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The lignocellulose degrading capability of Coniochaeta pulveracea CAB 683: an omics approach
Thesis (MSc)--Stellenbosch University, 2022.
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| Language: | English |
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Stellenbosch : Stellenbosch University
2022
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| _version_ | 1867614016504856576 |
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| access_status_str | Open Access |
| author | Borstlap, C. J. |
| author2 | Botha, Alfred
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| author_browse | Borstlap, C. J. Botha, Alfred |
| author_facet | Botha, Alfred
Borstlap, C. J. |
| author_sort | Borstlap, C. J. |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MSc)--Stellenbosch University, 2022. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/125073 |
| institution | Stellenbosch University (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:45:20.375Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/125073 The lignocellulose degrading capability of Coniochaeta pulveracea CAB 683: an omics approach Borstlap, C. J. Botha, Alfred Volschenk, Heinrich Stellenbosch University. Faculty of Science. Dept. of Microbiology. Lignocellulose -- Biodegradation Fungi -- Biotechnology Coniochaeta pulveracea -- Functional genomics Fungal enzymes Genomics -- Data processing UCTD Thesis (MSc)--Stellenbosch University, 2022. ENGLISH ABSTRACT: The biotechnological potential of fungi belonging to the genus Coniochaeta (Sordariomycetes) is progressively being studied by scientists across the globe. It is especially the wood degrading capabilities of coniochaetaceous fungi that have drawn the attention of research groups, since these fungi have the potential to be the source of novel industrially relevant lignocellulolytic enzymes. A representative from a particularly underexplored coniochaetaceous species, Coniochaeta pulveracea CAB 683, previously demonstrated the ability to secrete lignocellulolytic enzymes. However, due to a lack of genomic information on this species, the full potential of C. pulveracea for commercial exploitation remained vague. Therefore, during this project, we used genomics to catalogue the lignocellulolytic enzyme encoding genes of C. pulveracea. Moreover, using RNA-sequencing, we explored which enzymes are transcriptionally induced while the fungus grows on a complex lignocellulosic substrate. The genome of Coniochaeta pulveracea CAB 683 was assembled de novo into a 30 Mbp assembly and it was found to consist of 10,035 protein-encoding genes. Carbohydrate-active enzyme (CAZyme) annotation revealed that the CAB 683 genome contains 411 CAZyme encoding genes, of which the majority are involved in lignocellulose depolymerisation. Thereafter, we used information on the functional role of analogous CAZymes in closely related fungi to extrapolate the extent to which the CAZyme profile of CAB 683 would be able to depolymerise the different components of lignocellulose. Subsequently, we compared the CAZyme profile of CAB 683 to the profile of coniochaetaceous and non-coniochaetaceous fungi. Based on our comparisons, unique CAZyme profile characteristics of CAB 683 compared to non-coniochaetaceous fungi include significantly more CAZyme-encoding genes belonging to the families GH55, GH71, GH127 and CBM24. Additionally, no CAZy family within the genome of CAB 683 was found to be reduced in gene numbers compared to the genomes of non-coniochaetaceous fungi, i.e., representatives of Aspergillus niger, Fusarium oxysporum, Myceliophthora thermophila, Neurospora crassa, Podospora anserina and Trichoderma reesei. Finally, to gain further insight into how CAB 683 depolymerise woody material, we compared the genome-wide gene expression of this strain when cultured on a complex lignocellulosic substrate, milled Vachellia particles (MVP), to gene expression when the fungus was cultured on glucose as carbon source. The differential gene expression analysis revealed that in the presence of lignocellulose, the gene expression of several cellulolytic, hemicellulolytic and ligninolytic CAZymes are significantly upregulated compared to when the fungus was cultured on glucose. These included several industry-relevant CAZymes, i.e., β-glucosidases, lytic polysaccharide monooxygenases, xylanases, acetyl xylan esterases and laccases. Overall, the insights gained from our study