The production of multiple small peptaibol families by single 14-module Peptide synthetases in Trichoderma/Hypocrea

The most common sequences of peptaibiotics are 11-residue peptaibols found widely distributed in the genus Trichoderma/Hypocrea. Frequently associated are 14-residue peptaibols sharing partial sequence identity. Genome sequencing projects of three Trichoderma strains of the major clades reveal the presence of up to three types of nonribosomal peptide synthetases with 7, 14, or 18-20 amino acid-adding modules. Here, we provide evidence that the 14-module NRPS type found in T. virens, T. reesei (teleomorph Hypocrea jecorina), and T. atroviride produces both 11- and 14-residue peptaibols based on the disruption of the respective NRPS gene of T. reesei, and bioinformatic analysis of their amino acid-activating domains and modules. The sequences of these peptides may be predicted from the gene sequences and have been confirmed by analysis of families of 11- and 14-residue peptaibols from the strain 618, termed hypojecorins A (23 sequences determined, 4 new) and B (3 sequences determined, 2 new), and the recently established trichovirins A from T. virens. The distribution of 11- and 14-residue products is strain-specific and depends on growth conditions as well. Possible mechanisms of module skipping are discussed.     

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.     

Recent advances and future prospects in peptaibiotics, hydrophobin, and mycotoxin research, and their importance for chemotaxonomy of Trichoderma and Hypocrea

Fungi of the genus Trichoderma with teleomorphs in Hypocrea are abundant producers of a group of amphiphilic, non-ribosomal peptide antibiotics, which are rich in the non-proteinogenic amino acid Aib (alpha-aminoisobutyric acid). They are referred to as peptaibiotics, or peptaibols, if a 1,2-amino alcohol is present at the C-terminus. Trichoderma/Hypocrea, like other ascomycetous fungi, also produce hydrophobins, a class of small, cysteine-rich proteins. Advanced soft ionization mass spectrometric techniques such as LC-CID-MS, LC-ESI-MS(n), and IC-MALDI-TOF-MS enabled the high-throughput analysis, simultaneous detection and sequence determination of peptaibiotics and hydrophobins from minute quantities of fungal materials. Some Trichoderma species have been recognized to produce peptaibiotics as well as simple mycotoxins of the trichothecene group. The combination of sequence data of both groups of peptides with the pattern of low-molecular-weight secondary metabolites, including trichothecene-type mycotoxins, independently confirmed the results of morphological, molecular, and phylogenetic analyses. This approach established a new lineage in Trichoderma/Hypocrea, the Brevicompactum clade, comprising four new and one redescribed species. Notably, commercial preparations of single or mixed cultures of Trichoderma species, in particular T. harzianum, and T. koningii, are registered as biocontrol agents for soil and plant pathogens. In this context, it is emphasized that the four mycotoxin-producing species of the recently established Brevicompactum clade (T. brevicompactum, T. arundinaceum, T. turrialbense, and T. protrudens) are not closely related to any of the Trichoderma species currently used as biocontrol agents. Furthermore, possible health concerns about release of peptaibiotics in the biosphere are discussed with respect to their bioactivities and their use as drugs in human and veterinary medicine. Finally, future prospects regarding novel bioactivities and further research needs, including interdisciplinary taxonomic approaches, are outlined.     

