Penicillium janthinellum NCIM1366 shows improved biomass hydrolysis and a larger number of CAZymes with higher induction levels over Trichoderma reesei RUT-C30

Regulation of genes encoding polysaccharide-degrading enzymes in Penicillium

Penicillium fungi, including Penicillium oxalicum, can secrete a range of efficient plant-polysaccharide-degrading enzymes (PPDEs) that is very useful for sustainable bioproduction, using renewable plant biomass as feedstock. However, the low efficiency and high cost of PPDE production seriously hamper the industrialization of processes based on PPDEs. In Penicillium, the expression of PPDE genes is strictly regulated by a complex regulatory system and molecular breeding to modify this system is a promising way to improve fungal PPDE yields. In this mini-review, we present an update on recent research progress concerning PPDE distribution and function, the regulatory mechanism of PPDE biosynthesis, and molecular breeding to produce PPDE-hyperproducing Penicillium strains. This review will facilitate future development of fungal PPDE production through metabolic engineering and synthetic biology, thereby promoting PPDE industrial biorefinery applications. KEY POINTS: • This mini review summarizes PPDE distribution and function in Penicillium. • It updates progress on the regulatory mechanism of PPDE biosynthesis in Penicillium. • It updates progress on breeding of PPDE-hyperproducing Penicillium strains.

Rice straw hydrolysis using in-situ produced enzymes: Feedstock influences fungal enzyme composition and hydrolytic efficiency

Trichoderma reesei RUT-C30 was cultivated on differentially pretreated rice straw and pure cellulose as a carbon source/inducer for cellulase production, and the enzymes were evaluated for hydrolysis of sequential acid and alkali pretreated rice straw. Growth on pretreated rice straw enhanced protein secretion and cellulase activities compared to pure cellulose as a carbon source. The yield of cellulolytic enzymes was higher for alkali pretreated rice straw (ALP-RS), while H2O2-treated (HP-RS) could not induce cellulases to a larger level compared to pure cellulose. Protein concentration was 3.5-fold higher on ALP-RS as compared to pure cellulose, with a maximum filter-paper cellulase (FPase) activity of 1.76 IU/ml and carboxy-methyl cellulase (CMCase) activity of 40.16 IU/ml (2.18 fold higher). Beta-glucosidase (BGL) activity was more or less the same with the different substrates and supplementation of heterologous BGL could result in a quantum jump in hydrolytic efficiencies, which in the case of ALP-RS induced enzymes was 34% (increased from 69.26% to 92.51%). The use of lignocellulosic biomass (LCB) itself as a substrate for the production of cellulase is advantageous not only in terms of raw material costs but also for obtaining a more suitable enzyme profile for biomass hydrolysis.

Novel cyclic shifting of temperature strategy for simultaneous saccharification and fermentation for lignocellulosic bioethanol production

In the current study, a novel strategy using cyclic shifting of temperature was developed for simultaneous saccharification and fermentation (SSF) for bioethanol production from rice straw. The in-situ cellulase production, saccharification and fermentation was carried out using P. janthinellum and S. cerevisiae. Bioethanol titer of 14.98 g/l was obtained using base followed by acid pretreated rice straw by employing the cyclic shifting of temperature strategy "30 °C for 2 h to 40 °C for 2 h". The holding time was further tuned to increase the productivity and the tuned condition 30 °C(1.7 h) - 40 °C(2 h) improved the bioethanol titer to 15.9 g/l. Using this strategy, resulted 5.1-fold and 2.8-fold increment of bioethanol production compared to known approaches, SSF at mutual optimum temperature and prolong prehydrolysis followed by fermentation respectively. The application of cyclic shifting of temperature strategy can unleash a great potential in enhancing the yield and efficiency for a sustainable lignocellulosic bioethanol production.

