Biology subjects

Palhano, F.

Publications and source records attributed to Palhano, F..

5 recordsLinked to original sources

bioRxiv2025

Translation efficiency changes at heat shock in Saccharomyces cerevisiae

Both eukaryotic and prokaryotic cells respond to heat shock by engaging multiple regulatory mechanisms that preserve proteostasis, including adjustments in transcription, translation, and mRNA metabolism. Although the transcriptional response to heat stress in Saccharomyces cerevisiae has been well characterized, the extent to which translation efficiency (TE) is remodeled and how this remodeling contributes to protein synthesis remains less understood. Here, analysis of previously published ribosome profiling and RNA-seq data revealed that in S. cerevisiae, the TE varies during heat shock, depending on both temperature and stress duration. In contrast, TE remained largely stable in Escherichia coli under comparable conditions or during activation of {sigma}32, the main regulator of heat shock response in bacteria. In yeast, TE modulation patterns correlated with changes in protein abundance and differed markedly between early and late stages of stress. At 10 min, transcripts with short 5'UTRs and high codon optimality tended to display higher TE, primarily due to the easier ribosome engagement in these transcripts. By 30 min, the TE pattern across transcripts had changed drastically, suggesting increased availability of newly synthesized stress-response transcripts. These findings support a model in which early TE adjustments depend on intrinsic mRNA properties, whereas shifts in mRNA accessibility and transcriptional output shape later changes. The results highlight TE remodeling as a dynamic component of the heat-shock response in yeast and distinguish this behavior from the more buffered response observed in bacteria.

microbiology↗

bioRxiv2020

Natural variation of the cardiac transcriptome in humans

We investigated the gene-expression variation among humans by analyzing previously published mRNA-seq and ribosome footprint profiling (RP) of heart left-ventricles from healthy donors. We ranked the genes according to their coefficient of variation values and found that the top 5% most variable genes had special features compared to the rest of the genome, such as lower mRNA levels and shorter half-lives coupled to increased translation efficiency. We observed that these genes are mostly involved with immune response and have a pleiotropic effect on disease phenotypes, indicating that asymptomatic conditions contribute to the gene expression diversity of healthy individuals.

genomics↗

bioRxiv2019

Endogenous polybasic peptides cause slower movement of ribosomes but are not targets of the ribosome quality control complex (RQC)

Highly positively charged protein segments are known to result in poor translation efficiency. This effect is explained by ribosome stalling caused by electrostatic interactions between the nascent peptide and the negatively charged ribosome exit tunnel, leading to translation termination followed by protein degradation mediated by the RQC complex. These polybasic sequences are mainly studied in the context of artificial reporter systems. Examples of endogenous yeast proteins targeted by the RQC complex are Rqc1, a protein essential for RQC function, and Sdd1. Both contain polybasic sequences that are thought to activate the RQC, leading to protein down-regulation. Here, we investigated whether the RQC complex regulates other endogenous proteins with polybasic sequences. We show by bioinformatics, ribosome profiling data analysis, and western blot that endogenous proteins containing polybasic sequences similar to, or even more positively charged than those of Rqc1 and Sdd1, are not targeted by the RQC complex suggesting that endogenous polybasic sequences are not sufficient to induce this type of regulation. Finally, our results also suggest that Rqc1 is regulated post-translationally by the E3 component of the RQC complex Ltn1, in a manner independent of the RQC complex.

biochemistry↗

bioRxiv2019

Cerebral dopamine neurotrophic factor (CDNF) reduces myocardial ischemia/reperfusion injuries by the activation of PI3K-AKT via KDEL-receptor binding

CDNF (Cerebral Dopamine Neurotrophic Factor) belongs to a new family of NF, which presents several beneficial activities beyond the brain. Little is known about CDNF in the cardiac context. Herein we investigate CDNF effects in cardiomyocytes under endoplasmic reticulum (ER)-stress and in whole rat hearts subjected to ischemia/reperfusion (I/R). We showed that CDNF is secreted by cardiomyocytes stressed by thapsigargin and by isolated hearts subjected to I/R. CDNF protects human and mouse cardiomyocytes against ER-stress by restoring the calcium transient, and isolated heart against I/R injuries by reducing the infarct area and avoiding mitochondrial impairment. This protection is abrogated by wortmannin (PI3K-inhibitor) or by heptapeptides containing KDEL sequence, which block KDEL-receptor. These data suggest that CDNF induces cardioprotection via KDEL receptor binding and PI3K/AKT activation. This is the first study to propose CDNF as a cardiomyokine and to unravel the receptor and signaling pathway for this interesting family of NF.

physiology↗

bioRxiv2019

Icosahedral viruses defined by their positively charged domains: a signature for viral identity and capsid assembly strategy

Capsid proteins often present a positively charged arginine-rich region at the N and/or C-termini that for some icosahedral viruses has a fundamental role in genome packaging and particle stability. These sequences show little to no conservation at the amino-acid level and are structurally dynamic so that they cannot be easily detected by common sequence or structure comparison. As a result, the occurrence and distribution of positively charged protein domain across the viral and the overall protein universe are unknown. We developed a methodology based on the net charge calculation of discrete segments of the protein sequence that allows us to identify proteins containing amino-acid stretches with an extremely high net charge. We observed that among all organisms, icosahedral viruses are especially enriched in extremely positively charged segments (Q [≥] +17), with a distinctive bias towards arginine instead of lysine. We used viral particle structural data to calculate the total electrostatic charge derived from the most positively charged protein segment of capsid proteins and correlated these values with genome charge arising from the phosphates of each nucleotide. We obtained a positive correlation (r = 0.91, p-value < 0001) for a group of 17 viral families, corresponding to 40% of all families with icosahedral structures described so far. These data indicated that unrelated viruses with diverse genome types adopt a common underlying mechanism for capsid assembly and genome stabilization based on R-arms. Outliers from a linear fit pointed to families with alternative strategies of capsid assembly and genome packaging.\n\nSignificance StatementViruses can be characterized by the existence of a capsid, an intricate proteinaceous container that encases the viral genome. Therefore, capsid assembly and function are essential to viral replication. Here we specify virus families with diverse capsid structure and sequence, for each capsid packing capacity depends on a distinctive structural feature: a highly positively charged segment of amino acids residues, preferentially made of arginine. We also show that proteins with the same characteristics are rarely found in cellular proteins. Therefore, we identified a conserved viral functional element that can be used to infer capsid assembly mechanisms and inspire the design of protein nanoparticles and broad-spectrum antiviral treatments.

bioinformatics↗