, the cytochrome P450 (CYP450) inhibitor malathion and the glutathione S-transferase (GST) inhibitor 4-chloro-7-nitrobenzoxadiazole (NBD-Cl), increased the sensitivity of the R population to glufosinate. The results of subsequent RNA sequencing (RNA-seq) and quantitative real-time PCR (RT-qPCR) suggested that the constitutive overexpression of a GST gene (GSTU3) and three CYP450 genes (CYP94s and CYP71) may play an important role in glufosinate resistance. This study provides new insights into the resistance mechanism of E. indica.
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Affiliation(s)
- Sifen He
- Longping Branch, College of Biology, Hunan University, Changsha 410125, China
- Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Min Liu
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
| | - Wen Chen
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
| | - Dingyi Bai
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
| | - Yuxi Liao
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
| | - Lianyang Bai
- Longping Branch, College of Biology, Hunan University, Changsha 410125, China
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
- Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Lang Pan
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
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Hakim S, Imran A, Hussain MS, Mirza MS. RNA-Seq analysis of mung bean (Vigna radiata L.) roots shows differential gene expression and predicts regulatory pathways responding to taxonomically different rhizobia. Microbiol Res 2023; 275:127451. [PMID: 37478540 DOI: 10.1016/j.micres.2023.127451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 07/23/2023]
Abstract
Symbiotic interaction among legume and rhizobia is a complex phenomenon which results in the formation of nitrogen-fixing nodules. Mung bean is promiscuous host however expression profile of this important legume plant in response to rhizobial infection was particularly lacking and urgently needed. We have demonstrated the pattern of gene expression of mung bean roots inoculated with two symbionts Bradyrhizobium yuanmingense Vr50 and Sinorhizobium (Ensifer) aridi Vr33 and non-inoculated control (CK). The RNA-Seq data analyzed at two growth stages i.e., 1-3 h and 10-16 days post inoculation revealed significantly higher number of differentially expressed genes (DEGs) at nodulation stage. The DEGs encoding receptor kinases identified at early stage might be involved in perception of Nod factors produced by different rhizobia. At nodulation stage important genes involved in plant hormone signal transduction, nitrogen and sulfur metabolism were identified. KEGG pathway enrichment analysis showed that metabolic pathways were most prominent in both groups (Group 1: Vr33 vs CK; Group 2: Vr50 vs CK), followed by biosynthesis of secondary metabolites, plant hormone signal transduction and biosynthesis of amino acids. Furthermore, DEGs involved in cell communication and plant hormone signal transduction were found to be different among two symbiotic systems while DEGs involved in carbon, nitrogen and sulfur metabolism were similar but their expression varied in response to two rhizobial strains. This study provides the first insight into the mechanisms underlying interactions of mung bean host with two taxonomically different symbionts (Bradyrhizobium and Sinorhizobium) and the candidate genes for better understanding the mechanisms of symbiotic host-specificity.
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Affiliation(s)
- Sughra Hakim
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Asma Imran
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan
| | | | - M Sajjad Mirza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan.
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25
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Xie W, Li X, Xu H, Chen F, Cheng KW, Liu H, Liu B. Optimization of Heterotrophic Culture Conditions for the Microalgae Euglena gracilis to Produce Proteins. Mar Drugs 2023; 21:519. [PMID: 37888454 PMCID: PMC10608195 DOI: 10.3390/md21100519] [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: 08/31/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023] Open
Abstract
Euglena gracilis is one of the few permitted edible microalgae. Considering consumer acceptance, E. gracilis grown heterotrophically with yellow appearances have wider food industrial applications such as producing meat analogs than green cells. However, there is much room to improve the protein content of heterotrophic culture cells. In this study, the effects of nitrogen sources, temperature, initial pH, and C/N ratios on the protein production of E. gracilis were evaluated under heterotrophic cultivation. These results indicated that ammonium sulfate was the optimal nitrogen source for protein production. The protein content of E. gracilis cultured by ammonium sulfate increased by 113% and 44.7% compared with that cultured by yeast extract and monosodium glutamate, respectively. The manipulation of the low C/N ratio further improved E. gracilis protein content to 66.10% (w/w), which was 1.6-fold of that in the C/N = 25 group. Additionally, amino acid analysis revealed that the nitrogen-to-protein conversion factor (NTP) could be affected by nitrogen sources. A superior essential amino acid index (EAAI) of 1.62 and a balanced amino acid profile further confirmed the high nutritional value of E. gracilis protein fed by ammonium sulfate. This study highlighted the vast potency of heterotrophic cultured E. gracilis as an alternative dietary protein source.
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Affiliation(s)
- Weiying Xie
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Shenzhen University, Shenzhen 518060, China (H.X.)
- Shenzhen Key Laboratory of Food Nutrition and Health, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen518060, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Xiaojie Li
- Shenzhen Key Laboratory of Food Nutrition and Health, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen518060, China
| | - Huo Xu
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Shenzhen University, Shenzhen 518060, China (H.X.)
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Feng Chen
- Shenzhen Key Laboratory of Food Nutrition and Health, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen518060, China
| | - Ka-Wing Cheng
- Shenzhen Key Laboratory of Food Nutrition and Health, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen518060, China
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Bin Liu
- Shenzhen Key Laboratory of Food Nutrition and Health, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen518060, China
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Zhang W, Ni K, Long L, Ruan J. Nitrogen transport and assimilation in tea plant ( Camellia sinensis): a review. FRONTIERS IN PLANT SCIENCE 2023; 14:1249202. [PMID: 37810380 PMCID: PMC10556680 DOI: 10.3389/fpls.2023.1249202] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023]
Abstract
Nitrogen is one of the most important nutrients for tea plants, as it contributes significantly to tea yield and serves as the component of amino acids, which in turn affects the quality of tea produced. To achieve higher yields, excessive amounts of N fertilizers mainly in the form of urea have been applied in tea plantations where N fertilizer is prone to convert to nitrate and be lost by leaching in the acid soils. This usually results in elevated costs and environmental pollution. A comprehensive understanding of N metabolism in tea plants and the underlying mechanisms is necessary to identify the key regulators, characterize the functional phenotypes, and finally improve nitrogen use efficiency (NUE). Tea plants absorb and utilize ammonium as the preferred N source, thus a large amount of nitrate remains activated in soils. The improvement of nitrate utilization by tea plants is going to be an alternative aspect for NUE with great potentiality. In the process of N assimilation, nitrate is reduced to ammonium and subsequently derived to the GS-GOGAT pathway, involving the participation of nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), glutamate synthase (GOGAT), and glutamate dehydrogenase (GDH). Additionally, theanine, a unique amino acid responsible for umami taste, is biosynthesized by the catalysis of theanine synthetase (TS). In this review, we summarize what is known about the regulation and functioning of the enzymes and transporters implicated in N acquisition and metabolism in tea plants and the current methods for assessing NUE in this species. The challenges and prospects to expand our knowledge on N metabolism and related molecular mechanisms in tea plants which could be a model for woody perennial plant used for vegetative harvest are also discussed to provide the theoretical basis for future research to assess NUE traits more precisely among the vast germplasm resources, thus achieving NUE improvement.
