Biology subjects

Hudson, E. P.

Publications and source records attributed to Hudson, E. P..

16 recordsLinked to original sources

bioRxiv2026

CO2-concentrating nanoparticles drive progressive photosynthetic and cell-wall remodelling in Arabidopsis thaliana cells

Plant cells offer a distinctive platform for biohybrid engineering because they combine growth and proliferation with photosynthetic carbon acquisition and the continuous fabrication of structurally complex biomass. Harnessing these capabilities could enable living systems in which synthetic functionality develops together with cellular physiology and material organization. Yet nanomaterial engineering of proliferating plant cell populations remains largely unexplored. Here, we establish a biohybrid system combining photosynthetically active Arabidopsis thaliana suspension cells with chitosan-modified polyethyleneimine (gPEI-Chi) nanoparticles, a synthetic CO2-concentrating nanomaterial. By supplying fresh nanoparticles at each subculture, newly generated cell populations were successively functionalized, driving progressive changes in cellular and multicellular phenotypes. Nanoparticle functionalization reduced net headspace CO2 accumulation, increased chlorophyll content and induced stage-dependent reorganization of photosynthetic function and carbon-handling pathways. These physiological changes were accompanied by altered cell wall regeneration and progressive remodelling of cell wall composition, spatial organization and ultrastructure, ultimately promoting more cohesive multicellular aggregates. Our findings establish successive nanomaterial functionalization as a strategy to steer the evolving physiology and structural organization of proliferating plant cell populations, opening opportunities for plant biohybrid systems and engineered living materials.

plant biology↗

bioRxiv2026

β-lactoglobulin a new whey: Computational redesign improves stability and nutritional composition

Protein engineering and precision fermentation provide an opportunity to increase the value of food proteins by improving their solubility, stability, functionality, or nutritional composition. Here, we use {beta}-lactoglobulin ({beta}LG) as a model protein to investigate how state-of-the-art computational protein design approaches affect these properties. First, the deep learning-based design tool ProteinMPNN was used to alter up to 20% of {beta}LG residues for increased stability. Second, the physics-based modeling platform PyRosetta was used to find positions in {beta}LG accommodating increased branched-chain amino acid (BCAA) content and up to 10 residues were simultaneously exchanged. Experimental characterisation of ProteinMPNN and stabilised BCAA-enriched variants showed similar secondary structure and oligomeric state as native {beta}LG. ProteinMPNN variants gave increased titers and increased thermal stability up to 15 {degrees}C, and this correlated with changes in the rate of surface pressure in droplet tensiometry. Stabilized BCAA-enriched mutants had altered acid solubility. Correlations between computationally derived biophysical metrics and experimental properties are presented and suggest some predictive power for surface hydrophobicity on protein yield.

bioengineering↗

bioRxiv2026

Identifying Novel Targets of the Stringent Response in Plants and Cyanobacteria using chemoproteomics

Survival in dynamic environments requires photosynthetic organisms to rapidly sense and respond to stress. The stringent response, mediated by the signaling molecule guanosine-3,5-bisdiphosphate (ppGpp), is crucial for acclimation to environmental changes such as darkness and nitrogen limitation. While it has been extensively characterized in heterotrophic bacteria such as Escherichia coli, the molecular mechanisms and regulatory targets of ppGpp in photosynthetic organisms remain less understood. Here, we report large-scale chemoproteomic identification of ppGpp-binding proteins across plant chloroplasts and cyanobacteria, revealing both conserved and novel targets compared to E. coli. In plants, we found that ppGpp regulates pyrimidine metabolism by inhibiting the chloroplastic enzyme aspartate transcarbamoylase (PyrB). In cyanobacteria, we found that ppGpp activates glucose-1-phosphate adenylyltransferase (GlgC) involved in glycogen synthesis, activates citrate synthase (GltA), and induces carboxysome aggregation. These findings expand the known ppGpp regulatory network in photosynthetic organisms and provide a foundation for understanding how ppGpp coordinates adaptation to nutrient and environmental stresses.

systems biology↗

bioRxiv2026

Immobilization in nanocellulose matrix reallocates cyanobacterial proteome resources from growth to bioproduction

