In silico identification of AMPylating enzymes and study of their divergent evolution
In silico identification of AMPylating enzymes and study of their divergent evolution
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DOI：
10.1038/srep10804
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发表时间：
2015-06-03
影响因子：
4.6
通讯作者：
Mohanty, Debasisa
中科院分区：
文献类型：
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作者：
Khater, Shradha;Mohanty, Debasisa
AMPylation 是一种新型翻译后修饰 (PTM)，涉及 AMP 部分与蛋白质的苏氨酸/酪氨酸侧链的共价连接。属于三个不同家族的 AMP 化酶，即 Fic/Doc、GS-ATase 和 DrrA 已通过实验进行了表征。这些新型酶参与无数的生物过程，使它们成为全基因组搜索的有趣候选者。我们使用 SVM 和 HMM 开发了一种计算协议，用于识别 AMPylation 结构域并将其分类为催化 AMPylation、去AMPylation、磷酸化和磷酸胆碱转移的各种功能亚家族。我们的分析不仅在未注释的蛋白质中鉴定出新型 PTM 催化酶，而且还揭示了这种新型酶家族如何通过蛋白质序列/结构的细微变化而进化以产生功能多样性。 Fic/Doc 的系统发育分析揭示了三个新的同功能亚家族，从而增加了它们的功能分歧。此外，Fic/Doc 蛋白在高度移动和不稳定的基因组岛上频繁出现表明它们通过广泛的水平基因转移而进化。另一方面，系统发育分析表明 GS-ATase 家族的横向进化以及负责 GS-ATase AMPylation 和 deAMPylation 活性的早期重复事件。我们的分析还揭示了 DrrA 蛋白底物特异性的分子基础。
AMPylation is a novel post-translational modification (PTM) involving covalent attachment of an AMP moiety to threonine/tyrosine side chains of a protein. AMPylating enzymes belonging to three different families, namely Fic/Doc, GS-ATase and DrrA have been experimentally characterized. Involvement of these novel enzymes in a myriad of biological processes makes them interesting candidates for genome-wide search. We have used SVM and HMM to develop a computational protocol for identification of AMPylation domains and their classification into various functional subfamilies catalyzing AMPylation, deAMPylation, phosphorylation and phosphocholine transfer. Our analysis has not only identified novel PTM catalyzing enzymes among unannotated proteins, but has also revealed how this novel enzyme family has evolved to generate functional diversity by subtle changes in sequence/structures of the proteins. Phylogenetic analysis of Fic/Doc has revealed three new isofunctional subfamilies, thus adding to their functional divergence. Also, frequent occurrence of Fic/Doc proteins on highly mobile and unstable genomic islands indicated their evolution via extensive horizontal gene transfers. On the other hand phylogenetic analyses indicate lateral evolution of GS-ATase family and an early duplication event responsible for AMPylation and deAMPylation activity of GS-ATase. Our analysis also reveals molecular basis of substrate specificity of DrrA proteins.