Early cellular events and potential regulators of cellulase induction in Penicillium janthinellum NCIM 1366

Cellulase production by fungi is tightly regulated in response to environmental cues, and understanding this mechanism is a key pre-requisite in the efforts to improve cellulase secretion. Based on UniProt descriptions of secreted Carbohydrate Active enZymes (CAZymes), 13 proteins of the cellulase hyper-producer Penicillium janthinellum NCIM 1366 (PJ-1366) were annotated as cellulases- 4 cellobiohydrolases (CBH), 7 endoglucanases (EG) and 2 beta glucosidases (BGL). Cellulase, xylanase, BGL and peroxidase activities were higher for cultures grown on a combination of cellulose and wheat bran, while EG was stimulated by disaccharides. Docking studies indicated that the most abundant BGL- Bgl2- has different binding sites for the substrate cellobiose and the product glucose, which helps to alleviate feedback inhibition, probably accounting for the low level of glucose tolerance exhibited. Out of the 758 transcription factors (TFs) differentially expressed on cellulose induction, 13 TFs were identified whose binding site frequencies on the promoter regions of the cellulases positively correlated with their abundance in the secretome. Further, correlation analysis of the transcriptional response of these regulators and TF-binding sites on their promoters indicated that cellulase expression is possibly preceded by up-regulation of 12 TFs and down-regulation of 16 TFs, which cumulatively regulate transcription, translation, nutrient metabolism and stress response.

Comparison of the solid-state and submerged fermentation derived secretomes of hyper-cellulolytic Penicillium janthinellum NCIM 1366 reveals the changes responsible for differences in hydrolytic performance

Solid-state fermentation (SSF) and submerged fermentation (SmF) have often been compared for production of biomass hydrolyzing enzymes highlighting the superiority of the SSF produced enzymes, but the reasons for the performance differences are under-explored. Penicillium janthinellum NCIM 1366 culture extracts from SSF had better hydrolytic performance along with a higher initial rate of reaction. Secretome analyses of the SSF and SmF enzymes using LC/MS-MS, indicated that while the type of proteins secreted were similar in both modes, the abundance of specific beta glucosidases, lytic polysaccharide monooxygenases and hemicellulolytic enzymes were very high in SSF resulting in efficient initiation, low accumulation of cellobiose and high initial reaction rates. Key enzymes that catalyse lignocellulose breakdown under SSF and SmF are therefore different and the fungus may be speculated to have regulation mechanisms that aid differential expression under different cultivation modes.

Lignocellulose degradation by Penicillium janthinellum enzymes is influenced by its variable secretome and a unique set of feedstock characteristics

Substrate characteristics and proteins that affect lignocellulose-hydrolysis by the hypercellulolytic fungus Penicillium janthinellum NCIM 1366 (PJ-1366) were investigated. The hydrolysis rate of PJ-1366 enzymes was very high, with upto 75 % of the reaction being completed in initial 4 h. Comparison of the hydrolytic efficiencies on differently pretreated biomass indicated that the greatest (negative) effect was imparted by lignin, suggesting that improving ligninase activity of the PJ-1366 enzymes may help to improve hydrolysis. Larger pore sizes and higher crystallinity of substrates, which favor enzyme penetration and processive hydrolysis, positively influenced hydrolysis efficiency. For alkali-pretreated substrates, 16 FPU/g of PJ-1366 cellulases released the sugar-equivalent of using 10 FPU/g of a commercial biomass hydrolyzing enzyme. By correlation analysis, 41 proteins, including 20 CAZymes were identified, whose abundance in the secretome positively correlated with the cellulase activities of the culture filtrate. These proteins may be considered as the primary drivers of FPase/CMCase/pNPGase/xylanase activity in PJ-1366.

Comparison of various delignification/desilication pre-treatments and indigenous fungal cellulase for improved hydrolysis of paddy straw

The efficient removal of lignin and silica from paddy straw is essential for its volarization into biofuels and other value-added products. In this work, different chemical pre-treatments viz. acid/alkali, organosolv and deep eutectic solvents were carried out to assess the extent of delignification and desilication of paddy straw. Maximum lignin and silica removal of 96.08 and 95.51% was observed with two step acid (0.5% sulphuric acid) followed by alkali (4% sodium hydroxide) pre-treatment with significantly low total lignin (2.30%) and silica content (0.80%) of the treated straw residue. The treated straw residue contained significantly high holocellulose (91.65%), cellulose (75.01%) and hemicellulose content (16.64%). Among the four indigenous fungal isolates, Penicillium mallochii (JS17) cellulase showed better accessibility for the treated straw residue with maximum release of 504.18 mg g^-1 of reducing sugars and saccharification efficiency of 56.90%. The two-step acid/alkali pre-treatment of paddy straw was highly effective for removing lignin and silica from paddy straw, thereby, resulting in enhanced enzymatic accessibility of the substrate and more efficient hydrolysis of cellulose into fermentable sugars.

