Novel osmotic stress control strategy for improved pneumocandin B0 production in Glarea lozoyensis combined with a mechanistic analysis at the transcriptome level

Revealing the regulatory impact of nutrient on the production of (R)-2-(4-Hydroxyphenoxy)propanoic acid by Beauveria bassiana biofilms through comparative transcriptomics analyse

Carbon and nitrogen play a fundamental role in the architecture of fungal biofilm morphology and metabolite production. However, the regulatory mechanism of nutrients remains to be fully understood. In this study, the formation of Beauveria bassiana biofilm and the production of (R)-2-(4-Hydroxyphenoxy)propanoic acid in two media with different carbon and nitrogen sources (GY: Glucose as a carbon source and yeast extract as a nitrogen source, MT: Mannitol as a carbon source and tryptone as a nitrogen source) were compared. R-HPPA production increased 2.85-fold in media MT than in media GY. Different fungal biofilm morphology and architecture were discovered in media GY and MT. Comparative transcriptomics revealed up-regulation of mitogen-activated protein kinase (MAPK) pathway and polysaccharides degradation genes affecting mycelial morphology and polysaccharides yield of the extracellular polymeric substances (EPS) in MT medium biofilms. Upregulation of genes related to NADH synthesis (carbon metabolism, amino acid metabolism, glutamate cycle) causes NADH accumulation and triggers an increase in R-HPPA production. These data provide a valuable basis for future studies on regulating fungal biofilm morphology and improving the production of high-value compounds.

Efficient production of R-2-(4-hydroxyphenoxy) propionic acid by Beauveria bassiana using biofilm-based two-stage fermentation

In this work, a novel biofilm-based fermentation of Beauveria bassiana was employed to convert R-2- phenoxypropionic acid (R-PPA) to R-2-(4-hydroxyphenoxy) propionic acid (R-HPPA). The biofilm culture model of Beauveria bassiana produced a significantly higher R-HPPA titer than the traditional submerged fermentation method. Mannitol dosage, tryptone dosage, and initial pH were the factors that played a significant role in biofilm formation and R-HPPA synthesis. Under the optimal conditions, the maximum R-HPPA titer and productivity approached 22.2 g/L and 3.2 g/(L·d), respectively. A two-stage bioreactor combining agitation and static incubation was developed to further increase R-HPPA production. The process was optimized to achieve 100 % conversion of R-PPA, with a maximum R-HPPA titer of 50 g/L and productivity of 3.8 g/(L·d). This newly developed biofilm-based two-stage fermentation process provides a promising strategy for the industrial production of R-HPPA and related hydroxylated aromatic compounds.

Effect of fatty acids on intracellular pneumocandin B0 storage in the fermentation of Glarea lozoyensis

The natural product pneumocandin B0 is the precursor of the antifungal drug caspofungin. To explore the relationship between pneumocandin B0 and oil. We found that the addition of 1 g/L of oil to the fermentation medium is more conducive to the production of pneumocandin B0. The metabolic reaction mechanism was explored using different fatty acids and the results showed that stearic acid and acetic acid increased the total production of pneumocandin B0 by 22.98% and 9.08%, respectively, as well as increasing the content of intracellular lipid droplets. We also analyzed gene expression and pathway differences between the two different fatty acids using transcriptome analyses. The addition of both acetic acid and stearic acid promoted an active pentose phosphate pathway, providing cells with higher intracellular reducing power. We found that the addition of fatty acids can lead to lipid accumulation, and lipid droplets can sequester lipophilic secondary metabolites such as pneumocandin B0 to reduce cell damage. These results provide novel insights into the relationship between pneumocandin B0 biosynthesis and fatty acids in G. lozoyensis. In addition, this study provides important genetic information for improving the yield of pneumocandin B0 through a strategy of metabolic engineering in the future.

A comprehensive genomic analysis provides insights on the high environmental adaptability of Acinetobacter strains

Acinetobacter is ubiquitous, and it has a high species diversity and a complex evolutionary pattern. To elucidate the mechanism of its high ability to adapt to various environment, 312 genomes of Acinetobacter strains were analyzed using the phylogenomic and comparative genomics methods. It was revealed that the Acinetobacter genus has an open pan-genome and strong genome plasticity. The pan-genome consists of 47,500 genes, with 818 shared by all the genomes of Acinetobacter, while 22,291 are unique genes. Although Acinetobacter strains do not have a complete glycolytic pathway to directly utilize glucose as carbon source, most of them harbored the n-alkane-degrading genes alkB/alkM (97.1% of tested strains) and almA (96.7% of tested strains), which were responsible for medium-and long-chain n-alkane terminal oxidation reaction, respectively. Most Acinetobacter strains also have catA (93.3% of tested strains) and benAB (92.0% of tested strains) genes that can degrade the aromatic compounds catechol and benzoic acid, respectively. These abilities enable the Acinetobacter strains to easily obtain carbon and energy sources from their environment for survival. The Acinetobacter strains can manage osmotic pressure by accumulating potassium and compatible solutes, including betaine, mannitol, trehalose, glutamic acid, and proline. They respond to oxidative stress by synthesizing superoxide dismutase, catalase, disulfide isomerase, and methionine sulfoxide reductase that repair the damage caused by reactive oxygen species. In addition, most Acinetobacter strains contain many efflux pump genes and resistance genes to manage antibiotic stress and can synthesize a variety of secondary metabolites, including arylpolyene, β-lactone and siderophores among others, to adapt to their environment. These genes enable Acinetobacter strains to survive extreme stresses. The genome of each Acinetobacter strain contained different numbers of prophages (0-12) and genomic islands (GIs) (6-70), and genes related to antibiotic resistance were found in the GIs. The phylogenetic analysis revealed that the alkM and almA genes have a similar evolutionary position with the core genome, indicating that they may have been acquired by vertical gene transfer from their ancestor, while catA, benA, benB and the antibiotic resistance genes could have been acquired by horizontal gene transfer from the other organisms.

