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Brazilian Journal of Biology = Revista... 2022Brazil is one of the world leaders in the agribusiness sector tending to directly influence a growing dependence on imported inputs, specifically synthetic... (Review)
Review
Brazil is one of the world leaders in the agribusiness sector tending to directly influence a growing dependence on imported inputs, specifically synthetic agrochemicals. At the state level, in 2013, Tocantins stood out in first place in the ranking of agrochemical consumers, however, these products can cause several problems, such as poisoning to humans, environmental contamination, and increased resistance to phytopathogens. Biological control is an alternative to the use of agrochemicals towards eliminating pests naturally by using living organisms called Biological Control Agents (BCA). Currently, fungi of the Trichoderma genus are some of the most used organisms in biological pest control for their relevant characteristics that favor them in terms of survival in the environment, such as high capacity to adapt to ecological conditions, potential to colonize the rhizosphere of plants, mycoparasitism, production of volatile and non-volatile metabolites. In addition, it works on plant growth and productivity. In general, the use of Trichoderma favors the control of soil pathogens, such as Rhizoctonia, Pythium, Sclerotinia, and nematodes. Thus, this review aims to demonstrate the importance of using Trichoderma in biological control, as well as to present an overview and perspectives of research developed by respondents in the Brazilian Midwest region and Tocantins state.
Topics: Agrochemicals; Biological Control Agents; Brazil; Humans; Pest Control, Biological; Plant Diseases; Trichoderma
PubMed: 35946640
DOI: 10.1590/1519-6984.260161 -
Applied Microbiology and Biotechnology Mar 2011L-Arabinose is the second most abundant pentose beside D-xylose and is found in the plant polysaccharides, hemicellulose and pectin. The need to find renewable carbon... (Review)
Review
L-Arabinose is the second most abundant pentose beside D-xylose and is found in the plant polysaccharides, hemicellulose and pectin. The need to find renewable carbon and energy sources has accelerated research to investigate the potential of L-arabinose for the development and production of biofuels and other bioproducts. Fungi produce a number of extracellular arabinanases, including α-L-arabinofuranosidases and endo-arabinanases, to specifically release L-arabinose from the plant polymers. Following uptake of L-arabinose, its intracellular catabolism follows a four-step alternating reduction and oxidation path, which is concluded by a phosphorylation, resulting in D-xylulose 5-phosphate, an intermediate of the pentose phosphate pathway. The genes and encoding enzymes L-arabinose reductase, L-arabinitol dehydrogenase, L-xylulose reductase, xylitol dehydrogenase, and xylulokinase of this pathway were mainly characterized in the two biotechnological important fungi Aspergillus niger and Trichoderma reesei. Analysis of the components of the L-arabinose pathway revealed a number of specific adaptations in the enzymatic and regulatory machinery towards the utilization of L-arabinose. Further genetic and biochemical analysis provided evidence that L-arabinose and the interconnected D-xylose pathway are also involved in the oxidoreductive degradation of the hexose D-galactose.
Topics: Arabinose; Aspergillus niger; Metabolic Networks and Pathways; Polysaccharides; Trichoderma
PubMed: 21212945
DOI: 10.1007/s00253-010-3071-8 -
BMC Genomics Jun 2019The growing importance of the ubiquitous fungal genus Trichoderma (Hypocreales, Ascomycota) requires understanding of its biology and evolution. Many Trichoderma species... (Comparative Study)
Comparative Study
BACKGROUND
The growing importance of the ubiquitous fungal genus Trichoderma (Hypocreales, Ascomycota) requires understanding of its biology and evolution. Many Trichoderma species are used as biofertilizers and biofungicides and T. reesei is the model organism for industrial production of cellulolytic enzymes. In addition, some highly opportunistic species devastate mushroom farms and can become pathogens of humans. A comparative analysis of the first three whole genomes revealed mycoparasitism as the innate feature of Trichoderma. However, the evolution of these traits is not yet understood.