Solid-state photosynthetic cell factories transform dissolved and atmospheric carbon into chemicals and biomass, offering a platform for the sustainable production of industrially relevant compounds. Yet, how immobilisation affects cell physiology to favour biosynthesis over growth is unclear. Here, we fabricate photosynthetic biohybrids of cellulose nanofiber (CNF) and Synechocystis sp. PCC 6803 by osmotic dehydration. Osmotic dehydration resulted in an anisotropic distribution of the cyanobacterial colonies and provided excellent light distribution during cultivation. In an engineered sucrose-secreting Synechocystis strain, quantitative proteomics showed that immobilization downregulates ribosomal proteins while upregulating sucrose-synthesis and carbon concentrating machinery, as well as a stress signature of enhanced photosystem II repair, photoprotection, and ROS detoxification. These changes are consistent with a reallocation of constrained proteome resources from growth toward product synthesis. This principle may be extendable to photosynthetic production of compounds beyond sucrose.

microbiology↗

bioRxiv2026

Expression landscape of heterologous enzymes in Synechocystis sp. PCC 6803

Photosynthetic cyanobacteria are promising platforms for sustainable chemical production, as they can convert light and CO2 into valuable compounds. Achieving this often requires engineering cyanobacteria with non-native enzymes with strong promoters to maximize enzyme accumulation. However, despite extensive engineering efforts, the extent to which these enzymes misfold and undergo degradation in cyanobacteria remains unknown. Here, we systematically investigate the fate of recombinant proteins in Synechocystis sp. PCC 6803 by estimating protein loss due to protease degradation. To do this, we developed a quantitative approach that combines split-GFP reporting with inducible CRISPRi knockdown of Clp protease system, enabling estimation of portion of proteins that would otherwise be degraded. Applying this method to 103 heterologous proteins previously used in cyanobacterial metabolic engineering studies, we find that, on average, one-third of recombinant protein accumulation is lost to degradation, with some enzymes exhibiting more than 95% protein loss. Furthermore, we compare expression from identical expression constructs in E. coli and Synechocystis and find broad similarities in their protein accumulation patterns. Together, these findings provide the first quantitative overview of heterologous protein expression in cyanobacteria and identify enzymes that are suboptimal for their respective pathways, information usable to increase production titers in photosynthetic cell factories.

synthetic biology↗

bioRxiv2025

The fitness landscape of a Form II Rubisco in a photosynthetic bacterium guides engineering of oxygen tolerance

Rubisco is an important but challenging protein engineering target. Fast and selective rubiscos could enhance photosynthesis in plants and accelerate biobased production processes. To facilitate engineering of rubisco, we applied an in vivo screen that couples rubisco activity to growth rate of the photoautotrophic cyanobacterium Synechocystis sp. PCC 6803. We screened a barcoded mutagenesis library of the form II rubisco from Gallionella sp. containing 15,000 single-site and multi-site variants. Exchanges in loop 6 near the active site, at the dimer interface, and in potential gas tunnels improved rubisco fitness. The dataset also informed protein engineering, using recombination and a trained transformer model. In vitro characterisation of two high-fitness variants showed reduced catalytic efficiency for oxygenation (kcat/Ko) in both and an increased carboxylation turnover (kcatC) in one. This large labeled fitness dataset, containing examples of epistasis, can be useful for benchmarking computational models of rubisco. TeaserEvolving a foreign rubisco to photosynthesis leads to reduced oxygen sensitivity.

