Peptaibiomics: an advanced, rapid and selective analysis of peptaibiotics/peptaibols by SPE/LC-ES-MS

Untargeted Metabolomics Sheds Light on the Secondary Metabolism of Fungi Triggered by Choline-Based Ionic Liquids

Fungal secondary metabolites constitute a rich source of yet undiscovered bioactive compounds. Their production is often silent under standard laboratory conditions, but the production of some compounds can be triggered simply by altering the cultivation conditions. The usage of an organic salt – ionic liquid – as growth medium supplement can greatly impact the biosynthesis of secondary metabolites, leading to higher diversity of compounds accumulating extracellularly. This study examines if such supplements, specifically cholinium-based ionic liquids, can support the discovery of bioactive secondary metabolites across three model species: Neurospora crassa, Aspergillus nidulans, and Aspergillus fumigatus. Enriched organic extracts obtained from medium supernatant revealed high diversity in metabolites. The supplementation led apparently to increased levels of either 1-aminocyclopropane-1-carboxylate or α-aminoisobutyric acid. The extracts where bioactive against two major foodborne bacterial strains: Staphylococcus aureus and Escherichia coli. In particular, those retrieved from N. crassa cultures showed greater bactericidal potential compared to control extracts derived from non-supplemented cultures. An untargeted mass spectrometry analysis using the Global Natural Product Social Molecular Networking tool enabled to capture the chemical diversity driven by the ionic liquid stimuli. Diverse macrolides, among other compounds, were putatively associated with A. fumigatus; whereas an unexpected richness of cyclic (depsi)peptides with N. crassa. Further studies are required to understand if the identified peptides are the major players of the bioactivity of N. crassa extracts, and to decode their biosynthesis pathways as well.

Harnessing Chemical Ecology for Environment-Friendly Crop Protection

Heavy reliance on synthetic pesticides for crop protection has become increasingly unsustainable, calling for robust alternative strategies that do not degrade the environment and vital ecosystem services. There are numerous reports of successful disease control by various microbes used in small-scale trials. However, inconsistent efficacy has hampered their large-scale application. A better understanding of how beneficial microbes interact with plants, other microbes, and the environment and which factors affect disease control efficacy is crucial to deploy microbial agents as effective and reliable pesticide alternatives. Diverse metabolites produced by plants and microbes participate in pathogenesis and defense, regulate the growth and development of themselves and neighboring organisms, help maintain cellular homeostasis under various environmental conditions, and affect the assembly and activity of plant and soil microbiomes. However, research on the metabolites associated with plant health-related processes, except antibiotics, has not received adequate attention. This review highlights several classes of metabolites known or suspected to affect plant health, focusing on those associated with biocontrol and belowground plant-microbe and microbe-microbe interactions. The review also describes how new insights from systematic explorations of the diversity and mechanism of action of bioactive metabolites can be harnessed to develop novel crop protection strategies.

Structural Diversity and Bioactivities of Peptaibol Compounds From the Longibrachiatum Clade of the Filamentous Fungal Genus Trichoderma

This study examined the structural diversity and bioactivity of peptaibol compounds produced by species from the phylogenetically separated Longibrachiatum Clade of the filamentous fungal genus Trichoderma, which contains several biotechnologically, agriculturally and clinically important species. HPLC-ESI-MS investigations of crude extracts from 17 species of the Longibrachiatum Clade (T. aethiopicum, T. andinense, T. capillare, T. citrinoviride, T. effusum, T. flagellatum, T. ghanense, T. konilangbra, T. longibrachiatum, T. novae-zelandiae, T. pinnatum, T. parareesei, T. pseudokoningii, T. reesei, T. saturnisporum, T. sinensis, and T. orientale) revealed several new and recurrent 20-residue peptaibols related to trichobrachins, paracelsins, suzukacillins, saturnisporins, trichoaureocins, trichocellins, longibrachins, hyporientalins, trichokonins, trilongins, metanicins, trichosporins, gliodeliquescins, alamethicins and hypophellins, as well as eight 19-residue sequences from a new subfamily of peptaibols named brevicelsins. Non-ribosomal peptide synthetase genes were mined from the available genome sequences of the Longibrachiatum Clade. Their annotation and product prediction were performed in silico and revealed full agreement in 11 out of 20 positions regarding the amino acids predicted based on the signature sequences and the detected amino acids incorporated. Molecular dynamics simulations were performed for structural characterization of four selected peptaibol sequences: paracelsins B, H and their 19-residue counterparts brevicelsins I and IV. Loss of position R6 in brevicelsins resulted in smaller helical structures with higher atomic fluctuation for every residue than the structures formed by paracelsins. We observed the formation of highly bent, almost hairpin-like, helical structures throughout the trajectory, along with linear conformation. Bioactivity tests were performed on the purified peptaibol extract of T. reesei on clinically and phytopathologically important filamentous fungi, mammalian cells, and Arabidopsis thaliana seedlings. Porcine kidney cells and boar spermatozoa proved to be sensitive to the purified peptaibol extract. Peptaibol concentrations ≥0.3 mg ml⁻¹ deterred the growth of A. thaliana. However, negative effects to plants were not detected at concentrations below 0.1 mg ml⁻¹, which could still inhibit plant pathogenic filamentous fungi, suggesting that those peptaibols reported here may have applications for plant protection.

