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Alagarsamy M, Amal TC, Karuppan S, Adhimoolam K. Comparative proteomic analysis of resistant and susceptible cotton genotypes in response to leaf hopper infestation. J Proteomics 2024; 305:105258. [PMID: 39004338 DOI: 10.1016/j.jprot.2024.105258] [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: 05/17/2024] [Revised: 07/02/2024] [Accepted: 07/11/2024] [Indexed: 07/16/2024]
Abstract
The cotton leaf hopper is a major pest in cotton, causing a hopper burn in leaves. In this study, a comparative proteomic analysis of NDLH2010 (Resistant) and LRA5166 (Susceptible), infected with leaf hopper, was employed using a nano LC-MS/MS approach. A total of 1402 proteins varied significantly between leaf hopper-infected and control plants. The resistant and susceptible genotypes had differentially expressed proteins (DEPs) of 743 and 659, respectively. Functional annotation of DEPs revealed that the DEPs were primarily associated with stress response, hormone synthesis, photosynthesis, cell wall, and secondary metabolites. Notably, DEPs such as polyphenol oxidase, carboxypeptidase, heat shock proteins, protein BTR1-like isoform X2, chaperone protein ClpB1, and β glucosidase factors associated with environmental stress response were also detected. Quantitative real-time PCR (qRT-PCR) analysis confirmed a positive correlation between protein abundances and transcripts for all genes. Collectively, this study provides the molecular mechanisms associated with cotton defense responses against leaf hopper. SIGNIFICANCE STATEMENT: Cotton, a natural fiber, assumes a pivotal role as a raw material for textile industries, thereby bearing significant importance in the global economy. The cotton production sector is considerably affected by both biotic and abiotic stresses. The cotton leaf hopper (Amrasca biguttula biguttula (Ishida)) stands as a polyphagous insect, emerging as a dominant sap-feeding pest of the cotton crop. The continuous onslaught of sap-feeding insects on cotton plants has a detrimental impact, with leaf hoppers potentially causing yield reductions of up to 50%. Therefore, comprehending the molecular interplay between cotton and leaf hopper, elucidated at the proteome level, holds promise for more effective pest management strategies. This approach holds the potential to offer insights that contribute to the development of leaf hopper-resistant cotton varieties.
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Affiliation(s)
- Manivannan Alagarsamy
- ICAR-Central Institute for Cotton Research, Regional Station, Coimbatore, TN, India.
| | - Thomas Cheeran Amal
- ICAR-Central Institute for Cotton Research, Regional Station, Coimbatore, TN, India
| | | | - Karthikeyan Adhimoolam
- Subtropical Horticulture Research Institute, Jeju National University, Jeju, South Korea
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AbdElneam AI, Al‐Dhubaibi MS, Bahaj SS, Mohammed GF, Atef LM. The role of hsa-miR-193a-5p as an important factor for control of inositol in alopecia areata. Skin Res Technol 2024; 30:e13800. [PMID: 38925555 PMCID: PMC11197030 DOI: 10.1111/srt.13800] [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: 01/09/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND MicroRNAs (miRNAs) are small RNA molecules that play a regulatory role in various biological processes by acting as intracellular mediators. They hold great potential as therapeutic agents for targeting human disease pathways; however, there is still much to be uncovered about their mechanism of gene regulation. Alopecia areata (AA) is a commonly occurring inflammatory condition characterized by the infiltration of T cells that specifically target the anagen-stage hair follicle. The limited understanding of its precise cellular mechanism may be the reason behind the scarcity of effective treatments for AA. AIM The significance and function of hsa-miR-193a-5p as a genetic marker for AA and its potential influence on the advancement of the disease. SUBJECTS AND METHODS A case-control study comprised 77 individuals diagnosed with AA who were matched with 75 healthy controls. In order to measure the expression of miR-200c-3p in both groups, the real-time PCR technique was utilized. The prediction of suitable genes for hsa-miR-193a-5p, as well as the identification of pathways and gene-gene interactions, were carried out using bioinformatic tools. RESULTS The levels of hsa-miR-193a-5p expression were notably elevated in AA patients in comparison to healthy controls. Our prediction suggests that the involvement of hsa-miR-193a-5p in the development of AA is significant due to its influence on the inositol phosphorylation pathway and the Phosphatidylinositol signaling system, achieved through its direct impact on the IPPK gene. CONCLUSION For the first time, our study demonstrates the significant over-expression of a new miRNA, hsa-miR-193a-5p, in the blood of AA patients compared to controls, and highlights its impact on the IPPK gene and the inositol phosphorylation and Phosphatidylinositol signaling pathways, suggesting a potential therapeutic role for hsa-miR-193a-5p in AA.
