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PubMed1978

Bioproduction of [14C]ochratoxin A in submerged culture.

A number of Aspergillus and Penicillium species were tested for production of ochratoxin A (OA) in several media. After 8 days of static incubations of submerged cultures at 28 degrees C, toxin yields of 25 and 30 micrograms/ml were obtained with Aspergillus alliaceus NRRL 4181 in Ferreirás and 2% yeast extract-4% sucrose media, respectively. However, the largest production observed in the preliminary screening was 54 micrograms/ml; this highest level was produced by A. sulphureus NRRL 4077 in a modified Czapek solution. The medium contained the basal salts and sucrose of Czapek plus urea (3%) and corn steep liquor (0.5% solids). A time study of toxin production demonstrated maximum yield of 350 micrograms/ml by the A. sulphureus isolate in the modified Czapek medium after 11 days of static incubation at 28 degrees C. The optimal production conditions were employed in additional tests designed to measure the efficiency of 14C incorporation from sodium [1-14C]-acetate into OA. Samples (20 microCi) of sodium acetate were added to separate culture flasks at 24-h intervals during the initial 9 days of the fermentation. Addition of [14C]acetate on day 4 of incubation provided the maximum yield of labeled OA. The highest specific activity of labeled toxin obtained was 0.07 microCi/mg of OA and the maximum incorporation rate of labeled acetate was 5.3%.

Acetates↗
PubMed1977

Bioproduction of rubratoxin in a glucose-mineral salts broth with nutritional supplements and metabolic inhibitors.

A sterile glucose-salts broth fortified with various metabolic inhibitors and nutritional supplements was inoculated with conidia of Penicillium rubrum P3290, and incubated quiescently at 28 degrees C for 14 days. Potassium sulfite and sodium metabisulfite at all test concentrations caused moderate reduction in rubratoxin formation; at high concentrations (greater than or equal to 2.7 X 10(-2)M) accumulation of fungal tissue was also retarded. Production of rubratoxin and cell mass was inhibited by p-aminobenzoic acid; syntheses of toxin were completely blocked by 7.5 X 10(-2)M of the vitamin. Effects of sodium fluoride on P. rubrum cultures grown on inorganic nitrogen sources varied from inhibition of mold growth and (or) rubratoxin A production to reduction in formation of rubratoxin B. With organic nitrogen sources, fluoride caused a 30 and 60% reduction in synthesis of rubratoxins A and B, respectively. Sodium acetate at all test concentrations enhanced formation of rubratoxin; mold growth was enhanced when acetate concentration was larger than or equal to 6.0 X 10(-2)M. A moderate reduction in mold growth was caused by lower acetate concentrations (1.2 X 10(-2)M or 2.4 X 10(-2)M). Sodium arsenite and iodoacetate at test concentrations blocked mold growth and toxin formation; sodium azide and 2,4-dinitrophenol caused a marked reduction in mold growth but inhibited toxin formation completely. However, sodium azide permitted slight growth and toxin formation when mold cultures were incubated for 28 days.

4-Aminobenzoic Acid↗
PubMed1977

[Bioproduction of sterigmatocystine by Aspergillus versicolor (Vuill.) tiraboschi in dry fodder].

Lucerne and ray-grass, sterilized or not, were equilibrated at relative humidity (E.R.H.) 84, 88, 93 p. 100, and contaminated by spores of a highly toxinogenic A. Versicolor strain and maintained in these E.R.H. during 6 months. A peculiar technique for extraction and purification was necessary; the quantification limit for sterigmatocystin was 100 ppb; measurements had been done monthly in 3 replicates. Solvent water was estimated from water sorption isotherms: Toxin yield progressively increases, then lowers and, at last, becomes stable between 1200 and 2000 p.p.b.; The maximal yield is all the higher and the different evolution stages are all the shorter as E.R.H. is higher. The substrate nature influence is different according to E.R.H.; The toxin yields are about twice lower in unsterilized forages. The main parameter for fungal development and toxinogenesis, in low E.R.H. conditions, appears to be the solvent water concentration. Taking into consideration the weak yields of sterigmatocystin obtained in these conditions with a highly toxinogenic strain, the hazard of sterigmatocystin as a natural contaminant in these forages is low, in spite of the high frequency of this fungal species.