Improvement of beauvericin production by Fusarium oxysporum AB2 under solid-state fermentation using an optimised liquid medium and co-cultures

The production of beauvericin (BEA) by Fusarium oxysporum AB2 in liquid medium (SmF) was compared to that on solid medium (SSF) on inert support (polyurethane foam or PUF), using a previously optimised medium. The analysis included two different concentrations of the medium (1 × and 3 ×). Under SSF, the production of BEA (22.8 mg·L^-1) was higher relative to SmF (0.8 mg·L^-1). The production increased proportionally in the concentrated medium (3 ×) (65.3 mg·L^-1); using the concentrated medium in SmF, the production of BEA was completely inhibited, although more biomass was produced. The peak of BEA production was reached on day 7 and remained stable until day 11; sustained production after several days has not been achieved in similar reports. The presence of BEA was corroborated by high-performance liquid chromatography (HPLC) and mass spectrometry. The BEA production profile is shown performing mixed cultures of Fusarium oxysporum AB2 and Epicoccum nigrum TORT using the same system, increasing the production of BEA up to 84.6 mg·L^-1. We propose SSF using polyurethane foam (PUF) as a solid support as a new culture system for obtaining secondary metabolites such as BEA.

Simultaneous improvement of lincomycin A production and reduction of lincomycin B levels in Streptomyces lincolnensis using a combined medium optimization approach

Purpose

The current study aimed to optimize the culture and production parameters of industrial production of lincomycin A by Streptomyces lincolnensis using a statistical approach that could also reduce unwanted by-products.

Methods

The Plackett-Burman design, steepest ascent method, and response surface design were used to evaluate different factors that affect lincomycin A production.

Results

Using an optimized S. lincolnensis fermentation medium, lincomycin A production was increased up to 4600 mg/L in shaking flasks, which indicated a 28.3% improvement over previous production in an un-optimized medium (3585 mg/L). Additionally, the concentration of lincomycin B by-product was reduced to 0.8%, which was 82.2% lower than that in the un-optimized medium. Further, quantitative real-time PCR analysis revealed the optimized medium improved lincomycin A production by stimulating key genes in the lincomycin A biosynthesis pathway, as well as an osmotic stress gene.

Conclusions

Based on the results, the sequential optimization strategy in this study provides powerful means for the enhancement of lincomycin A with less by-product. We found that osmotic stress reduced the concentration of lincomycin B, which could also help reduce fermentation by-product yields in other actinobacteria.

Glyap1 regulates pneumocandin B0 synthesis by controlling the intracellular redox balance in Glarea lozoyensis

Pneumocandin B₀, the precursor of the antifungal drug caspofungin, is a lipohexapeptide produced by the fungus Glarea lozoyensis. Oxidative stress and the resulting production of reactive oxygen species (ROS) are known to be involved in the regulation of pneumocandin B₀ biosynthesis. In this study, the Glyap1 gene of Glarea lozoyensis, a homologue of the yeast redox regulator YAP1, was knocked out. The intracellular ROS levels of the resulting ΔGlyap1 strain were higher than in the wild-type strain, which was caused by the downregulated expression of superoxide dismutase (SOD) and catalase (CAT). Compared with the wild-type strain, ΔGlyap1 exhibited an oxidative phenotype throughout its life cycle, which resulted in significantly higher pneumocandin B₀ production per unit biomass. In addition, ΔGlyap1 showed growth inhibition and decreased pneumocandin B₀ production in the presence of CCl₄, which leads to strong oxidative stress. To overcome the strain's sensitivity, a three-stage antioxidant addition strategy was developed. This approach significantly improved the growth of ΔGlyap1 while maintaining a high pneumocandin B₀ production per unit biomass, which reached 38.78 mg/g DCW. Notably, this result represents a 50% increase over the wild-type strain. These findings provide new insights into the regulatory mechanisms that control pneumocandin B₀ production under oxidative stress, which may be applied to improve the production of other secondary metabolites. KEY POINTS: • Glyap1 is involved in expression of redox and pneumocandin B₀ synthesis-related genes. • Addition of a three-stage antioxidant alleviated the sensitivity of ΔGlyap1 strain. • The yield of pneumocandin B₀ per unit biomass of ΔGlyap1 strain was 38.78 mg/g DCW.