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Affiliation(s)
- Wenjing Zhang
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kang Ni
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Xihu National Agricultural Experimental Station for Soil Quality, Hangzhou, China
| | - Lizhi Long
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Jianyun Ruan
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Xihu National Agricultural Experimental Station for Soil Quality, Hangzhou, China
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27
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Lu Z, He S, Kashif M, Zhang Z, Mo S, Su G, Du L, Jiang C. Effect of ammonium stress on phosphorus solubilization of a novel marine mangrove microorganism Bacillus aryabhattai NM1-A2 as revealed by integrated omics analysis. BMC Genomics 2023; 24:550. [PMID: 37723472 PMCID: PMC10506230 DOI: 10.1186/s12864-023-09559-z] [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: 02/17/2023] [Accepted: 08/07/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Phosphorus is one of the essential nutrients for plant growth. Phosphate-solubilizing microorganisms (PSMs) can alleviate available P deficiency and enhance plant growth in an eco-friendly way. Although ammonium toxicity is widespread, there is little understanding about the effect of ammonium stress on phosphorus solubilization (PS) of PSMs. RESULTS In this study, seven PSMs were isolated from mangrove sediments. The soluble phosphate concentration in culture supernatant of Bacillus aryabhattai NM1-A2 reached a maximum of 196.96 mg/L at 250 mM (NH4)2SO4. Whole-genome analysis showed that B. aryabhattai NM1-A2 contained various genes related to ammonium transporter (amt), ammonium assimilation (i.e., gdhA, gltB, and gltD), organic acid synthesis (i.e., ackA, fdhD, and idh), and phosphate transport (i.e., pstB and pstS). Transcriptome data showed that the expression levels of amt, gltB, gltD, ackA and idh were downregulated, while gdhA and fdhD were upregulated. The inhibition of ammonium transporter and glutamine synthetase/glutamate synthase (GS/GOGAT) pathway contributed to reducing energy loss. For ammonium assimilation under ammonium stress, accompanied by protons efflux, the glutamate dehydrogenase pathway was the main approach. More 2-oxoglutarate (2-OG) was induced to provide abundant carbon skeletons. The downregulation of formate dehydrogenase and high glycolytic rate resulted in the accumulation of formic acid and acetic acid, which played key roles in PS under ammonium stress. CONCLUSIONS The accumulation of 2-OG and the inhibition of GS/GOGAT pathway played a key role in ammonium detoxification. The secretion of protons, formic acid and acetic acid was related to PS. Our work provides new insights into the PS mechanism, which will provide theoretical guidance for the application of PSMs.
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Affiliation(s)
- Zhaomei Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory for Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, China
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Sheng He
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defect prevention, Guangxi Zhuang Autonomous Region Women and Children Health Care Hospital, Nanning, 530033, China
| | - Muhammad Kashif
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory for Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, China
| | - Zufan Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Shuming Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Guijiao Su
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Linfang Du
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China.
| | - Chengjian Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China.
- Guangxi Key Laboratory for Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, China.
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28
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Bouzroud S, Henkrar F, Fahr M, Smouni A. Salt stress responses and alleviation strategies in legumes: a review of the current knowledge. 3 Biotech 2023; 13:287. [PMID: 37520340 PMCID: PMC10382465 DOI: 10.1007/s13205-023-03643-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 05/21/2023] [Indexed: 08/01/2023] Open
Abstract
Salinity is one of the most significant environmental factors limiting legumes development and productivity. Salt stress disturbs all developmental stages of legumes and affects their hormonal regulation, photosynthesis and biological nitrogen fixation, causing nutritional imbalance, plant growth inhibition and yield losses. At the molecular level, salt stress exposure involves large number of factors that are implicated in stress perception, transduction, and regulation of salt responsive genes' expression through the intervention of transcription factors. Along with the complex gene network, epigenetic regulation mediated by non-coding RNAs, and DNA methylation events are also involved in legumes' response to salinity. Different alleviation strategies can increase salt tolerance in legume plants. The most promising ones are Plant Growth Promoting Rhizobia, Arbuscular Mycorrhizal Fungi, seed and plant's priming. Genetic manipulation offers an effective approach for improving salt tolerance. In this review, we present a detailed overview of the adverse effect of salt stress on legumes and their molecular responses. We also provide an overview of various ameliorative strategies that have been implemented to mitigate/overcome the harmful effects of salt stress on legumes.
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Affiliation(s)
- Sarah Bouzroud
- Equipe de Microbiologie et Biologie Moléculaire, Centre de Biotechnologie Végétale et Microbienne Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 10000 Rabat, Morocco
| | - Fatima Henkrar
- Laboratoire de Biotechnologie et Physiologie Végétales, Centre de Biotechnologie Végétale et Microbienne Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 10000 Rabat, Morocco
- Laboratoire Mixte International Activité Minière Responsable “LMI-AMIR”, IRD/UM5R/INAU, 10000 Rabat, Morocco
| | - Mouna Fahr
- Laboratoire de Biotechnologie et Physiologie Végétales, Centre de Biotechnologie Végétale et Microbienne Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 10000 Rabat, Morocco
- Laboratoire Mixte International Activité Minière Responsable “LMI-AMIR”, IRD/UM5R/INAU, 10000 Rabat, Morocco
| | - Abdelaziz Smouni
- Laboratoire de Biotechnologie et Physiologie Végétales, Centre de Biotechnologie Végétale et Microbienne Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 10000 Rabat, Morocco
- Laboratoire Mixte International Activité Minière Responsable “LMI-AMIR”, IRD/UM5R/INAU, 10000 Rabat, Morocco
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Zhang Q, Shi Y, Hu H, Shi Y, Tang D, Ruan J, Fernie AR, Liu MY. Magnesium promotes tea plant growth via enhanced glutamine synthetase-mediated nitrogen assimilation. PLANT PHYSIOLOGY 2023; 192:1321-1337. [PMID: 36879396 PMCID: PMC10231486 DOI: 10.1093/plphys/kiad143] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/08/2023] [Accepted: 02/12/2023] [Indexed: 06/01/2023]
Abstract
Acidic tea (Camellia sinensis) plantation soil usually suffers from magnesium (Mg) deficiency, and as such, application of fertilizer containing Mg can substantially increase tea quality by enhancing the accumulation of nitrogen (N)-containing chemicals such as amino acids in young tea shoots. However, the molecular mechanisms underlying the promoting effects of Mg on N assimilation in tea plants remain unclear. Here, both hydroponic and field experiments were conducted to analyze N, Mg, metabolite contents, and gene expression patterns in tea plants. We found that N and amino acids accumulated in tea plant roots under Mg deficiency, while metabolism of N was enhanced by Mg supplementation, especially under a low N fertilizer regime. 15N tracing experiments demonstrated that assimilation of N was induced in tea roots following Mg application. Furthermore, weighted gene correlation network analysis (WGCNA) analysis of RNA-seq data suggested that genes encoding glutamine synthetase isozymes (CsGSs), key enzymes regulating N assimilation, were markedly regulated by Mg treatment. Overexpression of CsGS1.1 in Arabidopsis (Arabidopsis thaliana) resulted in a more tolerant phenotype under Mg deficiency and increased N assimilation. These results validate our suggestion that Mg transcriptionally regulates CsGS1.1 during the enhanced assimilation of N in tea plant. Moreover, results of a field experiment demonstrated that high Mg and low N had positive effects on tea quality. This study deepens our understanding of the molecular mechanisms underlying the interactive effects of Mg and N in tea plants while also providing both genetic and agronomic tools for future improvement of tea production.
