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Interstrand cross-links (ICLs) block replication and transcription and thus are highly cytotoxic. In higher eukaryotes, ICLs processing involves the Fanconi anemia (FA) pathway and homologous recombination. Stalled replication forks activate the eight-subunit FA core complex, which ubiquitylates FANCD2-FANCI. Once it is posttranslationally modified, this(More)
BACKGROUND The number of available genome sequences is increasing, and easy-to-use software that enables efficient comparative analysis is needed. RESULTS We developed GenomeMatcher, a stand-alone software package for Mac OS X. GenomeMatcher executes BLAST and MUMmer, and the detected similarities are displayed in two-dimensional and parallel views with(More)
The recent findings of various mobile catabolic genes have provided some insight into the evolution of microbial degradation systems for xenobiotic compounds. The catabolic genes undergo marked genetic rearrangements due to their presence on transposons or association with mobile genetic elements. Bacterial catabolic transposons fall into three defined(More)
Structural comparison of three different haloalkane dehalogenases suggested that substrate specificity of these bacterial enzymes could be significantly influenced by the size and shape of their entrance tunnels. The surface residue leucine 177 positioned at the tunnel opening of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26 was selected(More)
Toluene degrading (xyl) genes on a Pseudomonas TOL plasmid pWWO are located within a 39-kb DNA portion. The 56-kb region including these xyl genes and its 17-kb derivative with a deletion of the internal 39-kb portion transposed to various sites on target replicons such as pACYC184 and R388 in escherichia coli recA strains. Thus the 56- and 17-kb regions(More)
In response to iron limitationPseudomonas aeruginosa PAO induces production of pyoverdin, a low-molecular-weight siderophore able to capture ferric ion with a very high affinity. Thepvd genes involved in the pyoverdin biosynthesis are organized in a chromosomal region termed thepvd region, and expression of somepvd genes is regulated at the transcriptional(More)
Expression of the multidrug efflux system MexC-MexD-OprJ in nfxB mutants of Pseudomonas aeruginosa contributes to resistance to fluoroquinolones and the "fourth-generation" cephems (cefpirome and cefozopran), but not to most beta-lactams, including the ordinary cephems (ceftazidime and cefoperazone). nfxB mutants also express a second multidrug efflux(More)
Recent studies have indicated that the evolutionarily common catabolic gene clusters are loaded on structurally diverse toluene-catabolic (TOL) plasmids and their residing transposons. To elucidate the mechanisms supporting the diversification of catabolic plasmids and transposons, we determined here the complete 107,929 bp sequence of pWW53, a TOL plasmid(More)
Haloalkane dehalogenases catalyze cleavage of the carbon-halogen bond in halogenated aliphatic compounds, resulting in the formation of an alcohol, a halide, and a proton as the reaction products. Three structural features of haloalkane dehalogenases are essential for their catalytic performance: (i) a catalytic triad, (ii) an oxyanion hole, and (iii) the(More)
Transposable DNA elements occur naturally in the genomes of nearly all species of prokaryotes. A proposal for a uniform transposable element nomenclature was published prominently in the 1970s but is not, at present, available online even in abstract form, and many of the newly discovered elements have been named without reference to it. We propose here an(More)