Distribution and evolution of nonribosomal peptide synthetase gene clusters in the Ceratocystidaceae

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dc.contributor.author Sayari, Mohammad
dc.contributor.author Van der Nest, Magrieta Aletta
dc.contributor.author Steenkamp, Emma Theodora
dc.contributor.author Soal, Nicole Christine
dc.contributor.author Wilken, Pieter Markus
dc.contributor.author Wingfield, Brenda D.
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


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