Evolution of hydra, a recently evolved testis-expressed gene with nine alternative first exons in Drosophila melanogaster.
Evolution of hydra, a recently evolved testis-expressed gene with nine alternative first exons in Drosophila melanogaster.
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Hydra的进化是一种最近进化的睾丸表达的基因，在果蝇中有9个替代第一外显子。
DOI：
10.1371/journal.pgen.0030107
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发表时间：
2007-07
期刊：
影响因子：
4.5
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中科院分区：
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作者：
我们在这里描述了似乎在黑腹果蝇亚群中从头开始的果蝇基因hydra，并随后在黑腹果蝇及其兄弟物种的结构和表达水平上进化。D. melanogaster hydra编码一种约300个氨基酸的预测蛋白质，与任何已知的蛋白质没有明显的相似性。在D. ananassae和D. pseudoobscura中都发现了两侧水螅的同长区，但水螅只在黑腹蛇亚群中发现，表明其起源时间不到1300万年前。在D. melanogaster中，hydra的1号外显子经历了反复的重复，导致形成了9个串联交替的1号外显子。这些可选外显子中的7个在它们的3 '侧被转座子DINE-1（果蝇分散元件-1）所包围。我们证明了9个重复的外显子1中至少有4个可以作为替代转录起始位点。整个水螅座在拟龙和雪hellia中也有复制。黑腹水螅在睾丸近端表达最强烈，提示在后期精子发生中起作用。水螅编码区在种间具有较高的Ka/Ks比值，但在所有比较中该比值均小于1，说明水螅受功能约束。水螅的序列多态性和分化分析表明，水螅是在正向选择下进化而来的。围绕第一外显子的剧烈结构变化并不影响基因表达的组织特异性：hydra主要在D. melanogaster、D. simulans和D. yakuba的睾丸中表达。然而，我们发现D. melanogaster和D. simulans之间的表达水平发生了显著变化（约20倍）。虽然水螅最初是在没有附近转座元件插入的情况下进化的，但我们认为，随后水螅区域重复序列的积累可能通过诱导重排和引起局部异染色质化而促进了结构和表达水平的进化。我们的分析进一步表明，基因结构和表达水平的反复进化可能是新进化基因的特征。我们还认为，晚期精子发生是新进化和快速进化的男性特异性基因的功能靶点。相似的动物种群具有相似数量的基因，但并非所有这些基因都是相同的。虽然一些基因高度保守，可以很容易地在从酵母到植物到人类的物种中唯一地识别出来，但其他基因有时只在少数物种中甚至在单个物种中被发现。这种新进化的基因可能有助于产生使物种独特的特征。我们在这里描述了一种新进化的基因，叫做水螅，它只存在于果蝇物种的一个小亚群中。Hydra在睾丸中表达，表明它可能在男性生育能力中起作用。九头蛇的结构和蛋白质编码序列在物种间发生了显著的进化。作者以被赫拉克勒斯杀死的九头怪物命名hydra基因，因为在果蝇中，hydra有九个潜在的备选第一外显子。也许是由于这种或其他结构上的变化，水螅在一对物种之间产生的RNA水平有很大的不同。这一分析表明，新产生的基因可能在序列、结构和表达水平上迅速进化。
We describe here the Drosophila gene hydra that appears to have originated de novo in the melanogaster subgroup and subsequently evolved in both structure and expression level in Drosophila melanogaster and its sibling species. D. melanogaster hydra encodes a predicted protein of ~300 amino acids with no apparent similarity to any previously known proteins. The syntenic region flanking hydra on both sides is found in both D. ananassae and D. pseudoobscura, but hydra is found only in melanogaster subgroup species, suggesting that it originated less than ~13 million y ago. Exon 1 of hydra has undergone recurrent duplications, leading to the formation of nine tandem alternative exon 1s in D. melanogaster. Seven of these alternative exons are flanked on their 3′ side by the transposon DINE-1 (Drosophila interspersed element-1). We demonstrate that at least four of the nine duplicated exon 1s can function as alternative transcription start sites. The entire hydra locus has also duplicated in D. simulans and D. sechellia. D. melanogaster hydra is expressed most intensely in the proximal testis, suggesting a role in late-stage spermatogenesis. The coding region of hydra has a relatively high Ka/Ks ratio between species, but the ratio is less than 1 in all comparisons, suggesting that hydra is subject to functional constraint. Analysis of sequence polymorphism and divergence of hydra shows that it has evolved under positive selection in the lineage leading to D. melanogaster. The dramatic structural changes surrounding the first exons do not affect the tissue specificity of gene expression: hydra is expressed predominantly in the testes in D. melanogaster, D. simulans, and D. yakuba. However, we have found that expression level changed dramatically (~ >20-fold) between D. melanogaster and D. simulans. While hydra initially evolved in the absence of nearby transposable element insertions, we suggest that the subsequent accumulation of repetitive sequences in the hydra region may have contributed to structural and expression-level evolution by inducing rearrangements and causing local heterochromatinization. Our analysis further shows that recurrent evolution of both gene structure and expression level may be characteristics of newly evolved genes. We also suggest that late-stage spermatogenesis is the functional target for newly evolved and rapidly evolving male-specific genes. Similar groups of animals have similar numbers of genes, but not all of these genes are the same. While some genes are highly conserved and can be easily and uniquely identified in species ranging from yeast to plants to humans, other genes are sometimes found in only a small number or even in a single species. Such newly evolved genes may help produce traits that make species unique. We describe here a newly evolved gene called hydra that occurs only in a small subgroup of Drosophila species. hydra is expressed in the testes, suggesting that it may have a function in male fertility. hydra has evolved significantly in its structure and protein-coding sequence among species. The authors named the gene hydra after the nine-headed monster slain by Hercules because in one species, Drosophila melanogaster, hydra has nine potential alternative first exons. Perhaps because of this or other structural changes, the level of RNA made by hydra differs significantly between one pair of species. This analysis reveals that newly created genes may evolve rapidly in sequence, structure, and expression level.