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Fungal cryptic gene cluster

David J Newman
In this short review, I am discussing the relatively recent awareness of the role of symbionts in plant, marine-invertebrates and fungal areas. It is now quite obvious that in marine-invertebrates, a majority of compounds found are from either as yet unculturable or poorly culturable microbes, and techniques involving "state of the art" genomic analyses and subsequent computerized analyses are required to investigate these interactions. In the plant kingdom evidence is amassing that endophytes (mainly fungal in nature) are heavily involved in secondary metabolite production and that mimicking the microbial interactions of fermentable microbes leads to involvement of previously unrecognized gene clusters (cryptic clusters is one name used), that when activated, produce previously unknown bioactive molecules...
2016: Frontiers in Microbiology
Pranatchareeya Chankhamjon, Yuta Tsunematsu, Mie Ishida-Ito, Yuzuka Sasa, Florian Meyer, Daniela Boettger-Schmidt, Barbara Urbansky, Klaus-Dieter Menzel, Kirstin Scherlach, Kenji Watanabe, Christian Hertweck
The regioselective functionalization of non-activated carbon atoms such as aliphatic halogenation is a major synthetic challenge. A novel multifunctional enzyme catalyzing the geminal dichlorination of a methyl group was discovered in Aspergillus oryzae (Koji mold), an important fungus that is widely used for Asian food fermentation. A biosynthetic pathway encoded on two different chromosomes yields mono- and dichlorinated polyketides (diaporthin derivatives), including the cytotoxic dichlorodiaporthin as the main product...
September 19, 2016: Angewandte Chemie
Lena Studt, Sarah M Rösler, Immo Burkhardt, Birgit Arndt, Michael Freitag, Hans-Ulrich Humpf, Jeroen S Dickschat, Bettina Tudzynski
Filamentous fungi produce a vast array of secondary metabolites (SMs) and some play a role in agriculture or pharmacology. Sequencing of the rice pathogen Fusarium fujikuroi revealed the presence of far more SM-encoding genes than known products. SM production is energy-consuming and thus tightly regulated, leaving the majority of SM gene clusters silent under laboratory conditions. One important regulatory layer in SM biosynthesis involves histone modifications that render the underlying genes either silent or poised for transcription...
November 2016: Environmental Microbiology
Hsu-Hua Yeh, Manmeet Ahuja, Yi-Ming Chiang, C Elizabeth Oakley, Shauna Moore, Olivia Yoon, Heather Hajovsky, Jin-Woo Bok, Nancy P Keller, Clay C C Wang, Berl R Oakley
Fungal genome projects are revealing thousands of cryptic secondary metabolism (SM) biosynthetic gene clusters that encode pathways that potentially produce valuable compounds. Heterologous expression systems should allow these clusters to be expressed and their products obtained, but approaches are needed to identify the most valuable target clusters. The inp cluster of Aspergillus nidulans contains a gene, inpE, that encodes a proteasome subunit, leading us to hypothesize that the inp cluster produces a proteasome inhibitor and inpE confers resistance to this compound...
August 19, 2016: ACS Chemical Biology
Chi-Ching Tsang, Jasper F W Chan, Wai-Mei Pong, Jonathan H K Chen, Antonio H Y Ngan, Mei Cheung, Christopher K C Lai, Dominic N C Tsang, Susanna K P Lau, Patrick C Y Woo
"Engyodontium album" is an environmental saprobic mould and an emerging opportunistic pathogen able to cause both superficial and systemic infections. In this study, we isolated a mould from the skin lesion biopsy specimen of the right shin in a patient who received renal transplantation for end-stage renal failure with prednisolone, tacrolimus, and azathioprine immunosuppressant therapy. Histology of the skin biopsy showed mild squamous hyperplasia and neutrophilic infiltrate in the epidermis, active chronic inflammation in the dermis, and fat necrosis in the subcutis, with numerous fungal elements within the serum crusts...
October 1, 2016: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
Koji Narita, Ryota Chiba, Atsushi Minami, Motoichiro Kodama, Isao Fujii, Katsuya Gomi, Hideaki Oikawa
Heterologous expression of four candidate genes found in ophiobolin gene clusters from three fungal strains was employed to elucidate the late-stage biosynthetic pathway of phytotoxin ophiobolin. Expression of oblBAc (cytochrome P450) from the cryptic gene cluster gave unexpected products, and that of oblBBm/oblBEv from the gene cluster of ophiobolin producers, with oblDBm as the transporter, yielded intermediate ophiobolin C through an unusual four-step oxidation process. The observation made in this study may provide a useful guideline for the elucidation of genuine biosynthetic pathways of natural products...
