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6 Publications visible to you, out of a total of 6
Dissimilar pigment regulation in Serpula lacrymans and Paxillus involutus during inter-kingdom interactions.

Abstract (Expand)

Production of basidiomycete atromentin-derived pigments like variegatic acid (pulvinic acid-type) and involutin (diarylcyclopentenone) from the brown-rotter Serpula lacrymans and the ectomycorrhiza-forming … Paxillus involutus, respectively, is induced by complex nutrition, and in the case of S. lacrymans, bacteria. Pigmentation in S. lacrymans was stimulated by 13 different bacteria and cell-wall-damaging enzymes (lytic enzymes and proteases), but not by lysozyme or mechanical damage. The use of protease inhibitors with Bacillus subtilis or heat-killed bacteria during co-culturing with S. lacrymans significantly reduced pigmentation indicating that enzymatic hyphal damage and/or released peptides, rather than mechanical injury, was the major cause of systemic pigment induction. Conversely, no significant pigmentation by bacteria was observed from P. involutus. We found additional putative transcriptional composite elements of atromentin synthetase genes in P. involutus and other ectomycorrhiza-forming species that were absent from S. lacrymans and other brown-rotters. Variegatic and its precursor xerocomic acid, but not involutin, in return inhibited swarming and colony biofilm spreading of Bacillus subtilis, but did not kill B. subtilis. We suggest that dissimilar pigment regulation by fungal lifestyle was a consequence of pigment bioactivity and additional promoter motifs. The focus on basidiomycete natural product gene induction and regulation will assist in future studies to determine global regulators, signalling pathways and associated transcription factors of basidiomycetes.

Authors: J. P. Tauber, R. Gallegos-Monterrosa, A. T. Kovacs, E. Shelest, D. Hoffmeister

Date Published: 6th Dec 2017

Publication Type: Journal

Transcription Factors in Fungi: TFome Dynamics, Three Major Families, and Dual-Specificity TFs.

Abstract (Expand)

Transcription factors (TFs) are essential regulators of gene expression in a cell; the entire repertoire of TFs (TFome) of a species reflects its regulatory potential and the evolutionary history of … the regulatory mechanisms. In this work, I give an overview of fungal TFs, analyze TFome dynamics, and discuss TF families and types of particular interest. Whole-genome annotation of TFs in more than 200 fungal species revealed ~80 families of TFs that are typically found in fungi. Almost half of the considered genomes belonged to basidiomycetes and zygomycetes, which have been underrepresented in earlier annotations due to dearth of sequenced genomes. The TFomes were analyzed in terms of expansion strategies genome- and lineage-wise. Generally, TFomes are known to correlate with genome size; but what happens to particular families when a TFome is expanding? By dissecting TFomes into single families and estimating the impact of each of them, I show that in fungi the TFome increment is largely limited to three families (C6 Zn clusters, C2H2-like Zn fingers, and homeodomain-like). To see whether this is a fungal peculiarity or a ubiquitous eukaryotic feature, I also analyzed metazoan TFomes, where I observed a similar trend (limited number of TFome-shaping families) but also some important differences connected mostly with the increased complexity in animals. The expansion strategies of TF families are lineage-specific; I demonstrate how the patterns of the TF families' distributions, designated as "TF signatures," can be used as a taxonomic feature, e.g., for allocation of uncertain phyla. In addition, both fungal and metazoan genomes contain an intriguing type of TFs. While usually TFs have a single DNA-binding domain, these TFs possess two (or more) different DNA-binding specificities. I demonstrate that dual-specific TFs comprising various combinations of all major TF families are a typical feature of fungal and animal genomes and have an interesting evolutionary history involving gene duplications and domain losses.

Author: E. Shelest

Date Published: 20th May 2017

Publication Type: Not specified

antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification.

Abstract (Expand)

Many antibiotics, chemotherapeutics, crop protection agents and food preservatives originate from molecules produced by bacteria, fungi or plants. In recent years, genome mining methodologies have been … widely adopted to identify and characterize the biosynthetic gene clusters encoding the production of such compounds. Since 2011, the 'antibiotics and secondary metabolite analysis shell-antiSMASH' has assisted researchers in efficiently performing this, both as a web server and a standalone tool. Here, we present the thoroughly updated antiSMASH version 4, which adds several novel features, including prediction of gene cluster boundaries using the ClusterFinder method or the newly integrated CASSIS algorithm, improved substrate specificity prediction for non-ribosomal peptide synthetase adenylation domains based on the new SANDPUMA algorithm, improved predictions for terpene and ribosomally synthesized and post-translationally modified peptides cluster products, reporting of sequence similarity to proteins encoded in experimentally characterized gene clusters on a per-protein basis and a domain-level alignment tool for comparative analysis of trans-AT polyketide synthase assembly line architectures. Additionally, several usability features have been updated and improved. Together, these improvements make antiSMASH up-to-date with the latest developments in natural product research and will further facilitate computational genome mining for the discovery of novel bioactive molecules.

Authors: K. Blin, T. Wolf, M. G. Chevrette, X. Lu, C. J. Schwalen, S. A. Kautsar, H. G. Suarez Duran, E. L. C. de Los Santos, H. U. Kim, M. Nave, J. S. Dickschat, D. A. Mitchell, E. Shelest, R. Breitling, E. Takano, S. Y. Lee, T. Weber, M. H. Medema

Date Published: 2nd May 2017

Publication Type: Not specified

Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus.

Abstract (Expand)

BACKGROUND: The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent … carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus. RESULTS: We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli. CONCLUSIONS: Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.

