Bioinformatics deciphers the thebaine biosynthesis pathway in opium poppy: Hub genes, network analysis, and miRNA regulation

IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology
Zahra Shirazi , Mahsa Rostami , Abozar Ghorbani , Pietro Hiram Guzzi
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引用次数: 0

Abstract

Thebaine, a vital precursor in the codeine and morphine pathway, shows promise in addiction treatment. We conducted a comprehensive study on the thebaine biosynthesis pathway in opium poppy, utilizing bioinformatics tools. The dataset comprising the thirteen genes associated with the thebaine biosynthesis pathway was compiled from an extensive review of published literature and validated using the NCBI BLAST tool. Utilizing STRING and Cytoscape, we analyzed gene interactions and visualized the molecular interaction network, respectively. To identify hub proteins, CytoHubba was administered. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) at STRING were used for the enrichment analysis of the hub genes. CytoCluster was used to analyze the network in clusters. Promoter regions of hub genes and potential miRNAs were explored using MEME and the psRNATarget database. Hub genes crucial to thebaine biosynthesis were identified, contributing to essential cellular functions like growth, development, stress response, and signal transduction. Metabolic processes emerged as pivotal for thebaine production, indicating a broader role for the thebaine pathway gene network beyond primary metabolite production. Cell component subnetwork genes demonstrated associations with anatomical units, indicating involvement in plant defense responses. Dominant molecular functions drove plant defense responses. KEGG pathway analysis highlighted the significance of metabolic pathways and biosynthesis of secondary metabolites. Cluster analysis emphasized the relevance of the biosynthesis of amino acids, confirming the link between primary and secondary metabolites. Promoter analysis suggested the potential involvement of signal transduction in thebaine production. Hub genes were targeted by 40 miRNAs, suggesting potential novel biomarkers or target genes within the thebaine biosynthesis pathway. Based on the role of miRNAs identified in connection with the hub genes of the thebaine production process, the secondary metabolite pathway of thebaine appears to be associated with several key plant pathways, e.g. growth, development and stress response. However, these findings, based on bioinformatics analysis, warrant further experimental validation and promise to advance our understanding of the biosynthesis of thebaine and its interactions with other genes and metabolic pathways that influence the production of metabolites.

生物信息学破解罂粟中的蒂巴因生物合成途径:枢纽基因、网络分析和 miRNA 调控
蒂巴因是可待因和吗啡途径中的一种重要前体,有望用于成瘾治疗。我们利用生物信息学工具对罂粟中的生物合成途径进行了全面研究。与罂粟碱生物合成途径相关的 13 个基因的数据集是在广泛查阅已发表文献的基础上编制的,并使用 NCBI BLAST 工具进行了验证。我们利用 STRING 和 Cytoscape 分别分析了基因间的相互作用和可视化分子相互作用网络。为了识别枢纽蛋白,我们使用了 CytoHubba。在 STRING 中使用京都基因和基因组百科全书(KEGG)和基因本体(GO)对中心基因进行富集分析。使用 CytoCluster 对网络进行聚类分析。利用 MEME 和 psRNATarget 数据库探索了枢纽基因和潜在 miRNA 的启动子区域。结果发现了对茶碱生物合成至关重要的枢纽基因,它们对生长、发育、应激反应和信号转导等基本细胞功能做出了贡献。新陈代谢过程是产生巴豆碱的关键,这表明巴豆碱通路基因网络除了产生初级代谢物外,还能发挥更广泛的作用。细胞组分子网络基因与解剖单位相关,表明它们参与了植物防御反应。显性分子功能驱动植物防御反应。KEGG 通路分析强调了代谢通路和次生代谢物生物合成的重要性。聚类分析强调了氨基酸生物合成的相关性,证实了初级和次级代谢物之间的联系。启动子分析表明,信号转导可能参与了甜菜碱的生产。40 个 miRNA 靶向了枢纽基因,这表明在生物合成途径中存在潜在的新型生物标记或靶基因。根据已确定的 miRNA 与巴豆碱生产过程中枢基因的作用,巴豆碱的次级代谢物途径似乎与植物的几个关键途径有关,如生长、发育和胁迫反应。不过,这些基于生物信息学分析的发现还需要进一步的实验验证,并有望加深我们对巴豆碱的生物合成及其与影响代谢产物产生的其他基因和代谢途径之间的相互作用的理解。
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来源期刊
Journal of Genetic Engineering and Biotechnology
Journal of Genetic Engineering and Biotechnology Biochemistry, Genetics and Molecular Biology-Biotechnology
CiteScore
5.70
自引率
5.70%
发文量
159
审稿时长
16 weeks
期刊介绍: Journal of genetic engineering and biotechnology is devoted to rapid publication of full-length research papers that leads to significant contribution in advancing knowledge in genetic engineering and biotechnology and provide novel perspectives in this research area. JGEB includes all major themes related to genetic engineering and recombinant DNA. The area of interest of JGEB includes but not restricted to: •Plant genetics •Animal genetics •Bacterial enzymes •Agricultural Biotechnology, •Biochemistry, •Biophysics, •Bioinformatics, •Environmental Biotechnology, •Industrial Biotechnology, •Microbial biotechnology, •Medical Biotechnology, •Bioenergy, Biosafety, •Biosecurity, •Bioethics, •GMOS, •Genomic, •Proteomic JGEB accepts
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