New 19-Residue Peptaibols from Trichoderma Clade Viride

Trichoderma koningiopsis and T. gamsii belong to clade Viride of Trichoderma, the largest and most diverse group of this genus. They produce a wide range of bioactive secondary metabolites, including peptaibols with antibacterial, antifungal, and antiviral properties. The unusual amino acid residues of peptaibols, i.e., α-aminoisobutyric acid (Aib), isovaline (Iva), and the C-terminal 1,2-amino alcohol make them unique among peptides. In this study, the peptaibiomes of T. koningiopsis and T. gamsii were investigated by HPLC-ESI-MS. The examined strains appeared to produce 19-residue peptaibols, most of which are unknown from literature, but their amino acid sequences are similar to those of trikoningins, tricholongins, trichostrigocins, trichorzianins, and trichorzins. A new group of peptaibols detected in T. koningiopsis are described here under the name “Koningiopsin”. Trikoningin KA V, the closest peptaibol compound to the peptaibols produced by these two strains, was selected for structural investigation by short MD simulation, which revealed that many residues show high preference for left handed helix formation. The bioactivity of the peptaibol mixtures produced by T. koningiopsis and T. gamsii was tested on agar plates against bacteria, yeasts, and filamentous fungi. The results revealed characteristic differences in bioactivities towards the different groups of target microorganisms, which can be explained with the differences in their cell wall structures.

Identification of a novel fungus, Trichoderma asperellum GDFS1009, and comprehensive evaluation of its biocontrol efficacy

Due to its efficient broad-spectrum antimicrobial activity, Trichoderma has been established as an internationally recognized biocontrol fungus. In this study, we found and identified a novel strain of Trichoderma asperellum, named GDFS1009. The mycelium of T. asperellum GDFS1009 exhibits a high growth rate, high sporulation capacity, and strong inhibitory effects against pathogens that cause cucumber fusarium wilt and corn stalk rot. T. asperellum GDFS1009 secretes chitinase, glucanase, and protease, which can degrade the cell walls of fungi and contribute to mycoparasitism. The secreted xylanases are good candidates for inducing plant resistance and enhancing plant immunity against pathogens. RNA sequencing (RNA-seq) and gas chromatography-mass spectrometry (GC-MS) showed that T. asperellum GDFS1009 produces primary metabolites that are precursors of antimicrobial compounds; it also produces a variety of antimicrobial secondary metabolites, including polyketides and alkanes. In addition, this study speculated the presence of six antimicrobial peptides via ultra-performance liquid chromatography quadrupole time of flight mass spectrometry (UPLC-QTOF-MS/MS). Future studies should focus on these antimicrobial metabolites for facilitating widespread application in the field of agricultural bio-control.

Diversity Profile and Dynamics of Peptaibols Produced by Green Mould Trichoderma Species in Interactions with Their Hosts Agaricus bisporus and Pleurotus ostreatus

Certain Trichoderma species are causing serious losses in mushroom production worldwide. Trichoderma aggressivum and Trichoderma pleuroti are among the major causal agents of the green mould diseases affecting Agaricus bisporus and Pleurotus ostreatus, respectively. The genus Trichoderma is well-known for the production of bioactive secondary metabolites, including peptaibols, which are short, linear peptides containing unusual amino acid residues and being synthesised via non-ribosomal peptide synthetases (NRPSs). The aim of this study was to get more insight into the peptaibol production of T. aggressivum and T. pleuroti. HPLC/MS-based methods revealed the production of peptaibols closely related to hypomurocins B by T. aggressivum, while tripleurins representing a new group of 18-residue peptaibols were identified in T. pleuroti. Putative NRPS genes enabling the biosynthesis of the detected peptaibols could be found in the genomes of both Trichoderma species. In vitro experiments revealed that peptaibols are potential growth inhibitors of mushroom mycelia, and that the host mushrooms may have an influence on the peptaibol profiles of green mould agents.

Sequences of stilboflavin C: towards the peptaibiome of the filamentous fungus Stilbella (= Trichoderma) flavipes

Filamentous fungi of the genus Stilbella are recognized as an abundant source of naturally occurring α-aminoisobutyric acid-containing peptides. The culture broth of Stilbella (Trichoderma) flavipes CBS 146.81 yielded a mixture of peptides named stilboflavins (SF), and these were isolated and separated by preparative TLC into groups named SF-A, SF-B, and SF-C. Although all three of these groups resolved as single spots on thin-layer chromatograms, HPLC analysis revealed that each of the groups represents very microheterogeneous mixtures of closely related peptides. Here, we report on the sequence analysis of SF-C peptides, formerly isolated by preparative TLC. HPLC coupled to QqTOF-ESI-HRMS provided the sequences of 10 16-residue peptides and five 19-residue peptides, all of which were N-terminally acetylated. In contrast to the previously described SF-A and SF-B peptaibols, SF-C peptaibols contain Ser-Alaol or Ser-Leuol, which are rarely found as C-termini, and repetitive Leu-Aib-Gly sequences, which have not been detected in peptaibols before. Taking the previously determined sequences of SF-A and SF-B into account, the entirety of peptides produced by S. flavipes (the 'peptaibiome') approaches or exceeds 100 non-ribosomally biosynthesized peptaibiotics. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

