scholarly journals Metabolomic Analysis of The Chemical Diversity of South Africa Leaf Litter Fungal Species Using an Epigenetic Culture-Based Approach

Molecules ◽  
2021 ◽  
Vol 26 (14) ◽  
pp. 4262
Author(s):  
Rachel Serrano ◽  
Víctor González-Menéndez ◽  
Germán Martínez ◽  
Clara Toro ◽  
Jesús Martín ◽  
...  
Keyword(s):  
South Africa ◽  
Genome Mining ◽  
Fungal Species ◽  
Chemical Diversity ◽  
Fermentation Conditions ◽  
Metabolite Profiles ◽  
Different Populations ◽  
Fungal Genomes ◽  
Microbial Natural Products ◽  
Fermentation Media

Microbial natural products are an invaluable resource for the biotechnological industry. Genome mining studies have highlighted the huge biosynthetic potential of fungi, which is underexploited by standard fermentation conditions. Epigenetic effectors and/or cultivation-based approaches have successfully been applied to activate cryptic biosynthetic pathways in order to produce the chemical diversity suggested in available fungal genomes. The addition of Suberoylanilide Hydroxamic Acid to fermentation processes was evaluated to assess its effect on the metabolomic diversity of a taxonomically diverse fungal population. Here, metabolomic methodologies were implemented to identify changes in secondary metabolite profiles to determine the best fermentation conditions. The results confirmed previously described effects of the epigenetic modifier on the metabolism of a population of 232 wide diverse South Africa fungal strains cultured in different fermentation media where the induction of differential metabolites was observed. Furthermore, one solid-state fermentation (BRFT medium), two classic successful liquid fermentation media (LSFM and YES) and two new liquid media formulations (MCKX and SMK-II) were compared to identify the most productive conditions for the different populations of taxonomic subgroups.

scholarly journals New Method for Identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences

2021 ◽  
Vol 7 (3) ◽  
pp. 207
Author(s):  
Lene Lange ◽  
Kristian Barrett ◽  
Anne S. Meyer
Keyword(s):  
Fungal Species ◽  
Fungal Genome ◽  
Sequencing Data ◽  
Carbohydrate Active Enzymes ◽  
New Approach ◽  
Fungal Enzyme ◽  
Biomass Processing ◽  
Fungal Genomes ◽  
Robust Prediction ◽  
Fungal Kingdom

Fungal genome sequencing data represent an enormous pool of information for enzyme discovery. Here, we report a new approach to identify and quantitatively compare biomass-degrading capacity and diversity of fungal genomes via integrated function-family annotation of carbohydrate-active enzymes (CAZymes) encoded by the genomes. Based on analyses of 1932 fungal genomes the most potent hotspots of fungal biomass processing CAZymes are identified and ranked according to substrate degradation capacity. The analysis is achieved by a new bioinformatics approach, Conserved Unique Peptide Patterns (CUPP), providing for CAZyme-family annotation and robust prediction of molecular function followed by conversion of the CUPP output to lists of integrated “Function;Family” (e.g., EC 3.2.1.4;GH5) enzyme observations. An EC-function found in several protein families counts as different observations. Summing up such observations allows for ranking of all analyzed genome sequenced fungal species according to richness in CAZyme function diversity and degrading capacity. Identifying fungal CAZyme hotspots provides for identification of fungal species richest in cellulolytic, xylanolytic, pectinolytic, and lignin modifying enzymes. The fungal enzyme hotspots are found in fungi having very different lifestyle, ecology, physiology and substrate/host affinity. Surprisingly, most CAZyme hotspots are found in enzymatically understudied and unexploited species. In contrast, the most well-known fungal enzyme producers, from where many industrially exploited enzymes are derived, are ranking unexpectedly low. The results contribute to elucidating the evolution of fungal substrate-digestive CAZyme profiles, ecophysiology, and habitat adaptations, and expand the knowledge base for novel and improved biomass resource utilization.

