Genome structure of <i>Halobacterium halobium</i>: plasmid dynamics in gas vacuole deficient mutants

Pfeifer, Felicitas; Blaseio, Ulrike; Horne, Mary C.

doi:10.1139/m89-015

Cited by 17 publications

(11 citation statements)

References 14 publications

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“…The hypermutable gyp operon and most copies of the ISH are in the plasmid fraction, which is also consistent with the model. In H. salinarium, all characterized mutations are mediated by ISH elements (1,3,(8)(9)(10).…”

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Conservation of chromosomal arrangement among three strains of the genetically unstable archaeon Halobacterium salinarium

1994

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Phenotypic variants of Halobacterium salinarium NRC-1 arise at a frequency of 10-2. These result from transpositions of halobacterial insertion sequences and rearrangements mediated by halobacterial insertion sequences. We have tested the hypothesis that such mutations are confined to only a portion of the genome by comparing the chromosomal restriction map of H. salinarium NRC-1 and that of the derivative S9, which was made in 1969. The two chromosomes were mapped by using two-dimensional pulsed-field gel electrophoresis and the restriction enzymes AfIll, AseI, and Dral. A comparison of the two deduced maps showed a domain of about 210 kbp to be subject to many rearrangements, including an inversion in S9 relative to NRC-1. However, the rest of the chromosome was conserved among NRC-1, S9, and an independent Halobacterium isolate, GRB, previously mapped by St. Jean et al. (A. St. Jean, B. A. Trieselmann, and R. L. Charlebois, Nucleic Acids Res. 22:1476Res. 22: -1483Res. 22: , 1994). This concurs with data from eubacteria suggesting strong selective forces maintaining gene order even in the face of rearrangement events occurring at a high frequency.Halobacterium salinarium (formerly H. halobium) is an archaeon (20) that originally attracted attention as the source of bacteriorhodopsin, a light-dependent transmembrane proton pump (18). The cloning of the bacterio-opsin gene (bop) facilitated studies which showed that the high rate of mutation to the Bop-phenotype (1 cell in 500) resulted from insertional inactivation of the bop gene (15). A number of different mobile insertion sequences, named ISH (for halobacterial insertion sequences), which can transpose into the bop gene and adjacent regulatory genes have been identified (1, 8). The ability to form gas vesicles, encoded by the gyp operon, is lost at an even higher rate of about 10-2. The Gvp-phenotype results from two types of events: duplicative transpositions of ISH and deletion events consistent with abortive intramolecular transposition (3, 9, 10).It seems unlikely that all H. salinarium genes have the same inactivation rate; there must be domains of the genome that mutate much less readily. The genome can be divided into two fractions on the basis of GC content (4, 7). The FT fraction contains 68% GC and is believed to be the chromosome. The FII fraction contains 58% GC and corresponds to one or more plasmids and AT-rich islands of the chromosome (7). One plausible model for genome structure is one in which the plasmids represent a hypermutable domain where new functions are created by random transposition and recombination events. A selectively advantageous genetic element is rendered stable by transfer into the chromosome, where it would be resistant to rearrangement. This idea is consistent with the different GC contents of the two fractions of the genome, which suggest that the plasmids are recently acquired from another species. The hypermutable gyp operon and most copies of the ISH are in the plasmid fraction, which is also consistent with the m...

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Conservation of chromosomal arrangement among three strains of the genetically unstable archaeon Halobacterium salinarium

1994

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“…leading to mutation in phenotypic markers at frequencies of up to 10<-per cell per generation (6,7). Moreover, recombination between repeated copies of the elements occurs so frequently in some strains that a consistent and reproducible map of the genomiie might not exist (1,5,8). Important forces must therefore be acting to limit daimiaee to the genome and to maintain some measure of genetic integritY.…”

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“…(However, an analysis of gas vesicle gene disruption bN insertion elements [8] showed that the plasmild-enlcoded p-vwc [in FlI DNA] was inactivated more than a thous(and timnes More frequently than the chromosomally-encoded c-l'' in F! DNA].…”