biochemistry↗

bioRxiv2025

Deciphering the metabolic details of L-lysine toxicity in cyanobacteria

L-lysine (Lys) has been explored as a potential cyanobactericide due to its inhibitory effects on cyanobacterial growth at micromolar concentrations, comparable to many antibiotics. Here, we investigated the early metabolic and physiological responses of the model cyanobacterium Synechocystis sp. PCC 6803 to Lys exposure. Physiological analyses revealed cell enlargement, oxidative stress, and photosynthesis inhibition, leading to growth arrest. Metabolomic profiling indicated disruptions in peptidoglycan biosynthesis, evidenced by the accumulation of L-/D-alanine, meso-diaminopimelate, and D-Ala-D-Ala, suggesting interference with cell wall integrity. Furthermore, levels of energy metabolites and other amino acids including tyrosine, tryptophan, valine, and iso-/leucine were significantly altered, implying broader metabolic impacts of Lys toxicity. To explore potential resistance mechanisms, we used a CRISPRi-based genetic screen to identify key genes involved in relieving Lys toxicity. The Bgt permease system, responsible for basic amino acid uptake, was essential for acquiring Lys-resistance, as a bgtA mutant exhibited a normal growth on elevated Lys concentrations, thereby validating our CRISPRi-screen. Additionally, UirR, a DNA-binding response regulator, and genes linked to c-di-AMP signaling, seemed implicated in Lys metabolism. Deletion of c-di-AMP synthase gene increased Lys sensitivity, supporting a role for c-di-AMP in cell wall homeostasis and osmotic stress regulation. Altogether, our findings explored the early metabolic responses and physiological consequences of Lys exposure in Synechocystis, demonstrating its effects on peptidoglycan biosynthesis, amino acid metabolism, and nucleotide biosynthesis. The identification of key genetic factors contributing to Lys resistance provides new insights into cyanobacterial physiology and the potential application of Lys in bloom control strategies.

microbiology↗

bioRxiv2025

A cyanobacterial screening platform for Rubisco mutant variants

Rubisco is the main entry point of inorganic carbon into the biosphere and a central player in the global carbon system. Its relatively low catalytic constant as well as its tendency to also accept O2 as a substrate have made it a common target of enzyme engineering. We have developed an enzyme engineering and screening platform for Rubisco using the model cyanobacterium Synechocystis sp. PCC 6803. Starting with the Form II Rubisco from Gallionella, we first show that the enzyme can replace the native Form I Rubisco in Synechocystis and that growth rates become sensitive to CO2 and O2 levels. We address the challenge of designing a zero-shot input library, without prior experimental knowledge, by coupling the phylogenetically-guided model EVmutation with "in silico evolution". Starting with this targeted mutagenesis library, we used competitive growth coupled to deep sequencing to compare the properties of Rubisco protein variants under different cultivation conditions. We identified an amino acid exchange which increased the thermostability of Gallionella Rubisco and conveyed resilience to detrimental exchanges. The establishment of this platform is a first step towards high-throughput screening of Rubisco variants in Synechocystis and creating optimized enzyme variants to accelerate the Calvin-Benson-Bassham cycle in cyanobacteria and possibly chloroplasts. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/633911v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@b0e549org.highwire.dtl.DTLVardef@19d2a56org.highwire.dtl.DTLVardef@1468557org.highwire.dtl.DTLVardef@dc3e7e_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

The energy metabolism of Cupriavidus necator in different trophic conditions

The knallgas bacterium Cupriavidus necator is attracting interest for biotechnological applications due to its extremely versatile metabolism. C. necator can use hydrogen or formic acid as an energy source, fixes CO2 via the Calvin-Benson-Bassham (CBB) cycle, and also grows well on various other organic acids and sugars. Its tri-partite genome is notable for its size and manifold duplications of key genes (CBB cycle, hydrogenases, nitrate reductases). Comparatively little is known about which of these (iso-) enzymes and their cofactors are actually utilized for growth on different energy sources. Here, we investigated the energy metabolism of C. necator H16 by growing a barcoded transposon knockout library on various substrates including succinate, fructose, hydrogen (H2/CO2) and formic acid. The fitness contribution of each gene was determined from enrichment or depletion of the corresponding mutants. Fitness analysis revealed that 1) some, but not all, molybdenum cofactor biosynthesis genes were essential for growth on formate and nitrate respiration. 2) Soluble formate dehydrogenase (FDH) was the dominant enzyme for formate oxidation, not membrane-bound FDH. 3) For hydrogenases, both soluble and membrane-bound enzymes were beneficial for lithoautotrophic growth. 4) Of the six terminal respiratory complexes in C. necator H16, only some are utilized and utilization depends on the energy source. 5) Deletion of hydrogenase-related genes boosted heterotrophic growth, and we show that the relief from associated protein cost is responsible for this phenomenon. This study evaluates the contribution of each of C. necators genes to fitness in biotechnologically relevant growth regimes. Our results illustrate the genomic redundancy of this generalist bacterium, and may inspire future strategies for strain engineering. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/582058v2_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@1aac357org.highwire.dtl.DTLVardef@1fe970corg.highwire.dtl.DTLVardef@16ea53dorg.highwire.dtl.DTLVardef@122498d_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIa barcoded transposon library was used to assess gene fitness for hydrogenase, formate dehydrogenase and electron transport chain complexes C_LIO_LIthe utilization of terminal respiratory complexes is substrate specific C_LIO_LIsoluble formate dehydrogenase is more important than the membrane-bound enzyme C_LIO_LIsoluble hydrogenase and membrane-bound hydrogenase are equally utilized C_LIO_LIinactivation of hydrogenase and its accessory genes leads to faster heterotrophic growth C_LIO_LIwe demonstrate that faster growth is caused by the relief of protein synthesis burden C_LIO_LIfitness data is available in an interactive app at https://m-jahn.shinyapps.io/ShinyLib/ C_LI