Standing Out and Blending In: Contact-Based Research, Ethics, and Positionality

2021 ◽  
pp. 1-5
Author(s):  
Carolyn E. Holmes
Keyword(s):  
South Africa ◽  
Research Ethics ◽  
Political Science ◽  
Ethical Training ◽  
Research Outcomes ◽  
Different Populations ◽  
The Way

ABSTRACT This article explores the ethical difficulties that arise because of the interaction between fieldwork practitioners and their sites, in terms of the positionality of the researcher. What are the ethics of blending in or of standing out? This question stems from my experience of 12 months of fieldwork in South Africa in two distinct locales and among two different populations, one in which I could “pass” and another in which I was marked as various degrees of “outsider.” Drawing on this fieldwork, as well as an overview of the literature in political science on positionality, I argue that our discipline—because of the way it shapes interactions and research outcomes—must take positionality seriously in ethical training and practice.

scholarly journals Volatile organic compound patterns predict fungal trophic mode and lifestyle

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Yuan Guo ◽  
Werner Jud ◽  
Fabian Weikl ◽  
Andrea Ghirardo ◽  
Robert R. Junker ◽  
...  
Keyword(s):  
Organic Compound ◽  
Fungal Species ◽  
Chemical Diversity ◽  
Phenotypic Integration ◽  
Ecological Studies ◽  
Volatile Organic ◽  
Ecological Importance ◽  
Fungal Interactions ◽  
Computational Analyses ◽  
Different Levels

AbstractFungi produce a wide variety of volatile organic compounds (VOCs), which play central roles in the initiation and regulation of fungal interactions. Here we introduce a global overview of fungal VOC patterns and chemical diversity across phylogenetic clades and trophic modes. The analysis is based on measurements of comprehensive VOC profiles of forty-three fungal species. Our data show that the VOC patterns can describe the phyla and the trophic mode of fungi. We show different levels of phenotypic integration (PI) for different chemical classes of VOCs within distinct functional guilds. Further computational analyses reveal that distinct VOC patterns can predict trophic modes, (non)symbiotic lifestyle, substrate-use and host-type of fungi. Thus, depending on trophic mode, either individual VOCs or more complex VOC patterns (i.e., chemical communication displays) may be ecologically important. Present results stress the ecological importance of VOCs and serve as prerequisite for more comprehensive VOCs-involving ecological studies.

scholarly journals Chitin Degradation Machinery and Secondary Metabolite Profiles in the Marine Bacterium Pseudoalteromonas rubra S4059

Marine Drugs ◽  
2021 ◽  
Vol 19 (2) ◽  
pp. 108
Author(s):  
Xiyan Wang ◽  
Thomas Isbrandt ◽  
Mikael Lenz Strube ◽  
Sara Skøtt Paulsen ◽  
Maike Wennekers Nielsen ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Genetic Manipulation ◽  
Genome Mining ◽  
Hydrolytic Enzymes ◽  
Metabolite Profile ◽  
Chitinolytic Enzyme ◽  
Chitin Degradation ◽  
Metabolite Profiles ◽  
Bioactive Potential ◽  
Pseudoalteromonas Rubra

Genome mining of pigmented Pseudoalteromonas has revealed a large potential for the production of bioactive compounds and hydrolytic enzymes. The purpose of the present study was to explore this bioactivity potential in a potent antibiotic and enzyme producer, Pseudoalteromonas rubra strain S4059. Proteomic analyses (data are available via ProteomeXchange with identifier PXD023249) indicated that a highly efficient chitin degradation machinery was present in the red-pigmented P. rubra S4059 when grown on chitin. Four GH18 chitinases and two GH20 hexosaminidases were significantly upregulated under these conditions. GH19 chitinases, which are not common in bacteria, are consistently found in pigmented Pseudoalteromonas, and in S4059, GH19 was only detected when the bacterium was grown on chitin. To explore the possible role of GH19 in pigmented Pseudoalteromonas, we developed a protocol for genetic manipulation of S4059 and deleted the GH19 chitinase, and compared phenotypes of the mutant and wild type. However, none of the chitin degrading ability, secondary metabolite profile, or biofilm-forming capacity was affected by GH19 deletion. In conclusion, we developed a genetic manipulation protocol that can be used to unravel the bioactive potential of pigmented pseudoalteromonads. An efficient chitinolytic enzyme cocktail was identified in S4059, suggesting that this strain could be a candidate with industrial potential.

