Biology subjects

Radi, R.

Publications and source records attributed to Radi, R..

5 recordsLinked to original sources

bioRxiv2026

Tracing the Path from 4-Hydroxyphenylpyruvate to the Benzoquinone Ring of Q6 and the p-aminobenzoate pathway in Yeast

AbstractCoenzyme Q (ubiquinone, CoQ) is an essential component of the mitochondrial electron transport chain and a major lipid antioxidant in eukaryotic cells. Formation of its benzoquinone ring requires aromatic precursors whose metabolic origin remains incompletely defined. Here, we elucidate the biochemical link between tyrosine metabolism and the synthesis of the benzoquinone head group of coenzyme Q6 (Q6) in Saccharomyces cerevisiae through the 4-hydroxymandelate (4HMA) pathway. Using isotopic tracing with 13C6-tyrosine, 13C6-4-hydroxybenzoate, and 13C6-p-aminobenzoate (pABA), we demonstrate that tyrosine-derived 4-hydroxyphenylpyruvate is converted into 4-hydroxybenzaldehyde via benzoylformate decarboxylation, defining a functional 4HMA pathway in yeast. Chemical inhibition of benzoylformate decarboxylase with methylbenzoylphosphonate led to accumulation of pathway intermediates, which were identified by GCMS. Consistently, mutants lacking ARO10, DLD1, or DLD2 exhibited strongly decreased 4-hydroxybenzaldehyde formation. Despite disruption of the 4HMA pathway, the pABA route from chorismate compensated, demonstrating S. cerevisiaes metabolic flexibility to use pABA or 4-HB and maintain Q6 ring biosynthesis. Our results provide a mechanistic framework linking aromatic amino acid metabolism to respiratory quinone biosynthesis in eukaryotes and support the evolutionary conservation of the 4HMA-derived pathway as a source of 4-hydroxybenzoate for Q synthesis in higher organisms. O_FIG O_LINKSMALLFIG WIDTH=194 HEIGHT=200 SRC="FIGDIR/small/734323v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@79d684org.highwire.dtl.DTLVardef@f2a7a4org.highwire.dtl.DTLVardef@dc3f0borg.highwire.dtl.DTLVardef@1af14a6_HPS_FORMAT_FIGEXP M_FIG Graphical abstract.4-hydroxyphenylpyruvic acid (4HPP), 4-hydroxymandelate (4HMA), 4-hydroxybenzoic acid (4HB), p-aminobenzoic acid (pABA). C_FIG

biochemistry↗

bioRxiv2026

Evolution of allostery without shape shifting: Internal dynamics drives functional diversification of a transcriptional repressor superfamily

Allostery enables proteins to couple environmental signals to functional outputs, yet how allosteric mechanisms diversify during evolution remains poorly understood. Here, we address this question in the ubiquitous and functionally diverse arsenic repressor (ArsR) superfamily by integrating information-theoretic bioinformatics, structural characterization of DNA recognition and NMR measurements of fast internal dynamics. We identify conserved residues that define the structural scaffold of ArsR proteins and subfamily-specific positions that encode inducer and DNA specificity. In the persulfide sensor SqrR, the crystal structure of the DNA-bound complex reveals how operator specificity is encoded by a limited set of residues, consistent with sequence-derived predictions functionally validated by in vitro transcription assays across divergent ArsR regulators. We further show that allosteric inhibition of DNA binding in SqrR occurs without large-scale conformational rearrangements and is instead associated with changes in internal dynamics, as previously observed for the zinc sensor CzrA. Together, these results support a model in which conformational entropy preserves allosteric connectivity while relaxing sequence constraints, thereby enabling functional diversification within a protein superfamily.

biochemistry↗

bioRxiv2024

Differential effects of diphenyl diselenide (PhSe)2 on mitochondria-related pathways depending on the cellular energy status in Bovine Vascular Endothelial Cells