microbiology↗

bioRxiv2023

CRISPR interference screens reveal tradeoffs between growth rate and robustness in Synechocystis sp. PCC 6803 across trophic conditions

Barcoded mutant libraries are a powerful tool for elucidating gene function in microbes, particularly when screened in multiple growth conditions. Here, we screened a pooled CRISPR interference library of the model cyanobacterium Synechocystis sp. PCC 6803 in 11 bioreactor-controlled conditions, spanning multiple light regimes and carbon sources. This gene repression library contained 21,705 individual mutants with high redundancy over all open reading frames and non-coding RNAs. Comparison of the derived gene fitness scores revealed multiple instances of gene repression being beneficial in one condition while generally detrimental in others, particularly for genes within light harvesting and conversion, such as antennae components at high light and PSII subunits during photoheterotrophy. Suboptimal regulation of such genes likely represents a tradeoff of reduced growth speed for enhanced robustness to perturbation. The extensive dataset assigns condition-specific importance to many previously unannotated genes, and suggests new functions for central metabolic enzymes. Prk, GAPDH, and CP12 were critical for mixotrophy and photoheterotrophy, which implicates the ternary complex as important for redirecting metabolic flux in these conditions in addition to inactivation of the Calvin cycle in the dark. To predict the potency of sgRNA sequences, we applied machine learning on sgRNA sequences and gene repression data, which showed the importance of C enrichment and T depletion in the first 12 bp proximal to the PAM site. Fitness data for all genes in all conditions is compiled in an interactive web application.

systems biology↗

bioRxiv2022

Metabolite interactions in the bacterial Calvin cycle and implications for flux regulation

Metabolite-level regulation of enzyme activity is important for microbes to cope with environmental shifts. Knowledge of such regulations can also guide strain engineering to improve industrial phenotypes. Recently developed chemoproteomics workflows allow for genome-wide detection of metabolite-protein interactions that may regulate pathway activity. We applied limited proteolysis small molecule mapping (LiP-SMap) to identify and compare metabolite-protein interactions in the proteomes of two cyanobacteria and two lithoautotrophic bacteria that fix CO2 using the Calvin cycle. Clustering analysis of the hundreds of detected interactions showed that some metabolites interacted in a species-specific manner, such as interactions of glucose-6-phosphate in Cupriavidus necator and of glyoxylate in Synechocystis sp PCC 6803. These are interpreted in light of the different central carbon conversion pathways present. Metabolites interacting with the Calvin cycle enzymes fructose-1,6/sedoheptulose-1,7-bisphosphatase (F/SBPase) and transketolase were tested for effects on catalytic activity in vitro. The Calvin cycle intermediate glyceraldehyde-3-phosphate activated both Synechocystis and Cupriavidus F/SBPase, which suggests a feed-forward activation of the cycle in both photoautotrophs and chemolithoautotrophs. In contrast to the stimulating effect in reduced conditions, glyceraldehyde-3-phosphate inactivated the Synechocystis F/SBPase in oxidized conditions by accelerating protein aggregation. Thus, metabolite-level regulation of the Calvin cycle is more prevalent than previously appreciated and may act in addition to redox regulation.

