Evolutionary dynamics of origin and loss in the deep history of phospholipase D toxin genes
Evolutionary dynamics of origin and loss in the deep history of phospholipase D toxin genes
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DOI：
10.1186/s12862-018-1302-2
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发表时间：
2018-12-18
影响因子：
3.4
通讯作者：
Binford, Greta J.
中科院分区：
文献类型：
--
作者：
Cordes, Matthew H. J.;Binford, Greta J.
毒液表达的鞘磷脂酶D/磷脂酶D(sMase D/PLD)酶是由普遍存在的甘油磷酸二酯酶(GDPD)进化而来的。GDPD样SMaseD/PLD毒素在蜘蛛类和细菌中的表达激发了人们对侧向基因转移和汇聚招募在这一谱系进化史上的相对贡献的思考。以前的工作识别了两个不同的谱系，一个是包括蜘蛛类毒素的SinTox-like(ST-like)分支，另一个是包括细菌毒素和大量真菌同源物的类似放线杆菌(AT-like)的分支。ST-like分支现在包括了更广泛的节肢动物中的同源物以及Cnidaria中的一个姊妹群；AT-like分支现在包括了额外的真菌门和蛋白细菌同源物；我们报告了第三个在不同的水生后生动物分类群、一些单细胞真核生物和一些水生变形细菌中表达的分支。与GDPD类似的SMaseD/PLD在ST-like家族的螯合物和水生生物家族的纤毛虫中有着古老的存在。有根的系统发育树表明，这三个分支来自于变形杆菌GDPD样sMase D/PLD的一个基本类群，其中一些位于可移动的遗传元件上。与GDPD类似的SMase D/PLD具有一个签名的C-末端基序和一个缩短的1环，这是它们与GDPD的区别。这三个主要分支还具有活动站点循环签名，以区分它们与GDPD以及彼此之间的区别。基于生物亲缘关系的分子系统学分析揭示了一个动态的进化史，包括横向基因转移和基因复制/丢失。结论类似GDPD的SMaseD/PLD酶起源于一个古老的祖先，可能是蛋白质细菌，并至少部分通过横向基因转移辐射到不同的生物谱系。
BackgroundVenom-expressed sphingomyelinase D/phospholipase D (SMase D/PLD) enzymes evolved from the ubiquitous glycerophosphoryl diester phosphodiesterases (GDPD). Expression of GDPD-like SMaseD/PLD toxins in both arachnids and bacteria has inspired consideration of the relative contributions of lateral gene transfer and convergent recruitment in the evolutionary history of this lineage. Previous work recognized two distinct lineages, a SicTox-like (ST-like) clade including the arachnid toxins, and an Actinobacterial-toxin like (AT-like) clade including the bacterial toxins and numerous fungal homologs.ResultsHere we expand taxon sampling by homology detection to discover new GDPD-like SMase D/PLD homologs. The ST-like clade now includes homologs in a wider variety of arthropods along with a sister group in Cnidaria; the AT-like clade now includes additional fungal phyla and proteobacterial homologs; and we report a third clade expressed in diverse aquatic metazoan taxa, a few single-celled eukaryotes, and a few aquatic proteobacteria. GDPD-like SMaseD/PLDs have an ancient presence in chelicerates within the ST-like family and ctenophores within the Aquatic family. A rooted phylogenetic tree shows that the three clades derived from a basal paraphyletic group of proteobacterial GDPD-like SMase D/PLDs, some of which are on mobile genetic elements. GDPD-like SMase D/PLDs share a signature C-terminal motif and a shortened 1 loop, features that distinguish them from GDPDs. The three major clades also have active site loop signatures that distinguish them from GDPDs and from each other. Analysis of molecular phylogenies with respect to organismal relationships reveals a dynamic evolutionary history including both lateral gene transfer and gene duplication/loss.ConclusionsThe GDPD-like SMaseD/PLD enzymes derive from a single ancient ancestor, likely proteobacterial, and radiated into diverse organismal lineages at least in part through lateral gene transfer.