Systems metabolic engineering of the primary and secondary metabolism of Streptomyces albidoflavus enhances production of the reverse antibiotic nybomycin against multi-resistant Staphylococcus aureus

Nybomycin is an antibiotic compound with proven activity against multi-resistant Staphylococcus aureus, making it an interesting candidate for combating these globally threatening pathogens. For exploring its potential, sufficient amounts of nybomycin and its derivatives must be synthetized to fully study its effectiveness, safety profile, and clinical applications. As native isolates only accumulate low amounts of the compound, superior producers are needed. The heterologous cell factory S. albidoflavus 4N24, previously derived from the cluster-free chassis S. albidoflavus Del14, produced 860 μg L-1 of nybomycin, mainly in the stationary phase. A first round of strain development modulated expression of genes involved in supply of nybomycin precursors under control of the common Perm* promoter in 4N24, but without any effect. Subsequent studies with mCherry reporter strains revealed that Perm* failed to drive expression during the product synthesis phase but that use of two synthetic promoters (PkasOP* and P41) enabled strong constitutive expression during the entire process. Using PkasOP*, several rounds of metabolic engineering successively streamlined expression of genes involved in the pentose phosphate pathway, the shikimic acid pathway, supply of CoA esters, and nybomycin biosynthesis and export, which more than doubled the nybomycin titer to 1.7 mg L-1 in the sixth-generation strain NYB-6B. In addition, we identified the minimal set of nyb genes needed to synthetize the molecule using single-gene-deletion strains. Subsequently, deletion of the regulator nybW enabled nybomycin production to begin during the growth phase, further boosting the titer and productivity. Based on RNA sequencing along the created strain genealogy, we discovered that the nyb gene cluster was unfavorably downregulated in all advanced producers. This inspired removal of a part and the entire set of the four regulatory genes at the 3'-end nyb of the cluster. The corresponding mutants NYB-8 and NYB-9 exhibited marked further improvement in production, and the deregulated cluster was combined with all beneficial targets from primary metabolism. The best strain, S. albidoflavus NYB-11, accumulated up to 12 mg L-1 nybomycin, fifteenfold more than the basic strain. The absence of native gene clusters in the host and use of a lean minimal medium contributed to a selective production process, providing an important next step toward further development of nybomycin.

Chromogenic Escherichia coli reporter strain for screening DNA damaging agents

The presence of pollutants in soil and water has given rise to diverse analytical and biological approaches to detect and measure contaminants in the environment. Using bacterial cells as reporter strains represents an advantage for detecting pollutants present in soil or water samples. Here, an Escherichia coli reporter strain expressing a chromoprotein capable of interacting with soil or water samples and responding to DNA damaging compounds is validated. The reporter strain generates a qualitative signal and is based on the expression of the coral chromoprotein AmilCP under the control of the recA promoter. This strain can be used simply by applying soil or water samples directly and rendering activation upon DNA damage. This reporter strain responds to agents that damage DNA (with an apparent detection limit of 1 µg of mitomycin C) without observable response to membrane integrity damage, protein folding or oxidative stress generating agents, in the latter case, DNA damage was observed. The developed reporter strain reported here is effective for the detection of DNA damaging agents present in soils samples. In a proof-of-concept analysis using soil containing chromium, showing activation at 15.56 mg/L of Cr(VI) present in soil and leached samples and is consistent with Cr(III) toxicity at high concentrations (130 µg). Our findings suggest that chromogenic reporter strains can be applied for simple screening, thus reducing the number of samples requiring analytical techniques.

Impact of multigenerational exposure to AgNO3 or NM300K Ag NPs on antioxidant defense and oxidative stress in Caenorhabditis elegans

Adaptation of the nematode Caenorhabditis elegans towards NM300K silver nanoparticles (Ag NPs) has previously been demonstrated. In the current study, the sensitivity to a range of secondary stressors (CeO2 NP, Ce3+, Cu2+, Cd2+, and Paraquat) following the multigenerational exposure to silver nanoparticles (Ag NPs NM300K) or AgNO3 was investigated. This revealed improved tolerance to the ROS inducer Paraquat with higher fecundity after pre-exposure to Ag NP, indicating an involvement of reactive oxygen species (ROS) metabolism in the adaptive response to NM300K. The potential contribution of the antioxidant defenses related to adaptive responses was investigated across six generations of exposure using the sod-1::GFP reporter (GA508), and the Grx1-roGFP2 (GRX) biosensor strains. Results showed an increase in sod-1 expression by the F3 generation, accompanied by a reduction of GSSG/GSH ratios, from both AgNO3 and Ag NP exposures. Continuous exposure to AgNO3 and Ag NP until the F6 generation resulted in a decreased sod-1 expression, with a concomitant increase in GSSG/GSH ratios. The results thus show that despite an initial enhancement, the continuous exposure to Ag caused a severe impairment of the antioxidant defense capacity in C. elegans.

