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The molecular and metabolic effects of co-evolution on Saccharomyces cerevisiae
Thesis (PhDAgric)--Stellenbosch University, 2023.
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| Format: | Thesis |
| Language: | English |
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Stellenbosch : Stellenbosch University
2023
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| _version_ | 1867613913366921216 |
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| access_status_str | Open Access |
| author | Oosthuizen, Jennifer Rae |
| author2 | Bauer, Florian |
| author_browse | Bauer, Florian Oosthuizen, Jennifer Rae |
| author_facet | Bauer, Florian Oosthuizen, Jennifer Rae |
| author_sort | Oosthuizen, Jennifer Rae |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (PhDAgric)--Stellenbosch University, 2023. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/129331 |
| institution | Stellenbosch University (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:43:41.995Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/129331 The molecular and metabolic effects of co-evolution on Saccharomyces cerevisiae Oosthuizen, Jennifer Rae Bauer, Florian Naidoo-Blassoples, René Rossouw, Debra Stellenbosch University. Faculty of AgriSciences. Dept. of Viticulture & Oenology & Institute for Wine Biotechnology. Saccharomyces cerevisiae -- Biotechnology Coevolution Yeast -- Molecular aspects Genomics Chlorella sorokiniana Single nucleotide polymorphisms -- Variation UCTD Thesis (PhDAgric)--Stellenbosch University, 2023. ENGLISH ABSTRACT: Saccharomyces cerevisiae, as a cornerstone of both fundamental research and biotechnology, provides a versatile platform for exploring fundamental biological processes and engineering novel biotechnological solutions. S. cerevisiae has undergone extensive study in the monoculture context. However, despite the ubiquitous nature of environmental interactions that undeniably influence nearly all aspects of a species' existence, there exists a research gap concerning the impacts of interactivity and co-evolution on species. The functionality and application of existing monoculture systems can be further improved through the advantages of co-culturing and microbial consortia with other biotechnologically relevant species such as the microalga Chlorella sorokinana. The metabolic complementarity of an autotroph-heterotroph pairing makes it an ideal system to study the effects of symbiosis and co-evolutionary adaptation. This dissertation assessed the feasibility of employing both synthetic ecology and evolutionary engineering to better characterise and enhance the interactions between these species. Species that had previously been continuously co-evolved for a period of 100 generations within an obligate mutualism were investigated. Previous research showed that co-evolved strains displayed an adapted phenotype resulting in increased biomass accumulation under selective conditions. In order to study the effects of cell-contact on parental and co-evolved species a novel multi-membrane system was constructed that allowed for the co-culturing of species in either physical or metabolic contact while still exchanging metabolites. Parental and co-evolved strains co-cultured under both these conditions and changes were identified at the phenotypic and transcriptomic levels. Parental and co-evolved S. cerevisiae strain genomes were sequenced to identify any changes at the genomic level that could be attributed to the adapted co-evolved phenotype. Co-culturing the parental and co-evolved species in physical and metabolic contact resulted in distinct growth patterns under each condition, indicating the effects of cell-contact on growth of species in symbiosis and confirming that co-evolutionary adaptation observed is due to the metabolic exchange that takes place during mutualistic growth. Gene expression analysis using RNA sequencing unveiled distinct transcriptomic responses in co-evolved S. cerevisiae in response to the presence of C. sorokiniana compared to the parental yeast. Biological processes involved in the transport of amino acids, hexoses and sulphur were upregulated by co-evolved S. cerevisiae in physical contact compared to metabolic contact. Genomic sequencing showed that co-evolved S. cerevisiae strains had accumulated a number of single nucleotide polymorphisms (SNPs) during co-evolution. A functional analysis of high impact SNPs showed that the inactivation of two genes ETP1 and GAT1 could be directly attributed to the altered phenotype observed in co-evolved strains. Disrupting these genes in the parental S. cerevisiae showed improved biomass accumulation when paired with co-evolved C. sorokiniana strains and altered utilisation of carbon and nitrogen sources. These changes are highly relevant to the mutualism in which these species were co-evolved, whereby carbon and nitrogen were exchanged in a synthetic environment. Overall, the data indicate that these systems have the potential to explore the phenotypic and genetic modifications linked to the coevolution of trans-kingdom ecosystems. AFRIKAANSE OPSOMMING: Saccharomyces