Biology subjects

Benda, A.

Publications and source records attributed to Benda, A..

6 recordsLinked to original sources

bioRxiv2026

TRANSSULFURATION LINKS ASPARTATE-ASPARAGINE METABOLISM AND REDOX HOMEOSTASIS TO DRIVE TUMOR GROWTH

Cytosolic redox balance is tightly coupled to aspartate synthesis through the malate-aspartate shuttle, and limiting the malate-aspartate shuttle has been proposed to constrain tumor growth by restricting aspartate availability. Here we show that tumors derived from cancer cells lacking GOT1 and GOT2, the cytosolic and mitochondrial aspartate aminotransferases essential for as-partate production and malate-aspartate shuttle function, grow despite impaired canonical as-partate synthesis. This is because cytosolic redox state, not aspartate supply, is the primary metabolic bottleneck in GOT1/GOT2 knockout cells. Using single-cell transcriptomics, metabo-lite tracing, and a loss-of-function CRISPR screen, we find that these tumors engage an adaptive bypass in which availability of asparagine, a product of aspartate, enables serine- and methio-nine-dependent transsulfuration to generate -ketobutyrate, whose reduction regenerates cy-tosolic NAD and restores redox homeostasis. Pharmacological inhibition or genetic ablation of transsulfuration abrogates this asparagine-driven rescue. These findings define asparagine as a regulator of cytosolic NAD/NADH balance and reveal a link between amino acid metabolism and redox control that suggests transsulfuration as a targetable vulnerability in tumor redox maintenance. Significance statementAspartate synthesis and cytosolic redox balance are both coupled through the malate-aspartate shuttle. We show that the cytosolic NAD/NADH ratio, not aspartate supply, is a critical output of the malate-aspartate shuttle for tumor growth. Availability of asparagine, a product of aspar-tate, enables serine- and methionine-dependent transsulfuration to restore cytosolic NAD/NADH balance, proliferation and tumor growth independently of canonical aspartate pro-duction by the malate-aspartate shuttle. This defines asparagine as a regulator of cytosolic re-dox and identifies transsulfuration as a targetable vulnerability in tumor redox maintenance.

cancer biology↗

bioRxiv2026

Learning the structural diversity in random protein sequence space

The universe of possible protein sequences is astronomically large, yet our understanding of the sequence-structure relationship is confined to the infinitesimal fraction used currently by life. Determining whether "foldable" architectures are rare singularities or accessible solutions is critical for understanding protein evolution and designing novel proteins. Here, we map the structural landscape of random sequence space by screening one million synthetic proteins using a high-throughput in vivo FRET biosensor. We reveal that this space is structurally heterogeneous, populated not only by disordered chains and stress-inducing aggregates but also by "benign" compact structures that resemble globular proteins and evade cellular chaperone responses. By training machine learning models on these phenotypes, we show that structural potential is learnable and generalizes to natural proteomes. These findings demonstrate that biology-like folds are accessible from random sequences with surprising frequency, providing data required to expand generative protein design beyond evolutionary priors.

synthetic biology↗

bioRxiv2025

Post-transcriptional control of enamel matrix mineralization by TENT5A-mediated cytoplasmic polyadenylation

Tooth enamel formation, or amelogenesis, is a complex biomineralization process regulated by ameloblasts cells. These cells secrete enamel matrix proteins (EMPs), including Amelogenin (AMELX) and Ameloblastin (AMBN), which are essential for hydroxyapatite crystal deposition during enamel mineralization. Precise regulation of this process ensures the mechanical and chemical strength of dental enamel. Using Tent5a knock-out (KO) mouse, we demonstrated that TENT5A, a non-canonical poly(A) polymerase is crucial for the stability, translation, and secretion of EMP mRNAs, particularly AMELX, during amelogenesis. TENT5A-deficient mice exhibited Amelogenesis imperfecta, characterized by enamel hypomineralization, reduced thickness, and disrupted ultrastructure, as revealed by micro-computed tomography. Through nanopore direct mRNA sequencing, we identified that TENT5A polyadenylates Amelx and other mRNAs encoding secreted proteins, enhancing their stability and translation in the endoplasmic reticulum. Moreover, loss of TENT5A altered AMELX secretion and extracellular self-assembly, impairing matrix organization and hydroxyapatite deposition. This study highlights the role of TENT5A in post-transcriptional regulation during enamel formation, demonstrating its importance in enamel homeostasis. TeaserTENT5A adds poly(A) tails to specific mRNAs in enamel, enhancing their expression, which is crucial for dental mineralization.

