Biology subjects

Blank, L. M.

Publications and source records attributed to Blank, L. M..

At least 19 recordsLinked to original sources

bioRxiv2026

Rewiring central carbon metabolism reveals a trade-off between yield and production rate in poly-γ-glutamic acid synthesis by Bacillus subtilis

Improving carbon yield and process time is a key requirement for the industrially viable production of biopolymers. During poly-{gamma}-glutamic acid production with Bacillus subtilis, a considerable fraction of the carbon source is diverted into by-products. These originate from accumulating pyruvate, constraining carbon flux towards glutamate synthesis. Disrupting by-product pathways reduces their secretion, but the underlying imbalance at the pyruvate node persists. Here, we rewired the central carbon metabolism to redirect glycolytic flux from pyruvate formation towards oxaloacetate and 2-oxoglutarate in an improved medium. Deletion of pyruvate kinase combined with heterologous expression of phosphoenolpyruvate carboxylase established an alternative anaplerotic entry route into the TCA cycle. Subsequent disruption of gluconeogenetic reactions (OF5) reduced by-product formation by 81% and increased {gamma}-PGA yield to 0.41 g g-1 glucose, but lowered the glucose uptake rate. Alternatively, disruption of the TCA cycle downstream of 2-oxoglutarate combined with enhanced glutamate synthesis (OF4.2) increased substrate uptake and improved the {gamma}-PGA production rate by 39% compared to the wild type, while product and by-product titers remained comparable. Both strategies thus revealed a trade-off between improved yield or production rate. Subsequent 13C metabolic flux analysis and intracellular metabolite profiling revealed distinct carbon routing phenotypes. While strain OF5 maintained carbon within the TCA cycle, OF4.2 cycled carbon between oxaloacetate, malate and pyruvate, thereby altering redox and energy balances. These results highlight the need for coordinated control of carbon flux, redox metabolism and energy supply for improving {gamma}-PGA synthesis, and identify the oxaloacetate-malate-pyruvate node as a promising strain engineering target.

microbiology↗

bioRxiv2026

Adaptive laboratory evolution rewires Pseudomonas putida for resource-efficient acetate assimilation

Acetate is an attractive renewable two-carbon substrate for microbial biotechnology, but its toxicity limits growth and carbon-use efficiency at process-relevant concentrations. Here, we used adaptive laboratory evolution to improve acetate tolerance in a genome-reduced strain of Pseudomonas putida and combined whole-genome sequencing, reverse engineering, transcriptomics, proteomics, and 13C-acetate fluxomics to resolve the underlying adaptation mechanisms. Evolution under increasing acetate concentrations selected recurrent mutations in gacA and fabB, which encode a global response regulator and a fatty acid biosynthesis enzyme, respectively. Reverse engineering of these mutations recovered most of the evolved phenotype, including shorter lag phase and substantially higher biomass yield from acetate. Multi-omic analyses showed repression of type VI secretion systems, carbohydrate storage functions, fatty acid metabolism, and oxidative stress-associated proteins, indicating resource reallocation away from costly stress and non-essential programs. Fluxomics further revealed reduced EDEMP cycling and increased glyoxylate shunt flux, consistent with improved acetate-carbon retention in biomass. These results establish acetate tolerance in P. putida as a resource-efficiency phenotype and identify gacA and fabB as actionable targets for acetate-based bioproduction.

synthetic biology↗

bioRxiv2026

Improving acetate metabolism of Pseudomonas putida KT2440 by evolutionary and rational engineering

