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Saturday, 23 September 2017
Chromobacterium violaceum Pathway-Genome Database PDF Print

Pathway-genome databases (PGDBs) have advanced computational annotation, particularly concerning metabolic and other organizational information such as protein complexes for annotated microbial and more complex genomes. We have created and analyzed the genome of Chromobacterium violaceum strain ATCC 12472, recently sequenced by BRGene (Brazilian National Genome Project Consortium, 2003). C. violaceum is a remarkable bacterium with potential medical and biotechnological applications, and has been used in our group as a model organism to study quorum sensing and violacein production.


CvioCyc: a Pathway-Genome Database for Chromobacterium violaceum
Great efforts have been done to sequence and annotate whole genomes. The hallmark of those projects is the collaborative nature of the work involved. Several bioinformatics tools have been developed to computationally annotate genomes, but human intervention is still the preferred approach due to the belief that it produces more accurate and polished results. Pathway-genome databases (PGDBs) have advanced computational annotation, particularly concerning metabolic and other organizational information such as protein complexes to annotated microbial and more complex genomes. Chromobacterium violaceum is a remarkable bacterium with potential medical and biotechnological applications. This bacterium had its genome sequenced by the Brazilian National Genome Project Consortium in 2003. C. violaceum  has been used as a model organism to study quorum sensing and violacein production, so an useful database was required.

We created CvioCyc, a Pathway-Genome Database, using an academic license of the Pathway-Tools software provided by SRI International. Two hundred and thirty-three metabolic pathways were initially identified, most of them showing incomplete routes due to required missing reactions (enzymes). Pathway-Tools automatically generated reports were extensively used to investigate 64 metabolic pathways, and deletions and insertions were performed based on evidences found by the software, other databases, and literature investigation.

Violacein biosynthesis pathway and its related compounds were included in CvioCyc since that purple pigment is the most prominent phenotype feature of C. violaceum. Pathway analysis through the glyphs generated in CvioCyc was used to curate and re-annotate the Chromobacterium genome. It was shown that computational curation may substantially improve the quality of metabolic networks and physiological analysis of sequenced genomes.
 
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