Genomic and Transcriptomic Study for Screening Genes Involved in the Limonene Biotransformation of Penicillium digitatum DSM 62840

A fungal P450 enzyme from Fusarium equiseti HG18 with 7β-hydroxylase activity in biosynthesis of ursodeoxycholic acid

Cytochrome P450 enzyme with 7β-hydroxylation capacity has attracted widespread attentions due to the vital roles in the biosynthesis of ursodeoxycholic acid (UDCA), a naturally active molecule for the treatment of liver and gallbladder diseases. In this study, a novel P450 hydroxylase (P450FE) was screen out from Fusarium equiseti HG18 and identified by a combination of genome and transcriptome sequencing, as well as heterologous expression in Pichia pastoris. The biotransformation of lithocholic acid (LCA) by whole cells of recombinant Pichia pastoris further confirmed the C7β-hydroxylation with 5.2% UDCA yield. It was firstly identified a fungal P450 enzyme from Fusarium equiseti HG18 with the capacity to catalyze the LCA oxidation producing UDCA. The integration of homology modeling and molecular docking discovered the substrate binding to active pockets, and the key amino acids in active center were validated by site-directed mutagenesis, and revealed that Q112, V362 and L363 were the pivotal residues of P450FE in regulating the activity and selectivity of 7β-hydroxylation. Specifically, V362I mutation exhibited 2.6-fold higher levels of UDCA and higher stereospecificity than wild-type P450FE. This advance provided guidance for improving the catalytic efficiency and selectivity of P450FE in LCA hydroxylation, indicative of the great potential in green synthesis of UDCA from biologically toxic LCA.

Isolation, purification, and mass spectrometry identification of the enzyme involved in citrus flavor (+)-valencene biotransformation to (+)-nootkatone by Yarrowia lipolytica

BACKGROUND

(+)-Nootkatone is a highly valuable sesquiterpene compound that can be used as an aromatic in the food industry because of its grapefruit flavor and low sensory threshold. The unconventional yeast Yarrowia lipolytica has many unique physical and chemical properties, metabolic characteristics, and genetic structure, which has aroused the interest of researchers. Previous research showed that Y. lipolytica possesses the ability to transform the sesquiterpene (+)-valencene to (+)-nootkatone. The aim of this study was to isolate, purify, and identify the enzyme involved in the (+)-valencene bioconversion to (+)-nootkatone by Y. lipolytica.

RESULTS

In this study, ultrasonic-assisted extraction, ammonium sulfate precipitation, anion-exchange chromatography, and gel-filtration chromatography were used to separate and purify the enzyme involved in the (+)-valencene bioconversion by Y. lipolytica. The protein was identified as aldehyde dehydrogenase (ALDH) (gene0658) using sodium dodecyl sulfate polyacrylamide gel electrophoresis and liquid chromatography-tandem mass spectrometry analysis. The ALDH had the highest activity when the pH value was 6.0 and the temperature was 30 °C. The activity of ALDH was significantly stimulated by ferrous ions and inhibited by barium, calcium, and magnesium ions.

CONCLUSION

This is the first time that ALDH was found to participate in (+)-valencene biotransformation by Y. lipolytica. It may be involved in regulating the microbial transformation of (+)-valencene to (+)-nootkatone through redox characteristics. This study provides a theoretical basis and reference for the biological synthesis of citrus flavor (+)-nootkatone. © 2023 Society of Chemical Industry.

Transcriptomic Profile of Penicillium digitatum Reveals Novel Aspects of the Mode of Action of the Antifungal Protein AfpB