Acetate is a promising carbon source for microbial biotechnology as it can be produced sustainably from lignocellulosic biomass or C1 gases. Since acetate is directly activated to acetyl-CoA, it is especially suitable for producing acetyl-CoA-derived products, showcased here with the production of 3-(3-hydroxyalkanoyloxy) alkanoic acids (HAAs). P. putida KT2440 can natively metabolize acetate, but the weak acid has also inhibitory effects on microbial growth. We present an in-depth study on the physiology of P. putida KT2440 using acetate as carbon and energy source and evaluate acetate as feedstock for the biosynthesis of HAAs. Initially, a rational engineering approach to overexpress acetyl-CoA synthetase for acetate activation resulted in an improved growth rate of 16% and reduced lag phase by six hours. To further increase the performance of P. putida KT2440 on acetate, adaptive laboratory evolution was performed. This resulted in an improvement in the growth rate from 0.4 h-1 to 0.6 h-1 and enabled growth on up to 12.5 g L-1 acetate with a shortened lag phase compared to the wild type. Whole-genome sequencing revealed mutations in proteins involved in gene expression regulation and signal transduction. This evolutionary engineering approach informed the deletions of gacS and crc, which resulted in a reduction in the lag phase from seven hours to one hour and an improvement of the growth rate by 25 %, matching the growth properties of the evolved clones. Using the evolved strains for the production of HAAs resulted in faster biomass and product formation with product titers reaching up to 94 % of that of the wild type. In conclusion, we identified mechanisms in the acetate metabolism of P. putida KT2440 and improved the growth performance of the strain by rational and evolutionary engineering, demonstrating the potential of the promising, but challenging 3rd generation feedstock acetate.

microbiology↗

bioRxiv2026

Protein without farms: What comparative genomics reveals about ''Power-to-Food'' microbes

Conventional agriculture is increasingly incompatible with planetary boundaries, such as land and water demand, greenhouse-gas emissions, and disruption of the nitrogen cycle. Hydrogen-oxidizing bacteria (HOB) enable a scalable "power-to-food" approach in which aerobic gas fermentation turns CO2 and renewable H2, along with N2 in some strains, into protein-rich biomass, largely decoupling protein production from arable land and climate variability. The same chemistry is attractive for closed-loop space life support, where crew CO2 and electrolysis-derived H2 can be recycled into edible biomass. Here, we compare two leading HOB chassis strains, Cupriavidus necator H16 and Xanthobacter sp. SoF1, using standardized re-annotation, orthology-based comparison, pathway reconstruction, and safety-oriented genome screening. Importantly, SoF1 is the production strain for Solar Foods Solein(R), a dried microbial biomass ingredient, which is approved as a novel food in Singapore and has a self-affirmed GRAS status in the United States. H16 has a larger, multipartite genome of 7.41 Mb split across two chromosomes and the pHG1 megaplasmid, whereas SoF1 is more compact at 4.91 Mb and encoded on a single replicon. Both encode Calvin-Benson-Bassham CO2 fixation and multiple [NiFe]-hydrogenase systems supporting growth on CO2/H2, but nitrogen economy differentiates the hosts. SoF1 encodes a complete nitrogen-fixation module (nifHDK) and nitrate-assimilation genes, whereas H16 lacks nif and instead encodes nitrate/nitrite respiration for oxygen-limited flexibility. Safety screening revealed no evidence of canonical virulence determinants, integron or plasmid-linked antimicrobial resistant (AMR) cassettes, or high-confidence foodborne exotoxins under strict thresholds. These results convert genome-level features into actionable design constraints for selecting and engineering food-grade HOB, strengthening robust air-to-protein bioprocesses on Earth and informing a blueprint for closed-loop, space-compatible protein production. HighlightsO_LIHydrogen-oxidizing bacteria enable power-to-protein from CO2, H2 with minimal land use. C_LIO_LIHead-to-head genomics defines design rules for food-grade "air-to-protein" bioprocesses. C_LIO_LIContrasting nitrogen routes guide media design, nutrient inputs, and closed-loop operation. C_LIO_LICO2 fixation and hydrogenase gene sets reveal complementary robustness and control features. C_LIO_LIGenome architecture and COG shifts inform safety, stability, and regulatory-ready strain choice. C_LI

