Biology subjects

Dubrac, S.

Publications and source records attributed to Dubrac, S..

5 recordsLinked to original sources

bioRxiv2025

A connection between two ancient and essential cellular processes, iron-sulfur protein biogenesis and fatty acid synthesis, in Escherichia coli

Iron-sulfur [Fe-S] clusters are ubiquitous cofactors of a wide array of structural and functional diverse proteins. Acyl Carrier Protein (ACP) is the universal factor required for fatty acid (FA) synthesis. In this study in E. coli, we demonstrated that [Fe-S] and FA biosynthesis pathways are coordinated processes, driven by a physical interaction between ACP and the ISC [Fe-S] biogenesis machinery. Using bacterial two-hybrid assays, co-purification and biochemical analyses, we demonstrated a molecular interaction between ACP and IscS, the ISC machinery cysteine desulfurase that provides sulfur for [Fe-S] cluster formation. Structural modeling and directed mutagenesis pinpointed the ACP-binding site in a region of IscS shared for interactions with other components of the ISC [Fe-S] biogenesis system. At the cellular level, ACP depletion was found to disrupt ISC-dependent [Fe-S] cluster biogenesis, diminishing the activity of key [Fe-S]-dependent regulators (IscR, FNR, NsrR) and enzymes (aconitase, biotin synthase). Our findings underscore a functional link between [Fe-S] cluster biogenesis and fatty acid metabolism with far-reaching unexplored intricacies of metabolic coordination and cellular homeostasis. Comparison with eucaryotic systems highlight a strong evolutive driving force towards a link between [Fe-S] cluster and fatty acid biosynthesis in all living systems. ImportanceCellular functions rely on interconnected metabolic pathways, yet many regulatory links remain unexplored. Iron-sulfur [Fe-S] clusters are co-factors of proteins driving fundamental cellular processes, from respiration to gene regulation. Our study uncovers a direct connection between [Fe-S] cluster biogenesis and fatty acid biosynthesis. We demonstrate the molecular connection between these two essential cellular processes to lie within the interaction between the acyl carrier protein (ACP), a shuttle of fatty acid biosynthetic intermediates and IscS, the source of sulfur for [Fe-S] cluster assembly. Intriguingly, similar interactions between ACP and [Fe-S] building cysteine desulfurase have been observed in yeast and human models, yet resting on different molecular determinants. This points out the existence of a strong evolutive driving force towards establishing a link between [Fe-S] cluster and fatty acid biosynthesis in all living systems with far-reaching implications for metabolic coordination and cellular homeostasis.

microbiology↗

bioRxiv2025

Specificity and Mechanism of tRNA cleavage by the AriB Toprim nuclease of the PARIS bacterial immune system

Transfer RNA molecules have been recently recognized as widespread targets of bacterial immune systems. Translation inhibition through tRNA cleavage or modification inhibits phage propagation, thereby protecting the bacterial population. To counteract this, some viruses encode their own tRNA molecules, allowing infection to take place. The AriB effector of the PARIS defence system is a Toprim nuclease previously shown to target the E. coli tRNALys(UUU), but not a tRNALys(UUU) variant encoded by bacteriophage T5. We demonstrate here that the T5-tRNALys(UUU) is required but not sufficient to bypass PARIS immunity. Combining tRNA-sequencing, genetics, phage infection and in vitro biochemical data, we reveal that the E. coli tRNAThr(UGU), is another prime target of AriB and tRNAAsn(GUU) represents a secondary, yet biologically relevant, target of the PARIS effector. Activated AriB protein cleaves these targets in vitro, and the cleavage reaction is not dependent on the presence of specific tRNA modifications. We show that the overexpression of phage T5 tRNALys(UUU), tRNAThr(UGU) and tRNAAsn(GUU) variants is sufficient to inhibit PARIS anti-viral defence. Finally, we propose a model for tRNA recognition by the AriB dimer and provide molecular details of its nuclease activity and specificity.

microbiology↗

bioRxiv2025

Programmed in vivo excision of prophage {varphi}13 is an essential timing device for the Staphylococcus aureus infectious process

