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Herrera-Isidron L, Uribe-Lopez B, Barraza A, Cabrera-Ponce JL, Valencia-Lozano E. Analysis of Stress Response Genes in Microtuberization of Potato Solanum tuberosum L.: Contributions to Osmotic and Combined Abiotic Stress Tolerance. PLANTS (BASEL, SWITZERLAND) 2024; 13:2996. [PMID: 39519915 PMCID: PMC11548447 DOI: 10.3390/plants13212996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Revised: 10/23/2024] [Accepted: 10/25/2024] [Indexed: 11/16/2024]
Abstract
Wild Solanum species have contributed many introgressed genes during domestication into current cultivated potatoes, enhancing their biotic and abiotic stress resistance and facilitating global expansion. Abiotic stress negatively impacts potato physiology and productivity. Understanding the molecular mechanisms regulating tuber development may help solve this global problem. We made a transcriptomic analysis of potato microtuberization under darkness, cytokinins, and osmotic stress conditions. A protein-protein interaction (PPI) network analysis identified 404 genes with high confidence. These genes were involved in important processes like oxidative stress, carbon metabolism, sterol biosynthesis, starch and sucrose metabolism, fatty acid biosynthesis, and nucleosome assembly. From this network, we selected nine ancestral genes along with eight additional stress-related genes. We used qPCR to analyze the expression of the selected genes under osmotic, heat-osmotic, cold-osmotic, salt-osmotic, and combined-stress conditions. The principal component analysis (PCA) revealed that 60.61% of the genes analyzed were associated with osmotic, cold-osmotic, and heat-osmotic stress. Seven out of ten introgression/domestication genes showed the highest variance in the analysis. The genes H3.2 and GAPCP1 were involved in osmotic, cold-osmotic, and heat-osmotic stress. Under combined-all stress, TPI and RPL4 were significant, while in salt-osmotic stress conditions, ENO1, HSP70-8, and PER were significant. This indicates the importance of ancestral genes for potato survival during evolution. The targeted manipulation of these genes could improve combined-stress tolerance in potatoes, providing a genetic basis for enhancing crop resilience.
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Affiliation(s)
- Lisset Herrera-Isidron
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato (UPIIG), Instituto Politécnico Nacional, Av. Mineral de Valenciana 200, Puerto Interior, Silao de la Victoria 36275, Guanajuato, Mexico; (L.H.-I.); (B.U.-L.)
| | - Braulio Uribe-Lopez
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato (UPIIG), Instituto Politécnico Nacional, Av. Mineral de Valenciana 200, Puerto Interior, Silao de la Victoria 36275, Guanajuato, Mexico; (L.H.-I.); (B.U.-L.)
| | - Aaron Barraza
- CONAHCYT-Centro de Investigaciones Biológicas del Noreste, SC. Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz 23096, Baja California Sur, Mexico;
| | - José Luis Cabrera-Ponce
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico
| | - Eliana Valencia-Lozano
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico
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Tan L, Lu L, Sun W, Zhang X, Liu Y, Xiang Y, Yan H. Identification and validation of qRT-PCR reference genes for analyzing grape infection with gray mold. BMC Genomics 2024; 25:997. [PMID: 39448910 PMCID: PMC11515470 DOI: 10.1186/s12864-024-10889-9] [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: 06/02/2024] [Accepted: 10/09/2024] [Indexed: 10/26/2024] Open
Abstract
BACKGROUND Grapes are highly valued for their nutritional and economic benefits, and have been widely studied for their biological attributes such as fruit development, quality formation, and stress resistance. One significant threat to grape quality is gray mold, caused by Botrytis cinerea, which can infect the flowers, fruits, leaves, and stems. The quantitative real-time PCR (qRT-PCR), known for its high sensitivity and quantitative accuracy, is an essential tool for analyzing gene expression related to the pathogenesis of gray mold, thereby providing deeper insights into the disease. RESULT In this study, we aim to identify stable internal reference genes crucial for accurate gene expression analysis via qRT-PCR. Utilizing transcriptome data from grapes under various disease stresses, we identified twelve candidate reference genes with consistently high expression levels. The stability of these genes was assessed through delta-CT, geNorm, NormFinder, BestKeeper, and RefFinder analyses after establishing the cycling thresholds (Ct) in different grape varieties treated with Botrytis cinerea. CONCLUSIONS Our findings reveal that VIT-17s0000g02750 and VIT-06s0004g04280 exhibit stable expression and are suitable as new reference genes. This foundational work supports further research into the molecular mechanisms of grape biological processes.
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Affiliation(s)
- Lina Tan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Lijuan Lu
- Horticulture Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Wen Sun
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Xinyuan Zhang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Yanglin Liu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Hanwei Yan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China.
