Biology subjects

Baumgart, M.

Publications and source records attributed to Baumgart, M..

12 recordsLinked to original sources

bioRxiv2026

Buried Ion-Pairs Reshape Folding Pathways of Artificial Proteins

Ion-pairs are central charged motifs that control the biological function of several proteins. Yet, the physical principles linked to the formation of ion-pairs during protein folding remain poorly understood. Here, we show that buried ion-pairs of de novo-designed helical bundle proteins reshape the folding pathways by introducing kinetic barriers that are overcome by a hydrophobic collapse linked to packing of the protein core. By combining protein design with co-translational folding studies, nuclear magnetic resonance (NMR) spectroscopy, and molecular dynamics simulations, we show that introduction of a buried ion-pair leads to a shifted folding transition that balances desolvation and electrostatic interactions within the protein and the bulk solvent. Moreover, we find that the folding pathway is sensitive to modifications in non-polar interactions and motifs that electrostatically shield the ion-pair from its surroundings. Our combined findings provide a blueprint for understanding how functional motifs affect protein folding and how mutation of charged networks alter the stability of proteins.

biophysics↗

bioRxiv2025

Metabolic engineering of Corynebacterium glutamicum for production of the low-caloric natural sweetener D-allulose via phosphorylated intermediates

D-Allulose is a natural, low-calorie sweetener providing [~]70% of the sweetness of sucrose but [≤]10% of its caloric value, making it an attractive alternative to conventional sugars. Recently, a phosphorylation-dephosphorylation pathway for D-allulose production was established, involving the formation and irreversible dephosphorylation of D-allulose 6-phosphate. Although this pathway has been demonstrated in Escherichia coli, efficient production involved complex medium, complicating downstream processing. Here, we report D-allulose production in minimal medium by implementing the phosphorylation-dephosphorylation pathway in a Corynebacterium glutamicum strain unable to metabolize D-fructose. Growth- and production-based screenings identified fructokinase MakEC and D-allulose 6-phosphate 3-epimerase AlsEEC from E. coli, together with D-allulose 6-phosphate phosphatase AlsPCT from Clostridium thermocellum, as the most effective enzyme combination for D-allulose formation. Further metabolic engineering of C. glutamicum including deletion of zwf (D-glucose 6-phosphate dehydrogenase), overexpression of fbp (D-fructose 1,6-bisphosphatase), and downregulation of pgm (phosphoglucomutase) partially redirected central carbon flux toward D-allulose synthesis, resulting in a 2.3-fold increase in production. The engineered strain produced [~]3.6 g L-1 D-allulose from a D-glucose-D-fructose mixture with a yield of 9.1%.

bioengineering↗

bioRxiv2024

Efficient microbial glucose-fructose conversion at ambient temperature through adaptive laboratory evolution and application for D-allulose production

The low-calorie sugar D-allulose is a promising alternative to D-sucrose and high-fructose corn syrup, but its microbial production from D-glucose at mesophilic temperatures is limited by insufficient D-glucose isomerase (XylA) activity. Here, we overcome this bottleneck by evolving a Corynebacterium glutamicum selection strain whose growth strictly depends on XylA function. This strategy yielded a XylA variant with a nine-fold higher catalytic efficiency, sugar transporter variants (IolT1) with ten-fold increased activity for D-glucose and D-fructose, and hints for co-transport of these sugars by the D-sucrose transporter PtsS. Molecular dynamics simulations provided possible mechanistic explanations for the adaptive mutations. Combining the evolved enzymes with a suitable D-allulose 3-epimerase in a highly engineered chassis strain enabled whole-cell conversion of D-glucose to D-allulose with a 15% yield at 30 {degrees}C. This performance rivals immobilized enzyme processes performed at [~]60{degrees}C while avoiding enzyme purification and immobilization, offering an alternative for low-calorie sweetener production.

bioengineering↗

bioRxiv2024

Epigenetic clock and lifespan prediction in the short-lived killifish Nothobranchius furzeri

