1
|
Wang B, Yang R, Zhang Z, Huang S, Ji Z, Zheng W, Zhang H, Zhang Y, Feng F. Integration of miRNA and mRNA analysis reveals the role of ribosome in to anti-artificial aging in sweetcorn. Int J Biol Macromol 2023; 240:124434. [PMID: 37062384 DOI: 10.1016/j.ijbiomac.2023.124434] [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: 11/04/2022] [Revised: 03/03/2023] [Accepted: 03/31/2023] [Indexed: 04/18/2023]
Abstract
Sweetcorn is a kind of maize with high sugar content and has poor seed aging tolerance, which seriously limits its production. However, few studies have explored the artificial aging (AA) tolerance by miRNA-mRNA integration analysis in sweetcorn. Here, we characterized the physiological, biochemical and transcriptomic changes of two contrasting lines K62 and K107 treated with AA during time series. Both the germination indexes and antioxidant enzymes showed significant difference between two lines. The MDA content of AA-tolerant genotype K62 was significantly lower than that of K107 on the fourth and sixth day. Subsequently, 157 differentially expressed miRNAs (DEMIs) and 8878 differentially expressed mRNAs (DEMs) were identified by RNA-seq analysis under aging stress. The "ribosome" and "peroxisome" pathways were enriched to respond to aging stress, genes for both large units and small ribosomal subunits were significantly upregulated expressed and higher translation efficiency might exist in K62. Thirteen pairs of miRNA-target genes were obtained, and 8 miRNA-mRNA pairs might involve in ribosome protein and translation process. Our results elucidate the mechanism of sweetcorn response to AA at miRNA-mRNA level, and provide a new insight into sweetcorn AA response to stress.
Collapse
Affiliation(s)
- Bo Wang
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Ruichun Yang
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Zili Zhang
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Silin Huang
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Zhaoqian Ji
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Wenbo Zheng
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Huaxing Zhang
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Yafeng Zhang
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Faqiang Feng
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China.
| |
Collapse
|
2
|
Wu D, Hou Y, Cheng J, Han T, Hao N, Zhang B, Fan X, Ji X, Chen F, Gong D, Wang L, McGinn P, Zhao L, Chen S. Transcriptome analysis of lipid metabolism in response to cerium stress in the oleaginous microalga Nannochloropsis oculata. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156420. [PMID: 35660445 DOI: 10.1016/j.scitotenv.2022.156420] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/28/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Nannochloropsis oculata can accumulate large amounts of lipids under rare earth element (REE) conditions. However, the lipid accumulation mechanism responsible for REE stress has not been elucidated. In this study, the effects of cerium (the most abundant REE) on the growth and lipid accumulation of N. oculata were investigated. The de novo transcriptome data of N. oculata under cerium conditions were subsequently collected and analyzed. The results showed that N. oculata exhibited good cerium-resistance ability, showed slightly decrease in biomass but significantly increase in lipid content (55.8 % dry cell weight) under 6.0 mg/L cerium condition. Meanwhile, about 83.4 % cerium was biological fixated. Through transcriptome analysis, we found that the inhibited photosynthesis and carbon fixation pathways coupled with the stress-sensitive expression of ribosome biogenesis genes acclimatized the cells to REE stress. The active glycolysis pathway accelerated carbon flux to pyruvate and acetyl-CoA, and the upregulation of glycerol kinase and phosphatidate cytidylyltransferase genes further induced lipid accumulation. In addition, cerium downregulated the acyl-CoA oxidase and triacylglycerol lipase genes, which inhibited the degradation of lipids. Therefore, different responses to cerium demonstrate how N. oculata cells adapt to REE stress, and this knowledge may be used to extend our understanding of triacylglycerol (TAG) and the synthesis of other important metabolites.