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Affiliation(s)
- Qunfeng Zhang
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants (Ministry of Agriculture and Rural Affairs), Hangzhou 310008, China
| | - Yutao Shi
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
- College of Tea and Food Science, Wuyi University, Wuyishan 354300, China
| | - Hao Hu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuanzhi Shi
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants (Ministry of Agriculture and Rural Affairs), Hangzhou 310008, China
| | - Dandan Tang
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Jianyun Ruan
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants (Ministry of Agriculture and Rural Affairs), Hangzhou 310008, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Mei-Ya Liu
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants (Ministry of Agriculture and Rural Affairs), Hangzhou 310008, China
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Sharma N, Dabral S, Tyagi J, Yadav G, Aggarwal H, Joshi NC, Varma A, Koul M, Choudhary DK, Mishra A. Interaction studies of Serendipita indica and Zhihengliuella sp. ISTPL4 and their synergistic role in growth promotion in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1155715. [PMID: 37293679 PMCID: PMC10244739 DOI: 10.3389/fpls.2023.1155715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/17/2023] [Indexed: 06/10/2023]
Abstract
Rapid urbanization and globalization demand increasing agricultural productivity. Soil nutrient supply capacity is continuously decreasing due to soil erosion, degradation, salt deposition, undesired element, metal deposition, water scarcity, and an uneven nutrient delivery system. Rice cultivation requires a large amount of water which is becoming detrimental due to these activities. There is a need to increase its productivity. Microbial inoculants are becoming increasingly important in achieving sustainable agricultural production systems. The current study was conducted to investigate the interaction between the root endophytic fungus Serendipita indica (S. indica) and the actinobacterium Zhihengliuella sp. ISTPL4 (Z. sp. ISTPL4) and their synergistic effects on the growth of rice (Oryza sativa L). Both S. indica and Z. sp. ISTPL4 showed positive interactions. Growth of S. indica was observed at different days after Z. sp. ISTPL4 inoculation, and stimulated growth of S. indica was observed when Z. sp. ISTPL4 was inoculated at 5 dafi (days after fungal inoculation). Z. sp. ISTPL4 promoted the growth of S. indica as it increased spore germination. Furthermore, confocal and scanning electron microscopy (SEM) analyses showed a 27% increase in the spore size of S. indica in the presence of Z. sp. ISTPL4. In a liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis increased production of alanine and glutamic acid was observed in their sequential co-culture as compared with individual cultures. Sequential inoculation of S. indica and Z. sp. ISTPL4 significantly increased the biochemical and physical characteristics of rice as compared with their individual inoculum. Biochemical parameters such as chlorophyll content, total soluble sugar, and flavonoid content in the rice increased by up to 57%, 47%, and 39%, respectively, in the presence of the combined inoculum of S. indica and Z. sp. ISTPL4. This will be the first study, to the best of our knowledge, which shows the fungus and actinobacterium interaction and their synergistic roles in the growth promotion of rice. Furthermore, this novel combination can also be used to boost the growth of other crops to increase the agricultural yield.
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Affiliation(s)
- Neha Sharma
- Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, India
| | - Surbhi Dabral
- Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, India
| | - Jaagriti Tyagi
- Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, India
| | - Gaurav Yadav
- Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, India
| | - Himanshi Aggarwal
- Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, India
| | | | - Ajit Varma
- Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, India
| | - Monika Koul
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | | | - Arti Mishra
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
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Esmaeilzadeh-Salestani K, Tohidfar M, Ghanbari Moheb Seraj R, Khaleghdoust B, Keres I, Marawne H, Loit E. Transcriptome profiling of barley in response to mineral and organic fertilizers. BMC PLANT BIOLOGY 2023; 23:261. [PMID: 37193945 DOI: 10.1186/s12870-023-04263-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 05/04/2023] [Indexed: 05/18/2023]
Abstract
BACKGROUND Nitrogen is very important for crop yield and quality. Crop producers face the challenge of reducing the use of mineral nitrogen while maintaining food security and other ecosystem services. The first step towards understanding the metabolic responses that could be used to improve nitrogen use efficiency is to identify the genes that are up- or downregulated under treatment with different forms and rates of nitrogen. We conducted a transcriptome analysis of barley (Hordeum vulgare L.) cv. Anni grown in a field experiment in 2019. The objective was to compare the effects of organic (cattle manure) and mineral nitrogen (NH4NO3; 0, 40, 80 kg N ha-1) fertilizers on gene activity at anthesis (BBCH60) and to associate the genes that were differentially expressed between treatment groups with metabolic pathways and biological functions. RESULTS The highest number of differentially expressed genes (8071) was found for the treatment with the highest mineral nitrogen rate. This number was 2.6 times higher than that for the group treated with a low nitrogen rate. The lowest number (500) was for the manure treatment group. Upregulated pathways in the mineral fertilizer treatment groups included biosynthesis of amino acids and ribosomal pathways. Downregulated pathways included starch and sucrose metabolism when mineral nitrogen was supplied at lower rates and carotenoid biosynthesis and phosphatidylinositol signaling at higher mineral nitrogen rates. The organic treatment group had the highest number of downregulated genes, with phenylpropanoid biosynthesis being the most significantly enriched pathway for these genes. Genes involved in starch and sucrose metabolism and plant-pathogen interaction pathways were enriched in the organic treatment group compared with the control treatment group receiving no nitrogen input. CONCLUSION These findings indicate stronger responses of genes to mineral fertilizers, probably because the slow and gradual decomposition of organic fertilizers means that less nitrogen is provided. These data contribute to our understanding of the genetic regulation of barley growth under field conditions. Identification of pathways affected by different nitrogen rates and forms under field conditions could help in the development of more sustainable cropping practices and guide breeders to create varieties with low nitrogen input requirements.
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Affiliation(s)
- Keyvan Esmaeilzadeh-Salestani
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Fr. R.Kreutzwaldi 1, 51014, Tartu, Estonia.
| | - Masoud Tohidfar
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Rahele Ghanbari Moheb Seraj
- Department of Horticultural Sciences, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Banafsheh Khaleghdoust
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Fr. R.Kreutzwaldi 1, 51014, Tartu, Estonia
| | - Indrek Keres
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Fr. R.Kreutzwaldi 1, 51014, Tartu, Estonia
| | - Hashem Marawne
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Evelin Loit
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Fr. R.Kreutzwaldi 1, 51014, Tartu, Estonia
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Prabhakaran P, Raethong N, Thananusak R, Nazir MYM, Sapkaew C, Soommat P, Kingkaw A, Hamid AA, Vongsangnak W, Song Y. Revealing holistic metabolic responses associated with lipid and docosahexaenoic acid (DHA) production in Aurantiochytrium sp. SW1. Biochim Biophys Acta Mol Cell Biol Lipids 2023; 1868:159306. [PMID: 36907245 DOI: 10.1016/j.bbalip.2023.159306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/02/2023] [Accepted: 02/25/2023] [Indexed: 03/12/2023]
Abstract
Aurantiochytrium sp. SW1, a marine thraustochytrid, has been regarded as a potential candidate as a docosahexaenoic acid (DHA) producer. Even though the genomics of Aurantiochytrium sp. are available, the metabolic responses at a systems level are largely unknown. Therefore, this study aimed to investigate the global metabolic responses to DHA production in Aurantiochytrium sp. through transcriptome and genome-scale network-driven analysis. Of a total of 13,505 genes, 2527 differentially expressed genes (DEGs) were identified in Aurantiochytrium sp., unravelling the transcriptional regulations behinds lipid and DHA accumulation. The highest number of DEG were found for pairwise comparison between growth phase and lipid accumulating phase where a total of 1435 genes were down-regulated with 869 genes being up-regulated. These uncovered several metabolic pathways that contributing in DHA and lipid accumulation including amino acid and acetate metabolism which involve in the generation of crucial precursors. Upon applying network-driven analysis, hydrogen sulphide was found as potential reporter metabolite that could be associated with the genes related to acetyl-CoA synthesis for DHA production. Our findings suggest that the transcriptional regulation of these pathways is a ubiquitous feature in response to specific cultivation phases during DHA overproduction in Aurantiochytrium sp. SW1.
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Affiliation(s)
- Pranesha Prabhakaran
- Colin Ratledge Centre for Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, China; Interdisciplinary Graduate Programs in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Nachon Raethong
- Institute of Nutrition, Mahidol University, Nakhon Pathom, Thailand
| | - Roypim Thananusak
- Interdisciplinary Graduate Programs in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Mohamed Yusuf Mohamed Nazir
- Colin Ratledge Centre for Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, China; Department of Food Sciences, Faculty of Science and Technology, University Kebangsaan Malaysia, UKM, Bangi, Malaysia
| | - Chakkapan Sapkaew
- Interdisciplinary Graduate Programs in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Panyawarin Soommat
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand; Genetic Engineering and Bioinformatic Program, Graduate School, Kasetsart University, Bangkok, Thailand
| | - Amornthep Kingkaw
- Interdisciplinary Graduate Programs in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Aidil Abdul Hamid
- Department of Biological Science and Biotechnology, Faculty of Science and Technology, National University of Malaysia, Bangi, Malaysia.