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confidence: 99%

Physical map and set of overlapping cosmid clones representing the genome of the archaeonHalobacteriumsp. GRB

1994

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“…The resulting transpositional cost to the cell is compounded by the potential recombinational chaos mediated by interaction between members of each insertion sequence family. It has been suggested that a genomically pure clone of H. salinarium cannot be grown because of continual rearrangements which occur in plasmid DNA (27,30,36).The genus Haloferax is not as severely infested with insertion sequences as is H. salinarium. Nevertheless, Haloferax volcanii possesses at least 49 copies of the ISH51 family distributed throughout the genome (8), and there is good evidence for the existence of several other types of repeated sequences as well (35,37).…”

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Genomic stability in the archaeae Haloferax volcanii and Haloferax mediterranei

et al. 1995

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Through hybridization of available probes, we have added nine genes to the macrorestriction map of the Haloferax mediterranei chromosome and five genes to the contig map of Haloferax volcanii. Additionally, we hybridized 17 of the mapped cosmid clones from H. volcanii to the H. mediterranei genome. The resulting 35-point chromosomal comparison revealed only two inversions and a few translocations. Forces known to promote rearrangement, common in the haloarchaea, have been ineffective in changing global gene order throughout the nearly 10 7 years of these species' divergent evolution.One of the most notable characteristics of extremely halophilic archaea is their genetic instability (4,11,12,27). The haloarchaea are rich in insertion sequences which can disrupt genes at frequencies as high as 10 Ϫ2 in the case of Halobacterium salinarium (32,43). Most of the activity of these insertion sequences is confined to plasmid DNA or to FII DNA (which has a lower moles percent GϩC content) (13,28,31), but chromosomal genes are not spared from disruption. The bop gene, for instance, is inactivated by at least eight different types of insertion sequences (11, 27), resulting in a combined risk of about 10 Ϫ4 per generation (32). H. salinarium is known to possess hundreds of insertion sequences, in dozens of families (35). The resulting transpositional cost to the cell is compounded by the potential recombinational chaos mediated by interaction between members of each insertion sequence family. It has been suggested that a genomically pure clone of H. salinarium cannot be grown because of continual rearrangements which occur in plasmid DNA (27,30,36).The genus Haloferax is not as severely infested with insertion sequences as is H. salinarium. Nevertheless, Haloferax volcanii possesses at least 49 copies of the ISH51 family distributed throughout the genome (8), and there is good evidence for the existence of several other types of repeated sequences as well (35,37). Though H. volcanii is not as prone to genetic disruption as is H. salinarium, neither is it immune. Less is known about the number or distribution of insertion sequences in Haloferax mediterranei. Interestingly, the populous ISH51/27 family shared by H. volcanii and H. salinarium (29) is absent from H. mediterranei (37). Regardless, repeated sequences which can potentially facilitate genomic rearrangement are present (1).With physical and genetic maps available, we can now begin to address genomic stability in the haloarchaea. The first researchers to assess the degree of rearrangement in the haloarchaeal chromosome by using a comprehensive comparative mapping approach (15) found that much of the H. salinarium chromosome is conserved in structure among several strains, despite different complements of repetitive sequences in their genomes. Differences in the maps were observed to be confined to a few discrete, hypervariable blocks. H. salinarium NRC-1 and H. salinarium S9 maintain hundreds of insertion sequences within their genomes, and yet gene order is preserve...

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Genome structure of Halobacterium halobium: plasmid dynamics in gas vacuole deficient mutants

Cited by 17 publications

References 14 publications

Conservation of chromosomal arrangement among three strains of the genetically unstable archaeon Halobacterium salinarium

Conservation of chromosomal arrangement among three strains of the genetically unstable archaeon Halobacterium salinarium

Physical map and set of overlapping cosmid clones representing the genome of the archaeonHalobacteriumsp. GRB

Genomic stability in the archaeae Haloferax volcanii and Haloferax mediterranei

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