Lipopeptides as therapeutics: applications and in vivo quantitative analysis

A number of novel lipopeptides have been studied for their possible therapeutic potential. These studies should be supported by the appropriate analytical tools not only for novel potential drugs but also for their metabolites, precursors and side products. Lipopeptides have specific physicochemical properties that make them successful in medical applications. However, there are some difficulties with their qualitative and quantitative analyses in biological samples. Therefore, reliable, sensitive and robust analytical methods are in high demand. The main interest of our review is to describe a selection of specific and important properties of lipopeptides, and the analytical methods currently utilized for their characterization and determination in biological samples. A comparison of the pros and cons of immunomethods versus LC-MS methods is discussed in detail.

Trichopolyn VI: a new peptaibol insecticidal compound discovered using a recombinant Saccharomyces cerevisiae screening system

In the course of searching for insecticides from soil microorganisms, we found that a fermentation broth of the fungus, Trichoderma brevicompactum FKI-6324, produced Trichopolyn VI, a new peptaibol, which possessed significant insecticidal potential. Spectroscopic analysis showed the compound to be a new trichopolyn I derivative. This paper describes the isolation, structure elucidation and biological activity of trichopolyn VI.

Transcriptomic and metabolomic profiling of ionic liquid stimuli unveils enhanced secondary metabolism in Aspergillus nidulans

BACKGROUND

The inherent potential of filamentous fungi, especially of Ascomycota, for producing diverse bioactive metabolites remains largely silent under standard laboratory culture conditions. Innumerable strategies have been described to trigger their production, one of the simplest being manipulation of the growth media composition. Supplementing media with ionic liquids surprisingly enhanced the diversity of extracellular metabolites generated by penicillia. This finding led us to evaluate the impact of ionic liquids' stimuli on the fungal metabolism in Aspergillus nidulans and how it reflects on the biosynthesis of secondary metabolites (SMs).

RESULTS

Whole transcriptional profiling showed that exposure to 0.7 M cholinium chloride or 1-ethyl-3-methylimidazolium chloride dramatically affected expression of genes encoding both primary and secondary metabolism. Both ionic liquids apparently induced stress responses and detoxification mechanisms but response profiles to each stimulus were unique. Primary metabolism was up-regulated by choline, but down-regulated by 1-ethyl-3-methylimidazolium chloride; both stimulated production of acetyl-CoA (key precursor to numerous SMs) and non proteinogenic amino acids (building blocks of bioactive classes of SMs). In total, twenty one of the sixty six described backbone genes underwent up-regulation. Accordingly, differential analysis of the fungal metabolome showed that supplementing growth media with ionic liquids resulted in ca. 40 differentially accumulated ion masses compared to control conditions. In particular, it stimulated production of monodictyphenone and orsellinic acid, otherwise cryptic. Expression levels of genes encoding corresponding polyketide biosynthetic enzymes (i.e. backbone genes) increased compared to control conditions. The corresponding metabolite extracts showed increased cell polarity modulation potential in an ex vivo whole tissue assay (The lial Live Targeted Epithelia; theLiTE™).

CONCLUSIONS

Ionic liquids, a diverse class of chemicals composed solely of ions, can provide an unexpected means to further resolve the diversity of natural compounds, guiding discovery of fungal metabolites with clinical potential.

Front line defenders of the ecological niche! Screening the structural diversity of peptaibiotics from saprotrophic and fungicolous Trichoderma/Hypocrea species

Approximately 950 individual sequences of non-ribosomally biosynthesised peptides are produced by the genus Trichoderma/Hypocrea that belong to a perpetually growing class of mostly linear antibiotic oligopeptides, which are rich in the non-proteinogenic α-aminoisobutyric acid (Aib). Thus, they are comprehensively named peptaibiotics. Notably, peptaibiotics represent ca. 80 % of the total inventory of secondary metabolites currently known from Trichoderma/Hypocrea. Their unique membrane-modifying bioactivity results from amphipathicity and helicity, thus making them ideal candidates in assisting both colonisation and defence of the natural habitats by their fungal producers. Despite this, reports on the in vivo-detection of peptaibiotics have scarcely been published in the past. In order to evaluate the significance of peptaibiotic production for a broader range of potential producers, we screened nine specimens belonging to seven hitherto uninvestigated fungicolous or saprotrophic Trichoderma/Hypocrea species by liquid chromatography coupled to electrospray high resolution mass spectrometry. Sequences of peptaibiotics found were independently confirmed by analysing the peptaibiome of pure agar cultures obtained by single-ascospore isolation from the specimens. Of the nine species examined, five were screened positive for peptaibiotics. A total of 78 peptaibiotics were sequenced, 56 (=72 %) of which are new. Notably, dihydroxyphenylalaninol and O-prenylated tyrosinol, two C-terminal residues, which have not been reported for peptaibiotics before, were found as well as new and recurrent sequences carrying the recently described tyrosinol residue at their C-terminus. The majority of peptaibiotics sequenced are 18- or 19-residue peptaibols. Structural homologies with 'classical representatives' of subfamily 1 (SF1)-peptaibiotics argue for the formation of transmembrane ion channels, which are prone to facilitate the producer capture and defence of its substratum.

