Biology subjects

Alba, J.

Publications and source records attributed to Alba, J..

4 recordsLinked to original sources

bioRxiv2023

CryoEM architecture of a native stretch-sensitive membrane microdomain

Biological membranes are partitioned into functional zones containing specific lipids and proteins, termed membrane microdomains. Their composition and organization remain controversial owing to a paucity of techniques that can visualize lipids in situ without disrupting their native behavior1,2. The yeast eisosome, a membrane compartment scaffolded by the BAR-domain proteins Pil1 and Lsp1, senses and responds to mechanical stress by flattening and releasing sequestered factors3-7. Here, we isolated native eisosomes as helical filaments of Pil1/Lsp1 lattice bound to plasma membrane lipids and solved their structures by helical reconstruction. We observe remarkable organization within the lipid bilayer density from which we could assign headgroups of PI(4,5)P2 and phosphatidylserine bound to Pil1/Lsp1 and a pattern of membrane voids, signatures of sterols, beneath an amphipathic helix. We verified these assignments using in vitro reconstitutions and molecular dynamics simulations. 3D variability analysis of the native eisosomes revealed a dynamic stretching of the Pil1/Lsp1 lattice that affects functionally important lipid sequestration, supporting a mechanism in which membrane stretching liberates lipids otherwise anchored by the Pil1/Lsp1 coat. Our results provide mechanistic insight into how eisosome BAR-domain proteins create a mechanosensitive membrane microdomain and, more globally, resolve long-standing controversies about the architecture and nature of lipid microdomains.

biophysics↗

bioRxiv2022

Malonyl-CoA is an ancient physiological ATP-competitive mTORC1 inhibitor

Cell growth is regulated primarily by the mammalian/mechanistic Target of Rapamycin Complex 1 (mTORC1) that functions both as a nutrient sensor and a master controller of virtually all biosynthetic pathways 1. This ensures that cells are metabolically active only when conditions are optimal for growth. Notably, although mTORC1 is known to regulate fatty acid (FA) biosynthesis, how and whether the cellular lipid biosynthetic capacity signals back to fine-tune mTORC1 activity remains poorly understood. Here, we show that mTORC1 senses the capacity of a cell to synthesize FAs by detecting the levels of malonyl-CoA, an intermediate of this biosynthetic pathway. We find that, in both yeast and mammalian cells, this regulation is very direct, with malonyl-CoA binding to the mTOR catalytic pocket and acting as a specific ATP-competitive inhibitor. When ACC1 (acetyl-CoA carboxylase 1) is hyperactive or FASN (fatty acid synthase) is downregulated/inhibited, elevated malonyl-CoA levels are channelled to proximal mTOR molecules that form direct protein-protein interactions with ACC1 and FASN. Our findings represent a conserved, unique, homeostatic mechanism whereby impaired FA biogenesis leads to reduced mTORC1 activity to coordinatively link this metabolic pathway to the overall cellular biosynthetic output. Moreover, they reveal the first-described example of a physiological metabolite that directly inhibits the activity of a signalling kinase by competing with ATP for binding.

cell biology↗

bioRxiv2022

Impact of HIV infection and integrase strand transfer inhibitors-based treatment on gut virome

Viruses are the most abundant components of the microbiome in human beings with a significant impact on health and disease. However, the impact of human immunodeficiency virus (HIV) infection on gut virome has been scarcely analyzed. On the other hand, several studies suggested that not all antiretrovirals for treating HIV infection exert similar effects on the gut bacteriome, being the integrase strand transfers inhibitors (INSTIs) --first-choice treatment of naive HIV-infected patients nowadays-- those associated with a healthier gut. Thus, the aim of this study was to evaluate the effects of HIV infection and INSTIs in first line of treatment on gut virome composition. To accomplish this objective, 26 non-HIV-infected volunteers, 15 naive HIV-infected patients and 15 INSTIs-treated HIV-infected patients were recruited and gut virome composition was analysed using shotgun sequencing. The results showed that bacteriophages are the most abundant and diverse viruses in the gut independent from the HIV-status and the use of treatment. HIV infection was accompanied by a decrease in phage richness which was reverted after INSTIs-based treatment (p<0.01 naive vs. control Richness index and p<0.05 naive vs. control Fishers alpha index). {beta}-diversity of phages revealed that samples from HIV-infected samples clustered separately from those belonging to the control group (padj<0.01 naive vs. control and padj<0.05 INSTIs vs. control). However, it is worth mentioning that samples coming from INSTIs-treated patients were more grouped than those from naive patients. Differential abundant analysis of phages showed an increase of Caudoviricetes class in the naive group compared to control the group (padj<0.05) and a decrease of Malgrandaviricetes class in the INSTIs-treated group compared to the control group (padj<0.001). Besides, it was observed that INSTIs-based treatment was not able to reverse the increase of lysogenic phages associated with HIV infection (p<0.05 vs. control) or to modify the decrease observed on the relative abundance of Proteobacteria-infecting phages (p<0.05 vs. control). To sum up, our study describes for the first time the impact of HIV and INSTIs on gut virome and demonstrates that INSTIs-based treatments are able to partially restore gut dysbiosis not only at bacterial but also at viral level, which opens several opportunities for new studies focused on microbiota-based therapies. Author summaryThe impact of human immunodeficiency virus (HIV) infection and the effects of integrase strand transfer inhibitors (INSTIs)-based treatments --first-choice treatment of naive HIV-infected patients nowadays-- on gut virome are unknown. In this study, we have confirmed that phages are the most abundant viral component of the human gut virome. Besides, we have described for the first time that INSTIs-based treatments are able to partially restore gut dysbiosis induced by HIV infection not only at bacteria but also at viral level. This fact opens new opportunities for future studies and approaches focused on microbiota-based therapies in the context of HIV infection and treatment.

microbiology↗

bioRxiv2020

The full model of the pMHC-TCR-CD3 complex: a structural and kinetics characterization

The machinery involved in cytotoxic T-cell activation requires three main characters such as: the major histocompatibility complex class I (MHC I) bound to the peptide (p), the T-cell receptor (TCR), and the CD3-complex which is a multidimer interfaced with the intracellular side. The pMHC:TCR interaction has been largely studied both in experimental and computational models, giving a contribution in understanding the complexity of the TCR triggering process. Nevertheless, a detailed study of the structural and dynamical characterization of the full complex (pMHC:TCR:CD3-complex) is still missing, due to insufficient data available on the CD3-chains arrangement around the TCR. The recent determination of the TCR:CD3-complex structure by means of Cryo-EM technique has given a chance to build the entire proteins system essential in the activation of T-cell, and thus in the adaptive immune response. Here, we present the first full model of the pMHC interacting with the TCR:CD3-complex, built in a lipid environment. To describe the conformational behaviour associated with the unbound and the bound states, all atoms Molecular Dynamics simulations were performed for the TCR:CD3-complex and for two pMHC:TCR:CD3-complex systems, bound to two different peptides. Our data point out that a conformational change affecting the TCR Constant {beta} (C{beta}) region occurs after the binding to the pMHC, revealing a key role of such a region in the propagation of the signal. Moreover, we found that the TCR reduces the flexibility of the MHC I binding groove, confirming our previous results.

immunology↗