cerevisiae, wat 'n belangrike hoeksteen van beide fundamentele navorsing en biotegnologie is, bied 'n veelsydige platform om basiese biologiese prosesse te bestudeer en nuwe biotegnologiese oplossings te ontwikkel. S. cerevisiae is omvattend bestudeer in 'n monokultuur omgewing. Ten spyte van die feit dat alomteenwoordige omgewingsinteraksies 'n beduidende impak op alle aspekte van 'n spesie se bestaan het, is daar 'n gebrek aan navorsing oor die uitwerking van interaktiwiteit en ko-evolusie op hierdie spesie. Deur S. cerevisiae saam met ander relevante spesies te kweek, soos die mikroalg Chlorella sorokinana, kan die funksionaliteit en toepassing van bestaande monokultuurstelsels verbeter word. Die metaboliese aanvullendheid van 'n outotrofiese-heterotrofiese paring maak dit 'n ideale stelsel vir die bestudering van simbiose en ko-evolusionêre aanpassing. Hierdie tesis het ten doel gehad om die haalbaarheid van die gebruik van ‘n sintetiese ekologie en evolusionêre ingenieurswese te assesseer om die interaksies tussen hierdie spesies beter te verstaan en te verbeter. Die studie het gefokus op spesies wat voorheen vir 100 generasies saam-evolueer het binne 'n verpligte mutualisme. Vorige navorsing het getoon dat mede-geëvolueerde stamme 'n aangepaste fenotipe vertoon wat lei tot verhoogde biomassa-akkumulasie onder spesifieke toestande. Om die uitwerking van selkontak op ouer- en mede-geëvolueerde spesies te ondersoek, is 'n nuwe multi-membraanstelsel ontwerp om die mede-kweek van spesies in fisiese of metaboliese kontak moontlik te maak, terwyl dit steeds die uitruil van metaboliete moontlik maak. Die fenotipiese en transkriptomiese veranderinge in ouer- en mede-geëvolueerde stamme is onder beide toestande ontleed. Die genome van die ouerlike en saam-geëvolueerde S. cerevisiae-stamme is in volgordebepalingsanalise geplaas om enige genomiese veranderinge wat met die aangepaste saam-geëvolueerde fenotipe geassosieer word, te identifiseer. Die mede-kweek van die ouer- en mede-geëvolueerde spesies in fisiese en metaboliese kontak het tot afsonderlike groeipatrone onder elke toestand gelei. Dit dui aan dat selkontak die groei van spesies in simbiose beïnvloed, en bevestig dat die waargenome ko-evolusionêre aanpassing te wyte is aan metaboliese uitruiling tydens mutualistiese groei. RNA-volgordebepalingsanalise het verskillende transkriptomiese reaksies in mede-geëvolueerde Mede-geëvolueerde S. cerevisiae het opregulering getoon van biologiese prosesse betrokke by die vervoer van aminosure, heksose en swael in fisiese kontak in vergelyking met metaboliese kontak. Genomiese volgordebepaling het getoon dat saamgeëvolueerde S. cerevisiae-stamme verskeie enkelnukleotiedpolimorfismes (SNPs) tydens ko-evolusie versamel het. 'n Ontleding van die funksionele effekte van beduidende SNPs het aan die lig gebring dat die waargenome veranderinge in fenotipe in mede-geëvolueerde stamme direk toegeskryf kan word aan die inaktivering van twee gene, ETP1 en GAT1. Toe hierdie gene in die oorspronklike S. cerevisiae ontwrig was, was daar 'n toename in biomassa akkumulasie wanneer dit met mede-geëvolueerde C. sorokiniana stamme gepaar is, sowel as 'n verandering in die manier waarop koolstof- en stikstofbronne benut is. Hierdie veranderinge is veral belangrik in die konteks van die mutualisme waarin hierdie spesies saam geëvolueer het, aangesien koolstof en stikstof in 'n sintetiese omgewing uitgeruil is. Algeheel, dui die data daarop dat hierdie stelsels die potensiaal het om die veranderinge in fenotipe en genetika wat met die mede-evolusie van trans-koninkryk ekosisteme geassosieer word, te verken. Doctoral 2023-10-20T06:51:02Z 2024-02-20T07:48:38Z 2023-10-20T06:51:02Z 2024-02-20T07:48:38Z 2023-12 Thesis https://scholar.sun.ac.za/handle/10019.1/129331 en Stellenbosch University 130 pages : illustrations application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Saccharomyces cerevisiae -- Biotechnology Coevolution Yeast -- Molecular aspects Genomics Chlorella sorokiniana Single nucleotide polymorphisms -- Variation UCTD Oosthuizen, Jennifer Rae The molecular and metabolic effects of co-evolution on Saccharomyces cerevisiae |
| title | The molecular and metabolic effects of co-evolution on Saccharomyces cerevisiae |
| title_full | The molecular and metabolic effects of co-evolution on Saccharomyces cerevisiae |
| title_fullStr | The molecular and metabolic effects of co-evolution on Saccharomyces cerevisiae |
| title_full_unstemmed | The molecular and metabolic effects of co-evolution on Saccharomyces cerevisiae |
| title_short | The molecular and metabolic effects of co-evolution on Saccharomyces cerevisiae |
| title_sort | molecular and metabolic effects of co evolution on saccharomyces cerevisiae |
| topic | Saccharomyces cerevisiae -- Biotechnology Coevolution Yeast -- Molecular aspects Genomics Chlorella sorokiniana Single nucleotide polymorphisms -- Variation UCTD |
| url | https://scholar.sun.ac.za/handle/10019.1/129331 |
| work_keys_str_mv | AT oosthuizenjenniferrae themolecularandmetaboliceffectsofcoevolutiononsaccharomycescerevisiae AT oosthuizenjenniferrae molecularandmetaboliceffectsofcoevolutiononsaccharomycescerevisiae |