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Affiliation(s)
- Ahmed Ibrahim AbdElneam
- Department of Clinical Biochemistry, Department of Basic Medical Sciences, College of MedicineShaqra UniversityDawadmiSaudi Arabia
- Molecular Genetics and Enzymology DepartmentHuman Genetics and Genome Research Institute, National Research CenterDokkiCairoEgypt
| | | | - Saleh Salem Bahaj
- Department of Microbiology and Immunology, Faculty of Medicine and Health SciencesSana'a UniversitySana'aYemen
| | - Ghada Farouk Mohammed
- Department of Dermatology, Venereology, and Sexology, Faculty of MedicineSuez Canal UniversityIsmailiaEgypt
| | - Lina Mohammed Atef
- Department of Dermatology, Venereology, and Sexology, Faculty of MedicineSuez Canal UniversityIsmailiaEgypt
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Qiao L, Gao X, Jia Z, Liu X, Wang H, Kong Y, Qin P, Yang B. Identification of adult resistant genes to stripe rust in wheat from southwestern China based on GWAS and WGCNA analysis. PLANT CELL REPORTS 2024; 43:67. [PMID: 38341832 DOI: 10.1007/s00299-024-03148-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/02/2024] [Indexed: 02/13/2024]
Abstract
KEY MESSAGE In this study, genome-wide association studies combined with transcriptome data analysis were utilized to reveal potential candidate genes for stripe rust resistance in wheat, providing a basis for screening wheat varieties for stripe rust resistance. Wheat stripe rust, which is caused by the wheat stripe rust fungus (Puccinia striiformis f. sp. tritici, Pst) is one of the world's most devastating diseases of wheat. Genetic resistance is the most effective strategy for controlling diseases. Although wheat stripe rust resistance genes have been identified to date, only a few of them confer strong and broad-spectrum resistance. Here, the resistance of 335 wheat germplasm resources (mainly wheat landraces) from southwestern China to wheat stripe rust was evaluated at the adult stage. Combined genome-wide association study (GWAS) and weighted gene co-expression network analysis (WGCNA) based on RNA sequencing from stripe rust resistant accession Y0337 and susceptible accession Y0402, five candidate resistance genes to wheat stripe rust (TraesCS1B02G170200, TraesCS2D02G181000, TraesCS4B02G117200, TraesCS6A02G189300, and TraesCS3A02G122300) were identified. The transcription level analyses showed that these five genes were significantly differentially expressed between resistant and susceptible accessions post inoculation with Pst at different times. These candidate genes could be experimentally transformed to validate and manipulate fungal resistance, which is beneficial for the development of the wheat cultivars resistant to stripe rust.
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Affiliation(s)
- Liang Qiao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Xue Gao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Zhiqiang Jia
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Xingchen Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Huiyutang Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Yixi Kong
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Peng Qin
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Baoju Yang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China.
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Wu J, Liu X, Ge F, Li F, Liu N. Tolerance mechanism of rice (Oryza sativa L.) seedings towards polycyclic aromatic hydrocarbons toxicity: The activation of SPX-mediated signal transduction to maintain P homeostasis. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 341:123009. [PMID: 38006996 DOI: 10.1016/j.envpol.2023.123009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/01/2023] [Accepted: 11/18/2023] [Indexed: 11/27/2023]
Abstract
Plant tolerance to abiotic stress depends on fast molecular cascades involving stress perception, signal transduction, gene expression alterations, and metabolic rearrangement. This study sheds light on the tolerance mechanism of rice (Oryza sativa L.) towards the toxicity of the polycyclic aromatic hydrocarbons (PAHs), including phenanthrene (Phe), pyrene (Pyr), and benzo[a]pyrene (BaP). Results showed that three PAHs significantly activated the phosphoinositide signaling system involving the phosphorus (P) metabolism and homeostasis in rice roots. This activation increased phytic acid (IP6) levels to over 54.12% of the control (p < 0.05). Molecular docking verified that three PAHs occupied the IP6 binding site in SPX3, a negative regulatory factor of P homeostasis, where ARG229 interacted with PAHs via the van der Waals force. Moreover, the expression of gene encoding SPX3 was significantly downregulated 2.81-, 2.83-, and 2.18-fold under Phe, Pyr, and BaP stress, respectively, relative to the control. Conversely, the expression levels of the gene coding SDEL2 was significantly increased, promoting the degradation of SPX3. Ultimately, P absorption and nucleic acid synthesis were enhanced, alleviating the inhibition effect of PAHs on rice growth. Notably, Pyr demonstrated the strongest binding affinity for SPX3, confirming its critical interference with P homeostasis. These findings provide insight into the molecular mechanisms regulating plant responses to PAHs, and offer guidance for improving crop resistance against organic pollutants and protecting food security.