May 6, 2016: Organic Letters
Alexandra A Soukup, Nancy P Keller, Philipp Wiemann
Filamentous fungi are historically known as rich sources for production of biologically active natural products, so-called secondary metabolites. One particularly pharmaceutically relevant chemical group of secondary metabolites is the nonribosomal peptides synthesized by nonribosomal peptide synthetases (NRPSs). As most of the fungal NRPS gene clusters leading to production of the desired molecules are not expressed under laboratory conditions, efforts to overcome this impediment are crucial to unlock the full chemical potential of each fungal species...
2016: Methods in Molecular Biology
Scott Griffiths, Benedetta Saccomanno, Pierre J G M de Wit, Jérôme Collemare
Cladosporium fulvum is a non-obligate biotrophic fungal tomato pathogen for which fifteen secondary metabolite (SM) gene clusters were previously identified in its genome. However, most of these SM biosynthetic pathways remain cryptic during growth in planta and in different in vitro conditions. The sole SM produced in vitro is the pigment cladofulvin. In this study, we attempted to activate cryptic pathways in order to identify new compounds produced by C. fulvum. For this purpose, we manipulated orthologues of the global regulators VeA, LaeA and HdaA known to regulate SM biosynthesis in other fungal species...
November 2015: Fungal Genetics and Biology: FG & B
Daniel Montiel, Hahk-Soo Kang, Fang-Yuan Chang, Zachary Charlop-Powers, Sean F Brady
Large-scale sequencing of prokaryotic (meta)genomic DNA suggests that most bacterial natural product gene clusters are not expressed under common laboratory culture conditions. Silent gene clusters represent a promising resource for natural product discovery and the development of a new generation of therapeutics. Unfortunately, the characterization of molecules encoded by these clusters is hampered owing to our inability to express these gene clusters in the laboratory. To address this bottleneck, we have developed a promoter-engineering platform to transcriptionally activate silent gene clusters in a model heterologous host...
July 21, 2015: Proceedings of the National Academy of Sciences of the United States of America
Kristian F Nielsen, Thomas O Larsen
Having entered the Genomic Era, it is now evident that the biosynthetic potential of filamentous fungi is much larger than was thought even a decade ago. Fungi harbor many cryptic gene clusters encoding for the biosynthesis of polyketides, non-ribosomal peptides, and terpenoids - which can all undergo extensive modifications by tailoring enzymes - thus potentially providing a large array of products from a single pathway. Elucidating the full chemical profile of a fungal species is a challenging exercise, even with elemental composition provided by high-resolution mass spectrometry (HRMS) used in combination with chemical databases (e...
2015: Frontiers in Microbiology
Sylvie Pažoutová, Kamila Pešicová, Milada Chudíčková, Petr Šrůtka, Miroslav Kolařík
Claviceps purpurea is an ovarian parasite infecting grasses (Poaceae) including cereals and forage plants. This fungus produces toxic alkaloids and consumption of contaminated grains can cause ergotism in humans and other mammals. Recent molecular genetics studies have indicated that it included three cryptic species (G1, G2, G3). In this study, reproductive isolation amongst these groups and among material from Phragmites and Molinia was tested using gene flow statistics for five polymorphic loci, and to support these data, phylogenetic affiliations based on gene trees and a multigene phylogeny were used...
January 2015: Fungal Biology
Fang Li, Bo Wang, Long Wang, Bin Cao
One hundred isolates of Aspergillus fumigatus sensu lato mainly from China, as well as from Australia, France, India, Indonesia, Ireland, UK, and USA were analyzed to infer their sequence types (STs) and population diversity based on partial calmodulin, calcineurin regulatory subunit B, beta-tubulin, cytochrome C and calcineurin catalytic subunit A genes as well as their mating types, using ClonalFrame, Structure and MEGA software. Our results inferred 48 STs and showed that most of the STs or lineages evolved independently and without clear population structure among them...
October 2014: Mycopathologia
C E Negri, S S Gonçalves, H Xafranski, M D Bergamasco, V R Aquino, P T O Castro, A L Colombo
Aspergillus spp. are among the most common causes of opportunistic invasive fungal infections in tertiary care hospitals. Little is known about the prevalence and in vitro susceptibility of Aspergillus species in Latin America, because there are few medical centers able to perform accurate identification at the species level. The purpose of this study was to analyze the distribution of cryptic and rare Aspergillus species among clinical samples from 133 patients with suspected aspergillosis admitted in 12 medical centers in Brazil and to analyze the in vitro activity of different antifungal drugs...