Sterigmatocystin Limits Plasmodium falciparum Proliferation and Transmission

As part of our drug discovery program against malaria, the Penicillium janthinellum extract was discovered to inhibit P. falciparum proliferation in blood and transmission to mosquitoes. Bioactivity-guided fractionation of P. janthinellum extraction was carried out using chromatographic techniques. We determined the activities of fractions against Plasmodium falciparum asexual stage parasite proliferation in culture and sexual stage parasite transmission to mosquitoes using standard membrane feeding assays (SMFA). One active compound was isolated. Based on mass spectrometry and nuclear magnetic resonance profiles, the compound was structurally determined to be sterigmatocystin. Sterigmatocystin inhibited P. falciparum proliferation in the blood with an IC50 of 34 µM and limited the sexual parasites to infect mosquitoes with an IC50 of 48 µM. Meanwhile, sterigmatocystin did not show any acute toxicity to human kidney cells at a concentration of 64 µM or lower. Sterigmatocystin can be used as a drug lead for malaria control and as a probe to understand molecular mechanisms of malaria transmission.

Improving the catalytic performance of xylanase from Bacillus circulans through structure-based rational design

Endo-1,4-β-xylanase is one of the most important enzymes employed in biorefineries for obtaining fermentable sugars from hemicellulosic components. Herein, we aimed to improve the catalytic performance of Bacillus circulans xylanase (Bcx) using a structure-guided rational design. A systematic analysis of flexible motions revealed that the R49 component of Bcx (i) constrains the global conformational changes essential for substrate binding and (ii) is involved in modulating flexible motion. Site-saturated mutagenesis of the R49 residue led to the engineering of the active mutants with the trade-off between flexibility and rigidity. The most active mutant R49N improved the catalytic performance, including its catalytic efficiency (7.51-fold), conformational stability (0.7 °C improvement), and production of xylose oligomers (2.18-fold higher xylobiose and 1.72-fold higher xylotriose). The results discussed herein can be applied to enhance the catalytic performance of industrially important enzymes by controlling flexibility.

Dissecting Cellular Function and Distribution of β-Glucosidases in Trichoderma reesei

Trichoderma reesei has 11 putative β-glucosidases in its genome, playing key parts in the induction and production of cellulase. Nevertheless, the reason why the T. reesei genome encodes so many β-glucosidases and the distinct role each β-glucosidase plays in cellulase production remain unknown. In the present study, the cellular function and distribution of 10 known β-glucosidases (CEL3B, CEL3E, CEL3F, CEL3H, CEL3J, CEL1A, CEL3C, CEL1B, CEL3G, and CEL3D) were explored in T. reesei, leaving out BGL1 (CEL3A), which has been well investigated. We found that the overexpression of cel3b or cel3g significantly enhanced extracellular β-glucosidase production, whereas the overexpression of cel1b severely inhibited cellulase production by cellulose, resulting in nearly no growth of T. reesei. Four types of cellular distribution patterns were observed for β-glucosidases in T. reesei: (i) CEL3B, CEL3E, CEL3F, and CEL3G forming clearly separated protein secretion vesicles in the cytoplasm; (ii) CEL3H and CEL3J diffusing the whole endomembrane as well as the cell membrane with protein aggregation, like a reticular network; (iii) CEL1A and CEL3D in vacuoles; (iv) and CEL3C in the nucleus. β-glucosidases CEL1A, CEL3B, CEL3E, CEL3F, CEL3G, CEL3H, and CEL3J were identified as extracellular, CEL3C and CEL3D as intracellular, and CEL1B as unknown. The extracellular β-glucosidases CEL3B, CEL3E, CEL3F, CEL3H, and CEL3G were secreted through a tip-directed conventional secretion pathway, and CEL1A, via a vacuole-mediated pathway that was achieved without any signal peptide, while CEL3J was secreted via an unconventional protein pathway bypassing the endoplasmic reticulum (ER) and Golgi.