Learning to predict expression efficacy of vectors in recombinant protein production

BMC Bioinformatics

Research

Po-Huang Liang¹  Yan-Ping Shih¹  Ueng-Cheng Yang²  Wen-Ching Chan³  Wen-chang Lin⁴  Chun-Nan Hsu⁵ 

[1] Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan;Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan;Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan;Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan;Institute of Information Science, Academia Sinica, Taipei, Taiwan;Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan;Institute of Information Science, Academia Sinica, Taipei, Taiwan;

关键词: Attribute Vector;    Binary Classifier;    Recombinant Protein Production;    Recombinant Fusion Protein;    Codon Preference;   

DOI  :  10.1186/1471-2105-11-S1-S21

来源: Springer

【 摘 要 】

BackgroundRecombinant protein production is a useful biotechnology to produce a large quantity of highly soluble proteins. Currently, the most widely used production system is to fuse a target protein into different vectors in Escherichia coli (E. coli). However, the production efficacy of different vectors varies for different target proteins. Trial-and-error is still the common practice to find out the efficacy of a vector for a given target protein. Previous studies are limited in that they assumed that proteins would be over-expressed and focused only on the solubility of expressed proteins. In fact, many pairings of vectors and proteins result in no expression.ResultsIn this study, we applied machine learning to train prediction models to predict whether a pairing of vector-protein will express or not express in E. coli. For expressed cases, the models further predict whether the expressed proteins would be soluble. We collected a set of real cases from the clients of our recombinant protein production core facility, where six different vectors were designed and studied. This set of cases is used in both training and evaluation of our models. We evaluate three different models based on the support vector machines (SVM) and their ensembles. Unlike many previous works, these models consider the sequence of the target protein as well as the sequence of the whole fusion vector as the features. We show that a model that classifies a case into one of the three classes (no expression, inclusion body and soluble) outperforms a model that considers the nested structure of the three classes, while a model that can take advantage of the hierarchical structure of the three classes performs slight worse but comparably to the best model. Meanwhile, compared to previous works, we show that the prediction accuracy of our best method still performs the best. Lastly, we briefly present two methods to use the trained model in the design of the recombinant protein production systems to improve the chance of high soluble protein production.ConclusionIn this paper, we show that a machine learning approach to the prediction of the efficacy of a vector for a target protein in a recombinant protein production system is promising and may compliment traditional knowledge-driven study of the efficacy. We will release our program to share with other labs in the public domain when this paper is published.

【 授权许可】

Unknown   
© Chan et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.