- Title
- Sequence and structural investigation of the nonribosomal peptide synthetases of Bacillus atrophaeus UCMB 5137(63Z)
- Creator
- Ryan, Candice Nancy
- ThesisAdvisor
- Tastan Bishop, Özlem
- ThesisAdvisor
- Reva, Oleg
- Subject
- Bacillus (Bacteria)
- Subject
- Peptides--Synthesis
- Subject
- Antibiotics
- Subject
- Drug resistance in microorganisms
- Subject
- Amino acids
- Subject
- Phytopathogenic microorganisms
- Subject
- Trees--Phylogeny
- Subject
- Ligases
- Date
- 2013
- Date
- 2013-04-19
- Type
- Thesis
- Type
- Masters
- Type
- MSc
- Identifier
- vital:3891
- Identifier
- http://hdl.handle.net/10962/d1003057
- Identifier
- Bacillus (Bacteria)
- Identifier
- Peptides--Synthesis
- Identifier
- Antibiotics
- Identifier
- Drug resistance in microorganisms
- Identifier
- Amino acids
- Identifier
- Phytopathogenic microorganisms
- Identifier
- Trees--Phylogeny
- Identifier
- Ligases
- Description
- Due to increased plant resistance to the existing antibiotics produced, there is a need to develop alternatives. Nonribosomal peptides (NRPs) are important plant phytopathogens synthesized by nonribosomal peptide synthetases (NRPSs). In this study, a newly sequenced Bacillus strain Bacillus atrophaeus UCMB 5137 (63Z), found to have increased phytopathogenic activity, was investigated to gain insights to the possible reason behind this activity. NRPS modules were identified using a novel script that can act on unannotated, raw DNA sequences. The Structure Based Sequence Analysis Webserver was used to identify the amino acids incorporated into the final NRP, which were compared to the NRP database. Five NRPSs were found within the strain; fengycin/plipstatin, mycosubtilin, surfactin, bacillibactin and bacitracin. Some of the modules usually present for these NRPSs were not present in the test strain and only a few modules were found. A phylogenetic study was carried out and the topologies of the trees showed that genes were not transferred horizontally. It did, however, lead to the hypothesis that different NRPS genes are under different adaptive evolutionary pressures. Only slight conformational changes between L and D-conformation of amino acids were seen between the test and neighboring strains. All of the linker and terminal regions of synthetases were found to exhibit a large amount of conservation overall. Homology modeling was performed on the test strain on selected modules, TE and A-domains of fengycin and mycosubtilin synthetases. TE-domains between the different synthetases are different and specific for the NRP they facilitate release for. The NRPS from which the A-domain originates also influences substrate specificity as well as the module in which the A-domain occurs within the NRPS. Binding pockets of A-domains of differing substrate specificity were compared. Future work will include; refinement of the models and docking studies within the A-domain binding pocket.
- Description
- Microsoft� Word 2010
- Description
- Adobe Acrobat 9.54 Paper Capture Plug-in
- Format
- 147 p., pdf
- Publisher
- Rhodes University, Faculty of Science, Biochemistry, Microbiology and Biotechnology
- Language
- English
- Rights
- Ryan, Candice Nancy
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Collections
RU Department of Biochemistry, Microbiology and Biotechnology (end of 2014)
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