Graduate School of Nanobiosicences, Yokohama City University, Yokohama, Japan.
Microbiol Spectr. 2022 Feb 23;10(1):e0222521. doi: 10.1128/spectrum.02225-21. Epub 2022 Jan 5.
Chromids (secondary chromosomes) in bacterial genomes that are present in addition to the main chromosome appear to be evolutionarily conserved in some specific bacterial groups. In rare cases among these groups, a small number of strains from and were shown to possess a naturally fused single chromosome that was reported to have been generated through intragenomic homologous recombination between repeated sequences on the chromosome and chromid. Similar examples have never been reported in the family , a well-documented group that conserves chromids. Here, an in-depth genomic characterization was performed on a bacterium that was isolated from a soil bacterial consortium maintained on diesel fuel and mutagenic benzo[]pyrene. This organism, Cupriavidus necator strain KK10, was revealed to carry a single chromosome with unexpectedly large size (>6.6 Mb), and results of comparative genomics with the genome of C. necator N-1 indicated that the single chromosome of KK10 was generated through fusion of the prototypical chromosome and chromid at the rRNA operons. This fusion hypothetically occurred through homologous recombination with a crossover between repeated rRNA operons on the chromosome and chromid. Some metabolic functions that were likely expressed from genes on the prototypical chromid region were indicated to be retained. If this phenomenon-the bacterial chromosome-chromid fusion across the rRNA operons through homologous recombination-occurs universally in prokaryotes, the multiple rRNA operons in bacterial genomes may not only contribute to the robustness of ribosome function, but also provide more opportunities for genomic rearrangements through frequent recombination. A bacterial chromosome that was naturally fused with the secondary chromosome, or "chromid," and presented as an unexpectedly large single replicon was discovered in the genome of Cupriavidus necator strain KK10, a biotechnologically useful member of the family . Although is a well-documented group that conserves chromids in their genomes, this chromosomal fusion event has not been previously reported for this family. This fusion has hypothetically occurred through intragenomic homologous recombination between repeated rRNA operons and, if so, provides novel insight into the potential of multiple rRNA operons in bacterial genomes to lead to chromosome-chromid fusion. The harsh conditions under which strain KK10 was maintained-a genotoxic hydrocarbon-enriched milieu-may have provided this genotype with a niche in which to survive.
在一些特定的细菌群体中，除了主染色体之外，还存在着细菌基因组中的次染色体（Chromids），这些次染色体似乎在进化上是保守的。在这些群体中，有少数来自 和 的菌株被发现拥有自然融合的单条染色体，据报道，这些染色体是通过染色体和次染色体上重复序列之间的基因组内同源重组产生的。然而，在家族 中，这种情况从未被报道过，该家族是一个保存次染色体的记录良好的群体。在这里，对一种从柴油燃料和诱变剂苯并[]芘维持的土壤细菌联合体中分离出来的 细菌进行了深入的基因组特征分析。这种生物体，即铜绿假单胞菌 KK10 菌株，被发现携带一条大小异常大（>6.6 Mb）的单条染色体，与铜绿假单胞菌 N-1 基因组的比较基因组学结果表明，KK10 的单条染色体是通过原型染色体和次染色体在 rRNA 操纵子处的融合产生的。这种融合假设是通过染色体和次染色体上 rRNA 操纵子之间的重复序列之间的同源重组和交叉发生的。一些可能来自原型次染色体区域的基因表达的代谢功能被认为是保留的。如果这种现象——通过同源重组在 rRNA 操纵子处融合细菌染色体和次染色体——在原核生物中普遍存在，那么细菌基因组中的多个 rRNA 操纵子不仅可以为核糖体功能的稳健性做出贡献，而且还可以通过频繁的重组提供更多的基因组重排机会。在铜绿假单胞菌 KK10 菌株的基因组中发现了一种自然融合了次级染色体（“次染色体”）的细菌染色体，呈现出异常大的单个复制子，这是家族 中的一个生物技术有用成员。尽管 是一个记录良好的群体，其基因组中保存了次染色体，但该家族以前从未报道过这种染色体融合事件。这种融合假设是通过重复 rRNA 操纵子之间的基因组内同源重组发生的，如果是这样，那么这为细菌基因组中多个 rRNA 操纵子导致染色体-次染色体融合提供了新的见解。KK10 菌株所处的苛刻条件——富含遗传毒性碳氢化合物的环境——可能为这种基因型提供了一个生存的小生境。