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

Summary. “Proteomics” and “peptidomics” are used as technical terms to define the analysis and study of all proteins and peptides expressed in an organism or tissue. In analogy we propose the name peptaibiomics for the analysis of a group of fungal peptide antibiotics (peptaibiotics) containing the characteristic amino acid Aib (α-aminoisobutyric acid). In analogy to the peptidome the complete expression of peptaibiotics by fungal multienzyme complexes should be named the peptaibiome. Peptaibiotics are defined as peptides containing Aib and exerting a variety of bioactivities. They comprise the sub-groups of N-acetylated peptaibols, characterized also by a C-terminal amide-linked 2-amino alcohol, and lipopeptaibols having in place of an acetyl group a lipophilic fatty acid acyl group. Furthermore, lipoaminopeptides are also known with long-chain fatty acid on the N-termini, a lipoamino acid in position three and a strongly basic secondary or tertiary amine form a subgroup of mixed forms which could not be integrated in one of these three previously mentioned groups. Here we present a specific and rapid screening method on the peptaibiome applicable directly onto filamentous fungi cultured in a single Petri dish. The method comprises solid-phase extraction (SPE) of peptaibiotics followed by on-line reversed-phase HPLC coupled to an ion trap electrospray tandem mass spectrometer (ES-MS). The presence of these peptides is indicated by characteristic mass differences of Δm = 85.1 Da representing Aib-residues which can be observed in the b-series of acylium fragment ions resulting from ES-MS. Partial sequences can be deduced from the data and compared with structures compiled in electronic peptaibol data bases. The judgement is possible whether or not structures are novel, already known or related to known structures. Suitability of the method is demonstrated with the analysis of strains of Trichoderma and its teleomorph Hypocrea. New sequences of peptaibiotics are presented and those being related to established 10- to 18-residue peptaibols trichovirin, trichogin and trichotoxin, which have been described in the literature.     

Peptaibiomics: Towards a Myriad of Bioactive Peptides Containing Cα‐Dialkylamino Acids?

Fungi are generally regarded as a literally infinite resource of bioactive secondary metabolites displaying remarkable structural diversity. Research on a particular group of linear and cyclic peptide antibiotics comprehensively named peptaibiotics--as result of the abundance of the non-proteinogenic C(alpha)-dialkylated alpha-amino acids alpha-aminoisobutyric acid (Aib) and isovaline (Iva)--has been started 50 years ago. These peptides have gained constantly increasing interest because of their unique bioactivities and conformations. This review, reflecting the history of peptaibiotic research from 1958 to 2008, is focussed on introducing both the structural diversity and natural microheterogeneity of the peptaibiotics, as well as the biodiversity of their fungal producers. Recently introduced state-of-the-art methods for rapid screening and sequencing of peptaibiotics, such as peptaibiomics and intact-cell MALDI-TOF mass spectrometry, are discussed. Finally, future prospects in peptaibiotic research are presented. Owing to the ubiquity and biodiversity of the fungal producers in the biosphere, the discovery of a myriad of peptaibiotics within the next decade is predicted.     

Peptaibols and related peptaibiotics of Trichoderma. A review

Peptaibols and the related peptaibiotics are linear, amphipathic polypeptides. More than 300 of these secondary metabolites have been described to date. These compounds are composed of 5-20 amino acids and are generally produced in microheterogeneous mixtures. Peptaibols and peptaibiotics with unusual amino acid content are the result of non-ribosomal biosynthesis. Large multifunctional enzymes known as peptide synthetases assemble these molecules by the multiple carrier thiotemplate mechanism from a remarkable range of precursors, which can be N-methylated, acylated or reduced. Peptaibols and peptaibiotics show interesting physico-chemical and biological properties including the formation of pores in bilayer lipid membranes, as well as antibacterial, antifungal, occasionally antiviral activities, and may elicit plant resistance. The three-dimensional structure of peptaibols and peptaibiotics is characterized predominantly by one type of the helical motifs alpha-helix, 3(10)-helix and beta-bend ribbon spiral. The aim of this review is to summarize the data available about the biosynthesis, biological activity and conformational properties of peptaibols and peptaibiotics described from Trichoderma species.     

Peptaibol,Secondary‐Metabolite,and Hydrophobin Pattern of Commercial Biocontrol Agents Formulated with Species of the Trichoderma harzianum Complex