systems biology↗

bioRxiv2022

Inducible CRISPR/Cas9 allows for multiplexed and rapidly segregated single target genome editing in Synechocystis sp. PCC 6803

Establishing various synthetic biology tools is crucial for the development of cyanobacteria for biotechnology use, especially tools that allow for precise and markerless genome editing in a time-efficient manner. Here we describe a riboswitch-inducible CRISPR/Cas9 system, contained on one single replicative vector, for the model cyanobacteria Synechocystis sp. PCC 6803. A theophylline-responsive riboswitch allowed tight control of Cas9 expression, which enabled reliable transformation of the CRISPR/Cas9 vector into Synechocystis. Induction of the CRISPR/Cas9 mediated various types of genomic edits, specifically deletions and insertions of varying size. The editing efficiency varied depending on the target and intended edit; smaller edits overall performed better, reaching e.g. 100% for insertion of a FLAG-tag onto rbcL. Importantly, the single-vector CRISPR/Cas9 system described herein was also shown to mediate multiplexed editing of up to three targets in parallel in Synechocystis. All single-target and several double-target mutants were also fully segregated after the first round of induction, adding to the usefulness of this system. Further, a vector curing system that is separately induced by nickel and contained on the CRISPR/Cas9 vector itself, improved curing efficiencies by roughly 4-fold, enabling the final mutants to become truly markerless.

synthetic biology↗

bioRxiv2022

Thermodynamic limitations of metabolic strategies for PHB production from formate and fructose in Cupriavidus necator

The chemolithotroph Cupriavidus necator H16 is known as a natural producer of the bioplastic-polymer PHB, as well as for its metabolic versatility to utilize different substrates, including formate as the sole carbon and energy source. Depending on the entry point of the substrate, this versatility requires adjustment of the thermodynamic landscape to maintain sufficiently high driving forces for biological processes. Here we employed a model of the core metabolism of C. necator H16 to analyze the thermodynamic driving forces and PHB yields of different metabolic engineering strategies. For this, we enumerated elementary flux modes (EFMs) of the network and evaluated their PHB yields as well as thermodynamics via Max-min driving force (MDF) analysis and random sampling of driving forces. A heterologous ATP:citrate lyase reaction was predicted to increase driving force for producing acetyl-CoA. A heterologous phosphoketolase reaction was predicted to increase maximal PHB yields as well as driving forces. These enzymes were verified experimentally to enhance PHB titers between 60 and 300% in select conditions. The EFM analysis also revealed that metabolic strategies for PHB production from formate may be limited by low driving forces through citrate lyase and aconitase, as well as cofactor balancing, and identified reactions of the core metabolism associated with low and high PHB yield. The findings of this study aid in understanding metabolic adaptation. Furthemore, the outlined approach will be useful in designing metabolic engineering strategies in other non-model bacteria. HighlightsO_LIElementary flux modes of C. necator for PHB synthesis from fructose and formate. C_LIO_LIMetabolite sampling identified common reactions among EFMs with low driving force. C_LIO_LIPHB from formate shows low driving forces for aconitase, citrate lyase, NADPH synthesis. C_LIO_LIPhosphoketolase and ATP citrate lyase increased driving forces and PHB production. C_LI

bioengineering↗

bioRxiv2021

Synthetic metabolic pathways for conversion of CO2 into secreted short- to medium-chain hydrocarbons using cyanobacteria

