Complete genome sequence of lovastatin producer Aspergillus terreus ATCC 20542 and evaluation of genomic diversity among A. terreus strains

Screening and genetic engineering of marine-derived Aspergillus terreus for high-efficient production of lovastatin

BACKGROUND

Lovastatin has widespread applications thanks to its multiple pharmacological effects. Fermentation by filamentous fungi represents the major way of lovastatin production. However, the current lovastatin productivity by fungal fermentation is limited and needs to be improved.

RESULTS

In this study, the lovastatin-producing strains of Aspergillus terreus from marine environment were screened, and their lovastatin productions were further improved by genetic engineering. Five strains of A. terreus were isolated from various marine environments. Their secondary metabolites were profiled by metabolomics analysis using Ultra Performance Liquid Chromatography-Mass spectrometry (UPLC-MS) with Global Natural Products Social Molecular Networking (GNPS), revealing that the production of secondary metabolites was variable among different strains. Remarkably, the strain of A. terreus MJ106 could principally biosynthesize the target drug lovastatin, which was confirmed by High Performance Liquid Chromatography (HPLC) and gene expression analysis. By one-factor experiment, lactose was found to be the best carbon source for A. terreus MJ106 to produce lovastatin. To improve the lovastatin titer in A. terreus MJ106, genetic engineering was applied to this strain. Firstly, a series of strong promoters was identified by transcriptomic and green fluorescent protein reporter analysis. Then, three selected strong promoters were used to overexpress the transcription factor gene lovE encoding the major transactivator for lov gene cluster expression. The results revealed that compared to A. terreus MJ106, all lovE over-expression mutants exhibited significantly more production of lovastatin and higher gene expression. One of them, LovE-b19, showed the highest lovastatin productivity at a titer of 1512 mg/L, which represents the highest production level reported in A. terreus.

CONCLUSION

Our data suggested that combination of strain screen and genetic engineering represents a powerful tool for improving the productivity of fungal secondary metabolites, which could be adopted for large-scale production of lovastatin in marine-derived A. terreus.

Species-specific effects of the introduction of Aspergillus nidulans gfdB in osmophilic aspergilli

Industrial fungi need a strong environmental stress tolerance to ensure acceptable efficiency and yields. Previous studies shed light on the important role that Aspergillus nidulans gfdB, putatively encoding a NAD⁺-dependent glycerol-3-phosphate dehydrogenase, plays in the oxidative and cell wall integrity stress tolerance of this filamentous fungus model organism. The insertion of A. nidulans gfdB into the genome of Aspergillus glaucus strengthened the environmental stress tolerance of this xerophilic/osmophilic fungus, which may facilitate the involvement of this fungus in various industrial and environmental biotechnological processes. On the other hand, the transfer of A. nidulans gfdB to Aspergillus wentii, another promising industrial xerophilic/osmophilic fungus, resulted only in minor and sporadic improvement in environmental stress tolerance and meanwhile partially reversed osmophily. Because A. glaucus and A. wentii are phylogenetically closely related species and both fungi lack a gfdB ortholog, these results warn us that any disturbance of the stress response system of the aspergilli may elicit rather complex and even unforeseeable, species-specific physiological changes. This should be taken into consideration in any future targeted industrial strain development projects aiming at the fortification of the general stress tolerance of these fungi. KEY POINTS: • A. wentii c' gfdB strains showed minor and sporadic stress tolerance phenotypes. • The osmophily of A. wentii significantly decreased in the c' gfdB strains. • Insertion of gfdB caused species-specific phenotypes in A. wentii and A. glaucus.

Whole genome sequence characterization of Aspergillus terreus ATCC 20541 and genome comparison of the fungi A. terreus

Aspergillus terreus is well-known for lovastatin and itaconic acid production with biomedical and commercial importance. The mechanisms of metabolite formation have been extensively studied to improve their yield through genetic engineering. However, the combined repertoire of carbohydrate-active enzymes (CAZymes), cytochrome P450s (CYP) enzymes, and secondary metabolites (SMs) in the different A. terreus strains has not been well studied yet, especially with respect to the presence of biosynthetic gene clusters (BGCs). Here we present a 30 Mb whole genome sequence of A. terreus ATCC 20541 in which we predicted 10,410 protein-coding genes. We compared the CAZymes, CYPs enzyme, and SMs across eleven A. terreus strains, and the results indicate that all strains have rich pectin degradation enzyme and CYP52 families. The lovastatin BGC of lovI was linked with lovF in A. terreus ATCC 20541, and the phenomenon was not found in the other strains. A. terreus ATCC 20541 lacked a non-ribosomal peptide synthetase (AnaPS) participating in acetylaszonalenin production, which was a conserved protein in the ten other strains. Our results present a comprehensive analysis of CAZymes, CYPs enzyme, and SM diversities in A. terreus strains and will facilitate further research in the function of BGCs associated with valuable SMs.

