Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, VIC 3010, Australia.
Computational Systems Biochemistry, Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany.
Genes (Basel). 2024 Aug 26;15(9):1123. doi: 10.3390/genes15091123.
Australian isolates of , a square-shaped haloarchaeon, often harbor small cryptic plasmids of the pL6-family, approximately 6 kb in size, and five examples have been previously described. These plasmids exhibit a highly conserved gene arrangement and encode replicases similar to those of betapleolipoviruses. To assess their global distribution and recover more examples for analysis, fifteen additional plasmids were reconstructed from the metagenomes of seven hypersaline sites across four countries: Argentina, Australia, Puerto Rico, and Spain. Including the five previously described plasmids, the average plasmid size is 6002 bp, with an average G+C content of 52.5%. The tetramers GGCC and CTAG are either absent or significantly under-represented, except in the two plasmids with the highest %G+C. All plasmids share a similar arrangement of genes organized as outwardly facing replication and ATPase modules, but variations were observed in some core genes, such as F2, and some plasmids had acquired accessory genes. Two plasmids, pCOLO-c1 and pISLA-c6, shared 92.7% nt identity despite originating from Argentina and Spain, respectively. Numerous metagenomic CRISPR spacers matched sequences in the fifteen reconstructed plasmids, indicating frequent invasion of haloarchaea. Spacers could be assigned to haloarchaeal genera by mapping their associated direct repeats (DR), with half of these matching . Finally, strand-specific metatranscriptome (RNA-seq) data could be used to demonstrate the active transcription of two pL6-family plasmids, including antisense transcripts.
澳大利亚的 菌株是一种方形的盐古菌，通常含有大小约为 6kb 的小型隐性 pL6 家族质粒，此前已经描述了五个例子。这些质粒表现出高度保守的基因排列，并编码与 betapleolipoviruses 相似的复制酶。为了评估它们的全球分布并回收更多的例子进行分析，从四个国家（阿根廷、澳大利亚、波多黎各和西班牙）的七个高盐地点的宏基因组中重建了另外 15 个质粒。包括之前描述的五个质粒，平均质粒大小为 6002bp，平均 G+C 含量为 52.5%。四聚体 GGCC 和 CTAG 要么不存在，要么明显缺失，除了两个 G+C 含量最高的质粒。所有质粒都具有相似的基因排列，组织为外向复制和 ATP 酶模块，但在一些核心基因（如 F2）中观察到了变化，并且一些质粒获得了辅助基因。尽管分别来自阿根廷和西班牙，但质粒 pCOLO-c1 和 pISLA-c6 的核苷酸同一性高达 92.7%。许多宏基因组 CRISPR 间隔子与十五个重建质粒中的序列匹配，表明 haloarchaea 经常受到入侵。通过将其相关的直接重复序列 (DR) 映射到间隔子上，可以将间隔子分配给 haloarchaea 属，其中一半与 匹配。最后，链特异性宏转录组（RNA-seq）数据可用于证明两个 pL6 家族质粒的转录活性，包括反义转录本。