The sequences of the eleven-residue peptaibiotics: suzukacillins-B

The filamentous fungus designated 'Trichoderma viride' strain 63 C-1 simultaneously produces suzukacillins (SZs), two microheterogeneous groups of peptaibols, under submerged culture conditions. Both groups are readily distinguishable by TLC: the major group is designated SZ-A, whereas the minor group with a higher Rf value is named SZ-B. The peptide mixture was obtained from a MeOH extract of the mycelium. SZ-B was separated from SZ-A by Sephadex LH-20 column chromatography. Although it provided one single spot on silica-gel TLC plates, 15 individual peptides could be separated by C8 reversed-phase (RP) HPLC, and their sequences were determined by HPLC/QqTOF-ESI-HRMS. Fourteen peptides exhibit the C-terminal sequence Pro(6) -Lxx-Lxx-Aib-Pro-Vxxol/Lxxol(11) , which is common for eleven-residue peptaibols. The remaining peptide is tentatively assigned as a ten-residue sequence, in which the C-terminal 1,2-amino alcohol is deleted, thus terminating in free proline. Nine of the peptides carry an Ac-Aib residue at the N-terminus, very frequently found in eleven-residue peptaibols. Four peptides comprise the rare Ac-Ala N-terminus, and for two peptides, N-terminal Ac-D-Iva residues were identified. One peptide contains a C-terminal residue of yet undetermined structure. Comparison with previously reported eleven-residue peptaibol sequences reveals that eight of the peptides represent new sequence analogs.

Sequences of metanicins, 20-residue peptaibols from the ascomycetous fungus CBS 597.80

Four linear 20-residue peptaibols, named metanicins (MTCs) A-D, were isolated from submerged cultures of the ascomycetous fungus CBS 597.80. Structure elucidation was performed by a combination of fast-atom-bombardment mass spectrometry (FAB-MS), electrospray ionization MS, Edman degradation of isolated fragments, and amino acid analysis by ion-exchange and gas chromatography, and enantioselective HPLC. The sequences of MTC A(B) are (amino acid exchange in B and C in parentheses): Ac-Aib-Ala-Aib-Ala-Aib-Ala-Gln-Aib-Val-Aib-Gly-Leu-Aib-Pro-Val-Aib-Aib(D-Iva)-Gln-Gln-Pheol and of MTC C(D) Ac-Aib-Ala-Aib-Ala-Aib-Ala-Gln-Aib-Val-Aib-Gly-Leu-Aib-Pro-Val-Aib-Aib(D-Iva)-Gln-Gln-Pheol (Ac, acetyl; Aib, α-aminoisobutyric acid; Iva, isovaline; Pheol, L-phenylalaninol). The peptides are related, and some of the sequences are identical, to other 20-residue peptaibols isolated from Trichoderma species. MTCs show moderate activities against Micrococcus luteus, Enterococcus faecalis, and Staphylococcus aureus, and very low activities against Bacillus subtilis. The producer has originally been identified and deposited as Metarhizium anisopliae var. anisopliae CBS 597.80. Although this identification has been withdrawn by Centralbureau voor Schimmelcultures (CBS) in the meantime, the accession number will be retained - independently from any taxonomic revisions.

Screening the biosphere: the fungicolous fungus Trichoderma phellinicola, a prolific source of hypophellins, new 17-, 18-, 19-, and 20-residue peptaibiotics

To investigate the significance of antibiotics for the producing organism(s) in the natural habitat, we screened a specimen of the fungicolous fungus Trichoderma phellinicola (syn. Hypocrea phellinicola) growing on its natural host Phellinus ferruginosus. Results revealed that a particular group of non-ribosomal antibiotic polypeptides, peptaibiotics, which contain the non-proteinogenic marker amino acid, α-aminoisobutyric acid, was biosynthesized in the natural habitat by the fungicolous producer and, consequently, released into the host. By means of liquid chromatography coupled to electrospray high-resolution time-of-flight mass spectrometry, we detected ten 20-residue peptaibols in the specimen. Sequences of peptaibiotics found in vivo were independently confirmed by analyzing the peptaibiome of an agar plate culture of T. phellinicola CBS 119283 (ex-type) grown under laboratory conditions. Notably, this strain could be identified as a potent producer of 39 new 17-, 18-, and 19-residue peptaibiotics, which display the same building scheme as the 20-residue peptaibols found in the specimen. Two of the 19-residue peptaibols are tentatively assigned to carry tyrosinol, a novel C-terminal residue, as deduced from high-resolution tandem mass-spectrometry data. For the new peptaibiotics produced by T. phellinicola, the name 'hypophellin(s)', based on the teleomorph name, is introduced.

