LIRcentral: a manually curated online database of experimentally validated functional LIR motifs.

IF 14.6 1区 生物学 Q1 CELL BIOLOGY
Autophagy Pub Date : 2023-12-01 Epub Date: 2023-08-02 DOI:10.1080/15548627.2023.2235851
Agathangelos Chatzichristofi, Vasileios Sagris, Aristos Pallaris, Marios Eftychiou, Ioanna Kalvari, Nicholas Price, Theodosios Theodosiou, Ioannis Iliopoulos, Ioannis P Nezis, Vasilis J Promponas
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引用次数: 3

Abstract

Several selective macroautophagy receptor and adaptor proteins bind members of the Atg8 (autophagy related 8) family using short linear motifs (SLiMs), most often referred to as Atg8-family interacting motifs (AIMs) or LC3-interacting regions (LIRs). AIM/LIR motifs have been extensively studied during the last fifteen years, since they can uncover the underlying biological mechanisms and possible substrates for this key catabolic process of eukaryotic cells. Prompted by the fact that experimental information regarding LIR motifs can be found scattered across heterogeneous literature resources, we have developed LIRcentral (https://lircentral.eu), a freely available online repository for user-friendly access to comprehensive, high-quality information regarding LIR motifs from manually curated publications. Herein, we describe the development of LIRcentral and showcase currently available data and features, along with our plans for the expansion of this resource. Information incorporated in LIRcentral is useful for accomplishing a variety of research tasks, including: (i) guiding wet biology researchers for the characterization of novel instances of LIR motifs, (ii) giving bioinformaticians/computational biologists access to high-quality LIR motifs for building novel prediction methods for LIR motifs and LIR containing proteins (LIRCPs) and (iii) performing analyses to better understand the biological importance/features of functional LIR motifs. We welcome feedback on the LIRcentral content and functionality by all interested researchers and anticipate this work to spearhead a community effort for sustaining this resource which will further promote progress in studying LIR motifs/LIRCPs.Abbreviations: AIM, Atg8-family interacting motif; Atg8, autophagy related 8; GABARAP, GABA type A receptor-associated protein; LIR, LC3-interacting region; LIRCP, LIR-containing protein; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; PMID, PubMed identifier; PPI, protein-protein interaction; SLiM, short linear motif.

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LIRcentral:一个人工策划的在线数据库,包含实验验证的功能性LIR基序。
几种选择性大自噬受体和衔接蛋白使用短线性基序(SLiMs)结合Atg8(自噬相关8)家族的成员,最常被称为Atg8家族相互作用基序(AIMs)或LC3相互作用区(LIRs)。在过去的十五年里,AIM/LIR基序得到了广泛的研究,因为它们可以揭示真核细胞这一关键分解代谢过程的潜在生物学机制和可能的底物。由于LIR基序的实验信息可以分散在不同的文献资源中,我们开发了LIR中心(https://lircentral.eu),一个免费提供的在线存储库,可方便用户从手动策划的出版物中获取有关LIR主题的全面、高质量信息。在此,我们描述了LIR中心的开发,并展示了当前可用的数据和功能,以及我们扩展该资源的计划。LIR中心包含的信息有助于完成各种研究任务,包括:(i)指导湿生物学研究人员表征LIR基序的新实例,(ii)让生物信息学家/计算生物学家获得高质量的LIR基序,以构建LIR基阵和含LIR蛋白(LIRCP)的新预测方法,以及(iii)进行分析,以更好地理解功能性LIR基模的生物学重要性/特征。我们欢迎所有感兴趣的研究人员对LIR中心内容和功能的反馈,并预计这项工作将引领社区努力维持这一资源,这将进一步促进LIR基序/LIRCPs.Abbreviations:AIM,Atg8家族相互作用基序的研究进展;Atg8,自噬相关8;GABARAP,GABA型受体相关蛋白;LIR、LC3相互作用区;LIRCP、含有LIR的蛋白质;MAP1LC3/LC3、微管相关蛋白1轻链3;PMID,PubMed标识符;PPI,蛋白质-蛋白质相互作用;SLiM,短线性图案。
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来源期刊
Autophagy
Autophagy 生物-细胞生物学
CiteScore
21.30
自引率
2.30%
发文量
277
审稿时长
1 months
期刊介绍: Autophagy is a peer-reviewed journal that publishes research on autophagic processes, including the lysosome/vacuole dependent degradation of intracellular material. It aims to be the premier journal in the field and covers various connections between autophagy and human health and disease, such as cancer, neurodegeneration, aging, diabetes, myopathies, and heart disease. Autophagy is interested in all experimental systems, from yeast to human. Suggestions for specialized topics are welcome. The journal accepts the following types of articles: Original research, Reviews, Technical papers, Brief Reports, Addenda, Letters to the Editor, Commentaries and Views, and Articles on science and art. Autophagy is abstracted/indexed in Adis International Ltd (Reactions Weekly), EBSCOhost (Biological Abstracts), Elsevier BV (EMBASE and Scopus), PubMed, Biological Abstracts, Science Citation Index Expanded, Web of Science, and MEDLINE.
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