Collapse
Affiliation(s)
- Di Wu
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China
| | - Yuyong Hou
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Jie Cheng
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China
| | - Tong Han
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Nahui Hao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Bingjie Zhang
- Department of Food Engineering, Anhui Science and Technology Trade School, Bengbu 233080, China
| | - Xiang Fan
- Department of Food Engineering, Anhui Science and Technology Trade School, Bengbu 233080, China
| | - Xiang Ji
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China.
| | - Fangjian Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin, China.
| | - Donghui Gong
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China
| | - Lei Wang
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China
| | - Patrick McGinn
- National Research Council Canada, 1200 Montreal Road, Building M-58, Ottawa, Ontario K1A 0R6, Canada
| | - Lei Zhao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin, China.
| | - Shulin Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| |
Collapse
|
3
|
Pena LB, Matayoshi CL, Méndez AAE, Arán M, Moratto CJ, Vázquez-Ramos JM, Gallego SM. Metabolic rearrangements in imbibed maize (Zea mays L) embryos in the presence of oxidative stressors. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 155:560-569. [PMID: 32846391 DOI: 10.1016/j.plaphy.2020.08.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 08/06/2020] [Accepted: 08/13/2020] [Indexed: 06/11/2023]
Abstract
Cadmium (Cd) is a metal known to generate oxidative stress in plants and may be particularly harmful during germination. Herein, the growth and metabolic rearrangements of maize embryo axes subjected during the imbibition stage to Cd ions and other two well-known oxidative stressors, methyl viologen (MV) and hydrogen peroxide (H2O2), were assessed for 48 h. Similar decreases in embryo's length were detected for all stressed axes up to 48 h of imbibition. By this time, treated embryos revealed greater accumulation of reactive oxygen species (ROS) and increased levels of carbonylated and ubiquitinated proteins. The proteolytic activities were intensely enhanced in the treated axes, particularly at 48 h of imbibition, and several antioxidant enzymes were induced in most cases. NMR spectroscopy followed by principal component analysis (PCA) and hierarchical cluster analysis (HCA) showed that a large proportion of polar metabolites, mainly amino acids and organic acids, were decreased under stress conditions, while carbohydrates were increased at 48 h of imbibition, with significant increases in glucose and raffinose for treated embryos relatively to controls. We demonstrated that maize embryo axes were capable of shifting their metabolism to improve their antioxidant defense system, at the expense of their growth. Under these adverse conditions, proteolysis seems to play a key role by providing free amino acids needed for the de novo synthesis of defense-related proteins.
Collapse
Affiliation(s)
- Liliana B Pena
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina; Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Buenos Aires, Argentina
| | - Carolina L Matayoshi
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina
| | - Andrea A E Méndez
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina; Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Buenos Aires, Argentina
| | - Martín Arán
- Laboratorio de Resonancia Magnética Nuclear, Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - Camila J Moratto
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina
| | - Jorge M Vázquez-Ramos
- Universidad Nacional Autónoma de México, Facultad de Química, Departamento de Bioquímica, México DF, Mexico
| | - Susana M Gallego
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina; Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Buenos Aires, Argentina.
| |
Collapse
|
4
|
Cheng Q, Zhou Q, Jin Z, Jiang Y, Xu L, Jiang H, Zhao Y. Bioaccumulation, growth performance, and transcriptomic response of Dictyosphaerium sp. after exposure to nonylphenol. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 687:416-422. [PMID: 31212149 DOI: 10.1016/j.scitotenv.2019.06.136] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/07/2019] [Accepted: 06/08/2019] [Indexed: 06/09/2023]
Abstract
Algal cultures of Dictyosphaerium sp. were treated with a wide range (0-8 mg/L) of nonylphenol (NP) applications to investigate the species' potential to perform bioremediation of NP-contaminated wastewater and explore the mechanism of NP toxicity in algal cell. The algal species exhibited a high tolerance for NP and efficiently removed even high concentrations of NP. The accumulation of NP in algal cells tended to increase and the percentage of NP adhered to the cell walls tended to decrease as the NP concentration increased. The thylakoid density and the pyrenoid size also tended to decrease as the NP concentration rose. The key genes involved in the antioxidative pathways and photosynthetic pathways were down-regulated in the NP-treated algal cells. Algal ribosome genes were especially sensitive to NP. The results indicated that NP could induce oxidative stress in algal cells and that Dictyosphaerium sp. showed potential as a bioremediation agent.