Echinocandins: structural diversity, biosynthesis, and development of antimycotics

Abstract

Echinocandins are a clinically important class of non-ribosomal antifungal lipopeptides produced by filamentous fungi. Due to their complex structure, which is characterized by numerous hydroxylated non-proteinogenic amino acids, echinocandin antifungal agents are manufactured semisynthetically. The development of optimized echinocandin structures is therefore closely connected to their biosynthesis. Enormous efforts in industrial research and development including fermentation, classical mutagenesis, isotope labeling, and chemical synthesis eventually led to the development of the active ingredients caspofungin, micafungin, and anidulafungin, which are now used as first-line treatments against invasive mycosis. In the last years, echinocandin biosynthetic gene clusters have been identified, which allowed for the elucidation but also engineering of echinocandin biosynthesis on the molecular level. After a short description of the history of echinocandin research, this review provides an overview of the current knowledge of echinocandin biosynthesis with a special focus of the diverse structural elements, their biosynthetic background, and structure−activity relationships.

Key points

• Complex and highly oxidized lipopeptides produced by fungi.

• Crucial in the design of drugs: side chain, solubility, and hydrolytic stability.

• Genetic methods for engineering biosynthesis have recently become available.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-020-11022-y.

CRISPR/Cas9-Based Genome Editing in the Filamentous Fungus Glarea lozoyensis and Its Application in Manipulating gloF

Glarea lozoyensis is an important industrial fungus that produces the pneumocandin B0, which is used for the synthesis of antifungal drug caspofungin. However, because of the limitations and complications of traditional genetic tools, G. lozoyensis strain engineering has been hindered. In this study, we established an efficient CRISPR/Cas9-based gene editing tool in G. lozoyensis SIPI1208. With this method, gene mutagenesis efficiency in the target locus can be up to 80%, which enables the rapid gene knockout. According to the reports, GloF and Ap-HtyE, proline hydroxylases involved in pneumocandin and Echinocandin B biosynthesis, respectively, can catalyze the proline to generate different ratios of trans-3-hydroxy-l-proline to trans-4-hydroxy-l-proline. Heterologous expression of Ap-HtyE in G. lozoyensis decreased the ratio of pneumocandin C0 to (pneumocandin B0 + pneumocandin C0) from 33.5% to 11% without the addition of proline to the fermentation medium. Furthermore, the gloF was replaced by ap-htyE to study the production of pneumocandin C0. However, the gene replacement has been hampered by traditional gene tools since gloF and gloG, two contiguous genes indispensable in the biosynthesis of pneumocandins, are cotranscribed into one mRNA. With the CRISPR/Cas9 strategy, ap-htyE was knocked in and successfully replaced gloF, and results showed that the knock-in strain retained the ability to produce pneumocandin B0, but the production of pneumocandin C0 was abolished. Thus, this strain displayed a competitive advantage in the industrial production of pneumocandin B0. In summary, this study showed that the CRISPR/Cas9-based gene editing tool is efficient for manipulating genes in G. lozoyensis.

Comparative Transcriptomics Analysis of the Responses of the Filamentous Fungus Glarea lozoyensis to Different Carbon Sources

The natural product pneumocandin B₀ is the precursor of the antifungal drug caspofungin. We found that replacing glucose in the initial fermentation medium with 20 g/L fructose is more conducive to pneumocandin B₀ production and biomass accumulation. In order to explore the mechanism of the different metabolic responses to fructose and glucose, we used each as the sole carbon source, and the results showed that fructose increased the total pneumocandin B₀ yield and biomass by 54.76 and 13.71%, respectively. Furthermore, we analyzed the differences of gene expression and metabolic pathways between the two different carbon sources by transcriptomic analysis. When fructose was used as the carbon source, genes related to the pentose phosphate pathway (PPP), glycolysis and branched-chain amino acid metabolism were significantly upregulated, resulting in increased intracellular pools of NADPH and acetyl-CoA in Glarea lozoyensis for cell growth and pneumocandin B₀ product synthesis. Interestingly, the pneumocandin B₀ biosynthetic gene cluster and the genes of the TCA cycle were significantly downregulated, while the FAS genes were significantly upregulated, indicating that more acetyl-CoA was used for fatty acid synthesis. In particular, we found that excessive synthesis of fatty acids caused lipid accumulation, and lipid droplets can sequester lipophilic secondary metabolites such as pneumocandin B₀ to reduce cell damage, which may also be an important reason for the observed increase of pneumocandin B₀ yield. These results provide new insights into the relationship between pneumocandin B₀ biosynthesis and carbon sources in G. lozoyensis. At the same time, this study provides important genomic information for improving pneumocandin B₀ production through metabolic engineering strategies in the future.