CRISPR/Cas9-mediated genome editing directed by a 5S rRNA-tRNAGly hybrid promoter in the thermophilic filamentous fungus Humicola insolens

BACKGROUND

Humicola insolens is a filamentous fungus with high potential of producing neutral and heat- and alkali-resistant cellulase. However, the genetic engineering tools, particularly the genome-editing tool, are scarce, hindering the study of cellulase expression regulation in this organism.

RESULTS

Herein, a CRISPR/Cas9 genome-editing system was established in H. insolens based on a hybrid 5S rRNA-tRNA^Gly promoter. This system is superior to the HDV (hepatitis delta virus) system in genome editing, allowing highly efficient single gene destruction in H. insolens with rates of deletion up to 84.1% (37/44). With this system, a putative pigment synthesis gene pks and the transcription factor xyr1 gene were disrupted with high efficiency. Moreover, the extracellular protein concentration and cellulase activity largely decreased when xyr1 was deleted, demonstrating for the first time that Xyr1 plays an important role in cellulase expression regulation.

CONCLUSIONS

The established CRISPR/Cas9 system is a powerful genetic operation tool for H. insolens, which will accelerate studies on the regulation mechanism of cellulase expression and engineering of H. insolens for higher cellulase production.

Process strategies to improve biocatalytic depolymerization of post-consumer PET packages in bioreactors, and investigation on consumables cost reduction

Massive plastics production has raised concerns about low recycling rates and disposal of these materials in nature, causing environmental and economic impacts. Poly(ethylene terephthalate) (PET) is one of main polymers used for manufacture of plastic packaging (e.g. bottles, trays). Enzymatic recycling of PET has been a route of increasing study aiming at to recover its monomers (terephthalic acid and ethylene glycol), resulting in a circular production chain. In this study, investigation of pH control and fractionation of enzyme feeding were explored in post-consumed PET (PC-PET) hydrolysis reactions catalyzed by Humicola insolens cutinase (HiC) in stirred reactors. It was found that the unbuffered reaction provided of pH control by 0.5 M NaOH addition showed 2.39-fold improvement in the released monomers (to a total of 26.3 mM), comparatively to the Tris-HCl-buffered reaction. In addition, it was observed a possibility of reducing the enzyme loading used in the process by half, leading to an increase of 2.41-fold in the specific terephthalic acid concentration released per protein amount, whilst maintaining a high products concentration (97 mM). A simplified cost analysis of reaction consumables was performed, and the data reported here demonstrates that these alternative process strategies contribute to costs reduction on the enzymatic depolymerization reactions of PET.

A Novel CreA-Mediated Regulation Mechanism of Cellulase Expression in the Thermophilic Fungus Humicola insolens

The thermophilic fungus Humicola insolens produces cellulolytic enzymes that are of great scientific and commercial interest; however, few reports have focused on its cellulase expression regulation mechanism. In this study, we constructed a creA gene (carbon catabolite repressor gene) disruption mutant strain of H. insolens that exhibited a reduced radial growth rate and stouter hyphae compared to the wild-type (WT) strain. The creA disruption mutant also expressed elevated pNPCase (cellobiohydrolase activities), pNPGase (β-glucosidase activities), and xylanase levels in non-inducing fermentation with glucose. Unlike other fungi, the H. insolenscreA disruption mutant displayed lower FPase (filter paper activity), CMCase (carboxymethyl cellulose activity), pNPCase, and pNPGase activity than observed in the WT strain when fermentation was induced using Avicel, whereas its xylanase activity was higher than that of the parental strain. These results indicate that CreA acts as a crucial regulator of hyphal growth and is part of a unique cellulase expression regulation mechanism in H. insolens. These findings provide a new perspective to improve the understanding of carbon catabolite repression regulation mechanisms in cellulase expression, and enrich the knowledge of metabolism diversity and molecular regulation of carbon metabolism in thermophilic fungi.

Polysaccharide monooxygenase-catalyzed oxidation of cellulose to glucuronic acid-containing cello-oligosaccharides

BACKGROUND

Polysaccharide monooxygenases (PMOs) play an important role in the enzymatic degradation of cellulose. They have been demonstrated to able to C6-oxidize cellulose to produce C6-hexodialdoses. However, the biological function of C6 oxidation of PMOs remains unknown. In particular, it is unclear whether C6-hexodialdoses can be further oxidized to uronic acid (glucuronic acid-containing oligosaccharides).