The production of bioactive polypeptides (peptaibiotics) in vivo is a sophisticated adaptation strategy of both mycoparasitic and saprotrophic Trichoderma species for colonizing and defending their natural habitats. This feature is of major practical importance, as the detection of peptaibiotics in plant‐protective Trichoderma species, which are successfully used against economically relevant bacterial and fungal plant pathogens, certainly contributes to a better understanding of these complex antagonistic interactions. We analyzed five commercial biocontrol agents (BCAs), namely Canna^®, Trichosan^®, Vitalin^®, Promot^® WP, and TrichoMax^®, formulated with recently described species of the Trichoderma harzianum complex, viz. T. afroharzianum, T. simmonsii, and T. guizhouense. By using the well‐established, HPLC/MS‐based peptaibiomics approach, it could unequivocally be demonstrated that all of these formulations contained new and recurrent peptaibols, i.e., peptaibiotics carrying an acetylated N‐terminus, the C‐terminus of which is reduced to a 1,2‐amino alcohol. Their chain lengths, including the amino alcohol, were 11, 14, and 18 residues, respectively. Peptaibols were also to be the dominating secondary metabolites in plate cultures of the four strains obtained from four of the Trichoderma‐ based BCAs, contributing 95% of the UHPLC‐UV/VIS peak areas and 99% of the total ion count MS peak area from solid media. Furthermore, species‐specific hydrophobins, as well as non‐peptaibiotic secondary metabolites, were detected, the latter being known for their antifungal, siderophore, or plant‐growth‐promoting activities. Notably, none of the isolates produced low‐molecular weight mycotoxins.     

Facts and challenges in the understanding of the biosynthesis of peptaibols by Trichoderma

Species of the mitosporic filamentous fungal genus Trichoderma are prominent producers of both short (7-11 residues) and long (18-20 residues) peptaibols and peptaibiotics, which are thought to be involved in their interaction with other living systems. Numerous reviews are available regarding biodiversity, structure, and mode of action of these peptide derivatives, but little emphasis has been paid to the physiology and genetics of their formation. In this review article, we used the recent knowledge on biosynthesis and production of these components to speculate on some of the unknown points. We also highlight areas where further research is most urgently needed.     

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.     

Two classes of new peptaibols are synthesized by a single non-ribosomal peptide synthetase of Trichoderma virens

Peptaibols are a group of small peptides having a high α-aminoisobutyric acid (Aib) content and produced by filamentous fungi, especially by the members of the genus Trichoderma (anamorph Hypocrea). These antibiotics are economically important for their anti-microbial and anti-cancer properties as well as ability to induce systemic resistance in plants against microbial invasion. In this study we present sequences of two classes (11-residue and 14-residue) of peptaibols produced by the biocontrol fungus Trichoderma virens. Of the 35 11-residue peptaibols sequenced, 18 are hitherto not described, and all the 53 14-residue sequences described by us here are new. We have also identified a peptaibol synthetase (non-ribosomal peptide synthetase, NRPS) with 14 complete modules in the genome of this fungus and disruption of this single gene (designated as tex2) resulted in the loss of both the classes of peptaibols. We, thus present here an unprecedented case where a single NRPS encodes for two classes of peptaibols. The new peptaibols identified here could have applications as therapeutic agents for the management of human and plant health.     

Phylogeny of the genus trichoderma based on sequence analysis of the internal transcribed spacer region 1 of the rDNA cluster

Sequences of the internal transcribed spacer region 1 (ITS1) of the ribosomal DNA were used to determine the phylogenetic relationships of species of Trichoderma sect. Pachybasium. To this end, 85 strains-including all the available ex-type strains-were analyzed. Parsimony analysis demonstrated that the section is nonmonophyletic, distributing the 85 strains among three main groups that were supported by bootstrap values. Group A comprises two clades (A1 and A2), with A1 including T. polysporum, T. piluliferum, and T. minutisporum, while A2 included T. hamatum, T. pubescens, and T. strigosum in addition to species previously included in sect. Trichoderma (i.e., T. viride, T. atroviride, and T. koningii). The ex-type strain of T. fasciculatum formed a separate branch basal to clade A. Clade B contained the sect. Pachybasium members T. harzianum, T. fertile, T. croceum, T. longipile, T. strictipile, T. tomentosum, T. oblongisporum, T. flavofuscum, T. spirale, and the anamorphs of Hypocrea semiorbis and H. cf. gelatinosa. Sequence differences among clades A1, A2, and B were in the same order of magnitude as between each of them and T. longibrachiatum, which was used as an outgroup in these analyses. Sequence differences within clades A1, A2, and B were considerably smaller: in some cases (i.e., T. virens and T. flavofuscum; T. strictipile and H. cf. gelatinosa), the ITS1-sequences were identical, suggesting conspecifity. In other cases (e.g., T. crassum and T. longipile; T. harzianum, T. inhamatum, T. croceum, T. fertile, and H. semiorbis; T. hamatum and T. pubescens; and T. viride, T. atroviride, and T. koningii) differences were in the range of 1-3 nt only, suggesting a very close phylogenetic relationship. The sequence of a previously described aggressive mushroom competitor group of T. harzianum strains (Th2) was strikingly different from that of the ex-type strain of T. harzianum and closely related species and is likely to be a separate species. Copyright 1998 Academic Press.     

