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

Abstract

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...

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

“…The minichromosomes share a 145-kb region of identity within which exist 2 copies of 33-37-kb inverted repeats. The majority (69 of 91) of IS elements were also localized to the minichromosomes, which, along with the other genomic repeats, accounts for the dynamic nature of the genome (Charlebois and Doolittle 1989;Ng et al 1991;Hackett et al 1994). Altogether, 14% of the genome, including the 91 IS elements, 33-37-kb inverted repeats, and 145-kb duplication in pNRC100 and pNRC200, is repeated DNA.…”

Comparative genomic analysis of the Haloferax volcanii DS2 and Halobacterium salinarium GRB contig maps reveals extensive rearrangement

“…Only two variable regions were identified, the first spanning 240 kbp involving numerous changes to the restriction map, a large insertion-deletion, and an inversion and the second an insertion-deletion spanning approximately 10 kbp (19). While one would normally expect such conservation when looking at strains of the same species, the genetic instability of two of the strains in the comparison did not make this a forgone conclusion.…”

“…The most detailed maps among the Archaea are derived from the extreme halophiles. Maps of ordered cosmid libraries are available for Haloferax volcanii DS2 (8) and Halobacterium salinarium GRB (47), while highly detailed macrorestriction maps constructed by using two-dimensional gel electrophoresis are available for two additional strains of Halobacterium salinarium (19). The higher resolution of these maps compared to what is achieved with standard PFGE maps allows for more detailed and potentially informative comparisons to be made.…”

“…The latter scenario requires a more ancient origin of the chromosomal size difference. Although the Halobacterium mediterranei chromosome matches that of Haloferax volcanii in size (30), implying constancy since their divergence, a comparison within strains of Halobacterium salinarium (19) revealed recent small insertion-deletion events. Thus, neither mechanism can be excluded at this time.…”

“…To date, three archaeal genomic comparisons have been performed, one between two methanogens (46) and two between different members of the haloarchaea (19,31). The most detailed maps among the Archaea are derived from the extreme halophiles.…”