Rapid production of l-DOPA by Vibrio natriegens, an emerging next-generation whole-cell catalysis chassis

Small-scale fed-batch cultivations of Vibrio natriegens: overcoming challenges for early process development

Vibrio natriegens is a fast-growing microbial workhorse with high potential for biotechnological applications. However, handling the bacterium in batch processes is challenging due to its high overflow metabolism and mixed acid formation under microaerobic conditions. For early process development, technologies enabling small-scale fed-batch cultivation of V. natriegens Vmax are needed. In this study, fed-batch cultivations in 96-well microtiter plates were successfully online-monitored for the first time with a µTOM device. Using the online-monitored oxygen transfer rate, a scale up to membrane-based fed-batch shake flasks was performed. The overflow metabolism was efficiently minimized by choosing suitable feed rates, and mixed acid formation was prevented. A glucose soft sensor using the oxygen transfer rate provided accurate estimates of glucose consumption throughout the fermentation, eliminating the need for offline sampling. Analyzing the impact of the inducer IPTG on the recombinant production of the enzyme inulosucrase revealed concentration-dependent effects in batch processes. In contrast, fed-batch operating mode resulted in high inulosucrase activity even without induction. Overall, an inulosucrase titer of 80 U/mL was achieved. In conclusion, the advantages of small-scale fed-batch technologies supported by a glucose soft sensor have been demonstrated for early process development for V. natriegens Vmax.

Low-biomass pyruvate production with engineered Vibrio natriegens is accompanied by parapyruvate formation

BACKGROUND

Pyruvate is a precursor for various compounds in the chemical, drug, and food industries and is therefore an attractive target molecule for microbial production processes. The fast-growing bacterium Vibrio natriegens excels with its specific substrate uptake rate as an unconventional chassis for industrial biotechnology. Here, we aim to exploit the traits of V. natriegens for pyruvate production in fermentations with low biomass concentrations.

RESULTS

We inactivated the pyruvate dehydrogenase complex in V. natriegens Δvnp12, which harbors deletions of the prophage regions vnp12. The resulting strain V. natriegens Δvnp12 ΔaceE was unable to grow in minimal medium with glucose unless supplemented with acetate. In shaking flasks, the strain showed a growth rate of 1.16 ± 0.03 h- 1 and produced 4.0 ± 0.3 gPyr L- 1 within 5 h. We optimized the parameters in an aerobic fermentation process and applied a constant maintenance feed of 0.24 gAc h- 1 which resulted in a maximal biomass concentration of only 6.6 ± 0.4 gCDW L- 1 and yielded highly active resting cells with a glucose uptake rate (qS) of 3.5 ± 0.2 gGlc gCDW-1 h- 1. V. natriegens Δvnp12 ΔaceE produced 41.0 ± 1.8 gPyr L- 1 with a volumetric productivity of 4.1 ± 0.2 gPyr L- 1 h- 1. Carbon balancing disclosed a gap of 30%, which we identified partly as parapyruvate. Deletion of ligK encoding the HMG/CHA aldolase in V. natriegens Δvnp12 ΔaceE did not impact biomass formation but plasmid-based overexpression of ligK negatively affected growth and led to a 3-fold higher parapyruvate concentration in the culture broth. Notably, we also identified parapyruvate in supernatants of a pyruvate-producing Corynebacterium glutamicum strain. Cell-free bioreactor experiments mimicking the biological process also resulted in parapyruvate formation, pointing to a chemical reaction contributing to its synthesis.

CONCLUSIONS

We engineered metabolically highly active resting cells of V. natriegens producing pyruvate with high productivity at a low biomass concentration. However, we also found that pyruvate production is accompanied by parapyruvate formation in V. natriegens as well as in a pyruvate producing C. glutamicum strain. Parapyruvate formation seems to be a result of chemical pyruvate conversion and might be supported biochemically by an aldolase reaction.

