Evolutionary history of the poly(ADP-ribose) polymerase gene family in eukaryotes.
Evolutionary history of the poly(ADP-ribose) polymerase gene family in eukaryotes.
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DOI：
10.1186/1471-2148-10-308
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发表时间：
2010-10-13
影响因子：
3.4
通讯作者：
Lamb RS
中科院分区：
文献类型：
--
作者：
Citarelli M;Teotia S;Lamb RS
聚（ADP-核糖）聚合酶（PARP）超家族最初被鉴定为使用 NAD+ 作为底物催化 ADP-核糖亚基与靶蛋白附着的酶。该家族的特征是催化位点，称为 PARP 特征。虽然这些蛋白质可以在一系列真核生物中找到，但它们在哺乳动物中的研究最为深入。在这些生物体中，PARP 在 DNA 修复、基因组完整性和表观遗传调控方面具有关键功能。最近，人们发现 PARP 超家族中的蛋白质已经改变了催化位点，并且具有单（ADP-核糖）转移酶（mART）活性或酶促无活性。这些发现表明 PARP 签名具有最初预测的更广泛的功能。在这项研究中，我们研究了真核生物中 PARP 基因的进化史。我们通过计算机技术鉴定了来自 6 个真核超类群中 5 个的 77 个物种的 236 个 PARP 蛋白。我们对已识别的 PARP 进行了广泛的系统发育分析。它们存在于所有可获得序列的真核生物超群中，但超群内的一些个体谱系独立地丢失了这些基因。 PARP 超家族可分为 6 个分支。其中两个进化枝很可能是在最后的共同真核祖先中发现的。此外，我们还在生物体中发现了 PARP，而此前它们尚未在其中被描述过。我们的研究可以得出三个主要结论。首先，PARP 基因的广泛分布和代表性模式表明所有现存真核生物的祖先都编码这种类型的蛋白质。其次，祖先的PARP蛋白具有不同的功能和活性。其中一种蛋白质与人类 PARP1 相似，可能在 DNA 损伤反应中发挥作用。第二个祖先 PARP 的催化结构域已经进化出差异，表明这些蛋白质可能不具有聚（ADP-核糖基）化活性。第三，PARP超家族的多样性比之前记录的要大，这表明随着更多的真核基因组可用，该基因家族的数量和类型都将增长。
The Poly(ADP-ribose)polymerase (PARP) superfamily was originally identified as enzymes that catalyze the attachment of ADP-ribose subunits to target proteins using NAD+ as a substrate. The family is characterized by the catalytic site, termed the PARP signature. While these proteins can be found in a range of eukaryotes, they have been best studied in mammals. In these organisms, PARPs have key functions in DNA repair, genome integrity and epigenetic regulation. More recently it has been found that proteins within the PARP superfamily have altered catalytic sites, and have mono(ADP-ribose) transferase (mART) activity or are enzymatically inactive. These findings suggest that the PARP signature has a broader range of functions that initially predicted. In this study, we investigate the evolutionary history of PARP genes across the eukaryotes. We identified in silico 236 PARP proteins from 77 species across five of the six eukaryotic supergroups. We performed extensive phylogenetic analyses of the identified PARPs. They are found in all eukaryotic supergroups for which sequence is available, but some individual lineages within supergroups have independently lost these genes. The PARP superfamily can be subdivided into six clades. Two of these clades were likely found in the last common eukaryotic ancestor. In addition, we have identified PARPs in organisms in which they have not previously been described. Three main conclusions can be drawn from our study. First, the broad distribution and pattern of representation of PARP genes indicates that the ancestor of all extant eukaryotes encoded proteins of this type. Second, the ancestral PARP proteins had different functions and activities. One of these proteins was similar to human PARP1 and likely functioned in DNA damage response. The second of the ancestral PARPs had already evolved differences in its catalytic domain that suggest that these proteins may not have possessed poly(ADP-ribosyl)ation activity. Third, the diversity of the PARP superfamily is larger than previously documented, suggesting as more eukaryotic genomes become available, this gene family will grow in both number and type.
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