Biology subjects

Jallet, D.

Publications and source records attributed to Jallet, D..

6 recordsLinked to original sources

bioRxiv2026

Small but Mighty: The Surprising Metabolic Range of a Bacterial Microcompartment

Bacterial microcompartments (BMCs) are protein-based metabolic modules increasingly investigated as potential intracellular nanoreactors. In this study, we engineered Escherichia coli by chromosomally integrating the propanediol utilization (pdu) operon from Citrobacter freundii and evaluated the metabolic versatility of the heterologously produced Pdu BMCs. The formation of well-assembled, operational Pdu BMCs was confirmed in cellula. Oxygen was found to inhibit 1,2-propanediol utilization, an effect alleviated under microaerobic conditions. The engineered E. coli strain assimilated a range of diols and triols, demonstrating that Pdu BMCs process both their native substrate and glycerol and linear diols up to 1,2-butanediol (C4). This substrate promiscuity was exploited to produce high value-added compounds and revealed previously unrecognized potential for plastic upcycling through ethylene glycol metabolism. In keeping with molecular dynamics simulations indicating that the Pdu BMC shell does not impose significant diffusion barriers for longer chain diols and triols, the range of amenable substrates was successfully extended to 1,2-pentanediol (C5) by mutating the diol dehydratase large subunit (PduC). Together, these findings establish heterologous Pdu BMCs as promiscuous and genetically tunable metabolic modules in E. coli, highlighting their potential as scalable platforms for synthetic biology and biotechnological applications. ImportanceBacterial microcompartments (BMCs) are increasingly popular modular platforms for organizing and optimizing metabolic pathways, yet their substrate scope and engineering potential remain underexplored. Here, we demonstrate that heterologous Pdu BMCs expressed in Escherichia coli metabolize a substantially broader range of substrates than previously appreciated, including various diols and triols outside their native range. We further show that BMC performance is modulated by oxygen availability and can be predictably expanded by targeted enzyme engineering. These findings establish Pdu BMCs as flexible, genetically tunable metabolic modules capable of converting diverse feedstocks into value-added products, while also revealing an unanticipated capacity for plastic upcycling via ethylene glycol utilization. By integrating pathway engineering, physiological characterization, and computational modelling, this work advances the design of BMC-based systems for sustainable bioproduction and highlights their potential as customizable intracellular nanoreactors for biotechnology.

biochemistry↗

bioRxiv2025

Acetate as a metabolic booster for glucose-based bioproduction in Escherichia coli

Escherichia coli, a key workhorse in industrial biotechnology, is commonly grown on glucose, which supports rapid growth but leads to acetate overflow, which instead inhibits growth, diverts carbon from the production pathway, and reduces productivity. Recent studies suggest that acetate may also have beneficial effects in glucose-grown E. coli, but its potential in bioprocesses remains unexplored. In this study, we systematically investigated acetates impact on bioproduction using a kinetic model of glucose and acetate metabolism in E. coli. The model predicts that acetate can enhance bioproduction in glucose-grown E. coli through three mechanisms: (i) by minimizing acetate overflow, thereby reducing carbon loss, (ii) by increasing acetyl-CoA levels, thereby boosting the biosynthetic flux of acetyl-CoA-derived compounds, and (iii) by promoting biomass accumulation, thus improving overall productivity. We experimentally validated the predictions of the model for mevalonate and 3-hydroxypropionate production, where acetate supplementation increased productivity by 117% and 34%, respectively. Our findings provide a valuable framework for optimizing E. coli-based bioprocesses and highlight acetates underutilized potential in biotechnology. By leveraging acetate from waste streams as a metabolic booster, this approach could contribute to more sustainable and environmentally friendly bioprocesses. Highlights- A kinetic model was used for rational optimization of E. coli-based bioprocesses - Acetate can enhance growth and production of acetyl-CoA-derived bioproducts - Model predictions were validated for mevalonate and 3-hydroxypropionate production - Acetate can be used as a metabolic booster for glucose-based bioproduction in E. coli

systems biology↗

bioRxiv2024

Circadian regulation of key physiological processes by the RITMO1 clock protein in the marine diatom Phaeodactylum tricornutum

