A bioinformatic workflow for in silico secretome prediction with the lignocellulose degrading ascomycete fungus Parascedosporium putredinis NO1.
A bioinformatic workflow for in silico secretome prediction with the lignocellulose degrading ascomycete fungus Parascedosporium putredinis NO1.
复制标题
利用木质纤维素降解子囊菌真菌 Parascedosporium putredinis NO1 进行计算机分泌蛋白组预测的生物信息学工作流程。
DOI：
10.1111/mmi.15144
复制
发表时间：
2023
影响因子：
3.6
通讯作者：
Scott CJR
中科院分区：
文献类型：
--
作者：
Scott CJR
微生物基因组序列的不断增加为鉴定新的微生物酶提供了信息库。编码参与细胞外过程的蛋白质的基因特别令人感兴趣，因为这些蛋白质介导微生物与其环境的相互作用。然而，分泌组的蛋白质组学分析是具有挑战性的，并且经常捕获通过细胞死亡和裂解释放的细胞内蛋白质。来自序列数据的分泌组预测工作流程通常用于过滤通过蛋白质组学鉴定的蛋白质，但通常被简化为单个步骤，并且没有对其有效性进行生物信息学评估。在这里，一个工作流程来预测真菌分泌组的设计和应用到theParascedosporium putredinis NO1基因组的编码区。这种子囊菌是一种特殊的木质纤维素降解菌，以前已经鉴定出一种新的木质素降解酶。“分泌组分离”工作流程基于定位预测和分泌预测两种策略，每种策略均利用多种可用工具。该工作流程产生了三个最终的分泌组，其严格性水平不断增加。所有三个分泌组显示增加功能注释细胞外过程和减少注释细胞内过程。作为分泌组的一部分分离的多个序列缺乏任何功能注释，并为新酶的发现提供了令人兴奋的候选者。
The increasing availability of microbial genome sequences provides a reservoir of information for the identification of new microbial enzymes. Genes encoding proteins engaged in extracellular processes are of particular interest as these mediate the interactions microbes have with their environments. However, proteomic analysis of secretomes is challenging and often captures intracellular proteins released through cell death and lysis. Secretome prediction workflows from sequence data are commonly used to filter proteins identified through proteomics but are often simplified to a single step and are not evaluated bioinformatically for their effectiveness. Here, a workflow to predict a fungal secretome was designed and applied to the coding regions of theParascedosporium putredinisNO1 genome. This ascomycete fungus is an exceptional lignocellulose degrader from which a new lignin‐degrading enzyme has previously been identified. The ‘secretome isolation’ workflow is based on two strategies of localisation prediction and secretion prediction each utilising multiple available tools. The workflow produced three final secretomes with increasing levels of stringency. All three secretomes showed increases in functional annotations for extracellular processes and reductions in annotations for intracellular processes. Multiple sequences isolated as part of the secretome lacked any functional annotation and made exciting candidates for novel enzyme discovery.