The behavior of chromosomal inversions in Escherichia coli depends upon the region they affect. Regions flanking the replication terminus have been termed nondivisible zones (NDZ) because inversions ending in the region were either deleterious or not feasible. This regional phenomenon is further analyzed here. Thirty segments distributed between 23 and 29 min on the chromosome map have been submitted to an inversion test. Twenty-five segments either became deleterious when inverted or were noninvertible, but five segments tolerated inversion. The involvement of polar replication pause sites in this distribution was investigated. The results suggest that the Tus/pause site system may forbid some inversion events, but that other constraints to inversion, unrelated to this system, exist. Our current model for deleterious inversions is that the segments involved carry polar sequences acting in concert with other polar sequences located outside the segments. The observed patchwork of refractory and tolerant segments supports the existence of several NDZs in the 23- to 29-min region. Microscopic observations revealed that deleterious inversions are associated with high frequencies of abnormal nucleoid structure and distribution. Combined with other information, the data suggest that NDZs participate in the organization of the terminal domain of the nucleoid.

The E. coli chromosome replication arms are polarized by motifs such as RRNAGGGS oligomers, found preferentially on leading strands. Their skew increases regularly from the origin to dif (the site in the center of the terminus where chromosome dimer resolution occurs), to reach a value of 90% near dif. Convergent information indicates that polarization in opposite directions from the dif region controls tightly the activity of dif, probably by orienting mobilization of the terminus at cell division. Another example of polarization is the presence, in the region peripheral to the terminus, of small non-divisible zones whose inversion interferes with spatial separation of sister nucleoids. The two phenomena may contribute to the organization of the Ter macrodomain.

The presence of recessive growth-retarding alleles can reduce the fitness of industrial wine yeasts. In nature, these alleles are supposed to be eliminated through "genome renewal". We emulated this process in the laboratory to increase the fermentation vigor of wine yeasts. The procedure is simply to sporulate the yeast strains and select new homozygous single-spore descendants. Most of the yeasts achieve a faster onset of fermentation when recessive deleterious genes are eliminated. The increase of the degree of homozygosity has no relation, either direct or inverse, with the fermentation vigor of the yeasts or with the quality of the resulting wine. However, in some strains in which recessive growth-retarding alleles have been eliminated, the fermentation vigor and the quality of the wine were found to be improved simultaneously.

Regions close to the replication terminus of the Escherichia coli chromosome are strongly refractory to genomic inversions. Since these regions also harbour polar replication terminator-like sequences or pause sites, we have investigated the possibility that slowing of replication as a result of pausing at inverted pause sites is responsible for inability to isolate stable inversions affecting these regions. A mutation in the tus gene is known to abolish replication pausing at terminators. We show here that the distribution of invertible and noninvertible segments along the chromosome is not affected by tus mutations. This observation eliminates replication pausing as a cause for the reduced fitness of bacteria harbouring certain chromosomal inversions.

Inversion of many predetermined segments of the Escherichia coli chromosome was attempted by using a system for in vivo selection of genomic rearrangements. Two types of constraints on these inversions were observed: (i) a sensitivity to rich medium when the distance between oriC and the 86- to 91-min region (which carries loci essential for transcription and translation) is increased; (ii) a poor viability or inviability of inversions having at least one endpoint in the one-third of the chromosome around replication terminators (with an exception for some inversions ending between these terminators). Although the first constraint is simply explained by a decreased dosage of the region involved, the second one may result from disruption of two long-range chromosomal organizations. The nondivisible zones thus disclosed coincide remarkably well with the two zones that we have previously described, which are polarized with respect to their replication. It is proposed that the two phenomena result from a sequence-dependent and polarized organization of the terminal region of the chromosome, which defines chromosome replication arms and may participate in nucleoid organization.