Snapshot of a large dynamic replicon in a halophilic archaeon: Megaplasmidor minichromosome?

Extremely halophilic archaea, which flourish in hypersaline environments, a re known to contain a variety of large dynamic replicons. Previously, the a nalysis of one such replicon, pNRC100, in Halobacterium sp. strain NRC-1, s howed that it undergoes high-frequency insertion sequence (IS) element-medi ated insertions and deletions, as well as inversions via recombination betw een 39-kb-long inverted repeats (IRs). Now, the complete sequencing of pNRC 100, a 191,346-bp circle, has shown the presence of 27 IS elements represen ting eight families. A total of 176 ORFs or likely genes of 850-bp average size were found, 39 of which were repeated within the large IRs. More than one-half of the ORFs are likely to represent novel genes that have no known homologs in the databases. Among ORFs with previously characterized homolo gs, three different copies of putative plasmid replication and four copies of partitioning genes were found, suggesting that pNRC100 evolved from IS e lement-mediated fusions of several smaller plasmids. Consistent with this i dea, putative genes typically found on plasmids, including those encoding a restriction-modification system and arsenic resistance, as well as buoyant gas-filled vesicles and a two-component regulatory system, were found on p NRC100. However, additional putative genes not expected on an extrachromoso mal element, such as those encoding an electron transport chain cytochrome d oxidase, DNA nucleotide synthesis enzymes thioredoxin and thioredoxin red uctase, and eukaryotic-like TATA-binding protein transcription factors and a chromosomal replication initiator protein were also found. A multi-step I S element-mediated process is proposed to account for the acquisition of th ese chromosomal genes. The finding of essential genes on pNRC100 and its pr operty of resistance to curing suggest that this replicon may be evolving i nto a new chromosome.