RESULTS
We selected 12 most commonly occurring Trichoderma species and studied the evolution of their genome sequences. Trichoderma evolved in the time of the Cretaceous-Palaeogene extinction event 66 (±15) mya, but the formation of extant sections (Longibrachiatum, Trichoderma) or clades (Harzianum/Virens) happened in Oligocene. The evolution of the Harzianum clade and section Trichoderma was accompanied by significant gene gain, but the ancestor of section Longibrachiatum experienced rapid gene loss. The highest number of genes gained encoded ankyrins, HET domain proteins and transcription factors. We also identified the Trichoderma core genome, completely curated its annotation, investigated several gene families in detail and compared the results to those of other fungi. Eighty percent of those genes for which a function could be predicted were also found in other fungi, but only 67% of those without a predictable function.
CONCLUSIONS
Our study presents a time scaled pattern of genome evolution in 12 Trichoderma species from three phylogenetically distant clades/sections and a comprehensive analysis of their genes. The data offer insights in the evolution of a mycoparasite towards a generalist.
Topics: Biopolymers; Carbon; Evolution, Molecular; Extracellular Space; Fungal Proteins; Genes, Fungal; Genomics; Hydrolysis; Reproduction; Trichoderma
PubMed: 31189469
DOI: 10.1186/s12864-019-5680-7 -
Microbiological Research Jun 2022Trichoderma reesei has extraordinary potential for high-level protein production at large scales, and it need to be further explored through genetic engineering tools to... (Review)
Review
BACKGROUND
Trichoderma reesei has extraordinary potential for high-level protein production at large scales, and it need to be further explored through genetic engineering tools to obtain a thorough understanding of its cellular physiology. Understanding the genetic factors involved in the intrinsic regulatory network is crucial; without this information, there would be restrictions in expressing genes of interest. Past and present studies are concentrated on the application and expansion of novel expression systems using synthetic biology concepts. These approaches involve either using previously established promoters that are strong or genetically engineered promoters. Genomic and transcriptomic methods have also been employed to isolate strong promoters and expression systems such as light-inducible expression systems, copper-inducible expression systems, L-methionine inducible promoters, and Tet-On expression system etc. AIMS OF REVIEW: In this review, we will highlight various research endeavors related to tunable and constitutive promoters; the role of different promoters in homologous and heterologous protein expression; the identification of innovative promoters, and strategies that may be beneficial for future research aimed at improving and enhancing protein expression in T. reesei.
KEY SCIENTIFIC CONCEPTS OF THE REVIEW
The characterization of new promoters and implementation of novel expression systems that will result in a significant extension of the molecular toolbox that is accessible for the genetic engineering of innovative strains of T. reesei. Genetically engineered strong inducible promoters such as Pcbh1 through replacement of transcriptional repressors (cre1, ace1) with transcriptional activators (xyr1, ace2, ace3, hap2/3/5) and synthetic expression systems can result in elevated production of endoglucanases (EGLs), β-glucosidases (BGLs), and cellobiohydrolases (CBHs). Strong constitutive promoters such as Pcdna1 can be converted into genetically engineered synthetic hybrid promoters by integrating the activation region of strong inducible promoters, which can allow the induction and expression of cellulases even on repressing media. More efforts are necessary to identify innovative promoters and novel expression strategies for the enhanced expression of desirable proteins at industrial scales.
Topics: Cellulase; Fungal Proteins; Gene Expression Regulation, Fungal; Genetic Engineering; Hypocreales; Transcription Factors; Trichoderma
PubMed: 35339938
DOI: 10.1016/j.micres.2022.127011 -
Fungal Genetics and Biology : FG & B Nov 2010In recent years, considerable progress has been made in the elucidation of photoresponses and the mechanisms responsible for their induction in species of the genus... (Review)
Review
In recent years, considerable progress has been made in the elucidation of photoresponses and the mechanisms responsible for their induction in species of the genus Trichoderma. Although an influence of light on these fungi had already been reported five decades ago, their response is not limited to photoconidiation. While early studies on the molecular level concentrated on signaling via the secondary messenger cAMP, a more comprehensive scheme is available today. The photoreceptor-orthologs BLR1 and BLR2 are known to mediate almost all known light responses in these fungi and another light-regulatory protein, ENVOY, is suggested to establish the connection between light response and nutrient signaling. As a central regulatory mechanism, this light signaling machinery impacts diverse downstream pathways including vegetative growth, reproduction, carbon and sulfur metabolism, response to oxidative stress and biosynthesis of peptaibols. These responses involve several signaling cascades, for example the heterotrimeric G-protein and MAP-kinase cascades, resulting in an integrated response to environmental conditions.