Animal Feed↗
PubMed2025

Physiological and metabolic responses of Zymomonas mobilis to lignocellulosic hydrolysate.

Zymomonas mobilis is a promising biocatalyst for the sustainable conversion of lignocellulosic sugars into biofuels and bioproducts, yet its response to lignocellulosic hydrolysates remains poorly understood. Here, we investigate the physiological response of Z. mobilis to ammonia fiber expansion (AFEX)-pretreated switchgrass hydrolysate using a systems-level approach integrating LC-MS/MS-based lipidomics and shotgun proteomics. Growth on hydrolysate induced substantial shifts in fatty acid and membrane phospholipid composition, alongside broad proteomic remodeling. Notably, Z. mobilis exhibited a stress response characterized by the upregulation of heat shock proteins and efflux transporters and the downregulation of cell motility proteins. Unexpectedly, hydrolysate exposure also led to a robust upregulation of the Entner-Doudoroff pathway, the ethanol fermentation pathway, and other central carbon metabolism enzymes, indicating a substantial cellular investment potentially driven by additional nutrient availability in hydrolysate. These findings provide new insights into the metabolic adaptations of Z. mobilis to lignocellulosic hydrolysates, informing strategies to enhance its biofuel production capabilities.IMPORTANCEBiomass pretreatment processes release fermentable sugars from lignocellulosic biomass, but they also generate inhibitors that can impact microbial metabolism. This study provides a systems-level evaluation of how Zymomonas mobilis responds to hydrolysate stress, revealing distinct physiological and lipid membrane remodeling responses. While some stress responses overlap with those induced by ethanol and isobutanol toxicity, both valuable biofuels, hydrolysate exposure elicits unique metabolic shifts. These findings offer valuable insights for engineering Z. mobilis strains with improved tolerance and performance for efficient bioconversion of lignocellulosic hydrolysates into biofuels and bioproducts.

Zymomonas↗
PubMed1977

[Lipid metabolism in Aspergillus versicolor (Vuill.) Tiragoschi. Relation to biogenesis of sterigmatocystin].

Aspergillus versicolor is cultivated in a synthetic medium for 22 days. Bioproduction of lipids and sterigmatocystin are compared. The fatty acids of the neutral lipid and polar lipids fractions are mainly: C 16:0, C 18:0, C 18:1, C 18:2, C 18:3. Maximal yields of dry weight, neutral lipids and sterigmatocystin occur, respectively, on the 4th, the 7th and the 20th days. These results and their comparison with other works emphasize that a fall of concentration in lipids precedes the phase of highest concentration in secondary metabolites of polyketide type; it appears that fats and particularly palmitic acid are present in biogenesis of these derivatives.

Aspergillus↗
PubMed2026

Membrane and proteome allocation constraints in Escherichia coli models during overflow metabolism.

The allocation of finite cellular resources is a fundamental principle that dictates microbial metabolic strategies and gives rise to complex phenomena, such as overflow metabolism, characterized by the production of respiro-fermentative by-products, including acetate, during rapid growth. Although proteome-constrained models have successfully predicted overflow metabolism in Escherichia coli, they often overlook the distinct biophysical and energetic costs associated with protein localization. The cellular membrane, in particular, represents a critical and constrained compartment where competition for space and synthesis machinery can create significant metabolic bottlenecks. To investigate this, we developed the membrane-associated constrained flux balance analysis (MAFBA), a scalable, genome-scale metabolic model that introduces a tunable constraint on the total protein mass allocated to the cellular membrane. Our model demonstrates that the overall and membrane-associated proteome allocation constraints interact to improve the accuracy of predicting the onset of overflow metabolism. It mechanistically reveals that at high growth rates, competition for limited membrane allocation forces a trade-off between growth-essential functions and respiratory capacity, leading to acetate production. Furthermore, MAFBA quantitatively explains the widely observed experimental phenomenon that expressing heterologous membrane proteins imposes a significantly higher metabolic burden than expressing cytosolic proteins. This study establishes membrane resource allocation as a key constraint governing bacterial physiology, acting in concert with overall proteome limitations. The resulting MAFBA framework provides a powerful and accessible tool for synthetic biology and metabolic engineering, enabling the prediction of metabolic costs associated with expressing membrane-bound proteins and guiding strain design strategies, holding promise for applications in bioproduction and metabolic engineering.

