Ancestral reconstruction of polyethylene terephthalate degrading cutinases reveals a rugged and unexplored sequence-fitness landscape

IF 11.7 1区综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES

Science Advances Pub Date : 2025-05-14 DOI:10.1126/sciadv.ads8318

Vanessa Vongsouthi, Rosemary Georgelin, Dana S. Matthews, Jake Saunders, Brendon M. Lee, Jennifer Ton, Adam M. Damry, Rebecca L. Frkic, Matthew A. Spence, Colin J. Jackson

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Abstract

The use of protein engineering to generate enzymes for the degradation of polyethylene terephthalate (PET) is a promising route for plastic recycling, yet traditional engineering approaches often fail to explore protein sequence space for optimal enzymes. In this work, we use multiplexed ancestral sequence reconstruction (mASR) to address this, exploring the evolutionary sequence space of PET-degrading cutinases. Using 20 statistically equivalent phylogenies of the bacterial cutinase family, we generated 48 ancestral sequences revealing a wide range of PETase activities, highlighting the value of mASR in uncovering functional variants. Our findings show PETase activity can evolve through multiple pathways involving mutations remote from the active site. Moreover, analyzing the PETase fitness landscape with local ancestral sequence embedding (LASE) revealed that LASE can capture sequence features linked to PETase activity. This work highlights mASR’s potential in exploration of sequence space and underscores the use of LASE in readily mapping the protein fitness landscapes.

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聚对苯二甲酸乙二醇酯降解角质酶的祖先重建揭示了一个崎岖和未探索的序列适应度景观

利用蛋白质工程生成降解聚对苯二甲酸乙二醇酯（PET）的酶是一条很有前途的塑料回收途径，但传统的工程方法往往无法探索最佳酶的蛋白质序列空间。在这项工作中，我们使用多路祖先序列重建（mASR）来解决这个问题，探索pet降解角质酶的进化序列空间。利用细菌角质酶家族的20个统计上相等的系统发育，我们生成了48个祖先序列，揭示了广泛的PETase活性，突出了mASR在发现功能变异方面的价值。我们的研究结果表明，PETase活性可以通过多种途径进化，包括远离活性位点的突变。此外，利用局部祖先序列嵌入（LASE）分析了PETase适应度景观，发现LASE可以捕获与PETase活性相关的序列特征。这项工作突出了mASR在探索序列空间方面的潜力，并强调了LASE在绘制蛋白质适合度景观方面的使用。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Science Advances 综合性期刊-综合性期刊

CiteScore

21.40

自引率

1.50%

发文量

1937

审稿时长

29 weeks

期刊介绍： Science Advances, an open-access journal by AAAS, publishes impactful research in diverse scientific areas. It aims for fair, fast, and expert peer review, providing freely accessible research to readers. Led by distinguished scientists, the journal supports AAAS's mission by extending Science magazine's capacity to identify and promote significant advances. Evolving digital publishing technologies play a crucial role in advancing AAAS's global mission for science communication and benefitting humankind.