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Role of Escherichia coli DNA Polymerase IV in In Vivo Replication Fidelity. Wojciech Kuban, 2004.We have investigated whether DNA polymerase IV (Pol IV; the dinB gene product) contributes to the error rate of chromosomal DNA replication in Escherichia coli . We compared mutation frequencies in mismatch repair-defective strains that were either dinB positive or dinB deficient, using a series of mutational markers, including lac targets in both orientations on the chromosome . Virtually no contribution of Pol IV to the chromosomal mutation rate was observed . On the other hand, a significant effect of dinB was observed for reversion of a lac allele when the lac gene resided on an F'(pro-lac) episome . Bacteriophage ST64B, a Genetic Mosaic of Genes from Diverse Sources Isolated from Salmonella enterica Serovar Typhimurium DT 64. Princess T. Mmolawa, 2003.The complete sequence of the double-stranded DNA (dsDNA) genome of the Salmonella enterica serovar Typhimurium ST64B bacteriophage was determined . The 40,149-bp genomic sequence of ST64B has an overall G+C content of 51.3% and is distinct from that of P22 . The genome architecture is similar to that of the lambdoid phages, particularly that of coliphage  . Most of the putative tail genes showed sequence similarity to tail genes of Mu, a nonlambdoid phage . In addition, it is likely that these tail genes are not expressed due to insertions of fragments of genes related to virulence within some of the open reading frames . This, together with the inability of ST64B to produce plaques on a wide range of isolates, suggests that ST64B is a defective phage . In contrast to the tail genes, most of the head genes showed similarity to those of the lambdoid phages HK97 and HK022, but these head genes also have significant sequence similarities to those of several other dsDNA phages infecting diverse bacterial hosts, including Escherichia, Pseudomonas, Agrobacterium, Caulobacter, Mesorhizobium, and Streptomyces. This suggests that ST64B is a genetic mosaic that has acquired significant portions of its genome from sources outside the genus Salmonella .
Agrobacterium rhizogenes GALLS Protein Substitutes for Agrobacterium tumefaciens Single-Stranded DNA-Binding Protein VirE2. Larry D. Hodges, 2004.Agrobacterium tumefaciens and Agrobacterium rhizogenes transfer plasmid-encoded genes and virulence (Vir) proteins into plant cells . The transferred DNA (T-DNA) is stably inherited and expressed in plant cells, causing crown gall or hairy root disease . DNA transfer from A . tumefaciens into plant cells resembles plasmid conjugation; single-stranded DNA (ssDNA) is exported from the bacteria via a type IV secretion system comprised of VirB1 through VirB11 and VirD4 . Bacteria also secrete certain Vir proteins into plant cells via this pore . One of these, VirE2, is an ssDNA-binding protein crucial for efficient T-DNA transfer and integration . VirE2 binds incoming ssT-DNA and helps target it into the nucleus . Some strains of A . rhizogenes lack VirE2, but they still transfer T-DNA efficiently . We isolated a novel gene from A . rhizogenes that restored pathogenicity to virE2 mutant A . tumefaciens . The GALLS gene was essential for pathogenicity of A . rhizogenes . Unlike VirE2, GALLS contains a nucleoside triphosphate binding motif similar to one in TraA, a strand transferase conjugation protein . Despite their lack of similarity, GALLS substituted for VirE2 . Does Virus-Induced Lysis Contribute Significantly to Bacterial Mortality in the Oxygenated Sediment Layer of Shallow Oxbow Lakes?. Ulrike R. Fischer, 2003.Despite the recognition that viruses are ubiquitous components of aquatic ecosystems, the number of studies on viral abundance and the ecological role of viruses in sediments is scarce . In this investigation, the interactions between viruses and bacteria were studied in the oxygenated silty sediment layer of a mesotrophic oxbow lake . A long-term study (13 months) and a diel study revealed that viruses are a numerically important and dynamic component of the microbial community . The abundance and decay rates ranged from 4.3 x 109 to 7.2 x 109 particles ml of wet sediment-1 and from undetectable to 22.2 x 107 particles ml-1 h-1, respectively, and on average the values were 2 orders of magnitude higher than the values for the overlying water . In contrast to our expectations, viruses did not contribute significantly to the bacterial mortality in the sediment, since on average only 6% (range, 0 to 25%) of the bacterial secondary production was controlled by viruses . The low impact of viruses on the bacterial community may be associated with the quantitatively low viral burden that benthic bacteria have to cope with compared to the viral burden with which bacterial assemblages in the water column are confronted . The virus-to-bacterium ratio of the sediment varied between 0.9 and 3.2, compared to a range of 5.0 to 12.4 obtained for the water column . We speculate that despite high numbers of potential hosts, the possibility of encountering a host cell is limited by the physical conditions in the sediment, which is therefore not a favorable environment for viral proliferation . Our data suggest that viruses do not play an important role in the processing and transfer of bacterial carbon in the oxygenated sediment layer of the environment investigated .
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