Hypopulvins, novel peptaibiotics from the polyporicolous fungus Hypocrea pulvinata, are produced during infection of its natural hosts

In order to investigate the significance of antibiotics for the producing organism(s) in the natural habitat, we screened specimens of the polyporicolous fungus Hypocrea pulvinata growing on its natural hosts Piptoporus betulinus and Fomitopsis pinicola. Results showed that a particular group of nonribosomally biosynthesised antibiotic polypeptides, the peptaibiotics, which contain the nonproteinogenic marker amino acid α-aminoisobutyric acid (Aib), was produced in the natural habitat by the fungicolous producer and, consequently, released into the host. Using liquid chromatography coupled to electrospray high-resolution mass spectrometry we detected especially 19-, but also 11-, 18-, and 20-residue peptaibiotics in the five infected specimens analysed. Structures of peptaibiotics found were confirmed by analysing the peptaibiome of pure agar cultures obtained by single-ascospore isolation from the specimens. The 19-residue peptaibols were determined as deletion sequences of the trichosporins B lacking the Aib residue in position 6. Notably, 26 of the 28 peptaibiotics sequenced were novel; therefore the name 'hypopulvins' was introduced. Considering not only the ubiquity of both the two host species but also the highly specific association between H. pulvinata and P. betulinus/F. pinicola, and the abundance of this fungicolous species in north temperate regions of the world, a decisive role for the peptaibiotics detected in this study is predicted, which may act as mediators of the complex interactions between the basidiomycetous host and its fungicolous ascomycete 'partner'. Structural analogies of the hypopulvins, particularly with other 18-, 19-, and 20-residue peptaibiotics, suggest that the hypopulvins are forming transmembrane ion channels and could thus support the hypothesis of a parasitic lifestyle of the fungicolous producer.

Antifungal activity of extracts from endophytic fungi associated with Smallanthus maintained in vitro as autotrophic cultures and as pot plants in the greenhouse

The endophytic fungal assemblages associated with Smallanthus sonchifolius (Poepp.) H. Rob. and Smallanthus uvedalius (L.) Mack. ex Small growing in vitro autotrophic cultures and in the greenhouse were identified and evaluated for their ability to produce bioactive compounds. A total of 25 isolates were recovered that were genetically closely related to species of the genera Bionectria , Cladosporium , Colletotrichum , Fusarium , Gibberella , Hypocrea , Lecythophora , Nigrospora , Plectosphaerella , and Trichoderma . The endophytic assemblages of S. sonchifolius presented a greater diversity than the group isolated from S. uvedalius and demonstrated the presence of dominant generalist fungi. Extracts of all fungi were screened against the fungal plant pathogens. Ten extracts (41.6%) displayed antifungal activities; some of them had a broad antifungal activity. The phylotypes Lecythophora sp. 1, Lecythophora sp. 2, and Fusarium oxysporum were isolated from in vitro autotrophic cultures and displayed antifungal activity. The presence of bioactive endophytic fungi within S. sonchifolius and S. uvedalius suggests an ecological advantage against pathogenic attacks. This study revealed reduced numbers of endophytes in association with both Smallanthus species in controlled cultivation conditions compared with the endophytic communities of hosts collected in the wild environments. Even as reduced endophytic communities, these fungi continue to provide chemical protection for the host.

Translational research on Trichoderma: from 'omics to the field

Structural and functional genomics investigations are making an important impact on the current understanding and application of microbial agents used for plant disease control. Here, we review the case of Trichoderma spp., the most widely applied biocontrol fungi, which have been extensively studied using a variety of research approaches, including genomics, transcriptomics, proteomics, metabolomics, etc. Known for almost a century for their beneficial effects on plants and the soil, these fungi are the subject of investigations that represent a successful case of translational research, in which 'omics-generated novel understanding is directly translated in to new or improved crop treatments and management methods. We present an overview of the latest discoveries on the Trichoderma expressome and metabolome, of the complex and diverse biotic interactions established in nature by these microbes, and of their proven or potential importance to agriculture and industry.

Asperelines A-F, peptaibols from the marine-derived fungus Trichoderma asperellum

Fermentation of the marine-derived fungus Trichoderma asperellum, collected from the sediment of the Antarctic Penguin Island, resulted in the isolation of six new peptaibols named asperelines A-F (1-6), which are characterized by an acetylated N-terminus and a C-terminus containing an uncommon prolinol residue. Structures were determined by extensive 1D and 2D NMR ((1)H-(1)H COSY, HMQC, HMBC, NOESY) spectroscopic data analysis combined with ESIMS/MS fragmentation. The absolute configurations of the amino acid residues possessing a chiral alpha-carbon and of the prolinol residue were determined to be L and S, respectively, using a new method of (1)H NMR spectroscopic comparison of complexes formed between the chiral reagent Ru(D(4)-Por*)CO and amino acids derived from the peptaibols with those formed with reference standards.