Topics: Carbon; Fungal Proteins; Gene Expression Regulation, Fungal; Light; Mycelium; Oxidative Stress; Peptaibols; Receptors, Cell Surface; Signal Transduction; Sulfur; Transcription Factors; Trichoderma
PubMed: 20466064
DOI: 10.1016/j.fgb.2010.04.010 -
Applied and Environmental Microbiology Sep 2020Due to the rapid expansion in microbial taxonomy, precise identification of common industrially and agriculturally relevant fungi such as species is challenging. In...
Due to the rapid expansion in microbial taxonomy, precise identification of common industrially and agriculturally relevant fungi such as species is challenging. In this study, we introduce the online multilocus identification system (MIST) for automated detection of 349 species based on a set of three DNA barcodes. MIST is based on the reference databases of validated sequences of three commonly used phylogenetic markers collected from public databases. The databases consist of 414 complete sequences of the nuclear rRNA internal transcribed spacers (ITS) 1 and 2, 583 sequence fragments of the gene encoding translation elongation factor 1-alpha (), and 534 sequence fragments of the gene encoding RNA polymerase subunit 2 (). Through MIST, information from different DNA barcodes can be combined and the identification of species can be achieved based on the integrated parametric sequence similarity search (blastn) performed in the manner of a decision tree classifier. In the verification process, MIST provided correct identification for 44 species based on DNA barcodes consisting of and markers. Thus, MIST can be used to obtain an automated species identification as well as to retrieve sequences required for manual identification by means of phylogenetic analysis. The genus is important to humankind, with a wide range of applications in industry, agriculture, and bioremediation. Thus, quick and accurate identification of species is paramount, since it is usually the first step in -based research. However, it frequently becomes a limitation, especially for researchers who lack taxonomic knowledge of fungi. Moreover, as the number of -based studies has increased, a growing number of unidentified sequences have been stored in public databases, which has made the species identification more ambiguous. In this study, we provide an easy-to-use tool, MIST, for automated species identification, a list of species, and corresponding sequences of reference DNA barcodes. Therefore, this study will facilitate the research on the biodiversity and applications of the genus .
Topics: Base Sequence; DNA Barcoding, Taxonomic; DNA, Fungal; Multilocus Sequence Typing; RNA, Fungal; RNA, Ribosomal; Species Specificity; Trichoderma
PubMed: 32680870
DOI: 10.1128/AEM.01532-20 -
Applied and Environmental Microbiology Jun 2020Cerato-platanins (CPs) form a family of fungal small secreted cysteine-rich proteins (SSCPs) and are of particular interest not only because of their surface activity...
Cerato-platanins (CPs) form a family of fungal small secreted cysteine-rich proteins (SSCPs) and are of particular interest not only because of their surface activity but also their abundant secretion by fungi. We performed an evolutionary analysis of 283 CPs from 157 fungal genomes with the focus on the environmental opportunistic plant-beneficial and mycoparasitic fungus Our results revealed a long evolutionary history of CPs in Dikarya fungi that have undergone several events of lateral gene transfer and gene duplication. Three genes were maintained in the core genome of , while some species have up to four CP-encoding genes. All CPs evolve under stabilizing natural selection pressure. The functional genomic analysis of CPs in and revealed that only is active at all stages of development but that it plays a minor role in interactions with other fungi and bacteria. The deletion of this gene results in increased colonization of tomato roots by spp. Similarly, biochemical tests of EPL1 heterologously produced by support the claims described above. Based on the results obtained, we conclude that the function of CPs is probably linked to their surfactant properties and the ability to modify the hyphosphere of submerged mycelia and, thus, facilitate the nutritional versatility of fungi. The effector-like functions do not sufficiently describe the diversity and evolution of these proteins in fungi, as they are also maintained, duplicated, or laterally transferred in the genomes of nonherbivore fungi. Cerato-platanins (CPs) are surface-active small proteins abundantly secreted by filamentous fungi. Consequently, immune systems of plants and other organisms recognize CPs and activate defense mechanisms. Some CPs are toxic to plants and act as virulence factors in plant-pathogenic fungi. Our analysis, however, demonstrates that the interactions with plants do not explain the origin and evolution of CPs in the fungal kingdom. We revealed a long evolutionary history of CPs with multiple cases of gene duplication and events of interfungal lateral gene transfers. In the mycoparasitic spp., CPs evolve under stabilizing natural selection and hamper the colonization of roots. We propose that the ability to modify the hydrophobicity of the fungal hyphosphere is a key to unlock the evolutionary and functional paradox of these proteins.
