RPS:一种为合成代谢途径推荐宿主生物和外源酶的软件工具  

RPS:a Software Tool to Recommend Host Organisms and Exogenous Enzymes for Designing Synthetic Metabolic Pathways

作　　者：卢吉晓 黄毅然[1,2,3] 钟诚 LU Jixiao;HUANG Yiran;ZHONG Cheng(School of Computer and Electronics Information,Guangxi University,Nanning,530004;Guangxi Key Laboratory of Multimedia Communications Network Technology,Nanning,530004;Key Laboratory of Parallel,Distribution and Intelligent Computing in Guangxi Universities and Colleges,Nanning,530004)

机构地区：[1]广西大学计算机与电子信息学院,南宁530004 [2]广西多媒体通信网络技术重点实验室,南宁530004 [3]广西高校并行分布与智能计算重点实验室,南宁530004

出　　处：《基因组学与应用生物学》2024年第7期1186-1195,共10页Genomics and Applied Biology

基　　金：国家自然科学基金项目(62362004,61862006);广西自然科学基金项目(2020GXNSFAA159074)共同资助。

摘　　要：为合成代谢途径选择宿主生物,并为合成代谢途径中的外源反应确定外源酶是合成生物学和代谢工程的两大挑战问题。自然界中存在成千上万种微生物和生物合成反应,仅通过生物实验来确定这些目标既昂贵又耗时。本文设计开发了一种名为RPS(recommend metabolic pathway’s species)的新型生物推理软件系统,以辅助合成代谢途径的设计。RPS软件可根据竞争性内源反应的比例和途径末端代谢物的数量为合成代谢途径推荐合适的宿主生物,并通过酶的系统发育距离和反应动力学信息为宿主生物中的外源反应识别合适的外源酶。有别于已有的以宿主为中心的合成代谢途径设计工具,RPS软件以代谢途径为中心的特点可帮助研究人员以不同视角评估合成代谢途径设计。实验结果表明,RPS软件工具可准确识别合成代谢途径潜在的宿主生物,并为合成代谢途径中的外源反应发现合适的外源酶。用户可通过https://biolab.gxu.edu.cn/RPS在线使用RPS软件工具。Selecting host organisms for synthetic metabolic pathways and determining exogenous enzymes for exogenous reactions in synthetic metabolic pathways are two challenges of synthetic biology and metabolic engineering.Due to thousands of microorganisms and biosynthetic reactions existing in nature,it is expensive and time-consuming to identify such goals only via biological experiments.This paper develops a novel biological reasoning software called RPS(recommend metabolic pathway's species)for synthetic metabolic pathway design.For synthetic metabolic pathways,the RPS software tool suggests suitable host organisms based on the ratios of competing endogenous reactions and the number of dead-end metabolites,and identifies appropriate exogenous enzymes of exogenous reactions in host organism via phylogenetic distance and reaction kinetics of enzymes.These pathway-centered features distinguish the RPS software from the existing host-centered synthetic metabolic pathway design tools and enable researchers to assess the design of their synthetic metabolic pathways in a different view.Experimental results show that the RPS software tool can accurately identify potential host organisms for synthetic metabolic pathways and discover suitable exogenous enzymes for exogenous reactions in synthetic metabolic pathways.Users can execute the RPS software online via https://biolab.gxu.edu.cn/RPS.

关 键 词：宿主生物推荐 外源酶推荐 代谢途径设计 软件 

分 类 号：Q78[生物学—分子生物学] TP319[自动化与计算机技术—计算机软件与理论]