Functional genomics and systems biology of Cordyceps species for biotechnological applications.

The use of Cordyceps species for the manufacture of natural products has been established; however, the tremendous advances observed in recent years in genetic engineering and molecular biology have revolutionized the optimization of Cordyceps as cell factories and drastically expanded the biotechnological potential of these fungi. Here, we present a review of systems and synthetic biology studies of Cordyceps and their implications for fungal biology and industrial applications. We summarize the current status of synthetic biology for enhancing targeted metabolites in Cordyceps species, such as cordycepin, adenosine, polysaccharide, and pentostatin. Progress in the systems and synthetic biology of Cordyceps provides a strategy for comprehensively comprehensive controlling efficient cell factories of natural bioproducts and novel synthetic biology toolbox for targeted engineering.

Enhancing Genome-Scale Model by Integrative Exometabolome and Transcriptome: Unveiling Carbon Assimilation towards Sphingolipid Biosynthetic Capability of Cordyceps militaris.

Cordyceps militaris is an industrially important fungus, which is often used in Asia as traditional medicine. There has been a published genome-scale metabolic model (GSMM) of C. militaris useful for predicting its growth behaviors; however, lipid metabolism, which plays a vital role in cellular functions, remains incomplete in the GSMM of C. militaris. A comprehensive study on C. militaris was thus performed by enhancing GSMM through integrative analysis of metabolic footprint and transcriptome data. Through the enhanced GSMM of C. militaris (called iPC1469), it contained 1469 genes, 1904 metabolic reactions and 1229 metabolites. After model evaluation, in silico growth simulation results agreed well with the experimental data of the fungal growths on different carbon sources. Beyond the model-driven integrative data analysis, interestingly, we found key metabolic responses in alteration of lipid metabolism in C. militaris upon different carbon sources. The sphingoid bases (e.g., sphinganine, sphingosine, and phytosphingosine) and ceramide were statistically significant accumulated in the xylose culture when compared with other cultures; this study suggests that the sphingolipid biosynthetic capability in C. militaris was dependent on the carbon source assimilated for cell growth; this finding provides a comprehensive basis for the sphingolipid biosynthesis in C. militaris that can help to further redesign its metabolic control for medicinal and functional food applications.

A novel amylolytic/xylanolytic/cellulolytic multienzyme complex from Clostridium manihotivorum that hydrolyzes polysaccharides in cassava pulp.

Some anaerobic bacteria, particularly Clostridium species, produce extracellular cellulolytic and xylanolytic enzymes as multienzyme complexes (MECs). However, an amylolytic/xylanolytic/cellulolytic multienzyme complex (AXC-MEC) from anaerobic bacteria is rarely found. In this work, the glycoprotein AXC-MEC, composed of subunits of amylolytic, xylanolytic, and cellulolytic enzymes, was isolated from crude extracellular enzyme of the mesophilic anaerobic bacterium Clostridium manihotivorum CT4, grown on cassava pulp, using a milled cassava pulp column and Sephacryl S-500 gel filtration chromatography. The isolated AXC-MEC showed a single band upon native-polyacrylamide gel electrophoresis (native-PAGE). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) showed at least eight protein bands of the multienzyme complex which predominantly exhibited amylolytic enzyme activity, followed by xylanolytic and cellulolytic enzyme activities. The AXC-MEC is highly capable of degrading starch and non-starch polysaccharides present in cassava pulp into glucose and oligosaccharides, without conventional pretreatment. Base on the genomic analysis of C. manihotivorum CT4, we found no evidence of the known structural components of the well-known multienzyme complexes from Clostridium species, cellulosomes such as scaffoldin, cohesin, and dockerin, indicating that AXC-MEC from strain CT4 exhibit a different manner of assembly from the cellulosomes. These results suggest that AXC-MEC from C. manihotivorum CT4 is a new MEC capable of hydrolyzing cassava pulp into value-added products, which will benefit the starch industry. KEY POINTS: • Glycoprotein AXC-MEC was first reported in Clostridium manihotivorum. • Unlike cellulosomes, AXC-MEC consists of amylase, xylanase, and cellulase. • Glucose and oligosaccharides were hydrolysis products from cassava pulp by AXC-MEC.

Clostridium manihotivorum sp. nov., a novel mesophilic anaerobic bacterium that produces cassava pulp-degrading enzymes.

BACKGROUND: Cassava pulp is a promising starch-based biomasses, which consists of residual starch granules entrapped in plant cell wall containing non-starch polysaccharides, cellulose and hemicellulose. Strain CT4T, a novel mesophilic anaerobic bacterium isolated from soil collected from a cassava pulp landfill, has a strong ability to degrade polysaccharides in cassava pulp. This study explored a rarely described species within the genus Clostridium that possessed a group of cassava pulp-degrading enzymes. METHODS: A novel mesophilic anaerobic bacterium, the strain CT4T, was identified based on phylogenetic, genomic, phenotypic and chemotaxonomic analysis. The complete genome of the strain CT4T was obtained following whole-genome sequencing, assembly and annotation using both Illumina and Oxford Nanopore Technology (ONT) platforms. RESULTS: Analysis based on the 16S rRNA gene sequence indicated that strain CT4T is a species of genus Clostridium. Analysis of the whole-genome average amino acid identity (AAI) of strain CT4T and the other 665 closely related species of the genus Clostridium revealed a separated strain CT4T from the others. The results revealed that the genome consisted of a 6.3 Mb circular chromosome with 5,664 protein-coding sequences. Genome analysis result of strain CT4T revealed that it contained a set of genes encoding amylolytic-, hemicellulolytic-, cellulolytic- and pectinolytic enzymes. A comparative genomic analysis of strain CT4T with closely related species with available genomic information, C. amylolyticum SW408T, showed that strain CT4T contained more genes encoding cassava pulp-degrading enzymes, which comprised a complex mixture of amylolytic-, hemicellulolytic-, cellulolytic- and pectinolytic enzymes. This work presents the potential for saccharification of strain CT4T in the utilization of cassava pulp. Based on phylogenetic, genomic, phenotypic and chemotaxonomic data, we propose a novel species for which the name Clostridium manihotivorum sp. nov. is suggested, with the type strain CT4T (= TBRC 11758T = NBRC 114534T).

