Purification and characterization of an extracellular 24 kDa chitobiosidase from the mycoparasitic fungus Trichoderma saturnisporum

Microbial chitinases and their relevance in various industries

Chitin, the second most abundant biopolymer on earth after cellulose, is composed of β-1,4-N-acetylglucosamine (GlcNAc) units. It is widely distributed in nature, especially as a structural polysaccharide in the cell walls of fungi, the exoskeletons of crustaceans, insects, and nematodes. However, the principal commercial source of chitin is the shells of marine or freshwater invertebrates. Microbial chitinases are largely responsible for chitin breakdown in nature, and they play an important role in the ecosystem's carbon and nitrogen balance. Several microbial chitinases have been characterized and are gaining prominence for their applications in various sectors. The current review focuses on chitinases of microbial origin, their diversity, and their characteristics. The applications of chitinases in several industries such as agriculture, food, the environment, and pharmaceutical sectors are also highlighted.

Trichoderma longibrachiatum T6: A nematocidal activity of endochitinase gene exploration and its function identification

Endochitinase is a natural extracellular protein in Trichoderma longibrachiatum T6, which can degrade the eggshell of Heterodera avenae significantly, however the related genes that coding this protein was rarely characterized. In the present study, the endochitinase 18-5 gene (T6-Echi18-5) of T. longibrachiatum T6 was cloned and sequenced. The expression level of T6-Echi18-5 gene in T. longibrachiatum T6 was induced and increased after the H. avenae cysts inoculation. The full-length cDNA sequence of T6-Echi18-5 was 1671 bp that contained an ORF of 1275 bp, corresponding to 424 amino acids with a 45.9 kDa molecular weight. A single band of 60.04 kDa was detected and identified using SDS-PAGE and Western blot analysis after transferring the T6-Echi18-5 gene to Escherichia coli BL21 Rosetta (DE3). The concentration of purified recombinant T6-Echi18-5 protein was 1.53 mg·ml^-1, and the optimal temperature and pH were 50 °C and 5.0, respectively. The eggshell and content were dissolved and exuded from 4 to10 days after treatment with the purified recombinant T6-Echi18-5 protein. The relative inhibition rate of eggs hatching was 86.79 % at 12 days after treatment. Our study demonstrated the key role of T6-Echi18-5 gene in degrading the H. avenae eggshell and inhibiting the eggs hatching.

Management of bakanae disease of rice using biocontrol agents and insights into their biocontrol mechanisms

Bakanae disease is an emerging problem for the Basmati rice cultivation in India. Forty-seven endophytes isolated earlier along with three Talaromyces flavus isolates evaluated against Fusaium fujikuroi [Nirenberg] bakanae pathogen [isolate F250] through dual culture and enzymatic assays. Out of 50 isolates, 6 isolates namely, Tf₁, Tf₂, Tf₃, Fusarium equiseti, Fusarium sp. and Trichoderma sp. produced good inhibitory results under in vitro conditions and were proceeded with in planta studies and conducted microscopic studies and real-time PCR assays. Microscopic studies revealed that the defense response system of plants was activated to a longer extent in bioagent treatments, since the number of live nuclei (DAPI staining) and green stained live plant cells (FDA staining) were higher as seen in treated plants when compared to pathogen-inoculated and uninoculated control when observed under confocal laser scanning microscopy. The analysis of cell cycle-related genes expressed during the ROS activity showed increased expression of the cell cycle-related genes involved. The selected isolates were also tested under glasshouse for disease inhibition studies. F. equiseti, Fusarium sp. and Trichoderma sp. gave a disease inhibition of, 87%, 66% and 94%, respectively. Tf₂ and Tf₁ isolate dominantly inhibited the disease with 95% whereas Tf₃ also inhibited successfully with 70%. Through the results of our study, we can deduce that the T. flavus (Tf_1, Tf₂, Tf₃) isolates and the endophytes F. equiseti, Fusarium sp. and Trichoderma sp. may represent an important biocontrol agent to control the bakanae disease of rice and also implicated that could further be befitting to capitalize them for field evaluations.

Identification of plant beneficial Bacillus spp. for Resilient agricultural ecosystem

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The plant beneficial microbes from rhizosphere soils in cauliflower fields were characterized for plants beneficial attributes such as phosphorus solubilization, siderophore, chitinase and protease activity, and indole acetic acid type of growth regulator.

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The antagonistic behavior of these isolates against fusarium oxysporum and sclerotinia sclerotiorum revealed their potential in combating the biotic stresses.

