Novel Families of Archaeo-Eukaryotic Primases Associated with Mobile Genetic Elements of Bacteria and Archaea.
Novel Families of Archaeo-Eukaryotic Primases Associated with Mobile Genetic Elements of Bacteria and Archaea.
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DOI：
10.1016/j.jmb.2017.11.014
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发表时间：
2018-03-02
影响因子：
5.6
通讯作者：
Krupovic M
中科院分区：
文献类型：
--
作者：
Kazlauskas D;Sezonov G;Charpin N;Venclovas Č;Forterre P;Krupovic M
细胞生物在不同的生命领域使用结构不相关的，非同源的DNA引物来合成DNA复制的引物。古细菌和真核生物编码古真核引物酶（AEP）超家族的酶，而细菌则统一使用DnaG家族的引物酶。然而，AEP基因在细菌基因组中广泛存在，对其来源和功能提出了疑问。在这里，我们使用由pTN2质粒编码的古细菌引物聚合酶PolpTN2作为序列相似性搜索的种子，从12个高度不同的门的细菌中恢复了800多个AEP同源物。这些序列形成了一个超群PrimPol-PV1，并可划分为5个新的AEP家族，其特征是含有可能参与核苷酸结合的精氨酸残基的保守基序。功能分析证实了该基序对PolpTN2引物聚合酶的催化活性的重要性。进一步的分析表明，细菌AEPs显示了一系列的结构域组织，并发现了一些新的解旋酶家族的候选者。此外，序列和结构比较表明，经常与AEP结构域融合的PriCT-1和PriCT-2结构域彼此相关，并且与古细菌和真核生物引物的非催化大亚基有关，与最近发现的古细菌引物的PriX亚基有关。最后，基因组邻域分析表明，细菌基因组中编码的AEPs几乎完全与高度多样化的整合移动遗传元件相关，包括整合共轭质粒和噬菌体。古真核引物酶（AEP）超家族的引物酶在细菌中广泛存在。我们描述了5个新的AEP家族的细菌属于12个不同的门。新的AEP家族显示了一个保守的特征基序，可能涉及核苷酸结合。引物酶结构域融合到不同的功能结构域，揭示了新的假定解旋酶家族。新的引物被编码在高度多样化的集成移动遗传元件中。
Cellular organisms in different domains of life employ structurally unrelated, non-homologous DNA primases for synthesis of a primer for DNA replication. Archaea and eukaryotes encode enzymes of the archaeo-eukaryotic primase (AEP) superfamily, whereas bacteria uniformly use primases of the DnaG family. However, AEP genes are widespread in bacterial genomes raising questions regarding their provenance and function. Here, using an archaeal primase–polymerase PolpTN2 encoded by pTN2 plasmid as a seed for sequence similarity searches, we recovered over 800 AEP homologs from bacteria belonging to 12 highly diverse phyla. These sequences formed a supergroup, PrimPol-PV1, and could be classified into five novel AEP families which are characterized by a conserved motif containing an arginine residue likely to be involved in nucleotide binding. Functional assays confirm the essentiality of this motif for catalytic activity of the PolpTN2 primase–polymerase. Further analyses showed that bacterial AEPs display a range of domain organizations and uncovered several candidates for novel families of helicases. Furthermore, sequence and structure comparisons suggest that PriCT-1 and PriCT-2 domains frequently fused to the AEP domains are related to each other as well as to the non-catalytic, large subunit of archaeal and eukaryotic primases, and to the recently discovered PriX subunit of archaeal primases. Finally, genomic neighborhood analysis indicates that the identified AEPs encoded in bacterial genomes are nearly exclusively associated with highly diverse integrated mobile genetic elements, including integrative conjugative plasmids and prophages. Primases of the archaeo-eukaryotic primase (AEP) superfamily are widespread in bacteria. We describe five new AEP families in bacteria belonging to 12 diverse phyla. The new AEP families display a conserved signature motif likely involved in nucleotide binding. The primase domains are fused to diverse functional domains, revealing new families of putative helicases. The novel primases are encoded within highly diverse integrated mobile genetic elements.
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影响因子：
14.9
作者：
Guilliam TA;Keen BA;Brissett NC;Doherty AJ
通讯作者：
Doherty AJ
影响因子：
16
作者：
Bianchi, Julie;Rudd, Sean G.;Jozwiakowski, Stanislaw K.;Bailey, Laura J.;Soura, Violetta;Taylor, Elaine;Stevanovic, Irena;Green, Andrew J.;Stracker, Travis H.;Lindsay, Howard D.;Doherty, Aidan J.
通讯作者：
Doherty, Aidan J.
DOI：
10.1093/bioinformatics/btw108
发表时间：
2016-07-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Katoh K;Standley DM
通讯作者：
Standley DM
影响因子：
14.9
作者：
Finn RD;Clements J;Arndt W;Miller BL;Wheeler TJ;Schreiber F;Bateman A;Eddy SR
通讯作者：
Eddy SR
影响因子：
4.8
作者：
Galal, Wiebke Chemnitz;Pan, Miao;Hurwitz, Jerard
通讯作者：
Hurwitz, Jerard