Induction and the regulation of production of cellulase by fungi

Efficient System Wide Metabolic Pathway Comparisons in Multiple Microbes Using Genome to KEGG Orthology (G2KO) Pipeline Tool

Comparison of system-wide metabolic pathways among microbes provides valuable insights of organisms' metabolic capabilities that can further assist in rationally screening organisms in silico for various applications. In this work, we present a much needed, efficient and user-friendly Genome to KEGG Orthology (G2KO) pipeline tool that facilitates efficient comparison of system wide metabolic networks of multiple organisms simultaneously. The optimized strategy primarily involves automatic retrieval of the KEGG Orthology (KO) identifiers of user defined organisms from the KEGG database followed by overlaying and visualization of the metabolic genes using the KEGG Mapper reconstruct pathway tool. We demonstrate the applicability of G2KO via two case studies in which we processed 24,314 genes across 15 organisms, mapped on to 530 reference pathways in KEGG, while focusing on pathways of interest. First, an in-silico designing of synthetic microbial consortia towards bioprocessing of cellulose to valuable products by comparing the cellulose degradation and fermentative pathways of microbes was undertaken. Second, we comprehensively compared the amino acid biosynthetic pathways of multiple microbes and demonstrated the potential of G2KO as an efficient tool for metabolic studies. We envisage the tool will find immensely useful to the metabolic engineers as well as systems biologists. The tool's web-server, along with tutorial is publicly available at https://faculty.iitmandi.ac.in/~shyam/tools/g2ko/g2ko.cgi . Also, standalone tool can be downloaded freely from https://sourceforge.net/projects/g2ko/ , and from the supplementary.

Mini review: Advances in understanding regulation of cellulase enzyme in white-rot basidiomycetes

White-rot basidiomycetic fungi have gained a lot of scientific attention in recent years owing to their ability to produce cellulase enzymes that are of great importance in numerous industrial applications. This has seen a rise in number of studies seeking to comprehend both physical and molecular mechanisms that regulate the production of cellulase enzymes in these fungi. Cellulase has several applications in production of food and beverages, biofuel, biological detergents, pharmaceuticals, and deinking in paper and pulp industry. Enhanced understanding of genetic mechanisms that regulate cellulase production would have utility for optimal cellulase production in white-rot basidiomycetes using biotechnology approaches. Carbon catabolite repression and various transcriptional factors such as XlnR, Cre, Clr, Ace, and gna1 control expression of genes encoding cellobiohydrolase (CBH), endoglucanase (EGL) and β-glucosidase (BGL). In this review, we have consolidated and summarised some of recent findings on genetic regulation of cellulase with an aim of highlighting the general regulatory mechanisms that underlie cellulase expressions in white-rot fungi. This review further outlines some of important transcription factors that regulate cellulase genes, and key research gaps that may need to be addressed by future research.

Quantitative multiplexed profiling of Penicillium funiculosum secretome grown on polymeric cellulase inducers and glucose

Filamentous fungi respond to the need to secure utilisable carbon from their growth milieu by secreting unique extracellular proteins depending upon the types of polymeric substrates. We have here profiled the variations in the secretome pattern of a non-model hypercellulolytic fungus - Penicillium funiculosum, grown in minimal media containing four different polymeric cellulase inducers, i.e., Avicel, wheat bran, ammonium-pretreated wheat straw and Avicel & wheat bran, and glucose over its early and late log phases of growth. Of the 137 secreted proteins validated at 1% FDR, we identified the quantified proteins in three clusters as early, persistently or lately expressed. The type of carbon substrate present in the culture media significantly affected the levels of cellulolytic enzymes expression by the fungus. The top abundant proteins quantified in the secretome for Avicel and wheat bran were cellobiohydrolaseI [GH7-CBM1], cellobiohydrolaseII [GH6-CBM1], β-glucosidase [GH3], arabinofuranosidase [GH51] and β-xylosidase [GH3], with bicupin being highest in case of wheat straw. Our results further suggested that the fungus secreted the extracellular proteins in waves, such that the initial responders act to hydrolyse the composite substrates in the culture environment before the second wave of proteins which tend to be more tailored to the specific substrate in the cultivating media.