The use of synthetic pesticides and chemicals to continuously increase agricultural productivity is causing severe damage to our ecosystem. Therefore, there is need to enhance our understanding about the factors which can contribute to soil processes and play key role in developing sustainable agricultural ecosystem. In this context, the bacteria from cauliflower rhizosphere were isolated and characterized for different plants beneficial attributes. The relationship of soil bacteria and its elemental composition was examined using canonical correspondence analysis. The elemental composition analysis of soil samples revealed presence of Mg, Al, Si, P, K, Ca, Fe and their oxides. In addition, the isolates were found positive for phosphorus solubilization, siderophore, chitinase and protease activity, and indole acetic acid type of growth regulator. The direct confrontation assay revealed antagonistic behavior of these isolates against Fusarium oxysporum and Sclerotinia sclerotiorum. The promising isolates were identified and affiliated to closely related species of genus Bacillus in phylogenetic relationship. The canonical correspondence analysis revealed distribution of elements and their relationship with the identified species in particular area. The characteristics of these isolates revealed their potential in alleviating the biotic and abiotic stresses and hence enhancing crops yield without the usage of synthetic fertilizers and pesticides. The present study is first of its kind and will open new avenues to explore microbial community structure across different farmlands soils to develop resilience agricultural ecosystem.

Genomic Organization of Streptomyces flavotricini NGL1 and Streptomyces erythrochromogenes HMS4 Reveals Differential Plant Beneficial Attributes and Laccase Production Capabilities

The genus Streptomyces has been explored in industrial sectors due to its endurance to environmental stresses, the production of a plethora of biomolecules, the biological remediation of soils, and alleviating plant stresses. The whole genome of NGL1 and HMS4 was sequenced due to the specific laccase activity against 2,6-dimethoxyphenol (2,6-DMP) and differential plant beneficial attributes. The deduced genome of 8.85 Mbp and 7.73 Mbp in size with a G+C content of 72.03% and 72.3% was obtained for NGL1 and HMS4, respectively. A total of 8438 and 7322 protein coding genes, 155 (130 tRNA, 25 rRNA) and 145 tRNA (121 tRNA, 24 rRNA) coding genes were predicted in NGL1 and HMS4, respectively. The comparative genomics of NGL1 and HMS4 showed 185 and 162 genes encoding for carbohydrate-active enzymes, respectively. The genomic ability of these strains to encode carbohydrate-active enzymes, laccase, and diversity of BGCs, along with plant beneficial attributes to suppress the plant pathogens can be used for several industrial and agricultural applications.

Molecular imprints of plant beneficial Streptomyces sp. AC30 and AC40 reveal differential capabilities and strategies to counter environmental stresses

Streptomyces and their biomolecules are well explored for antibiotics production, bioremediation and alleviating the plant stresses due to their plant beneficial attributes. Therefore, due to plethora of biological attributes, the accurate portraying of molecular capabilities of these microorganisms at genomic level is of paramount importance. Here, we have evaluated biochemical attributes of two Streptomyces sp. AC30and AC40 for different plant beneficial activities which are antagonistic to Fusarium oxysporum, Alternaria solani, Sclerotinia sclerotium and Phytopthora infestans. In parallel, the draft genomes of these strains were deduced to understand their genomic capabilities using Illumina platform. The complete genome of AC30and AC40 were 11,284,599 bp and 12,636,188 bp in size with total G + C content of 62.36 and 54.75 %, respectively. Overall, higher number of genes (14,024) was reported for AC40 as compared to AC30 (12,476). The comparative genome organization revealed sharing of a few biosynthetic clusters as well as some exclusive biosynthetic clusters among both the strains. Further, expansion in the chitinases and glucanases was found in the genome of AC40. In addition, genes for 3-phytase and glycosyl hydrolase family 19 were restricted to AC40 only. The comparative genome study revealed presence of plant induced nitrilase in AC40 which is predicted for its role in IAA biosynthesis, release of ammonia, biotransformation of nitrile compounds to corresponding acids and bioremediation of soil containing nitrile compounds. For IAA and secondary metabolites biosynthesis, flavin-dependent monooxygenase, a rate limiting factor in Trp-dependent auxin biosynthesis pathway was found exclusive to AC30 genome. The comparative study revealed the diversification of few pathways/strategies to suppress plant pathogens and promote plant growth by Streptomyces strains.

