Insights into Co-Expression Network Analysis of MicroProteins and their Target Transcription Factors in Plant Embryo Development

IF 2.4 3区生物学 Q3 BIOCHEMICAL RESEARCH METHODS

Current Bioinformatics Pub Date : 2024-06-26 DOI:10.2174/0115748936304167240530091051

Khadijeh Shokri, Naser Farrokhi, Asadollah Ahmadikhah, Mahdi Safaeizade, Amir Mousavi

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引用次数: 0

Abstract

Background: Gene expression is regulated in a spatiotemporal manner, and the roles of microProteins (MiPs) in this concept have started to become clear in plants. Methods: Here, a microarray data analysis was carried out to decipher the spatiotemporal role of MiPs in embryo development. The guilt-by-association method was used to determine the corresponding regulatory factors. Results: Module network analyses and protein-protein interaction (PPI) assays suggested 13 modules for embryo development in the Arabidopsis model plant. Various biological processes such as metabolite biosynthesis, hormone transition and regulation, fatty acid and storage protein biosynthesis, and photosynthesis-related processes were prevalent. Different transcription factors (TFs) at different stages of embryo development were found and reviewed. Furthermore, 106 putative MiPs were identified that might be involved in the regulation of embryo development. Candidate hub MiPs (15) at embryo developmental stages were identified by PPI network analysis and their putative regulatory roles were discussed. Previously reported MiPs, AT1G14760 (KNOX), AT5G39860 (PRE1), and AT2G46410 (CPC), were noted to be present in modules M3 and M8. Conclusion: Molecular comprehension of regulatory factors including MiPs and TFs during embryo development allows targeted breeding of the corresponding traits and genome-based engineering of value-added new varieties.

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植物胚胎发育过程中微蛋白及其目标转录因子共表达网络分析的启示

背景：基因表达是以时空方式调控的，而微蛋白（MiPs）在这一概念中的作用在植物中已开始变得清晰。方法：本文通过微阵列数据分析来揭示 MiPs 在胚胎发育中的时空作用。采用 "逐个关联 "法（guilty-by-association）确定相应的调控因子。结果模块网络分析和蛋白质-蛋白质相互作用（PPI）分析表明，拟南芥模式植物的胚胎发育有 13 个模块。各种生物过程，如代谢物生物合成、激素转换和调节、脂肪酸和贮藏蛋白生物合成以及光合作用相关过程都普遍存在。发现并综述了胚胎发育不同阶段的不同转录因子（TFs）。此外，还发现了 106 个可能参与胚胎发育调控的推定 MiPs。通过PPI网络分析确定了胚胎发育阶段的候选中枢MiPs（15个），并讨论了它们的推测调控作用。之前报道的 MiPs AT1G14760（KNOX）、AT5G39860（PRE1）和 AT2G46410（CPC）被发现存在于模块 M3 和 M8 中。结论通过对胚胎发育过程中的调控因子（包括 MiPs 和 TFs）的分子理解，可对相应性状进行有针对性的育种，并基于基因组工程技术培育出高附加值的新品种。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Current Bioinformatics 生物-生化研究方法

CiteScore

6.60

自引率

2.50%

发文量

审稿时长

>12 weeks

期刊介绍： Current Bioinformatics aims to publish all the latest and outstanding developments in bioinformatics. Each issue contains a series of timely, in-depth/mini-reviews, research papers and guest edited thematic issues written by leaders in the field, covering a wide range of the integration of biology with computer and information science. The journal focuses on advances in computational molecular/structural biology, encompassing areas such as computing in biomedicine and genomics, computational proteomics and systems biology, and metabolic pathway engineering. Developments in these fields have direct implications on key issues related to health care, medicine, genetic disorders, development of agricultural products, renewable energy, environmental protection, etc.