Topics: Evolution, Molecular; Fungal Proteins; Fungi; Gene Transfer, Horizontal; Genome, Fungal; Solanum lycopersicum; Multigene Family; Plant Roots; Trichoderma
PubMed: 32332135
DOI: 10.1128/AEM.00696-20 -
Microbial Cell Factories May 2019Studies carried out with novel 13 strains of Trichoderma, isolated from mangrove sediments (PE, Brazil) using morphophysiological and molecular characterization,...
BACKGROUND
Studies carried out with novel 13 strains of Trichoderma, isolated from mangrove sediments (PE, Brazil) using morphophysiological and molecular characterization, followed evaluation of biocontrol using Fusarium strains isolated from Caatinga soil (PE, Brazil). Trichoderma strains were characterized by polyphasic taxonomic approach, and the extracted DNA was amplified with primers ITS 1 and 4, and sequenced. The biocontrol evaluation was conducted at 24 and 48 h of growth intervals by Tukey test, with a significance of 5%. Antibiosis tests were assessed in vitro by dual plate and partition plate techniques against Fusarium strains.
RESULTS
Trichoderma molecular identification, sequences of 500 bp were amplified, deposited into GenBank, and used for phylogenetic analyses. The strains were identified as T. asperellum (10), as T. harzianum (2) and one as T. longibrachiatum. Growth rate presented an average of 0.1207 cm h for Trichoderma and lower growth rate of 0.031 cm h for Fusarium spp., respectively. Antibiosis tests presented the best antagonist level of efficiency for T. asperellum UCP 0149 against F. solani UCP 1395 (82.2%) and F. solani UCP 1075 (70.0%), followed by T. asperellum UCP 0319 against F. solani UCP1083 (73.4%) and T. asperellum UCP 0168 against F. solani UCP1098 (71.5%), respectively.
CONCLUSIONS
The data obtained in this study as tool for identification of novel Trichoderma strains serve as basis for development of several sustainable use for biotechnological processes. Those Trichoderma strains found promising for the management antagonistic potential and interaction could aid the conduct of biotechnological biocontrol of contaminants, and improve environmental conditions for the health of plants.
Topics: Antibiosis; Biodiversity; Biological Control Agents; Brazil; Fusarium; Geologic Sediments; Phylogeny; Plants; Soil Microbiology; Trichoderma; Wetlands
PubMed: 31122261
DOI: 10.1186/s12934-019-1108-y -
Microbiology Spectrum Dec 2021Trichoderma spp. represent one of the most important fungal genera to mankind and in natural environments. The genus harbors prolific producers of wood-decaying enzymes,...
Complete Genome Sequences and Genome-Wide Characterization of Biocontrol Agents Provide New Insights into their Evolution and Variation in Genome Organization, Sexual Development, and Fungal-Plant Interactions.