Collapse
Affiliation(s)
- Qilu Cheng
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qifa Zhou
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhuo Jin
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying Jiang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ligen Xu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hui Jiang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuhua Zhao
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
5
|
Deng K, Yu L, Zheng X, Zhang K, Wang W, Dong P, Zhang J, Ren M. Target of Rapamycin Is a Key Player for Auxin Signaling Transduction in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2016; 7:291. [PMID: 27014314 PMCID: PMC4786968 DOI: 10.3389/fpls.2016.00291] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 02/23/2016] [Indexed: 05/08/2023]
Abstract
Target of rapamycin (TOR), a master sensor for growth factors and nutrition availability in eukaryotic species, is a specific target protein of rapamycin. Rapamycin inhibits TOR kinase activity viaFK506 binding protein 12 kDa (FKBP12) in all examined heterotrophic eukaryotic organisms. In Arabidopsis, several independent studies have shown that AtFKBP12 is non-functional under aerobic condition, but one study suggests that AtFKBP12 is functional during anaerobic growth. However, the functions of AtFKBP12 have never been examined in parallel under aerobic and anaerobic growth conditions so far. To this end, we cloned the FKBP12 gene of humans, yeast, and Arabidopsis, respectively. Transgenic plants were generated, and pharmacological examinations were performed in parallel with Arabidopsis under aerobic and anaerobic conditions. ScFKBP12 conferred plants with the strongest sensitivity to rapamycin, followed by HsFKBP12, whereas AtFKBP12 failed to generate rapamycin sensitivity under aerobic condition. Upon submergence, yeast and human FKBP12 can significantly block cotyledon greening while Arabidopsis FKBP12 only retards plant growth in the presence of rapamycin, suggesting that hypoxia stress could partially restore the functions of AtFKBP12 to bridge the interaction between rapamycin and TOR. To further determine if communication between TOR and auxin signaling exists in plants, yeast FKBP12 was introduced into DR5::GUS homozygous plants. The transgenic plants DR5/BP12 were then treated with rapamycin or KU63794 (a new inhibitor of TOR). GUS staining showed that the auxin content of root tips decreased compared to the control. DR5/BP12 plants lost sensitivity to auxin after treatment with rapamycin. Auxin-defective phenotypes, including short primary roots, fewer lateral roots, and loss of gravitropism, occurred in DR5/BP12 plants when seedlings were treated with rapamycin+KU63794. This indicated that the combination of rapamycin and KU63794 can significantly inhibit TOR and auxin signaling in DR5/BP12 plants. These studies demonstrate that TOR is essential for auxin signaling transduction in Arabidopsis.
Collapse
Affiliation(s)
- Kexuan Deng
- School of Life Sciences, Chongqing UniversityChongqing, China
| | - Lihua Yu
- School of Life Sciences, Chongqing UniversityChongqing, China
| | - Xianzhe Zheng
- School of Life Sciences, Chongqing UniversityChongqing, China
| | - Kang Zhang
- School of Life Sciences, Chongqing UniversityChongqing, China
| | - Wanjing Wang
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Pan Dong
- School of Life Sciences, Chongqing UniversityChongqing, China
| | - Jiankui Zhang
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Maozhi Ren
- School of Life Sciences, Chongqing UniversityChongqing, China
- *Correspondence: Maozhi Ren
| |
Collapse
|
6
|
Yu X, Li A, Li W. How membranes organize during seed germination: three patterns of dynamic lipid remodelling define chilling resistance and affect plastid biogenesis. PLANT, CELL & ENVIRONMENT 2015; 38:1391-403. [PMID: 25474382 PMCID: PMC4766844 DOI: 10.1111/pce.12494] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 11/18/2014] [Accepted: 11/22/2014] [Indexed: 05/20/2023]
Abstract
Imbibitional chilling injury during germination causes agricultural losses, but this can be overcome by osmopriming. It remains unknown how membranes reorganize during germination. Herein, we comparatively profiled changes of membrane lipids during imbibition under normal and chilling temperatures in chilling-tolerant and -sensitive soybean seeds. We found three patterns of dynamic lipid remodelling during the three phases of germination. Pattern 1 involved a gradual increase in plastidic lipids during phases I and II, with an abrupt increase during phase III. This abrupt increase was associated with initiation of photosynthesis. Pattern 3 involved phosphatidic acid (PA) first decreasing, then increasing, and finally decreasing to a low level. Patterns 1 and 3 were interrupted in chilling-sensitive seeds under low temperature, which lead a block in plastid biogenesis and accumulation of harmful PA, respectively. However, they were rescued and returned to their status under normal temperature after polyethylene glycol osmopriming. We specifically inhibited phospholipase D (PLD)-mediated PA formation in chilling-sensitive seeds of soybean, cucumber, and pea, and found their germination under low temperature was significantly improved. These results indicate that membranes undergo specific and functional reorganization of lipid composition during germination and demonstrate that PLD-mediated PA causes imibibitional chilling injury.
