Identification, characterization and classification of prokaryotic nucleoid‐associated proteins,Molecular Microbiology

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Identification, characterization and classification of prokaryotic nucleoid‐associated proteins
Molecular Microbiology ( IF 2.6 ) Pub Date : 2024-07-23 , DOI: 10.1111/mmi.15298
Samuel Schwab _{1,

2,

3} , Remus T Dame _{1,

2,

3}

Affiliation

Common throughout life is the need to compact and organize the genome. Possible mechanisms involved in this process include supercoiling, phase separation, charge neutralization, macromolecular crowding, and nucleoid‐associated proteins (NAPs). NAPs are special in that they can organize the genome at multiple length scales, and thus are often considered as the architects of the genome. NAPs shape the genome by either bending DNA, wrapping DNA, bridging DNA, or forming nucleoprotein filaments on the DNA. In this mini‐review, we discuss recent advancements of unique NAPs with differing architectural properties across the tree of life, including NAPs from bacteria, archaea, and viruses. To help the characterization of NAPs from the ever‐increasing number of metagenomes, we recommend a set of cheap and simple in vitro biochemical assays that give unambiguous insights into the architectural properties of NAPs. Finally, we highlight and showcase the usefulness of AlphaFold in the characterization of novel NAPs.

中文翻译：

原核类核相关蛋白的鉴定、表征和分类

一生中常见的是压缩和组织基因组的需要。该过程涉及的可能机制包括超螺旋、相分离、电荷中和、大分子拥挤和类核相关蛋白（NAP）。 NAP 的特殊之处在于它们可以在多个长度尺度上组织基因组，因此通常被认为是基因组的建筑师。 NAP 通过弯曲 DNA、包裹 DNA、桥接 DNA 或在 DNA 上形成核蛋白丝来塑造基因组。在这篇小型评论中，我们讨论了生命树中具有不同结构特性的独特 NAP 的最新进展，包括来自细菌、古细菌和病毒的 NAP。为了帮助从数量不断增加的宏基因组中表征 NAP，我们推荐了一套廉价且简单的体外生化测定，可以对 NAP 的结构特性提供明确的见解。最后，我们强调并展示了 AlphaFold 在表征新型 NAP 方面的有用性。

更新日期：2024-07-23

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