Molecular characterization of β-endoglucanase from antagonistic Trichoderma saturnisporum isolate GITX-Panog (C) induced under mycoparasitic conditions

The endoglucanase belonging to glycoside hydrolase family 61 are little studied. In present study, a β-endoglucanase of ~37 kDa induced on autoclaved mycelium of Fusarium oxysporum was cloned and characterized. The molecular characterization of β-endoglucanase encoding gene revealed presence of a single intron and an open reading frame of 1044-bp which encoded a protein of 347 amino acid residues. The phylogenetic analysis of Eglu revealed its similarity to endo-β-glucanases of other Trichoderma spp. The catalytic site of β-endoglucanase contained Asp, Asn, His and Tyr residues. The cDNA encoding β-glucanase was cloned into E. coli and Pichia pastoris using pQUA-30 and pPIC9K vector system, respectively. The comparison of structure revealed that most similar structure to Eglu is Hypocrea jecorina template 5o2w.1.A of glycoside hydrolase family 61.The biochemical characterization of β-endoglucanase purified from T. saturnisporum isolate and the recombinant protein expressed in E. coli and P. pastoris was active under acidic conditions with a pH optima of 5 and temperature optima of 60 °C. The purified and expressed enzyme preparation was able to inhibit growth of F.oxysporum at 1 × 10⁵ spores/mL which clearly revealed its significance in plant pathogen suppression.

Integrated Translatome and Proteome: Approach for Accurate Portraying of Widespread Multifunctional Aspects of Trichoderma

Genome-wide studies of transcripts expression help in systematic monitoring of genes and allow targeting of candidate genes for future research. In contrast to relatively stable genomic data, the expression of genes is dynamic and regulated both at time and space level at different level in. The variation in the rate of translation is specific for each protein. Both the inherent nature of an mRNA molecule to be translated and the external environmental stimuli can affect the efficiency of the translation process. In biocontrol agents (BCAs), the molecular response at translational level may represents noise-like response of absolute transcript level and an adaptive response to physiological and pathological situations representing subset of mRNAs population actively translated in a cell. The molecular responses of biocontrol are complex and involve multistage regulation of number of genes. The use of high-throughput techniques has led to rapid increase in volume of transcriptomics data of Trichoderma. In general, almost half of the variations of transcriptome and protein level are due to translational control. Thus, studies are required to integrate raw information from different “omics” approaches for accurate depiction of translational response of BCAs in interaction with plants and plant pathogens. The studies on translational status of only active mRNAs bridging with proteome data will help in accurate characterization of only a subset of mRNAs actively engaged in translation. This review highlights the associated bottlenecks and use of state-of-the-art procedures in addressing the gap to accelerate future accomplishment of biocontrol mechanisms.

Elucidation of biocontrol mechanisms of Trichoderma harzianum against different plant fungal pathogens: Universal yet host specific response

In the present study, different transcripts of Trichoderma harzianum ThHP-3 were evaluated for their response against four fungal pathogens Fusarium oxysporum, Colletotrichum capsici, Colletotrichum truncatum and Gloesercospora sorghi using RT-qPCR. The time course study of T. harzianum transcripts related to signal transduction, lytic enzymes, secondary metabolites and various transporters revealed variation in expression against four fungal pathogens. In a broader term, the transcripts were upregulated at various time intervals but the optimum expression of cyp3, abc, nrp, tga1, pmk, ech42 and glh20 varied with respect to host fungi. Additionally, the expression of transcripts related to transporters/cytochromes was also observed against Fusarium oxysporum after 96h whereas transcripts related to secondary metabolites and lytic enzymes showed significant difference in expression against Colletotrichum spp. from 72 to 96h. This is first study on transcriptomic response of T. harzianum against pathogenic fungi which shows their host specific response.

The Modes of Action of ChiIII, a Chitinase from Mushroom Coprinopsis cinerea, Shift with Changes in the Length of GlcNAc Oligomers

A putative class III endochitinase (ChiIII) was reported previously to be expressed dominantly in fruiting bodies of Coprinopsis cinerea, and its expression levels increased with the maturation of the fruiting bodies. This paper further reports that ChiIII is a novel chitinase with exo- and endoactivities. When the substrate was (GlcNAc)3-5, ChiIII exhibited exoactivity, releasing GlcNAc processively from the reducing end of (GlcNAc)3-5; when the substrate was (GlcNAc)6-7, the activity of ChiIII shifted to an endoacting enzyme, randomly splitting chitin oligosaccharides to various shorter oligosaccharides. This shift in the mode of action of ChiIII may be related to its stronger hydrolytic capacity to degrade chitin in fungal cell walls. The predicted structure of ChiIII shows that it lacks the α+β domain insertion; however, its substrate binding cleft seems to be deeper than that of common endochitinases but shallower and more open than that of common exochitinases, which may be related to its exo- and endohydrolytic activities.

