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

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dc.contributor.advisor Isokpehi, Raphael
dc.contributor.advisor Tekere, Memory
dc.contributor.author Kashim, Zainab Abimbola
dc.date.accessioned 2017-11-17T09:46:35Z
dc.date.available 2017-11-17T09:46:35Z
dc.date.issued 2016-09
dc.date.submitted 2017-08
dc.identifier.citation Kashim, Zainab Abimbola (2016) Genomic context analytics of genes for universal stress proteins from petroleum-degrading Alcanivorax, University of South Africa, Pretoria, <http://hdl.handle.net/10500/23365>
dc.identifier.uri http://hdl.handle.net/10500/23365
dc.description.abstract Alcanivorax species are gram negative bacteria that usually require aliphatic hydrocarbon as the sole carbon source for growth. The ability to use petroleum in polluted environments as energy source makes Alcanivorax species biotechnologically relevant in bioremediation. Universal stress proteins confer ability to respond to unfavourable environments, thus the present study was done to analyse the genomic context of genes for universal stress proteins in Alcanivorax genomes. A combination of bioinformatics and visual analytics approaches were used to analyze genome-enabled data including sequences and gene expression datasets. On the basis of transcription unit and adjacent genes, two types of Alcanivorax USP genes observed were (i) adjacent to cyclic nucleotide-binding and oxygen sensing functions; and (ii) adjacent to sulfate transporter function. Both types of genes encode two universal stress protein domains (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 investigated. This dissertation research evaluated data from Alcanivorax borkumensis cells (grown on either pyruvate or hexadecane as carbon source) that were stressed with 1-octanol and data collected at 15 min, 30 min, 60 min and 90 min after 1-octanol addition. The two genes for Alcanivorax borkumensis SK2 universal stress proteins, ABO_1340 and ABO_1511, had the same direction of expression for adjacent genes. A limitation of this research was that findings based on bioinformatics and visual analytics methods may need confirmation by molecular methods. The differences observed may also reflect the quality of the annotations provided for genes. The sequence and structural characteristics of each of the four USP domains in Alcanivorax needs to be further investigated. Further research is needed on the relationship between 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 genomic context of the universal stress protein in Alcanivorax genome. The knowledge discovered from this genome context analytics research could contribute to improving the performance of Alcanivorax species in bioremediation of environments polluted with petroleum en
dc.format.extent 1 online resource (xi, 79 leaves : color illustrations, color graphs) en
dc.language.iso en en
dc.subject.ddc 622.338
dc.subject.lcsh Petroleum -- Biodegradation en
dc.subject.lcsh Genes -- Research en
dc.subject.lcsh Heat shock proteins -- Research en
dc.title Genomic context analytics of genes for universal stress proteins from petroleum-degrading Alcanivorax en
dc.type Dissertation en
dc.description.department College of Agriculture and Environmental Sciences en
dc.description.degree M. Sc. (Environmental Science)


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  • Unisa ETD [8700]
    Electronic versions of theses and dissertations submitted to Unisa since 2003

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