Escherichia coli↗
PubMed2026

Unravelling the genomic potential of sponge-associated Streptomyces sp. BLC 17-3 from Indonesia for mannooligosaccharide production.

This research aims to show the promising capacity of Streptomyces sp. BLC 17-3 to produce high β-mannanase enzymes and generate mannooligosaccharide (MOS) such as mannobiose, mannotriose, mannotetraose and mannopentaose when exposed to mannan polymers. Streptomyces sp. BLC 17-3 was isolated from the sponge (Rhabdastrella globostellata) Put4 obtained from the marine waters of Putus Island in Bitung, North Sulawesi, Indonesia. The characterization results showed that the peak enzyme activity was achieved at 50 mM sodium acetate, 6.0 pH, and 60 °C temperature on the seventh day of production with a value of 155.77 ± 3.21 U/mL. The SDS-PAGE and zymograms also showed that the size of the enzyme molecule was approximately ±34.8-49.1 kDa. Moreover, whole-genome sequencing was conducted to identify the genetic basis of MOS-synthesizing capabilities in the selected strain, followed by functional annotation of genes encoding mannan degradation and associated functions. The results showed an 8,248,862 Mb complete draft genome of the strain which comprised 111 predicted gene models. Gene annotation also provided important information about the location and function of protein-encoding genes. A total of 6 mannan degradation-related genes encoding mannanase-related metabolism were identified and the three-dimensional structures were predicted using AlphaFold 3. This characterization and modeling further enhanced the bioprospecting and development of this strain which exhibited efficient mannose metabolism. The results showed Streptomyces sp. BLC 17-3 as a promising microorganism for the future bioproduction of MOS which were discovered to have the capability of serving as a potential prebiotic substance to enhance digestion and promote health.

Bioprospecting↗
PubMed2025

The Elements of Life, Photosynthesis and Genomics.

I am a Professor of Biochemistry, Biophysics and Structural Biology and Plant and Microbial Biology at the University of California in Berkeley. I was born and raised in India, emigrated to the United States to attend university, earning a B.S. in Molecular Biology and a Ph.D. in Biochemistry at the University of Wisconsin in Madison. Following post-doctoral studies with Lawrence Bogorad at Harvard University where I became interested in genetic control of trace element quotas, I joined the department of Chemistry and Biochemistry at UCLA. One of the first to appreciate essential trace metals as potential regulators of gene expression, I articulated the details of the nutritional Cu regulon in Chlamydomonas. In parallel, I used genetic approaches to discover the genes governing missing steps in tetrapyrrole metabolism, including the attachment of heme to apocytochromes in the thylakoid lumen and the factors catalyzing the formation of ring V in chlorophyll. After biochemistry and classical genetics, I embraced genomics, taking a leadership role on the Joint Genome Institute's efforts on the Chlamydomonas genome and more recently, contributing to high quality assemblies of several genomes in the green algal radiation, and large transcriptomic and proteomic datasets - focusing on the diel metabolic cycle in synchronized cultures and acclimation to key environmental and nutritional stressors - that are well-used and appreciated by the community. A new venture in Berkeley is the promotion of Auxenochlorella protothecoides as the true "green yeast" and as a platform for engineering algae to produce useful bioproducts.

Photosynthesis↗
PubMed2026

Biosynthesis and heterologous production of the α-agarofuran scaffold of Celangulin V from Celastrus angulatus.