Plant Secondary Metabolites as Modulators of Mitochondrial Health: An Overview of Their Anti-Oxidant, Anti-Apoptotic, and Mitophagic Mechanisms

Plant secondary metabolites (PSMs) are a diverse group of bioactive compounds, including flavonoids, polyphenols, saponins, and terpenoids, which have been recognised for their critical role in modulating cellular functions. This review provides a comprehensive analysis of the effects of PSMs on mitochondrial health, with particular emphasis on their therapeutic potential. Emerging evidence shows that these metabolites improve mitochondrial function by reducing oxidative stress, promoting mitochondrial biogenesis, and regulating key processes such as apoptosis and mitophagy. Mitochondrial dysfunction, a hallmark of many pathologies, including neurodegenerative disorders, cardiovascular diseases, and metabolic syndrome, has been shown to benefit from the protective effects of PSMs. Recent studies show that PSMs can improve mitochondrial dynamics, stabilise mitochondrial membranes, and enhance bioenergetics, offering significant promise for the prevention and treatment of mitochondrial-related diseases. The molecular mechanisms underlying these effects, including modulation of key signalling pathways and direct interactions with mitochondrial proteins, are discussed. The integration of PSMs into therapeutic strategies is highlighted as a promising avenue for improving treatment efficacy while minimising the side effects commonly associated with synthetic drugs. This review also highlights the need for future research to elucidate the specific roles of individual PSMs and their synergistic interactions within complex plant matrices, which may further optimise their therapeutic utility. Overall, this work provides valuable insights into the complex role of PSMs in mitochondrial health and their potential as natural therapeutic agents targeting mitochondrial dysfunction.

The new chassis in the flask: Advances in Vibrio natriegens biotechnology research

Biotechnology has been built on the foundation of a small handful of well characterized and well-engineered organisms. Recent years have seen a breakout performer gain attention as a new entrant into the bioengineering toolbox: Vibrio natriegens. This review covers recent research efforts into making V. natriegens a biotechnology platform, using a large language model (LLM) and knowledge graph to expedite the literature survey process. Scientists have made advancements in research pertaining to the fundamental metabolic characteristics of V. natriegens, development and characterization of synthetic biology tools, systems biology analysis and metabolic modeling, bioproduction and metabolic engineering, and microbial ecology. Each of these subcategories has relevance to the future of V. natriegens for bioengineering applications. In this review, we cover these recent advancements and offer context for the impact they may have on the field, highlighting benefits and drawbacks of using this organism. From examining the recent bioengineering research, it appears that V. natriegens is on the precipice of becoming a platform bacterium for the future of biotechnology.

Vibrio natriegens: Application of a Fast-Growing Halophilic Bacterium

The fast growth accompanied with high substrate consumption rates and a versatile metabolism paved the way to exploit Vibrio natriegens as unconventional host for biotechnological applications. Meanwhile, a wealth of knowledge on the physiology, the metabolism, and the regulation in this halophilic marine bacterium has been gathered. Sophisticated genetic engineering tools and metabolic models are available and have been applied to engineer production strains and first chassis variants of V. natriegens. In this review, we update the current knowledge on the physiology and the progress in the development of synthetic biology tools and provide an overview of recent advances in metabolic engineering of this promising host. We further discuss future challenges to enhance the application range of V. natriegens.

Engineering xylose induction in Vibrio natriegens for biomanufacturing applications

Xylose is an abundant, inexpensive and readily available carbohydrate common in minimally processed feedstocks such as seaweed and algae. While a wide variety of marine microbes have evolved to utilize seaweed and algae, only a few currently have the requisite characteristics and genetic engineering tools necessary to entertain the use of these underutilized feedstocks. The rapidly growing Gram-negative halophilic bacterium Vibrio natriegens is one such chassis. In this study, we engineered and tested xylose induction in V. natriegens as a tool for scalable bioproduction applications. First, we created a sensing construct based on the xylose operon from Escherichia coli MG1665 and measured its activity using a fluorescent reporter and identified that cellular import plays a key role in induction strength and that expression required the XylR transcription factor. Next, we identified that select deletions of the promoter region enhance gene expression, limiting the effect of carbohydrate repression when xylose is used as an inducer in the presence of industrially relevant carbon sources. Lastly, we used the optimized constructs to produce the biopolymer melanin using seawater mimetic media. One of these formulations utilized a nori-based seaweed extract as an inducer and demonstrated melanin yields comparable to previously optimized methods using a more traditional and costly inducer. Together, the results demonstrate that engineering xylose induction in V. natriegens can provide an effective and lower cost option for timed biosynthesis in scalable biomanufacturing applications using renewable feedstocks.

Unraveling the impact of pH, sodium concentration, and medium osmolality on Vibrio natriegens in batch processes

BACKGROUND

Vibrio natriegens, a halophilic marine γ-proteobacterium, holds immense biotechnological potential due to its remarkably short generation time of under ten minutes. However, the highest growth rates have been primarily observed on complex media, which often suffer from batch-to-batch variability affecting process stability and performance. Consistent bioprocesses necessitate the use of chemically defined media, which are usually optimized for fermenters with pH and dissolved oxygen tension (DOT) regulation, both of which are not applied during early-stage cultivations in shake flasks or microtiter plates. Existing studies on V. natriegens' growth on mineral media report partially conflicting results, and a comprehensive study examining the combined effects of pH buffering, sodium concentration, and medium osmolality is lacking.

