Functional Annotation of Proteins Encoded by the Minimal Bacterial Genome Based on Secondary Structure Element Alignment

Journal of Proteome Research
Zhiyuan Yang, Stephen Kwok-Wing Tsui

Abstract

In synthetic biology, one of the key focuses is building a minimal artificial cell which can provide basic chassis for functional study. Recently, the J. Craig Venter Institute published the latest version of the minimal bacterial genome JCVI-syn3.0, which only encoded 438 essential proteins. However, among them functions of 149 proteins remain unknown because of the lack of effective annotation method. Here, we report a secondary structure element alignment method called SSEalign based on an effective training data set extracting from various bacterial genomes. The experimentally validated homologous genes in different species were selected as training positives, while unrelated genes in different species were selected as training negatives. Moreover, SSEalign used a set of well-defined basic alignment elements with the backtracking line search algorithm to derive the best parameters for accurate prediction. Experimental results showed that SSEalign achieved 88.2% test accuracy, which is better than the existing prediction methods. SSEalign was subsequently applied to identify the functions of those unannotated proteins in the latest published minimal bacteria genome JCVI-syn3.0. Results indicated that at least 136 proteins ou...Continue Reading

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Citations

Aug 4, 2020·Computational Biology and Chemistry·Zhiyuan YangStephen Kwok-Wing Tsui
Nov 21, 2020·Current Genomics·Girik MalikPrashanth Suravajhala
Jul 22, 2021·Molecular Systems Biology·Jean-Christophe LachanceSébastien Rodrigue

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