Snapshot of a Large Dynamic Replicon in a Halophilic Archaeon: Megaplasmid or Minichromosome?

Ng, Wailap Victor; Ciufo, Stacy; Smith, T. M. F.; Bumgarner, Roger E.; Baskin, Dale; Faust, Janet; Hall, Barbara; Loretz, Carol; Seto, Jason; Slagel, Joseph; Hood, Leroy; DasSarma, Shiladitya

doi:10.1101/gr.8.11.1131

Cited by 106 publications

(109 citation statements)

References 51 publications

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“…Moreover, since it carries substantially more IS elements and MITEs than Sulfolobus tokodaii, or than Sulfolobus acidocaldarius, which probably lacks active mobile elements (4,9,11), it was proposed that the genomic rearrangements are driven primarily by mobile-element-dependent mechanisms (5). This proposal complements the earlier hypothesis that the megaplasmid pNRC100 of the euryarchaeon Halobacterium halobium arose via a multistep IS element-mediated process (10,20).…”

supporting

confidence: 72%

Mutations and Rearrangements in the Genome ofSulfolobus solfataricusP2

Redder

Garrett

2006

J Bacteriol

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The genome of Sulfolobus solfataricus P2 carries a larger number of transposable elements than any other sequenced genome from an archaeon or bacterium and, as a consequence, may be particularly susceptible to rearrangement and change. In order to gain more insight into the natures and frequencies of different types of mutation and possible rearrangements that can occur in the genome, the pyrEF locus was examined for mutations that were isolated after selection with 5-fluoroorotic acid. About two-thirds of the 130 mutations resulted from insertions of mobile elements, including insertion sequence (IS) elements and a single nonautonomous mobile element, SM2. For each of these, the element was identified and shown to be present at its original genomic position, consistent with a progressive increase in the copy numbers of the mobile elements. In addition, several base pair substitutions, as well as small deletions, insertions, and a duplication, were observed, and about one-fifth of the mutations occurred elsewhere in the genome, possibly in an orotate transporter gene. One mutant exhibited a 5-kb genomic rearrangement at the pyrEF locus involving a two-step IS element-dependent reaction, and its boundaries were defined using a specially developed "in vitro library" strategy. Moreover, while searching for the donor mobile elements, evidence was found for two major changes that had occurred in the genome of strain P2, one constituting a single deletion of about 4% of the total genome (124 kb), while the other involved the inversion of a 25-kb region. Both were bordered by IS elements and were inferred to have arisen through recombination events. The results underline the caution required in working experimentally with an organism such as S. solfataricus with a continually changing genome.

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supporting

confidence: 72%

Mutations and Rearrangements in the Genome ofSulfolobus solfataricusP2

Redder

Garrett

2006

J Bacteriol

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“…The megaplasmid contains almost 25% of the IS element content of the genome. It is possible that IS elements contributed to formation of pMP118 by a cointegration mechanism, which was suggested for the formation of an archaeal megaplasmid (24). Overall, L. salivarius possesses both the highest number and diversity of IS elements in Lactobacillus genomes sequenced to date.…”

Section: Resultsmentioning

confidence: 99%

“…22 and 23) and may include minichromosomes, which are difficult to formally distinguish from megaplasmids (24). We designated pMP118 as a megaplasmid for the following reasons: It contains neither tRNA nor rRNA genes; it has plasmid-related replication and partition proteins; and it does not contain the only copy in the genome of any known essential gene.…”

Section: Resultsmentioning

confidence: 99%

Multireplicon genome architecture of Lactobacillus salivarius

Claesson

Li²,

Leahy³

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

199

185

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Lactobacillus salivarius subsp. salivarius strain UCC118 is a bacteriocin-producing strain with probiotic characteristics. The 2.13-Mb genome was shown by sequencing to comprise a 1.83 Mb chromosome, a 242-kb megaplasmid (pMP118), and two smaller plasmids. Megaplasmids previously have not been characterized in lactic acid bacteria or intestinal lactobacilli. Annotation of the genome sequence indicated an intermediate level of auxotrophy compared with other sequenced lactobacilli. No single-copy essential genes were located on the megaplasmid. However, contingency amino acid metabolism genes and carbohydrate utilization genes, including two genes for completion of the pentose phosphate pathway, were megaplasmid encoded. The megaplasmid also harbored genes for the Abp118 bacteriocin, a bile salt hydrolase, a presumptive conjugation locus, and other genes potentially relevant for probiotic properties. Two subspecies of L. salivarius are recognized, salivarius and salicinius, and we detected megaplasmids in both subspecies by pulsed-field gel electrophoresis of sizes ranging from 100 kb to 380 kb. The discovery of megaplasmids of widely varying size in L. salivarius suggests a possible mechanism for genome expansion or contraction to adapt to different environments.megaplasmid ͉ probiotic ͉ heterofermentation

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“…Halobacterium NRC-1, the single halophile to have its genome sequenced thus far, grows optimally in a 4.5 M NaCl medium supplemented with amino acids and other nutrients and is capable of both aerobic and phototropic growth (Ng et al 1998. This organism is easy to culture and manipulate in the laboratory, which has made it an excellent model organism among the archaea.…”

mentioning

confidence: 99%

Understanding the Adaptation of Halobacterium Species NRC-1 to Its Extreme Environment through Computational Analysis of Its Genome Sequence

Kennedy¹,

Ng²,

Salzberg³

et al. 2001

Genome Res.

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303

267

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The genome of the halophilic archaeon Halobacterium sp. NRC-1 and predicted proteome have been analyzed by computational methods and reveal characteristics relevant to life in an extreme environment distinguished by hypersalinity and high solar radiation: (1) The proteome is highly acidic, with a median pI of 4.9 and mostly lacking basic proteins. This characteristic correlates with high surface negative charge, determined through homology modeling, as the major adaptive mechanism of halophilic proteins to function in nearly saturating salinity. (2) Codon usage displays the expected GC bias in the wobble position and is consistent with a highly acidic proteome. (3) Distinct genomic domains of NRC-1 with bacterial character are apparent by whole proteome BLAST analysis, including two gene clusters coding for a bacterial-type aerobic respiratory chain. This result indicates that the capacity of halophiles for aerobic respiration may have been acquired through lateral gene transfer. (4) Two regions of the large chromosome were found with relatively lower GC composition and overrepresentation of IS elements, similar to the minichromosomes. These IS-element-rich regions of the genome may serve to exchange DNA between the three replicons and promote genome evolution. (5) GC-skew analysis showed evidence for the existence of two replication origins in the large chromosome. This finding and the occurrence of multiple chromosomes indicate a dynamic genome organization with eukaryotic character.

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Snapshot of a Large Dynamic Replicon in a Halophilic Archaeon: Megaplasmid or Minichromosome?

Cited by 106 publications

References 51 publications

Mutations and Rearrangements in the Genome ofSulfolobus solfataricusP2

Mutations and Rearrangements in the Genome ofSulfolobus solfataricusP2

Multireplicon genome architecture of Lactobacillus salivarius

Understanding the Adaptation of Halobacterium Species NRC-1 to Its Extreme Environment through Computational Analysis of Its Genome Sequence

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