Different Proteins Mediate Step-Wise Chromosome Architectures in Thermoplasma acidophilum and Pyrobaculum calidifontis
Different Proteins Mediate Step-Wise Chromosome Architectures in Thermoplasma acidophilum and Pyrobaculum calidifontis
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DOI：
10.3389/fmicb.2020.01247
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发表时间：
2020-03
影响因子：
5.2
通讯作者：
Hugo Maruyama;E. Prieto;Takayuki Nambu;Chiho Mashimo;Kosuke Kashiwagi;T. Okinaga;H. Atomi;K. Takeyasu
中科院分区：
文献类型：
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作者：
Hugo Maruyama;E. Prieto;Takayuki Nambu;Chiho Mashimo;Kosuke Kashiwagi;T. Okinaga;H. Atomi;K. Takeyasu
古细菌物种编码多种不同的谱系特异性染色体蛋白。我们之前已经表明，在柯达热球菌中，组蛋白、Alba和TrmBL2在染色体组织中起着不同的作用。尽管我们对单个古菌染色体蛋白的了解一直在进步，但古菌染色体如何折叠成高阶结构以及它们如何被调节在很大程度上是未知的。在这里，我们研究了来自不同古细菌谱系的古细菌染色体的初级和高级结构。原子力显微镜观察嗜酸热原体（Thermoplasma acidophilum）和焦杆菌（Pyrobaculum calidifontis）细胞外的染色体展布，发现10 nm的纤维和30 - 40 nm的球状结构，提示发生了高阶染色体折叠。我们的结果还表明，染色体紧实发生在固定期。微球菌核酸酶酶切结果表明，嗜酸t和kodakarensis存在染色体基本结构单元，而calidifontis和Sulfolobus solfataricus不存在。体外重构表明，嗜酸乳杆菌中细菌HU蛋白同源物HTa通过包裹DNA形成6 nm的纤维，而Alba则通过沿DNA结合而不包裹DNA形成10 nm的纤维。值得注意的是，Alba可以在体外与组蛋白或HTa在DNA上形成不同的高阶复合物。质谱法在嗜酸t染色体中检测到HTa，而在其他物种中未检测到。在P. calidifontis染色体上发现了一个AsnC/Lrp家族的转录调节因子（Pcal_1183），但在其他物种的染色体上没有发现。在研究的三种古细菌（包括T. acidophilum， P. calidifontis和T. kodakarensis）的染色体中检测到假定的膜相关蛋白。总的来说，我们的数据表明，古细菌使用不同的蛋白质组合来实现染色体结构和功能调节。
Archaeal species encode a variety of distinct lineage-specific chromosomal proteins. We have previously shown that in Thermococcus kodakarensis, histone, Alba, and TrmBL2 play distinct roles in chromosome organization. Although our understanding of individual archaeal chromosomal proteins has been advancing, how archaeal chromosomes are folded into higher-order structures and how they are regulated are largely unknown. Here, we investigated the primary and higher-order structures of archaeal chromosomes from different archaeal lineages. Atomic force microscopy of chromosome spreads out of Thermoplasma acidophilum and Pyrobaculum calidifontis cells revealed 10-nm fibers and 30–40-nm globular structures, suggesting the occurrence of higher-order chromosomal folding. Our results also indicated that chromosome compaction occurs toward the stationary phase. Micrococcal nuclease digestion indicated that fundamental structural units of the chromosome exist in T. acidophilum and T. kodakarensis but not in P. calidifontis or Sulfolobus solfataricus. In vitro reconstitution showed that, in T. acidophilum, the bacterial HU protein homolog HTa formed a 6-nm fiber by wrapping DNA, and that Alba was responsible for the formation of the 10-nm fiber by binding along the DNA without wrapping. Remarkably, Alba could form different higher-order complexes with histone or HTa on DNA in vitro. Mass spectrometry detected HTa in the T. acidophilum chromosome but not in other species. A putative transcriptional regulator of the AsnC/Lrp family (Pcal_1183) was detected on the P. calidifontis chromosome, but not on that of other species studied. Putative membrane-associated proteins were detected in the chromosomes of the three archaeal species studied, including T. acidophilum, P. calidifontis, and T. kodakarensis. Collectively, our data show that Archaea use different combinations of proteins to achieve chromosomal architecture and functional regulation.