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand; Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, Thailand.
| | - Yuanda Song
- Colin Ratledge Centre for Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, China.
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Tan J, Zhao S, Chen J, Pan X, Li C, Liu Y, Wu C, Li W, Zheng M. Preparation of nitrogen-doped carbon dots and their enhancement on lettuce yield and quality. J Mater Chem B 2023; 11:3113-3123. [PMID: 36947418 DOI: 10.1039/d2tb02817d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Nanotechnology is an effective way to stimulate the yield potential of crops. Various nano-fertilizers and nano-carriers are gradually being developed to bring about a technological revolution in the agricultural industry. As a biocompatible water-soluble nanomaterial, carbon dots (CDs) have attracted the attention of researchers for applications in agriculture. In this study, we prepared nitrogen-doped CDs (N-CDs) as a type of water-soluble carbon nanofertilizer by a one-pot hydrothermal method, and investigated its effects on lettuce biomass and quality. 100 and 200 mg L-1 of N-CDs substantially promoted lettuce biomass accumulation (41.70%), elevated lettuce nutrient content, as well as promoted the accumulation of major nutrients. Moreover, 100 mg L-1 N-CDs increased the chlorophyll a content by 12.68%, significantly increased the electron transport rate (ETR) by 38.61%, significantly increased the light energy conversion efficiency (Y(II)) by 31.24% and increased the Rubisco activity by 60.61%, which are important reasons for its increase in actual photosynthesis rate. N-CDs also have a positive effect on plant nitrogen metabolism by promoting the activity of glutamine synthetase. The significant benefits of N-CDs on lettuce make them have great potential for agricultural yield increase and quality improvement.
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Affiliation(s)
- Jieqiang Tan
- Key Laboratory for Biobased Materials and Energy of Ministry of Education, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, People's Republic of China.
| | - Shili Zhao
- Key Laboratory for Biobased Materials and Energy of Ministry of Education, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, People's Republic of China.
| | - Junyu Chen
- Key Laboratory for Biobased Materials and Energy of Ministry of Education, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, People's Republic of China.
| | - Xiaoqin Pan
- Key Laboratory for Biobased Materials and Energy of Ministry of Education, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, People's Republic of China.
| | - Chen Li
- Key Laboratory for Biobased Materials and Energy of Ministry of Education, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, People's Republic of China.
| | - Yingliang Liu
- Key Laboratory for Biobased Materials and Energy of Ministry of Education, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, People's Republic of China.
| | - Caijuan Wu
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525100, China
| | - Wei Li
- Key Laboratory for Biobased Materials and Energy of Ministry of Education, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, People's Republic of China.
| | - Mingtao Zheng
- Key Laboratory for Biobased Materials and Energy of Ministry of Education, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, People's Republic of China.
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525100, China
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Jie L, Sanagi M, Luo Y, Maeda H, Fukao Y, Chiba Y, Yanagisawa S, Yamaguchi J, Takagi J, Sato T. Histone chaperone NUCLEOSOME ASSEMBLY PROTEIN 1 proteins affect plant growth under nitrogen deficient conditions in Arabidopsis thaliana. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2023; 40:93-98. [PMID: 38439935 PMCID: PMC10910346 DOI: 10.5511/plantbiotechnology.22.1219a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/19/2022] [Indexed: 03/06/2024]
Abstract
Nitrogen (N) availability is one of the most important factors regulating plant metabolism and growth as it affects global gene expression profiles. Dynamic changes in chromatin structure, including histone modifications and nucleosome assembly/disassembly, have been extensively shown to regulate gene expression under various environmental stresses in plants. However, the involvement of chromatin related changes in plant nutrient responses has been demonstrated only in a few studies to date. In this study, we investigated the function of histone chaperone NUCLEOSOME ASSEMBLY PROTEIN1 (NAP1) proteins under N deficient conditions in Arabidopsis. In the nap1;1 nap1;2 nap1;3 triple mutant (m123-1), the expression of N-responsive marker genes and growth of lateral roots were decreased under N deficient conditions. In addition, the m123-1 plants showed a delay in N deficiency-induced leaf senescence. Taken together, these results suggest that NAP1s affect plant growth under N deficient conditions in Arabidopsis.
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Affiliation(s)
- Linnan Jie
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Miho Sanagi
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Yongming Luo
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Haruna Maeda
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Yoichiro Fukao
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Yukako Chiba
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Shuichi Yanagisawa
- Plant Functional Biotechnology, Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Junji Yamaguchi
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Junpei Takagi
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Takeo Sato
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
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Ding S, Lv J, Hu Z, Wang J, Wang P, Yu J, Foyer CH, Shi K. Phytosulfokine peptide optimizes plant growth and defense via glutamine synthetase GS2 phosphorylation in tomato. EMBO J 2023; 42:e111858. [PMID: 36562188 PMCID: PMC10015362 DOI: 10.15252/embj.2022111858] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 12/05/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
Phytosulfokine (PSK) is a plant pentapeptide hormone that fulfills a wide range of functions. Although PSK has frequently been reported to function in the inverse regulation of growth and defense in response to (hemi)biotrophic pathogens, the mechanisms involved remain largely unknown. Using the tomato (Solanum lycopersicum) and Pseudomonas syringae pv. tomato (Pst) DC3000 pathogen system, we present compelling evidence that the PSK receptor PSKR1 interacts with the calcium-dependent protein kinase CPK28, which in turn phosphorylates the key enzyme of nitrogen assimilation glutamine synthetase GS2 at two sites (Serine-334 and Serine-360). GS2 phosphorylation at S334 specifically regulates plant defense, whereas S360 regulates growth, uncoupling the PSK-induced effects on defense responses and growth regulation. The discovery of these sites will inform breeding strategies designed to optimize the growth-defense balance in a compatible manner.
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Affiliation(s)
- Shuting Ding
- Department of HorticultureZhejiang UniversityHangzhouChina
| | - Jianrong Lv
- Department of HorticultureZhejiang UniversityHangzhouChina
| | - Zhangjian Hu
- Department of HorticultureZhejiang UniversityHangzhouChina
| | - Jiao Wang
- Department of HorticultureZhejiang UniversityHangzhouChina
| | - Ping Wang
- Department of HorticultureZhejiang UniversityHangzhouChina
| | - Jingquan Yu
- Department of HorticultureZhejiang UniversityHangzhouChina
- Hainan Institute, Yazhou Bay Science and Technology CityZhejiang UniversitySanyaChina
- Key Laboratory of Horticultural Plant Growth and DevelopmentMinistry of Agriculture and Rural AffairsHangzhouChina
| | - Christine H Foyer
- School of Biosciences, College of Life and Environmental SciencesUniversity of BirminghamBirminghamUK
| | - Kai Shi
- Department of HorticultureZhejiang UniversityHangzhouChina
- Hainan Institute, Yazhou Bay Science and Technology CityZhejiang UniversitySanyaChina
- Key Laboratory of Horticultural Plant Growth and DevelopmentMinistry of Agriculture and Rural AffairsHangzhouChina
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Alam I, Zhang H, Du H, Rehman NU, Manghwar H, Lei X, Batool K, Ge L. Bioengineering Techniques to Improve Nitrogen Transformation and Utilization: Implications for Nitrogen Use Efficiency and Future Sustainable Crop Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:3921-3938. [PMID: 36842151 DOI: 10.1021/acs.jafc.2c08051] [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: 06/18/2023]
Abstract
Nitrogen (N) is crucial for plant growth and development, especially in physiological and biochemical processes such as component of different proteins, enzymes, nucleic acids, and plant growth regulators. Six categories, such as transporters, nitrate absorption, signal molecules, amino acid biosynthesis, transcription factors, and miscellaneous genes, broadly encompass the genes regulating NUE in various cereal crops. Herein, we outline detailed research on bioengineering modifications of N metabolism to improve the different crop yields and biomass. We emphasize effective and precise molecular approaches and technologies, including N transporters, transgenics, omics, etc., which are opening up fascinating opportunities for a complete analysis of the molecular elements that contribute to NUE. Moreover, the detection of various types of N compounds and associated signaling pathways within plant organs have been discussed. Finally, we highlight the broader impacts of increasing NUE in crops, crucial for better agricultural yield and in the greater context of global climate change.