Aging, characterized by a gradual decline in organismal fitness, is the primary risk factor for numerous diseases including cancer, cardiovascular, and neurodegenerative disorders. The inter-individual variability in aging and disease susceptibility has led to the concept of "biological age," an indirect measure of an individuals relative fitness. Epigenetic changes, particularly DNA methylation, have emerged as reliable biomarkers for estimating biological age, leading to the development of predictive models known as epigenetic clocks. Initially created for humans, these clocks have been extended to various mammalian species. Here we set to expand these tools for the short-lived killifish, Nothobranchius furzeri. This species, with its remarkably short lifespan and expression of canonical aging hallmarks, offers a unique model for experimental aging studies. We developed an epigenetic clock for N. furzeri using reduced-representation bisulfite sequencing (RRBS) to analyze DNA methylation in brain and caudal fin tissues across different ages. Our study involved generating comprehensive DNA methylation datasets and employing machine learning to create predictive models based on individual CpG sites and co-methylation modules. These models demonstrated high accuracy in estimating chronological age, with a median absolute error of 3 weeks (7.5% of median lifespan) for a clock based on methylation of individual CpG and 1.5 weeks (3.7% of median lifespan) for an eigenvector-based clock. Our investigation extended to assessing epigenetic age acceleration in different strains and the potential resetting effect of regeneration on fin tissue. Notably, our models indicated that a shorter-lived strain has accelerated epigenetic aging and that regeneration does not reset, but may decelerate epigenetic aging. Additionally, we used longitudinal data to develop an "epigenetic timer" for direct prediction of individual lifespan based on fin biopsies and eigenvector-based method, achieving a median absolute error of 4.5 weeks in the prediction of actual age of death. This surprising result underscores the existence of intrinsic determinants of lifespan established early in life. This study presents the first epigenetic clocks and lifespan predictors for N. furzeri, highlighting their potential as aging biomarkers and sets the stage for future research on life-extending interventions in this model organism.

genomics↗

bioRxiv2023

A comprehensive atlas of the aging vertebrate brain reveals signatures of progressive proteostasis dysfunction

Aging and neurodegeneration entail diverse cellular and molecular hallmarks. Here, we studied the effects of aging on the transcriptome, translatome, and multiple layers of the proteome in the brain of a short-lived killifish. We reveal that aging causes widespread reduction of proteins enriched in basic amino acids that is independent of mRNA regulation, and it is not due to impaired proteasome activity. Instead, we identify a cascade of events where aberrant translation pausing leads to reduced ribosome availability resulting in proteome remodeling independently of transcriptional regulation. Our research uncovers a vulnerable point in the aging brains biology - the biogenesis of basic DNA/RNA binding proteins. This vulnerability may represent a unifying principle that connects various aging hallmarks, encompassing genome integrity and the biosynthesis of macromolecules. One-Sentence SummaryTranslation pausing reshapes the aging brain proteome, revealing vulnerabilities in the biogenesis of nucleic-acid protein.

systems biology↗

bioRxiv2022

A deep neural network provides an ultraprecise transcriptomic clock of the short-lived fish Nothobranchius furzeri and identifies predictive genes translatable to human aging.

A key and unresolved question in aging research is how to quantify aging at the individual level that led to development of "aging clocks", machine learning algorhythms trained to predict individual age from high-dimensional molecular data under the the assumption that individual deviations of the predicted age from the chronological age contain information on the individual condition (often referred to as "biological age"). A full validation of such clocks as biomarkers for clinical studies of ageing would require a comparison of their predictions with information on actual lifespan and long-term health. Such studies take decades in humans, but could be conducted in a much shorter time-frame in animal models. We developed a transcriptomic clock in the turquoise killifish Nothobranchius furzeri. This species is the shortest-lived vertebrate that can be cultured in captivity and is an emerging model organism for genetic and experimental studies on aging. We developed a proprietary deep learning architecture that autonomously selects a customizable number of input genes to use for its predictions in order to reduce overfitting and increase interpretability, and adopts an adversarial learning framework to identify tissue-independent transcriptional patterns. We called this architecture the Selective Adversarial Deep Neural Network (SA-DNN) and trained it on a multi-tissue transcriptomic dataset of N. furzeri. This SA-DNN predicted age of the test set with an accuracy of 1 day, i.e. less than 1% of the total species lifespan and detected genetic, pharmacological and environmental interventions that are known to influence lifespan in this species. Finally, a human transcriptomic multi-tissue clock that uses as input the orthologs of the genes selected by our SA-DNN in N. furzeri reaches an average error of[~] 3 years rivalling epigenetic clocks. Our SA-DNN represents the prototype of a new class of aging clocks that provide biomarkers applicable to intervention studies in model organisms and humans.

