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Burkholderia cepacia

ABSTRACT: Opportunistic pathogen

PROVIDER: PRJNA12340 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	DRR015635_1.fastq.gz	Fastqsanger.gz
	DRR015635_2.fastq.gz	Fastqsanger.gz
	DRR015636_1.fastq.gz	Fastqsanger.gz
	DRR015636_2.fastq.gz	Fastqsanger.gz

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An investigation of Burkholderia cepacia complex methylomes via SMRT sequencing and mutant analysis

Project description:While nucleotide sequences determine an organism’s proteins, methylation of the nucleotides themselves can confer additional properties. In bacteria, differences in methylation can be used to identify incoming DNA, for example from bacteriophages. Restriction enzymes detect the methylation status at specific sequence motifs, and cleave improperly methylated, foreign DNA. Furthermore, methylation of key genetic regions can influence gene expression and hence phenotype. In this study, we determined the methylated motifs of three strains from the closely-related Burkholderia cepacia complex of opportunistic pathogens. Three of these motifs were novel, while two are methylated throughout this group of bacteria and beyond and had already been assigned putative causative genes. To investigate the contribution of the enzymes that methylate and cut DNA, we deleted the genes encoding them from a representative strain. We found that these genes are important for traits including motility, biofilm formation, cell shape and production of iron acquisition elements. The mutant strain showed marked defects in replicon partitioning and was more efficient at acquiring foreign DNA, illustrating the importance of methylation in maintaining genome integrity. Interestingly, we found that one methylase, part of an integrated bacteriophage genome, was essential for maintaining the phage in a dormant state.

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DNA-Based diagnostic approaches for identification of Burkholderia cepacia complex, Burkholderia vietnamiensis, Burkholderia multivorans, Burkholderia stabilis, and Burkholderia cepacia genomovars I and III.

Project description:Bacteria of the Burkholderia cepacia complex consist of five discrete genomic species, including genomovars I and III and three new species: Burkholderia multivorans (formerly genomovar II), Burkholderia stabilis (formerly genomovar IV), and Burkholderia vietnamiensis (formerly genomovar V). Strains of all five genomovars are capable of causing opportunistic human infection, and microbiological identification of these closely related species is difficult. The 16S rRNA gene (16S rDNA) and recA gene of these bacteria were examined in order to develop rapid tests for genomovar identification. Restriction fragment length polymorphism (RFLP) analysis of PCR-amplified 16S rDNA revealed sequence polymorphisms capable of identifying B. multivorans and B. vietnamiensis but insufficient to discriminate strains of B. cepacia genomovars I and III and B. stabilis. RFLP analysis of PCR-amplified recA demonstrated sufficient nucleotide sequence variation to enable separation of strains of all five B. cepacia complex genomovars. Complete recA nucleotide sequences were obtained for 20 strains representative of the diversity of the B. cepacia complex. Construction of a recA phylogenetic tree identified six distinct clusters (recA groups): B. multivorans, B. vietnamiensis, B. stabilis, genomovar I, and the subdivision of genomovar III isolates into two recA groups, III-A and III-B. Alignment of recA sequences enabled the design of PCR primers for the specific detection of each of the six latter recA groups. The recA gene was found on the largest chromosome within the genome of B. cepacia complex strains and, in contrast to the findings of a previous study, only a single copy of the gene was present. In conclusion, analysis of the recA gene of the B. cepacia complex provides a rapid and robust nucleotide sequence-based approach to identify and classify this taxonomically complex group of opportunistic pathogens.

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