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Zhang Y, Peng Y, Zhang H, Gao Q, Song F, Cui X, Mo F. Genome-Wide Identification of APX Gene Family in Citrus maxima and Expression Analysis at Different Postharvest Preservation Times. Genes (Basel) 2024; 15:911. [PMID: 39062690 PMCID: PMC11276291 DOI: 10.3390/genes15070911] [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: 05/31/2024] [Revised: 07/01/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Ascorbate peroxidase (APX) is a crucial enzyme involved in cellular antioxidant defense and plays a pivotal role in modulating reactive oxygen species (ROS) levels under various environmental stresses in plants. This study utilized bioinformatics methods to identify and analyze the APX gene family of pomelo, while quantitative real-time PCR (qRT-PCR) was employed to validate and analyze the expression of CmAPXs at different stages of fruit postharvest. This study identified 96 members of the CmAPX family in the entire pomelo genome, with uneven distribution across nine chromosomes and occurrences of gene fragment replication. The subcellular localization includes peroxisome, cytoplasm, chloroplasts, and mitochondria. The CmAPX family exhibits a similar gene structure, predominantly consisting of two exons. An analysis of the upstream promoter regions revealed a significant presence of cis-acting elements associated with light (Box 4, G-Box), hormones (ABRE, TCA-element), and stress-related (MBS, LTR, ARE) responses. Phylogenetic and collinearity analyses revealed that the CmAPX gene family can be classified into three subclasses, with seven collinear gene pairs. Furthermore, CmAPXs are closely related to citrus, pomelo, and lemon, followed by Arabidopsis, and exhibit low homology with rice. Additionally, the transcriptomic heat map and qPCR results revealed that the expression levels of CmAPX57, CmAPX34, CmAPX50, CmAPX4, CmAPX5, and CmAPX81 were positively correlated with granulation degree, indicating the activation of the endogenous stress resistance system in pomelo cells by these genes, thereby conferring resistance to ROS. This finding is consistent with the results of GO enrichment analysis. Furthermore, 38 miRNAs were identified as potential regulators targeting the CmAPX family for post-transcriptional regulation. Thus, this study has preliminarily characterized members of the APX gene family in pomelo and provided valuable insights for further research on their antioxidant function and molecular mechanism.
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Affiliation(s)
- Yu Zhang
- Key Laboratory of Beibu Gulf Environment Change and Resources Utilization of Ministry of Education, Nanning Normal University, Nanning 530001, China
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Yujiao Peng
- Key Laboratory of Beibu Gulf Environment Change and Resources Utilization of Ministry of Education, Nanning Normal University, Nanning 530001, China
- Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning 530001, China
| | - Huixin Zhang
- Key Laboratory of Beibu Gulf Environment Change and Resources Utilization of Ministry of Education, Nanning Normal University, Nanning 530001, China
- Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning 530001, China
| | - Qiuyu Gao
- Key Laboratory of Beibu Gulf Environment Change and Resources Utilization of Ministry of Education, Nanning Normal University, Nanning 530001, China
- Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning 530001, China
| | - Fangfei Song
- Key Laboratory of Beibu Gulf Environment Change and Resources Utilization of Ministry of Education, Nanning Normal University, Nanning 530001, China
- Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning 530001, China
| | - Xueyu Cui
- Key Laboratory of Beibu Gulf Environment Change and Resources Utilization of Ministry of Education, Nanning Normal University, Nanning 530001, China
- Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning 530001, China
| | - Fulei Mo
- Key Laboratory of Beibu Gulf Environment Change and Resources Utilization of Ministry of Education, Nanning Normal University, Nanning 530001, China
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
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Gaona-López C, Méndez-Álvarez D, Moreno-Rodríguez A, Bautista-Martínez JL, De Fuentes-Vicente JA, Nogueda-Torres B, García-Torres I, López-Velázquez G, Rivera G. TATA-Binding Protein-Based Virtual Screening of FDA Drugs Identified New Anti-Giardiasis Agents. Int J Mol Sci 2024; 25:6238. [PMID: 38892424 PMCID: PMC11172525 DOI: 10.3390/ijms25116238] [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: 05/01/2024] [Revised: 05/27/2024] [Accepted: 06/01/2024] [Indexed: 06/21/2024] Open
Abstract
Parasitic diseases, predominantly prevalent in developing countries, are increasingly spreading to high-income nations due to shifting migration patterns. The World Health Organization (WHO) estimates approximately 300 million annual cases of giardiasis. The emergence of drug resistance and associated side effects necessitates urgent research to address this growing health concern. In this study, we evaluated over eleven thousand pharmacological compounds sourced from the FDA database to assess their impact on the TATA-binding protein (TBP) of the early diverging protist Giardia lamblia, which holds medical significance. We identified a selection of potential pharmacological compounds for combating this parasitic disease through in silico analysis, employing molecular modeling techniques such as homology modeling, molecular docking, and molecular dynamics simulations. Notably, our findings highlight compounds DB07352 and DB08399 as promising candidates for inhibiting the TBP of Giardia lamblia. Also, these compounds and DB15584 demonstrated high efficacy against trophozoites in vitro. In summary, this study identifies compounds with the potential to combat giardiasis, offering the prospect of specific therapies and providing a robust foundation for future research.