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Affiliation(s)
- Intikhab Alam
- College of Forestry and Landscape Architecture, Department of Grassland Science, South China Agricultural University (SCAU), Guangzhou 510642, China
- College of Life Sciences, SCAU, Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
| | - Hanyin Zhang
- College of Forestry and Landscape Architecture, Department of Grassland Science, South China Agricultural University (SCAU), Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
| | - Huan Du
- College of Forestry and Landscape Architecture, Department of Grassland Science, South China Agricultural University (SCAU), Guangzhou 510642, China
- College of Life Sciences, SCAU, Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
| | - Naveed Ur Rehman
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
| | - Hakim Manghwar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, SCAU, Guangzhou 510642, China
| | - Xiao Lei
- College of Forestry and Landscape Architecture, Department of Grassland Science, South China Agricultural University (SCAU), Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
| | - Khadija Batool
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liangfa Ge
- College of Forestry and Landscape Architecture, Department of Grassland Science, South China Agricultural University (SCAU), Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
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Kiefl E, Esen OC, Miller SE, Kroll KL, Willis AD, Rappé MS, Pan T, Eren AM. Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution. SCIENCE ADVANCES 2023; 9:eabq4632. [PMID: 36812328 DOI: 10.1126/sciadv.abq4632] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Comprehensive sampling of natural genetic diversity with metagenomics enables highly resolved insights into the interplay between ecology and evolution. However, resolving adaptive, neutral, or purifying processes of evolution from intrapopulation genomic variation remains a challenge, partly due to the sole reliance on gene sequences to interpret variants. Here, we describe an approach to analyze genetic variation in the context of predicted protein structures and apply it to a marine microbial population within the SAR11 subclade 1a.3.V, which dominates low-latitude surface oceans. Our analyses reveal a tight association between genetic variation and protein structure. In a central gene in nitrogen metabolism, we observe decreased occurrence of nonsynonymous variants from ligand-binding sites as a function of nitrate concentrations, revealing genetic targets of distinct evolutionary pressures maintained by nutrient availability. Our work yields insights into the governing principles of evolution and enables structure-aware investigations of microbial population genetics.
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Affiliation(s)
- Evan Kiefl
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Ozcan C Esen
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Samuel E Miller
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Kourtney L Kroll
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Michael S Rappé
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI 96822, USA
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
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Liu C, Duan N, Chen X, Li X, Zhao N, Cao W, Li H, Liu B, Tan F, Zhao X, Li Q. Transcriptome Profiling and Chlorophyll Metabolic Pathway Analysis Reveal the Response of Nitraria tangutorum to Increased Nitrogen. PLANTS (BASEL, SWITZERLAND) 2023; 12:895. [PMID: 36840241 PMCID: PMC9962214 DOI: 10.3390/plants12040895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/04/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
To identify genes that respond to increased nitrogen and assess the involvement of the chlorophyll metabolic pathway and associated regulatory mechanisms in these responses, Nitraria tangutorum seedlings were subjected to four nitrogen concentrations (N0, N6, N36, and N60: 0, 6, 36, and 60 mmol·L-1 nitrogen, respectively). The N. tangutorum seedling leaf transcriptome was analyzed by high-throughput sequencing (Illumina HiSeq 4000), and 332,420 transcripts and 276,423 unigenes were identified. The numbers of differentially expressed genes (DEGs) were 4052 in N0 vs. N6, 6181 in N0 vs. N36, and 3937 in N0 vs. N60. Comparing N0 and N6, N0 and N36, and N0 and N60, we found 1101, 2222, and 1234 annotated DEGs in 113, 121, and 114 metabolic pathways, respectively, classified in the Kyoto Encyclopedia of Genes and Genomes database. Metabolic pathways with considerable accumulation were involved mainly in anthocyanin biosynthesis, carotenoid biosynthesis, porphyrin and chlorophyll metabolism, flavonoid biosynthesis, and amino acid metabolism. N36 increased δ-amino levulinic acid synthesis and upregulated expression of the magnesium chelatase H subunit, which promoted chlorophyll a synthesis. Hence, N36 stimulated chlorophyll synthesis rather than heme synthesis. These findings enrich our understanding of the N. tangutorum transcriptome and help us to research desert xerophytes' responses to increased nitrogen in the future.
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Affiliation(s)
- Chenggong Liu
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing 100091, China
| | - Na Duan
- Experimental Center of Desert Forestry, Chinese Academy of Forestry, Dengkou 015200, China
- National Long-Term Scientific Research Base of Ulan Buh Desert Comprehensive Control, National Forestry and Grassland Administration, Dengkou 015200, China
| | - Xiaona Chen
- Experimental Center of Desert Forestry, Chinese Academy of Forestry, Dengkou 015200, China
- National Long-Term Scientific Research Base of Ulan Buh Desert Comprehensive Control, National Forestry and Grassland Administration, Dengkou 015200, China
| | - Xu Li
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing 100091, China
| | - Naqi Zhao
- Experimental Center of Desert Forestry, Chinese Academy of Forestry, Dengkou 015200, China
- National Long-Term Scientific Research Base of Ulan Buh Desert Comprehensive Control, National Forestry and Grassland Administration, Dengkou 015200, China
| | - Wenxu Cao
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing 100091, China
| | - Huiqing Li
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing 100091, China
| | - Bo Liu
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing 100091, China
| | - Fengsen Tan
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing 100091, China
| | - Xiulian Zhao
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing 100091, China
| | - Qinghe Li
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing 100091, China
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Li J, Yu C, Liu Z, Wang Y, Wang F. Microplastic accelerate the phosphorus-related metabolism of bacteria to promote the decomposition of methylphosphonate to methane. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:160020. [PMID: 36356736 DOI: 10.1016/j.scitotenv.2022.160020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/08/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
Microplastic (MP) contaminants in marine water have become a global public health concern because of their persistence and potentially adverse effects on organisms. MP can affect the growth and metabolism of marine microorganisms and further impact the microbial environmental functions. The molecular impact mechanisms of MP on specific functional microbes with the capability of decomposing methylphosphonate (MPn) to release methane (CH4) in oxygenated water have rarely been reported upon. Herein, we investigated the effects of MP on microbes and concomitant methanogenesis via the microbial degradation of MPn. Furthermore, the specific perturbation was revealed at the molecular level combined with transcriptomics and metabolomics. The results showed that intracellular phosphorus utilization by MPn-degrading strain Burkholderia sp. HQL1813 was enhanced by accelerating the catabolism of MPn. Phosphorus transport-related genes (phnG-M, pstSCAB, phnCDE) were upregulated in the MP exposure groups. Amino acid metabolism, the phosphotransferase system and nucleotide metabolism were also perturbed after MP exposure. Notably, released CH4 increased by 24 %, 29 % and 14 % in the exposure group. In addition, the responses of the strain were dose-independent with increasing MP doses. These findings are beneficial for clarifying the effect of MP on specific functional microbes at the molecular level and their degradation of CH4 by MPn.
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Affiliation(s)
- Junhong Li
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, 100083 Beijing, China; School of Environment, Beijing Normal University, 19 Xinjiekouwai Street, 100875 Beijing, China
| | - Chan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, 430062 Wuhan, China
| | - Zeqin Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, 430062 Wuhan, China
| | - Yan Wang
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, 100083 Beijing, China
| | - Fei Wang
- School of Environment, Beijing Normal University, 19 Xinjiekouwai Street, 100875 Beijing, China.
