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折返式DNA壳调节多聚磷酸盐凝聚物的大小。

Reentrant DNA shells tune polyphosphate condensate size.

作者信息

Chawla Ravi, Tom Jenna K A, Boyd Tumara, Grotjahn Danielle A, Park Donghyun, Deniz Ashok A, Racki Lisa R

机构信息

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.

出版信息

bioRxiv. 2023 Sep 15:2023.09.13.557044. doi: 10.1101/2023.09.13.557044.

Abstract

The ancient, inorganic biopolymer polyphosphate (polyP) occurs in all three domains of life and affects myriad cellular processes. An intriguing feature of polyP is its frequent proximity to chromatin, and in the case of many bacteria, its occurrence in the form of magnesium-enriched condensates embedded in the nucleoid, particularly in response to stress. The physical basis of the interaction between polyP and DNA, two fundamental anionic biopolymers, and the resulting effects on the organization of both the nucleoid and polyP condensates remain poorly understood. Given the essential role of magnesium ions in the coordination of polymeric phosphate species, we hypothesized that a minimal system of polyP, magnesium ions, and DNA (polyP-Mg-DNA) would capture key features of the interplay between the condensates and bacterial chromatin. We find that DNA can profoundly affect polyP-Mg coacervation even at concentrations several orders of magnitude lower than found in the cell. The DNA forms shells around polyP-Mg condensates and these shells show reentrant behavior, primarily forming in the concentration range close to polyP-Mg charge neutralization. This surface association tunes both condensate size and DNA morphology in a manner dependent on DNA properties, including length and concentration. Our work identifies three components that could form the basis of a central and tunable interaction hub that interfaces with cellular interactors. These studies will inform future efforts to understand the basis of polyP granule composition and consolidation, as well as the potential capacity of these mesoscale assemblies to remodel chromatin in response to diverse stressors at different length and time scales.

摘要

古老的无机生物聚合物多聚磷酸盐(polyP)存在于生命的所有三个域中,并影响无数细胞过程。多聚磷酸盐的一个有趣特征是它经常靠近染色质,在许多细菌中,它以富含镁的凝聚物形式存在于类核中,特别是在应激反应时。多聚磷酸盐与DNA这两种基本的阴离子生物聚合物之间相互作用的物理基础,以及由此对类核和多聚磷酸盐凝聚物组织产生的影响,仍然知之甚少。鉴于镁离子在聚合磷酸物种配位中的重要作用,我们假设多聚磷酸盐、镁离子和DNA的最小系统(polyP-Mg-DNA)将捕捉凝聚物与细菌染色质之间相互作用的关键特征。我们发现,即使在比细胞中低几个数量级的浓度下,DNA也能深刻影响多聚磷酸盐-镁凝聚作用。DNA在多聚磷酸盐-镁凝聚物周围形成壳层,这些壳层表现出折返行为,主要在接近多聚磷酸盐-镁电荷中和的浓度范围内形成。这种表面结合以依赖于DNA特性(包括长度和浓度)的方式调节凝聚物大小和DNA形态。我们的工作确定了三个可以构成与细胞相互作用体相互作用的核心且可调节的相互作用枢纽基础的成分。这些研究将为未来理解多聚磷酸盐颗粒组成和巩固的基础,以及这些中尺度组装体在不同长度和时间尺度上响应各种应激源重塑染色质的潜在能力提供参考。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf67/10515899/bce0969ffe36/nihpp-2023.09.13.557044v1-f0001.jpg

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