Fitness Effects of Single Amino Acid Insertions and Deletions in TEM-1 β-Lactamase
Fitness Effects of Single Amino Acid Insertions and Deletions in TEM-1 β-Lactamase
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DOI：
10.1016/j.jmb.2019.04.030
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发表时间：
2019-05-31
影响因子：
5.6
通讯作者：
Ostermeier, Marc
中科院分区：
文献类型：
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作者：
Gonzalez, Courtney E.;Roberts, Paul;Ostermeier, Marc
短插入和缺失（InDels）是自然界中常见的突变类型，也是蛋白质工程中有用的变异来源。InDel事件在蛋白质进化中具有重要影响，通常为适应开辟新的途径。然而，与点突变和氨基酸取代相比，人们对InDels的影响知之甚少。特别是，关于突变适应度效应分布的深度诱变研究几乎完全集中在氨基酸取代上。在这里，我们对TEM-1 β -内酰胺酶中单个氨基酸indel的适应度效应进行了近乎全面的分析。虽然我们发现InDels在很大程度上是有害的，但在整个蛋白质中观察到部分重叠的缺失耐受性和插入耐受性区域，特别是在非结构化区域和螺旋末端。TEM-1的信号序列比成熟蛋白更能耐受InDels。蛋白质的大多数区域耐受插入多于缺失，但少数区域耐受缺失多于插入。我们研究了InDel耐受性与各种措施之间的关系，以帮助了解其起源。这些指标包括β -内酰胺酶的进化变异、二级结构同一性、对氨基酸取代的耐受性、溶剂可及性和侧链加权接触数。我们发现A类β -内酰胺酶的二级结构、加权接触数和进化变异在一定程度上可以预测InDel适应度效应。(C) 2019 Elsevier Ltd.版权所有。
Short insertions and deletions (InDels) are a common type of mutation found in nature and a useful source of variation in protein engineering. InDel events have important consequences in protein evolution, often opening new pathways for adaptation. However, much less is known about the effects of InDels compared to point mutations and amino acid substitutions. In particular, deep mutagenesis studies on the distribution of fitness effects of mutations have focused almost exclusively on amino acid substitutions. Here, we present a near-comprehensive analysis of the fitness effects of single amino acid InDels in TEM-1 beta-lactamase. While we found InDels to be largely deleterious, partially overlapping deletion-tolerant and insertion-tolerant regions were observed throughout the protein, especially in unstructured regions and at the end of helices. The signal sequence of TEM-1 tolerated InDels more than the mature protein. Most regions of the protein tolerated insertions more than deletions, but a few regions tolerated deletions more than insertions. We examined the relationship between InDel tolerance and a variety of measures to help understand its origin. These measures included evolutionary variation in beta-lactamases, secondary structure identity, tolerance to amino acid substitutions, solvent accessibility, and side-chain weighted contact number. We found secondary structure, weighted contact number, and evolutionary variation in class A beta-lactamases to be the somewhat predictive of InDel fitness effects. (C) 2019 Elsevier Ltd. All rights reserved.