RESULTS

A PMO gene, Hipmo1, was isolated from Humicola insolens and expressed in Pichia pastoris. This PMO (HiPMO1), belonging to the auxiliary activity 9 (AA9) family, was shown to able to cleave cellulose to yield non-oxidized and oxidized cello-oligosaccharides. The enzyme oxidizes C6 positions in cellulose to form glucuronic acid-containing cello-oligosaccharides, followed by hydrolysis with beta-glucosidase and beta-glucuronidase to yield glucose, glucuronic acid, and saccharic acid. This indicates that HiPMO1 can catalyze C6 oxidation of hydroxyl groups of cellulose to carboxylic groups.

CONCLUSIONS

HiPMO1 oxidizes C6 of cellulose to form glucuronic acid-containing cello-oligosaccharides followed by hydrolysis with beta-glucosidase and beta-glucuronidase to yield glucose, glucuronic acid, and saccharic acid, and even possibly by beta-eliminative cleavage to produce unsaturated cello-oligosaccharides. This study provides a new mechanism for cellulose cleavage by C6 oxidation of HiPMO1.

The use of Agrobacterium-mediated insertional mutagenesis sequencing to identify novel genes of Humicola insolens involved in cellulase production

A transfer DNA (T-DNA)-tagged mutant library of Humicola insolens was screened for mutants with altered cellulase production using the plate-clearing zone assay. Three selected mutants (5-A7, 5-C6, and 13-B7) exhibited significantly depressed FPase, CMCase and xylanase activities compared with the wild-type strain upon shake-flask fermentation, while the pNPCase and pNPGase activities of the three mutants were relatively higher than those of the parental strain. Combined with the results of SDS-PAGE and mass spectrometry, we suggest that expression of the CMCases Cel6B, Cel7B, CMC3, and XynA/B/C was reduced in the mutant strains. Twelve putative T-DNA insertion sites were identified in the three mutants via Agrobacterium-mediated insertional mutagenesis sequencing (AIM-Seq). Bioinformatics analysis suggested that a putative dolichyl pyrophosphate phosphatase, two hypothetical proteins encoding genes of unknown function, and/or nine intergenic fragments may be involved in cellulase and hemicellulase production by H. insolens. This provides promising new candidate genes relevant to cellulase production by the fungus, which will be crucial not only for our understanding of the molecular mechanism underlying cellulase production, but also for strain improvement.

Production of rice straw hydrolysis enzymes by the fungi Trichoderma reesei and Humicola insolens using rice straw as a carbon source

Rice straw was evaluated as a carbon source for the fungi, Trichoderma reesei and Humicola insolens, to produce enzymes for rice straw hydrolysis. The enzyme activity of T. reesei and H. insolens cultivated in medium containing non-treated rice straw were almost equivalent to the enzyme of T. reesei cultivated in Avicel medium, a form of refined cellulose. The enzyme activity of T. reesei cultivated in medium containing NH₄OH-treated rice straw was 4-fold higher than enzyme from cultures grown in Avicel medium. In contrast, H. insolens enzyme from cultures grown in NH₄OH-treated rice straw had significantly lower activity compared with non-treated rice straw or Avicel. The combined use of T. reesei and H. insolens enzymes resulted in a significant synergistic enhancement in enzymatic activity. Our data suggest that rice straw is a promising low-cost carbon source for fungal enzyme production for rice straw hydrolysis.

Cell dispersion culture for the effective growth of Humicola insolens and efficient enzyme production

We have developed a method for the effective growth of Humicola insolens conducive to efficient enzyme production using a medium containing glucose as a carbon source and extruded soybean meal (ExSBM) as a nitrogen source. Enzymes from Humicola sp. hold promise for biomass degradation, especially of lignocellulosic materials such as rice straw, wood chips, and corn stover. The strain, however, is hard to disperse, so an aggregated form of the fungus in a liquid culture media is generally used, resulting in poor control of the growth process and low enzyme production. This has greatly limited the utilization of this strain, in spite of its potential as an enzyme producer. Surprisingly, the addition of ExSBM improves mycelium dispersion and enzyme production of H. insolens, and the dispersive effect is applicable to other fungi such as Trichoderma and Aspergillus sp. In contrast, defatted soybean meal not treated with an extrusion process has little effect on mycelium cohesion. It therefore appears that the specific three-dimensional structure of ExSBM arising from the extrusion process provides a favorable environment for cell growth, since the composition of ExSBM and soybean meal is essentially identical. The optimum medium for cell dispersion culture essentially consisted of 5% glucose and 0.3% ExSBM.