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Affiliation(s)
- Jianjian Wu
- Department of Environment, College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China; Key Laboratory of Environmental and Ecological Health, Hunan, College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China
| | - Xinyue Liu
- Department of Environment, College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China; Key Laboratory of Environmental and Ecological Health, Hunan, College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China
| | - Fei Ge
- Department of Environment, College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China; Key Laboratory of Environmental and Ecological Health, Hunan, College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China
| | - Feng Li
- Department of Environment, College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China; Key Laboratory of Environmental and Ecological Health, Hunan, College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China
| | - Na Liu
- Department of Environment, College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China; Key Laboratory of Environmental and Ecological Health, Hunan, College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China.
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Abdi H, Alipour H, Bernousi I, Jafarzadeh J, Rodrigues PC. Identification of novel putative alleles related to important agronomic traits of wheat using robust strategies in GWAS. Sci Rep 2023; 13:9927. [PMID: 37336905 DOI: 10.1038/s41598-023-36134-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/30/2023] [Indexed: 06/21/2023] Open
Abstract
Principal component analysis (PCA) is widely used in various genetics studies. In this study, the role of classical PCA (cPCA) and robust PCA (rPCA) was evaluated explicitly in genome-wide association studies (GWAS). We evaluated 294 wheat genotypes under well-watered and rain-fed, focusing on spike traits. First, we showed that some phenotypic and genotypic observations could be outliers based on cPCA and different rPCA algorithms (Proj, Grid, Hubert, and Locantore). Hubert's method provided a better approach to identifying outliers, which helped to understand the nature of these samples. These outliers led to the deviation of the heritability of traits from the actual value. Then, we performed GWAS with 36,000 single nucleotide polymorphisms (SNPs) based on the traditional approach and two robust strategies. In the conventional approach and using the first three components of cPCA as population structure, 184 and 139 marker-trait associations (MTAs) were identified for five traits in well-watered and rain-fed environments, respectively. In the first robust strategy and when rPCA was used as population structure in GWAS, we observed that the Hubert and Grid methods identified new MTAs, especially for yield and spike weight on chromosomes 7A and 6B. In the second strategy, we followed the classical and robust principal component-based GWAS, where the first two PCs obtained from phenotypic variables were used instead of traits. In the recent strategy, despite the similarity between the methods, some new MTAs were identified that can be considered pleiotropic. Hubert's method provided a better linear combination of traits because it had the most MTAs in common with the traditional approach. Newly identified SNPs, including rs19833 (5B) and rs48316 (2B), were annotated with important genes with vital biological processes and molecular functions. The approaches presented in this study can reduce the misleading GWAS results caused by the adverse effect of outlier observations.
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Affiliation(s)
- Hossein Abdi
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Hadi Alipour
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Iraj Bernousi
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran.
