Chromosome architecture in an archaeal species naturally lacking structural maintenance of chromosomes proteins.

Proteins in the structural maintenance of chromosomes (SMC) superfamily play key roles in chromosome organization and are ubiquitous across all domains of life. However, SMC proteins are notably absent in the Desulfurococcales of phylum Crenarchaeota. Intrigued by this observation, we performed chromosome conformation capture experiments in the model Desulfurococcales species Aeropyrum pernix. As in other archaea, we observe chromosomal interaction domains across the chromosome. The boundaries between chromosomal interaction domains show a dependence on transcription and translation for their definition. Importantly, however, we reveal an additional higher-order, bipartite organization of the chromosome—with a small high-gene-expression and self-interacting domain that is defined by transcriptional activity and loop structures. Viewing these data in the context of the distribution of SMC superfamily proteins in the Crenarchaeota, we suggest that the organization of the Aeropyrum genome represents an evolutionary antecedent of the compartmentalized architecture observed in the Sulfolobus lineage. SMC proteins are key architects of chromosome organization across all domains of life, yet in their absence, A. pernix relies on transcription, anchored loops and self-interaction domains to maintain genome architecture.

染色体结构维持（SMC）超家族中的蛋白质在染色体组织中起关键作用，并且在所有生命领域中普遍存在。然而，在泉古菌门的热球菌目中明显不存在SMC蛋白。受这一观察结果的启发，我们在热球菌目模式物种激烈火球菌中进行了染色体构象捕获实验。与在其他古菌中一样，我们在整个染色体上观察到染色体相互作用结构域。染色体相互作用结构域之间的边界在其界定上依赖于转录和翻译。然而，重要的是，我们揭示了染色体的一种额外的高阶二分组织——具有一个由转录活性和环结构界定的小的高基因表达和自相互作用结构域。结合泉古菌中SMC超家族蛋白质的分布情况来看这些数据，我们认为激烈火球菌基因组的组织代表了在硫化叶菌谱系中所观察到的分隔式结构的进化前身。 SMC蛋白是所有生命领域中染色体组织的关键构建者，然而在缺乏它们的情况下，激烈火球菌依靠转录、锚定环和自相互作用结构域来维持基因组结构。