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Campolo N, Mastrogiovanni M, Mariotti M, Issoglio FM, Estrin D, Hägglund P, Grune T, Davies MJ, Bartesaghi S, Radi R. Multiple oxidative post-translational modifications of human glutamine synthetase mediate peroxynitrite-dependent enzyme inactivation and aggregation. J Biol Chem 2023; 299:102941. [PMID: 36702251 PMCID: PMC10011836 DOI: 10.1016/j.jbc.2023.102941] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/25/2023] Open
Abstract
Glutamine synthetase (GS), which catalyzes the ATP-dependent synthesis of L-glutamine from L-glutamate and ammonia, is a ubiquitous and conserved enzyme that plays a pivotal role in nitrogen metabolism across all life domains. In vertebrates, GS is highly expressed in astrocytes, where its activity sustains the glutamate-glutamine cycle at glutamatergic synapses and is thus essential for maintaining brain homeostasis. In fact, decreased GS levels or activity have been associated with neurodegenerative diseases, with these alterations attributed to oxidative post-translational modifications of the protein, in particular tyrosine nitration. In this study, we expressed and purified human GS (HsGS) and performed an in-depth analysis of its oxidative inactivation by peroxynitrite (ONOO-) in vitro. We found that ONOO- exposure led to a dose-dependent loss of HsGS activity, the oxidation of cysteine, methionine, and tyrosine residues and also the nitration of tryptophan and tyrosine residues. Peptide mapping by LC-MS/MS through combined H216O/H218O trypsin digestion identified up to 10 tyrosine nitration sites and five types of dityrosine cross-links; these modifications were further scrutinized by structural analysis. Tyrosine residues 171, 185, 269, 283, and 336 were the main nitration targets; however, tyrosine-to-phenylalanine HsGS mutants revealed that their sole nitration was not responsible for enzyme inactivation. In addition, we observed that ONOO- induced HsGS aggregation and activity loss. Thiol oxidation was a key modification to elicit aggregation, as it was also induced by hydrogen peroxide treatment. Taken together, our results indicate that multiple oxidative events at various sites are responsible for the inactivation and aggregation of human GS.
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Affiliation(s)
- Nicolás Campolo
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Mauricio Mastrogiovanni
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Michele Mariotti
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Federico M Issoglio
- CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Darío Estrin
- CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina; Departamento de Química Inorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Analítica y Química Física, Buenos Aires, Argentina
| | - Per Hägglund
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Tilman Grune
- Department of Molecular Toxicology, German Institute of Human Nutrition, Potsdam-Rehbrücke, Nuthetal, Germany; German Center for Cardiovascular Research (DZHK), Berlin, Germany; Department of Physiological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Michael J Davies
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Silvina Bartesaghi
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Rafael Radi
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
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Effects of nitrate and ammonium on assimilation of nitric oxide by Heterosigma akashiwo. Sci Rep 2023; 13:621. [PMID: 36635297 PMCID: PMC9837059 DOI: 10.1038/s41598-023-27692-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/05/2023] [Indexed: 01/13/2023] Open
Abstract
The harmful alga Heterosigma akashiwo possesses a hybrid nitrate reductase (NR) enzyme, NR2-2/2HbN, which has the potential to convert NO to nitrate for assimilation into biomass. In previous research, NR transcription in H. akashiwo was induced by nitrate while NR activity was inhibited by ammonium. Here, the capacity of H. akashiwo to use NO in the presence of nitrate and/or ammonium was investigated to understand the regulation of NO assimilation. Continuous cultures of H. akashiwo were acclimated to growth on nitrate, ammonium, or a mixture of both. Aliquots from these cultures were spiked with 15N-labeled NO. The expression of genes involved in nitrogen assimilation was evaluated, as well as nitrate reductase activity and assimilation of 15N-labeled nitrogen into algal biomass. Results showed that NO induced expression and activity of NR, and upregulated expression of GOGAT regardless of the presence of other inorganic nitrogen sources, while GS expression decreased over time. Furthermore, 15NO uptake and assimilation was significantly higher in cultures acclimated for growth on ammonium compared to cultures acclimated for growth on nitrate alone. Assimilation of NO may provide H. akashiwo with a competitive advantage in N-poor environments or areas with elevated NO.
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Zhang Y, Li B, Luo P, Xian Y, Xiao R, Wu J. Glutamine synthetase plays an important role in ammonium tolerance of Myriophyllum aquaticum. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157596. [PMID: 35905951 DOI: 10.1016/j.scitotenv.2022.157596] [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: 12/06/2021] [Revised: 06/30/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
High-strength ammonium (NH4+), the main characteristic of swine wastewater, poses a significant threat to the rural ecological environment. As a novel phytoremediation technology, Myriophyllum aquaticum wetlands have high tolerance and removal rate of NH4+. Glutamine synthetase (GS), a pivotal enzyme in nitrogen (N) metabolism, is hypothesized to play an important role in the tolerance of M. aquaticum to high NH4+. Herein, the responses of M. aquaticum to GS inhibition by 0.1 mM methionine sulfoximine (MSX) under 15 mM NH4+ were investigated. After 5 days, visible NH4+ toxicity symptoms were observed in MSX-treated plants. Compared with the control, the NH4+ accumulation in the leaves increased by 20.99 times, while that of stems and roots increased by 3.27 times and 47.76 %, suggesting that GS inhibition had a greater impact on the leaves. GS inhibition decreased pigments in the leaves by 8.64 %-41.06 %, triggered oxidative stress, and affected ions concentrations in M. aquaticum. The concentrations of glutamine (Gln) and asparagine decreased by 63.46 %-97.43 % and 12.37 %-76.41 %, respectively, while the concentrations of most other amino acids increased after 5 days of MSX treatment, showing that GS inhibition reprogrammed the amino acids synthesis. A decrease in Gln explains the regulations of N-related genes, including increased expression of AMT in roots and decreased expression of GS, GOGAT, GDH, and AS, which would cause further NH4+ accumulation via promoting NH4+ uptake and decreasing NH4+ assimilation in M. aquaticum. This study revealed for the first time that GS inhibition under high NH4+ condition can lead to phytotoxicity in M. aquaticum due to NH4+ accumulation. The physiological and molecular responses of the leaves, stems, and roots confirmed the importance of GS in the high NH4+ tolerance of M. aquaticum. These findings provide new insights into NH4+ tolerance mechanisms in M. aquaticum and a theoretical foundation for the phytoremediation of high NH4+-loaded swine wastewater.
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Affiliation(s)
- Ying Zhang
- Key Laboratory of Agro-ecological Processes in Subtropical Region/Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, PR China; College of Resources and Environment, Hunan Agricultural University, Changsha, Hunan 410128, PR China
| | - Baozhen Li
- Key Laboratory of Agro-ecological Processes in Subtropical Region/Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, PR China.
| | - Pei Luo
- Key Laboratory of Agro-ecological Processes in Subtropical Region/Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, PR China
| | - Yingnan Xian
- Key Laboratory of Agro-ecological Processes in Subtropical Region/Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, PR China
| | - Runlin Xiao
- Key Laboratory of Agro-ecological Processes in Subtropical Region/Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, PR China
| | - Jinshui Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Region/Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, PR China
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Cohen M, Hertweck K, Itkin M, Malitsky S, Dassa B, Fischer AM, Fluhr R. Enhanced proteostasis, lipid remodeling, and nitrogen remobilization define barley flag leaf senescence. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6816-6837. [PMID: 35918065 DOI: 10.1093/jxb/erac329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Leaf senescence is a developmental process allowing nutrient remobilization to sink organs. We characterized flag leaf senescence at 7, 14, and 21 d past anthesis in two near-isogenic barley lines varying in the allelic state of the HvNAM1 transcription factor gene, which influences senescence timing. Metabolomics and microscopy indicated that, as senescence progressed, thylakoid lipids were transiently converted to neutral lipids accumulating in lipid droplets. Senescing leaves also exhibited an accumulation of sugars including glucose, while nitrogen compounds (nucleobases, nucleotides, and amino acids) decreased. RNA-Seq analysis suggested lipid catabolism via β-oxidation and the glyoxylate cycle, producing carbon skeletons and feeding respiration as a replacement of the diminished carbon supply from photosynthesis. Comparison of the two barley lines highlighted a more prominent up-regulation of heat stress transcription factor- and chaperone-encoding genes in the late-senescing line, suggesting a role for these genes in the control of leaf longevity. While numerous genes with putative roles in nitrogen remobilization were up-regulated in both lines, several peptidases, nucleases, and nitrogen transporters were more highly induced in the early-senescing line; this finding identifies processes and specific candidates which may affect nitrogen remobilization from senescing barley leaves, downstream of the HvNAM1 transcription factor.
