Genetic Context Significantly Influences the Maintenance and Evolution of Degenerate Pathways.
Genetic Context Significantly Influences the Maintenance and Evolution of Degenerate Pathways.
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DOI：
10.1093/gbe/evab082
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发表时间：
2021-06-08
影响因子：
3.3
通讯作者：
Marx CJ
中科院分区：
文献类型：
--
作者：
Bruger EL;Chubiz LM;Rojas Echenique JI;Renshaw CJ;Espericueta NV;Draghi JA;Marx CJ
了解新的生理特征的进化对于扩展生物系统的表征和操作是高度相关的。新性状的获得可以通过水平基因转移(HGT)实现。在这里，我们调查了促进或阻止HGT驱动的退化的维持的驱动因素，当进程通过不相同的组件完成相同的功能时发生。随后的进化可以优化新获得的功能；例如，在一株经过工程改造的甲基紫罗兰菌株中发现的有益等位基因使其能够利用“外来”甲醛氧化途径取代其本地途径进行甲基营养生长。我们研究了当这些等位基因与本地途径或两者(双重)途径结合时，这些等位基因之间相互作用的适合性结果。与它们进化的外来途径环境不同，当这些等位基因进入这些不同的遗传背景时，它们往往是中性的或有害的。然而，有些情况下，多个等位基因的组合会产生比单个等位基因替换所能提供的更高的适合度结果。重要的是，伴随这些等位基因替换的遗传背景显著改变了适应度格局，移动了局部适应度峰值，并限制了一组可访问的进化轨迹。这些发现突显了遗传背景如何负面影响维持天然功能和HGT引入的功能的可能性，从而使退化难以进化。然而，在通过增加影响这些通路功能的进化等位基因来减轻维持退化的成本的情况下，我们观察到发生通路共同进化的罕见机会。总之，我们的结果强调了遗传背景和由此产生的上位性在保留或丧失HGT获得性退化功能方面的重要性。
Understanding the evolution of novel physiological traits is highly relevant for expanding the characterization and manipulation of biological systems. Acquisition of new traits can be achieved through horizontal gene transfer (HGT). Here, we investigate drivers that promote or deter the maintenance of HGT-driven degeneracy, occurring when processes accomplish identical functions through nonidentical components. Subsequent evolution can optimize newly acquired functions; for example, beneficial alleles identified in an engineered Methylorubrum extorquens strain allowed it to utilize a “Foreign” formaldehyde oxidation pathway substituted for its Native pathway for methylotrophic growth. We examined the fitness consequences of interactions between these alleles when they were combined with the Native pathway or both (Dual) pathways. Unlike the Foreign pathway context where they evolved, these alleles were often neutral or deleterious when moved into these alternative genetic backgrounds. However, there were instances where combinations of multiple alleles resulted in higher fitness outcomes than individual allelic substitutions could provide. Importantly, the genetic context accompanying these allelic substitutions significantly altered the fitness landscape, shifting local fitness peaks and restricting the set of accessible evolutionary trajectories. These findings highlight how genetic context can negatively impact the probability of maintaining native and HGT-introduced functions together, making it difficult for degeneracy to evolve. However, in cases where the cost of maintaining degeneracy was mitigated by adding evolved alleles impacting the function of these pathways, we observed rare opportunities for pathway coevolution to occur. Together, our results highlight the importance of genetic context and resulting epistasis in retaining or losing HGT-acquired degenerate functions.
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影响因子：
12.3
作者：
Xie G;Bonner CA;Brettin T;Gottardo R;Keyhani NO;Jensen RA
通讯作者：
Jensen RA
影响因子：
56.9
作者：
Chistoserdova, L;Vorholt, JA;Lidstrom, ME
通讯作者：
Lidstrom, ME
DOI：
10.1098/rstb.2016.0424
发表时间：
2017-12-05
影响因子：
6.3
作者：
Hall, James P. J.;Brockhurst, Michael A.;Harrison, Ellie
通讯作者：
Harrison, Ellie
影响因子：
5.7
作者：
Ghosh S;O'Connor TJ
通讯作者：
O'Connor TJ
影响因子：
4.5
作者：
Chou HH;Delaney NF;Draghi JA;Marx CJ
通讯作者：
Marx CJ