Dynamics and adaptive benefits of protein domain emergence and arrangements during plant genome evolution.
Dynamics and adaptive benefits of protein domain emergence and arrangements during plant genome evolution.
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DOI：
10.1093/gbe/evs004
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发表时间：
2012
影响因子：
3.3
通讯作者：
Grath S
中科院分区：
文献类型：
--
作者：
Kersting AR;Bornberg-Bauer E;Moore AD;Grath S
植物基因组通常非常大，大多是古多倍体，并且具有大量基因重复和复杂的基因组特征，例如重复和转座元件。人们假设其中许多特征能够使无法轻易逃脱环境挑战的植物能够快速适应。另一种机制是蛋白质编码基因的模块化重排，最近被充分描述为细菌、动物和真菌快速适应的主要促进者，但尚未适用于植物。由于基于图谱的方法具有高精度，通过表征蛋白质结构域及其结构、功能和进化构件的出现、丢失和重排，可以在蛋白质水平上很好地捕获重排。在这里，我们研究了结构域重排的动态，并探索了它们在 27 种植物和 3 种藻类基因组中的适应性益处。我们使用系统发育学方法，通过单步事件（例如域的融合、裂变和末端丢失）来解释 88% 排列的形成。我们发现每个谱系都有许多域丢失，但至少有 500 个域是新颖的，也就是说，它们是绿色植物所独有的，并且或多或少是最近才出现的。这些新的结构域比古老的结构域更容易在其基因组内复制和重新排列，并且过多地参与应激反应和发育创新。与古代结构域相比，新结构域更频繁地影响调节蛋白并表现出更高程度的结构紊乱。尽管存在相对较大且保守的单结构域蛋白质核心集，但长的多结构域排列往往具有物种特异性。我们发现重复的基因更经常参与重排。尽管裂变事件通常会影响代谢蛋白，但融合事件通常会产生环境传感所必需的新信号蛋白。总而言之，植物基因组中单个结构域的高波动性和复杂排列证明了模块化对于植物环境适应性的重要性。
Plant genomes are generally very large, mostly paleopolyploid, and have numerous gene duplicates and complex genomic features such as repeats and transposable elements. Many of these features have been hypothesized to enable plants, which cannot easily escape environmental challenges, to rapidly adapt. Another mechanism, which has recently been well described as a major facilitator of rapid adaptation in bacteria, animals, and fungi but not yet for plants, is modular rearrangement of protein-coding genes. Due to the high precision of profile-based methods, rearrangements can be well captured at the protein level by characterizing the emergence, loss, and rearrangements of protein domains, their structural, functional, and evolutionary building blocks. Here, we study the dynamics of domain rearrangements and explore their adaptive benefit in 27 plant and 3 algal genomes. We use a phylogenomic approach by which we can explain the formation of 88% of all arrangements by single-step events, such as fusion, fission, and terminal loss of domains. We find many domains are lost along every lineage, but at least 500 domains are novel, that is, they are unique to green plants and emerged more or less recently. These novel domains duplicate and rearrange more readily within their genomes than ancient domains and are overproportionally involved in stress response and developmental innovations. Novel domains more often affect regulatory proteins and show a higher degree of structural disorder than ancient domains. Whereas a relatively large and well-conserved core set of single-domain proteins exists, long multi-domain arrangements tend to be species-specific. We find that duplicated genes are more often involved in rearrangements. Although fission events typically impact metabolic proteins, fusion events often create new signaling proteins essential for environmental sensing. Taken together, the high volatility of single domains and complex arrangements in plant genomes demonstrate the importance of modularity for environmental adaptability of plants.
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DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
4.5
作者：
Baucom RS;Estill JC;Chaparro C;Upshaw N;Jogi A;Deragon JM;Westerman RP;Sanmiguel PJ;Bennetzen JL
通讯作者：
Bennetzen JL
影响因子：
3.5
作者：
Amoutzias, GD;Weiner, J;Bornberg-Bauer, E
通讯作者：
Bornberg-Bauer, E
影响因子：
2.6
作者：
Cartwright, Paulyn;Collins, Allen
通讯作者：
Collins, Allen
影响因子：
5.6
作者：
Apic, G;Gough, J;Teichmann, SA
通讯作者：
Teichmann, SA