Biology subjects

Aldea, M.

Publications and source records attributed to Aldea, M..

8 recordsLinked to original sources

bioRxiv2025

Concerted remodelling of the postsynaptic spine and RNA granule by cLTP

Synaptic plasticity is the cellular foundation of learning and memory and, for these plastic changes to be stabilised into long-term memory, proteins must be synthesised at the synapse1,2. RNA granules ensure that specific mRNAs are delivered and translated at the right time and place3,4, but the signalling mechanisms linking synaptic activation to local translation are still largely unknown. Here, to investigate how postsynaptic signals modulate the RNA granule, we employed a spatially-restricted biotinylation approach to quantify protein accessibility and proximity in the postsynaptic and RNA granule subproteomes. Upon chemical long-term potentiation (cLTP), we observed a sharp increase in the accessibility of ribosomes, translation factors and RNA binding proteins belonging to the RNA granule. Similarly, strong alterations were observed in proteins of the postsynaptic density, but mostly in those involved in signalling. Specific proximity to DBN1 and IGF2BP1 as postsynaptic and RNA granule reporters unveiled a shift of the translation machinery towards the postsynaptic compartment, whereas specific translation initiation factors and RNA helicases displayed marked changes in their proximity to DBN1 and/or IGF2BP1. Finally, alteration of synapse development and signalling by DBN1 downregulation caused a highly significant decrease in the proximity of RNA granule proteins to IGF2BP1 after synaptic stimulation, establishing a causal link between postsynaptic events and RNA granule dynamics.

neuroscience↗

bioRxiv2023

The PI3K-AKT-mTOR axis persists as a therapeutic dependency in KRASG12D-driven non-small cell lung cancer

IntroductionKRASG12C and KRASG12D inhibitors represent a major translational breakthrough for non-small cell lung cancer (NSCLC) and cancer in general by directly targeting its most mutated oncoprotein. However, resistance to these small molecules has highlighted the need for rational combination partners necessitating a critical understanding of signaling downstream of KRAS mutant isoforms. MethodsWe contrasted tumor development between KrasG12Cand KrasG12D genetically engineered mouse models (GEMMs). To corroborate findings and determine mutant subtype-specific dependencies, isogenic models of KrasG12C and KrasG12D initiation and adaptation were profiled by RNA sequencing. We also employed cell line models of established KRAS mutant NSCLC and determined therapeutic vulnerabilities through pharmacological inhibition. We analysed differences in survival outcomes for patients affected by advanced KRASG12C or KRASG12D-mutant NSCLC. ResultsKRASG12D exhibited higher potency in vivo, manifesting as more rapid lung tumor formation and reduced survival of KRASG12D GEMMs compared to KRASG12C. This increased potency, recapitulated in an isogenic initiation model, was associated with enhanced PI3K-AKT-mTOR signaling. However, KRASG12C oncogenicity and downstream pathway activation were comparable with KRASG12D at later stages of tumorigenesis in vitro and in vivo, consistent with similar clinical outcomes in patients. Despite this, established KRASG12D NSCLC models depended more on the PI3K-AKT-mTOR pathway, while KRASG12C models on the MAPK pathway. Specifically, KRASG12D inhibition was synergistically enhanced by AKT inhibition. ConclusionsOur data highlight a unique combination treatment vulnerability and suggest that patient selection strategies for combination approaches using direct KRAS inhibitors should be i) contextualised to individual RAS mutants, and ii) tailored to their downstream signaling.

cancer biology↗

bioRxiv2022

Transcriptomic balance and optimal growth are determined by cell size

Cell size and growth are intimately related across the evolutionary scale, and the molecular pathways underlying cell size homeostasis have received much attention over the last decades. However, whether cell size is important to attain maximal growth or fitness is still an open question, and the reasons why a critical size is needed for triggering key transitions of the cell cycle are unknown. We show that growth is a non-monotonic function of volume in yeast cells, with maximal values around the critical size. Comparing small to normal, large and outsized cells, the transcriptome undergoes an extensive inversion that correlates with RNA polymerase II occupancy. Accordingly, highly expressed genes impose strong negative effects on growth when their DNA/mass ratio is altered. A similar transcriptomic inversion is displayed by mouse liver cells of different sizes, suggesting that the uncovered mechanistic implications of cell size on growth and fitness are universal. We propose that cell size is set to attain a properly balanced transcriptome and, hence, maximize growth during cell proliferation.

