Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE 412 96, Sweden.
Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch F 67401, France.
Nucleic Acids Res. 2021 May 7;49(8):4550-4563. doi: 10.1093/nar/gkab236.
The nucleocapsid (NC) protein plays key roles in Human Immunodeficiency Virus 1 (HIV-1) replication, notably by condensing and protecting the viral RNA genome and by chaperoning its reverse transcription into double-stranded DNA (dsDNA). Recent findings suggest that integration of viral dsDNA into the host genome, and hence productive infection, is linked to a small subpopulation of viral complexes where reverse transcription was completed within the intact capsid. Therefore, the synthesized dsDNA has to be tightly compacted, most likely by NC, to prevent breaking of the capsid in these complexes. To investigate NC's ability to compact viral dsDNA, we here characterize the compaction of single dsDNA molecules under unsaturated NC binding conditions using nanofluidic channels. Compaction is shown to result from accumulation of NC at one or few compaction sites, which leads to small dsDNA condensates. NC preferentially initiates compaction at flexible regions along the dsDNA, such as AT-rich regions and DNA ends. Upon further NC binding, these condensates develop into a globular state containing the whole dsDNA molecule. These findings support NC's role in viral dsDNA compaction within the mature HIV-1 capsid and suggest a possible scenario for the gradual dsDNA decondensation upon capsid uncoating and NC loss.
核衣壳（NC）蛋白在人类免疫缺陷病毒 1（HIV-1）复制中发挥关键作用，特别是通过浓缩和保护病毒 RNA 基因组，并通过伴侣介导其逆转录成双链 DNA（dsDNA）。最近的研究结果表明，病毒 dsDNA 整合到宿主基因组中，从而导致产生感染，与逆转录在完整衣壳内完成的一小部分病毒复合物有关。因此，合成的 dsDNA 必须紧密压缩，最有可能由 NC 来完成，以防止这些复合物中的衣壳破裂。为了研究 NC 压缩病毒 dsDNA 的能力，我们在这里使用纳米流通道描述了在不饱和 NC 结合条件下单个 dsDNA 分子的压缩特性。压缩是由 NC 在一个或几个压缩位点上的积累引起的，导致小的 dsDNA 凝聚物。NC 优先在 dsDNA 的柔性区域（如富含 AT 的区域和 DNA 末端）起始压缩。随着进一步的 NC 结合，这些凝聚物发展成包含整个 dsDNA 分子的球形状态。这些发现支持 NC 在成熟 HIV-1 衣壳内病毒 dsDNA 压缩中的作用，并提出了衣壳脱壳和 NC 丢失时 dsDNA 逐渐去凝聚的可能情况。