Peanut Web Blotch: I. Cultural Characteristics and Identity of Causal Fungus1

1984 ◽  
Vol 11 (2) ◽  
pp. 109-114 ◽  
Author(s):  
R. A. Taber ◽  
R. E. Pettit ◽  
G. L. Philley
Keyword(s):  
South Africa ◽  
Cultural Studies ◽  
Mycelial Growth ◽  
Fungal Species ◽  
Optimum Temperature ◽  
Cultural Characteristics ◽  
Foliar Disease ◽  
The Usa

Abstract A foliar disease of peanuts, previously unreported in the USA, was found in Texas in 1972. The pathogen was identified as a species of Ascochyta. Further cultural studies have revealed this fungus to be Phoma arachidicola Marasas, Pauer, and Boerema. Pycnidia form profusely at 20 C and 25 C. Pycnidiospores are borne on short pycnidiosphores and are predominantly one-celled in culture. Spores produced in pycnidia on infected leaflets become 1 septate. Large 1-septate spores, as well as an occasional 2-septate spore, may form in culture. Optimum temperature for mycelial growth in 20 C; little or no growth occurs at 5 C or above 30 C. The teleomorphic state develops in the field on fallen leaflets and can be induced to form in the laboratory on sterilized peanut leaflets between 15 and 20 C. Cultures derived from single ascospores form pseudothecia. Pycnidiospores, ascospores, and chlamydospores are all infective units. Because this fungus produces hyaline ascospores and pseudoparaphyses, it has been transferred to the genus Didymella as Didymella arachidicola (Choch.) comb. nov. Comparisons with 15 isolates causing web blotch of peanut in the USA, Argentina, and South Africa indicate that web blotch symptoms are produced by the same fungal species.

scholarly journals Recent Advances in Discovery of Lead Structures from Microbial Natural Products: Genomics- and Metabolomics-Guided Acceleration

Molecules ◽  
2021 ◽  
Vol 26 (9) ◽  
pp. 2542
Author(s):  
Linda Sukmarini
Keyword(s):  
Natural Products ◽  
Genome Mining ◽  
Screening Methods ◽  
Technological Advancement ◽  
Natural Origin ◽  
Drug Discovery And Development ◽  
New Methodologies ◽  
Analytical Instrumentation ◽  
Microbial Natural Products ◽  
Drug Leads

Natural products (NPs) are evolutionarily optimized as drug-like molecules and remain the most consistently successful source of drugs and drug leads. They offer major opportunities for finding novel lead structures that are active against a broad spectrum of assay targets, particularly those from secondary metabolites of microbial origin. Due to traditional discovery approaches’ limitations relying on untargeted screening methods, there is a growing trend to employ unconventional secondary metabolomics techniques. Aided by the more in-depth understanding of different biosynthetic pathways and the technological advancement in analytical instrumentation, the development of new methodologies provides an alternative that can accelerate discoveries of new lead-structures of natural origin. This present mini-review briefly discusses selected examples regarding advancements in bioinformatics and genomics (focusing on genome mining and metagenomics approaches), as well as bioanalytics (mass-spectrometry) towards the microbial NPs-based drug discovery and development. The selected recent discoveries from 2015 to 2020 are featured herein.

scholarly journals Uncovering the unexplored diversity of thioamidated ribosomal peptides in Actinobacteria using the RiPPER genome mining tool