BIOLOGICAL SIGNIFICANCE

In this article, we have comprehensively examined the dynamics of the secretome of a non-model hypercellulolytic fungus produced in response to model and composite cellulase inducers. Our study has provided additional insights into how the fungus enzyme machinery responds to the presence of different polymeric cellulase inducers over the two different growth phases (early growth and late growth phase). The comprehensive typing and quantification of the different proteins present in the secretomes of the cellulolytic fungal strains in response to diverse nutrient sources hold many prospects in understanding the fungus unique enzyme machinery and dynamics for the downstream biotechnological applications.

Self-induction system for cellulase production by cellobiose produced from glucose in Rhizopus stolonifer

Cellulolytic fungi have evolved a sophisticated genetic regulatory network of cellulase synthesis to adapt to the natural environment. Even in the absence of lignocellulose, it still secretes low levels of “constitutive” cellulase for standby application. However, the mechanisms of this constitutive expression remain incompletely understood. Here we identified a cellobiose synthetase (CBS) from Rhizopus stolonifer, which has the capacity to catalyse the synthesis of cellobiose from uridine diphosphate glucose (UDPG). Through the construction of R. stolonifer Δcbs strain, we found that CBS plays a key role in the synthesis of cellulase. Further analysis of cellulase synthesis under glucose culture reveals that the cellobiose-responsive regulator CLR1 was activated by CBS-synthesized cellobiose, thereby promoting the expression of CLR2 and finally opening the transcription of cellulase genes. Our results suggest that R. stolonifer can be induced by self-synthesized cellobiose to produce cellulase, which can be used to reconstruct the expression regulation network to achieve rapid production of cellulase using simple carbon source. Based on our data, the “constitutive expression” of cellulase actually derives from the induction of cellobiose that synthesized by CBS from carbohydrate metabolites, which updates our knowledge of cellulase, and provides a novel insight into the regulation of cellulase synthesis.

Effects of Momordica charantia Saponins on In vitro Ruminal Fermentation and Microbial Population

This study was conducted to investigate the effects of Momordica charantia saponin (MCS) on ruminal fermentation of maize stover and abundance of selected microbial populations in vitro. Five levels of MCS supplements (0, 0.01, 0.06, 0.30, 0.60 mg/mL) were tested. The pH, NH3-N, and volatile fatty acid were measured at 6, 24, 48 h of in vitro mixed incubation fluids, whilst the selected microbial populations were determined at 6 and 24 h. The high dose of MCS increased the initial fractional rate of degradation at t-value = 0 (FRD0) and the fractional rate of gas production (k), but decreased the theoretical maximum of gas production (V F) and the half-life (t0.5) compared with the control. The NH3-N concentration reached the lowest concentration with 0.01 mg MCS/mL at 6 h. The MSC inclusion increased (p<0.001) the molar proportion of butyrate, isovalerate at 24 h and 48 h, and the molar proportion of acetate at 24 h, but then decreased (p<0.05) them at 48 h. The molar proportion of valerate was increased (p<0.05) at 24 h. The acetate to propionate ratio (A/P; linear, p<0.01) was increased at 24 h, but reached the least value at the level of 0.30 mg/mL MCS. The MCS inclusion decreased (p<0.05) the molar proportion of propionate at 24 h and then increased it at 48 h. The concentration of total volatile fatty acid was decreased (p<0.001) at 24 h, but reached the greatest concentration at the level of 0.01 mg/mL and the least concentration at the level of 0.60 mg/mL. The relative abundance of Ruminococcus albus was increased at 6 h and 24 h, and the relative abundance of Fibrobacter succinogenes was the lowest (p<0.05) at 0.60 mg/mL at 6 h and 24 h. The relative abundance of Butyrivibrio fibrisolvens and fungus reached the greatest value (p<0.05) at low doses of MCS inclusion and the least value (p<0.05) at 0.60 mg/mL at 24 h. The present results demonstrates that a high level of MCS quickly inhibits in vitro fermentation of maize stover, while MCS at low doses has the ability to modulate the ruminal fermentation pattern by regulating the number of functional rumen microbes including cellulolytic bacteria and fungi populations, and may have potential as a feed additive applied in the diets of ruminants.