confirm that Coniochaeta pulveracea is indeed a potentially rich source of novel key lignocellulolytic enzymes, which can be used commercially as individual enzymes or in enzyme cocktails. AFRIKAANSE OPSOMMING: Fungi vanuit die genus Coniochaeta (Sordariomycetes) is besig om te styg na prominensie a.g.v. hul biotegnologiese vooruitsigte, veral as ‘n onondersoekte bron van ensieme wat lignosellulose afbreek. Een van die mees onondersoekte spesies, Coniochaeta pulveracea, het voorheen die vermoë om lignosellulolitiese ensieme te produseer, getoon. Alhoewel hierdie fungus potensiaal toon, is daar ‘n tekort aan genomiese informasie vir hierdie spesie wat veroorsaak dat die werklike potensiaal van C. pulveracea vir kommersiële uitbuiting nog vaag is. Gedurende hierdie projek het ons dus genomika gebruik om die lignosellulolitiese ensieme van C. pulveracea te klasifiseer. Bowendien, het ons RNA-volgordebepaling gebruik om te bepaal watter van hierdie ensieme se geen transkripsie word geïnduseer in die teenwoordigheid van ‘n komplekse lignosellulose substraat. Die genoom van Coniochaeta pulveracea CAB 683 was de novo saamgestel in ‘n 30 Mbp samestelling wat uit 10,035 proteïen-koderende gene bestaan. Die annotasie van koolhidraat-aktiewe ensieme (CAZyme) het geopenbaar dat daar 411 gene in die genoom van CAB 683 is wat kodeer vir CAZyme, waarvan die meerderheid betrokke is in die depolimerisasie van lignosellulose. Daarna het ons informasie oor die funksionele rol van analoog CAZyme in na verwante fungi gebruik om te bepaal tot watter mate die CAZyme profiel van CAB 683 die verskillende komponente van lignosellulose kan afbreek. Ons het ook die CAZy profiel van CAB 683 vergelyk met die CAZy profiel van coniochaetaceous en nie-coniochaetaceous fungi. Unieke CAZyme profiel karaktereienskappe van CAB 683 in vergelyking met die nie-coniochaetaceous fungi sluit in aansienlik meer CAZyme-koderende gene wat aan die ensiem families GH55, GH71, GH127 en CBM24 behoort. Asook dat daar geen ensiem familie in die CAZyme profiel van CAB 683 was wat aansienlik minder CAZyme-koderende gene gehad het nie in vergelyking met die nie-coniochaetaceous fungi. Laastens het ons die genoom-wye geen uitdrukking van CAB 683 wat gegroei het op ‘n komplekse lignosellulose substraat, gemaalde Vachellia deeltjies, vergelyk met die geen uitdrukking van die fungus toe dit gegroei was op glukose as a koolstof bron. Die differensiële geenuitdrukking analise het gewys dat ‘n verskeidenheid sellulolitiese, hemisellulolitiese en ligninolitiese CAZyme se geen uitdrukking was aansienlik opgereguleer in die teenwoordigheid van lignosellulose in vergelyking toe die fungus op glukose gegroei was. Dit sluit in ‘n verskeidenheid industriële relavante CAZyme soos β-glukosidase, litiese polisakkaried monooksigenase, xylanase, asetiel xilaan esterase en laccase. Altesaam bevestig die insigte verkry gedurende hierdie studie dat Coniochaeta pulveracea wel ‘n ryk bron van lignosellulolitiese ensieme is waarvan kommersiële ensiem mengsels mee opgebou en/of aangevul word. Masters 2022-03-09T11:43:40Z 2022-04-29T12:52:48Z 2022-03-09T11:43:40Z 2022-03-09 Thesis http://hdl.handle.net/10019.1/125073 en Stellenbosch University xv, 119 pages : illustrations, maps application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Lignocellulose -- Biodegradation Fungi -- Biotechnology Coniochaeta pulveracea -- Functional genomics Fungal enzymes Genomics -- Data processing UCTD Borstlap, C. J. The lignocellulose degrading capability of Coniochaeta pulveracea CAB 683: an omics approach |
| title | The lignocellulose degrading capability of Coniochaeta pulveracea CAB 683: an omics approach |
| title_full | The lignocellulose degrading capability of Coniochaeta pulveracea CAB 683: an omics approach |
| title_fullStr | The lignocellulose degrading capability of Coniochaeta pulveracea CAB 683: an omics approach |
| title_full_unstemmed | The lignocellulose degrading capability of Coniochaeta pulveracea CAB 683: an omics approach |
| title_short | The lignocellulose degrading capability of Coniochaeta pulveracea CAB 683: an omics approach |
| title_sort | lignocellulose degrading capability of coniochaeta pulveracea cab 683 an omics approach |
| topic | Lignocellulose -- Biodegradation Fungi -- Biotechnology Coniochaeta pulveracea -- Functional genomics Fungal enzymes Genomics -- Data processing UCTD |
| url | http://hdl.handle.net/10019.1/125073 |
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