Antifungal proteins (AFPs) from filamentous fungi are promising biomolecules to control fungal pathogens. Understanding their biological role and mode of action is essential for their future application. AfpB from the citrus fruit pathogen Penicillium digitatum is highly active against fungal phytopathogens, including its native fungus. Our previous data showed that AfpB acts through a multitargeted three-stage process: interaction with the outer mannosylated cell wall, energy-dependent cell internalization, and intracellular actions that result in cell death. Here, we extend these findings by characterizing the functional role of AfpB and its interaction with P. digitatum through transcriptomic studies. For this, we compared the transcriptomic response of AfpB-treated P. digitatum wild type, a ΔafpB mutant, and an AfpB-overproducing strain. Transcriptomic data suggest a multifaceted role for AfpB. Data from the ΔafpB mutant suggested that the afpB gene contributes to the overall homeostasis of the cell. Additionally, these data showed that AfpB represses toxin-encoding genes, and they suggest a link to apoptotic processes. Gene expression and knockout mutants confirmed that genes coding for acetolactate synthase (ALS) and acetolactate decarboxylase (ALD), which belong to the acetoin biosynthetic pathway, contribute to the inhibitory activity of AfpB. Moreover, a gene encoding a previously uncharacterized extracellular tandem repeat peptide (TRP) protein showed high induction in the presence of AfpB, whereas its TRP monomer enhanced AfpB activity. Overall, our study offers a rich source of information to further advance in the characterization of the multifaceted mode of action of AFPs. IMPORTANCE Fungal infections threaten human health worldwide and have a negative impact on food security, damaging crop production and causing animal diseases. At present, only a few classes of fungicides are available due to the complexity of targeting fungi without affecting plant, animal, or human hosts. Moreover, the intensive use of fungicides in agriculture has led to the development of resistance. Therefore, there is an urgent need to develop antifungal biomolecules with new modes of action to fight human-, animal-, and plant-pathogenic fungi. Fungal antifungal proteins (AFPs) offer great potential as new biofungicides to control deleterious fungi. However, current knowledge about their killing mechanism is still limited, which hampers their potential applicability. AfpB from P. digitatum is a promising molecule with potent and specific fungicidal activity. This study further characterizes its mode of action, opening avenues for the development of new antifungals.

SPME-GC-MS combined with chemometrics to assess the impact of fermentation time on the components, flavor, and function of Laoxianghuang

Laoxianghuang, fermented from Citrus medica L. var. Sarcodactylis Swingle of the Rutaceae family, is a medicinal food. The volatiles of Laoxianghuang fermented in different years were obtained by solid-phase microextraction combined with gas chromatography–mass spectrometry (SPME-GC–MS). Meanwhile, the evolution of its component-flavor function during the fermentation process was explored in depth by combining chemometrics and performance analyses. To extract the volatile compounds from Laoxianghuang, the fiber coating, extraction time, and desorption temperature were optimized in terms of the number and area of peaks. A polydimethylsiloxane/divinylbenzene (PDMS/DVB) with a thickness of 65 μm fiber, extraction time of 30 min, and desorption temperature of 200 °C were shown to be the optimal conditions. There were 42, 44, 52, 53, 53, and 52 volatiles identified in the 3rd, 5th, 8th, 10th, 15th, and 20th years of fermentation of Laoxianghuang, respectively. The relative contents were 97.87%, 98.50%, 98.77%, 98.85%, 99.08%, and 98.36%, respectively. Terpenes (mainly limonene, γ-terpinene and cymene) displayed the highest relative content and were positively correlated with the year of fermentation, followed by alcohols (mainly α-terpineol, β-terpinenol, and γ-terpineol), ketones (mainly cyclohexanone, D(+)-carvone and β-ionone), aldehydes (2-furaldehyde, 5-methylfurfural, and 1-nonanal), phenols (thymol, chlorothymol, and eugenol), esters (bornyl formate, citronellyl acetate, and neryl acetate), and ethers (n-octyl ether and anethole). Principal component analysis (PCA) and hierarchical cluster analysis (HCA) showed a closer relationship between the composition of Laoxianghuang with similar fermentation years of the same gradient (3rd-5th, 8th-10th, and 15th-20th). Partial least squares discriminant analysis (PLS-DA) VIP scores and PCA-biplot showed that α-terpineol, γ-terpinene, cymene, and limonene were the differential candidate biomarkers. Flavor analysis revealed that Laoxianghuang exhibited wood odor from the 3rd to the 10th year of fermentation, while herb odor appeared in the 15th and the 20th year. This study analyzed the changing pattern of the flavor and function of Laoxianghuang through the evolution of the composition, which provided a theoretical basis for further research on subsequent fermentation.