Celangulin V is a widely used biopesticide derived from Celastrus angulatus, and features antifeedant and insecticidal properties as a dihydro-β-agarofuran (DHβAF) sesquiterpenoid. Its biosynthesis remains largely unexplored. Here, we assemble a chromosome-level and haplotype-resolved reference genome of C. angulatus, with each haplotype assembled into 23 pseudochromosomes and achieving scaffold N50 of 14.31 and 14.01 Mb, respectively. This high-quality genome reveals that a recent β whole-genome triplication (β-WGT) event occurred ~34.3 million years ago, and that the expansion of sesquiterpene synthases and cytochrome P450s from the CYP71BE family results from whole-genome duplication (WGD) event and tandem duplication, respectively. We identify CaTPS16 as a γ-eudesmol synthase, and show that CYP71BE416 further catalyzes the γ-eudesmol to tetrahydrofuran ring α-agarofuran for Celangulin V biosynthesis. We further achieve the de novo synthesis of α-agarofuran in Saccharomyces cerevisiae through combined coexpression of these genes. This study has significantly increases the available genomic resources of the Celastraceae family, improves our understanding of the biosynthetic origins and evolution of the tetrahydrofuran ring in DHβAF sesquiterpenoids, and enables its heterologous bioproduction in microbial chassis.

Celastrus↗
PubMed2025

Engineering of xylose metabolic pathways in Rhodotorula toruloides for sustainable biomanufacturing.

The oleaginous yeast Rhodotorula toruloides is a promising microbial cell factory for the sustainable production of biofuels and value-added chemicals from renewable carbon sources. Unlike the conventional yeast Saccharomyces cerevisiae, R. toruloides can naturally metabolize xylose, the second most abundant sugar in lignocellulosic hydrolysates. However, its native xylose metabolism is inefficient, characterized by slow xylose uptake and accumulation of D-arabitol. Moreover, despite its phenotype, research on the enzymes involved in xylose metabolism has yet to reach a consensus. Therefore, this review provides a comprehensive analysis of the non-canonical xylose metabolism in R. toruloides, focusing on the properties of key enzymes involved in xylose metabolism. Native xylose reductase and xylitol dehydrogenase exhibit broad substrate promiscuity compared to their counterparts in the xylose-fermenting Scheffersomyces stipitis. Additionally, the absence of xylulokinase expression under xylose-utilizing conditions redirects metabolism toward D-arabitol accumulation. Consequently, D-arabitol dehydrogenases and ribulokinase play essential roles in the xylose metabolism of R. toruloides. These findings highlight the fundamental differences between R. toruloides xylose metabolism and the oxidoreductase pathways observed in other xylose-fermenting yeast, providing insights for metabolic engineering strategies to improve xylose utilization and enhance bioconversion of cellulosic hydrolysates to different bioproducts by R. toruloides.

Xylose↗
PubMed2025

Evolution and applications of genome-scale metabolic models in yeast systems biology studies.

Genome-scale metabolic models (GEMs) can be used to simulate the metabolic network of an organism in a systematic and holistic way. Different yeast species, including Saccharomyces cerevisiae, have emerged as powerful cell factories for bioproduction. Recently, with the dedicated efforts from the scientific community, significant progress has been made in the development of yeast GEMs. Numerous versions of yeast GEMs and the derived multiscale models have been released, facilitating integrative omics analysis and rational strain design for different types of yeast cell factories. These advancements reflected the evolution and maturation of yeast GEMs together with a model ecosystem around them. This review will summarize the development and expansion of yeast GEMs and discuss their applications in yeast systems biology studies. It is anticipated that yeast GEMs will continue to play an increasingly important role in pioneering yeast physiological and metabolic studies in coming years.

Systems Biology↗
PubMed2025

Engineering recombination machinery facilitates the construction of yeast cell factories.

Advances in genome editing have been promoted by programmable nucleases like CRISPR-Cas9, which triggers endogenous DNA repair mechanisms by inducing double-strand break (DSB). Cellular responses to DSBs are governed by competing repair pathways: error-prone non-homologous end joining (NHEJ) and high-fidelity homologous recombination (HR). This review systematically compares the molecular mechanisms and key regulators of NHEJ and HR, with a focus on recent breakthroughs in recombination engineering in non-conventional yeasts. These advances address challenges in precise genome editing, enabling robust metabolic engineering of yeast cell factories for sustainable bioproduction.

