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Comparative genomics study of completely sequenced Thermus sp. strains to enhance and facilitate their application in biotechnology
Thesis (PhD)--University of Pretoria, 2013.
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| Format: | Thesis |
| Language: | English |
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University of Pretoria
2014
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| _version_ | 1867613497082249216 |
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| access_status_str | Open Access |
| author2 | Reva, Oleg N. |
| author_browse | Reva, Oleg N. |
| author_facet | Reva, Oleg N. |
| collection | Thesis |
| dc_rights_str_mv | © 2013 University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. |
| description | Thesis (PhD)--University of Pretoria, 2013. |
| format | Thesis |
| id | oai:repository.up.ac.za:2263/40247 |
| institution | University of Pretoria (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:37:05.077Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UPSpace — University of Pretoria Institutional Repository |
| publishDate | 2014 |
| publishDateRange | 2014 |
| publishDateSort | 2014 |
| publisher | University of Pretoria |
| publisherStr | University of Pretoria |
| record_format | dspace |
| source_str | UPSpace — University of Pretoria Institutional Repository |
| spelling | oai:repository.up.ac.za:2263/40247 Comparative genomics study of completely sequenced Thermus sp. strains to enhance and facilitate their application in biotechnology Reva, Oleg N. benjkum@gmail.com Litthauer, Derek Kumwenda, Benjamin Enzymes Thermus species Amino acid substitutions UCTD Thesis (PhD)--University of Pretoria, 2013. Thermus bacteria are of special interest because of their ability to live in high temperature environments. Their enzymes exhibit higher and stable activity in industry as compared to mesophilic or synthetic counterparts. Thermus bacteria are capable of reducing heavy metals which is essential in eradication of heavy metal pollution and controlling global warming. Genome rearrangements were investigated in Thermus species and the extent to which they affected the distribution of functionally related genes on the chromosome and its implication on the coherence of the metabolic network. The contribution of horizontal gene transfer to genome rearrangements and the shuffling of genes on the chromosome were analysed. Horizontally transferred genes were identified alongside their donors and recipients, their age and relative time of insertion. Metabolic networks were clustered and compared to determine the extent to which they were affected by rearrangements as a measure of evolutionary pressures experienced by organisms. Factors that enhance protein thermostability were analysed by determining dominant substitutions for amino acid residues and their properties. Protein thermostability was measured using the UNAFold algorithm. Amino acid substitutions were compared between less and highly thermophilic orthologous sequences in T. scotoductus SA-01 and T. thermophilus HB27 respectively. Protein structures were modelled for orthologs that met a defined selection criterion. Dominant amino acid substitutions were analysed in the structures to determine their locations. The contribution of dominant substitutions to energy changes in structures was analysed using FoldX program. Results revealed a uniform distribution of functionally related genes among thermophilic and mesophilic organisms. The contribution of horizontal gene transfer to genome rearrangements was found to be insignificant. Metabolic networks for Thermus species were poorly clustered in correlation with their optimum environmental growth temperatures. Non-polar, small and charged amino acids were found to significantly enhance thermostability. Higher occurrence of alanine substituted by serine and threonine; and arginine substituted by glutamine and lysine were observed to influence thermostability. Structural comparison showed that mutations were mostly located on the surfaces and helices of structures. The positions of mutations appeared to influence their energy contribution to the overall structure as measured by FoldX algorithm. gm2014 Biochemistry unrestricted 2014-06-17T13:06:00Z 2014-06-17T13:06:00Z 2014-04-09 2013 Thesis Kumwenda, B 2013, Comparative genomics study of completely sequenced Thermus sp. strains to enhance and facilitate their application in biotechnology, PhD thesis, University of Pretoria, Pretoria, viewed yymmdd <http://hdl.handle.net/2263/40247> D14/4/115/gm http://hdl.handle.net/2263/40247 en © 2013 University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. application/pdf University of Pretoria |
| spellingShingle | Enzymes Thermus species Amino acid substitutions UCTD Comparative genomics study of completely sequenced Thermus sp. strains to enhance and facilitate their application in biotechnology |
| title | Comparative genomics study of completely sequenced Thermus sp. strains to enhance and facilitate their application in biotechnology |
| title_full | Comparative genomics study of completely sequenced Thermus sp. strains to enhance and facilitate their application in biotechnology |
| title_fullStr | Comparative genomics study of completely sequenced Thermus sp. strains to enhance and facilitate their application in biotechnology |
| title_full_unstemmed | Comparative genomics study of completely sequenced Thermus sp. strains to enhance and facilitate their application in biotechnology |
| title_short | Comparative genomics study of completely sequenced Thermus sp. strains to enhance and facilitate their application in biotechnology |
| title_sort | comparative genomics study of completely sequenced thermus sp strains to enhance and facilitate their application in biotechnology |
| topic | Enzymes Thermus species Amino acid substitutions UCTD |
| url | http://hdl.handle.net/2263/40247 |