Multiple RNA- and DNA-binding proteins exhibit direct transfer of polynucleotides with implications for target-site search.
Multiple RNA- and DNA-binding proteins exhibit direct transfer of polynucleotides with implications for target-site search.
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DOI：
10.1073/pnas.2220537120
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发表时间：
2023-06-27
影响因子：
11.1
通讯作者：
Cech, Thomas R.
中科院分区：
文献类型：
--
作者：
Hemphill, Wayne O.;Voong, Calvin K.;Fenske, Regan;Goodrich, James A.;Cech, Thomas R.
传统上，蛋白质-配体复合物的寿命被认为是一种内在性质，不受游离溶液中竞争分子的影响。相比之下，已经观察到一些寡聚核酸结合蛋白在其结合位点交换竞争配体，因此它们的寿命随着竞争剂浓度而降低。我们的研究结果表明，这种“直接转移”能力可能是核酸结合蛋白的一个更普遍的性质。因此，许多DNA和RNA结合蛋白可以通过直接转移到核小体DNA而不是完全依赖于三维扩散来减少它们寻找靶位点的维度。此外，从新生RNA到DNA的直接转移可以解释为什么这么多DNA结合蛋白也结合RNA。我们以前证明，polycomb阻遏复合物2染色质修饰酶可以直接在RNA和DNA之间转移，而没有游离酶的中间状态。模拟表明，这种直接转移机制通常可能是RNA将蛋白质募集到染色质所必需的，但直接转移能力的普遍性尚不清楚。在此，我们使用荧光偏振分析，并观察到几个良好的特征核酸结合蛋白的直接转移：三总理修复核酸外切酶1，异质核核糖核蛋白U，Fem-3结合因子2，和MS 2噬菌体外壳蛋白。对于TREX 1，在单分子测定中另外观察到直接转移机制，并且数据表明直接转移通过具有部分缔合的多核苷酸的不稳定的三元中间体发生。通常，直接转移可以允许许多DNA和RNA结合蛋白对其靶位点进行一维搜索。此外，结合RNA和DNA的蛋白质可能能够容易地在这些配体之间移位。
Classically, the lifetime of a protein–ligand complex is presumed to be an intrinsic property, unaffected by competitor molecules in free solution. By contrast, a few oligomeric nucleic acid–binding proteins have been observed to exchange competing ligands in their binding sites, and consequently their lifetimes decrease with competitor concentration. Our findings suggest that this “direct transfer” capability may be a more general property of nucleic acid– binding proteins. Thus, many DNA- and RNA-binding proteins could reduce the dimensionality of their search for their target sites by direct transfer to nucleosome DNA, instead of relying entirely on three-dimensional diffusion. Furthermore, direct transfer from nascent RNA to DNA may explain why so many DNA-binding proteins also bind RNA. We previously demonstrated that the polycomb repressive complex 2 chromatin–modifying enzyme can directly transfer between RNA and DNA without a free-enzyme intermediate state. Simulations suggested that such a direct transfer mechanism may be generally necessary for RNA to recruit proteins to chromatin, but the prevalence of direct transfer capability is unknown. Herein, we used fluorescence polarization assays and observed direct transfer for several well-characterized nucleic acid–binding proteins: three-prime repair exonuclease 1, heterogeneous nuclear ribonucleoprotein U, Fem-3-binding factor 2, and MS2 bacteriophage coat protein. For TREX1, the direct transfer mechanism was additionally observed in single-molecule assays, and the data suggest that direct transfer occurs through an unstable ternary intermediate with partially associated polynucleotides. Generally, direct transfer could allow many DNA- and RNA-binding proteins to conduct a one-dimensional search for their target sites. Furthermore, proteins that bind both RNA and DNA might be capable of readily translocating between those ligands.
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影响因子：
7.2
作者：
Gillooly, James F.;Hein, Andrew;Damiani, Rachel
通讯作者：
Damiani, Rachel
影响因子：
5.6
作者：
BRESLOFF, JL;CROTHERS, DM
通讯作者：
CROTHERS, DM
DOI：
10.1073/pnas.0805050105
发表时间：
2008-09-16
影响因子：
11.1
作者：
Doucleff, Michaeleen;Clore, G. Marius
通讯作者：
Clore, G. Marius
影响因子：
4.8
作者：
Fye, Jason M.;Orebaugh, Clinton D.;Perrino, Fred W.
通讯作者：
Perrino, Fred W.
影响因子：
5.6
作者：
Giuntoli, Rebecca D.;Linzer, Nora B.;Marko, John F.
通讯作者：
Marko, John F.