Differential proteomic analysis of citrus flavor (+)-valencene biotransformation to (+)-nootkatone by Yarrowia lipolytica

Natural products (+)-nootkatone is an important sesquiterpene compound and is widely used in pharmaceutical, cosmetic, agricultural and food industries. The aim of this study was to analyze the differentially expressed proteins (DEPs) during citrus aroma compound (+)-valencene biotransformation to (+)-nootkatone by Yarrowia lipolyticaby with high-throughput LC-MS/MS. A total of 778 proteins were differentially expressed, 385 DEPs were significantly up-regulated and 393 DEPs were markedly down-regulated. It was found that the enzymes transformed (+)-valencene to (+)-nootkatone were mainly existed in yeast intracellular and precipitated under the condition of 30-40 % ammonium sulfate. Most DEPs involved in amino acid and fatty acid metabolism were down-regulated during (+)-valencene biotransformation. The DEPs related to the carbohydrate metabolism, energy metabolism and most of transporter proteins were significantly up-regulated. Furthermore, the key enzymes involved in (+)-valencene transformation might be related to cytochrome P450s (gene2215 and gene2911) and dehydrogenases (gene6493). This is the first time that proteomics was used to investigate the metabolism mechanism of Yarrowia lipolytica during (+)-valencene biotransformation. The proteomic analysis of Yarrowia lipolytica provided a foundation for the molecular regulatory mechanism in the biotransformation to (+)-nootkatone from (+)-valencene.

Identification of functional genes associated with the biotransformation of limonene to trans-dihydrocarvone in Klebsiella sp. O852

BACKGROUND

Natural dihydrocarvone has been widely used in the food, cosmetics, agrochemicals and pharmaceuticals industries because of its sensory properties and physiological effects. In our previous study, Klebsiella sp. O852 was shown to be capable of converting limonene to trans-dihydrocarvone with high catalytic efficiency. Thus, it was essential to identify and characterize the functional genes involved in limonene biotransformation using genome sequencing and heterologous expression.

RESULTS

The 5.49-Mb draft genome sequence of Klebsiella sp. O852 contained 5218 protein-encoding genes. Seven candidate genes participating in the biotransformation of limonene to trans-dihydrocarvone were identified by genome analysis. Heterologous expression of these genes in Escherichia coli BL21(DE3) indicated that 0852_GM005124 and 0852_GM003417 could hydroxylate limonene in the six position to yield carveol, carvone and trans-dihydrocarvone. 0852_GM002332 and 0852_GM001602 could catalyze the oxidation of carveol to carvone and trans-dihydrocarvone. 0852_GM000709, 0852_GM001600 and 0852_GM000954 had high carvone reductase activity toward the hydrogenation of carvone to trans-dihydrocarvone.

CONCLUSION

The results obtained in the present study suggest that the seven genes described above were responsible for converting limonene to trans-dihydrocarvone. The present study contributes to providing a foundation for the industrial production of trans-dihydrocarvone in microbial chassis cells using synthetic biology strategies. © 2021 Society of Chemical Industry.

Draft Genome Assembly and Annotation for Cutaneotrichosporon dermatis NICC30027, an Oleaginous Yeast Capable of Simultaneous Glucose and Xylose Assimilation

The identification of oleaginous yeast species capable of simultaneously utilizing xylose and glucose as substrates to generate value-added biological products is an area of key economic interest. We have previously demonstrated that the Cutaneotrichosporon dermatis NICC30027 yeast strain is capable of simultaneously assimilating both xylose and glucose, resulting in considerable lipid accumulation. However, as no high-quality genome sequencing data or associated annotations for this strain are available at present, it remains challenging to study the metabolic mechanisms underlying this phenotype. Herein, we report a 39,305,439 bp draft genome assembly for C. dermatis NICC30027 comprised of 37 scaffolds, with 60.15% GC content. Within this genome, we identified 524 tRNAs, 142 sRNAs, 53 miRNAs, 28 snRNAs, and eight rRNA clusters. Moreover, repeat sequences totaling 1,032,129 bp in length were identified (2.63% of the genome), as were 14,238 unigenes that were 1,789.35 bp in length on average (64.82% of the genome). The NCBI non-redundant protein sequences (NR) database was employed to successfully annotate 11,795 of these unigenes, while 3,621 and 11,902 were annotated with the Swiss-Prot and TrEMBL databases, respectively. Unigenes were additionally subjected to pathway enrichment analyses using the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins (COG), Clusters of orthologous groups for eukaryotic complete genomes (KOG), and Non-supervised Orthologous Groups (eggNOG) databases. Together, these results provide a foundation for future studies aimed at clarifying the mechanistic basis for the ability of C. dermatis NICC30027 to simultaneously utilize glucose and xylose to synthesize lipids.

