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dc.contributor.author | Sayari, Mohammad![]() |
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dc.contributor.author | Van der Nest, Magrieta Aletta![]() |
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dc.contributor.author | Steenkamp, Emma Theodora![]() |
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dc.contributor.author | Soal, Nicole Christine![]() |
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dc.contributor.author | Wilken, Pieter Markus![]() |
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dc.contributor.author | Wingfield, Brenda D.![]() |
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dc.date.accessioned | 2020-08-24T07:27:26Z | |
dc.date.available | 2020-08-24T07:27:26Z | |
dc.date.issued | 2019-04-30 | |
dc.description | Supplementary file S1. Genome sequence information for the 16 Sordariomycetes representative included in this study. Secondary metabolite unique regions finder (SMURF; www.jcvi.org/smurf/; (22) was used to predict NRPS genes from the Sordariomycetes genomes available from the Joint Genome Institute (JGI; https://jgi.doe.gov/ our-science/science-programs/fungal-genomics/) and the National Centre for Biotechnology Information (NCBI; http://blast.ncbi.nlm.nih.gov/). | en_ZA |
dc.description | Supplementary file S2. To confirm the order of genes within the di erent NRPS clusters identified, a PCR-based approach was used. For each cluster type, primers were designed that allow amplification of individual genes, as well as the regions between them. Correlation between predicted and observed fragment sizes were used as evidence that the specific cluster was correctly assembled. | en_ZA |
dc.description | Supplementary file S3. Blast hits for putative Ceratocystidaceae NRPS biosynthetic cluster genes. For confirmation of the antiSMASH results, we utilized secondary metabolite unique regions finder (SMURF; www.jcvi.org/smurf/; (22). For this purpose, genes that were 15 Kb upstream and downstream of the identified NRPS genes were retrieved and submitted to the BLASTp server at the National Center for Biotechnology Information (NCBI, ftp://ftp.ncbi.nih.gov/blast/) for identification. | en_ZA |
dc.description | Supplementary file S4. The tables below show the predicted nonribosomal peptide synthetase (NRPS) gene clusters predicted by SMURF (secondary metabolite unique regions finder) (22; 37). | en_ZA |
dc.description | Supplementary file S5. Top 10 BLASTp hits for each NRPS sequence. BLASTp search was done against the non-redundant protein sequences in the National Centre for Biotechnology Information database (NCBI; http://blast.ncbi.nlm.nih.gov/), and the top 10 hits are indicated with species where they are found, E-value, percent sequence identity, and coverage. Supplementary file S6. Mapping of RNA reads to di erent genes of the NRPS gene clusters of C. fimbriata, H. moniliformis, and H. omanensis. This included the genes of the monomodular NRPS gene clusters: A, hypothetical protein; B, nonribosomal peptide synthetase; C, siderophore transporter; D, siderophore biosynthesis; E, oxidoreductase; F, ABC transporter; and G, transporter. It also included mapping of RNA reads to di erent genes of multimodular NRPS gene clusters of C. fimbriata, H. moniliformis, and H. omanensis. A, nonribosomal peptide synthetase; B, orntithine monooxygenase; C, endothiapepsin; D, RNA polymerase transcription subunit; and E, aldehyde dehydrogenase. Reads in green and red represent forward and reverse orientation, respectively. | en_ZA |
dc.description | Supplementary file S5. Top 10 BLASTp hits for each NRPS sequence. BLASTp search was done against the non-redundant protein sequences in the National Centre for Biotechnology Information database (NCBI; http://blast.ncbi.nlm.nih.gov/), and the top 10 hits are indicated with species where they are found, E-value, percent sequence identity, and coverage. | en_ZA |
dc.description | Supplementary file S6. Mapping of RNA reads to di erent genes of the NRPS gene clusters of C. fimbriata, H. moniliformis, and H. omanensis. This included the genes of the monomodular NRPS gene clusters: A, hypothetical protein; B, nonribosomal peptide synthetase; C, siderophore transporter; D, siderophore biosynthesis; E, oxidoreductase; F, ABC transporter; and G, transporter. It also included mapping of RNA reads to di erent genes of multimodular NRPS gene clusters of C. fimbriata, H. moniliformis, and H. omanensis. A, nonribosomal peptide synthetase; B, orntithine monooxygenase; C, endothiapepsin; D, RNA polymerase transcription subunit; and E, aldehyde dehydrogenase. Reads in green and red represent forward and reverse orientation, respectively. | en_ZA |
dc.description.abstract | In filamentous fungi, genes in secondary metabolite biosynthetic pathways are generally clustered. In the case of those pathways involved in nonribosomal peptide production, a nonribosomal peptide synthetase (NRPS) gene is commonly found as a main element of the cluster. Large multifunctional enzymes are encoded by members of this gene family that produce a broad spectrum of bioactive compounds. In this research, we applied genome-based identification of nonribosomal peptide biosynthetic gene clusters in the family Ceratocystidaceae. For this purpose, we used the whole genome sequences of species from the genera Ceratocystis, Davidsoniella, Thielaviopsis, Endoconidiophora, Bretziella, Huntiella, and Ambrosiella. To identify and characterize the clusters, di erent bioinformatics and phylogenetic approaches, as well as PCR-based methods were used. In all genomes studied, two highly conserved NRPS genes (one monomodular and one multimodular) were identified and their potential products were predicted to be siderophores. Expression analysis of two Huntiella species (H. moniliformis and H. omanensis) confirmed the accuracy of the annotations and proved that the genes in both clusters are expressed. Furthermore, a phylogenetic analysis showed that both NRPS genes of the Ceratocystidaceae formed distinct and well supported clades in their respective phylograms, where they grouped with other known NRPSs involved in siderophore production. Overall, these findings improve our understanding of the diversity and evolution of NRPS biosynthetic pathways in the family Ceratocystidaceae. | en_ZA |
dc.description.department | Biochemistry | en_ZA |
dc.description.department | Forestry and Agricultural Biotechnology Institute (FABI) | en_ZA |
dc.description.department | Genetics | en_ZA |
dc.description.department | Microbiology and Plant Pathology | en_ZA |
dc.description.librarian | am2020 | en_ZA |
dc.description.sponsorship | The University of Pretoria, the South African National Research Foundation (NRF) and the South African Department of Science and Technology (DST) via the Centers of Excellence program (Center of Excellence in Tree Heath Biotechnology) and the South African Research Chairs Initiative | en_ZA |
dc.description.uri | www.mdpi.com/journal/genes | en_ZA |
dc.description.uri | http://www.mdpi.com/journal/genes | en_ZA |
dc.identifier.citation | Sayari, M., Van der Nest, M.A., Steenkamp, E.T. et al. 2019, 'Distribution and evolution of nonribosomal peptide synthetase gene clusters in the Ceratocystidaceae', Genes, vol. 10, art. 328, pp. 1-17. | en_ZA |
dc.identifier.issn | 2073-4425 (online) | |
dc.identifier.other | 10.3390/genes10050328 | |
dc.identifier.uri | http://hdl.handle.net/2263/75854 | |
dc.language.iso | en | en_ZA |
dc.publisher | MDPI Publishing | en_ZA |
dc.rights | © 2019 by the authors. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license. | en_ZA |
dc.subject | Nonribosomal peptide production | en_ZA |
dc.subject | Ceratocystidaceae | en_ZA |
dc.subject | Siderophore production | en_ZA |
dc.subject | Nonribosomal peptide synthetase (NRPS) | en_ZA |
dc.title | Distribution and evolution of nonribosomal peptide synthetase gene clusters in the Ceratocystidaceae | en_ZA |
dc.type | Article | en_ZA |