基于环境活性的蛋白质分析,从自然群落中发现功能驱动的酶。

IF 6.2 2区 环境科学与生态学 Q1 GENETICS & HEREDITY
Sabrina Ninck, Thomas Klaus, Tatiana V Kochetkova, Sarah P Esser, Leonard Sewald, Farnusch Kaschani, Christopher Bräsen, Alexander J Probst, Ilya V Kublanov, Bettina Siebers, Markus Kaiser
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引用次数: 0

摘要

背景:微生物群落是全球生物地球化学循环、异生物解毒以及有机物分解的重要驱动力。它们在生态系统功能中的主要新陈代谢作用由一组独特的酶来保证,提供了巨大的但大多隐藏的酶潜能。因此,探索这套酶不仅有助于更好地了解微生物如何在自然环境中发挥作用,从而促进生态学研究,而且还能进一步将微生物群落(尤其是极端生境中的微生物群落)变成发现新型酶的宝贵资源,从而在生物技术领域获得潜在应用。目前已经出现了不同的发掘策略,如生物勘探,这主要依赖于元基因组方法与基于序列的生物信息学分析相结合;然而,对其蛋白质组进行准确的功能预测和破译酶的体内活性仍然具有挑战性:在这里,我们介绍了基于环境活性的蛋白质分析(eABPP),这是一种多组学方法,它将基因组解析的元基因组学与基于质谱的 ABPP 结合在一起。eABPP因此弥补了环境基因组学、正确的功能注释和体内酶活性之间的差距。作为展示,我们报告了从俄罗斯堪察加半岛两个独立温泉的天然微生物群落的 eABPP 中成功鉴定出活性恒温丝氨酸水解酶的情况:通过报告生态系统中原生状态下的酶活性,我们预计 eABPP 不仅能推进当前从环境生态系统中发现同源序列酶的方法,以促进后续生物催化剂的开发,而且还能通过剖析微生物群落相互作用的潜在分子机制,为微生物群落相互作用的生态学研究做出贡献。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Environmental activity-based protein profiling for function-driven enzyme discovery from natural communities.

Background: Microbial communities are important drivers of global biogeochemical cycles, xenobiotic detoxification, as well as organic matter decomposition. Their major metabolic role in ecosystem functioning is ensured by a unique set of enzymes, providing a tremendous yet mostly hidden enzymatic potential. Exploring this enzymatic repertoire is therefore not only relevant for a better understanding of how microorganisms function in their natural environment, and thus for ecological research, but further turns microbial communities, in particular from extreme habitats, into a valuable resource for the discovery of novel enzymes with potential applications in biotechnology. Different strategies for their uncovering such as bioprospecting, which relies mainly on metagenomic approaches in combination with sequence-based bioinformatic analyses, have emerged; yet accurate function prediction of their proteomes and deciphering the in vivo activity of an enzyme remains challenging.

Results: Here, we present environmental activity-based protein profiling (eABPP), a multi-omics approach that extends genome-resolved metagenomics with mass spectrometry-based ABPP. This combination allows direct profiling of environmental community samples in their native habitat and the identification of active enzymes based on their function, even without sequence or structural homologies to annotated enzyme families. eABPP thus bridges the gap between environmental genomics, correct function annotation, and in vivo enzyme activity. As a showcase, we report the successful identification of active thermostable serine hydrolases from eABPP of natural microbial communities from two independent hot springs in Kamchatka, Russia.

Conclusions: By reporting enzyme activities within an ecosystem in their native state, we anticipate that eABPP will not only advance current methodological approaches to sequence homology-guided enzyme discovery from environmental ecosystems for subsequent biocatalyst development but also contributes to the ecological investigation of microbial community interactions by dissecting their underlying molecular mechanisms.

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来源期刊
Environmental Microbiome
Environmental Microbiome Immunology and Microbiology-Microbiology
CiteScore
7.40
自引率
2.50%
发文量
55
审稿时长
13 weeks
期刊介绍: Microorganisms, omnipresent across Earth's diverse environments, play a crucial role in adapting to external changes, influencing Earth's systems and cycles, and contributing significantly to agricultural practices. Through applied microbiology, they offer solutions to various everyday needs. Environmental Microbiome recognizes the universal presence and significance of microorganisms, inviting submissions that explore the diverse facets of environmental and applied microbiological research.
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