Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of DNA methylations in Burkholderia pseudomallei.
Project description:Array-CGH analysis and Burkholderia pseudomallei isolates pre and post ceftazidime relapse. Genomic DNA from both the parental strains and variant strains were labeled with Cy3 or Cy5 fluorescent dyes and hybridized onto a customized microarray with probes designed from the reference Bp K96243 genome. Log2 signal ratios of parental strain over the variant strains were then computed after normalization to find genomic loss or gain in the variant strains.
Project description:Many microbial pathogens express specific virulence traits at distinct growth phases. To investigate the molecular pathways linking bacterial growth to pathogenicity, we characterized the genome-wide growth transcriptome of the tropical pathogen Burkholderia pseudomallei (Bp), the causative agent of melioidosis. Using fine-scale sampling, approximately 17% of all Bp genes were found to display regulated expression during growth, manifested primarily as discrete waves of gene expression tightly associated with distinct growth phases and transition points. A functional curation of these clusters provided evidence of a global ‘just-in-time’ production strategy to ensure the synthesis of molecular constituents only when needed. We observed regulation of multiple virulence factors at all growth phases, and by analyzing the early-phase transcriptome data, we identified and experimentally validated serC as a novel virulence factor in mice. Immunization of mice with serC-disrupted Bp also conferred protection against subsequent challenges with different wild-type Bp strains, demonstrating the potential utility of the serC mutant as an attenuated vaccine. We found a significant bias in early phase genes on Chromosome 1, supporting its proposed role as the ancestral Burkholderia chromosome, and utilized a chromosomally ordered co-expression metric to define ~100 putative operons throughout the Bp genome. These results extend our knowledge of virulence pathways in Bp, and suggest that molecular events at all growth phases, including early phase, are likely to play important roles in microbial pathogenicity." Keywords: Time Series Comparison Bp (K96243)
Project description:We report the methylome sequencing and annotation of Burkholderia pseudomallei D286 based on high-throughput profiling using PacBio SMRT technology
Project description:Bacterial transcriptomes are dynamic, context-specific and condition-dependent. Infection by the soil bacterium, Burkholderia pseudomallei, causes melioidosis, an often fatal infectious disease of humans and animals. Possessing a large multi-chromosomal genome, B. pseudomallei is able to persist and survive in a multitude of environments. To obtain a comprehensive overview of B. pseudomallei expressed transcripts, we initiated whole-genome transcriptome profiling covering a broad spectrum of conditions and exposures – a so-called “condition compendium”. Using the compendium, we confirmed many previously-annotated genes and operons, and also identified hundreds of novel transcripts including anti-sense transcripts and non-coding RNAs. By systematically examining genes exhibiting highly similar expression patterns, we ascribed putative functions to previously uncharacterized genes, and identified novel regulatory elements controlling these expression patterns. We also used the compendium to elucidate candidate virulence pathways associated with quorum-sensing and infection in mice. Our study showcases the power of a B. pseudomallei condition compendium as a valuable resource for understanding microbial physiology and the pathogenesis of melioidosis.
Project description:B. pseudomallei strain K96243 is sensitive to the drug ceftazidime (CAZ), but has been shown to exhibit transient CAZ tolerance when in a biofilm form. To investigate an observed shift in gene expression profile during ceftazidime (CAZ) tolerance and to better understand the mechanistic aspects of this transient tolerance, RNA-sequencing was performed on B. pseudomallei K96243 from the following three growth states: planktonic-free, biofilm, and planktonic shedding cells. Results indicated that the expression of 651 genes (10.97%) were significantly changed in both biofilm (resistant) and planktonic shedding (sensitive) cells in comparison to the planktonic state. Burkholderia biofilm shifts its transcriptome in response to ceftazidime exposure by regulating iron-sulfur stabilizing and metabolic-related genes.