2018 ◽  
Author(s):  
Javier Santos-Aberturas ◽  
Govind Chandra ◽  
Luca Frattaruolo ◽  
Rodney Lacret ◽  
Thu H. Pham ◽  
...  
Keyword(s):  
Genome Mining ◽  
Gene Clusters ◽  
Chemical Diversity ◽  
Bioactive Molecules ◽  
Post Translational Modification ◽  
Biosynthetic Gene Clusters ◽  
New Family ◽  
The Family ◽  
Modified Peptides ◽  
Mining Tool

ABSTRACTThe rational discovery of new specialized metabolites by genome mining represents a very promising strategy in the quest for new bioactive molecules. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a major class of natural product that derive from genetically encoded precursor peptides. However, RiPP gene clusters are particularly refractory to reliable bioinformatic predictions due to the absence of a common biosynthetic feature across all pathways. Here, we describe RiPPER, a new tool for the family-independent identification of RiPP precursor peptides and apply this methodology to search for novel thioamidated RiPPs in Actinobacteria. Until now, thioamidation was believed to be a rare post-translational modification, which is catalyzed by a pair of proteins (YcaO and TfuA) in Archaea. In Actinobacteria, the thioviridamide-like molecules are a family of cytotoxic RiPPs that feature multiple thioamides, and it has been proposed that a YcaO-TfuA pair of proteins also catalyzes their formation. Potential biosynthetic gene clusters encoding YcaO and TfuA protein pairs are common in Actinobacteria but the chemical diversity generated by these pathways is almost completely unexplored. A RiPPER analysis reveals a highly diverse landscape of precursor peptides encoded in previously undescribed gene clusters that are predicted to make thioamidated RiPPs. To illustrate this strategy, we describe the first rational discovery of a new family of thioamidated natural products, the thiovarsolins from Streptomyces varsoviensis.

scholarly journals Eutypa, Eutypella, and Cryptovalsa Species (Diatrypaceae) Associated with Prunus Species in South Africa

Plant Disease ◽  
2018 ◽  
Vol 102 (7) ◽  
pp. 1402-1409 ◽  
Author(s):  
Providence Moyo ◽  
Ulrike Damm ◽  
Lizel Mostert ◽  
Francois Halleen
Keyword(s):  
South Africa ◽  
Phylogenetic Analyses ◽  
Fruit Trees ◽  
Fungal Species ◽  
Stone Fruit ◽  
Prunus Species ◽  
Internal Transcribed Spacer Region ◽  
Eutypa Lata ◽  
Eutypa Dieback ◽  
Prunus Spp

Stone fruit trees (Prunus spp.) are economically important fruit trees cultivated in South Africa. These trees are often grown in close proximity to vineyards and are to a large extent affected by the same trunk disease pathogens as grapevines. The aim of the present study was to determine whether stone fruit trees are inhabited by Diatrypaceae species known from grapevines and whether these trees could act as alternative hosts for these fungal species. Isolations were carried out from symptomatic wood of Prunus species (almond, apricot, cherry, nectarine, peach, and plum) in stone fruit growing areas in South Africa. Identification of isolates was based on phylogenetic analyses of the internal transcribed spacer region and β-tubulin gene. Forty-six Diatrypaceae isolates were obtained from a total of 380 wood samples, from which five species were identified. All five species have also been associated with dieback of grapevine. The highest number of isolates was found on apricot followed by plum. No Diatrypaceae species were isolated from peach and nectarine. Eutypa lata was the dominant species isolated (26 isolates), followed by Cryptovalsa ampelina (7), Eutypa cremea (5), Eutypella citricola (5), and Eutypella microtheca (3). First reports from Prunus spp. are E. cremea, E. citricola, and E. microtheca. Pathogenicity tests conducted on apricot and plum revealed that all these species are pathogenic to these hosts, causing red-brown necrotic lesions like those typical of Eutypa dieback on apricot.

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