In silico engineering of Pseudomonas metabolism reveals new biomarkers for increased biosurfactant production

PeerJ

article

Annalisa Occhipinti¹  Filmon Eyassu¹  Thahira J. Rahman²  Pattanathu K. S. M. Rahman²  Claudio Angione¹ 

[1] Department of Computer Science and Information Systems, Teesside University;Technology Futures Institute, School of Science, Engineering and Design, Teesside University;Institute of Biological and Biomedical Sciences, School of Biological Sciences, University of Portsmouth

关键词: Pseudomonas;    Rhamnolipids;    Biosurfactants;    Flux balance analysis;    Metabolic engineering;    Pseudomonas putida;    Multi-omics;    Genome-scale metabolic model;    Regression;    Machine learning;   

DOI  :  10.7717/peerj.6046

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

Background Rhamnolipids, biosurfactants with a wide range of biomedical applications, are amphiphilic molecules produced on the surfaces of or excreted extracellularly by bacteria including Pseudomonas aeruginosa. However, Pseudomonas putida is a non-pathogenic model organism with greater metabolic versatility and potential for industrial applications. Methods We investigate in silico the metabolic capabilities of P. putida for rhamnolipids biosynthesis using statistical, metabolic and synthetic engineering approaches after introducing key genes (RhlA and RhlB) from P. aeruginosa into a genome-scale model of P. putida. This pipeline combines machine learning methods with multi-omic modelling, and drives the engineered P. putida model toward an optimal production and export of rhamnolipids out of the membrane. Results We identify a substantial increase in synthesis of rhamnolipids by the engineered model compared to the control model. We apply statistical and machine learning techniques on the metabolic reaction rates to identify distinct features on the structure of the variables and individual components driving the variation of growth and rhamnolipids production. We finally provide a computational framework for integrating multi-omics data and identifying latent pathways and genes for the production of rhamnolipids in P. putida. Conclusions We anticipate that our results will provide a versatile methodology for integrating multi-omics data for topological and functional analysis of P. putida toward maximization of biosurfactant production.

【 授权许可】

CC BY