Sequence and thermodynamic characteristics of terminators revealed by FlowSeq and the discrimination of terminators strength  

作　　者：Weiji Zhai Yanting Duan Xiaomei Zhang Guoqiang Xu Hui Li Jinsong Shi Zhenghong Xu Xiaojuan Zhang 

机构地区：[1]Biotechnology of Ministry of Education,School of Biotechnology,Jiangnan University,Wuxi,China [2]National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing,Jiangnan University,Wuxi,China [3]School of Life Science and Health Engineering,Jiangnan University,Wuxi,214122,China [4]Jiangsu Provincial Engineering Research Center for Bioactive Product Processing,Jiangnan University,1800 Lihu Avenue,Wuxi,214122,China

出　　处：《Synthetic and Systems Biotechnology》2022年第4期1046-1055,共10页合成和系统生物技术（英文）

基　　金：This study was supported by the National Key Research and Development Program of China[2018YFA0900300];National Natural Science Foundation of China[32171421].

摘　　要：The intrinsic terminator in prokaryotic forms secondary RNA structure and terminates the transcription.However,leaking transcription is common due to varied terminator strength.Besides of the representative hairpin and U-tract structure,detailed sequence and thermodynamic features of terminators were not completely clear,and the effect of terminator on the upstream gene expression was unclearly.Thus,it is still challenging to use terminator to control expression with higher precision.Here,in E.Coli,we firstly determined the effect of the 3′-end sequences including spacer sequences and terminator sequences on the expression of upstream and downstream genes.Secondly,terminator mutation library was constructed,and the thermodynamic and sequence features differing in the termination efficiency were analyzed using the FlowSeq technique.The result showed that under the regulation of terminators,a negative correlation was presented between the expression of upstream and downstream genes(r=0.60),and the terminators with lower free energy corelated with higher upstream gene expression.Meanwhile,the terminator with longer stem length,more compact loop and perfect U-tract structure was benefit to the transcription termination.Finally,a terminator strength classification model was established,and the verification experiment based on 20 synthetic terminators indicated that the model can distinguish strong and weak terminators to certain extent.The results help to elucidate the role of terminators in gene expression,and the key factors identified are crucial for rational design of terminators,and the model provided a method for terminator strength prediction.

关 键 词：Intrinsic terminator Transcription termination Machine learning Structure-activity relationship FlowSeq Free energy 

分 类 号：O414.1[理学—理论物理]