cell biology↗

bioRxiv2022

Exploring the Regulation of Cdc42 Stability and Turnover in Yeast

Rho GTPases govern many cellular processes, including actin cytoskeleton dynamics and signal transduction pathways. Rho GTPase levels can be regulated by stability and turnover, yet many aspects of this type of regulation remain largely unexplored. We report here a new environmental stress, high temperature (37{degrees}C), that stimulates yeast Cdc42p turnover to impact its biological functions. At 37{degrees}C, Cdc42p turnover required the NEDD4 ubiquitin ligase Rsp5p and HSP40/HSP70 chaperones. Specific lysine residues promoted Cdc42p degradation at 37{degrees}C [K166; and residues in the Poly-Basic (PB) domain: K183, K184, K186, K187], which occurred in both the 26S proteosome and ESCRT-to-vacuole pathway. Degradation of Cdc42p at 37{degrees}C reduced the sensitivity to mating pheromone, demonstrating biological role for Cdc42p turnover in this context. Stabilization of Cdc42p at high temperatures restored pheromone sensitivity but caused growth and polarity defects, suggesting a tradeoff between sexual propagation and cellular fitness. One lysine residue (K16) in the P-loop of the protein was critical for stability. Overproduction of the protein, expression of Cdc42pK16R in a mutant where the protein accumulates, and other types of proteostatic stress led to the formation of Cdc42p aggregates in aging mother cells. These new aspects of Cdc42p protein quality control may extend to other members of the Rho GTPase family of proteins. Summary statementRho GTPases regulate cell polarity and signaling (e.g. MAPK) pathways. Here, we discovered that yeast Cdc42p is targeted for degradation at 37{degrees}C by a NEDD4 ubiquitin ligase and HSP40 and HSP70 chaperones through lysine residues in the C-terminus of the protein. At 37{degrees}C, Cdc42p was degraded both by the 26S proteasome and in an ESCRT-dependent manner in the vacuole. Preventing Cdc42p turnover at 37{degrees}C resulted in improved mating sensitivity but also viability and polarity defects, suggesting a tradeoff between sexual responses and fitness. In addition, one residue (K16) was critical for Cdc42p stability. Cdc42pK16R formed aggregates in aging mother cells, and aggregates were also observed in cells undergoing proteostatic stress. Protein quality control regulation of a Rho-type GTPase therefore has ramification in the regulation of cellular responses, evolutionary tradeoffs, and protein aggregation in ways that might impact aging. HIGHLIGHTSO_LIHigh temperatures (37{degrees}C) induce turnover of the Rho GTPase Cdc42p C_LIO_LITurnover of Cdc42p at 37{degrees}C requires the HSP40/HSP70 proteins and the NEDD4-type E3 ubiquitin ligase Rsp5p. C_LIO_LIK166 and four lysines at the extreme C-terminus [poly-basic (PB: K183, K184, K186, K187] promote turnover of Cdc42p at 37{degrees}C C_LIO_LICdc42p is degraded at 37{degrees}C by the proteosome and the ESCRT-to-vacuole pathways. C_LIO_LIGTP-Cdc42p does not accumulate in ESCRT mutants and is not turned over in the vacuole. C_LIO_LITurnover of Cdc42p at 37{degrees}C inhibits sensitivity to mating pheromone Preventing Cdc42p turnover restores pheromone sensitivity at the cost of cell viability and proper cell polarity. These results reveal a tradeoff between sexual responses and overall cellular fitness. C_LIO_LIAn internal lysine residue (K16) is required for Cdc42p stability. O_LIverproduction of the protein, or accumulation of Cdc42pK16R in certain mutants induces protein aggregation in aging mother cells. C_LI C_LI

cell biology↗

bioRxiv2020

Whi5 is diluted and protein synthesis does not dramatically increase in pre-Start G1