Aib and iva in the biosphere: neither rare nor necessarily extraterrestrial

Fourty-nine species and strains of filamentous fungi of the genera Acremonium, Bionectria, Clonostachys, Emericellopsis, Hypocrea/Trichoderma, Lecythophora, Monocillium, Nectriopsis, Niesslia, Tolypocladium, and Wardomyces, deposited with the culture collection of the Centraalbureau voor Schimmelcultures (CBS) in Utrecht, The Netherlands, were grown on nutrient agar plates. Organic extracts of mycelia were analyzed after acidic total hydrolysis and derivatization by GC/SIM-MS on Chirasil-L-Val for the presence of Aib (=alpha-aminoisobutyric acid, 2-methylalanine) and DL-Iva (=isovaline, 2-ethylalanine). In 37 of the hydrolysates, Aib was detected, and in several of them D-Iva or mixtures of D- and L-Iva. Non-proteinogenic Aib, in particular, is a highly specific marker for a distinctive group of fungal polypeptides named peptaibols or, comprehensively, peptaibiotics, i.e., peptides containing Aib and displaying (anti)biotic activities. The biotic synthesis of these amino acids by filamentous fungi contradicts the still widespread belief that alpha,alpha-dialkyl-alpha-amino acids do not or rarely occur in the biosphere and, if detected, are of extraterrestrial origin. The abundant production of peptaibiotics by cosmopolitan species of microfungi has also to be considered in the discussion on the occurrence of Aib and Iva in ancient and recent sediments. The detection of trace amounts of Aib in ice samples of Antarctica that are devoid of meteorites might also be related to the presence of Aib-producing microorganisms, being either indigenous psychrophiles, or being transported and localized by mechanisms related to bioaerosols and cryoconites. The presence of microfungi being capable of producing alpha,alpha-dialkyl alpha-amino acids in terrestrial samples, and possible contamination of extraterrestrial materials are pointed out to be of relevance for the reliable interpretation of cosmogeochemical data.

The production and characterisation of trichotoxin peptaibols, by Trichoderma asperellum

Trichoderma spp. are regularly found as a constituent of the mycoflora of many soils and are noted for their antagonistic activity against bacteria and other fungi. This latter property is the basis for the widespread interest in their use in the biological control of soil-borne fungal plant pathogens. This antagonism is partly based on their ability to produce an impressive inventory of secondary metabolites. An important group of bioactive metabolites produced by Trichoderma spp. are the non-ribosomal peptides (NRPs), especially the peptaibols. A virulent antagonistic strain, T. asperellum, which had been used in biological control strategies in Malaysia and previously examined for mycolytic enzyme production, has been studied for its potential for peptaibol production. The present research demonstrated the ability of T. asperellum to produce at least two metabolites which were identified as acid trichotoxin 1704E (Ac-Aib-Gly-Aib-Leu-Aib-Gln-Aib-Aib-Aib-Ala-Ala-Aib-Pro-Leu-Aib-Iva-Glu-Vol) and neutral trichotoxin 1717A (Ac-Aib-Gly-Aib-Leu-Aib-Gln-Aib-Aib-Aib-Ala-Aib-Aib-Pro-Leu-Aib-Iva-Gln-Vol). Addition of free Aib to the culture medium enhanced the production of trichotoxins. Biological activity of these substances was investigated against Bacillus stearothermophilus. The general characteristics of peptaibols, also found in the trichotoxins, include the presence of high proportions of the uncommon amino acid Aib, the protection of the N- and C-termini by an acetyl group and reduction of the C-terminus to 2-amino alcohols, respectively, amphipathy and microheterogeneity.

Natural cyclopeptaibiotics and related cyclic tetrapeptides: structural diversity and future prospects

Linearity is not considered a prerequisite anymore, and extension of the current definition of 'peptaibiotics' to cyclic, Aib-containing peptides is proposed. Sequences and bioactivities, together with ecophysiological importance of cyclopeptaibiotics and related cyclic tetrapeptides, and their fungal-taxonomic relationships, are discussed.