genomics↗

bioRxiv2026

Engineering Pseudomonas putida KT2440 for open-loop upcycling of mixed plastics

Current mechanical and chemical recycling strategies address less than 10% of global plastic waste, necessitating alternative valorization routes. Biological upcycling via enzymatic depolymerization combined with microbial conversion of the resulting monomers offers a promising pathway to transform mixed plastic waste into valuable alternatives. Here, we employed a single engineered Pseudomonas putida KT2440 for simultaneous co-utilization of five plastic monomers including ethylene glycol, terephthalic acid, adipic acid, 1,4-butanediol, and L-lactic acid, which can be derived from enzymatic hydrolysis of polyethylene terephthalate (PET), polybutylene adipate-co-terephthalate (PBAT), polyester-polyurethanes (PUs), and polylactic acid (PLA). Continuous fermentation over 21 days with alternating mixed-monomer feeds achieved steady state growth and complete substrate depletion, yielding adaptive mutations that informed iterative strain improvement. Further engineering enabled the biosynthesis of (R)-3-hydroxybutyrate (R-3HB), and 0.70 g L-1 R-3HB was produced directly from enzymatic hydrolysates of blended PET, PBAT, and TPU. These results establish a viable bio-based approach for upcycling realistic mixed plastics into value-added bioproducts.

microbiology↗

bioRxiv2026

Bioconversion of p-coumaric acid to cis,cis-muconic acid using an engineered A. baylyi ADP1 - E. coli co-culture

Lignin-derived aromatics are abundant in depolymerized lignin but remain remain untilized as carbon sources for commercial production of bulk chemicals. Among these aromatics, p-coumaric acid can be funnelled through the {beta}-ketoadipate pathway toward cis,cis-muconic acid (ccMA), a precursor of bio-based adipic and terephthalic acids. However, efficient ccMA production by Acinetobacter baylyi ADP1 is constrained by toxicity of catechol (the immediate precursor of ccMA), inefficient channelling of protocatechuate (PCA) metabolism towards ccMA production, and absence of PCA decarboxylase for converting PCA to catechol. Therefore, in this study, we engineered a modular co-culture system, combining engineered strains of A. baylyi and E. coli, for ccMA production from synthetic p-coumaric acid. Deletion of catB and catC genes and overexpression of catA in A. baylyi GJS_catA strain enabled near-stoichiometric conversion of catechol to ccMA ([~]90% carbon yield) with titres up to 56.4 mM ([~] 8 g/L) under controlled fed-batch feeding. The strain was further engineered (A. baylyi GJS2_catA) to convert p-coumaric acid to PCA. Due to the inactivity of heterologous PCA decarboxylase (aroY gene) in A. baylyi, this gene was incorporated in E. coli where it exhibited activity through PCA to catechol conversion. Upon its production by E.coli_aroY in the co-culture, catechol is instantaneously converted to ccMA by A. baylyi GJS2_catA strain. In a two-step process, 22 mM p-coumaric acid was initially converted to 20.6 mM PCA (A. baylyi GJS2_catA), which was further converted to catechol (E.coli_aroY) and finally to 18.55 mM ccMA (2.63 g L-{superscript 1}) by A. baylyi GJS2_catA. This process was validated by the valorization of lignin-derived p-coumaric acid to ccMA. While the modular strategy developed in this study substantially improves ccMA titres, it also highlights the bottlenecks in A. baylyi metabolic pathway engineering for lignin valorization. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=147 SRC="FIGDIR/small/709578v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@a83daborg.highwire.dtl.DTLVardef@168c6b6org.highwire.dtl.DTLVardef@1ce0abdorg.highwire.dtl.DTLVardef@23200b_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

Itaconic acid production from acetate by Ustilago maydis: A step towards land-free biotechnology

Itaconic acid is a versatile bio-based platform chemical produced from sugar-based feedstocks, linking its production to arable land use. As global food demand rises, alternative carbon sources that decouple industrial biotechnology from agriculture are required. The C2 compound acetate can be derived from lignocellulosic biomass and industrial side streams. Emerging routes enable the direct synthesis of acetate from C1 carbon sources such as CO2, CO, and methane. Here, we show that the smut fungus Ustilago maydis can efficiently produce itaconic acid using acetate as the sole carbon source. To overcome weak-acid toxicity and pH-related stress, a combined pH-stat and DO-triggered feeding strategy was applied in a 1 L-scale fed-batch bioreactor, enabling an itaconate titer of 97 g L-1 and an overall yield of 0.41 g g-1. Key performance indicators were comparable to those of a glucose-based reference process. Despite substantially lower biomass formation on acetate, biomass-specific production rates were markedly higher than on glucose, indicating highly efficient channeling of carbon toward product formation. Overall, our results establish acetate as a competitive and sustainable feedstock for fungal itaconic acid production and position acetate-based processes as a viable route toward land-free biotechnology.