| | - Jafar Jafarzadeh
- Dryland Agricultural Research Institute (DARI), Agriculture Research, Education and Extension Organization (AREEO), Maragheh, Iran
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Chen Q, Qu M, Chen Q, Meng X, Fan H. Phosphoproteomics analysis of the effect of target of rapamycin kinase inhibition on Cucumis sativus in response to Podosphaera xanthii. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 197:107641. [PMID: 36940522 DOI: 10.1016/j.plaphy.2023.107641] [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: 01/01/2023] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
Target of rapamycin (TOR) kinase is a conserved sensor of cell growth in yeasts, plants, and mammals. Despite the extensive research on the TOR complex in various biological processes, large-scale phosphoproteomics analysis of TOR phosphorylation events upon environmental stress are scarce. Powdery mildew caused by Podosphaera xanthii poses a major threat to the quality and yield of cucumber (Cucumis sativus L.). Previous studies concluded that TOR participated in abiotic and biotic stress responses. Hence, studying the underlying mechanism of TOR-P. xanthii infection is particularly important. In this study, we performed a quantitative phosphoproteomics studies of Cucumis against P. xanthii attack under AZD-8055 (TOR inhibitor) pretreatment. A total of 3384 phosphopeptides were identified from the 1699 phosphoproteins. The Motif-X analysis showed high sensitivity and specificity of serine sites under AZD-8055-treatment or P. xanthii stress, and TOR exhibited a unique preference for proline at +1 position and glycine at -1 position to enhance the phosphorylation response to P. xanthii. The functional analysis suggested that the unique responses were attributed to proteins related to plant hormone signaling, mitogen-activated protein kinase cascade signaling, phosphatidylinositol signaling system, and circadian rhythm; and calcium signaling- and defense response-related proteins. Our results provided rich resources for understanding the molecular mechanism of how the TOR kinase controlled plant growth and stress adaptation.
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Affiliation(s)
- Qiumin Chen
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Mengqi Qu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, China
| | - Qinglei Chen
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xiangnan Meng
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, China; Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, China; Key Laboratory of Biology and Genetic Improvement of Fruit Vegetables of Shenyang, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Haiyan Fan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, China; Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, China; Key Laboratory of Biology and Genetic Improvement of Fruit Vegetables of Shenyang, Shenyang Agricultural University, Shenyang, 110866, China.
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Liu TH, Zhao L, Zhang CY, Li XY, Wu TL, Dai YY, Sheng YY, Ren YL, Xue YZ. Gut microbial evidence chain in high-salt diet exacerbates intestinal aging process. Front Nutr 2022; 9:1046833. [PMID: 36386919 PMCID: PMC9650087 DOI: 10.3389/fnut.2022.1046833] [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: 09/17/2022] [Accepted: 10/07/2022] [Indexed: 11/29/2022] Open
Abstract
Although excessive salt consumption appears to hasten intestinal aging and increases susceptibility to cardiovascular disease, the molecular mechanism is unknown. In this study, mutual validation of high salt (HS) and aging fecal microbiota transplantation (FMT) in C56BL/6 mice was used to clarify the molecular mechanism by which excessive salt consumption causes intestinal aging. Firstly, we observed HS causes vascular endothelial damage and can accelerate intestinal aging associated with decreased colon and serum expression of superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and increased malondialdehyde (MDA); after transplantation with HS fecal microbiota in mice, vascular endothelial damage and intestinal aging can also occur. Secondly, we also found intestinal aging and vascular endothelial damage in older mice aged 14 months; and after transplantation of the older mice fecal microbiota, the same effect was observed in mice aged 6–8 weeks. Meanwhile, HS and aging significantly changed gut microbial diversity and composition, which was transferable by FMT. Eventually, based on the core genera both in HS and the aging gut microbiota network, a machine learning model was constructed which could predict HS susceptibility to intestinal aging. Further investigation revealed that the process of HS-related intestinal aging was highly linked to the signal transduction mediated by various bacteria. In conclusion, the present study provides an experimental basis of potential microbial evidence in the process of HS related intestinal aging. Even, avoiding excessive salt consumption and actively intervening in gut microbiota alteration may assist to delay the aging state that drives HS-related intestinal aging in clinical practice.
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Affiliation(s)
- Tian-hao Liu
- Department of Gastroenterology, Affiliated Hospital of Jiangnan University, Wuxi, China
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Lin Zhao
- Department of Gastroenterology, Affiliated Hospital of Jiangnan University, Wuxi, China
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Chen-yang Zhang
- Department of Gastroenterology, Affiliated Hospital of Jiangnan University, Wuxi, China
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Xiao-ya Li
- College of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Tie-long Wu
- Department of Gastroenterology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Yuan-yuan Dai
- Department of Gastroenterology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Ying-yue Sheng
- Department of Gastroenterology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Yi-lin Ren
- Department of Gastroenterology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Yu-zheng Xue
- Department of Gastroenterology, Affiliated Hospital of Jiangnan University, Wuxi, China
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- *Correspondence: Yu-zheng Xue
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