RESULTS

This study evaluates the influence of sodium concentration, pH buffering, and medium osmolality on the growth of V. natriegens under unregulated small-scale conditions. The maximum growth rate, time of glucose depletion, as well as the onset of stationary phase were observed through online-monitoring the oxygen transfer rate. The results revealed optimal growth conditions at an initial pH of 8.0 with a minimum of 300 mM MOPS buffer for media containing 20 g/L glucose or 180 mM MOPS for media with 10 g/L glucose. Optimal sodium chloride supplementation was found to be between 7.5 and 15 g/L, lower than previously reported ranges. This is advantageous for reducing industrial corrosion issues. Additionally, an osmolality range of 1 to 1.6 Osmol/kg was determined to be optimal for growth. Under these optimized conditions, V. natriegens achieved a growth rate of 1.97 ± 0.13 1/h over a period of 1 h at 37 °C, the highest reported rate for this organism on a mineral medium.

CONCLUSION

This study provides guidelines for cultivating V. natriegens in early-stage laboratory settings without pH and DOT regulation. The findings suggest a lower optimal sodium chloride range than previously reported and establish an osmolality window for optimal growth, thereby advancing the understanding of V. natriegens' physiology. In addition, this study offers a foundation for future research into the effects of different ions and carbon sources on V. natriegens.

Rhizosphere bacteria G-H27 significantly promoted the degradation of chlorpyrifos and fosthiazate

Microbial remediation of polluted environments is the most promising and significant research direction in the field of bioremediation. In this study, chlorpyrifos and fosthiazate were selected as representative organophosphorus pesticides, wheat was the tested plant, and fluorescently labeled degrading Bacillus cereus G-H27 were the film-forming bacteria. Exogenous strengthening technology was used to establish degrading bacterial biofilms on the root surface of wheat. The influence of root surface-degrading bacterial biofilms on the enrichment of chlorpyrifos and fosthiazate in wheat was comprehensively evaluated. First, the fluorescently-labeled degrading bacteria G-H27 was constructed, and its film-forming ability was investigated. Second, the growth- promoting characteristics and degradation ability of the bacteria G-H27 were investigated. Finally, the degradation effect of the root surface-degrading bacterial biofilm on chlorpyrifos and fosthiazate was determined. The above research provides an important material basis and method for the bioremediation of pesticide-contaminated soil.

High-Performance Production of N-Acetyl-d-Neuraminic Acid with Whole Cells of Fast-Growing Vibrio natriegens via a Thermal Strategy

High performance is the core objective that biotechnologists pursue, of which low efficiency, low titer, and side products are the chief obstacles. Here, a thermal strategy is proposed for simultaneously addressing the obstacles of whole-cell catalysis that is widely applied in the food industry. The strategy, by combining fast-growing Vibrio natriegens, thermophilic enzymes, and high-temperature whole-cell catalysis, was successfully applied for the high-performance production of N-acetyl-d-neuraminic acid (Neu5Ac) that plays essential roles in the fields of food (infant formulas), healthcare, and medicine. By using this strategy, we realized the highest Neu5Ac titer and productivity of 126.1 g/L and up to 71.6 g/(L h), respectively, 7.2-fold higher than the productivity of Escherichia coli. The major byproduct acetic acid was also eliminated via quenching complex metabolic side reactions enabled by temperature elevation. This study offers a broadly applicable strategy for producing chemicals relevant to the food industry, providing insights for its future development.

Rapid, high-titer biosynthesis of melanin using the marine bacterium Vibrio natriegens

Melanin is one of the most abundant natural biomolecules on Earth. These macromolecular biopolymers display several unique physical and chemical properties and have garnered interest as biomaterials for various commercial and industrial applications. To this end, extensive research has gone into refining methods for the synthesis and extraction of melanin from natural and recombinant sources. In this study, we developed and refined a procedure using a recombinant microbial system for the biosynthesis of melanin using the tyrosinase enzyme Tyr1 and tyrosine as a substrate. Using the emergent microbial chassis organisms Vibrio natriegens, we achieved maximal yields of 7.57 g/L, and one of the highest reported volumetric productivities of 473 mg L-1 h-1 with 100% conversion rates in an optimized, minimally defined medium. Additionally, we identified and investigated the use of a native copper responsive promoter in V. natriegens for stringent regulation of heterologous protein expression as a cost effective alternative to traditional IPTG-based induction. This research represents a promising advancement towards a green, rapid, and economical alternative for the biomanufacture of melanin.

