A workflow for annotating the knowledge gaps in metabolic reconstructions using known and hypothetical reactions

Author:

Vayena Evangelia1ORCID,Chiappino-Pepe Anush1,MohammadiPeyhani Homa1,Francioli Yannick1,Hadadi Noushin1,Ataman Meriç1,Hafner Jasmin1,Pavlou Stavros23ORCID,Hatzimanikatis Vassily1ORCID

Affiliation:

1. Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, 1015 Lausanne, Switzerland

2. Department of Chemical Engineering, University of Patras, 26504 Patras, Greece

3. Institute of Chemical Engineering Sciences (FORTH/ICE-HT), 26504 Patras, Greece

Abstract

Advances in medicine and biotechnology rely on a deep understanding of biological processes. Despite the increasingly available types and amounts of omics data, significant knowledge gaps remain, with current approaches to identify and curate missing annotations being limited to a set of already known reactions. Here, we introduce N etwork I ntegrated C omputational E xplorer for G ap A nnotation of Me tabolism (NICEgame), a workflow to identify and curate nonannotated metabolic functions in genomes using the ATLAS of Biochemistry and genome-scale metabolic models (GEMs). To resolve gaps in GEMs, NICEgame provides alternative sets of known and hypothetical reactions, assesses their thermodynamic feasibility, and suggests candidate genes to catalyze these reactions. We identified metabolic gaps and applied NICEgame in the latest GEM of Escherichia coli , iML1515, and enhanced the E. coli genome annotation by resolving 47% of these gaps. NICEgame, applicable to any GEM and functioning from open-source software, should thus enhance all GEM-based predictions and subsequent biotechnological and biomedical applications.

Publisher

Proceedings of the National Academy of Sciences

Subject

Multidisciplinary

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3