O_LIPhasing biological and physiological processes to periodic light-dark cycles is crucial for the life of most organisms. Marine diatoms, as many phytoplanktonic species, exhibit biological rhythms, yet their molecular timekeepers remain largely uncharacterized. Recently, the bHLH-PAS protein RITMO1 has been proposed to act as a regulator of circadian rhythms. C_LIO_LIIn this study, we first determined the physiological conditions to monitor circadian clock activity and its perturbation in the diatom model species Phaeodactylum tricornutum by using cell fluorescence as a circadian output. Employing ectopic overexpression, targeted gene mutagenesis, and functional complementation, we then investigated the role of RITMO1 in various circadian processes. C_LIO_LIOur findings reveal that RITMO1 significantly influences the P. tricornutum circadian rhythms not only of cellular fluorescence, but also of photosynthesis and of the expression of clock-controlled genes, including transcription factors and putative clock input/output components. RITMO1 effects on rhythmicity are unambiguously detectable under free running conditions. C_LIO_LIBy uncovering the complex regulation of biological rhythms in P. tricornutum, these results provide a key step in understanding the endogenous regulators of phytoplankton physiological responses to environmental changes. Furthermore, these studies position diatoms as instrumental and novel model systems for elucidating key mechanistic principles of oscillator functions in marine ecosystems. C_LI

molecular biology↗

bioRxiv2024

Integrative in vivo analysis of the ethanolamine utilization bacterial microcompartment in Escherichia coli.

Bacterial microcompartments (BMCs) are self-assembling protein megacomplexes that encapsulate metabolic pathways. Although approximately 20% of sequenced bacterial genomes contain operons encoding putative BMCs, few have been thoroughly characterized, nor any in the most studied Escherichia coli strains. We used an interdisciplinary approach to gain deep molecular and functional insights into the ethanolamine utilization (Eut) BMC system encoded by the eut operon in E. coli K-12. The eut genotype was linked with the ethanolamine utilization phenotype using deletion and overexpression mutants. The subcellular dynamics and morphology of the E. coli Eut BMC were characterized in cellula by fluorescence microscopy and electron (cryo)microscopy. The minimal proteome reorganization required for ethanolamine utilization and the in vivo stochiometric composition of the Eut BMC were determined by quantitative proteomics. Finally, the first flux map connecting the Eut BMC with central metabolism in cellula was obtained by genome scale modelling and 13C-fluxomics. Our results reveal that, contrary to previous suggestions, ethanolamine serves both as a nitrogen and a carbon source in E. coli K-12, while also contributing significant metabolic overflow. Overall, this study provides a quantitative molecular and functional understanding of the BMCs involved in ethanolamine assimilation by E. coli. ImportanceThe properties of BMCs make them an ideal tool to build orthogonal network structures with minimal interactions with native metabolic and regulatory networks. However, this requires an understanding of how BMCs work natively. In this study, we combined genetic manipulation, multi-omics, modelling and microscopy to address this issue for Eut BMCs. We show that the Eut BMC in E. coli turns ethanolamine into usable carbon and nitrogen substrates to sustain growth. These results improve our understanding of compartmentalization in a widely used bacterial chassis.

microbiology↗

bioRxiv2021

Integration of physiologically relevant photosynthetic energy flows into whole genome models of light-driven metabolism

Characterizing photosynthetic productivity is necessary to understand the ecological contributions and biotechnology potential of plants, algae, and cyanobacteria. Light capture efficiency and photophysiology have long been characterized by measurements of chlorophyll fluorescence dynamics. However, these investigations typically do not consider the metabolic network downstream of light harvesting. In contrast, genome-scale metabolic models capture species-specific metabolic capabilities but have yet to incorporate the rapid regulation of the light harvesting apparatus. Here we combine chlorophyll fluorescence parameters defining photosynthetic and non-photosynthetic yield of absorbed light energy with a metabolic model of the pennate diatom Phaeodactylum tricornutum. This integration increases the model predictive accuracy regarding growth rate, intracellular oxygen production and consumption, and metabolic pathway usage. Additionally, our simulations recapitulate the link between mitochondrial dissipation of photosynthetically-derived electrons and the redox state of the photosynthetic electron transport chain. We use this framework to assess engineering strategies for rerouting cellular resources toward bioproducts. Overall, we present a methodology for incorporating a common, informative data type into computational models of light-driven metabolism for characterization, monitoring and engineering of photosynthetic organisms.

systems biology↗

bioRxiv2020

Mitotic interhomolog recombination drives genomic diversity in diatoms

Diatoms, an evolutionarily successful group of microalgae, display high levels of intraspecific variability in natural populations. However, the process generating such diversity is unknown. Here we estimated the variability within a natural diatom population and subsequently mapped the genomic changes arising within cultures clonally propagated from single diatom cells. We demonstrate that genome rearrangements and mitotic recombination between homologous chromosomes underlie clonal variability, resulting in haplotype diversity accompanied by the appearance of novel protein variants and loss of heterozygosity resulting in the fixation of alleles. The frequency of interhomolog mitotic recombination exceeds 4 out of 100 cell divisions and increases under environmental stress. We propose that this plastic response in the interhomolog mitotic recombination rate increases the evolutionary potential of diatoms, contributing to their ecological success. One Sentence SummaryRecombination between homologous chromosomes in diatom vegetative cells leads to extensive genomic diversity in clonal populations.

genomics↗