genomics↗

bioRxiv2022

A live attenuated vaccine confers superior mucosal and systemic immunity to SARS-CoV-2 variants

Vaccines are a cornerstone in COVID-19 pandemic management. Here, we compare immune responses to and preclinical efficacy of the mRNA vaccine BNT162b2, an adenovirus-vectored spike vaccine, and the live-attenuated-virus vaccine candidate sCPD9 after single and double vaccination in Syrian hamsters. All regimens containing sCPD9 showed superior efficacy. The robust immunity elicited by sCPD9 was evident in a wide range of immune parameters after challenge with heterologous SARS-CoV-2 including rapid viral clearance, reduced tissue damage, fast differentiation of pre-plasmablasts, strong systemic and mucosal humoral responses, and rapid recall of memory T cells from lung tissue. Our results demonstrate that use of live-attenuated vaccines may offer advantages over available COVID-19 vaccines, specifically when applied as booster, and may provide a solution for containment of the COVID-19 pandemic.

immunology↗

bioRxiv2021

A TPR scaffold couples signal detection to OdhI phosphorylation in metabolic control by the protein kinase PknG

Signal transduction is essential for bacteria to adapt to changing environmental conditions. Among many forms of post-translational modifications, reversible protein phosphorylation has evolved as a ubiquitous molecular mechanism of protein regulation in response to specific stimuli. The Ser/Thr protein kinase PknG modulates the fate of intracellular glutamate by controlling the phosphorylation status of the 2-oxoglutarate dehydrogenase regulator OdhI, a function that is conserved among diverse actinobacteria. PknG has a modular organization characterized by the presence of regulatory domains surrounding the catalytic domain. Here we present an investigation through in vivo experiments as well as biochemical and structural methods of the molecular bases of the regulation of PknG from C. glutamicum (CgPknG), in the light of previous knowledge available for the kinase from M. tuberculosis (MtbPknG). We found that OdhI phosphorylation by CgPknG is regulated by a conserved mechanism that depends on a C-terminal domain composed of tetratricopeptide repeats (TPR) essential for metabolic homeostasis. Furthermore, we identified a conserved structural motif that physically connects the TPR domain and a flexible N-terminal extension of the kinase that is involved in docking interactions with OdhI. Based on our results and previous reports, we propose a model in which the TPR domain of PknG couples signal detection to the specific phosphorylation of OdhI. Overall, the available data indicate that conserved PknG domains in distant actinobacteria retain their roles in kinase regulation in response to nutrient availability. IMPORTANCEBacteria control the metabolic processes by which they obtain nutrients and energy in order to adapt to the environment. In this way, the metabolic characteristics of a microorganism determine its ecological role and its usefulness in industrial processes. Here, we use genetic, biochemical, and structural approaches to study a key component in a system that regulates glutamate production in C. glutamicum, a species that is used for the industrial production of amino acids. We elucidated molecular mechanisms involved in metabolic control in C. glutamicum, which are conserved in related pathogenic bacteria. The findings have broader significance for diverse actinobacteria, including microorganisms that cause disease as well as environmental species used to produce billions of dollars of amino acids and antibiotics every year.

biochemistry↗

bioRxiv2019

Mosaic heterochrony in neural progenitors sustains accelerated brain growth and neurogenesis in the juvenile killifish N. furzeri

