Dissecting cellobiose metabolic pathway and its application in biorefinery through consolidated bioprocessing in Myceliophthora thermophila

Rewiring metabolic flux to simultaneously improve malate production and eliminate by-product succinate accumulation by Myceliophthora thermophila

Although a high titre of malic acid is achieved by filamentous fungi, by-product succinic acid accumulation leads to a low yield of malic acid and is unfavourable for downstream processing. Herein, we conducted a series of metabolic rewiring strategies in a previously constructed Myceliophthora thermophila to successfully improve malate production and abolish succinic acid accumulation. First, a pyruvate carboxylase CgPYC variant with increased activity was obtained using a high-throughput system and introduced to improve malic acid synthesis. Subsequently, shifting metabolic flux to malate synthesis from mitochondrial metabolism by deleing mitochondrial carriers of pyruvate and malate, led to a 53.7% reduction in succinic acid accumulation. The acceleration of importing cytosolic succinic acid into the mitochondria for consumption further decreased succinic acid formation by 53.3%, to 2.12 g/L. Finally, the importer of succinic acid was discovered and used to eliminate by-product accumulation. In total, malic acid production was increased by 26.5%, relative to the start strain JG424, to 85.23 g/L and 89.02 g/L on glucose and Avicel, respectively, in the flasks. In a 5-L fermenter, the titre of malic acid reached 182.7 g/L using glucose and 115.8 g/L using raw corncob, without any by-product accumulation. This study would accelerate the industrial production of biobased malic acid from renewable plant biomass.

Independent metabolism of oligosaccharides is the keystone of synchronous utilization of cellulose and hemicellulose in Myceliophthora

The effective utilization of cellulose and hemicellulose, the main components of plant biomass, is a key technical obstacle that needs to be overcome for the economic viability of lignocellulosic biorefineries. Here, we firstly demonstrated that the thermophilic cellulolytic fungus Myceliophthora thermophila can simultaneously utilize cellulose and hemicellulose, as evidenced by the independent uptake and intracellular metabolism of cellodextrin and xylodextrin. When plant biomass serviced as carbon source, we detected the cellodextrin and xylodextrin both in cells and in the culture medium, as well as high enzyme activities related to extracellular oligosaccharide formation and intracellular oligosaccharide hydrolysis. Sugar consumption assay revealed that in contrast to inhibitory effect of glucose on xylose and cellodextrin/xylodextrin consumption in mixed-carbon media, cellodextrin and xylodextrin were synchronously utilized in this fungus. Transcriptomic analysis also indicated simultaneous induction of the genes involved in cellodextrin and xylodextrin metabolic pathway, suggesting carbon catabolite repression (CCR) is triggered by extracellular glucose and can be eliminated by the intracellular hydrolysis and metabolism of oligosaccharides. The xylodextrin transporter MtCDT-2 was observed to preferentially transport xylobiose and tolerate high cellobiose concentrations, which helps to bypass the inhibition of xylobiose uptake. Furthermore, the expression of cellulase and hemicellulase genes was independently induced by their corresponding inducers, which enabled this strain to synchronously utilize cellulose and hemicellulose. Taken together, the data presented herein will further elucidate the degradation of plant biomass by fungi, with implications for the development of consolidated bioprocessing-based lignocellulosic biorefinery.

Unveiling a classical mutant in the context of the GH3 β-glucosidase family in Neurospora crassa

Classical fungal mutant strains obtained by mutagenesis have helped to elucidate fundamental metabolic pathways in the past. In the filamentous fungus Neurospora crassa, the gluc-1 strain was isolated long ago and characterized by its low level of β-glucosidase activity, which is essential for the degradation of cellulose, the most abundant biopolymer on Earth and the main polymeric component of the plant cell wall. Based on genomic resequencing, we hypothesized that the causative mutation resides in the β-glucosidase gene gh3-3 (bgl6, NCU08755). In this work, growth patterns, enzymatic activities and sugar utilization rates were analyzed in several mutant and overexpression strains related to gluc-1 and gh3-3. In addition, different mutants affected in the degradation and transport of cellobiose were analyzed. While overexpression of gh3-3 led to the recovery of β-glucosidase activity in the gluc-1 mutant, as well as normal utilization of cellobiose, the full gene deletion strain Δgh3-3 was found to behave differently than gluc-1 with lower secreted β-glucosidase activity, indicating a dominant role of the amino acid substitution in the point mutated gh3-3 gene of gluc-1. Our results furthermore confirm that GH3-3 is the major extracellular β-glucosidase in N. crassa and demonstrate that the two cellodextrin transporters CDT-1 and CDT-2 are essential for growth on cellobiose when the three main N. crassa β-glucosidases are absent. Overall, these findings provide valuable insight into the mechanisms of cellulose utilization in filamentous fungi, being an essential step in the efficient production of biorefinable sugars from agricultural and forestry plant biomass.

