mobileOG-db: a Manually Curated Database of Protein Families Mediating the Life Cycle of Bacterial Mobile Genetic Elements.
mobileOG-db: a Manually Curated Database of Protein Families Mediating the Life Cycle of Bacterial Mobile Genetic Elements.
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DOI：
10.1128/aem.00991-22
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发表时间：
2022-09-22
影响因子：
4.4
通讯作者：
Zhang, Liqing
中科院分区：
文献类型：
--
作者：
Brown, Connor L.;Mullet, James;Hindi, Fadi;Stoll, James E.;Gupta, Suraj;Choi, Minyoung;Keenum, Ishi;Vikesland, Peter;Pruden, Amy;Zhang, Liqing
关键词：
细菌移动的遗传元件（MGE）编码执行元件的核心和辅助功能两者的功能模块，其中后者通常仅与元件瞬时相关。这些辅助基因的存在，这往往是密切的同源物，主要是固定的基因，招致高的假阳性率，因此，限制了这些数据库的MGE注释的可用性。为了克服这一局限性，我们分析了来自8个MGE数据库的10，776，849个蛋白质序列，以编译一组全面的6，140个手动策划的蛋白质家族，这些蛋白质家族与质粒的“生命周期”（整合/切除，复制/重组/修复，转移，稳定性/转移/防御和噬菌体特异性过程），整合，整合，转座和接合元件有关。我们覆盖实验信息，以创建一个分层的注释方案的高质量的注释和注释推断完全通过生物信息学证据。我们还为每个条目提供MGE类标签（例如，质粒或整合元件），并为每个条目分配主要和次要类别。由此产生的数据库，mobileOG-db（移动的orthogonal组），包括超过700，000个重复序列，包括5个主要的mobileOG类别和50多个次要类别，提供了一个结构化的语言和可解释的基础上，MGE为中心的分析阵列。mobileOG-db可以在mobileogdb.flsi.cloud.vt.edu/访问，用户可以在这里选择、优化和分析动态mobilome的自定义子集。基因组数据中细菌移动的遗传元件（MGE）的分析是分析抗生素耐药性、表型或代谢多样性以及细菌属进化的根本原因的关键一步。现有的MGE注释方法对生物和计算专业知识造成了很高的障碍，无法正确利用。为了弥补这一差距，我们系统地分析了来自8个MGE数据库的10，776，849种蛋白质，以鉴定6，140个MGE蛋白质家族，这些蛋白质家族可以作为候选标志，即，这些蛋白质可用作MGE的“签名”以帮助注释。由此产生的资源，mobileOG-db，提供了一个多层次的分类方案，包括质粒，噬菌体，整合和转座因子蛋白家族分为5个主要mobileOG类别和50多个小类别。因此，mobileOG-db为简单直观的元素注释提供了丰富的资源，可以无缝集成到现有的MGE检测管道和共定位分析中。
Bacterial mobile genetic elements (MGEs) encode functional modules that perform both core and accessory functions for the element, the latter of which are often only transiently associated with the element. The presence of these accessory genes, which are often close homologs to primarily immobile genes, incur high rates of false positives and, therefore, limits the usability of these databases for MGE annotation. To overcome this limitation, we analyzed 10,776,849 protein sequences derived from eight MGE databases to compile a comprehensive set of 6,140 manually curated protein families that are linked to the “life cycle” (integration/excision, replication/recombination/repair, transfer, stability/transfer/defense, and phage-specific processes) of plasmids, phages, integrative, transposable, and conjugative elements. We overlay experimental information where available to create a tiered annotation scheme of high-quality annotations and annotations inferred exclusively through bioinformatic evidence. We additionally provide an MGE-class label for each entry (e.g., plasmid or integrative element), and assign to each entry a major and minor category. The resulting database, mobileOG-db (for mobile orthologous groups), comprises over 700,000 deduplicated sequences encompassing five major mobileOG categories and more than 50 minor categories, providing a structured language and interpretable basis for an array of MGE-centered analyses. mobileOG-db can be accessed at mobileogdb.flsi.cloud.vt.edu/, where users can select, refine, and analyze custom subsets of the dynamic mobilome. IMPORTANCE The analysis of bacterial mobile genetic elements (MGEs) in genomic data is a critical step toward profiling the root causes of antibiotic resistance, phenotypic or metabolic diversity, and the evolution of bacterial genera. Existing methods for MGE annotation pose high barriers of biological and computational expertise to properly harness. To bridge this gap, we systematically analyzed 10,776,849 proteins derived from eight databases of MGEs to identify 6,140 MGE protein families that can serve as candidate hallmarks, i.e., proteins that can be used as “signatures” of MGEs to aid annotation. The resulting resource, mobileOG-db, provides a multilevel classification scheme that encompasses plasmid, phage, integrative, and transposable element protein families categorized into five major mobileOG categories and more than 50 minor categories. mobileOG-db thus provides a rich resource for simple and intuitive element annotation that can be integrated seamlessly into existing MGE detection pipelines and colocalization analyses.
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通讯作者：
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