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AGODB：一个全面的 Argonaute 蛋白结构域注释数据库。

AGODB: a comprehensive domain annotation database of argonaute proteins.

机构信息

Medical College, Guizhou University, Guiyang, Guizhou 550025, China.

School of Health Care Technology, Chengdu Neusoft University, Chengdu, Sichuan 611844, China.

出版信息

Database (Oxford). 2022 Sep 7;2022. doi: 10.1093/database/baac078.

DOI:10.1093/database/baac078
PMID:36068786
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9448894/
Abstract

UNLABELLED

Argonaute (Ago) proteins are widely expressed in almost all organisms. Eukaryotic Ago (eAgo) proteins bind small RNA guides forming RNA-induced silencing complex that silence gene expression, and prokaryotic Ago (pAgo) proteins defend against invading nucleic acids via binding small RNAs or DNAs. pAgo proteins have shown great potential as a candidate 'scissors' for gene editing. Protein domains are fundamental units of protein structure, function and evolution; however, the domains of Ago proteins are not well annotated/curated currently. Therefore, full functional domain annotation of Ago proteins is urgently needed for researchers to understand the function and mechanism of Ago proteins. Herein, we constructed the first comprehensive domain annotation database of Ago proteins (AGODB). The database curates detailed information of 1902 Ago proteins, including 1095 eAgos and 807 pAgos. Especially for long pAgo proteins, all six domains are annotated and curated. Gene Ontology (GO) enrichment analysis revealed that Ago genes in different species were enriched in the following GO terms: biological processes (BPs), molecular function and cellular compartment. GO enrichment analysis results were integrated into AGODB, which provided insights into the BP that Ago genes may participate in. AGODB also allows users to search the database with a variety of options and download the search results. We believe that the AGODB will be a useful resource for understanding the function and domain components of Ago proteins. This database is expected to cater to the needs of scientific community dedicated to the research of Ago proteins.

DATABASE URL

http://i.uestc.edu.cn/agodb/.

摘要

未加标签

Argonaute（AGO）蛋白广泛存在于几乎所有生物体中。真核 AGO（eAGO）蛋白结合小 RNA 向导，形成 RNA 诱导沉默复合物，沉默基因表达，而原核 AGO（pAGO）蛋白通过结合小 RNA 或 DNA 来抵御入侵的核酸。pAGO 蛋白已显示出作为基因编辑候选“剪刀”的巨大潜力。蛋白质结构域是蛋白质结构、功能和进化的基本单位；然而，AGO 蛋白的结构域目前注释/编纂得并不完善。因此，为了让研究人员了解 AGO 蛋白的功能和机制，迫切需要对 AGO 蛋白进行全面的功能结构域注释。在此，我们构建了第一个 AGO 蛋白综合结构域注释数据库（AGODB）。该数据库详细整理了 1902 种 AGO 蛋白的信息，包括 1095 种 eAGO 和 807 种 pAGO。特别是对于长 pAGO 蛋白，所有六个结构域都被注释和整理。GO 富集分析显示，不同物种的 AGO 基因在以下 GO 术语中富集：生物过程（BP）、分子功能和细胞区室。GO 富集分析结果被整合到 AGODB 中，这为 AGO 基因可能参与的 BP 提供了深入了解。AGODB 还允许用户使用各种选项搜索数据库并下载搜索结果。我们相信，AGODB 将成为理解 AGO 蛋白功能和结构域组成的有用资源。该数据库有望满足致力于 AGO 蛋白研究的科学界的需求。

数据库网址

http://i.uestc.edu.cn/agodb/。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c75b/9448894/3ddade6041ba/baac078f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c75b/9448894/27bb93fa18a2/baac078f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c75b/9448894/1f67881c1625/baac078f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c75b/9448894/6a1a846fc51a/baac078f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c75b/9448894/26603d06c44f/baac078f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c75b/9448894/b572d012b8b4/baac078f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c75b/9448894/3ddade6041ba/baac078f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c75b/9448894/27bb93fa18a2/baac078f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c75b/9448894/1f67881c1625/baac078f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c75b/9448894/6a1a846fc51a/baac078f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c75b/9448894/26603d06c44f/baac078f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c75b/9448894/b572d012b8b4/baac078f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c75b/9448894/3ddade6041ba/baac078f6.jpg

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本文引用的文献

1
Argonaute proteins: structures and their endonuclease activity.Argonaute 蛋白：结构及其内切核酸酶活性。
Mol Biol Rep. 2021 May;48(5):4837-4849. doi: 10.1007/s11033-021-06476-w. Epub 2021 Jun 11.
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KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis.KOBAS-i：用于基因富集分析的生物学功能智能优先级排序和探索性可视化。
Nucleic Acids Res. 2021 Jul 2;49(W1):W317-W325. doi: 10.1093/nar/gkab447.
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Protein domain identification methods and online resources.蛋白质结构域鉴定方法及在线资源。
Comput Struct Biotechnol J. 2021 Feb 2;19:1145-1153. doi: 10.1016/j.csbj.2021.01.041. eCollection 2021.
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Thermus thermophilus Argonaute Functions in the Completion of DNA Replication.嗜热栖热菌 Argonaute 在 DNA 复制完成中的作用。
Cell. 2020 Sep 17;182(6):1545-1559.e18. doi: 10.1016/j.cell.2020.07.036. Epub 2020 Aug 25.
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NCBI Taxonomy: a comprehensive update on curation, resources and tools.NCBI 分类学：在管理、资源和工具方面的全面更新。
Database (Oxford). 2020 Jan 1;2020. doi: 10.1093/database/baaa062.
6
DNA targeting and interference by a bacterial Argonaute nuclease.细菌 Argonaute 核酸内切酶的 DNA 靶向和干扰作用。
Nature. 2020 Nov;587(7835):632-637. doi: 10.1038/s41586-020-2605-1. Epub 2020 Jul 30.
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Argonaute proteins: Structural features, functions and emerging roles.Argonaute蛋白：结构特征、功能及新出现的作用
J Adv Res. 2020 Apr 29;24:317-324. doi: 10.1016/j.jare.2020.04.017. eCollection 2020 Jul.
8
AGONOTES: A Robot Annotator for Argonaute Proteins.AGONOTES：Argonaute 蛋白的机器人标注器。
Interdiscip Sci. 2020 Mar;12(1):109-116. doi: 10.1007/s12539-019-00349-4. Epub 2019 Nov 18.
9
DNA-guided DNA cleavage at moderate temperatures by Clostridium butyricum Argonaute.梭菌 Argonaute 在中等温度下引导 DNA 切割双链 DNA
Nucleic Acids Res. 2019 Jun 20;47(11):5809-5821. doi: 10.1093/nar/gkz306.
10
The Expanded Universe of Prokaryotic Argonaute Proteins.原核 Argonaute 蛋白的扩展宇宙。
mBio. 2018 Dec 18;9(6):e01935-18. doi: 10.1128/mBio.01935-18.