Cellular energy metabolism varies depending on tissue and cell type, as well as the availability of energy substrates and energy demands. We recently investigated the variations in cellular metabolism and antioxidant responses in primary bovine vascular endothelial cells (BAECs) under different energetic substrate conditions in vitro, specifically glucose or galactose. In this context, pharmacological agents may affect cells differently depending on their energy metabolism status. In this study, we aimed to characterize the effects of diphenyl diselenide ((PhSe)2), a redox-active molecule known for its prominent cardiovascular effects, on redox-bioenergetic cellular pathways under glycolytic or oxidative conditions in BAECs. Under glucose conditions, (PhSe)2 positively impacted mitochondrial oxidative capacity, as assessed by respirometry, and was associated with changes in mitochondrial cellular dynamics. However, these changes were not observed in cells cultured with galactose. Although (PhSe)2 induced the nuclear translocation of the redox sensitive nuclear factor erythroid 2-related factor 2 (Nrf2) in both glucose and galactose media, Nrf2 remained in the nuclei of cells cultured in galactose for a longer duration. Additionally, activation of another redox sensitive transcription factor, forkhead O3 (FOXO3a) was only detected in galactose media. Notably, (PhSe)2 induced the expression of genes controlling mitochondrial antioxidant capacity and glutathione synthesis and recycling in glucose media, whereas its effects in galactose media were primarily focused on glutathione homeostasis. In conclusion, our findings underscore the critical influence of cellular metabolic status on the antioxidant capacity of redox-active molecules such as (PhSe)2.

biochemistry↗

bioRxiv2021

Thiol-based mucolytics exhibit antiviral activity against SARS-CoV-2 through allosteric disulfide disruption in the spike glycoprotein

Small molecule therapeutics targeting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have lagged far behind the development of vaccines in the fight to control the COVID-19 pandemic. Here, we show that thiol-based mucolytic agents, P2119 and P2165, potently inhibit infection by human coronaviruses, including SARS-CoV-2, and decrease the binding of spike glycoprotein to its receptor, angiotensin-converting enzyme 2 (ACE2). Proteomics and reactive cysteine profiling link the antiviral activity of repurposed mucolytic agents to the reduction of key disulfides, specifically, by disruption of the Cys379-Cys432 and Cys391-Cys525 pairs distal to the receptor binding motif (RBM) in the receptor binding domain (RBD) of the spike glycoprotein. Computational analyses provide insight into conformation changes that occur when these disulfides break or form, consistent with an allosteric role, and indicate that P2119/P2165 target a conserved hydrophobic binding pocket in the RBD with the benzyl thiol warhead pointed directly towards Cys432. These collective findings establish the vulnerability of human coronaviruses to repurposed thiol-based mucolytics and lay the groundwork for developing these compounds as a potential treatment, preventative and/or adjuvant against infection.

microbiology↗

bioRxiv2021

Increased mitochondrial activity upon CatSper channel activation is required for sperm capacitation.

To fertilize an oocyte, sperm must become hyperactive. However, whether they obtain ATP for hyperactivated motility via glycolysis or mitochondrial respiration is unclear. Here, high-resolution respirometry, flow cytometry, and confocal microscopy experiments revealed that mitochondrial respiration and membrane potential increased during mouse sperm capacitation. Treatment with inhibitors of mitochondrial respiration prevented sperm from hyperactivating and fertilizing an oocyte. Mitochondrial respiration was impaired in sperm from mice lacking the calcium channel CatSper. We developed a method to image mitochondrial calcium in sperm and found that CatSper activation led to increased mitochondrial calcium concentration. Finally, treating sperm with an inhibitor of mitochondrial calcium import impaired mitochondrial function and sperm hyperactivation. Together, our results uncover a new role of sperm mitochondria and reveal a new pathway connecting calcium influx through CatSper to mitochondrial activity and the sperm hyperactivation required to fertilize an oocyte. SummaryThe source of ATP for sperm hyperactivation is unclear. Ferreira et al. show that mitochondrial activity increases during, and is required for, hyperactivation and fertilization ability. Increased mitochondrial activity depends on calcium influx through the channel CatSper.

cell biology↗