The transcriptional factor Clr-5 is involved in cellulose degradation through regulation of amino acid metabolism in Neurospora crassa

BACKGROUND

Filamentous fungi are efficient degraders of plant biomass and the primary producers of commercial cellulolytic enzymes. While the transcriptional regulation mechanisms of cellulases have been continuously explored in lignocellulolytic fungi, the induction of cellulase production remains a complex multifactorial system, with several aspects still largely elusive.

RESULTS

In this study, we identified a Zn2Cys6 transcription factor, designated as Clr-5, which regulates the expression of cellulase genes by influencing amino acid metabolism in Neurospora crassa during growth on cellulose. The deletion of clr-5 caused a significant decrease in secreted protein and cellulolytic enzyme activity of N. crassa, which was partially alleviated by supplementing with yeast extract. Transcriptomic profiling revealed downregulation of not only the genes encoding main cellulases but also those related to nitrogen metabolism after disruption of Clr-5 under Avicel condition. Clr-5 played a crucial role in the utilization of multiple amino acids, especially leucine and histidine. When using leucine or histidine as the sole nitrogen source, the Δclr-5 mutant showed significant growth defects on both glucose and Avicel media. Comparative transcriptomic analysis revealed that the transcript levels of most genes encoding carbohydrate-active enzymes and those involved in the catabolism and uptake of histidine, branched-chain amino acids, and aromatic amino acids, were remarkably reduced in strain Δclr-5, compared with the wild-type N. crassa when grown in Avicel medium with leucine or histidine as the sole nitrogen source. These findings underscore the important role of amino acid metabolism in the regulation of cellulase production in N. crassa. Furthermore, the function of Clr-5 in regulating cellulose degradation is conserved among ascomycete fungi.

CONCLUSIONS

These findings regarding the novel transcription factor Clr-5 enhance our comprehension of the regulatory connections between amino acid metabolism and cellulase production, offering fresh prospects for the development of fungal cell factories dedicated to cellulolytic enzyme production in bio-refineries.

Development of an efficient protein expression system in the thermophilic fungus Myceliophthora thermophila

BACKGROUND

Thermophilic fungus Myceliophthora thermophila has been widely used in industrial applications due to its ability to produce various enzymes. However, the lack of an efficient protein expression system has limited its biotechnological applications.

RESULTS

In this study, using a laccase gene reporting system, we developed an efficient protein expression system in M. thermophila through the selection of strong constitutive promoters, 5'UTRs and signal peptides. The expression of the laccase was confirmed by enzyme activity assays. The results showed that the Mtpdc promoter (Ppdc) was able to drive high-level expression of the target protein in M. thermophila. Manipulation of the 5'UTR also has significant effects on protein expression and secretion. The best 5'UTR (NCA-7d) was identified. The transformant containing the laccase gene under the Mtpdc promoter, NCA-7d 5'UTR and its own signal peptide with the highest laccase activity (1708 U/L) was obtained. In addition, the expression system was stable and could be used for the production of various proteins, including homologous proteins like MtCbh-1, MtGh5-1, MtLPMO9B, and MtEpl1, as well as a glucoamylase from Trichoderma reesei.

CONCLUSIONS

An efficient protein expression system was established in M. thermophila for the production of various proteins. This study provides a valuable tool for protein production in M. thermophila and expands its potential for biotechnological applications.

Thermophiles: potential chassis for lignocellulosic biorefinery

Lignocellulosic thermophiles can speed up lignocellulose hydrolysis and promote efficient degradation, but limited genetic tools and heavy metabolic burden narrow the spectrum of potential products. Constructing synthetic microbial consortia is a potential strategy to address this bottleneck and improves the efficiency of lignocellulosic biorefineries.

LpNOL-knockdown suppression of heat-induced leaf senescence in perennial ryegrass involving regulation of amino acid and organic acid metabolism

The nonyellow COLORING 1-like gene (NOL) is known for its roles in accelerating leaf senescence, but the underlying metabolic mechanisms for heat-induced leaf senescence remain unclear. The objectives of this study were to identify metabolites and associated metabolic pathways regulated by knockdown of NOL in perennial ryegrass (Lolium perenne) and to determine the metabolic mechanisms of NOL controlling heat-induced leaf senescence. Wild-type (WT; cv. "Pinnacle") and two lines (Noli-1 and Noli-2) of perennial ryegrass with LpNOL knockdown were exposed to heat stress at 35/33°C (day/night) or nonstress control temperatures at 25/22°C (day/night) for 30 days in growth chambers. Leaf electrolyte leakage, chlorophyll (Chl) content, photochemical efficiency (F_v /F_m ), and net photosynthetic rate (Pn) were measured as physiological indicators of leaf senescence, while gas chromatography-mass spectrometry was performed to identify metabolites regulated by LpNOL. Knockdown of LpNOL suppressed heat-induced leaf senescence and produced a stay-green phenotype in perennial ryegrass, as manifested by increased Chl content, photochemical efficiency, net photosynthetic rate, and cell membrane stability in Noli-1 and Noli-2. Five metabolites (valine, malic acid, threonic acid, shikimic acid, chlorogenic acid) were uniquely upregulated in LpNOL plants exposed to heat stress, and six metabolites (aspartic acid, glutamic acid, 5-oxoproline, phenylalanine, proline, tartaric acid) exhibited more pronounced increases in their content in LpNOL plants than the WT. LpNOL could regulate heat-induced leaf senescence in perennial ryegrass through metabolic reprogramming in the pathways of respiration, secondary metabolism, antioxidant metabolism, and protein synthesis.

