Applied Microbiology and Biotechnology最新文献

Identifying hormone-like quorum sensing (QS) molecules in streptomycetes is challenging due to low production levels but is essential for understanding secondary metabolite biosynthesis and morphological differentiation. This work reports the discovery of a novel γ-butenolide-type signaling molecule (SFB1) via overexpressing its biosynthetic gene (orf18) in Streptomyces fradiae. SFB1 was found to be essential for production of tylosin through dissociating the binding of its receptor TylP (a transcriptional repressor) to target genes, thus activating the expression of tylosin biosynthetic gene cluster (tyl). Meanwhile, SFB1 biosynthesis is negatively regulated by TylQ (another transcriptional repressor); the disruption of its coding gene tylQ led to increased production of SFB1, which in turn increased the yield of tylosin. Using tylQ disrupted mutant as chassis cell, co-overexpressing transcriptional activators TylR and TylS further increased tylosin yield to 3926 ± 110 mg/L, representing a 2.93-fold improvement over the wild-type strain. Since the quorum sensing signaling system can affect the biosynthesis of many secondary metabolites, thereby this strategy may also be readily applied for improving the titers of other microbial metabolites.

• SFB1 is a novel γ-butenolide-type quorum sensing signaling molecule of S. fradiae.

• SFB1 regulates the production of tylosin.

• Engineering SFB1 regulatory cascade improves tylosin production.

Improving ale or lager yeasts by conventional breeding is a non-trivial task. Domestication of lager yeasts, which are hybrids between Saccharomyces cerevisiae and Saccharomyces eubayanus, has led to evolved strains with severely reduced or abolished sexual reproduction capabilities, due to, e.g. postzygotic barriers. On the other hand, S. cerevisiae ale yeasts, particularly Kveik ale yeast strains, were shown to produce abundant viable spores (~ 60%; Dippel et al. Microorganisms 10(10):1922, 2022). This led us to investigate the usefulness of Kveik yeasts for conventional yeast breeding. Surprisingly, we could isolate heterothallic colonies from germinated spores of different Kveik strains. These strains presented stable mating types in confrontation assays with pheromone-sensitive tester strains. Heterothallism was due to inactivating mutations in their HO genes. These led to amino acid exchanges in the Ho protein, revealing a known G223D mutation and also a novel G217R mutation, both of which abolished mating type switching. We generated stable MATa or MATα lines of four different Kveik yeasts, named Odin, Thor, Freya and Vör. Analyses of bud scar positions in these strains revealed both axial and bipolar budding patterns. However, the ability of Freya and Vör to form viable meiotic offspring with haploid tester strains demonstrated that these strains are haploid. Fermentation analyses indicated that all four yeast strains were able to ferment maltose and maltotriose. Odin was found to share not only mutations in the HO gene, but also inactivating mutations in the PAD1 and FDC1 genes with lager yeasts, which makes this strain POF-, i.e. not able to generate phenolic off-flavours, a key feature of lager yeasts. These haploid ale yeast-derived strains may open novel avenues also for generating novel lager yeast strains by breeding or mutation and selection utilizing the power of yeast genetics, thus lifting a block that domestication of lager yeasts has brought about.

• Haploid Kveik ale yeasts with stable MATa and MATα mating types were isolated.

• Heterothallic strains bear mutant HO alleles leading to a novel inactivating G217R amino acid change.

• One strain was found to be POF- due to inactivating mutations in the PAD1 and FDC1 gene rendering it negative for phenolic off-flavor production.

• These strains are highly accessible for beer yeast improvements by conventional breeding, employing yeast genetics and mutation and selection regimes.

Monoclonal antibodies are extensively used as biotherapeutics for treatment of a variety of diseases. Glycosylation of therapeutic antibodies is considered a critical quality attribute as it influences the effector function, circulatory half-life, immunogenicity, and eventually efficacy and patient safety. During upstream process development, media components play a significant role in determining the glycosylation profile. In this study, we have evaluated 20 media additives (metal ions, vitamins, sugars, nucleosides). Six of the additives were shortlisted for their impact and then used to modulate the glycosylation profile of an in-house produced mAb (G0 2.38 ± 0.08%, G0F 75.58 ± 0.45%, G1F 10.07 ± 0.04%, G2F 0.54 ± 0.01%, G0F-N 5.84 ± 0.32%, sialylation 1.60 ± 0.33%, mannosylation 1.56 ± 0.39%) to achieve the glycan profile of a commercially available reference product (G0 2.49 ± 0.07%, G0F 37.83 ± 0.37%, G1F 34.77 ± 0.03%, G2F 4.87 ± 0.01%, G0F-N 2.34 ± 0.12%, sialylation 9.84 ± 0.30%, mannosylation 2.86 ± 0.29%). The proposed approach yielded us a glycan profile (G0 2.10 ± 0.07%, G0F 38.00 ± 0.49%, G1F 31.92 ± 0.09%, G2F 5.26 ± 0.54%, G0F-N 1.92 ± 0.02%, sialylation 10.28 ± 1.68%, mannosylation 3.12 ± 0.29%) that was near identical to that of the reference product. Equally importantly, other quality attributes including charge variants, aggregates, titer, and viability were not found to be significantly impacted by the addition of the additives under consideration.