Purification, characterization and physiological significance of a chitinase from the pilei of Coprinopsis cinerea fruiting bodies

We purified a chitinase from pilei extractions of Coprinopsis cinerea fruiting bodies by ammonium sulfate precipitation and CM Sepharose cation exchange chromatography. MALDI-TOF/TOF MS analysis characterized this purified chitinase as a putative class V chitinase, ChiB1. ChiB1 hydrolyzed colloidal chitin and chitosan, whereas it did not hydrolyze chitin powder. ChiB1 cleaved only pNP-(GlcNAc)2, rather than pNP-GlcNAc or pNP-(Glc-NAc)3, to release nitrophenol. ChiB1 preferably and progressively released (GlcNAc)2 from (GlcNAc)6 and digested (GlcNAc)6 to two molecules of (GlcNAc)3 in a small proportion, but did not split (GlcNAc)2, so it is an exochitinase. ChiB1 has an optimum temperature range of 35°C to 40°C and an optimum pH of 5.0. ChiB1 exhibited Km and Vmax values of 2.63 mg ml(-1) and 2.31 μmol min(-1) mg protein(-1) for colloidal chitin, respectively. The ChiB1 gene, along with another putative endochitinase (class III chitinase gene), was expressed dominantly among eight predicted chitinase genes in the genome, and its expression level increased with the maturation of fruiting bodies. ChiB1 incubation released a large amount of soluble β-glucan fractions from alkali-insoluble cell wall fractions of C. cinerea fruiting bodies, thereby it may promote the degradation of cell walls in synergy with the β-1,3-glucanases during pileus autolysis.

Trichoderma saturnisporum, a new biological control agent

BACKGROUND

Biocontrol agents (BCAs) could be a viable alternative to chemicals in the management of fungal crop diseases. Screening for potential biocontrol and plant growth promoter isolates from a soil in Cádiz (Spain) was conducted. Several isolates showed antagonism in in vitro tests to several plant pathogens.

RESULTS

Two isolates of Trichoderma saturnisporum (Ascomycetes, Hypocreales) were identified by sequencing of the rDNA region. One isolate was selected for further in vivo plant growth promotion and biological control assays. Results indicate that substrate application of T. saturnisporum improved plant quality and showed biological control activity against Phytophthora capsici and Phytophthora parasitica (Peronosporales, Peronosporaceae).

CONCLUSION

There are a few references to T. saturnisporum isolated from different media but not its ability to promote plant growth or biocontrol. This is the first report of T. saturnisporum as a seedling growth promoter and as biological control agent.

Chitinase Expression Due to Reduction in Fusaric Acid Level in an Antagonistic Trichoderma harzianum S17TH

To study the effect of reduction in phytotoxin level on fungal chitinases, antagonistic Trichoderma spp. were screened for their ability to reduce the level of fusaric acid (FA), the phytotoxin produced by Fusarium spp. A T. harzianum isolate S17TH was able to tolerate high levels of FA (up to 500 ppm) but was unable to reduce the toxin to a significant level (non-toxic) added to minimal synthetic broth (MSB). However, the isolate was able to reduce 400 ppm FA in the liquid medium after 7 days to a non-toxic level and displayed similar level of antagonism over the control (without FA). In studies of the effect of the reduction in FA (400 ppm) level on chitinase gene expression in PCR assays, nag1 was significantly repressed but ech42 expression was only slightly repressed. Chitinase activity was either reduced or absent in the extracellular proteins of MSB supplemented with 400 ppm FA, which could be attributed to the effect of residual FA or its breakdown products through unknown mechanisms. Selection of S17TH as a toxin insensitive isolate that could commensurate the negative effect on chitinase activity makes it a potential antagonist against Fusarium spp.

Chitinolytic microorganisms and their possible application in environmental protection

This paper provides a review of the latest research findings on the applications of microbial chitinases to biological control. Microorganisms producing these enzymes can inhibit the growth of many fungal diseases that pose a serious threat to global crop production. Currently, efforts are being made to discover producers of chitinolytic enzymes. The potential exists that natural biofungicides will replace chemical fungicides or will be used to supplement currently used fungicides, which would reduce the negative impact of chemicals on the environment and support the sustainable development of agriculture and forestry.