The objective of this study was to implement direct sunlight-driven conversion of CO2 into a naturally excreted ready-to-use fuel. We engineered four different synthetic metabolic modules for biosynthesis of short-to medium-chain length hydrocarbons in the model cyanobacterium Synechocystis sp. PCC 6803. In module 1, the combination of a truncated clostridial n-butanol pathway with over-expression of the native cyanobacterial aldehyde deformylating oxygenase resulted in small quantities of propane when cultured under closed conditions. Direct conversion of CO2 into propane was only observed in strains with CRISPRi-mediated repression of three native putative aldehyde reductases. In module 2, three different pathways towards pentane were evaluated based on the polyunsaturated fatty acid linoleic acid as an intermediate. Through combinatorial evaluation of bioreaction ingredients it was concluded that linoleic acid undergoes a spontaneous non-enzymatic reaction to yield pentane and hexanal. When Synechocystis was added to the bioreaction, hexanal was converted into 1-hexanol, but there was no further stimulation of pentane biosynthesis. For modules 3 and 4, several different acyl-ACP thioesterases were evaluated in combination with two different decarboxylases. Small quantities of 1-heptene and 1-nonene were observed in strains expressing the desaturase-like enzyme UndB from Pseudomonas mendocina in combination with C8-C10 preferring thioestersaes. When UndB instead was combined with a C12-specific UcFatB1 thioesterase, this resulted in ten-fold increase of alkene biosynthesis. When UndB was replaced with the light-dependent FAP decarboxylase, both undecane and tridecane accumulated, albeit with a 10-fold drop in productivity. Optimization of the RBS, promoter and gene order in these synthetic operons resulted in 1-alkene bioproductivity of 230 mg/L after 10 d with 15% carbon partitioning. In conclusion, the direct bioconversion of CO2 into secreted and ready-to-use hydrocarbon fuel was accomplished and optimal results were obtained with UndB and a C12 chain-length specific thioesterase. HighlightsO_LIMultiple repression of endogenous aldehyde reductases/dehydrogenases by CRISPRi enabled propane biosynthesis C_LIO_LIBiosynthesis of short-medium chain hydrocarbons (C7-C11) in a cyanobacterium was demonstrated for the first time C_LIO_LIThe final enzymes of the hydrocarbon pathways influenced both productivity and product profile C_LIO_LIAll volatile products were naturally secreted and accumulated outside of the cell C_LI

synthetic biology↗

bioRxiv2021

Protein allocation and utilization in the versatile chemolithoautotroph Cupriavidus necator

Bacteria must balance the different needs for substrate assimilation, growth functions, and resilience in order to thrive in their environment. Of all cellular macromolecules, the bacterial proteome is by far the most important resource and its size is limited. Here, we investigated how the highly versatile knallgas bacterium Cupriavidus necator reallocates protein resources when grown on different limiting substrates and with different growth rates. We determined protein quantity by mass spectrometry and estimated enzyme utilization by resource balance analysis modeling. We found that C. necator invests a large fraction of its proteome in functions that are hardly utilized. Of the enzymes that are utilized, many are present in excess abundance. One prominent example is the strong expression of CBB cycle genes such as Rubisco during growth on fructose. Modeling and mutant competition experiments suggest that CO2-reassimilation through Rubisco does not provide a fitness benefit for heterotrophic growth, but is rather an investment in readiness for autotrophy. HighlightsO_LIA large fraction of the C. necator proteome is not utilized and not essential C_LIO_LIHighly utilized enzymes are more abundant and less variable C_LIO_LIAutotrophy related enzymes are largely underutilized C_LIO_LIRe-assimilation of CO2 via the CBB cycle is unlikely to provide a fitness benefit C_LI

systems biology↗

bioRxiv2019

Pooled CRISPRi screening of the cyanobacterium Synechocystis sp. PCC 6803 for enhanced growth, tolerance, and chemical production

We developed an inducible CRISPRi gene repression library in the cyanobacterium Synechocystis sp. PCC 6803, where all annotated genes are targeted for repression. We used the library to estimate gene fitness in multiple conditions. The library revealed several mutants with increased specific growth rates (up to 17%), and transcriptomics of these mutants revealed common upregulation of genes within photosynthetic electron flow. We challenged the library with L-lactate stress to find more tolerant mutants. Repression of the peroxiredoxin Bcp2 increased growth rate by 49% in the presence of 0.1 M L-lactate. Finally, the library was transformed into a L-lactate-secreting strain, and droplet microfluidics sorting of top producers enriched sgRNAs targeting nutrient assimilation, redox modulation, and cyclic-electron flow. Several clones showed increased productivity in batch cultivations (up to 75%). In some cases, tolerance or productivity was enhanced by partial repression of essential genes, which are difficult to access by transposon insertion.

microbiology↗