Distribution and evolution of nonribosomal peptide synthetase gene clusters in the Ceratocystidaceae
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Date
Authors
Sayari, Mohammad
Van der Nest, Magrieta Aletta
Steenkamp, Emma Theodora
Soal, Nicole Christine
Wilken, Pieter Markus
Wingfield, Brenda D.
Journal Title
Journal ISSN
Volume Title
Publisher
MDPI Publishing
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.
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/).
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.
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.
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).
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.
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.
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.
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.
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).
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.
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.
Keywords
Nonribosomal peptide production, Ceratocystidaceae, Siderophore production, Nonribosomal peptide synthetase (NRPS)
Sustainable Development Goals
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.