Bioprocessing of Two Crop Residues for Animal Feeding into a High-Yield Lovastatin Feed Supplement

Simple Summary

Lovastatin is a fungal secondary metabolite that can mitigate rumen methane production. This work aimed at evaluating the lovastatin production by solid-state fermentation from selected crop residues and A. terreus strains, considering the post-fermented residues as feed supplements for ruminants. Fermented oat straw by A. terreus CDBB H-194 exhibited the highest lovastatin yield (23.8 mg/g DM fed). GC–MS analysis identified only a couple of compounds from the residues fermented by CDBB H-194 (1,3-dipalmitin trimethylsilyl ether in the fermented oat straw) and stearic acid hydrazide in the fermented wheat bran) that could negatively affect ruminal bacteria and fungi.

Abstract

This work aimed to evaluate the lovastatin (Lv) production by solid-state fermentation (SSF) from selected crop residues, considering the post-fermented residues as feed supplements for ruminants. The SSF was performed with two substrates (wheat bran and oat straw) and two A. terreus strains (CDBB H-194 and CDBB H-1976). The Lv yield, proximate analysis, and organic compounds by GC–MS in the post-fermented residues were assessed. The combination of the CDBB H-194 strain with oat straw at 16 d of incubation time showed the highest Lv yield (23.8 mg/g DM fed) and the corresponding degradation efficiency of hemicellulose + cellulose was low to moderate (24.1%). The other three treatments showed final Lv concentrations in decreasing order of 9.1, 6.8, and 5.67 mg/g DM fed for the oat straw + CDBB H-1976, wheat bran + CDBB H-194, and wheat bran + CDBB H-1976, respectively. An analysis of variance of the 2² factorial experiment of Lv showed a strong significant interaction between the strain and substrate factors. The kinetic of Lv production adequately fitted a zero-order model in the four treatments. GC–MS analysis identified only a couple of compounds from the residues fermented by A. terreus CDBB H-194 (1,3-dipalmitin trimethylsilyl ether in the fermented oat straw and stearic acid hydrazide in the fermented wheat bran) that could negatively affect ruminal bacteria and fungi. Solid-state fermentation of oat straw with CDBB H-194 deserves further investigation due to its high yield of Lv; low dietary proportions of this post-fermented oat straw could be used as an Lv-carrier supplement for rumen methane mitigation.

High molecular weight DNA extraction methods lead to high quality filamentous ascomycete fungal genome assemblies using Oxford Nanopore sequencing

During the last two decades, whole-genome sequencing has revolutionized genetic research in all kingdoms, including fungi. More than 1000 fungal genomes have been submitted to sequence databases, mostly obtained through second generation short-read DNA sequencing. As a result, highly fragmented genome drafts have typically been obtained. However, with the emergence of third generation long-read DNA sequencing, the assembly challenge can be overcome and highly contiguous assemblies obtained. Such attractive results, however, are extremely dependent on the ability to extract highly purified high molecular weight (HMW) DNA. Extraction of such DNA is currently a significant challenge for all species with cell walls, not least fungi. In this study, four isolates of filamentous ascomycetes (Apiospora pterospermum, Aspergillus sp. (subgen. Cremei), Aspergillus westerdijkiae, and Penicillium aurantiogriseum) were used to develop extraction and purification methods that result in HMW DNA suitable for third generation sequencing. We have tested and propose two straightforward extraction methods based on treatment with either a commercial kit or traditional phenol-chloroform extraction both in combination with a single commercial purification method that result in high quality HMW DNA from filamentous ascomycetes. Our results demonstrated that using these DNA extraction methods and coverage, above 75 x of our haploid filamentous ascomycete fungal genomes result in complete and contiguous assemblies.