Mining of genes encoding for DNA-manipulating enzymes from hot springs using metagenomic techniques.

Show simple item record Mokoena, Morena India 2022-01-28T04:18:37Z 2022-01-28T04:18:37Z 2019-09
dc.description M. Tech. (Department of Biotechnology, Faculty of Applied and Computer Sciences), Vaal University of Technology. en_US
dc.description.abstract The use of conventional culture-based approach results in vast majority of microbes (90 - 99%) unaccounted for. However, over the past years, the use of metagenomics, which is a culture-independent comprehensive approach has enabled researchers to access nearly 100% of the microbiome. In this study, three hot springs (44 – 70 oC) in Limpopo province of South Africa were investigated as potential sources of genes encoding for DNA-manipulating enzymes (DNA polymerase, DNA ligase and endonuclease), which are central in genetic engineering. They are usually grouped into four broad classes (nucleases, ligases, polymerases and modifying enzymes) depending on the type of the reaction they catalyze. Accordingly, hot spring metagenomic DNA was successfully extracted using modified SDS-CTAB method involving gel purification and electroelution. Consequently, a portion of the extracted metagenomic DNA was used for sequencing and another for fosmid library construction. Sequencing was done using Illumina MiSeq next generation sequencing platform and sequence data analyzed and de novo-assembled using CLC Genomic Workbench, which resulted in 5 681 662 reads and 7 338 contigs. A metagenome expression fosmid library of approximately 2.16 x 103 clones was also constructed using CopyControl™ HTP Fosmid Library Production Kit with pCC2FOS™ Vector. A BLAST algorithm in NCBI revealed 57 distinct genes for DNA polymerase, 29 genes for DNA ligase and more than 100 genes for endonuclease II enzymes. Hence, three genes related to thermophiles representing genes for DNA polymerase, DNA ligase and endonuclease II were selected. Accordingly, the three genes were codon-optimized, synthesized and successfully cloned into pET- 30a (+) and overexpressed in Escherichia coli BL21 (DE3) by inducing with 0.5 mM IPTG and incubating overnight at 16ºC. The cells were lysed using B-PER Reagent, protein extracted and purified using AKTA start protein purification system and purity of 85- 95 % was achieved. From this study, it can be concluded that metagenomics as an approach, can be used to mine for putative DNA-manipulating enzymes from hot spring metagenome. Besides, further study should be conducted to formulate the developed DNA-manipulating enzymes and study the practical application and chart way for commercialization. Moreover, the constructed fosmid library could also be screened for potentially novel thermo-stable biomolecules of industrial and therapeutic importance. en_US
dc.language.iso en en_US
dc.publisher Vaal University of Technology en_US
dc.subject Hot spring en_US
dc.subject Metagenomic library en_US
dc.subject DNA-manipulating enzymes en_US
dc.subject Sequencing en_US
dc.subject Cloning en_US
dc.subject Expression en_US
dc.subject.lcsh Dissertations, Academic -- South Africa en_US
dc.subject.lcsh Metagenomics en_US
dc.subject.lcsh Biotechnology en_US
dc.subject.lcsh DNA -- Synthesis en_US
dc.subject.lcsh Enzymes en_US
dc.title Mining of genes encoding for DNA-manipulating enzymes from hot springs using metagenomic techniques. en_US
dc.type Thesis en_US
dc.contributor.supervisor Feto, Naser Aliye, Dr Rashamuse, K., Dr.

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