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Affiliation(s)
- Carlos Gaona-López
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico;
| | - Domingo Méndez-Álvarez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico;
| | - Adriana Moreno-Rodríguez
- Laboratorio de Estudios Epidemiológicos, Clínicos, Diseños Experimentales e Investigación, Facultad de Ciencias Químicas, Universidad Autónoma “Benito Juárez” de Oaxaca, Oaxaca 68120, Mexico; (A.M.-R.); (J.L.B.-M.)
| | - Juan Luis Bautista-Martínez
- Laboratorio de Estudios Epidemiológicos, Clínicos, Diseños Experimentales e Investigación, Facultad de Ciencias Químicas, Universidad Autónoma “Benito Juárez” de Oaxaca, Oaxaca 68120, Mexico; (A.M.-R.); (J.L.B.-M.)
| | | | - Benjamín Nogueda-Torres
- Departamento de Parasitología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico;
| | - Itzhel García-Torres
- Laboratorio de Biomoléculas y Salud Infantil, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico; (I.G.-T.); (G.L.-V.)
| | - Gabriel López-Velázquez
- Laboratorio de Biomoléculas y Salud Infantil, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico; (I.G.-T.); (G.L.-V.)
| | - Gildardo Rivera
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico;
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Gaona-López C, Martínez-Vázquez AV, Villalobos-Rocha JC, Juárez-Rendón KJ, Rivera G. Analysis of Giardia lamblia Nucleolus as Drug Target: A Review. Pharmaceuticals (Basel) 2023; 16:1168. [PMID: 37631082 PMCID: PMC10457859 DOI: 10.3390/ph16081168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Giardia lamblia (G. lamblia) is the main causative agent of diarrhea worldwide, affecting children and adults alike; in the former, it can be lethal, and in the latter a strong cause of morbidity. Despite being considered a predominant disease in low-income and developing countries, current migratory flows have caused an increase in giardiasis cases in high-income countries. Currently, there is a wide variety of chemotherapeutic treatments to combat this parasitosis, most of which have potentially serious side effects, such as genotoxic, carcinogenic, and teratogenic. The necessity to create novel treatments and discover new therapeutic targets to fight against this illness is evident. The current review centers around the controversial nucleolus of G. lamblia, providing a historical perspective that traces its apparent absence to the present evidence supporting its existence as a subnuclear compartment in this organism. Additionally, possible examples of ncRNAs and proteins ubiquitous to the nucleolus that can be used as targets of different therapeutic strategies are discussed. Finally, some examples of drugs under research that could be effective against G. lamblia are described.