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Affiliation(s)
- Maja Cohen
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Kendra Hertweck
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Maxim Itkin
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Sergey Malitsky
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Andreas M Fischer
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Robert Fluhr
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
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Arora N, Lo E, Philippidis GP. A two-prong mutagenesis and adaptive evolution strategy to enhance the temperature tolerance and productivity of Nannochloropsis oculata. BIORESOURCE TECHNOLOGY 2022; 364:128101. [PMID: 36241066 DOI: 10.1016/j.biortech.2022.128101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Incorporation of microalgae in biorefineries intended to help society reach carbon neutrality is hindered by algal growth inhibition at high temperatures, necessitating the use of costly and carbon-intensive cooling systems. In the present study, a two-prong strategy of random mutagenesis and adaptive laboratory evolution to generate robust thermotolerant strains of Nannochloropsis oculata, was used. The best mutants demonstrated increased productivity at 35 °C, which was 10 °C higher than the optimal temperature of the wild type. In a 2-L photobioreactor at 35 °C, biomass and lipid productivity were 1.43-fold and 2.24-fold higher, respectively, than wild type at 25 °C. Higher pigment and carbohydrate content contributed to the mutants' rapid growth and enhanced photosynthetic efficiency. Metabolomics and lipidomics showed rewiring of the central carbon metabolism and membrane lipid synthesis in thermotolerant strains to ensure cellular homeostasis without compromising productivity. Tagatose and phosphatidylethanolamine upregulation were identified as future genetic targets for further enhancing lipid production.
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Affiliation(s)
- Neha Arora
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, USA
| | - Enlin Lo
- Department of Chemical, Biological and Materials Engineering, University of South Florida, Tampa, FL, USA
| | - George P Philippidis
- Patel College of Global Sustainability, University of South Florida, Tampa, FL, USA.
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Comprehensive Analysis of Transcriptome and Metabolome Elucidates the Molecular Regulatory Mechanism of Salt Resistance in Roots of Achnatherum inebrians Mediated by Epichloë gansuensis. J Fungi (Basel) 2022; 8:jof8101092. [PMID: 36294657 PMCID: PMC9605608 DOI: 10.3390/jof8101092] [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: 07/07/2022] [Revised: 09/15/2022] [Accepted: 10/13/2022] [Indexed: 11/17/2022] Open
Abstract
Salinization of soil is a major environmental risk factor to plant functions, leading to a reduction of productivity of crops and forage. Epichloë gansuensis, seed-borne endophytic fungi, establishes a mutualistic symbiotic relationship with Achnatherum inebrians and confers salt tolerance in the host plants. In this study, analysis of transcriptome and metabolome was used to explore the potential molecular mechanism underlying the salt-adaptation of A. inebrians roots mediated by E. gansuensis. We found that E. gansuensis played an important role in the gene expression of the host’s roots and regulated multiple pathways involved in amino acid metabolism, carbohydrate metabolism, TCA cycle, secondary metabolism, and lipid metabolism in the roots of A. inebrians. Importantly, E. gansuensis significantly induced the biological processes, including exocytosis, glycolytic process, fructose metabolic process, and potassium ion transport in roots of host plants at transcriptional levels, and altered the pathways, including inositol phosphate metabolism, galactose metabolism, starch, and sucrose metabolism at metabolite levels under NaCl stress. These findings provided insight into the molecular mechanism of salt resistance in roots of A. inebrians mediated by E. gansuensis and could drive progress in the cultivation of new salt-resistance breeds with endophytes.
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Chen X, Tang K, Zhang M, Liu S, Chen M, Zhan P, Fan W, Chen CTA, Zhang Y. Genome-centric insight into metabolically active microbial population in shallow-sea hydrothermal vents. MICROBIOME 2022; 10:170. [PMID: 36242065 PMCID: PMC9563475 DOI: 10.1186/s40168-022-01351-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/22/2022] [Indexed: 05/20/2023]
Abstract
BACKGROUND Geothermal systems have contributed greatly to both our understanding of the functions of extreme life and the evolutionary history of life itself. Shallow-sea hydrothermal systems are ecological intermediates of deep-sea systems and terrestrial springs, harboring unique and complexed ecosystems, which are well-lit and present physicochemical gradients. The microbial communities of deep-sea and terrestrial geothermal systems have been well-studied at the population genome level, yet little is known about the communities inhabiting the shallow-sea hydrothermal systems and how they compare to those inhabiting other geothermal systems. RESULTS Here, we used genome-resolved metagenomic and metaproteomic approaches to probe into the genetic potential and protein expression of microorganisms from the shallow-sea vent fluids off Kueishantao Island. The families Nautiliaceae and Campylobacteraceae within the Epsilonbacteraeota and the Thiomicrospiraceae within the Gammaproteobacteria were prevalent in vent fluids over a 3-year sampling period. We successfully reconstructed the in situ metabolic modules of the predominant populations within the Epsilonbacteraeota and Gammaproteobacteria by mapping the metaproteomic data back to metagenome-assembled genomes. Those active bacteria could use the reductive tricarboxylic acid cycle or Calvin-Benson-Bassham cycle for autotrophic carbon fixation, with the ability to use reduced sulfur species, hydrogen or formate as electron donors, and oxygen as a terminal electron acceptor via cytochrome bd oxidase or cytochrome bb3 oxidase. Comparative metagenomic and genomic analyses revealed dramatic differences between submarine and terrestrial geothermal systems, including microbial functional potentials for carbon fixation and energy conversion. Furthermore, shallow-sea hydrothermal systems shared many of the major microbial genera that were first isolated from deep-sea and terrestrial geothermal systems, while deep-sea and terrestrial geothermal systems shared few genera. CONCLUSIONS The metabolic machinery of the active populations within Epsilonbacteraeota and Gammaproteobacteria at shallow-sea vents can mirror those living at deep-sea vents. With respect to specific taxa and metabolic potentials, the microbial realm in the shallow-sea hydrothermal system presented ecological linkage to both deep-sea and terrestrial geothermal systems. Video Abstract.
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Affiliation(s)
- Xiaofeng Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China.
| | - Mu Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Shujing Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Mingming Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Peiwen Zhan
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Wei Fan
- Ocean College, Zhejiang University, Zhoushan, China
| | - Chen-Tung Arthur Chen
- Institute of Marine Geology and Chemistry, National Sun Yat-Sen University, Taiwan, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
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Pankievicz VCS, Delaux PM, Infante V, Hirsch HH, Rajasekar S, Zamora P, Jayaraman D, Calderon CI, Bennett A, Ané JM. Nitrogen fixation and mucilage production on maize aerial roots is controlled by aerial root development and border cell functions. FRONTIERS IN PLANT SCIENCE 2022; 13:977056. [PMID: 36275546 PMCID: PMC9583020 DOI: 10.3389/fpls.2022.977056] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Exploring natural diversity for biological nitrogen fixation in maize and its progenitors is a promising approach to reducing our dependence on synthetic fertilizer and enhancing the sustainability of our cropping systems. We have shown previously that maize accessions from the Sierra Mixe can support a nitrogen-fixing community in the mucilage produced by their abundant aerial roots and obtain a significant fraction of their nitrogen from the air through these associations. In this study, we demonstrate that mucilage production depends on root cap and border cells sensing water, as observed in underground roots. The diameter of aerial roots correlates with the volume of mucilage produced and the nitrogenase activity supported by each root. Young aerial roots produce more mucilage than older ones, probably due to their root cap's integrity and their ability to produce border cells. Transcriptome analysis on aerial roots at two different growth stages before and after mucilage production confirmed the expression of genes involved in polysaccharide synthesis and degradation. Genes related to nitrogen uptake and assimilation were up-regulated upon water exposure. Altogether, our findings suggest that in addition to the number of nodes with aerial roots reported previously, the diameter of aerial roots and abundance of border cells, polysaccharide synthesis and degradation, and nitrogen uptake are critical factors to ensure efficient nitrogen fixation in maize aerial roots.
