SummaryWe present evidence for the existence of two large (Ϸ50 kb) excisable segments in the chromosome of Salmonella typhimurium. The two elements -designated Gifsy-1 and Gifsy-2 -cover, respectively, the 57 units and the 24 units of the genetic map where they contribute indicative rare restriction sites. The two elements are closely interrelated and both contain a region of sequence similarity to the recE locus of the Rac prophage of Escherichia coli. Mutations within this region of Gifsy-1 yield the classical 'Sbc' phenotype: they suppress the recombination defect of recB mutants, apparently by activating a normally silent recE-like gene. At the same time, these 'sbcE ' mutations activate a Xis-type function that promotes excision of one or other of the two elements. Predictably, curing of Gifsy-1 results in the loss of recB mutant suppression. Surprisingly, the suppressor phenotype is also lost in cells cured for Gifsy-2 even though the Gifsy-1-associated sbcE mutation is still present. Moreover, the excision frequency of Gifsy-1 drops dramatically in Gifsy-2-cured cells. Thus, both elements must co-operate in the activation of recombination and excision functions. Overall, the data presented here suggest that Gifsy-1 and Gifsy-2 are cryptic prophages. They are distinct from previously described Fels prophages. Unlike Fels, they are not specific to S. typhimurium strain LT2 since they are both also found in a virulent S. typhimurium isolate (ATCC 14028s).

1. A series of CS revertants has been selected from various strains (both omega+ and omega-) carrying a CR mitochondrial mutation at the RIB1 locus. The properties of mitochondrial recombination exhibited by these CS revertants in various crosses, have been examined systematically. The omega allele of the CS revertants has been defined in crosses with omega+ and omega- tester strains using two criteria: the polarity of recombination and a new criterium called relative output coefficient. We found that mutations of omega appear frequently associated with the mutations at the RIB1 locus selected from omega- strains but not with those selected from omega+ strains. A new allelic form of omega (omega n) which had not been found amongst wild type yeast strains is characterised. Similarly omega n mutation was found frequently associated with CR mutants at the RIB1 locus selected from omega- CS strains but not with those selected from omega+ CS strains. The omega n mutants, and the omega+ and omega- strains, explain the groups of polarity previously observed by Coen et al. (1970). 2. Main features of mitochondrial crosses with omega n strains (omega+ x omega n, omega- x omega n and omega n x omega n) are analysed. Recombination is possible between the different mitochondrial genetic markers. No high polarity of recombination is observed and the frequency of recombinants are similar to those found in homosexual crosses (omega+ x omega+ and omega- x omega-). A striking property, observed for the first time, exists in crosses between zota+ omega n CS strains and some zota- CREO mutants: the zota- CREO are unable to integrate by recombination their CR allele into the zota+ mit-DNA of omega n CS strains while being capable of integrating it into omega+ CS or omega- CS genomes. 3. It is proposed that the omega locus is the site of initiation of non reciprocal recombination events, the omega+/omega- pairing specifically initiates the non-reciprocal act while omega+/omega n or omega-/omega n pairings do not. 4. The molecular nature of the omega n mutation and its bearing on the structure of the omega locus are discussed. It is suggested that omega n mutations correspond to macrolesions (probably deletions) of a segment of the mit-DNA covering the omega and RIB1 loci. If omega n is a partial deletions of the omega- sequence the omega+ could be an additionnal deletion of the omega n sequence. 5. The occurrence of spontaneous CR and ER mitochondrial mutations has been analysed by the Luria and Delbrück fluctuation test in omega- and omega n isonuclear strains. Results of these tests indicate that an intracellular selection of resistant copies preexisting the action of the anttibiotic occurs.

Complete eukaryote chromosomes were investigated for intrachromosomal duplications of nucleotide sequences. The analysis was performed by looking for nonexact repeats on two complete genomes, Saccharomyces cerevisiae and Caenorhabditis elegans, and four partial ones, Drosophila melanogaster, Plasmodium falciparum, Arabidopsis thaliana, and Homo sapiens. Through this analysis, we show that all eukaryote chromosomes exhibit similar characteristics for their intrachromosomal repeats, suggesting similar dynamics: many direct repeats have their two copies physically close together, and these close direct repeats are more similar and shorter than the other repeats. On the contrary, there are almost no close inverted repeats. These results support a model for the dynamics of duplication. This model is based on a continuous genesis of tandem repeats and implies that most of the distant and inverted repeats originate from these tandem repeats by further chromosomal rearrangements (insertions, inversions, and deletions). Remnants of these predicted rearrangements have been brought out through fine analysis of the chromosome sequence. Despite these dynamics, shared by all eukaryotes, each genome exhibits its own style of intrachromosomal duplication: the density of repeated elements is similar in all chromosomes issued from the same genome, but is different between species. This density was further related to the relative rates of duplication, deletion, and mutation proper to each species. One should notice that the density of repeats in the X chromosome of C. elegans is much lower than in the autosomes of that organism, suggesting that the exchange between homologous chromosomes is important in the duplication process.

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The complete genome of the yeast Saccharomyces cerevisiae was investigated for intrachromosomal duplications at the level of nucleotide sequences. The analysis was performed by looking for long approximate repeats (from 30 to 3,885 bp) present on each of the chromosomes. We show that direct and inverted repeats exhibit very different characteristics: the two copies of direct repeats are more similar and longer than those of inverted repeats. Furthermore, contrary to the inverted repeats, a large majority of direct repeats appear to be closely spaced. The distance (delta) between the two copies is generally smaller than 1 kb. Further analysis of these "close direct repeats" shows a negative correlation between delta and the percentage of identity between the two copies, and a positive correlation between delta and repeat length. Moreover, contrary to the other categories of repeats, close direct repeats are mostly located within coding sequences (CDSs). We propose two hypotheses in order to interpret these observations: first, the deletion/conversion rate is negatively correlated with delta; second, there exists an active duplication mechanism which continuously creates close direct repeats, the other intrachromosomal repeats being the result, by chromosomal rearrangements of these "primary repeats."