Compaction of bulky DNA is a universal issue for all DNA-based life forms. Chloroplast nucleoids (chloroplast DNA–protein complexes) are critical for chloroplast DNA maintenance and transcription, thereby supporting photosynthesis, but their detailed structure remains enigmatic. Our proteomic analysis of chloroplast nucleoids of the green alga Chlamydomonas reinhardtii identified a protein (HBD1) with a tandem repeat of two DNA-binding high mobility group box (HMG-box) domains, which is structurally similar to major mitochondrial nucleoid proteins transcription factor A, mitochondrial (TFAM), and ARS binding factor 2 protein (Abf2p). Disruption of the HBD1 gene by CRISPR-Cas9–mediated genome editing resulted in the scattering of chloroplast nucleoids. This phenotype was complemented when intact HBD1 was reintroduced, whereas a truncated HBD1 with a single HMG-box domain failed to complement the phenotype. Furthermore, ectopic expression of HBD1 in the mitochondria of yeast Δabf2 mutant successfully complemented the defects, suggesting functional similarity between HBD1 and Abf2p. Furthermore, in vitro assays of HBD1, including the electrophoretic mobility shift assay and DNA origami/atomic force microscopy, showed that HBD1 is capable of introducing U-turns and cross-strand bridges, indicating that proteins with two HMG-box domains would function as DNA clips to compact DNA in both chloroplast and mitochondrial nucleoids.

大体积 DNA 的压实是所有基于 DNA 的生命形式的普遍问题。叶绿体类核素（叶绿体 DNA-蛋白质复合物）对于叶绿体 DNA 的维持和转录至关重要，从而支持光合作用，但它们的详细结构仍然是个谜。我们对绿藻莱茵衣藻叶绿体类核蛋白的蛋白质组学分析鉴定了一种蛋白质 (HBD1)，该蛋白质 (HBD1) 具有两个 DNA 结合高迁移率群盒 (HMG-box) 域的串联重复，其在结构上与主要线粒体类核蛋白转录因子 A 相似、线粒体 (TFAM) 和 ARS 结合因子 2 蛋白 (Abf2p)。HBD1 的中断通过 CRISPR-Cas9 介导的基因组编辑的基因导致叶绿体类核的散射。当重新引入完整的 HBD1 时，这种表型得到了补充，而具有单个 HMG-box 结构域的截断 HBD1 未能补充表型。此外，HBD1 在酵母Δabf2突变体线粒体中的异位表达成功地补充了缺陷，表明 HBD1 和 Abf2p 之间的功能相似。此外，HBD1 的体外测定，包括电泳迁移率变化测定和 DNA 折纸/原子力显微镜，表明 HBD1 能够引入 U 形转弯和交叉链桥，表明具有两个 HMG-box 结构域的蛋白质将作为DNA 剪辑以压缩叶绿体和线粒体类核中的 DNA。