Coordination of consolidated bioprocessing technology and carbon dioxide fixation to produce malic acid directly from plant biomass in Myceliophthora thermophila

BACKGROUND

Consolidated bioprocessing (CBP) technique is a promising strategy for biorefinery construction, producing bulk chemicals directly from plant biomass without extra hydrolysis steps. Fixing and channeling CO₂ into carbon metabolism for increased carbon efficiency in producing value-added compounds is another strategy for cost-effective bio-manufacturing. It has not been reported whether these two strategies can be combined in one microbial platform.

RESULTS

In this study, using the cellulolytic thermophilic fungus Myceliophthora thermophila, we designed and constructed a novel biorefinery system DMCC (Direct microbial conversion of biomass with CO₂ fixation) through incorporating two CO₂ fixation modules, PYC module and Calvin-Benson-Bassham (CBB) pathway. Harboring the both modules, the average rate of fixing and channeling ¹³CO₂ into malic acid in strain CP51 achieved 44.4, 90.7, and 80.7 mg/L/h, on xylose, glucose, and cellulose, respectively. The corresponding titers of malic acid were up to 42.1, 70.4, and 70.1 g/L, respectively, representing the increases of 40%, 10%, and 7%, respectively, compared to the parental strain possessing only PYC module. The DMCC system was further improved by enhancing the pentose uptake ability. Using raw plant biomass as the feedstock, yield of malic acid produced by the DMCC system was up to 0.53 g/g, with ¹³C content of 0.44 mol/mol malic acid, suggesting DMCC system can produce 1 t of malic acid from 1.89 t of biomass and fix 0.14 t CO₂ accordingly.

CONCLUSIONS

This study designed and constructed a novel biorefinery system named DMCC, which can convert raw plant biomass and CO₂ into organic acid efficiently, presenting a promising strategy for cost-effective production of value-added compounds in biorefinery. The DMCC system is one of great options for realization of carbon neutral economy.

Metabolic engineering of the cellulolytic thermophilic fungus Myceliophthora thermophila to produce ethanol from cellobiose

BACKGROUND

Cellulosic biomass is a promising resource for bioethanol production. However, various sugars in plant biomass hydrolysates including cellodextrins, cellobiose, glucose, xylose, and arabinose, are poorly fermented by microbes. The commonly used ethanol-producing microbe Saccharomyces cerevisiae can usually only utilize glucose, although metabolically engineered strains that utilize xylose have been developed. Direct fermentation of cellobiose could avoid glucose repression during biomass fermentation, but applications of an engineered cellobiose-utilizing S. cerevisiae are still limited because of its long lag phase. Bioethanol production from biomass-derived sugars by a cellulolytic filamentous fungus would have many advantages for the biorefinery industry.

RESULTS

We selected Myceliophthora thermophila, a cellulolytic thermophilic filamentous fungus for metabolic engineering to produce ethanol from glucose and cellobiose. Ethanol production was increased by 57% from glucose but not cellobiose after introduction of ScADH1 into the wild-type (WT) strain. Further overexpression of a glucose transporter GLT-1 or the cellodextrin transport system (CDT-1/CDT-2) from N. crassa increased ethanol production by 131% from glucose or by 200% from cellobiose, respectively. Transcriptomic analysis of the engineered cellobiose-utilizing strain and WT when grown on cellobiose showed that genes involved in oxidation-reduction reactions and the stress response were downregulated, whereas those involved in protein biosynthesis were upregulated in this effective ethanol production strain. Turning down the expression of pyc gene results the final engineered strain with the ethanol production was further increased by 23%, reaching up to 11.3 g/L on cellobiose.

CONCLUSIONS

This is the first attempt to engineer the cellulolytic fungus M. thermophila to produce bioethanol from biomass-derived sugars such as glucose and cellobiose. The ethanol production can be improved about 4 times up to 11 grams per liter on cellobiose after a couple of genetic engineering. These results show that M. thermophila is a promising platform for bioethanol production from cellulosic materials in the future.