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探索细菌和古菌的酶库及其与代谢图谱的关联。

Exploring the enzymatic repertoires of Bacteria and Archaea and their associations with metabolic maps.

作者信息

Tenorio-Salgado Silvia, Villalpando-Aguilar José Luis, Hernandez-Guerrero Rafael, Poot-Hernández Augusto César, Perez-Rueda Ernesto

机构信息

Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica del Estado de Yucatán, Mérida, Yucatán, México.

Tecnológico Nacional de México, Instituto Tecnológico de Mérida, Av. Tecnológico km. 4.5, 97118, Merida, Yucatan, Mexico.

出版信息

Braz J Microbiol. 2024 Dec;55(4):3147-3157. doi: 10.1007/s42770-024-01462-3. Epub 2024 Jul 25.

DOI:10.1007/s42770-024-01462-3
PMID:39052173
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11711735/
Abstract

The evolution, survival, and adaptation of microbes are consequences of gene duplication, acquisition, and divergence in response to environmental challenges. In this context, enzymes play a central role in the evolution of organisms, because they are fundamental in cell metabolism. Here, we analyzed the enzymatic repertoire in 6,467 microbial genomes, including their abundances, and their associations with metabolic maps. We found that the enzymes follow a power-law distribution, in relation to the genome sizes. Therefore, we evaluated the total proportion enzymatic classes in relation to the genomes, identifying a descending-order proportion: transferases (EC:2.-), hydrolases (EC:3.-), oxidoreductases (EC:1.-), ligases (EC:6.-), lyases (EC:4.-), isomerases (EC:5.-), and translocases (EC:7-.). In addition, we identified a preferential use of enzymatic classes in metabolism pathways for xenobiotics, cofactors and vitamins, carbohydrates, amino acids, glycans, and energy. Therefore, this analysis provides clues about the functional constraints associated with the enzymatic repertoire of functions in Bacteria and Archaea.

摘要

微生物的进化、生存和适应是基因复制、获取以及因应环境挑战而发生分歧的结果。在此背景下，酶在生物体的进化中起着核心作用，因为它们在细胞代谢中至关重要。在这里，我们分析了6467个微生物基因组中的酶库，包括它们的丰度以及与代谢图谱的关联。我们发现，就基因组大小而言，酶遵循幂律分布。因此，我们评估了酶类在基因组中的总比例，确定了一个降序比例：转移酶（EC:2.-）、水解酶（EC:3.-）、氧化还原酶（EC:1.-）、连接酶（EC:6.-）、裂合酶（EC:4.-）、异构酶（EC:5.-）和转位酶（EC:7-.）。此外，我们确定了酶类在异生素、辅因子和维生素、碳水化合物、氨基酸、聚糖及能量的代谢途径中的优先使用情况。因此，该分析为与细菌和古菌中酶功能库相关的功能限制提供了线索。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/43a9/11711735/dca2bbfeeff7/42770_2024_1462_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/43a9/11711735/cc0ea661dcf1/42770_2024_1462_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/43a9/11711735/ba0f44ffc909/42770_2024_1462_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/43a9/11711735/5621b744cd72/42770_2024_1462_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/43a9/11711735/3d2a15550a72/42770_2024_1462_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/43a9/11711735/c2128745a6c1/42770_2024_1462_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/43a9/11711735/dca2bbfeeff7/42770_2024_1462_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/43a9/11711735/cc0ea661dcf1/42770_2024_1462_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/43a9/11711735/ba0f44ffc909/42770_2024_1462_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/43a9/11711735/5621b744cd72/42770_2024_1462_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/43a9/11711735/3d2a15550a72/42770_2024_1462_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/43a9/11711735/c2128745a6c1/42770_2024_1462_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/43a9/11711735/dca2bbfeeff7/42770_2024_1462_Fig6_HTML.jpg

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KEGG for taxonomy-based analysis of pathways and genomes.KEGG 用于基于分类的途径和基因组分析。
Nucleic Acids Res. 2023 Jan 6;51(D1):D587-D592. doi: 10.1093/nar/gkac963.
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Metabolic adaptation to vitamin auxotrophy by leaf-associated bacteria.叶片相关细菌对维生素营养缺陷的代谢适应。
ISME J. 2022 Dec;16(12):2712-2724. doi: 10.1038/s41396-022-01303-x. Epub 2022 Aug 20.
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A Genomic Perspective Across Earth's Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy.从基因组角度审视地球微生物群落发现，古菌和细菌的基因组大小与生态系统类型及营养策略相关。
Front Microbiol. 2022 Jan 5;12:761869. doi: 10.3389/fmicb.2021.761869. eCollection 2021.
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Enzyme nomenclature and classification: the state of the art.酶命名法和分类：现状。
FEBS J. 2023 May;290(9):2214-2231. doi: 10.1111/febs.16274. Epub 2022 Jan 3.
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