Biology subjects

Valverde, J. R.

Publications and source records attributed to Valverde, J. R..

3 recordsLinked to original sources

bioRxiv2026

Functional diversification of UBP6 in plant immunity through N-degron pathway regulation

Deubiquitylases are key proteolytic regulators of ubiquitin-dependent cellular processes, catalyzing the removal or remodelling of ubiquitin modifications on substrate proteins, including those targeted for proteasomal degradation. UBIQUITIN PROTEASE (UBP)6 is a deubiquitylase that promotes the abundance of NONEXPRESSOR OF PATHOGENESIS RELATED GENES (NPR)1, a conserved master regulator of plant immunity. Here, we show that the Arabidopsis thaliana protease METACASPASE (MC)9 site-specifically processes UBP6, generating the E157-UBP6 proteoform, whose stability is controlled by the Arginyl-transferase (ATE) N-degron pathway. We observed that pathogen recognition both triggers UBP6 cleavage and leads to conditional stabilisation of E157 UBP6, which is enhanced as the defence response intensifies. Our data suggest that E157 UBP6, which lacks deubiquitylating activity, may induce inhibition of the proteasome, elevating NPR1 levels and enhancing salicylic acid (SA) induced gene activation, all of which collectively contribute to restricting pathogen growth. Thus, UBP6 cleavage and N-degron pathway regulation provide distinct proteoforms of UBP6 with specific effects on the immune processes.

plant biology↗

bioRxiv2026

Exploiting outer-membrane protein promiscuity to induce transient collateral sensitivity via efflux pump competition

In the fight against antimicrobial resistance, the identification of robust collateral sensitivity (CS) patterns could form the basis of successful sequential and combinatorial antimicrobial therapies. While most of the focus has been devoted to study stable CS due to mutations, CS can be transiently induced in Pseudomonas aeruginosa using dequalinium chloride (DC), which increases the expression of the efflux operon mexCD-oprJ. This leads to transient CS to the aminoglycoside tobramycin, whose molecular mechanism remains unclear. Using a combination of experimental results, mechanistic mathematical models and structural simulations, we show that the inactivation of NfxB by DC not only increases mexCD expression but also reduces the effective amount of the MexXY-OprM aminoglycosides efflux pump. Our data suggest that, under conditions of high MexCD production, this efflux pump can outcompete MexXY for the outer-membrane protein OprM, thereby inducing CS to tobramycin. Bayesian fits accurately reproduce measured mexCD expression and minimal inhibitory concentration (MIC) shifts across DC doses. Model predictions were validated in P. aeruginosa PA14 mutants lacking functional outer-membrane channels. Loss of OprJ preserves DC-induced CS to tobramycin, whereas loss of OprM abolishes it. These results identify competition for OprM as the proximal cause of DC-induced, transient CS and provide a generalizable framework for eliciting CS by perturbing shared components of multidrug efflux systems. This strategy suggests immediate avenues to enhance aminoglycoside efficacy while minimizing selection for stable resistance.

microbiology↗

bioRxiv2025

The unique role of nucS-mediated non-canonical mismatch repair in Mycobacterium tuberculosis resistance evolution

DNA surveillance mechanisms play a vital role in maintaining genome stability and minimizing mutation rates. One such mechanism, post-replicative mismatch repair (MMR), corrects replication errors that escape DNA polymerase proofreading activity. In most bacteria and eukaryotes, MMR is orchestrated by MutS and MutL proteins. However, certain archaeal and actinobacterial species, including the major human pathogen Mycobacterium tuberculosis, lack these components. Instead, they rely on the nuclease EndoMS/NucS, a structurally distinct enzyme that governs a non-canonical MMR pathway. Given that M. tuberculosis acquires drug resistance exclusively through chromosomal mutations, understanding mutation rate regulation in this pathogen is critical. Nevertheless, despite its anticipated significance, the role of NucS in drug resistance evolution remains largely unexplored in this organism. This study investigates NucS function in M. tuberculosis and uncovers a unique resistance dynamic distinct from other Actinobacteria. While nucS deletion alters the mutational spectrum, it minimally affects the emergence of rifampicin-, isoniazid-, and ethambutol-resistant mutations, in stark contrast to its role in other Actinobacteria. We demonstrated that this atypical behaviour is not attributable to the presence of a single NucS polymorphism, R144S, in the NucS sequence of the M. tuberculosis reference strain H37Rv, which differs from the NucS consensus sequence. Constructing and analysing an H37Rv variant possessing the NucS consensus sequence revealed a subtly altered mutational spectrum but unchanged mutation rates. Notably, database analysis of the R144S polymorphism in clinical isolates revealed its prevalence and significant association with ethambutol resistance. These findings challenge the established view that nucS serves as a genome stability guardian that minimizes mutation rates in M. tuberculosis, suggesting additional mismatch repair mechanisms beyond NucS or a highly efficient replication system in this pathogen.

microbiology↗