New Trichobrachins, 11-residue peptaibols from a marine strain of Trichoderma longibrachiatum

A marine strain of Trichoderma longibrachiatum isolated from blue mussels (Mytilus edulis) was investigated for short peptaibol production. Various 11-residue peptaibols, obtained as microheterogenous mixtures after a chromatographic fractionation, were identified by positive mass spectrometry fragmentation (ESI-IT-MS(n), CID-MS(n) and GC/EI-MS). Thirty sequences were identified, which is the largest number of analogous sequences so far observed at once. Twenty-one sequences were new, and nine others corresponded to peptaibols already described. These peptaibols belonged to the same peptidic family based on the model Ac-Aib-xxx-xxx-xxx-Aib-Pro-xxx-xxx-Aib-Pro-xxol. They were named trichobrachin A when the residue in position 2 was an Asn, and trichobrachin C when it was a Gln. Major chromatographic sub-fractions, corresponding to purified peptaibols, were assayed for their cytotoxic activity. Trichobrachin A-IX and trichobrachin C exhibited the highest activities. There was an exponential relation between their relative hydrophobicity and their cytotoxicity on KB cells.     

The occurrence of peptaibols and structurally related peptaibiotics in fungi and their mass spectrometric identification via diagnostic fragment ions.

Peptaibols and related peptide antibiotics (peptaibiotics) display diagnostically useful fragmentation patterns during mass spectrometry (FAB-MS, ESI-CID-MS/MS and CID-MSn]. The paper compiles fragmentation data of pseudo-molecular ions reported in the literature as a guide to the rational identification of recurrently isolated and new peptaibols and peptaibiotics. Taxonomic and ecological aspects of microorganisms producing peptaibols and peptaibiotics are discussed.     

Multiple non-ribosomal peptide synthetase genes determine peptaibol synthesis in Trichoderma virens

Trichoderma virens, an imperfect fungus, is used as a biocontrol agent to suppress plant disease caused by soilborne fungal pathogens. Antimicrobial peptides it produces include peptaibols of 11, 14, and 18 amino acids in length. These peptaibols were previously reported to be synthesized by a non-ribosomal peptide synthetase (NRPS) encoded by the Tex1 gene in strain Tv29-8. The present study examined the Tex1 homolog in a commercially relevant T. virens strain, G20. Although the gene in G20 was 99% identical in DNA sequence to Tex1 in the 15.8 kb compared, gene disruption results indicate that it is only responsible for the production of an 18-mer peptaibol, and not 11-mer and 14-mer peptaibols. Additional NRPS adenylate domains were identified in T. virens and one was found to be part of a 5-module NRPS gene. Although the multimodule gene is not needed for peptaibol synthesis, sequence comparisons suggest that two of the individual adenylate domain clones might be part of a separate peptaibol synthesis NRPS gene. The results indicate a significant diversity of NRPS genes in T. virens that is unexpected from the literature.     

辽宁木霉属(Trichoderma)真菌的形态分类研究

对采自辽宁省内14个地方的173份土样和植物组织材料进行分离,获得了54株Trichoderma菌株,采用形态学分类方法鉴定出12种木霉菌,分别是拟康氏木霉(Trichoderma pseudokoningii)、长枝木霉(T.longi-brachiatum)、粘绿木霉(T.virens)、卷曲木霉(T.spirale)、顶孢木霉(T.fertile)、粗壮木霉(T.strigosum)、长孢木霉(T.longipile)、钩状木霉(T.hamatum)、绿色木霉(T.viride)、康氏木霉(T.koningii)、深绿木霉(T.atroviri-de)和哈茨木霉(T.harzianum)。其中长孢木霉为中国新记录种,粗壮木霉和卷曲木霉为东北地区首次报道。文中列有辽宁省木霉属真菌的分种检索表,并附有各木霉菌的生境和分布。     