microbiology↗

bioRxiv2025

Optimization of a T7 RNA polymerase expression system for high-yield protein production in Cupriavidus necator H16

Many chemical manufacturing routes are being replaced with enzymatic processes to improve sustainability. In biocatalysis, enzyme production is often the main bottleneck. Bacterial proteins are frequently produced using the workhorse E. coli BL21(DE3) and its derivatives. However, other bacteria with beneficial characteristics can also be engineered for this purpose. Cupriavidus necator H16 (C. necator), for example, is a Gram-negative bacterium well-known for its chemolithoautotrophic metabolism and high polyhydroxybutyrate (PHB) accumulation. Previous studies have demonstrated protein production without inclusion body formation, which is one of the main challenges when producing enzymes in E. coli. Nevertheless, high-yield protein production in C. necator remains an understudied field. Here, we investigated the bottlenecks limiting protein production in C. necator. We optimized a T7 RNA polymerase genetic system and quantified the impact of several genetic elements such as T7 promoter, RBS strength and codon usage towards GFP production. Codon usage was the main factor limiting protein production in C. necator. Tuning the RBS strength and selecting a different T7 promoter strongly influenced expression leakiness. We then produced the ene-reductase YqjM from Bacillus subtilis in C. necator, analyzing the performance of the engineered C. necator strain and our previously developed pMVRha expression plasmid. C. necator produced high amounts of soluble protein and outperformed the gold standard, E. coli BL21(DE3) in producing FMN-loaded enzyme. This result highlights the potential of non-model bacteria to achieve high-yield enzyme production and promote the transition to biocatalysis-driven chemical synthesis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/688765v2_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@1a6584corg.highwire.dtl.DTLVardef@1ef094dorg.highwire.dtl.DTLVardef@4bb4c3org.highwire.dtl.DTLVardef@489c85_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2025

Engineering of Pseudomonas putida KT2440 for Broad-Chain-Length 3-Hydroxy Fatty Acid Biosynthesis

3-Hydroxy fatty acids (3-HFAs) are versatile intermediates for bio-based polymers, fuels, and surfactants, and are advancing circular economy manufacturing. We built an acyl- CoA ligase-deficient chassis of Pseudomonas putida KT2440, thereby blocking 3-HFA activation and preventing its use as carbon source. This strategy decoupled synthesis from catabolism and enabled 3-HFA accumulation. We then compared two different routes for modifying the free 3-HFA composition. 1. In a direct route, overexpressing native PhaG produced C8, C10, C12, and C14 3-HFAs, achieving a total titer of 0.73 g/L in shake flasks. Functional analyses under our tested conditions support a re-assignment of PhaG: rather than acting primarily as a 3-hydroxyacyl-ACP:CoA transacylase, it functions mainly as a thioesterase, liberating free 3-HFAs from hydroxyacyl-ACP. 2. In an indirect route, overexpressing RhlA variants generated hydroxyalkanoyl-alkanoates (HAAs) that were converted to free 3-HFAs by endogenous esterase(s): RhlA from Pseudomonas aeruginosa PAO1 favored C8-C12 and yielded 0.47 g/L 3-HFAs, whereas RhlA from Burkholderia plantarii PG1 favored C10-C14 with 0.14 g/L, of which 80% was C14. Finally, we demonstrated process feasibility by up-scaling the PhaG pathway in a stirred-tank reactor. These results establish modular, stable, chassis-compatible routes for tailoring 3-HFA chain-length distributions, thereby providing a foundation for scalable, bio-based monomer supply in a circular economy.

