Genome sequence and functional comparison of thermus NXM2 A.1
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Date
2013-05
Authors
Tlalajoe, Nokuthula
Journal Title
Journal ISSN
Volume Title
Publisher
University of the Free State
Abstract
The aim of this project was to sequence the whole genome of Thermus sp. NMX2 A.1 strain and compare it to the whole genome sequence of T. scotoductus SA-01.Therafter attempt to use experimental data to confirm functionality within the genomes and lastly isolate a new Thermus sp. from the fissure water samples routinely collected from the deep gold mines of South Africa and the Northam Platinum mine. The genus Thermus has been extensively studied since the discovery of T. aquaticus in 1969 by Brock and Freeze and hundreds of species had been isolated ever since. However, up to date only eight validly described species are comprised in the genus Thermus. Moreover, amongst this handful amount of species from the genus Thermus; great discoveries have been made and highlighted parts drew further attention in studying this genus even more. Their metabolism is one of the aspects looked into especially the denitrification respiration. With the application of a nitrate operon it is known that a few species within this genus are able to grow under such conditions, meanwhile; others are modified by genetically manipulating them to do so, for instance T. thermophilus HB27. Subsequently, T. scotoductus SA-01 is reported to naturally possess the nitrate operon allowing it to grow in oxygen restricted conditions without any genetic manipulation applied. Recently, another strain was discovered to have the same functionalities as T. scotoductus SA-01 when grown under denitrification respiration with the supplement of potassium nitrate. In addition to that, many phylogenetic similarities and identical remarks were also observed between T. scotoductus SA-01 and the newly sequence Thermus sp. NMX2 A.1 strain such as the ones carried out using the BOX-PCR fingerprinting. Comparison was, therefore, carried out on genome level to verify the phylogenetic similarities; of which was seen that the two strains shared up to (81.6%) similarities. The remaining percentage represented a set of genes that where uniquely found in the newly sequenced strain such entailed the Calvin cycle. It is however, understandable as to why there might be differences between the two strains since the T. scotoductus SA-01 was isolated in the deep gold mines of South Africa and Thermus sp. NMX2 A.1 strain from the thermal hot springs of New Mexico in the USA. As a result; T. scotoductus SA-01 also indicated islands within its genome in which were not found in the newly sequenced strain. A detailed experimental procedure was carried out to further support the theoretical similarities of the two strains with the presence of their genes that participate within the nitrate operon. Their functionalities were therefore analyzed using the profile of the nitrite detection as initial step of nitrate reduction, of which they showed an identical profile from the beginning of the incubation period until the end. Lastly, with the advantages of a variety of fissure water samples collected from the different deep gold mines of South Africa and the Northam platinum mine a search for possible Thermus isolate was in addition performed. A range of different applications were implemented to obtain pure Gram negatives cells. This however, didn‟t successfully yield the expected results; even though there were numerous indications that the Gram negative cells where present and one could even hypothesize that those Gram negative cells were a genus Thermus since the “rotund bodies” characteristics were seen amongst these fissure water-samples. Unfortunately this directive was not achieved but the search continues to extend the known Thermus sp. isolations and exploration into their metabolic versatility.
Description
Keywords
Dissertation (M.Sc. (Microbial, Biochemical and Food Biotechnology))--University of the Free State, 2013, Genomes, Gene mapping, Nucleotide sequence, Thermus sp. NMX2 A.1, Next generation sequence, Nitrate reduction thermophiles, Calvin cycle