Characterisation of the peptaibiome of the biocontrol fungus Trichoderma atroviride by liquid chromatography/tandem mass spectrometry

The present study describes the liquid chromatography/tandem mass spectrometry (LC/MS/MS)-based screening and characterisation of linear antibiotic alpha-aminoisobutyric acid (Aib)-containing non-ribosomal peptides (NRP) in culture samples of the filamentous fungus Trichoderma atroviride ATCC 74058. Fungal culture filtrates were enriched by solid-phase extraction (SPE) and separated by reversed-phase high-performance liquid chromatography (HPLC), prior to mass spectrometric (MS) and tandem mass spectrometric (MS/MS) analysis on a triple quadrupole-linear ion trap tandem mass spectrometer. A workflow consisting of two alternative screening strategies was applied to search for NRP. Various MS full scan and MS/MS measurement modes led to the identification of 16 trichorzianines and diagnostic in-source fragment ions of another four trichorzianines. Furthermore, we detected 15 novel Aib-containing peptides with putative molecular weights ranging from 951.7 to 1043.7 g/mol (monoisotopic masses), composed of up to 9 amino acids. While the amino acid sequences of the novel peptaibiotics showed typical microheterogeneity and consisted of the amino acids Leu/Ile, Aib, Ser, Val/Iva, Gly, Ac-Aib, Tyr and Phe, the mass increments at the C-termini of the peptides were not assignable to any residues described in the literature. The amino acid sequences were confirmed and structure proposals made for both molecule termini by high-resolution MS and MS/MS analysis. We propose the group name 'trichoatrokontins' for the newly identified peptaibiotics. As no other peptaibiotics were found in the culture samples, the peptaibiome of the investigated strain of T. atroviride consists of at least 20 trichorzianines and 15 trichoatrokontins.

Intact-cell MALDI-TOF mass spectrometry analysis of peptaibol formation by the genus Trichoderma/Hypocrea: can molecular phylogeny of species predict peptaibol structures?

Peptaibols are characteristic linear alpha-aminoisobutyrate-containing peptides produced by certain Ascomycetes, especially of the genus Hypocrea/Trichoderma [Hypocrea and Trichoderma are the names for the teleo- and anamorph forms of the same taxon; where known to occur in nature, the teleomorph is used to name the species. To aid the inexperienced reader, both names (the less well known one in parentheses) are given at the first mention of each species.] Here we have investigated whether phylogenetic relationships within Trichoderma permit a prediction of the peptaibol production profiles. To this end, representative strains from a third (28) of the known species of Trichoderma, identified by the sequences of diagnostic genes and covering most clades of the established multilocus phylogeny of Trichoderma/Hypocrea, were investigated by intact-cell MALDI-TOF mass spectrometry. Peptaibols were detected in all strains, and some strains were found to produce up to five peptide families of different sizes. Comparison of the data with phylogenies derived from rRNA spacer regions (ITS1 and 2) and RNA polymerase subunit B (rpb2) gene sequences did not show a strict correlation with the types and sequences of the peptaibols produced, but the production of some groups of peptaibols appears to be found only in some clades or sections of the genus, which could be used for more targeted screening of novel compounds of this type. In an analysis of peptaibol structures, we have defined conserved key positions and have further identified and compared sequences of the corresponding adenylate domains within non-ribosomal peptide synthetases producing trichovirins, paracelsins and atroviridins. These phylogenies are not concordant with those of their producers Hypocrea virens, Hypocrea jecorina and Hypocrea atroviridis as obtained from ITS1 and 2, and rpb2, respectively, and therefore hint at a complex history of peptaibol diversity.

β-Lactoglobulin as source of bioactive peptides

Beta-lactoglobulin (beta-Lg) is currently an important source of biologically active peptides. These peptides are inactive within the sequence of the precursor protein, but they can be released by in vivo or in vitro enzymatic proteolysis. Once released, these peptides play important roles in the human health, including antihypertensive, antioxidant and antimicrobial activities as well as opioid-like features and ability to decrease the body-cholesterol levels. Bioactive peptides derived from beta-Lg are currently a point of intensive research. Their structure, biological significance and mechanism of action are briefly presented and discussed in this review.

Toxicity assessment of peptaibols and contaminated sediments on Crassostrea gigas embryos

Peptaibols are known membrane-modifying peptides that were recently detected in marine sediments and mussels collected from a shellfish farming area (Fier d'Ars, Atlantic coast, France). In this investigation, embryotoxicity bioassays with oysters (Crassostrea gigas) were performed to assess acute toxicity of alamethicin and different groups of peptaibols produced by a Trichoderma longibrachiatum strain isolated from marine environment. C. gigas embryos appeared very sensitive to all the metabolites examined with higher toxic effects for long-sequence peptides (EC50 ranging from 10 to 64 nM). D-shaped larvae with mantle abnormality were particularly noticed when peptaibol concentrations increased. Disturbances of embryogenesis were also observed following exposure to organic and aqueous extract of sediments from Fier d'Ars (EC50=42.4 and 6.6 g L(-1) dry weight, respectively). Although peptaibol concentrations measured in these sediments could explain only a part of the toxic effects observed, this study suggests that these mycotoxins can induce larval abnormalities in a population of exposed animals at environmentally realistic concentrations. Their detection in coastal areas devoted to bivalve culture should be taken into account.

