School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland.
School of Microbiology, Environmental Research Institute, APC Microbiome Institute, SUSFERM Fermentation Science Centre, University College Cork, Cork T12 K8AF, Ireland.
FEMS Yeast Res. 2022 Jun 30;22(1). doi: 10.1093/femsyr/foac024.
Kluyveromyces marxianus is an interesting and important yeast because of particular traits such as thermotolerance and rapid growth, and for applications in food and industrial biotechnology. For both understanding its biology and developing bioprocesses, it is important to understand how K. marxianus responds and adapts to changing environments. For this, a full suite of omics tools to measure and compare global patterns of gene expression and protein synthesis is needed. We report here the development of a ribosome profiling method for K. marxianus, which allows codon resolution of translation on a genome-wide scale by deep sequencing of ribosome locations on mRNAs. To aid in the analysis and sharing of ribosome profiling data, we added the K. marxianus genome as well as transcriptome and ribosome profiling data to the publicly accessible GWIPS-viz and Trips-Viz browsers. Users are able to upload custom ribosome profiling and RNA-Seq data to both browsers, therefore allowing easy analysis and sharing of data. We also provide a set of step-by-step protocols for the experimental and bioinformatic methods that we developed.
马克斯克鲁维酵母是一种有趣且重要的酵母，因为它具有耐热和快速生长等特殊特性，并且在食品和工业生物技术中有应用。为了理解其生物学并开发生物工艺，了解马克斯克鲁维酵母如何响应和适应不断变化的环境非常重要。为此，需要一套全面的组学工具来测量和比较基因表达和蛋白质合成的全局模式。我们在这里报告了一种用于马克斯克鲁维酵母的核糖体分析方法的开发，该方法通过对 mRNA 上核糖体位置的深度测序，允许在全基因组范围内对翻译进行密码子分辨率。为了便于分析和共享核糖体分析数据，我们将马克斯克鲁维酵母基因组以及转录组和核糖体分析数据添加到了可公开访问的 GWIPS-viz 和 Trips-Viz 浏览器中。用户可以将自定义的核糖体分析和 RNA-Seq 数据上传到这两个浏览器，从而可以轻松地分析和共享数据。我们还提供了一套用于我们开发的实验和生物信息学方法的分步协议。
