Evolution of genetic architecture and gene regulation in biphenyl/PCB-degrading bacteria

A variety of bacteria in the environment can utilize xenobiotic compounds as a source of carbon and energy. The bacterial strains degrading xenobiotics are suitable models to investigate the adaptation and evolutionary processes of bacteria because they appear to have emerged relatively soon after the release of these compounds into the natural environment. Analyses of bacterial genome sequences indicate that horizontal gene transfer (HGT) is the most important contributor to the bacterial evolution of genetic architecture. Further, host bacteria that can use energy effectively by controlling the expression of organized gene clusters involved in xenobiotic degradation will have a survival advantage in harsh xenobiotic-rich environments. In this review, we summarize the current understanding of evolutionary mechanisms operative in bacteria, with a focus on biphenyl/PCB-degrading bacteria. We then discuss metagenomic approaches that are useful for such investigation

Distribution of Camphor Monooxygenase Genes in Soil Bacteria

In microbial degradation of camphor, the first step is oxidation by multiunit enzyme, camphor monooxygenase, encoded by cam genes (camA,B,C). Seven camphor-utilizing bacterial strains have been isolated from soil at various locations. CamA,B,C genes of Pseudomonas putida strain PpG1 and strain GF2001 were used as probes to explore their abundance in the camphor-utilizing bacteria. Southern analysis revealed that all of the cam genes of GF2001 could hybridize well to the SpeI-digested genomic DNA of strains tested, whereas PpG1 cam genes were not. This result suggested that the GF2001 type cam genes are widely distributed among the camphorutilizing strains in the environment. Thus strain GF2001 and seven newly isolated strains share a common evolutionary origin. Key words: Camphor monooxygenase genes, gene distribution, sail bacteria

Identification, cloning and heterologous expression of biosynthetic gene cluster for desertomycin

From our in-house microbial genome database of secondary metabolite producers, we identified a candidate biosynthetic gene cluster for desertomycin from Streptomyces nobilis JCM4274. We report herein the cloning of the 127-kb entire gene cluster for desertomycin biosynthesis using bacterial artificial chromosome vector. The entire biosynthetic gene cluster for desertomycin was introduced in the heterologous host, Streptomyces lividans TK23, with an average yield of more than 130 mg l(-1)

Photoemission from the gas phase using soft x-ray fs pulses: An investigation of the space-charge effects

An experimental and computational investigation of the space-charge effects occurring in ultrafast photoelectron spectroscopy from the gas phase is presented. The target sample CF$_3$I is excited by ultrashort (100 fs) far-ultraviolet radiation pulses produced by a free-electron laser. The modification of the energy distribution of the photoelectrons, i.e. the shift and broadening of the spectral structures, is monitored as a function of the pulse intensity. A novel computational approach is presented in which a survey spectrum acquired at low radiation fluence is used to determine the initial energy distribution of the electrons after the photoemission event. The spectrum modified by the space-charge effects is then reproduced by $N$-body calculations that simulate the dynamics of the photoelectrons subject to the mutual Coulomb repulsion and to the attractive force of the positive ions. The employed numerical method allows to reproduce the complete photoelectron spectrum and not just a specific photoemission structure. The simulations also provide information on the time evolution of the space-charge effects on the picosecond scale. Differences with the case of photoemission from solid samples are highlighted and discussed. The presented simulation procedure constitutes an effective tool to predict and account for space-charge effect in time-resolved photoemission experiments with high-intensity pulsed sources.Comment: 18 pages, 4 figures, 1 tabl

Novel Approach to Quantitative Detection of Specific rRNA in a Microbial Community, Using Catalytic DNA

We developed a novel method for the quantitative detection of the 16S rRNA of a specific bacterial species in the microbial community by using deoxyribozyme (DNAzyme), which possesses the catalytic function to cleave RNA in a sequence-specific manner. A mixture of heterogeneous 16S rRNA containing the target 16S rRNA was incubated with a species-specific DNAzyme. The cleaved target 16S rRNA was separated from the intact 16S rRNA by electrophoresis, and then their amounts were compared for the quantitative detection of target 16S rRNA. This method was used to determine the abundance of the 16S rRNA of a filamentous bacterium, Sphaerotilus natans, in activated sludge, which is a microbial mixture used in wastewater treatment systems. The result indicated that this DNAzyme-based approach would be applicable to actual microbial communities

Metagenomic Screening for Bleomycin Resistance Genes▿ †

A metagenomic library of activated sludge was screened for bleomycin resistance genes. Two genes were identified that differed greatly from each other, from the genes of bleomycin-producing actinomycetes, and from those of clinical isolates. Therefore, the nonclinical environment is a rich reservoir of new resistance elements, and metagenomics can be used to sample the resistome rapidly