rifampin and Chromosome-Deletion

The presence of repeated DNA sequences is a genomic liability, because interrepeat recombination can result in chromosomal rearrangements. The mismatch repair system prevents recombination between nonidentical repeats, but the mechanism of antirecombination has not been established. Although the MutS protein binds to base pair mismatches in heteroduplex DNA, the role of the MutL protein in preventing recombination is unknown. In a screen designed to identify new cellular functions that suppress deletion formation involving nonidentical DNA repeats, we isolated a mutL mutant having a separation-of-function phenotype. The mutant showed an increased frequency of deletions but not of mutations. The split phenotype is due to a decreased MutL level, indicating that recombination, but not replication editing, is highly sensitive to MutL level. By altering the MutL level, we found that the frequency of deletion-generating recombination is inversely related to the amount of cellular MutL. DNA sequence analysis of the recombined repeats shows that the tolerance of base pair mismatches in heteroduplex DNA is also inversely correlated with MutL level. Unlike recombination, correction of misincorporation errors by mismatch repair is insensitive to fluctuations in MutL level. Overproduction of MutS does not affect either of these phenotypes, suggesting that, unlike MutL, MutS is not limiting for mismatch repair activities. These results indicate that MutL (i) determines effective DNA homology in recombination processes and (ii) fine tunes the process of deletion formation involving repeated, diverged DNA sequences.

Topics: Adenosine Triphosphatases; Chromosome Deletion; Chromosomes, Bacterial; Drug Resistance, Bacterial; Escherichia coli; Escherichia coli Proteins; Mutation; MutL Proteins; MutS DNA Mismatch-Binding Protein; Nalidixic Acid; Phenotype; Recombinant Proteins; Recombination, Genetic; Rifampin

The DNA sequence requirements of two T4 tertiary replication origins have been characterized by a deletion analysis of origin-containing plasmids. Maximal replication of each origin-containing plasmid required both an intact gpmotA-dependent middle-mode promoter sequence and approximately 50 base pairs of the downstream region. In contrast, gpmotA-dependent transcription from the origin promoter was found to be independent of the downstream region. The requirement for a promoter element within the tertiary origins is striking, particularly since the replication of tertiary origin-containing plasmids is resistant to the RNA polymerase inhibitor rifampicin.

Topics: Base Sequence; Chromosome Deletion; Drug Resistance, Microbial; Plasmids; Promoter Regions, Genetic; Rifampin; T-Phages; Transcription, Genetic; Virus Replication

The oriT site of the broad host-range multicopy IncQ plasmid RSF1010 was cloned onto the 2.2 kb pBR322-derived vector pED825. By successive subcloning and construction of deletions, the oriT region was localised on an 80-88 bp segment of DNA. This segment was contained within the HaeII fragment of RSF1010 that is known to include the relaxation nick site. The oriT region was sequenced and inverted repeats and sequences homologous to the oriT regions of ColE1 and RK2 were identified. A striking 10 bp inverted repeat at one end of the 88 bp oriT segment may be important for recognition of oriT, and its possible role in transfer is discussed. As for other plasmids, the oriT region served as the site for recA-independent, transfer-dependent, site-specific recombination. This provides genetic evidence that strand breakage and re-joining occur at oriT during transfer. Mobilization was independent of transcription by RNA polymerase in the donor cell, as shown by the lack of effect of rifampicin. Inversion of the oriT site with respect to the plasmid oriV site showed that there was no functional dependence of oriT on oriV for synthesis of primers possibly involved in recipient conjugal DNA synthesis. Alternative mechanisms are discussed.

Topics: Base Composition; Base Sequence; Chromosome Deletion; Cloning, Molecular; Crosses, Genetic; DNA Restriction Enzymes; Escherichia coli; Genes, Bacterial; Plasmids; Rifampin

Significant portion (up to 20%) of dominant mutations (rifd mutations) was observed among spontaneous mutations of rifampicin resistance picked up in cells of haploid Escherichia coli strain. These mutations are similar to rifd mutations obtained earlier when selecting them in rif-s/rif-s merodiploids. On the basis of analysis of nucleotide substitutions taking place in formation of spontaneous and induced mutations, it is established that rifd mutations are caused by single nucleotide substitution. The majority of rifd mutations are localized in a small region of the central part of RNA polymerase beta-subunit gene covering less than 200 base pairs. A rifd mutant has been described which occurred as a result of micro-deletion in one of the "hot" spots of the central region of beta-subunit gene.

Topics: Amino Acid Sequence; Base Sequence; Chromosome Deletion; DNA-Directed RNA Polymerases; Drug Resistance, Microbial; Escherichia coli; Genes, Bacterial; Genes, Dominant; Lysogeny; Mutation; Phenotype; Rifampin