In vivo assessment of silver nanoparticle induced reactive oxygen species reveals tissue specific effects on cellular redox status in the nematode Caenorhabditis elegans

The current study provides an in vivo analysis of the production of reactive oxygen species (ROS) and oxidative stress in the nematode Caenorhabditis elegans following exposure to EU reference silver nanoparticles NM300K and AgNO₃. Induction of antioxidant defenses was measured through the application of a SOD-1 reporter, and the HyPer and GRX biosensor strains to monitor changes in the cellular redox state. Both forms of Ag resulted in an increase in sod-1 expression, elevated H₂O₂ levels and an imbalance in the cellular GSSG/GSH redox status. Microscopy analysis of the strains revealed that AgNO₃ induced ROS-related effects in multiple tissues, including the pharynx, intestinal cells and muscle tissues. In contrast, NM300K resulted in localized ROS production and oxidative stress, specifically in tissues surrounding the intestinal lumen. This indicates that Ag from AgNO₃ exposure was readily transported across the whole body, while Ag or ROS from NM300K exposure was predominantly confined within the luminal tissues. Concentrations resulting in an increase in ROS production and changes in GSSG/GSH ratio were in line with the levels associated with observed physiological toxic effects. However, sod-1 was not induced at the lowest Ag concentrations, although reprotoxicity was seen at these levels. While both forms of Ag caused oxidative stress, impaired development, and reprotoxicity, the results suggest different involvement of ROS production to the toxic effects of AgNO₃versus NM300K.

Development and characterization of Escherichia coli triple reporter strains for investigation of population heterogeneity in bioprocesses

Background

Today there is an increasing demand for high yielding robust and cost efficient biotechnological production processes. Although cells in these processes originate from isogenic cultures, heterogeneity induced by intrinsic and extrinsic influences is omnipresent. To increase understanding of this mechanistically poorly understood phenomenon, advanced tools that provide insights into single cell physiology are needed.

Results

Two Escherichia coli triple reporter strains have been designed based on the industrially relevant production host E. coli BL21(DE3) and a modified version thereof, E. coli T7E2. The strains carry three different fluorescence proteins chromosomally integrated. Single cell growth is followed with EmeraldGFP (EmGFP)-expression together with the ribosomal promoter rrnB. General stress response of single cells is monitored by expression of sigma factor rpoS with mStrawberry, whereas expression of the nar-operon together with TagRFP657 gives information about oxygen limitation of single cells. First, the strains were characterized in batch operated stirred-tank bioreactors in comparison to wildtype E. coli BL21(DE3). Afterwards, applicability of the triple reporter strains for investigation of population heterogeneity in bioprocesses was demonstrated in continuous processes in stirred-tank bioreactors at different growth rates and in response to glucose and oxygen perturbation simulating gradients on industrial scale. Population and single cell level physiology was monitored evaluating general physiology and flow cytometry analysis of fluorescence distributions of the triple reporter strains. Although both triple reporter strains reflected physiological changes that were expected based on the expression characteristics of the marker proteins, the triple reporter strain based on E. coli T7E2 showed higher sensitivity in response to environmental changes. For both strains, noise in gene expression was observed during transition from phases of non-growth to growth. Apparently, under some process conditions, e.g. the stationary phase in batch cultures, the fluorescence response of EmGFP and mStrawberry is preserved, whereas TagRFP657 showed a distinct response.

Conclusions

Single cell growth, general stress response and oxygen limitation of single cells could be followed using the two triple reporter strains developed in this study. They represent valuable tools to study population heterogeneity in bioprocesses significantly increasing the level of information compared to the use of single reporter strains.

Nybomycin-producing Streptomyces isolated from carpenter ant Camponotus vagus

A novel strain of Actinomycetes was isolated from the body of an ant (Camponotus vagus Scopoli) and its genetic and morphological properties were characterized. The 16S rDNA gene sequence analysis of the isolate revealed its high phylogenetic relationship with type strains of Streptomyces violaceochromogenes NBRC 13100^T. As a result of antimicrobial activity assessment, it was found that the fermentation broth of the isolated strain both inhibited the growth and induced the SOS response in E. coli BW25113 ΔtolC strain cells. Using bioassay-guided fractionation, mass spectrometric and NMR analyses we identified the active compound to be nybomycin, a previously described antibiotic. Here we report for the first time Streptomyces producer of nybomycin in association with carpenter ants and demonstrate cytotoxic activity of nybomycin against human cell lines.

Significance of the class II hydrophobin FgHyd5p for the life cycle of Fusarium graminearum

Hydrophobins are small secreted proteins ubiquitously found in filamentous fungi. Some hydrophobins were shown to have functions in fungal development, while others lack known function. Class II hydrophobins from Fusarium graminearum and Fusarium culmorum are characterized by formation of low stability aggregates and their solubility in organic solvents. They are economically relevant to the brewing industry because they can induce beer gushing. Since cellular functions of Hyd5p's are still unknown, we analyzed the influence of FgHyd5p on growth and morphology of F. graminearum using FgΔhyd5 knock-out mutants expressing sGFP under the control of the hyd5 promoter and compared them with the performance of the parent wild type strain. Results demonstrate that FgHyd5p does not affect the colony and hyphal morphology. FgHyd5p affects the hydrophobicity of aerial mycelia but had no obvious function in penetration of hyphae through the water air interface. The hydrophobin affects the morphology of conidia, but not their fitness. Different sources of carbon and nitrogen as well as different pH have no effect on the expression of the hyd5 gene, which was demonstrated to be expressed upon growth of F. graminearum on hydrophobic surfaces.