Cellulase production by a thermophilic clostridium species

Strain M7, a thermophilic, anaerobic, terminally sporing bacterium (0.6 by 4.0 mum) was isolated from manure. It degraded filter paper in 1 to 2 days at 60 C in a minimal cellulose medium but was stimulated by yeast extract. It fermented a wide variety of sugars but produced cellulase only in cellulose or carboxymethyl-cellulose media. Cellulase synthesis not only was probably repressed by 0.4% glucose and 0.3% cellobiose, but also cellulase activity appeared to be inhibited by these sugars at these concentrations. Both C(1) cellulase (degrades native cellulose) and C(x) cellulase (beta-1,4-glucanase) activities in strain M7 cultures were assayed by measuring the liberation of reducing sugars with dinitrosalicylic acid. Both activities had optima at pH 6.5 and 67 C. One milliliter of a 48-h culture of strain M7 hydrolyzed 0.044-meq of glucose per min from cotton fibers. The cellulase(s) from strain M7 was extracellular, produced during exponential growth, but was not free in the growth medium until approximately 30% of the cellulose was hydrolyzed. Glucose and cellobiose were the major soluble products liberated from cellulose by the cellulase. ZnCl(2) precipitation appeared initially to be a good method for the concentration of cellulase activity, but subsequent purification was not successful. Isoelectric focusing indicated the presence of four C(x) cellulases (pI 4.5, 6.3, 6.8, and 8.7). The rapid production and high activity of cellulases from this organism strongly support the basic premise that increased hydrolysis of native cellulose is possible at elevated temperature.

Induction and Catabolite Repression of beta-Glucosidase Synthesis in Myceliophthora thermophila D-14 (= ATCC 48104)

beta-Glucosidase activity in Myceliophthora thermophila D-14 (= ATCC 48104) was inducible and was produced in culture filtrate during growth with various inducers, of which PNPG (p-nitrophenyl-beta-d-glucoside) was the most efficient. Induction of beta-glucosidase also occurred when the organism was grown in medium supplemented with different carbon sources. Carboxymethyl cellulose, cellobiose, and Solka-Floc were found effective for induction of enzyme biosynthesis. The addition of glucose to the culture medium severely repressed beta-glucosidase synthesis, which could not be reversed by exogenous cyclic AMP or dibutyryl cyclic AMP.

News & Notes: Effect of Surfactants on Cellulase Production by Nectria catalinensis

The effect of different nonionic surfactants (Tween 80, Tween 20, Triton X-100) and polyethylene glycol (PEG 6000) was tested on cellulolytic enzyme system production. Tween 80 gave the highest yield of endoglucanase, exoglucanase, and cellobiase at the 20th day of growth, presumably by causing increased permeability of cell membranes and/or by promoting the release of cell-bound enzymes. Maximal yield of endoglucanase was achieved with 1.7 mM Tween 80, whereas exoglucanase and cellobiase were at 0.85 mM. In the same way, this compound increased fungal growth. On the other hand, Tween 20 and Triton X-100 inhibited growth and cellulolytic enzyme production. High yields of endoglucanase and exoglucanase were achieved with PEG 6000 in comparison with the control, presumably by increasing enzyme stability.

Regulation, initiation, and termination of the cenA and cex transcripts of Cellulomonas fimi

We characterized the in vivo transcripts of two Cellulomonas fimi genes, the cenA gene, which encodes an extracellular endo-beta-1,4-glucanase (EC 3.2.1.4) and the cex gene, which encodes an extracellular exo-beta-1,4-glucanase (EC 3.2.1.91). By Northern blot analysis, cenA mRNA was detected in C. fimi RNA preparations from glycerol- and carboxymethyl cellulose-grown cells but not from glucose-grown cells. In contrast, cex mRNA was detected only in the preparations from carboxymethyl cellulose-grown cells. Therefore, the transcription of these genes is subject to regulation by the carbon source provided to C. fimi. By nuclease S1 protection studies with unique 5'-labeled DNA probes and C. fimi RNA isolated in vivo, 5' termini were found 51 and 62 bases before the cenA translational initiation codon and 28 bases before the cex translational initiation codon. S1 mapping with unlabeled DNA probes and C. fimi RNA which had been isolated in vivo but which had been 5' labeled in vitro with guanylyltransferase and [alpha-32P]GTP confirmed that true transcription initiation sites for cenA and cex mRNA had been identified. Comparative analysis of the DNA sequences immediately upstream of the initiation sites of the cenA and cex mRNAs revealed a 30-base-pair region where these two sequences display at least 66% homology. S1 mapping was also used to locate the 3' termini of the cenA and cex transcripts. Three 3' termini were found for cenA messages, whereas only one 3' terminus was identified for cex mRNA. The transcripts of both genes terminate in regions where their corresponding DNA sequences contain inverted repeats.

