Department of Microbiology and Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA.
Ulritech, LLC, Mount Pleasant, SC 29466, USA.
Nucleic Acids Res. 2024 Jan 5;52(D1):D647-D653. doi: 10.1093/nar/gkad847.
Signal transduction systems in bacteria and archaea link environmental stimuli to specific adaptive cellular responses. They control gene expression, motility, biofilm formation, development and other processes that are vital to survival. The microbial signal transduction (MiST) database is an online resource that stores tens of thousands of genomes and allows users to explore their signal transduction profiles, analyze genomes in bulk using the database application programming interface (API) and make testable hypotheses about the functions of newly identified signaling systems. However, signal transduction in metagenomes remained completely unexplored. To lay the foundation for research in metagenomic signal transduction, we have prepared a new release of the MiST database, MiST 4.0, which features over 10 000 metagenome-assembled genomes (MAGs), a scaled representation of proteins and detailed BioSample information. In addition, several thousands of new genomes have been processed and stored in the database. A new interface has been developed that allows users to seamlessly switch between genomes and MAGs. MiST 4.0 is freely available at https://mistdb.com; metagenomes and MAGs can also be explored using the API available on the same page.
细菌和古菌中的信号转导系统将环境刺激与特定的适应性细胞反应联系起来。它们控制着基因表达、运动性、生物膜形成、发育和其他对生存至关重要的过程。微生物信号转导 (MiST) 数据库是一个在线资源，它存储了数万基因组，并允许用户探索它们的信号转导谱，使用数据库应用程序编程接口 (API) 批量分析基因组，并对新发现的信号系统的功能做出可测试的假设。然而，宏基因组中的信号转导仍然完全没有被探索过。为了为宏基因组信号转导研究奠定基础，我们准备了 MiST 数据库的新版本 MiST 4.0，其中包含超过 10000 个宏基因组组装基因组 (MAGs)，这是蛋白质的比例表示和详细的生物样本信息。此外，还处理和存储了数千个新的基因组。开发了一个新的界面，允许用户在基因组和 MAG 之间无缝切换。MiST 4.0 可在 https://mistdb.com 上免费获得；也可以使用同一页面上提供的 API 来探索宏基因组和 MAG。