In their manuscript, Litsios et al.1 report a new model for how cell growth and biosynthetic activity control the G1/S transition in budding yeast. In essence, Litsios et al. claim that Start is driven by an increasing concentration of the G1 cyclin Cln3 due to a dramatic acceleration of protein synthesis in pre-Start G1 and not by the dilution of the cell cycle inhibitor Whi5. While we previously reported that Start was in part driven by cell growth during G1 diluting out the Start inhibitor Whi52, Litsios et al. report that Whi5 remains at constant concentration during G1, and changes in Whi5 concentration therefore do not contribute to Start. Since Litsios et al. directly contradict several key points of our own model of how cell growth triggers Start, we decided to investigate their claims and data. More specifically, we decided to investigate Litsios et al.s three major claims: O_LIWhi5 concentration remains constant during G1 C_LIO_LICln3 concentration strongly increases prior to Start C_LIO_LIGlobal protein synthesis rates increase by 2-3 fold prior to Start C_LI We investigated each of these three claims and found that the evidence presented by Litsios et al. does not support their claims due to inadequate analysis methods and flaws in their experiments.

molecular biology↗

bioRxiv2020

Stress granules display bistable dynamics modulated by Cdk

Stress granules are conserved biomolecular condensates that originate in response to many stress conditions. These membraneless organelles contain nontranslating mRNAs and a diverse subproteome, but our knowledge on their regulation and functional relevance is still incipient. Here we describe a mutual-inhibition interplay between stress granules and Cdc28, the budding yeast Cdk. Amongst Cdc28 interactors acting as negative modulators of Start we have identified Whi8, an RNA-binding protein that localizes to SGs and recruits the mRNA of CLN3, the most upstream G1 cyclin, for efficient translation inhibition and Cdk inactivation under stress. However, Whi8 also contributes to recruiting Cdc28 to SGs, where it acts to promote their dissolution. As predicted by a mutual-inhibition framework, the SG constitutes a bistable system that is modulated by Cdk. Since mammalian cells display a homologous mechanism, we propose that the opposing functions of specific mRNA-binding proteins and Cdks subjugate SG dynamics to a conserved hysteretic switch.

cell biology↗

bioRxiv2019

Proteostasis collapse halts G1 progression and delimits replicative lifespan

Loss of proteostasis and cellular senescence are key hallmarks of cell aging, but whether they are subject to direct cause-effect relationships is not known. We show that most yeast cells arrest in G1 before death with low nuclear levels of cyclin Cln3, a key activator of Start extremely sensitive to chaperone status. Chaperone availability is seriously compromised in aged cells, and the G1 arrest coincides with massive aggregation of a metastable chaperone-activity reporter. A mathematical model integrating autocatalytic protein aggregation and a minimal Start network recapitulates empirical observations. As key predictions, G1-cyclin overexpression increases lifespan in a chaperone-dependent manner, and lifespan reduction by enforced protein aggregation is greatly alleviated by increased expression of specific chaperones or cyclin Cln3. Overall, our data indicate the crucial role of chaperone malfunction in setting lifespan in yeast cells, and configure a molecular pathway whereby proteostasis breakdown acts as a direct effector of cell senescence.

cell biology↗

bioRxiv2018

The chaperone-client network subordinates cell-cycle entry to growth and stress

The precise coordination of growth and proliferation has a universal prevalence in cell homeostasis. As a prominent property, cell size is modulated by the coordination between these processes in bacterial, yeast and mammalian cells, but the underlying molecular mechanisms are largely unknown. Here we show that multifunctional chaperone systems play a concerted and limiting role in cell-cycle entry, specifically driving nuclear accumulation of the G1 Cdk-cyclin complex. Based on these findings, we establish and test a molecular competition model that recapitulates cell-cycle-entry dependence on growth rate. As key predictions at a single-cell level, we show that availability of the Ydj1 chaperone and nuclear accumulation of the G1 cyclin Cln3 are inversely dependent on growth rate and readily respond to changes in protein synthesis and stress conditions that alter protein folding requirements. Thus, chaperone workload would subordinate Start to the biosynthetic machinery and dynamically adjust proliferation to the growth potential of the cell.

molecular biology↗