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Li W, Liu J, Li Z, Ye R, Chen W, Huang Y, Yuan Y, Zhang Y, Hu H, Zheng P, Fang Z, Tao Z, Song S, Pan R, Zhang J, Tu J, Sheen J, Du H. Mitigating growth-stress tradeoffs via elevated TOR signaling in rice. MOLECULAR PLANT 2024; 17:240-257. [PMID: 38053337 PMCID: PMC11271712 DOI: 10.1016/j.molp.2023.12.002] [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: 09/18/2023] [Revised: 11/29/2023] [Accepted: 12/01/2023] [Indexed: 12/07/2023]
Abstract
Rice production accounts for approximately half of the freshwater resources utilized in agriculture, resulting in greenhouse gas emissions such as methane (CH4) from flooded paddy fields. To address this challenge, environmentally friendly and cost-effective water-saving techniques have become widely adopted in rice cultivation. However, the implementation of water-saving treatments (WSTs) in paddy-field rice has been associated with a substantial yield loss of up to 50% as well as a reduction in nitrogen use efficiency (NUE). In this study, we discovered that the target of rapamycin (TOR) signaling pathway is compromised in rice under WST. Polysome profiling-coupled transcriptome sequencing (polysome-seq) analysis unveiled a substantial reduction in global translation in response to WST associated with the downregulation of TOR activity. Molecular, biochemical, and genetic analyses revealed new insights into the impact of the positive TOR-S6K-RPS6 and negative TOR-MAF1 modules on translation repression under WST. Intriguingly, ammonium exhibited a greater ability to alleviate growth constraints under WST by enhancing TOR signaling, which simultaneously promoted uptake and utilization of ammonium and nitrogen allocation. We further demonstrated that TOR modulates the ammonium transporter AMT1;1 as well as the amino acid permease APP1 and dipeptide transporter NPF7.3 at the translational level through the 5' untranslated region. Collectively, these findings reveal that enhancing TOR signaling could mitigate rice yield penalty due to WST by regulating the processes involved in protein synthesis and NUE. Our study will contribute to the breeding of new rice varieties with increased water and fertilizer utilization efficiency.
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Affiliation(s)
- Wei Li
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Yu-Hang-Tang Road No. 866, Hangzhou 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Jiaqi Liu
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Yu-Hang-Tang Road No. 866, Hangzhou 310058, China
| | - Zeqi Li
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Yu-Hang-Tang Road No. 866, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Ruiqiang Ye
- National Key Laboratory of Plant Molecular Genetics, CAS, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wenzhen Chen
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Yu-Hang-Tang Road No. 866, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Yuqing Huang
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Yu-Hang-Tang Road No. 866, Hangzhou 310058, China
| | - Yue Yuan
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Yu-Hang-Tang Road No. 866, Hangzhou 310058, China
| | - Yi Zhang
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Yu-Hang-Tang Road No. 866, Hangzhou 310058, China
| | - Huayi Hu
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Yu-Hang-Tang Road No. 866, Hangzhou 310058, China
| | - Peng Zheng
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Yu-Hang-Tang Road No. 866, Hangzhou 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Zhongming Fang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Agricultural Sciences, Guizhou University, Guiyang 550025, China
| | - Zeng Tao
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Yu-Hang-Tang Road No. 866, Hangzhou 310058, China
| | - Shiyong Song
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Yu-Hang-Tang Road No. 866, Hangzhou 310058, China
| | - Ronghui Pan
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Yu-Hang-Tang Road No. 866, Hangzhou 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Jian Zhang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Jumim Tu
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Yu-Hang-Tang Road No. 866, Hangzhou 310058, China
| | - Jen Sheen
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Hao Du
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Yu-Hang-Tang Road No. 866, Hangzhou 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China; Hainan Institute of Zhejiang University, Sanya 572025, China.
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Zhuang X, Liu T, Wei L, Gao Y, Gao J. RNA sequencing reveals the mechanism of FTO in inhibiting inflammation and excessive proliferation of lipopolysaccharide-induced human glomerular mesangial cells. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2023; 396:3835-3846. [PMID: 37358794 DOI: 10.1007/s00210-023-02570-x] [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: 04/07/2023] [Accepted: 06/06/2023] [Indexed: 06/27/2023]
Abstract
Chronic glomerulonephritis (CGN) is a leading cause of end-stage renal disease in China; thus, there is an urgent need for effective therapeutic targets and strategies for CGN treatment. However, studies on CGN pathogenesis are limited. In this study, we found that the fat mass and obesity-associated protein (FTO) was significantly decreased in the lipopolysaccharide (LPS)-induced human glomerular mesangial cells (HGMCs) (P < 0.01) and kidney tissues of CGN patients (P < 0.05). Moreover, double-labeling immunofluorescence and flow cytometry assays demonstrated that the overexpression of FTO could inhibit inflammation and excessive proliferation of HGMCs. Furthermore, RNA-sequencing (RNA-seq) and real-time quantitative polymerase chain reaction (RT-qPCR) analyses revealed that FTO overexpression induced differential expression of 269 genes (absolute fold change ≥ 2 and P-value < 0.05), including 143 upregulated and 126 downregulated genes. Further functional analysis of these differentially expressed genes by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses suggested that FTO possibly mediates its inhibitory function by regulating the mammalian target of rapamycin (mTOR) signaling pathway and substance metabolism. Lastly, analysis of the PPI network and further identification of the top 10 hub genes (RPS15, RPS18, RPL18A, GNB2L1, RPL19, EEF1A1, RPS25, FAU, UBA52, and RPS6) indicated that FTO mediates its function by affecting the ribosomal proteins. Therefore, in this study, we elucidated the important role of FTO in the regulation of inflammation and excessive proliferation of HGMCs, suggesting FTO administration as a suitable therapeutic intervention for CGN.
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Affiliation(s)
- Xingxing Zhuang
- Department of Pharmacy, Chaohu Hospital of Anhui Medical University, No. 64 North Chaohu Road, Chaohu, 238000, Anhui, China
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, No. 117 Meishan Road, Hefei, 230012, Anhui, China
| | - Tao Liu
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, No. 117 Meishan Road, Hefei, 230012, Anhui, China
| | - Liangbing Wei
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, No. 117 Meishan Road, Hefei, 230012, Anhui, China
| | - Yachen Gao
- Department of Nephropathy, The First Affiliated Hospital of Anhui University of Chinese Medicine, No. 117 Meishan Road, Hefei, 230012, Anhui, China
| | - Jiarong Gao
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, No. 117 Meishan Road, Hefei, 230012, Anhui, China.
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