developmental biology↗

bioRxiv2024

Bioenergetics of human spermatozoa in patients with testicular germ cell tumour

In testicular germ cell tumour (TGCT) patients, sperm cryopreservation prior to anti-cancer treatment represents the main fertility preservation approach. However, it is associated with low sperm recovery rate after thawing. Since sperm is a high-energy demanding cell, which is supplied by glycolysis and oxidative phosphorylation (OXPHOS), mitochondrial dysfunctionality can directly result in sperm anomalies. In this study, we investigated the bioenergetic pattern of cryopreserved sperm of TGCT patients in comparison with normozoospermic samples using two state-of-the-art methods; the Extracellular Flux Analyzer (XF Analyzer) and Two-Photon Fluorescence Lifetime imaging (2P-FLIM), in order to assess the contributions of OXPHOS and glycolysis to energy provision. A novel protocol for combined measurement of OXPHOS (Oxygen Consumption Rate - OCR) and glycolysis (Extracellular Acidification Rate - ECAR) using the XF Analyzer was developed together with a unique customized AI-based approach for semiautomated processing of 2P-FLIM images. Our study delivers optimized Low-HEPES modified Human Tubal Fluid media (mHTF) for sperm handling during pre-analytical and analytical phases to maintain sperm physiological parameters and optimal OCR, equivalent of OXPHOS. The negative effect of cryopreservation was signified by deterioration of both bioenergetic pathways represented by modified OCR and ECAR curves and the derived parameters. This was true for normozoospermic as well as TGCT samples, which showed even a stronger damage within the respiratory chain compared to the level of glycolytic activity impairment. The impact of cryopreservation and pathology are supported by 2P-FLIM analysis showing a significant decrease in bound NADH in contrast to unbound NAD(P)H which reflects decreased metabolic activity in samples from TGCT patients. Our study provides novel insight into the impact of TGCT on sperm bioenergetics and delivers a verified protocol to be used for assessment of human sperm metabolic activity, which can be a valuable tool for further research and clinical andrology. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=182 SRC="FIGDIR/small/595824v2_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@130b9eeorg.highwire.dtl.DTLVardef@1fec841org.highwire.dtl.DTLVardef@d401forg.highwire.dtl.DTLVardef@1eccff8_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2020

Clustering of CD3ζ is sufficient to initiate T cell receptor signaling

T cell activation is initiated when ligand binding to the T cell receptor (TCR) triggers intracellular phosphorylation of the TCR-CD3 complex. However, it remains unknown how biophysical properties of TCR engagement result in biochemical phosphorylation events. Here, we constructed an optogenetic tool that induces spatial clustering of CD3{zeta} chains in a light controlled manner. We showed that spatial clustering of the CD3{zeta} intracellular tail alone was sufficient to initialize T cell triggering including phosphorylation of CD3{zeta}, Zap70, PLC{gamma}, ERK and initiated Ca2+ flux. In reconstituted COS-7 cells, only Lck expression was required to initiate CD3{zeta} phosphorylation upon CD3{zeta} clustering, which leads to the recruitment of tandem SH2 domain of Zap70 from cell cytosol to the newly formed CD3{zeta} clusters at the plasma membrane. Taken together, our data suggest that clustering of the TCR can initialize proximal TCR signaling and thus constitute a biophysical mechanism of TCR triggering.

immunology↗

bioRxiv2020

Single-color Fluorescence Lifetime Cross-Correlation Spectroscopy in vivo

The ability to quantify protein concentrations and to measure protein interactions in vivo is key information needed for the understanding of complex processes inside cells, but the acquisition of such information from living cells is still demanding. Fluorescence based methods like two-color fluorescence cross-correlation spectroscopy can provide this information but measurement precision is hampered by various sources of errors caused by instrumental or optical limitations such as imperfect overlap of detection volumes or detector cross-talk. Furthermore, the nature and properties of used fluorescent proteins or fluorescent dyes, such as labeling efficiency, fluorescent protein maturation, photo-stability, bleaching and fluorescence brightness can have an impact. Here we take advantage of lifetime differences as a mean to discriminate fluorescent proteins with similar spectral properties and to use them for single-color fluorescence lifetime cross-correlation spectroscopy (sc-FLCCS). By using only one excitation and one detection wavelength, this setup avoids all sources of errors resulting from chromatic aberrations and detector cross-talk. To establish sc-FLCCS we first engineered and tested multiple GFP-like fluorescent proteins for their suitability. This identified a novel GFP variant termed slmGFP (short lifetime monomeric GFP) with the so-far shortest lifetime. Monte-Carlo simulations were employed to explore the suitability of different combinations of GFP variants. Two GFPs, Envy and slmGFP were predicted to constitute the best performing couple for sc-FLCCS measurements. We demonstrated application of this GFP pair for measuring protein interactions between the proteasome and interacting proteins and for measuring protein interactions between three partners when combined with a red florescent protein. Together, our findings establish sc-FLCCS as a valid alternative for conventional dual-color(dc)-FCCS measurements. STATEMENT OF SIGNIFICANCEThe quantification of protein concentrations and protein-protein interactions in vivo is a crucial information needed for the understanding of complex processes inside cells. Determination of such information is unfortunately still challenging. Fluorescence-based method like fluorescence cross-correlation spectroscopy (FCCS) is the only method which provides this information in vivo and almost in the real time, however it suffers from limitations caused by experimental setup and biological origin of fluorescent proteins. We present single-color fluorescence lifetime cross-correlation spectroscopy as an alternative to FCCS, which uses the information of fluorescence lifetime to overcome some of these limitations. We challenged the method and determined its advantages and limitations and demonstrated the applicability of the method on the proteins of yeast proteasome.

cell biology↗