Ploidy in Vibrio natriegens: Very Dynamic and Rapidly Changing Copy Numbers of Both Chromosomes

Vibrio natriegens is the fastest-growing bacterium, with a doubling time of approximately 12-14 min. It has a high potential for basic research and biotechnological applications, e.g., it can be used for the cell-free production of (labeled) heterologous proteins, for synthetic biological applications, and for the production of various compounds. However, the ploidy level in V. natriegens remains unknown. At nine time points throughout the growth curve, we analyzed the numbers of origins and termini of both chromosomes with qPCR and the relative abundances of all genomic sites with marker frequency analyses. During the lag phase until early exponential growth, the origin copy number and origin/terminus ratio of chromosome 1 increased severalfold, but the increase was lower for chromosome 2. This increase was paralleled by an increase in cell volume. During the exponential phase, the origin/terminus ratio and cell volume decreased again. This highly dynamic and fast regulation has not yet been described for any other species. In this study, the gene dosage increase in origin-adjacent genes during the lag phase is discussed together with the nonrandom distribution of genes on the chromosomes of V. natriegens. Taken together, the results of this study provide the first comprehensive overview of the chromosome dynamics in V. natriegens and will guide the optimization of molecular biological characterization and biotechnological applications.

Isolation and Characterization of a Novel Vibrio natriegens—Infecting Phage and Its Potential Therapeutic Application in Abalone Aquaculture

Phage-based pathogen control (i.e., phage therapy) has received increasing scientific attention to reduce and prevent the emergence, transmission, and detrimental effects of antibiotic resistance. In the current study, multidrug-resistant Vibrio natriegens strain AbY-1805 was isolated and tentatively identified as a pathogen causing the death of juvenile Pacific abalones (Haliotis discus hannai Ino). In order to apply phage therapy, instead of antibiotics, to treat and control V. natriegens infections in marine aquaculture environments, a lytic phage, vB_VnaS-L3, was isolated. It could effectively infect V. natriegens AbY-1805 with a short latent period (40 min) and high burst size (~890 PFU/cell). Treatment with vB_VnaS-L3 significantly reduced the mortality of juvenile abalones and maintained abalone feeding capacity over a 40-day V. natriegens challenge experiment. Comparative genomic and phylogenetic analyses suggested that vB_VnaS-L3 was a novel marine Siphoviridae-family phage. Furthermore, vB_VnaS-L3 had a narrow host range, possibly specific to the pathogenic V. natriegens strains. It also exhibited viability at a wide range of pH, temperature, and salinity. The short latent period, large burst size, high host specificity, and broad environmental adaptation suggest that phage vB_VnaS-L3 could potentially be developed as an alternative antimicrobial for the control and prevention of marine animal infections caused by pathogenic V. natriegens.

Overexpression of recombinant proteins containing non-canonical amino acids in Vibrio natriegens: p-azido-L-phenylalanine as coupling site for 19F-tags

Vibrio natriegens is the fastest growing organism identified so far. The minimum doubling time of only 9.4 min, the ability to utilize over 60 different carbon sources and its non-pathogenic properties make it an interesting alternative to E. coli as a new production host for recombinant proteins. We investigated the ability of the engineered V. natriegens strain, Vmax™ Express, to incorporate the non-canonical amino acid (ncAA) p-azido-L-phenylalanine (AzF) into recombinant proteins for NMR applications. AzF was incorporated into enhanced yellow fluorescent protein (EYFP) and MlaC, an intermembrane transport protein, by stop codon suppression. AzF incorporation into EYFP resulted in an improved suppression efficiency (SE) of up to 35.5 ± 0.8% and a protein titer of 26.7 ± 0.7 mg/L. The expression levels of MlaC-AzF even exceeded those of E. coli BL21 cells. For the recording of 1H-15N and 19F NMR spectra, EYFP-AzF was expressed and isotopically labeled in minimal medium and the newly introduced azido-group was used as coupling site for NMR sensitive 19F-tags. Our findings show that Vmax is a flexible expression host, suitable for the incorporation of ncAAs in recombinant proteins with the potential to surpass protein yields of E. coli. The presented method suggests the implementation of V. natriegens for expression of isotopically labeled proteins containing ncAAs, which can be chemically modified for the application in protein-observed 19F-NMR.