扩展 PROXIMAL 预测人类肠道微生物群中酚类化合物的降解途径。

IF 3.5 2区 生物学 Q1 MATHEMATICAL & COMPUTATIONAL BIOLOGY
Francesco Balzerani, Telmo Blasco, Sergio Pérez-Burillo, Luis V Valcarcel, Soha Hassoun, Francisco J Planes
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引用次数: 0

摘要

尽管在重建基因组规模的代谢网络方面取得了重大进展,但人们对许多生物的细胞代谢的了解仍然不全面。阐明细胞新陈代谢的一个有前途的方法是分析酶的全部杂交范围,这利用了酶与非注释底物结合并产生新反应的能力。为了指导费时费力的实验,人们提出了不同的计算方法来探索酶的杂合性。其中一种相关算法是 PROXIMAL,它主要依靠 KEGG 来定义通用反应规则,并将特定分子亚结构与相关化学转化联系起来。在这里,我们介绍一种全新的管道 PROXIMAL2,它克服了对 KEGG 数据的依赖。此外,与前一版本相比,PROXIMAL2 引入了两项相关改进:i)正确处理多步反应;ii)跟踪转化过程中的电荷。我们比较了 PROXIMAL 和 PROXIMAL2 从 KEGG 反应中的底物恢复注释产物的情况,发现其准确性有了非常显著的提高。然后,我们将 PROXIMAL2 应用于预测人类肠道微生物群中酚类化合物的降解反应。我们将结果与 RetroPath RL(一种不同的相关酶杂合方法)进行了比较。我们发现这两种方法之间有明显的重叠,但也有互补的结果,这为研究营养学中的这一相关问题开辟了新的研究方向。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota.

Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota.

Despite significant advances in reconstructing genome-scale metabolic networks, the understanding of cellular metabolism remains incomplete for many organisms. A promising approach for elucidating cellular metabolism is analysing the full scope of enzyme promiscuity, which exploits the capacity of enzymes to bind to non-annotated substrates and generate novel reactions. To guide time-consuming costly experimentation, different computational methods have been proposed for exploring enzyme promiscuity. One relevant algorithm is PROXIMAL, which strongly relies on KEGG to define generic reaction rules and link specific molecular substructures with associated chemical transformations. Here, we present a completely new pipeline, PROXIMAL2, which overcomes the dependency on KEGG data. In addition, PROXIMAL2 introduces two relevant improvements with respect to the former version: i) correct treatment of multi-step reactions and ii) tracking of electric charges in the transformations. We compare PROXIMAL and PROXIMAL2 in recovering annotated products from substrates in KEGG reactions, finding a highly significant improvement in the level of accuracy. We then applied PROXIMAL2 to predict degradation reactions of phenolic compounds in the human gut microbiota. The results were compared to RetroPath RL, a different and relevant enzyme promiscuity method. We found a significant overlap between these two methods but also complementary results, which open new research directions into this relevant question in nutrition.

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来源期刊
NPJ Systems Biology and Applications
NPJ Systems Biology and Applications Mathematics-Applied Mathematics
CiteScore
5.80
自引率
0.00%
发文量
46
审稿时长
8 weeks
期刊介绍: npj Systems Biology and Applications is an online Open Access journal dedicated to publishing the premier research that takes a systems-oriented approach. The journal aims to provide a forum for the presentation of articles that help define this nascent field, as well as those that apply the advances to wider fields. We encourage studies that integrate, or aid the integration of, data, analyses and insight from molecules to organisms and broader systems. Important areas of interest include not only fundamental biological systems and drug discovery, but also applications to health, medical practice and implementation, big data, biotechnology, food science, human behaviour, broader biological systems and industrial applications of systems biology. We encourage all approaches, including network biology, application of control theory to biological systems, computational modelling and analysis, comprehensive and/or high-content measurements, theoretical, analytical and computational studies of system-level properties of biological systems and computational/software/data platforms enabling such studies.
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