title: Snapshot of a large dynamic replicon in a halophilic archaeon: megaplasmid or minichromosome?
abstract: Extremely halophilic archaea, which flourish in hypersaline environments, are known to contain a variety of large dynamic replicons. Previously, the analysis of one such replicon, pNRC100, in Halobacterium sp. strain NRC-1, showed that it undergoes high-frequency insertion sequence (IS) element-mediated insertions and deletions, as well as inversions via recombination between 39-kb-long inverted repeats (IRs). Now, the complete sequencing of pNRC100, a 191,346-bp circle, has shown the presence of 27 IS elements representing 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 homologs, three different copies of putative plasmid replication and four copies of partitioning genes were found, suggesting that pNRC100 evolved from IS element-mediated fusions of several smaller plasmids. Consistent with this idea, 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 pNRC100. However, additional putative genes not expected on an extrachromosomal element, such as those encoding an electron transport chain cytochrome d oxidase, DNA nucleotide synthesis enzymes thioredoxin and thioredoxin reductase, and eukaryotic-like TATA-binding protein transcription factors and a chromosomal replication initiator protein were also found. A multi-step IS element-mediated process is proposed to account for the acquisition of these chromosomal genes. The finding of essential genes on pNRC100 and its property of resistance to curing suggest that this replicon may be evolving into a new chromosome.
authors.affiliation: Department of Molecular Biotechnology, University of Washington, Seattle, Washington 98195, USA.
authors.forename: W V
authors.initials: WV
authors.lastname: Ng
authors.forename: S A
authors.initials: SA
authors.lastname: Ciufo
authors.forename: T M
authors.initials: TM
authors.lastname: Smith
authors.forename: R E
authors.initials: RE
authors.lastname: Bumgarner
authors.forename: D
authors.initials: D
authors.lastname: Baskin
authors.forename: J
authors.initials: J
authors.lastname: Faust
authors.forename: B
authors.initials: B
authors.lastname: Hall
authors.forename: C
authors.initials: C
authors.lastname: Loretz
authors.forename: J
authors.initials: J
authors.lastname: Seto
authors.forename: J
authors.initials: J
authors.lastname: Slagel
authors.forename: L
authors.initials: L
authors.lastname: Hood
authors.forename: S
authors.initials: S
authors.lastname: DasSarma
mesh_terms: D002874:Chromosome Mapping; D019847:Chromosomes, Archaeal / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D019641:DNA, Archaeal / Q000737:chemistry / Q000235:genetics; D015723:Gene Library; D019766:Genes, Archaeal / Q000235:genetics; D006217:Halobacterium / Q000235:genetics*; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D010957:Plasmids / Q000235:genetics; D012093:Replicon; D017422:Sequence Analysis, DNA
chemical_list: D004251:DNA Transposable Elements; D019641:DNA, Archaeal