Schwab Samuel, Dame Remus T
Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands.
Mol Microbiol. 2025 Mar;123(3):206-217. doi: 10.1111/mmi.15298. Epub 2024 Jul 22.
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.
在整个生命过程中，压缩和组织基因组的需求很常见。参与这一过程的可能机制包括超螺旋、相分离、电荷中和、大分子拥挤以及类核相关蛋白（NAPs）。NAPs的特别之处在于它们能够在多个长度尺度上组织基因组，因此常被视为基因组的建筑师。NAPs通过弯曲DNA、缠绕DNA、桥接DNA或在DNA上形成核蛋白丝来塑造基因组。在这篇小型综述中，我们讨论了在生命之树上具有不同结构特性的独特NAPs的最新进展，包括来自细菌、古菌和病毒的NAPs。为了帮助表征来自数量不断增加的宏基因组中的NAPs，我们推荐了一组廉价且简单的体外生化分析方法，这些方法能对NAPs的结构特性提供明确的见解。最后，我们强调并展示了AlphaFold在新型NAPs表征中的有用性。