Combined transcriptome and metabolome analyses reveal the potential mechanism for the inhibition of Penicillium digitatum by X33 antimicrobial oligopeptide

Penicillium digitatum is the primary spoilage fungus that causes green mold during postharvest in citrus. To reduce economic losses, developing more efficient and less toxic natural antimicrobial agents is urgently required. We previously found that the X33 antimicrobial oligopeptide (X33 AMOP), produced by Streptomyces lavendulae X33, exhibited a sterilization effect on P. digitatum. In this study, the effects, and physiological mechanisms of X33 AMOP as an inhibitor of P. digitatum were investigated. The transcriptional and metabolome profiling of P. digitatum exposed to X33 AMOP revealed 3648 genes and 190 metabolites that were prominently changed. The omics analyses suggested that X33 AMOP mainly inhibited P. digitatum growth by affecting cell integrity, genetic information delivery, oxidative stress tolerance, and energy metabolism. These findings provide helpful information regarding the antimicrobial mechanism of X33 AMOP against P. digitatum at the molecular level and indicate that X33 AMOP is a potential candidate to control P. digitatum.

Advances on (+)-nootkatone microbial biosynthesis and its related enzymes

(+)-Nootkatone is an important functional sesquiterpene and is comprehensively used in pharmaceutical, cosmetic, agricultural and food flavor industries. However, (+)-nootkatone is accumulated trace amounts in plants, and the demand for industry is mainly met by chemical methods which is harmful to the environment. The oxygen-containing sesquiterpenes prepared using microbial methods can be considered as "natural." Microbial transformation has the advantages of mild reaction conditions, high efficiency, environmental protection, and strong stereoselectivity, and has become an important method for the production of natural spices. The microbial biosynthesis of (+)-nootkatone from the main precursor (+)-valencene is summarized in this paper. Whole-cell systems of fungi, bacteria, microalgae, and plant cells have been employed. It was described that the enzymes involved in the microbial biosynthesis of (+)-nootkatone, including cytochrome p450 enzymes, laccase, lipoxygenase, and so on. More recently, the related enzymes were expressed in microbial hosts to heterologous produce (+)-nootkatone, such as Escherichia coli, Pichia pastoris, Yarrowia lipolytica, and Saccharomyces cerevisiae. Finally, the development direction of research for realizing industrialization of microbial transformation was summarized and it provided many options for future improved bioprocesses.

Sequencing and Comparative Genomic Analysis of a Highly Metal-Tolerant Penicillium janthinellum P1 Provide Insights Into Its Metal Tolerance

Heavy metal pollution is a global knotty problem and fungi hold promising potential for the remediation of wastewater containing heavy metals. Here, a new highly chromium-tolerance species, Penicillium janthinellum P1, is investigated. The genome of P1 was sequenced and assembled into 30 Mb genome size containing 10,955 predicted protein-coding genes with a GC content of 46.16% through an integrated method of Illumina short-read sequencing and single-molecule real-time Pacific Biosciences sequencing platforms. Through a phylogenetic analysis with model species of fungi, the evolutionary divergence time of Penicillium janthinellum P1 and Penicillium oxalicum 114-2 was estimated to be 74 MYA. 33 secondary metabolism gene clusters were identified via antiSMASH software, mainly including non-ribosomal peptide synthase genes and T1 polyketide synthase genes. 525 genes were annotated to encode enzymes that act on carbohydrates, involving 101 glucose-degrading enzymes and 24 polysaccharide synthase. By whole-genome sequence analysis, large numbers of metal resistance genes were found in strain P1. Especially ABC transporter and Superoxide dismutase ensure that the P1 fungus can survive in a chromium-polluted environment. ChrA and ChrR were also identified as key genes for chromium resistance. Analysis of their genetic loci revealed that the specific coding-gene arrangement may account for the fungus’s chromium resistance. Genetic information and comparative analysis of Penicillium janthinellum are valuable for further understanding the mechanism of high resistance to heavy metal chromium, and gene loci analysis provides a new perspective for identifying chromium-resistant strains.