Kramer Elena M, Su Huei-Jiun, Wu Cheng-Chiang, Hu Jer-Ming
Dept. of Organismic and Evolutionary Biology, Harvard University, Cambridge MA 02138, USA.
BMC Evol Biol. 2006 Mar 24;6:30. doi: 10.1186/1471-2148-6-30.
The evolution of type II MADS box genes has been extensively studied in angiosperms. One of the best-understood subfamilies is that of the Arabidopsis gene APETALA3 (AP3). Previous work has demonstrated that the ancestral paleoAP3 lineage was duplicated at some point within the basal eudicots to give rise to the paralogous TM6 and euAP3 lineages. This event was followed in euAP3 orthologs by the replacement of the C-terminal paleoAP3 motif with the derived euAP3 motif. It has been suggested that the new motif was created by an eight-nucleotide insertion that produced a translational frameshift.
The addition of 25 eudicot AP3 homologs to the existing dataset has allowed us to clarify the process by which the euAP3 motif evolved. Phylogenetic analysis indicates that the euAP3/TM6 duplication maps very close to the base of the core eudicots, associated with the families Trochodendraceae and Buxaceae. We demonstrate that although the transformation of paleoAP3 into euAP3 was due to a frameshift mutation, this was the result of a single nucleotide deletion. The use of ancestral character state reconstructions has allowed us to demonstrate that the frameshift was accompanied by few other nucleotide changes. We further confirm that the sequence is evolving as coding region.
This study demonstrates that the simplest of genetic changes can result in the remodeling of protein sequence to produce a kind of molecular 'hopeful monster.' Moreover, such a novel protein motif can become conserved almost immediately on the basis of what appears to be a rapidly generated new function. Given that the existing data on the function of such C-terminal motifs are somewhat disparate and contradictory, we have sought to synthesize previous findings within the context of the current analysis and thereby highlight specific hypotheses that require further investigation before the significance of the euAP3 frameshift event can be fully understood.
II型MADS盒基因的进化在被子植物中已得到广泛研究。研究得最透彻的亚家族之一是拟南芥基因APETALA3（AP3）所在的亚家族。先前的研究表明，古老的paleoAP3谱系在基部真双子叶植物的某个时期发生了复制，从而产生了同源的TM6和euAP3谱系。在euAP3直系同源基因中，这一事件之后是C末端的paleoAP3基序被衍生的euAP3基序所取代。有人提出，新的基序是由一个八核苷酸插入产生的，该插入导致了翻译移码。
在现有数据集中增加了25个真双子叶植物AP3同源基因，这使我们能够阐明euAP3基序的进化过程。系统发育分析表明，euAP3/TM6复制图谱非常接近核心真双子叶植物的基部，与昆栏树科和黄杨科相关。我们证明，虽然paleoAP3向euAP3的转变是由于移码突变，但这是单个核苷酸缺失的结果。祖先特征状态重建的使用使我们能够证明，移码伴随着很少的其他核苷酸变化。我们进一步证实该序列作为编码区在进化。
本研究表明，最简单的基因变化可导致蛋白质序列重塑，从而产生一种分子“有希望的怪物”。此外，这样一个新的蛋白质基序几乎可以立即基于一种似乎是快速产生的新功能而变得保守。鉴于关于此类C末端基序功能的现有数据有些不同且相互矛盾，我们试图在当前分析的背景下综合先前的发现，从而突出在能够充分理解euAP3移码事件的重要性之前需要进一步研究的特定假设。