Authors: R. P. de Vries, R. Riley, A. Wiebenga, G. Aguilar-Osorio, S. Amillis, C. A. Uchima, G. Anderluh, M. Asadollahi, M. Askin, K. Barry, E. Battaglia, O. Bayram, T. Benocci, S. A. Braus-Stromeyer, C. Caldana, D. Canovas, G. C. Cerqueira, F. Chen, W. Chen, C. Choi, A. Clum, R. A. Dos Santos, A. R. Damasio, G. Diallinas, T. Emri, E. Fekete, M. Flipphi, S. Freyberg, A. Gallo, C. Gournas, R. Habgood, M. Hainaut, M. L. Harispe, B. Henrissat, K. S. Hilden, R. Hope, A. Hossain, E. Karabika, L. Karaffa, Z. Karanyi, N. Krasevec, A. Kuo, H. Kusch, K. LaButti, E. L. Lagendijk, A. Lapidus, A. Levasseur, E. Lindquist, A. Lipzen, A. F. Logrieco, A. MacCabe, M. R. Makela, I. Malavazi, P. Melin, V. Meyer, N. Mielnichuk, M. Miskei, A. P. Molnar, G. Mule, C. Y. Ngan, M. Orejas, E. Orosz, J. P. Ouedraogo, K. M. Overkamp, H. S. Park, G. Perrone, F. Piumi, P. J. Punt, A. F. Ram, A. Ramon, S. Rauscher, E. Record, D. M. Riano-Pachon, V. Robert, J. Rohrig, R. Ruller, A. Salamov, N. S. Salih, R. A. Samson, E. Sandor, M. Sanguinetti, T. Schutze, K. Sepcic, E. Shelest, G. Sherlock, V. Sophianopoulou, F. M. Squina, H. Sun, A. Susca, R. B. Todd, A. Tsang, S. E. Unkles, N. van de Wiele, D. van Rossen-Uffink, J. V. Oliveira, T. C. Vesth, J. Visser, J. H. Yu, M. Zhou, M. R. Andersen, D. B. Archer, S. E. Baker, I. Benoit, A. A. Brakhage, G. H. Braus, R. Fischer, J. C. Frisvad, G. H. Goldman, J. Houbraken, B. Oakley, I. Pocsi, C. Scazzocchio, B. Seiboth, P. A. vanKuyk, J. Wortman, P. S. Dyer, I. V. Grigoriev

Date Published: 16th Feb 2017

Publication Type: Not specified

CASSIS and SMIPS: promoter-based prediction of secondary metabolite gene clusters in eukaryotic genomes

Abstract (Expand)

MOTIVATION: Secondary metabolites (SM) are structurally diverse natural products of high pharmaceutical importance. Genes involved in their biosynthesis are often organized in clusters, i.e., are … co-localized and co-expressed. In silico cluster prediction in eukaryotic genomes remains problematic mainly due to the high variability of the clusters' content and lack of other distinguishing sequence features. RESULTS: We present Cluster Assignment by Islands of Sites (CASSIS), a method for SM cluster prediction in eukaryotic genomes, and Secondary Metabolites by InterProScan (SMIPS), a tool for genome-wide detection of SM key enzymes ('anchor' genes): polyketide synthases, non-ribosomal peptide synthetases and dimethylallyl tryptophan synthases. Unlike other tools based on protein similarity, CASSIS exploits the idea of co-regulation of the cluster genes, which assumes the existence of common regulatory patterns in the cluster promoters. The method searches for 'islands' of enriched cluster-specific motifs in the vicinity of anchor genes. It was validated in a series of cross-validation experiments and showed high sensitivity and specificity. AVAILABILITY AND IMPLEMENTATION: CASSIS and SMIPS are freely available at https://sbi.hki-jena.de/cassis CONTACT: thomas.wolf@leibniz-hki.de or ekaterina.shelest@leibniz-hki.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Authors: T. Wolf, V. Shelest, N. Nath,

Date Published: 9th Dec 2015

Publication Type: Not specified

Multimodular type I polyketide synthases in algae evolve by module duplications and displacement of AT domains in trans

Abstract (Expand)

BACKGROUND: Polyketide synthase (PKS) catalyzes the biosynthesis of polyketides, which are structurally and functionally diverse natural products in microorganisms and plants. Here, we have analyzed … available full genome sequences of microscopic and macroscopic algae for the presence of type I PKS genes. RESULTS: Type I PKS genes are present in 15 of 32 analyzed algal species. In chlorophytes, large proteins in the MDa range are predicted in most sequenced species, and PKSs with free-standing acyltransferase domains (trans-AT PKSs) predominate. In a phylogenetic tree, PKS sequences from different algal phyla form clades that are distinct from PKSs from other organisms such as non-photosynthetic protists or cyanobacteria. However, intermixing is observed in some cases, for example polyunsaturated fatty acid (PUFA) and glycolipid synthases of various origins. Close relationships between type I PKS modules from different species or between modules within the same multimodular enzyme were identified, suggesting module duplications during evolution of algal PKSs. In contrast to type I PKSs, nonribosomal peptide synthetases (NRPSs) are relatively rare in algae (occurrence in 7 of 32 species). CONCLUSIONS: Our phylogenetic analysis of type I PKSs in algae supports an evolutionary scenario whereby integrated AT domains were displaced to yield trans-AT PKSs. Together with module duplications, the displacement of AT domains may constitute a major mechanism of PKS evolution in algae. This study advances our understanding of the diversity of eukaryotic PKSs and their evolutionary trajectories.

Authors: , N. Heimerl, M. Fichtner,

Date Published: 26th Nov 2015

Publication Type: Not specified

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