Collapse
Affiliation(s)
- Xiamei Yu
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Aihua Li
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Weiqi Li
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| |
Collapse
|
7
|
Durut N, Sáez-Vásquez J. Nucleolin: dual roles in rDNA chromatin transcription. Gene 2015; 556:7-12. [PMID: 25225127 DOI: 10.1016/j.gene.2014.09.023] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/08/2014] [Accepted: 09/09/2014] [Indexed: 01/17/2023]
Abstract
Nucleolin is a major nucleolar protein conserved in all eukaryotic organisms. It is a multifunctional protein involved in different cellular aspects like chromatin organization and stability, DNA and RNA metabolism, assembly of ribonucleoprotein complexes, cytokinesis, cell proliferation and stress response. The multifunctionality of nucleolin is linked to its tripartite structure, post-translational modifications and its ability of shuttling from and to the nucleolus/nucleoplasm and cytoplasm. Nucleolin has been now studied for many years and its activities and properties have been described in a number of excellent reviews. Here, we overview the role of nucleolin in RNA polymerase I (RNAPI) transcription and describe recent results concerning its functional interaction with rDNA chromatin organization. For a long time, nucleolin has been associated with rRNA gene expression and pre-rRNA processing. However, the functional connection between nucleolin and active versus inactive rRNA genes is still not fully understood. Novel evidence indicates that the nucleolin protein might be required for controlling the transcriptional ON/OFF states of rDNA chromatin in both mammals and plants.
Collapse
Affiliation(s)
- Nathalie Durut
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France; Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
| | - Julio Sáez-Vásquez
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France; Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France.
| |
Collapse
|
8
|
Garrocho-Villegas V, Aguilar C R, Sánchez de Jiménez E. Insights into the TOR-S6K signaling pathway in maize (Zea mays L.). pathway activation by effector-receptor interaction. Biochemistry 2013; 52:9129-40. [PMID: 24358933 DOI: 10.1021/bi401474x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The primordial TOR pathway, known to control growth and cell proliferation, has still not been fully described for plants. Nevertheless, in maize, an insulin-like growth factor (ZmIGF) peptide has been reported to stimulate this pathway. This research provides further insight into the TOR pathway in maize, using a biochemical approach in cultures of fast-growing (FG) and slow-growing (SG) calli, as a model system. Our results revealed that addition of either ZmIGF or insulin to SG calli stimulated DNA synthesis and increased the growth rate through cell proliferation and increased the rate of ribosomal protein (RP) synthesis by the selective mobilization of RP mRNAs into polysomes. Furthermore, analysis of the phosphorylation status of the main TOR and S6K kinases from the TOR pathway revealed stimulation by ZmIGF or insulin, whereas rapamycin inhibited its activation. Remarkably, a putative maize insulin-like receptor was recognized by a human insulin receptor antibody, as demonstrated by immunoprecipitation from membrane protein extracts of maize callus. Furthermore, competition experiments between ZmIGF and insulin for the receptor site on maize protoplasts suggested structural recognition of the putative receptor by either effector. These data were confirmed by confocal immunolocalization within the cell membrane of callus cells. Taken together, these data indicate that cell growth and cell proliferation in maize depend on the activation of the TOR-S6K pathway through the interaction of an insulin-like growth factor and its receptor. This evidence suggests that higher plants as well as metazoans have conserved this biochemical pathway to regulate their growth, supporting the conclusion that it is a highly evolved conserved pathway.
Collapse
|