Metabolic Engineering↗
PubMed2026

Yeast Strain Development and Process Intensification in High-Gravity Fermentation.

High- and very-high-gravity (HG/VHG) fermentation increases substrate loading and product titers, thereby improving fermenter utilisation and potentially reducing water use and downstream processing requirements. Initially developed for brewing and fuel ethanol production, these approaches are now applied more broadly in food, beverage, and bioproduct manufacturing. This MiniReview summarises operational definitions and industrial drivers of HG/VHG fermentation and examines the associated constraints in rheology, mass and heat transfer, osmotic and ethanol stress, nutrient availability, and oxidative damage. Yeast improvement strategies are reviewed, including adaptive laboratory evolution, mutagenesis, genome shuffling, multiplex genome editing, non-conventional yeasts, and multi-omics-guided selection. Process developments such as no-cook simultaneous liquefaction, saccharification and fermentation (SLSF), enzyme formulation, nutrient management, and in situ product recovery are considered together with applications in alcoholic beverages, organic acids, microbial lipids, and other value-added products. The review also discusses coproduct valorisation and the need to integrate strain development with process design. Current evidence supports HG/VHG fermentation as a useful process-intensification platform, although performance and sustainability depend strongly on feedstock, operating conditions, product requirements, and the basis used to report fermentation outcomes.

circular bioeconomy↗
PubMed2024

Genetic modification of the shikimate pathway to reduce lignin content in switchgrass (Panicum virgatum L.) significantly impacts plant microbiomes.

UNLABELLED: Switchgrass (Panicum virgatum L.) is considered a sustainable biofuel feedstock, given its fast-impact growth, low input requirements, and high biomass yields. Improvements in bioenergy conversion efficiency of switchgrass could be made by reducing its lignin content. Engineered switchgrass that expresses a bacterial 3-dehydroshikimate dehydratase (QsuB) has reduced lignin content and improved biomass saccharification due to the rerouting of the shikimate pathway towards the simple aromatic protocatechuate at the expense of lignin biosynthesis. However, the impacts of this QsuB trait on switchgrass microbiome structure and function remain unclear. To address this, wild-type and QsuB-engineered switchgrass were grown in switchgrass field soils, and samples were collected from inflorescences, leaves, roots, rhizospheres, and bulk soils for microbiome analysis. We investigated how QsuB expression influenced switchgrass-associated fungal and bacterial communities using high-throughput Illumina MiSeq amplicon sequencing of ITS and 16S rDNA. Compared to wild-type, QsuB-engineered switchgrass hosted different microbial communities in roots, rhizosphere, and leaves. Specifically, QsuB-engineered plants had a lower relative abundance of arbuscular mycorrhizal fungi (AMF). Additionally, QsuB-engineered plants had fewer Actinobacteriota in root and rhizosphere samples. These findings may indicate that changes in the plant metabolism impact both AMF and Actinobacteriota similarly or potential interactions between AMF and the bacterial community. This study enhances understanding of plant-microbiome interactions by providing baseline microbial data for developing beneficial bioengineering strategies and by assessing nontarget impacts of engineered plant traits on the plant microbiome. IMPORTANCE: Bioenergy crops provide an important strategy for mitigating climate change. Reducing the lignin in bioenergy crops could improve fermentable sugar yields for more efficient conversion into bioenergy and bioproducts. In this study, we assessed how switchgrass engineered for low lignin impacted aboveground and belowground switchgrass microbiome. Our results show unexpected reductions in mycorrhizas and actinobacteria in belowground tissues, raising questions on the resilience and function of genetically engineered plants in agricultural systems.

Panicum↗
PubMed2026

Characterization of carbon metabolism in a highly adhesive bacterium Acinetobacter sp. Tol 5 capable of assimilating diverse hydrocarbons and aromatic compounds.

