Genomic context analytics of genes for universal stress proteins from petroleum-degrading Alcanivorax
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Authors
Kashim, Zainab Abimbola
Issue Date
2016-09
Type
Dissertation
Language
en
Keywords
Alternative Title
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
Description
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>