October 2014: Journal of Clinical Microbiology
Eva-Maria Niehaus, Slavica Janevska, Katharina W von Bargen, Christian M K Sieber, Henning Harrer, Hans-Ulrich Humpf, Bettina Tudzynski
The fungus F. fujikuroi is well known for its production of gibberellins causing the 'bakanae' disease of rice. Besides these plant hormones, it is able to produce other secondary metabolites (SMs), such as pigments and mycotoxins. Genome sequencing revealed altogether 45 potential SM gene clusters, most of which are cryptic and silent. In this study we characterize a new non-ribosomal peptide synthetase (NRPS) gene cluster that is responsible for the production of the cyclic tetrapeptide apicidin F (APF). This new SM has structural similarities to the known histone deacetylase inhibitor apicidin...
2014: PloS One
Xiao-Long Yang, Takayoshi Awakawa, Toshiyuki Wakimoto, Ikuro Abe
Induced production of tetronate derivatives: We activated a dormant PKS-NRPS gene cluster in Aspergillus niger ATCC 1015 by expressing its dedicated transcription activator (caaR). As a result, the transformant expressing caaR produces three acyltetronate derivatives: carlosic acid (1), agglomerin F (2), and carlosic acid methyl ester (3).
July 21, 2014: Chembiochem: a European Journal of Chemical Biology
Ye Wang, Lynette Lim, Lina Madilao, Ljerka Lah, Joerg Bohlmann, Colette Breuil
To successfully colonize and eventually kill pine trees, Grosmannia clavigera (Gs cryptic species), the main fungal pathogen associated with the mountain pine beetle (Dendroctonus ponderosae), has developed multiple mechanisms to overcome host tree chemical defenses, of which terpenoids are a major component. In addition to a monoterpene efflux system mediated by a recently discovered ABC transporter, Gs has genes that are highly induced by monoterpenes and that encode enzymes that modify or utilize monoterpenes [especially (+)-limonene]...
August 2014: Applied and Environmental Microbiology
Susanne Altermann, Steven D Leavitt, Trevor Goward, Matthew P Nelsen, H Thorsten Lumbsch
The inclusion of molecular data is increasingly an integral part of studies assessing species boundaries. Analyses based on predefined groups may obscure patterns of differentiation, and population assignment tests provide an alternative for identifying population structure and barriers to gene flow. In this study, we apply population assignment tests implemented in the programs STRUCTURE and BAPS to single nucleotide polymorphisms from DNA sequence data generated for three previous studies of the lichenized fungal genus Letharia...
2014: PloS One
Maisa Ciampi-Guillardi, Cristina Baldauf, Anete Pereira Souza, Geraldo José Silva-Junior, Lilian Amorim
Citrus crops in São Paulo State, Brazil, have been severely affected by postbloom fruit drop disease (PFD), which is caused by Colletotrichum acutatum. This disease leads to the drop of up to 100% of young fruits. Previous studies have assumed that this pathogen exhibits a clonal reproductive mode, although no population genetic studies have been conducted so far. Thus, the genetic structure of six C. acutatum populations from sweet orange orchards showing PFD symptoms was determined using nine microsatellite markers, enabling inference on predominant mode of reproduction...
July 2014: Phytopathology
Christoffer B Harder, Thomas Læssøe, Tobias G Frøslev, Flemming Ekelund, Søren Rosendahl, Rasmus Kjøller
Phylogenetic analyses of Mycena sect. Calodontes using ITS previously suggested ten cryptic monophyletic ITS lineages within the Mycena pura morphospecies. Here, we compare ITS data (645 bp incl. gaps) from 46 different fruit bodies that represent the previously described ITS diversity with partial tEF-1-α (423 bp) and RNA polymerase II (RPB1) (492 bp) sequence data to test the genealogical concordance. While neither of the markers were in complete topological agreement, the branches differing between the tEF and RPB1 trees had a low bootstrap (<50) support, and the partition homogeneity incongruence length difference (ILD) tests were not significant...
November 2013: Fungal Biology
Franck O P Stefani, Rodney H Jones, Tom W May
This study aims to delimit species of Australian dermocyboid fungi (Cortinarius, Agaricales) using genealogical concordance on well-characterised phenotypic species and to assess the utility of seven loci for DNA barcoding Australian Cortinarius taxa. Eighty-six collections of dermocyboid Cortinarius were sampled from across southern Australia. Phenotypic species were first recognised by performing clustering analyses on a comprehensive phenotypic dataset including morphological, colour and pigment data. Then phylogenetic species were delimited from the concordance of seven locus genealogies (ITS, nLSU, gpd, mcm7, rpb1, rpb2 and tef1)...
February 2014: Molecular Phylogenetics and Evolution
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