Trichoderma spp. represent one of the most important fungal genera to mankind and in natural environments. The genus harbors prolific producers of wood-decaying enzymes, biocontrol agents against plant pathogens, plant-growth-promoting biofertilizers, as well as model organisms for studying fungal-plant-plant pathogen interactions. Pursuing highly accurate, contiguous, and chromosome-level reference genomes has become a primary goal of fungal research communities. Here, we report the chromosome-level genomic sequences and whole-genome annotation data sets of four strains used as biocontrol agents or biofertilizers ( Gv29-8, FT-333, FT-101, and P1). Our results provide comprehensive categorization, correct positioning, and evolutionary detail of both nuclear and mitochondrial genomes, including telomeres, AT-rich blocks, centromeres, transposons, mating-type loci, nuclear-encoded mitochondrial sequences, as well as many new secondary metabolic and carbohydrate-active enzyme gene clusters. We have also identified evolutionarily conserved core genes contributing to plant-fungal interactions, as well as variations potentially linked to key behavioral traits such as sex, genome defense, secondary metabolism, and mycoparasitism. The genomic resources we provide herein significantly extend our knowledge not only of this economically important fungal genus, but also fungal evolution and basic biology in general. Telomere-to-telomere and gapless reference genome assemblies are necessary to ensure that all genomic variants are studied and discovered, including centromeres, telomeres, AT-rich blocks, mating type loci, biosynthetic, and metabolic gene clusters. Here, we applied long-range sequencing technologies to determine the near-completed genome sequences of four widely used biocontrol agents or biofertilizers: Gv29-8 and FT-333, FT-101, and P1. Like those of three Trichoderma reesei wild isolates [QM6a, CBS999.97() and CBS999.97()] we reported previously, these four biocontrol agent genomes each contain seven nuclear chromosomes and a circular mitochondrial genome. Substantial intraspecies and intragenus diversities are also discovered, including single nucleotide polymorphisms, chromosome shuffling, as well as genomic relics derived from historical transposition events and repeat-induced point (RIP) mutations.
Topics: Biological Control Agents; Evolution, Molecular; Fertilizers; Genetic Variation; Genome, Fungal; Phylogeny; Plants; Secondary Metabolism; Trichoderma
PubMed: 34908505
DOI: 10.1128/Spectrum.00663-21 -
Molecules (Basel, Switzerland) Apr 2022: The genus is widely spread in the environment, mainly in soils. Trichoderma are filamentous fungi and are used in a wide range of fields to manage plant patho-genic...
: The genus is widely spread in the environment, mainly in soils. Trichoderma are filamentous fungi and are used in a wide range of fields to manage plant patho-genic fungi. They have proven to be effective biocontrol agents due to their high reproducibility, adaptability, efficient nutrient mobilization, ability to colonize the rhizosphere, significant inhibitory effects against phytopathogenic fungi, and efficacy in promoting plant growth. In the present study, the antagonist Trichoderma isolates were characterized from the soil of Abha region, Saudi Arabia. Soil samples were collected from six locations of Abha, Saudi Arabia to isolate having the antagonistic potential against plant pathogenic fungi. The soil dilution plate method was used to isolate ( Specific Medium (TSM)). Isolated were evaluated for their antagonistic potential against , and . The antagonist activity was assessed by dual culture assay, and the effect of volatile metabolites and culture filtrate of In addition, the effect of different temperature and salt concentrations on the growth of isolates were also evaluated. The most potent species were identified by using ITS4 and ITS 5 primers. Total 48 isolates were isolated on (TSM) from the soil samples out of those six isolates were found to have antagonist potential against the tested plant pathogenic fungi. In general, strains A (1) 2.1 T, A (3) 3.1 T and A (6) 2.2 T were found to be highly effective in reducing the growth of tested plant pathogenic fungi. A (1) 2.1 T was highly effective against (82%), whereas A (6) 2.2 T prevented the maximal growth of (77%) according to the dual culture data. Furthermore, A (1) 2.1 T volatile metabolites hindered growth. The volatile metabolite of A (6) 2.2 T, on the other hand, had the strongest activity against (45%). The A (1) 2.1 T culture filtrate was proven to be effective in suppressing the growth of (47%). The temperature range of 26 °C to 30 °C was observed to be optimum for growth. isolates grew well at salt concentrations (NaCl) of 2%, and with the increasing salt concentration the growth of isolates decreased. The molecular analysis of potent fungi by ITS4 and ITS5 primers confirmed that the isolates A (1) 2.1 T, A (3) 3.1 and A (6) 2.2 T were , , and , respectively. The study concludes that the soil of the Abha region contains a large population of diverse fungi including Trichoderma, which can be explored further to be used as biocontrol agents.
Topics: Fusarium; Plant Diseases; Plants; Reproducibility of Results; Saudi Arabia; Soil; Soil Microbiology; Trichoderma
PubMed: 35458723
DOI: 10.3390/molecules27082525