synthetic biology↗

bioRxiv2025

A physiologically-based model of bile acid metabolism in humans

Altered serum BA profiles have been reported for several chronic liver diseases. However, relevant modifications in bile acid disposition are difficult to investigate mechanistically due to the interference of the various physiological processes involved at various levels of bile acid metabolism. In this regard, validated computational models represent a promising tool to understand the functional effect of disease-related alterations on bile acid composition along the gut-liver-axis through mechanistic analyses of the underlying physiological processes. We applied a physiologically-based models of bile acid metabolism in humans comprising the five predominant bile acids. The model describes various physiological aspects of bile acid metabolism including synthesis, enterohepatic circulation, hepatic and microbial conversions, postprandial gall bladder emptying as well as excretion via feces and urine. Model development was based on 39 previously published studies in patients without any liver diseases. In the future, the established model may serve as reference for analysis of the role of bile acids in health and disease.

systems biology↗

bioRxiv2025

Yeast strain development for enhanced polyphosphate production

Withdrawal StatementAfter publication, we discovered that the data presented in the manuscript do not correspond to the microbial strains described in the text. Specifically, the strains were mixed up during the analysis, which compromises the validity of the main conclusions. We take full responsibility for this oversight and are currently working to resolve the issue. In the interest of scientific accuracy and integrity, we believe that withdrawal is the most appropriate course of action at this time. Therefore, we do not wish this work to be cited as reference fort he project. We apologize for any confusion this may have caused and thank you for your understanding. If you have any questions, please contact the corresponding author.

molecular biology↗

bioRxiv2024

A consortium-based approach to adaptive laboratory evolution of Acinetobacter baylyi ADP1 for lignin valorization

The utility of Acinetobacter baylyi ADP1 (ADP1) for lignin valorization has yet to be sufficiently investigated compared to other organisms such as Pseudomonas, Rhodococcus, etc. In this study, a two-step Adaptive Laboratory Evolution (ALE) process was used to evolve a unique ADP1 strain (A. baylyi SAG_185). Initially, several ADP1 strains were evolved for substrate tolerance to specific lignin-related aromatics (LRAs). Subsequently, a consortium of these strains was adaptively evolved in a mixture of LRAs, which resulted in the evolution of SAG_185. This strain was capable of simultaneous utilization of multiple LRAs at higher concentrations as well as grow on a depolymerized lignin-rich residue obtained from enzymatic hydrolysis of pre-treated corncob. This is the first report on such an evolutionary strategy. Whole-genome sequence analysis of all the evolved strains revealed large-scale mutations involving insertion sequences (IS). In particular, SAG_185 revealed a critical mutation in the vanR repressor gene, resulting in the up-regulation of vanAB genes required to convert vanillate to the key intermediate, protocatechuate (PCA). Additionally, there were two large deletions of 9kb and 38kb DNA segments, including genes for putative transcriptional regulators of LysR, MarR and AraC family. The evolved strains also showed mutations in the hcaE gene, responsible for the uptake of LRAs. The vast number of mutations in hypothetical proteins, transporter and regulatory sequences indicate the underlying effects of these regions on the uptake of multiple LRAs. Overall, our findings provide potential targets for reverse engineering of A. baylyi ADP1 for lignin valorization. IMPORTANCEThis study shows a novel strategy for adaptive laboratory evolution, which can be generically adopted to evolve bacterial strains for taking up multiple substrates which are toxic at higher concentrations. We developed a two-step evolutionary strategy to evolve a unique strain, A. baylyi SAG_185, which could take up multiple lignin-related aromatic monomers at higher concentrations as well as grow on depolymerized lignin. Initially, individual strains were adapted to utilize single aromatic monomers at higher concentrations. After many unsuccessful attempts to adapt these strains for utilizing multiple monomers, a consortium of the five evolved strains were grown on a mixture of aromatics and adapted to utilize all the monomers at high concentrations. The adapted consortia resulted in the evolution of SAG_185. Whole-genome sequence analysis of all these strains gave rise to many interesting insights on potential genetic targets for reverse engineering of A. baylyi ADP1 for lignin valorization.

