Genomic context analytics of genes for universal stress proteins from petroleum-degrading Alcanivorax

Résumé fourni par la source

Alcanivorax species are gram negative bacteria that usually require aliphatic hydrocarbon \nas the sole carbon source for growth. The ability to use petroleum in polluted environments as \nenergy source makes Alcanivorax species biotechnologically relevant in bioremediation. \nUniversal stress proteins confer ability to respond to unfavourable environments, thus the present \nstudy was done to analyse the genomic context of genes for universal stress proteins in \nAlcanivorax genomes. A combination of bioinformatics and visual analytics approaches were \nused to analyze genome-enabled data including sequences and gene expression datasets. On the \nbasis of transcription unit and adjacent genes, two types of Alcanivorax USP genes observed \nwere (i) adjacent to cyclic nucleotide-binding and oxygen sensing functions; and (ii) adjacent to \nsulfate transporter function. Both types of genes encode two universal stress protein domains \n(pfam00582) also referred to as tandem-type universal stress proteins. The sequence and structural characteristics of each of the four USP domains in Alcanivorax needs to be further \ninvestigated. This dissertation research evaluated data from Alcanivorax borkumensis cells \n(grown on either pyruvate or hexadecane as carbon source) that were stressed with 1-octanol and \ndata collected at 15 min, 30 min, 60 min and 90 min after 1-octanol addition. The two genes for \nAlcanivorax borkumensis SK2 universal stress proteins, ABO_1340 and ABO_1511, had the \nsame direction of expression for adjacent genes. A limitation of this research was that findings \nbased on bioinformatics and visual analytics methods may need confirmation by molecular \nmethods. The differences observed may also reflect the quality of the annotations provided for \ngenes. The sequence and structural characteristics of each of the four USP domains in \nAlcanivorax needs to be further investigated. Further research is needed on the relationship \nbetween number, length and order of genes in operons that include genes for universal stress proteins. Additionally, in vitro studies to confirm the functional prediction made from the \ngenomic context of the universal stress protein in Alcanivorax genome. The knowledge \ndiscovered from this genome context analytics research could contribute to improving the \nperformance of Alcanivorax species in bioremediation of environments polluted with petroleum

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