Greive Sandra J, Fung Herman K H, Chechik Maria, Jenkins Huw T, Weitzel Stephen E, Aguiar Pedro M, Brentnall Andrew S, Glousieau Matthieu, Gladyshev Grigory V, Potts Jennifer R, Antson Alfred A
York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK.
York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK Department of Biology, University of York, York YO10 5DD, UK.
Nucleic Acids Res. 2016 Jan 29;44(2):776-89. doi: 10.1093/nar/gkv1467. Epub 2015 Dec 15.
The helix-turn-helix (HTH) motif features frequently in protein DNA-binding assemblies. Viral pac site-targeting small terminase proteins possess an unusual architecture in which the HTH motifs are displayed in a ring, distinct from the classical HTH dimer. Here we investigate how such a circular array of HTH motifs enables specific recognition of the viral genome for initiation of DNA packaging during virus assembly. We found, by surface plasmon resonance and analytical ultracentrifugation, that individual HTH motifs of the Bacillus phage SF6 small terminase bind the packaging regions of SF6 and related SPP1 genome weakly, with little local sequence specificity. Nuclear magnetic resonance chemical shift perturbation studies with an arbitrary single-site substrate suggest that the HTH motif contacts DNA similarly to how certain HTH proteins contact DNA non-specifically. Our observations support a model where specificity is generated through conformational selection of an intrinsically bent DNA segment by a ring of HTHs which bind weakly but cooperatively. Such a system would enable viral gene regulation and control of the viral life cycle, with a minimal genome, conferring a major evolutionary advantage for SPP1-like viruses.
螺旋-转角-螺旋（HTH）基序在蛋白质与DNA结合的组装体中频繁出现。靶向病毒包装位点（pac位点）的小型末端酶蛋白具有一种不同寻常的结构，其中HTH基序呈环状排列，这与经典的HTH二聚体不同。在此，我们研究这种HTH基序的环状阵列如何在病毒组装过程中实现对病毒基因组的特异性识别，从而启动DNA包装。通过表面等离子体共振和分析超速离心，我们发现芽孢杆菌噬菌体SF6小型末端酶的单个HTH基序与SF6及相关SPP1基因组的包装区域结合较弱，几乎没有局部序列特异性。对任意单一位点底物进行的核磁共振化学位移扰动研究表明，HTH基序与DNA的接触方式类似于某些HTH蛋白非特异性接触DNA的方式。我们的观察结果支持这样一种模型：特异性是通过HTH环对内在弯曲的DNA片段进行构象选择而产生的，HTH环结合较弱但具有协同性。这样一个系统能够以最小的基因组实现病毒基因调控和病毒生命周期的控制，为类SPP1病毒带来重大的进化优势。
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