microbiology↗

bioRxiv2024

Using Cupriavidus necator H16 to provide a roadmap for increasing electroporation efficiency in non-model bacteria

Bacteria are a treasure trove of metabolic reactions, but most industrial biotechnology applications rely on a limited set of established host organisms. In contrast, adopting non-model bacteria for the production of various chemicals of interest is often hampered by their limited genetic amenability coupled with their low transformation efficiency. In this study, we propose a series of steps that can be taken to increase electroporation efficiency in non-model bacteria. As a test strain, we use Cupriavidus necator H16, a lithoautotrophic bacterium that has been engineered to produce a wide range of products from CO2 and hydrogen. However, its low electroporation efficiency hinders the high-throughput genetic modifications required to develop C. necator into an industrially relevant host organism. First, we propose a species-independent technique based on natively methylated DNA and Golden Gate assembly to increase one-pot cloning and electroporation efficiency by 70-fold. Second, bioinformatic tools were used to predict defense systems and develop a restriction avoidance strategy that was used to introduce suicide plasmids by electroporation to obtain a domesticated strain. The results are discussed in the context of metabolic engineering of non-model bacteria. TABLE OF CONTENT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=161 SRC="FIGDIR/small/596136v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@dfc76aorg.highwire.dtl.DTLVardef@19d130forg.highwire.dtl.DTLVardef@14e6ed3org.highwire.dtl.DTLVardef@4e0024_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2024

Synthetic bacterial consortium for degradation of plastic pyrolysis oil waste

The plasic crisis is ominipresent, from littering macroplastic to reports that document plastic in every niche of this planet, including the human body. In order to achieve higher recycling quotas, especially of mixed plastic waste, pyrolysis seems to be a viable option. However, depending on the process parameters, plastic pyrolysis oil waste is encountered, which is difficult to valorize, due to the enormous spread of the molecules included. To reduce the molecular heterogeneity, we here artificially compounded, monitored, and optimized the performance of a bacterial consortium, which has the ability to tolerate organic pollutants and use them as energy and carbon sources for their own metabolic activity. The primary constituents of the here used plastic pyrolysis oil waste (PPOW) were alkanes and {varepsilon}-caprolactam. The bacterial community exhibited noteworthy efficacy in eliminating alkanes of diverse chain lengths ranging from 71% to 100%. Additionally, within 7-days, the microbial community demonstrated a removal efficiency surpassing 50% for various aromatic hydrocarbons, along with complete eradication of {varepsilon}-caprolactam and naphthalene. Besides, a back-propagation (BP) neural network method is applied to evaluate O2 consumption as a measure of microbial activity. The insights gained were used to build a model, which is able to predict O2 depletion in long-time experiments and other experimental conditions. The results are discussed in the context of a developing (open) circular plastic economy. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/590079v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@628f68org.highwire.dtl.DTLVardef@b5274eorg.highwire.dtl.DTLVardef@1278ceaorg.highwire.dtl.DTLVardef@194887a_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightO_LISynthetic bacterial communities are used to remove plastic hydrolysis oil waste C_LIO_LIThe optimized biphase reaction system can remove the majority of pollutants C_LIO_LIThe biodegradation process can be monitored in a real-time bioprocess software C_LIO_LINeural network techniques are used to model and predict the removal process C_LI

bioengineering↗

bioRxiv2024

Establishing a straight-forward I-SceI mediated recombination one plasmid system for efficient genome editing in P. putida KT2440