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Affiliation(s)
| | - Pierre-Marc Delaux
- Department of Bacteriology and Agronomy, University of Wisconsin-Madison, Madison, WI, United States
| | - Valentina Infante
- Department of Bacteriology and Agronomy, University of Wisconsin-Madison, Madison, WI, United States
| | - Hayley H. Hirsch
- Department of Bacteriology and Agronomy, University of Wisconsin-Madison, Madison, WI, United States
| | - Shanmugam Rajasekar
- Department of Bacteriology and Agronomy, University of Wisconsin-Madison, Madison, WI, United States
| | - Pablo Zamora
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Dhileepkumar Jayaraman
- Department of Bacteriology and Agronomy, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Alan Bennett
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Jean-Michel Ané
- Department of Bacteriology and Agronomy, University of Wisconsin-Madison, Madison, WI, United States
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Over-Expression of Phosphoserine Aminotransferase-Encoding Gene ( AtPSAT1) Prompts Starch Accumulation in L. turionifera under Nitrogen Starvation. Int J Mol Sci 2022; 23:ijms231911563. [PMID: 36232863 PMCID: PMC9570139 DOI: 10.3390/ijms231911563] [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: 07/31/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
It has been demonstrated that the phosphorylation pathway of L-serine (Ser) biosynthesis (PPSB) is very important in plant growth and development, but whether and how PPSB affects nitrogen metabolism and starch accumulation has not been fully elucidated. In this study, we took the energy plant duckweed (strain Lemna turionifera 5511) as the research object and used a stable genetic transformation system to heterologously over-expressing Arabidopsis AtPSAT1 (the gene encoding phosphoserine aminotransferase, the second enzyme of PPSB). Our results showed that, under nitrogen starvation, the transgenic plants grew faster, with higher values of Fv/Fm, rETR, and Y(II), as well as fresh and dry weight, than the wild-type. More promisingly, the accumulation of starch was also found to be significantly improved when over-expressing AtPSAT1 in the transgenic plants. qRT-PCR analysis results showed that the expression of genes related to nitrogen assimilation, carbon metabolism, and starch biosynthesis was up-regulated, while the expression of starch degradation-related genes was down-regulated by AtPSAT1 over-expression. We propose that the increased starch accumulation caused by AtPSAT1 over-expression may result from both elevated photosynthetic capacity and nitrogen utilization efficiency. This research sheds new light on the mechanism underlying the ability of PPSB to coordinate nitrogen and carbon metabolism, and provides a feasible way to improve starch production, that is, through engineering PPSB in crops.
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Zhang K, Li S, Xu Y, Zhou Y, Ran S, Zhao H, Huang W, Xu R, Zhong F. Effect of Nickel Ions on the Physiological and Transcriptional Responses to Carbon and Nitrogen Metabolism in Tomato Roots under Low Nitrogen Levels. Int J Mol Sci 2022; 23:ijms231911398. [PMID: 36232700 PMCID: PMC9569439 DOI: 10.3390/ijms231911398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/20/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Nickel (Ni) is an essential trace element for plant growth and a component of the plant body that has many different functions in plants. Although it has been confirmed that nickel ions (Ni2+) havea certain regulatory effect on nitrogen (N) metabolism, there are not enough data to prove whether exogenous Ni2+ can increase the carbon (C) and N metabolism in the roots of tomato seedlingsunder low-nitrogen (LN) conditions. Therefore, through the present experiment, we revealed the key mechanism of Ni2+-mediated tomato root tolerance to LN levels. Tomato plants were cultured at two different N levels (7.66 and 0.383 mmol L−1) and two different Ni2+ levels (0 and 0.1 mg L−1 NiSO4 6H2O) under hydroponic conditions. After nine days, we collected roots for physiological, biochemical, and transcriptome sequencing analyses and found that the activities of N assimilation-related enzymes decreased at LN levels. In contrast, Ni2+ significantly increased the activities of N assimilation-related enzymes and increased the contents of nitrate (NO3−), ammonium (NH4+), and total amino acids. Through root transcriptomic analysis, 3738 differentially expressed genes (DEGs) were identified. DEGs related to C and N metabolism were downregulated after LN application. However, after Ni2+ treatment, PK, PDHB, GAPDH, NR, NiR, GS, GOGAT, and other DEGs related to C and N metabolism were significantly upregulated. In conclusion, our results suggest that Ni2+ can regulate the C and N metabolism pathways in tomato roots to alleviate the impact of LN levels.
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Affiliation(s)
- Kun Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuhao Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yang Xu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuqi Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shengxiang Ran
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huanhuan Zhao
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | | | - Ru Xu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Fenglin Zhong
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence:
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50
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Chattha MS, Ali Q, Haroon M, Afzal MJ, Javed T, Hussain S, Mahmood T, Solanki MK, Umar A, Abbas W, Nasar S, Schwartz-Lazaro LM, Zhou L. Enhancement of nitrogen use efficiency through agronomic and molecular based approaches in cotton. FRONTIERS IN PLANT SCIENCE 2022; 13:994306. [PMID: 36237509 PMCID: PMC9552886 DOI: 10.3389/fpls.2022.994306] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/22/2022] [Indexed: 05/22/2023]
Abstract
Cotton is a major fiber crop grown worldwide. Nitrogen (N) is an essential nutrient for cotton production and supports efficient crop production. It is a crucial nutrient that is required more than any other. Nitrogen management is a daunting task for plants; thus, various strategies, individually and collectively, have been adopted to improve its efficacy. The negative environmental impacts of excessive N application on cotton production have become harmful to consumers and growers. The 4R's of nutrient stewardship (right product, right rate, right time, and right place) is a newly developed agronomic practice that provides a solid foundation for achieving nitrogen use efficiency (NUE) in cotton production. Cropping systems are equally crucial for increasing production, profitability, environmental growth protection, and sustainability. This concept incorporates the right fertilizer source at the right rate, time, and place. In addition to agronomic practices, molecular approaches are equally important for improving cotton NUE. This could be achieved by increasing the efficacy of metabolic pathways at the cellular, organ, and structural levels and NUE-regulating enzymes and genes. This is a potential method to improve the role of N transporters in plants, resulting in better utilization and remobilization of N in cotton plants. Therefore, we suggest effective methods for accelerating NUE in cotton. This review aims to provide a detailed overview of agronomic and molecular approaches for improving NUE in cotton production, which benefits both the environment and growers.
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Affiliation(s)
- Muhammad Sohaib Chattha
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Qurban Ali
- Laboratory of Integrated Management of Crop Diseases and Pests, Department of Plant Pathology, College of Plant Protection, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Muhammad Haroon
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | | | - Talha Javed
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sadam Hussain
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Tahir Mahmood
- Department of Plant Breeding & Genetics, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Manoj K. Solanki
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Aisha Umar
- Institute of Botany, University of the Punjab, Lahore, Pakistan
| | - Waseem Abbas
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Shanza Nasar
- Department of Botany, University of Gujrat Hafiz Hayat Campus, Gujrat, Pakistan
| | - Lauren M. Schwartz-Lazaro
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Lei Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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