While developmental mechanisms driving increase in brain size during vertebrate evolution are actively studied, we know less of evolutionary strategies allowing to boost brain growth speed. In zebrafish and other vertebrates studied to date, radial glia (RG) constitute the primary neurogenic progenitor population throughout life (Kriegstein and Alvarez-Buylla, 2009); thus, RG activity is a determining factor of growth speed. Here, we ask whether enhanced RG activity is the mechanism selected to drive explosive growth, in adaptation to an ephemeral habitat. In post-hatching larvae of the turquoise killifish, which display drastic developmental acceleration, we show that the dorsal telencephalon (pallium) grows three times faster than in zebrafish. Rather than resulting from enhanced RG activity, we demonstrate that pallial growth is the product of a second type of progenitors (that we term AP for apical progenitors) that actively sustains neurogenesis and germinal zone self-renewal. Intriguingly, AP appear to retain, at larval stages, features of early embryonic progenitors. In parallel, RG enter premature quiescence and express markers of astroglial function. Together, we propose that mosaic heterochrony within the neural progenitor population may permit rapid pallial growth by safeguarding both continued neurogenesis and astroglial function.

developmental biology↗

bioRxiv2019

Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation

A progressive loss of protein homeostasis is characteristic of aging and a driver of neurodegeneration. To investigate this process quantitatively, we characterized proteome dynamics during brain aging in the short-lived vertebrate Nothobranchius furzeri combining transcriptomics and proteomics. We detected a progressive reduction in the correlation between protein and mRNA, mainly due to post-transcriptional mechanisms that account for over 40% of the age-regulated proteins. These changes cause a progressive loss of stoichiometry in several protein complexes, including ribosomes, which show impaired assembly / dis-assembly and are enriched in protein aggregates in old brains. Mechanistically, we show that reduction of proteasome activity is an early event during brain aging and is sufficient to induce proteomic signatures of aging and loss of stoichiometry in vivo. Using longitudinal transcriptomic data, we show that the magnitude of early life decline in proteasome levels is the major risk factor for mortality. Our work defines causative events in the aging process that can be targeted to prevent loss of protein homeostasis and delay the onset of age-related neurodegeneration. HighlightsO_LIProgressive loss of stoichiometry affects multiple protein complexes C_LIO_LIRibosomes aggregate in old brains C_LIO_LIPartial reduction of proteasome activity is sufficient to induce loss of stoichiometry C_LIO_LIReduced proteasome levels are a major risk factor for early death in killifish C_LI

systems biology↗

bioRxiv2019

Mitohormetic effects of rotenone drastically depend on age

Hormesis refers to a biphasic intensity-dependent response to stressors where low-intensity or short-duration exposure to potentially noxious stressors induces long-lasting adaptations that have positive physiological effects [1]. It was proposed that life-extending interventions, such as calorie restriction, retard aging via their hormetic action [2]. More recently, it was shown that a transient burst of reactive oxygen species is required to induce the effects of calorie restriction [3], physical exercise [4], inhibition of the insulin/IGF-I pathway [5] and metformin [6]. We have previously shown that partial inhibition of complex I of the respiratory chain by a low dose of the poison rotenone (ROT) administered in middle age increases the lifespan and reverts the transcriptomic signature of aging in a vertebrate species [7], an example of a hormetic effect. Here, we asked whether ROT treatment started at young age induces larger effects on life-span and transcriptome.

pharmacology and toxicology↗

bioRxiv2017

A miRNA catalogue and ncRNA annotation of theshort-living fish Nothobranchius furzeri

Background: The short-lived fish Nothobranchius furzeri is the shortest-lived vertebrate that can be cultured in captivity and was recently established as a model organism for aging research. Small non-coding RNAs, especially miRNAs, are implicated in age-dependent control of gene expression.\n\nResults: Here, we present a comprehensive catalogue of miRNAs and several other non-coding RNA classes (ncRNAs) for Nothobranchius furzeri. Analyzing multiple small RNA-Seq libraries, we show most of these identified miRNAs are expressed in at least one of seven Nothobranchius species. Additionally, duplication and clustering of N. furzeri miRNAs was analyzed and compared to the four fish species Danio rerio, Oryzias latipes, Gasterosteus aculeatus and Takifugu rubripes. A peculiar characteristic of N. furzeri as compared to other teleosts was a duplication of the miR-29 cluster.\n\nConclusion: The completeness of the catalogue we provide is comparable to that of zebrafish. This catalogue represents a basis to investigate the role of miRNAs in aging and development in this species.\n\nAvailability: All supplementary material can be found online at http://www.rna.uni-jena.de/en/supplements/nothobranchius-furzeri-mirnome/.

genomics↗