Wednesday, May 23, 2012

Transposome-based mutagenesis to develop a Planctomycetes model organism

Microbial geneticists continue to use the EZ-Tn5 in vivo transposomics tools for establishing genetic systems in novel bacteria. Jogler et al. report on the Planctomycetes phylum of bacteria which is a major component of the global nitrogen and carbon cycles. These bacteria perform reactions such as the anaerobic oxidation of ammonium ions. Many Planctomycetes strains are difficult to cultivate, so the researchers developed a model system using the P. limnophilus strain due to its cultivability, sensitivity to kanamycin, rapid growth, and availability of the genome sequence.

The authors used the EZ-Tn5 <R6Kgamma/KAN-2> Transposome in a standard in vivo transposition reaction to generate mutants that were detected by i) Kan resistance and ii) modified arbitrary PCR. The mutants were screened using a second arbitrary PCR step. Analysis showed that nine mutations were generated that were pinpointed to specific regions on the chromosome. The authors comment that there appeared to be only insignificant regional bias in the insertion sites. The authors further noted that the intracellular membrane and the condensed nucleoid did not appear to have any negative effect on the transposition; thus, the likelihood of gene transfer and mutagenesis in Planctobacillus spp. appears to be quite good. These results will enable future in-depth genetic analysis of Planctomycetes.

ResearchBlogging.orgJogler, C. et al. (2011). Characterization of Planctomyces limnophilus and Development of Genetic Tools for Its Manipulation Establish It as a Model Species for the Phylum Planctomycetes Applied and Environmental Microbiology, 77 (16), 5826-5829 DOI: 10.1128/AEM.05132-11

Friday, May 4, 2012

BAC library provides clue to transmissible tumors in Tasmanian devils

The Tasmanian devil was recently listed as an endangered species, primarily due to the emergence of a fatal, transmissible cancer known as devil facial tumour disease (DFTD). The disease was recently reported in Northern Tasmania, and has resulted in depletion of populations that could ultimately make the animals extinct within 25 to 35 years. Recently, Deakin et al. conducted a genetic survey of a BAC library created with the CopyControl™ BAC Library Construction Kit (EcoR I) from genomic DNA extracted from the liver of a deceased two-year-old male Tasmanian devil. Physical maps were compared to the genomes of other marsupials to determine the genesis of this particular disease.

The results showed that massive genomic restructuring appears to be a catalyst for development of the DFTD syndrome, based on chromosome painting and fluorescence in situ hybridization (FISH) experiments conducted using the BAC library. The authors developed a detailed map of the global chromosome restructuring and intricate gene rearrangements that characterize DFTD. Only limited regions of the genome were found to be highly rearranged. After the rearrangements occur, the tumor karyotype is remarkably stable during its clonal transmission from animal to animal. By anchoring genes to a reference and tumor maps, the authors believe that they can predict the locations of common tumor suppressor genes and oncogenes. This study provides an important framework for future genomic studies into DFTD and enhances the value of the creation of large-insert genomic libraries.

ResearchBlogging.orgDeakin, J. et al. (2012). Genomic Restructuring in the Tasmanian Devil Facial Tumour: Chromosome Painting and Gene Mapping Provide Clues to Evolution of a Transmissible Tumour PLoS Genetics, 8 (2) DOI: 10.1371/journal.pgen.1002483