• Screened 20 media additives to evaluate their effect on glycosylation of mAbs.

• Developed glycosylation indices models to evaluate the effect of various additives.

• Additive concentrations were optimized to target the reference product profile.

Butenyl-spinosyn, derived from Saccharopolyspora pogona, is a broad-spectrum and effective bioinsecticide. However, the regulatory mechanism affecting butenyl-spinosyn synthesis has not been fully elucidated, which hindered the improvement of production. Here, a high-production strain S. pogona H2 was generated by Cobalt-60 γ-ray mutagenesis, which showed a 2.7-fold increase in production compared to the wild-type strain S. pogona ASAGF58. A comparative transcriptomic analysis between S. pogona ASAGF58 and H2 was performed to elucidate the high-production mechanism that more precursors and energy were used to synthesize of butenyl-spinosyn. Fortunately, a PurR family transcriptional regulator TF00350 was discovered. TF00350 overexpression strain RS00350 induced morphological differentiation and butenyl-spinosyn production, ultimately leading to a 5.5-fold increase in butenyl-spinosyn production (141.5 ± 1.03 mg/L). Through transcriptomics analysis, most genes related to purine metabolism pathway were downregulated, and the butenyl-spinosyn biosynthesis gene was upregulated by increasing the concentration of c-di-GMP and decreasing the concentration of c-di-AMP. These results provide valuable insights for further mining key regulators and improving butenyl-spinosyn production.

• A high production strain of S. pogona H2 was obtained by ⁶⁰Co γ-ray mutagenesis.

• Positive regulator TF00350 identified by transcriptomics, increasing butenyl-spinosyn production by 5.5-fold.

• TF00350 regulated of butenyl-spinosyn production by second messengers.

L-valine holds wide-ranging applications in medicine, food, feed, and various industrial sectors. Escherichia coli, a pivotal strain in industrial L-valine production, features a concise fermentation period and a well-defined genetic background. This study focuses on mismatch repair genes (mutH, mutL, mutS, and recG) and genes associated with mutagenesis (dinB, rpoS, rpoD, and recA), employing a high-glucose adaptive culture in conjunction with metabolic modifications to systematically screen for superior phenotypes. This approach enhances the spontaneous survival rate of stress cells and facilitates the enrichment of positive mutations. Leveraging a multi-fragment seamless recombination technique, we successfully assembled the ilvBN, ilvC, ilvE, and ilvD pathway enzyme genes, transforming E. coli from a non-producer into a proficient L-valine producer capable of generating up to 6.62 g/L. Through a synergistic application of self-evolution engineering and metabolic engineering strategies, the engineered E. coli strain exhibited significantly enhanced tolerance and demonstrated heightened accumulation of L-valine.

• The innovation centered on mutated genes and mismatch repair genes

• By integrating modification with adaptive culture, a superior phenotype was attained

• Double plasmids expressing enzymes for L-valine production in E. coli were obtained

A new strategy has been developed to successfully produce the active component danshensu ex vivo. For this purpose, phenylalanine dehydrogenase from Bacillus sphaericus was combined with the novel hydroxyphenylpyruvate reductase from Mentha x piperita, thereby providing an in situ cofactor regeneration throughout the conversion process. The purified enzymes were co-immobilized and subsequently employed in batch biotransformation, resulting in 60% conversion of 10 mM L-dopa within 24 h, with a catalytic amount of NAD⁺ as cofactor. Furthermore, the bienzymatic system was implemented as a packed-bed reactor in continuous flow, achieving a conversion rate up to 80% with 60 min retention time. The process was further intensified by implementing a 48-h flow bioreaction. The biocatalysts demonstrated remarkable stability, retaining 62% of their initial activity at the end of the process. The final productivity of the isolated compound (96% purity) was calculated to be 1.84 g L⁻¹ h⁻¹ yielding a sustainable synthesis of danshensu.

