Enzyme annotation for orphan reactions and its applications in biomanufacturing

作     者：Zhen Zhang Chun Li Zhen Zhang;Chun Li

作者机构：Key Lab for Industrial BiocatalysisMinistry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijing100084China Center for Synthetic&Systems BiologyDepartment of Chemical EngineeringTsinghua UniversityBeijing100084China 

出 版 物：《Green Chemical Engineering》 (绿色化学工程（英文）)

年 卷 期：2023年第4卷第2期

页      面：137-145页

核心收录：

学科分类：08[工学] 082203[工学-发酵工程] 0822[工学-轻工技术与工程] 

基　　金：supported by the National Natural Science Foundation of China(22138006) 

主　　题：Enzyme annotation Orphan reactions Reaction similarity Gene mining Computational enzyme design 

摘      要：There are lots of biochemical reactions in the biosynthetic pathway without associated *** predicted by retro-biosynthetic tools are not assigned gene ***,non-natural reactions designed with novel functions also lack suitable *** these reactions can be categorized as orphan *** absence of protein-encoding genes in these orphan reactions limits their direct experimental *** tools have been developed to find candidate enzymes for these orphan ***,we discuss recent advances in these computational tools,including reaction similarity-based methods for calculating the substructural similarity between orphan reactions and known enzymatic reactions;sequence-based tools combine metabolic knowledge base and phenotypic information with genomic,transcriptomic,and metabolomic data to mine appropriate enzymes for orphan reactions;and approaches based on the creation of enzyme variants for orphan reactions as enzyme engineering modifications and de novo design of *** believe that our review will greatly facilitate the design of microbial cell factories and contribute to the development of the biomanufacturing field.