Abstract
The first Lactobacillus delbrueckii ssp. bulgaricus genome sequence revealed the presence of a very large inverted repeat (IR), a DNA sequence arrangement which thus far seemed inconceivable in a non-manipulated circular bacterial chromosome, at the replication terminus. This intriguing observation prompted us to investigate if similar IRs could be found in other bacteria. IRs with sizes varying from 38 to 76 kbp were found at the replication terminus of all 5 L. delbrueckii ssp. bulgaricus chromosomes analysed, but in none of 1373 other chromosomes. They represent the first naturally occurring very large IRs detected in circular bacterial genomes. A comparison of the L. bulgaricus replication terminus regions and the corresponding regions without IR in 5 L. delbrueckii ssp. lactis genomes leads us to propose a model for the formation and evolution of the IRs. The DNA sequence data are consistent with a novel model of chromosome rescue after premature replication termination or irreversible chromosome damage near the replication terminus, involving mechanisms analogous to those proposed in the formation of very large IRs in human cancer cells. We postulate that the L. delbrueckii ssp. bulgaricus-specific IRs in different strains derive from a single ancestral IR of at least 93 kbp.
Highlights
Dimer) would result in the inversion of a part of the dimer rather than its resolution[5,10]
We present a comparative analysis of 10 L. delbrueckii genome sequences, representing 5 strains of the ssp. lactis and 5 strains of the ssp. bulgaricus, with a focus on the replication terminus region
The genomes of the L. delbrueckii subspecies bulgaricus and lactis are in an active phase of evolution, as witnessed by an aberrant GC content at third codon positions[5] and remarkably high numbers of pseudogenes in both subspecies[4,5]
Summary
Dimer) would result in the inversion of a part of the dimer rather than its resolution[5,10] These observations prompted us to investigate if similar IRs could be found in other genomes. Bulgaricus, with a focus on the replication terminus region. We show that very large naturally occurring IRs are found in the replication terminus region of all 5 ssp. Lactis genomes leads us to propose a model for the formation and evolution of the IRs. The DNA sequence data are consistent with a novel model of chromosome rescue after premature replication termination or irreversible chromosome damage near the replication terminus, involving the formation of a very large IR through mechanisms analogous to those proposed in the formation of very large IRs in human cancer cells
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