• Characterization of the hydroxyphenylpyruvate reductase from Mentha x piperita

• Bi-enzymatic system in a cascade reaction to produce danshensu

• Purification and isolation of the active compound danshensu

The animal gut microbiome is a complex system of diverse, predominantly anaerobic microbiota with secondary metabolite potential. These metabolites likely play roles in shaping microbial community membership and influencing animal host health. As such, novel secondary metabolites from gut microbes hold significant biotechnological and therapeutic interest. Despite their potential, gut microbes are largely untapped for secondary metabolites, with gut fungi and obligate anaerobes being particularly under-explored. To advance understanding of these metabolites, culture-based and (meta)genome-based approaches are essential. Culture-based approaches enable isolation, cultivation, and direct study of gut microbes, and (meta)genome-based approaches utilize in silico tools to mine biosynthetic gene clusters (BGCs) from microbes that have not yet been successfully cultured. In this mini-review, we highlight recent innovations in this area, including anaerobic biofoundries like ExFAB, the NSF BioFoundry for Extreme & Exceptional Fungi, Archaea, and Bacteria. These facilities enable high-throughput workflows to study oxygen-sensitive microbes and biosynthetic machinery. Such recent advances promise to improve our understanding of the gut microbiome and its secondary metabolism.

• Gut microbial secondary metabolites have therapeutic and biotechnological potential

• Culture- and (meta)genome-based workflows drive gut anaerobe metabolite discovery

• Anaerobic biofoundries enable high-throughput workflows for metabolite discovery

The production of biodegradable and biobased polymers is one way to overcome the present plastic pollution while using cheap and abundant feedstocks. Polyhydroxyalkanoates are a promising class of biopolymers that can be produced by various microorganisms. Within the production process, batch-to-batch variation occurs due to changing feedstock composition when using waste streams, slightly different starting conditions, or biological variance of the microorganisms. Therefore, reliable and online-capable measurement methods of the product concentration are required to monitor and eventually react to those fluctuations. In this work, we present a flexible approach to determine polyhydroxyalkanoate concentrations based on a simple mathematical model. The data-driven model correlates polyhydroxyalkanoate concentrations with optical densities measured at 600 nm, a widespread, fast, and cheap lab measurement. We found that with different cultivation conditions, the correlation needs to be updated for a reasonable PHA determination during the process. We test this approach for the production of poly(3-hydroxybutyrate) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) in Cupriavidus necator using fructose and propionic acid as carbon sources. This flexible approach allows a simple estimation of PHA concentrations and offers the possibility to further enhance biopolymer production when combined with advanced control strategies.

(bullet ) Development of a simple mathematical model to estimate polyhydroxyalkanoate concentrations.

(bullet ) Optical density measurement is used to determine polyhydroxyalkanoate concentration.

(bullet ) The approach is tested for the production of PHB and PHBV with C. necator.

The widespread use of antibiotics has led to the emergence of multidrug-resistant bacteria, which pose significant threats to animal health and food safety. Host defense peptides (HDPs) have emerged as promising alternatives because of their unique antimicrobial properties and minimal resistance induction. However, the high costs associated with HDP production and incorporation into animal management practices hinder their widespread application. Alternatively, promoting endogenous HDP expression has gained attention as a sustainable and cost-effective approach. This study summarizes the latest research findings on the modulation of HDP expression by the gut microbiota and its metabolites. By exploring the intricate relationships among the gut microbiota, metabolites, and HDP expression, this study aims to provide a theoretical foundation for the development of targeted strategies to increase endogenous HDP production, thereby promoting animal health and resistance to infectious diseases.

• Host defense peptides (HDPs) are expressed via various factors, such as nutrients, the gut microbiota, and microbial metabolites.

• Recent trends include mechanisms among the gut microbiota, microbiota metabolites, and the intestine on HDP expression.

• A comprehensive overview of mechanisms of HDP expression and gut microbiota–host interaction is provided.

One of the most significant bacteriophage technologies is phage display, in which heterologous peptides are exhibited on the virion surface. This work describes the display of λ decorative protein D_λ linked to the E protein domain III of Zika virus (D_λ-ZE_DIII), to the GFP protein (D_λ-GFP), or to different domain III epitopes of the E_ZIKV protein (D_λ-TD), exhibited on the surface of an in vitro evolved lambda phage (λ_evo). This phage harbors a gene D deletion and was subjected to directed evolution using Escherichia coli W3110/pD_λ-ZE_DIII as background. After 20 days (20 cycles of dilution), the λ_evo phage developed a ~ 22% genome deletion affecting the non-essential λ b region, rendering a more stable phage that exhibited fusion proteins D_λ-ZE_DIII or D_λ-GFP but not D_λ-TD. Despite the λ_evo system was able to decorate itself with the D_λ-ZE_DIII protein, the production of viral particles was ~ 1000-fold lower than the λ wild-type, due to the unexpected D_λ-ZE_DIII protein aggregation into bacterial inclusion bodies. Decorated phages (10⁶ PFU (plaque forming units)/100 µl) were inoculated into BALB/c mice, and subsequent dot blot and Western blot immunoassays proved the production of murine antibodies against ZIKV (Zika virus). This multipurpose λ_evo phage display platform may be used interchangeably with other more soluble peptides, providing better yields.

• λ_evo platform for displaying recombinant peptides.

• Directed evolution to generate λ_evo with more efficient decoration.

• Antigenic reaction in BALB/c mice by inoculating λ_evo with recombinant peptides.