Sustainable bioproduction requires developing robust microbial chassis with broad metabolic versatility and suitability for industrial applications. Acinetobacter sp. Tol 5 is a highly adhesive bacterium capable of utilizing various hydrocarbons, making it a promising chassis candidate for immobilized whole-cell catalysis. In this study, we characterized the carbon metabolism of Tol 5 by reconstructing metabolic pathway maps from its genomic data and analyzing the transcriptomes of cells grown on ethanol, hexadecane, toluene, and phenol. Genomic analysis revealed that Tol 5 has limited capacity for sugar utilization but possesses a wide range of metabolic pathways for alkane and aromatic compounds, including five distinct aromatic degradation routes that expand the known metabolic diversity of the genus Acinetobacter. Transcriptome analysis identified the specific pathway genes induced in response to each carbon source. During growth on phenol, alkylbenzene degradation genes were upregulated alongside phenol monooxygenase genes, suggesting possible substrate-dependent cross-regulation between aromatic degradation pathways. Gene disruption experiments indicated that phenol monooxygenase is required for phenol assimilation, whereas toluene dioxygenase may contribute to earlier entry into exponential growth while potentially limiting final biomass accumulation. These findings provide a comprehensive view of the carbon metabolism of Tol 5 and a basis for assessing its potential in bioprocesses using non-sugar carbon sources.

Acinetobacter↗
PubMed1979

[Feedstuffs contamination by Penicillium cyclopium Westling. Frequency of penicillic acid producing strains (author's transl)].

For the last six years, 246 samples of feedstuffs, suspected for animal disorder, have been subjected to mycological examination, Penicillium cyclopium was present with more than 10(3) and 10(5) propagules per gram respectively in 42% and 6% of samples. The feeds mainly concerned are, in decreasing order of P. cyclopium frequency and contamination level : barley, maïze mixed feeds (50%), the straw (41%), hays (21%) and milk replacers (10%) (table 1). The penicillic acid bioproduction by fifty strains freshly isolated from these feedstuffs is investigated on wet crushed corn (60% water). After incubation at 25 degrees C for a week, extraction by ethyl acetate and purification, quantification is done by fluorodensitometry on TLC plates after exposure to concentrated ammonia (fig. 1). Among the strains, 50% produces less than 5 ppm, 4% between 10-100 ppm, 20% (100-1 000), 20% (1 000-5 000) and 6% (5 000-10 000 ppm) (table 2). Maximal yield obtained was 8 240 mg/kg. Hypothesis of a log-normal distribution of toxigenic strength is not rejected (fig. 2). On the whole, frequency and toxic yields are higher for strains originating from cereals. One may think that only a quarter of the strains might be considered as actual potential penicillic acid producers in agricultural conditions.

Animal Feed↗
PubMed2026

Multivalent Display of Antimicrobial Peptides on Plant Virus Scaffolds Enhances Killing of Drug-Resistant Bacteria.

Multidrug-resistant (MDR) bacteria pose a significant challenge to global health. Antimicrobial peptides (AMPs) have emerged as promising candidates against MDR bacteria due to their rapid and broad-spectrum activity; however, their clinical translation is hindered by compromised activity, toxicity, and poor stability under in vivo conditions. Here, we report the development of RPG (rod-based peptide grids), a plant virus-based antimicrobial platform that harnesses the structural scaffold of high-aspect-ratio Potato virus X (PVX) for the multivalent and modular display of AMPs. Our data show that RPG enhances the efficacy of AMPs by more than 9700-fold, maintaining activity under in vivo salt conditions. RPG eradicates MDR pathogens within 10-30 min, surpassing the efficacy of last-resort antibiotics (vancomycin, tigecycline, and cefiderocol), while exhibiting low measurable cytotoxicity to mammalian cells at high therapeutic doses. Due to structural complexity, RPG demonstrates stability in serum and resistance to proteases. Multivalent display of peptide variants enabled enhanced broad-spectrum killing at low doses. This work establishes plant virus-AMP conjugates as a safe, potent, broad-spectrum antimicrobial platform, offering a versatile strategy for addressing antibiotic resistance.

Antimicrobial Peptides↗