Enzyme annotation for orphan reactions and its applications in biomanufacturing  

作　　者：Zhen Zhang Chun Li 

机构地区：[1]Key Lab for Industrial Biocatalysis,Ministry of Education,Department of Chemical Engineering,Tsinghua University,Beijing,100084,China [2]Center for Synthetic&Systems Biology,Department of Chemical Engineering,Tsinghua University,Beijing,100084,China

出　　处：《Green Chemical Engineering》2023年第2期137-145,共9页绿色化学工程（英文）

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

摘　　要：There are lots of biochemical reactions in the biosynthetic pathway without associated enzymes.Reactions predicted by retro-biosynthetic tools are not assigned gene sequences.Besides,non-natural reactions designed with novel functions also lack suitable enzymes.All these reactions can be categorized as orphan reactions.The absence of protein-encoding genes in these orphan reactions limits their direct experimental implementation.Computational tools have been developed to find candidate enzymes for these orphan reactions.Herein,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 enzymes.We believe that our review will greatly facilitate the design of microbial cell factories and contribute to the development of the biomanufacturing field.

关 键 词：Enzyme annotation Orphan reactions Reaction similarity Gene mining Computational enzyme design 

分 类 号：Q814[生物学—生物工程]