Metabolic engineering of long chain-polyunsaturated fatty acid biosynthetic pathway in oleaginous fungus for dihomo-gamma linolenic acid production.

Microbial lipids are promising alternative sources of long chain-polyunsaturated fatty acids (LC-PUFAs) for food, feed, nutraceutical and pharmaceutical sectors. Dihomo-γ-linolenic acid (C20:3Δ(8,11,14); DGLA) is an important LC-PUFAs with anti-inflammatory and anti-proliferative effects. To generate a DGLA-producing strain, fatty acid reconstitution in Aspergillus oryzae was performed by metabolic engineering through co-expression of codon-optimized Pythium Δ(6)-desaturase and Δ(6)-elongase, which had high conversion rates of substrates to respective products as compared to the native enzymes. The Δ(6)-desaturated and Δ(6)-elongated products, γ-linolenic acid (C18:3Δ(6,9,12); GLA) and DGLA, were accumulated in phospholipids rather than triacylglycerol. Interestingly, the manipulation of lipid quality in the oleaginous fungus did not affect growth and lipid phenotypes. This strategy might expand to development of the oleaginous fungal strain for producing other tailor-made oils with industrial applications.

The codon-optimized Δ(6)-desaturase gene of Pythium sp. as an empowering tool for engineering n3/n6 polyunsaturated fatty acid biosynthesis.

BACKGROUND: The ∆(6)-desaturase gene, encoding a key enzyme in the biosynthesis of polyunsaturated fatty acids, has potential in pharmaceutical and nutraceutical applications. RESULTS: The ∆(6)-desaturase gene has been isolated from a selected strain of Oomycetes, Pythium sp. BCC53698. The cloned gene (PyDes6) contained an open reading frame (ORF) of 1401 bp encoding 466 amino acid residues. The deduced amino acid sequence shared a high similarity to those of other ∆(6)-desaturases that contained the signature features of a membrane-bound ∆(6)-desaturase, including a cytochrome b 5 and three histidine-rich motifs and membrane-spanning regions. Heterologous expression in Saccharomyces cerevisiae showed that monoene, diene and triene fatty acids having ∆(9)-double bond were substrates for PyDes6. No distinct preference between the n-3 and n-6 polyunsaturated fatty acyl substrates was found. The ∆(6)-desaturated products were markedly increased by codon optimization of PyDes6. CONCLUSION: The codon-optimized ∆(6)-desaturase gene generated in this study is a promising tool for further reconstitution of the fatty acid profile, in a host system of choice, for the production of economically important fatty acids, particularly the n-3 and n-6 polyunsaturated fatty acids.

Novel elongase of Pythium sp. with high specificity on Δ(6)-18C desaturated fatty acids.

We identified a novel elongase gene from a selected strain of the Oomycete, Pythium sp. BCC53698. Using a PCR approach, the cloned gene (PyElo) possessed an open reading frame (ORF) of 834 bp encoding 277 amino acid residues. A similarity search showed that it had homology with the PUFA elongases of several organisms. In addition, the signature characteristics, including four conserved motifs, a histidine-rich catalytic motif and membrane-associated feature were present in the Pythium gene. Heterologous expression in Saccharomyces cerevisiae showed that it was specific for fatty acid substrates, having a double bond at Δ(6)-position, which included γ-linolenic acid (GLA) and stearidonic acid (STA), and preferentially elongated the n3-18C PUFA. This is an elongase in Oomycete fungi, which displays very high specificity on Δ(6)-18C desaturated fatty acids. This will be a powerful tool to engineer PUFA biosynthesis in organisms of interest through the n-6 series pathway for producing value-added fatty acids.

Up-regulated expression of desaturase genes of Mucor rouxii in response to low temperature associates with pre-existing cellular fatty acid constituents.

Transcriptional response of desaturase genes to low temperature was investigated in the dimorphic fungus Mucor rouxii. The two morphological forms of M. rouxii, yeast-like and mycelial cells containing different fatty acid profiles were shifted from 30 to 10°C. Both cultures exhibited significantly altered fatty acid composition, whose content in polyunsaturated fatty acids increased as consequence of the temperature shift and was accompanied by a reduction of C18:1Δ(9) about 2 h after the temperature shift. These changes were particularly significant in phosphatidylcholine and phosphatidylethanolamine fractions. Moreover, the fatty acid profiles of monoacylglycerol and diacylglycerol were also modulated in response to the lower temperature of incubation. The changes of membrane lipids of M. rouxii were due to the cold-induced expression of Δ(9)-, Δ(12)- and Δ(6)-desaturase genes. Although the mRNA levels of the three desaturases were transiently induced by lowering the temperature, the pre-existing composition of fatty acid profiles of mycelial and yeast-like forms of M. rouxii may have lead to different expression profiles of desaturase genes that modified their membrane physical state under cold shock. While expression of Δ(12)-desaturase gene contributed mainly to cold acclimation of mycelia, Δ(9)-desaturase expression was the main transcript identified in the yeast-like culture after temperature shift.