Peptaibiomics: microheterogeneity, dynamics, and sequences of trichobrachins, peptaibiotics from Trichoderma parceramosum Bissett (T. longibrachiatum Rifai)

From the culture broth of the filamentous fungus Trichoderma parceramosum, strain CBS 936.69, a mixture of polypeptide antibiotics (pepaibiotics), named trichobrachin (TB), was isolated. Three major groups designated TB I, TB II, and TB III could be separated and isolated by preparative TLC on silica gel. Individual peptides of these three groups were sequenced by on-line LC/ESI-MS(n). The mixture of N-acetylated peptides comprises ten 19-residue peptides with a free C-terminal Gln residue (TB I peptides), two 18-residue peptides with a free C-terminal Gln residue (TB II 1 and 2), seven 20-residue peptides with a C-terminal amide-bound phenylalaninol (TB II 3-10), and 34 eleven-residue peptides with either a C-terminal leucinol or isoleucinol or valinol (TB III 1-34). Monitoring production and degradation of peptaibiotics in a pilot experiment revealed that the biosynthesis of TB II and TB III peptides starts two days after the beginning of fermentation. After five days of fermentation, the concentration of TB II decreased, whereas the amount of TB I increased. This observation unequivocally demonstrates that those two 18-residue TB I and TB II peptides with the free carboxy terminus result from enzymatic C-terminal degradation of the 20-residue TB II peptides. In analogy to the technical terms proteome and proteomics, the terms peptaibiome and peptaibiomics have recently been proposed for the entirety and dynamics of the Aib-containing peptides (comprehensively named peptaibiotics). Consequently, the entire peptaibiome of T. parceramosum grown under submerse conditions in shake-flasks for five days comprises at least 54 peptides differing in main-chain length and microheterogeneity, i.e., exchange of amino acids and the C-terminal 1,2-amino alcohol.

New Sequences, Constituents, and Producers of Peptaibiotics: An Updated Review

To date, 18 genera of imperfect and ascomycetous fungi have been recognized to produce ca. 700 individual sequences of peptaibiotics. These are linear polypeptide antibiotics which i) have a molecular weight between 500 and 2,200 Dalton, thus containing 5-21 residues; ii) show a high content of alpha-aminoisobutyric acid; iii) are characterized by the presence of other nonproteinogenic amino acids and/or lipoamino acids; iv) possess an acylated N-terminus, and v) have a C-terminal residue that, in most of them, consists of a free or acetylated amide-bonded 1,2-amino alcohol, but might also be an amine, amide, free amino acid, 2,5-dioxopiperazine, or sugar alcohol. From April 2003 until present, ca. 300 new individual sequences of peptaibiotics have been published in the literature, but most of them have not yet been included in databases. To summarize these new sequences and novel constituents, as well as to introduce fungal species hitherto unknown as producers of peptaibiotics, the relevant literature is reviewed. Furthermore, ecophysiological and taxonomic aspects of the producing fungi are discussed.

Peptaibols of trichoderma

The fungal genus Trichoderma has various applications in industry and in medicine, and several species have economic importance as sources of enzymes, antibiotics, plant growth promoters, decomposers of xenobiotics, and as commercial biofungicides. Peptaibiotics and peptaibols are a class of linear peptides synthesized by such fungi, and more than 300 have been described to date. Of this class, those compounds exhibiting antimicrobial activity are referred to as antibiotic peptides. In this review, the biosynthesis, fermentation, structure elucidation (by MS and NMR techniques in particular) and biological activity of antibiotic peptides from Trichoderma species are described.

Profiling of trichorzianines in culture samples of Trichoderma atroviride by liquid chromatography/tandem mass spectrometry

Peptaibols are bioactive linear peptides of 5-20 amino acid residues and contain specific non-proteinogenic amino acids such as alpha-aminoisobutyric acid (Aib). They are antibiotic secondary metabolites of moulds belonging predominantly to the genus Trichoderma, some species of which are successfully used as biocontrol organisms to fight against plant diseases. In the present study we developed a profiling method for the relative quantification of 16 trichorzianine peptaibols in culture samples of T. atroviride and the comparison of their expression patterns by liquid chromatography/electrospray ionisation tandem mass spectrometry (LC/ESI-MS/MS). The method is based on selected reaction monitoring (SRM) in a triple-quadrupole tandem mass spectrometer using three SRM transitions per compound. The trichorzianines were enriched by solid-phase extraction (SPE) on C(18) cartridges. SPE recoveries were evaluated for diluted trichorzianine standard solutions and ranged from 72-97%. Suppression of the ionisation of the peptaibols in the ESI source ranged from 67-128% for most of the trichorzianines in culture filtrates of two different strains of T. atroviride and in spiked culture medium. In the case of trichorzianines TA Vb, TA VIa and TA VIb the presence of matrix components in the fungal culture samples caused a reduction of the SRM signal, with intensities between 34% and 56% relative to pure standard solutions. Finally, the profiling method was successfully applied to culture samples of T. atroviride P1 wild-type and two deletion mutants showing different trichorzianine expression patterns characteristic for the investigated fungal strains. This is the first LC-SRM profiling method for peptaibols for the investigation of peptaibol expression patterns in fungal culture samples.