Characterization and synthesis regulation of Penicillium italicum 1,6-beta-glucanase

The filamentous fungus Penicillium italicum when grown in a synthetic medium, produced and secreted 1,6-beta-glucanase into the culture medium. This enzyme has been partially purified by gel filtration. After this step the active fractions were free of 1,3-beta-glucanase, alpha-amylase and beta-glucosidase activities. Only four proteins, one associated with the enzyme, were found by polyacrylamide gel electrophoresis under non denaturing conditions. The enzyme behaves as an acidic protein (pI 4.65) with an optimum pH of 5 and an endohydrolytic mode of action. The activity was also found associated with the mycelium. Its synthesis was repressed by glucose or growth-promoting sugars. Derepression in low glucose containing medium required protein synthesis. 8-Hydroxyquinoline, an RNA synthesis inhibitor, added during the derepression period did permit some increase in the specific activity but prevented it when added at the beginning of that period.

[Cleavage of alpha-L-arabinofuranoside, beta-D-glucopyranoside and beta-cellobioside of 4-nitrophenol by enzymes of various fungi - a contribution to increase the selectivity of tumor therapy]

To carry out long-term experiments as part of a therapy concept of malignant tumours using inactive transport forms of cancerostatic substances and their specific cleavage in the acidic pH region of the tumours by application of extraneous enzymes, we require enzymes with similar catalytic and pharmacokinetic properties which differ from each other in immunological respect. In the search for such enzymes, the alpha-L-arabinofuranosidases from 12 different fungi, among them 9 basidiomycetes, were studied. The enzymes mentioned were demonstrable in all fungi. Optimum pH values ranged between 2.5 and 5.5. The Km values for the cleavage of alpha-L-arabinofuranoside were, in most cases, 0.5 to 1.8 moles-liter-1-10(-3). With regard to pH dependence, the alpha-L-arabinofuranosidases of most of the fungi investigated proved adequate for the long-term trials envisaged. 4-nitrophenyl-beta-D-glucopyranoside and -beta-cellobioside were also cleaved by enzyme preparations of all the 11 fungi investigated. The beta-D-glucopyranosidases showed a less favourable pH dependence than the alpha-L-arabinofuranosidases. The cleavage of 4-nitrophenyl-beta-cellobioside, on the contrary, showed mostly a comparatively favourable pH dependence. On the basis of the coinciding optimal pH values and the occurrence of 4-nitrophenyl-beta-D-glucopyranoside as an intermediate product in the cleavage of the corresponding cellobioside, we assume that both substrates are cleaved by beta-glucosidase. Because the occurrence of the glucoside during the cleavage of cellobioside is undesirable for the therapeutic trial, a method is proposed for selection of an appropriate cellobioside splitting enzyme basing on the present studies and the relevant literature.

Control of Extracellular beta-1,3-glucanase activity in a basidiomycete species

The basidiomycete QM 806 excreted large amounts of beta-1,3-glucanase into the culture medium. Synthesis and excretion of the enzyme were triggered by a critically low concentration of carbon source. The extracellular beta-1,3-glucanase exhibited a remarkable stability. Addition of glucose or other carbon sources to a culture after consumption of the initial carbon source led to an inactivation of the extracellular beta-1,3-glucanase by an inactivating system, which could be separated from the cells. The inactivation of beta-1,3-glucanse was prevented by cycloheximide. This indicates the necessity of active protein synthesis for the inactivation process but does not prove that the inactivating system itself is a protein. Marked changes in the electrophoretic mobility and immunological properties of beta-1,3-glucanase indicate rather profound alterations of the enzyme protein in the course of inactivation.

Effect of phenethyl alcohol and other organic substances on cellulas production

Cellulase can be produced from growth in noncellulosic substrate if the growth rate of the producing organism is restricted. Phenethyl alcohol (PEA) is a growth inhibitor and was used to control the growth of M. verrucaria in attempts to obtain increased cellulase production. Cellulase yield was found to be increased without a restriction in growth rate when PEA was present in low concentrations (0.03% v/v). The effect was observed for other organisms but notably L. trabea, which produced considerable enzyme from a small quantity of mycelium. Here increased cellulase synthesis was concomitant with restricted growth. Other chemicals with PEA-like structure (e.g. benzyl alcohol) resulted in similar or more extensive cellulase synthesis. Of the substances tried, propyl alcohol was most effective, followed by acetone. PEA causes a swelling of cell walls and inhibits spore formation. This and other data given suggest that PEA affects the cytoplasmic membrane or the cell wall or both. Cellulase synthesis is considered to take place in the membrane and wall region of the cell.