Pseudomonas putida has become an increasingly important chassis for the production of valuable bioproducts. This development is not at least due to the ever-improving genetic toolbox, including gene and genome editing techniques. Here, we present a novel, one plasmid design of a key genetic tool, the pEMG/pSW system, guaranteeing one engineering cycle to be finalized in three days. The pEMG/pSW system proved in the last decade to be valuable for targeted gensome engineering in Pseudomonas, as it enables the deletion of large regions of the genome, the integration of heterologous gene clusters or targeted generation of point mutations. Here, to expedite genetic engineering, two alternative plasmids were constructed: 1) the sacB gene from Bacillus subtilis was integrated into the I-SceI expressing plasmid pSW-2 as counterselection marker to accelerated plasmid curing; 2) double strand break introducing gene I-SceI and SacB counterselection marker were integrated into the backbone of the original pEMG vector, named pEMG-RIS. The single plasmid of pEMG-RIS allows rapid genome editing despite the low transcriptional activity of a single copy of the I-SceI encoding gene. Here, the usability of the pEMG-RIS is shown in P. putida KT2440 by integrating an expression cassette including a msfGFP gene in three days. In addition, a large fragment of almost 16 kb was also integrated. In summary, an updated pEMG/pSW genome editing system is presented that allows efficient and rapid genome editing in P. putida. The pEMG-RIS will be available via the Addgene platform.

microbiology↗

bioRxiv2023

Yeast9: A Consensus Yeast Metabolic Model Enables Quantitative Analysis of Cellular Metabolism By Incorporating Big Data

Genome-scale metabolic models (GEMs) can facilitate metabolism-focused multi-omics integrative analysis. Since Yeast8, the yeast-GEM of Saccharomyces cerevisiae, published in 2019, has been continuously updated by the community. This have increased the quality and scope of this model, culminating now in Yeast9. To evaluate its predictive performance, we generated 163 condition-specific GEMs constrained by single-cell transcriptomics from osmotic pressure or normal conditions. Comparative flux analysis showed that yeast adapting to high osmotic pressure benefits from upregulating fluxes through the central carbon metabolism. Furthermore, combining Yeast9 with proteomics revealed metabolic rewiring underlying its preference in nitrogen sources. Lastly, we created strain-specific GEMs (ssGEMs) constrained by transcriptomics for 1229 mutant strains. Well able to predict the strains growth rates, fluxomics from those large-scale ssGEMs outperformed transcriptomics in predicting functional categories for all studied genes in machine-learning models. Based on those findings we anticipate that Yeast9 will empower systems biology studies of yeast metabolism.

systems biology↗

bioRxiv2023

Bioprocess optimization enables enhanced protopanaxadiol production in yeast

Ginsenosides are the primary active metabolites of ginseng and have been used in traditional herbal medicine in Asia for more than 4,000 years. Protopanaxadiol (PPD) is the precursor of dammarane-type ginsenosides, exhibiting different pharmacological activities. However, extraction of PPD from plant material is cumbersome because of its low concentration. Precision fermentation using recombinant yeast is a promising alternative strategy to produce PPD. For increasing PPD production, the medium and fermentation conditions were optimized by a Design of Experiment (DoE) approach. PPD production increased by 7.5-fold in the final cultivation condition compared to the reference condition. The PPD titer reached 1.2 g/L during simple 500 mL shake flask cultivations, the highest PPD production in shake flasks to date. The protocol presented facilitates parallel evaluation of recombinant yeast, thereby contributing to the much-needed sustainable synthesis of the versatile molecule class of triterpenoids.

synthetic biology↗

bioRxiv2023

Itaconic acid production by co-feeding of Ustilago maydis: a combined approach of experimental data, design of experiments and metabolic modeling

Itaconic acid is a platform chemical with a range of applications in polymer synthesis and is also discussed for biofuel production. While produced in industry from glucose or sucrose, co-feeding of glucose and acetate was recently discussed to increase itaconic acid production by the smut fungus Ustilago maydis. In this study, we investigate the optimal co-feeding conditions by interlocking experimental and computational methods. Flux balance analysis indicates that acetate improves the itaconic acid yield up to a share of 40 % acetate on a carbon molar basis. A design of experiment results in the maximum yield of 0.14 itaconic acid per carbon source from 100 g L-1 glucose and 12 g L-1 acetate. The yield is improved by around 22 % when compared to feeding of glucose as sole carbon source. To further improve the yield, gene deletion targets are discussed that were identified using the metabolic optimization tool OptKnock. The study contributes ideas to reduce land use for biotechnology, by incorporating acetate as co-substrate, a C2-carbon source that is potentially derived from carbon dioxide.

microbiology↗