Peptaibols: stable markers of fungal development in the marine environment

Different peptaibols were observed in both fresh and frozen marine sediments collected from a marine area devoted to bivalve culture (Fier d'Ars, Atlantic coast, France). The identification of the peptaibols was based on a three-step mass-spectrometric analysis: observation of doubly charged ions with a characteristic isotopic profile, cleavage and observation of C- and N-terminal fragments, and partial sequencing of the N-terminal segments. The MS characteristics indicated numerous similarities between the peptaibols detected and those produced by different strains of Trichoderma species isolated from fresh sediments. Peptaibols were also detected in mussel samples collected at the same site. This constitutes the first observation of contamination of the marine human-food chain by fungal metabolites. Since peptaibols were readily observed both in fresh sediments and in samples kept frozen for several years, these compounds can be considered as stable markers of the development of Trichoderma in the marine environment.     

Isolation and characterisation of a partial peptide synthetase gene from Trichoderma asperellum

Many species of Trichoderma have attracted interest as agents for the biological control of soil borne fungal pathogens of a range of crop plants. Research on the biochemical mechanisms associated with this application has focused on the ability of these fungi to produce enzymes which lyse fungal cell walls, and antifungal antibiotics. An important group of the latter are the non-ribosomal peptides called peptaibols. In this study Trichoderma asperellum, a strain used in biological control in Malaysia, was found to produce the peptaibol, trichotoxin. This type of peptide molecule is synthesised by a peptide synthetase (PES) enzyme template encoded by a peptide synthetase (pes) gene. Using nucleotide sequences amplified from adenylation (A-) domains as probes, to hybridise against a lambda FIXII genomic library from T. asperellum, 25 clones were recovered. These were subsequently identified as representative of four groups based on their encoding properties for specific amino acid incorporation modules in a PES. This was based on analysis of their amino acid sequences which showed up to 86% identity to other PESs including TEX 1.     

Antimicrobial peptaibols induce defense responses and systemic resistance in tobacco against tobacco mosaic virus

Trichoderma spp. are well-known biocontrol agents because of their antimicrobial activity against bacterial and fungal phytopathogens. However, the biochemical mechanism of their antiviral activity remains largely unknown. In this study, we found that Trichokonins, antimicrobial peptaibols isolated from Trichoderma pseudokoningii SMF2, could induce defense responses and systemic resistance in tobacco (Nicotiana tabacum var. Samsun NN) against tobacco mosaic virus (TMV) infection. Local Trichokonin (100 nM) treatment led to 54% lesion inhibition, 57% reduction in average lesion diameter and 30% reduction in average lesion area in systemic tissue of tobacco compared with control, indicating that Trichokonins induced resistance in tobacco against TMV infection. Trichokonin treatment increased the production of reactive oxygen species and phenolic compounds in tobacco. Additionally, application of Trichokonins significantly increased activities of pathogenesis-related enzymes PAL and POD, and upregulated the expression of several plant defense genes. These results suggested that multiple defense pathways in tobacco were involved in Trichokonin-mediated TMV resistance. We report on the antivirus mechanism of peptaibols, which sheds light on the potential of peptaibols in plant viral disease control.     

Detection of peptaibols and partial cloning of a putative peptaibol synthetase gene fromT. harzianum CECT 2413

The characterization of 11- and 18-residue peptaibols (peptides synthesized by peptide synthetases) at Trichoderma harzianum CECT 2413 (a filamentous fungus) was performed. Using a heterologous probe from tex1, the only peptaibol synthetase cloned and characterized so far in Trichoderma species, was cloned; a region that comprised 11676 bp of a second peptide synthetase gene detected in these strain (called salps2) and sequenced. The deduced sequence of Salps2 (3891 amino acids) contained three complete and a fourth incomplete module of a peptide synthetase, in which the typical adenylation, thiolation and condensation domains were found, but also an additional dehydrogenase/reductase domain in the C-terminus of the last module. Based on sequence similarity and analysis of its modular structure, it is proposed that Salps2 is a peptaibol synthetase. Additionally, analysis of =4.4-kb sequence downstream of salps2 was done and the signature sequences of Salps2 were identified and compared with those of available sequences of the other Trichoderma peptaibol synthetases.