Mobile genetic elements play an essential part in the infectious process of major pathogens, yet the role of prophage dynamics in Staphylococcus aureus pathogenesis is still not well understood. Here we studied the impact of the {Phi}13 hlb- converting prophage, whose integration inactivates the hlb {beta}-toxin gene, on staphylococcal pathogenesis. We showed that prophage {Phi}13 is lost in approximately half the bacterial population during the course of infection. Inactivation of the {Phi}13 int recombinase gene, essential for insertion/excision, locked the prophage in the bacterial chromosome, leading to a significant loss of virulence in a murine systemic infection model. In contrast, the non-lysogen strain ({Delta}{Phi}13), where the hlb beta-hemolysin gene is reconstituted, displayed strongly increased virulence. Accordingly, histopathological analyses revealed more severe nephritis in mice infected with bacteria lacking prophage {Phi}13 ({Delta}{Phi}13), compared to infection with the parental strain. Infection with the {Delta}int mutant, where beta-hemolysin production is abolished, led to the least severe renal lesions. Cytokine induction in a human neutrophil model showed significantly increased IL-6 expression following infection with the beta-hemolysin producing strain ({Delta}{Phi}13). Our results indicate that timely in vivo excision of the {Phi}13 prophage is essential for progression of the Staphylococcus aureus infectious process: early excision leads to rapid host death whereas the inability to excise the prophage significantly reduces staphylococcal virulence. IMPORTANCEThis study highlights prophage {Phi}13 excision as a critical factor in S. aureus pathogenesis, influencing infection outcomes by balancing rapid host killing with reduced bacterial virulence. This mechanism may represent a bet-hedging strategy in genetic regulation, resulting in a mixed bacterial population capable of rapidly switching between two processes: bacterial colonization and host damage. Unraveling this dynamic opens new possibilities for developing targeted therapies to disrupt or modulate prophage activity, offering a novel approach to mitigating S. aureus infections.

microbiology↗

bioRxiv2023

Epidermal barrier dysregulation in atopic skin predisposes for excessive growth of the allergy-associated yeast Malassezia

The skin barrier is vital for protection against environmental threats including insults caused by skin-resident microbes. Dysregulation of the barrier is a hallmark of atopic dermatitis (AD) and ichthyosis, with variable consequences for host immune control of colonizing commensals and opportunistic pathogens. While sensitisation to Malassezia, the most abundant commensal fungus of the skin, is common in AD, its relevance for pathogenesis remains unclear. Here we show that in barrier-disrupted skin, Malassezia acquires enhanced fitness. This is not a consequence of the dysregulated allergic immune status characteristic for AD but is rather explained by structural and metabolic changes in the cutaneous niche that provide increased accessibility and a favourable lipid profile, to which the lipid-dependent yeast adapts for enhanced nutrient assimilation. These findings reveal fundamental insights into the role of the mycobiota in the pathogenesis of common skin barrier disorders.

microbiology↗

bioRxiv2020

Fatty Acyl Availability Modulates Cardiolipin Composition and Alters Mitochondrial Function in HeLa Cells

The molecular assembly of cells depends not only on their balance between anabolism and catabolism, but to a large degree also on the building blocks available in the environment. For cultivated mammalian cells, this is largely determined by the composition of the growth medium used. Here we study the impact of medium lipids on mitochondrial membrane architecture and function by combining LC-MS/MS lipidomics and functional tests with lipid supplementation experiments in an otherwise serum- and lipid-free cell culture model. We demonstrate that the composition of mitochondrial cardiolipins (CL) strongly depends on the lipid environment in cultured cells and prefers the incorporation of essential linoleic acid over other fatty acids. Simultaneously, the mitochondrial respiratory complex I activity was altered, whereas the matrix-localized enzyme citrate synthase was unaffected. This suggests a link between membrane composition and respiratory capacity. In summary, we find a strong dependency of central mitochondrial features on the type of lipids contained in the growth medium. Thus, this underlines the importance of considering these factors when using and establishing cell culture models in biomedical research. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=76 SRC="FIGDIR/small/937433v2_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@1960166org.highwire.dtl.DTLVardef@135d267org.highwire.dtl.DTLVardef@88868forg.highwire.dtl.DTLVardef@13a3c83_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