Biology subjects

Carvalho, P. C.

Publications and source records attributed to Carvalho, P. C..

4 recordsLinked to original sources

bioRxiv2025

Bclaf1 biomolecular condensates protect nuclear PTK2 from ubiquitin-proteasome system promoting cardiomyocyte survival during oxidative stress

PTK2, a non-receptor tyrosine kinase, plays a critical role in regulating essential cellular functions, including cell survival, by reducing p53 levels and activating the PI3K/AKT pathway. However, the mechanism underlying PTK2 stabilization during stress remains unclear. In this study, we identified Bclaf1, a multifunctional protein known to stabilize partners, as a PTK2 interactor. Using advanced microscopy techniques we identified nuclear Bclaf1 biomolecular condensates containing PTK2 in cardiomyocytes under oxidative stress. While diffuse PTK2 in the nucleus was susceptible to ubiquitination, PTK2 sequestered in the Bclaf1 condensates was protected from the ubiquitin-proteasome system (UPS). The K926 residue was identified as a ubiquitination site on PTK2, and subsequent proteasome inhibition experiments confirmed the role of the UPS in PTK2 homeostasis. Furthermore, disrupting Bclaf1 biomolecular condensates lead to PTK2 degradation, subsequently increasing p53 levels and activating apoptosis. Our findings support the role of Bclaf1 in the formation of pro-survival nuclear condensates that sequester and stabilize PTK2, promoting cardiomyocyte survival during oxidative stress. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/636487v3_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@15377a9org.highwire.dtl.DTLVardef@d5325forg.highwire.dtl.DTLVardef@de0ac9org.highwire.dtl.DTLVardef@196325d_HPS_FORMAT_FIGEXP M_FIG C_FIG In BriefMoretto et al. demonstrated that Bclaf1 undergo liquid-liquid phase separation (LLPS) during doxorubicin (Dox) induced oxidative stress to generate membraneless organelles where PTK2 is sequestered and protected from the ubiquitin-proteasome system (UPS). The maintenance of PTK2 stability may favor the p53 and Mdm2 interaction, which results in p53 ubiquitination and degradation, promoting cell survival. Loss of Bclaf1 disrupts PTK2 stabilization, leading to the ubiquitination and degradation of this kinase and downstream upregulation of p53, increasing cell death. HighlightsO_LIBclaf1 undergoes LLPS to stabilize protein partners during stress. C_LIO_LIPTK2 inside the Bclaf1 biomolecular condensates is protected from the UPS to promote cardiomyocyte survival during dox-induced oxidative stress. C_LIO_LIThe PTK2 ubiquitination site, lysine 926, was identified and the action of the UPS on PTK2 proteostasis was confirmed. C_LIO_LIBclaf1 knockdown results in overall protein ubiquitination and in PTK2 ubiquitination and degradation, resulting in increased levels of p53 and PUMA. C_LI

cell biology↗

bioRxiv2024

The genetic history of Portugal over the past 5,000 years

BackgroundRecent ancient DNA studies uncovering large-scale demographic events in Iberia have focused primarily on Spain, with limited reports for Portugal, a country located at the westernmost edge of continental Eurasia. Here, we introduce the largest collection of ancient Portuguese genomic datasets (n = 68) to date, spanning 5,000 years, from the Neolithic to the 19th century. ResultsWe found evidence of patrilocality in Neolithic Portugal, with admixture from local hunter-gatherers and Anatolian farmers, and persistence of Upper Paleolithic Magdalenian ancestry. This genetic profile persists into the Chalcolithic, reflecting diverse local hunter- gatherer contributions. During the Bronze Age, local genetic ancestry persisted, particularly in southern Iberia, despite influences from the North Pontic Steppe and early Mediterranean contacts. The Roman period highlights Idanha-a-Velha as a hub of migration and interaction, with a notably diverse genetic profile. The Early Medieval period is marked by Central European ancestry linked to Suebi/Visigoth migrations, adding to coeval local, African, and Mediterranean influences. The Islamic and Christian Conquest periods show strong genetic continuity in northern Portugal and significant African admixture in the south, with persistent Jewish and Islamic ancestries suggesting enduring influences in the post-Islamic period. ConclusionsThis study represents the first attempt to reconstruct the genetic history of Portugal from the analysis of ancient individuals. We reveal dynamic patterns of migration and cultural exchange across millennia, but also the persistence of local ancestries. Our findings integrate genetic information with historical and archaeological data, enhancing our understanding of Iberias ancient heritage.

genomics↗

bioRxiv2024

Optimised in-solution enrichment of over a million ancient human SNPs

In-solution hybridisation enrichment of genetic markers is a method of choice in paleogenomic studies, where the DNA of interest is generally heavily fragmented and contaminated with environmental DNA, and where the retrieval of genetic data comparable between individuals is challenging. Here, we benchmarked the commercial "Twist Ancient DNA" reagent from Twist Biosciences using sequencing libraries from ancestrally diverse ancient human samples with low to high endogenous DNA content (0.1-44%). For each library, we tested one and two rounds of enrichment, and assessed performance compared to deep shotgun sequencing. We find that the "Twist Ancient DNA" assay provides robust enrichment of [~]1.2M target SNPs without introducing allelic bias that may interfere with downstream population genetics analyses. Additionally, we show that pooling up to 4 sequencing libraries and performing two rounds of enrichment is both reliable and cost-effective for libraries with less than 27% endogenous DNA content. Above 38% endogenous content, a maximum of one round of enrichment is recommended for cost-effectiveness and to preserve library complexity. In conclusion, we provide researchers in the field of human paleogenomics with a comprehensive understanding of the strengths and limitations of different sequencing and enrichment strategies, and our results offer practical guidance for optimising experimental protocols.

genomics↗

bioRxiv2023

PROTEOME-SCALE RECOMBINANT STANDARDS AND A ROBUST HIGH-SPEED SEARCH ENGINE TO ADVANCE CROSS-LINKING MS-BASED INTERACTOMICS

AO_SCPLOWBSTRACTC_SCPLOWAdvancing data analysis tools for proteome-wide cross-linking mass spectrometry (XL-MS) requires ground-truth standards that mimic biological complexity. Here, we develop wellcontrolled XL-MS standards comprising hundreds of recombinant proteins that are systematically mixed for cross-linking. We use one standard dataset to guide the development of Scout, a search engine for XL-MS with MS-cleavable cross-linkers. Using other, independent datasets from our standards as well as published datasets, we benchmark the performance of Scout and existing XL-MS software. This demonstrates that Scout offers the best combination of speed, sensitivity, and false-discovery rate control. These results illustrate how our large recombinant standards can support the development of XL-MS analysis tools and evaluation of XL-MS results.

bioinformatics↗