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Affiliation(s)
- Carlos Gaona-López
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
| | | | - Juan Carlos Villalobos-Rocha
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico;
| | - Karina Janett Juárez-Rendón
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico; (A.V.M.-V.); (K.J.J.-R.)
| | - Gildardo Rivera
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
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Zhong XD, Chen LJ, Xu XY, Liu YJ, Tao F, Zhu MH, Li CY, Zhao D, Yang GJ, Chen J. Berberine as a potential agent for breast cancer therapy. Front Oncol 2022; 12:993775. [PMID: 36119505 PMCID: PMC9480097 DOI: 10.3389/fonc.2022.993775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/09/2022] [Indexed: 01/02/2023] Open
Abstract
Breast cancer (BC) is a common malignancy that mainly occurred in women and it has become the most diagnosed cancer annually since 2020. Berberine (BBR), an alkaloid extracted from the Berberidacea family, has been found with broad pharmacological bioactivities including anti-inflammatory, anti-diabetic, anti-hypertensive, anti-obesity, antidepressant, and anticancer effects. Mounting evidence shows that BBR is a safe and effective agent with good anticancer activity against BC. However, its detailed underlying mechanism in BC treatment remains unclear. Here, we will provide the evidence for BBR in BC therapy and summarize its potential mechanisms. This review briefly introduces the source, metabolism, and biological function of BBR and emphasizes the therapeutic effects of BBR against BC via directly interacting with effector proteins, transcriptional regulatory elements, miRNA, and several BBR-mediated signaling pathways. Moreover, the novel BBR-based therapeutic strategies against BC improve biocompatibility and water solubility, and the efficacies of BBR are also briefly discussed. Finally, the status of BBR in BC treatment and future research directions is also prospected.
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Affiliation(s)
- Xiao-Dan Zhong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, China
| | - Li-Juan Chen
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, China
| | - Xin-Yang Xu
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, China
| | - Yan-Jun Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, China
| | - Fan Tao
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, China
| | - Ming-Hui Zhu
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, China
| | - Chang-Yun Li
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, China
| | - Dan Zhao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, China
- *Correspondence: Guan-Jun Yang, ; Jiong Chen, ; Dan Zhao,
| | - Guan-Jun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, China
- *Correspondence: Guan-Jun Yang, ; Jiong Chen, ; Dan Zhao,
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, China
- *Correspondence: Guan-Jun Yang, ; Jiong Chen, ; Dan Zhao,
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Li H, Shi L, Gao W, Zhang Z, Zhang L, Wang G. dPromoter-XGBoost: Detecting promoters and strength by combining multiple descriptors and feature selection using XGBoost. Methods 2022; 204:215-222. [PMID: 34998983 DOI: 10.1016/j.ymeth.2022.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/13/2021] [Accepted: 01/02/2022] [Indexed: 12/12/2022] Open
Abstract
Promoters play an irreplaceable role in biological processes and genetics, which are responsible for stimulating the transcription and expression of specific genes. Promoter abnormalities have been found in some diseases, and the level of promoter-binding transcription factors can be used as a marker before a disease occurs. Hence, detecting promoters from DNA sequences has important biological significance, particular, distinguishing strong promoters can help to elucidate differences in gene expression and the mechanisms of specific diseases. With the introduction of third-generation sequencing, it is difficult to match the speed of sequencing to the speed of labeling promoters experimentally. Many computing models have been designed to fill this gap and identify unlabeled DNA. However, their feature representation methods are very singular, which cannot reflect the information contained in the original samples. With the aim of avoiding information loss, we propose a computational model based on multiple descriptors and feature selection to jointly express samples. It is worth mentioning that a new feature descriptor called K-mer word vector is defined. The promoter model of multiple feature descriptors dominated by K-mer word vector achieves similar performance to existing methods, the sensitivity of 85.72% can distinguish the promoter more effectively than other methods. Furthermore, the performance of the promoter strength has surpassed published methods, and accuracy of 77.00% greatly improves the ability to distinguish between strong and weak promoters.
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Affiliation(s)
- Hongfei Li
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China; Yangtze Delta Region Institute, University of Electronic Science and Technology, Quzhou,China
| | - Lei Shi
- Department of Spine Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Wentao Gao
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Zixiao Zhang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Lichao Zhang
- School of Intelligent Manufacturing and Equipment, Shenzhen Institute of Information Technology, Shenzhen, China
| | - Guohua Wang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China.
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