Biology subjects

Cuervo, A.

Publications and source records attributed to Cuervo, A..

4 recordsLinked to original sources

bioRxiv2023

ICAM-1 nanoclusters regulate hepatic epithelial cell polarity by leukocyte adhesion-independent control of apical actomyosin

Epithelial Intercellular Adhesion Molecule (ICAM)-1 is apically polarized, interacts with and guides leukocytes across epithelial barriers. Polarized hepatic epithelia organize their apical membrane domain into bile canaliculi and ducts, which are not accessible to circulating immune cells but that nevertheless confine most of ICAM-1. Here, by analyzing ICAM-1_KO human hepatic cells, liver organoids from ICAM-1_KO mice and rescue-of-function experiments, we show that ICAM-1 regulates epithelial apicobasal polarity in a leukocyte adhesion-independent manner. ICAM-1 signals to an actomyosin network at the base of canalicular microvilli, thereby controlling the dynamics and size of bile canalicular-like structures (BCs). We identified the scaffolding protein EBP50/NHERF1/SLC9A3R1, which connects membrane proteins with the underlying actin cytoskeleton, in the proximity interactome of ICAM-1. EBP50 and ICAM-1 form nano-scale domains that overlap in microvilli, from which ICAM-1 regulates EBP50 nano-organization. Indeed, EBP50 expression is required for ICAM-1-mediated control of BC morphogenesis and actomyosin. Our findings indicate that ICAM-1 regulates the dynamics of epithelial apical membrane domains beyond its role as a heterotypic cell-cell adhesion molecule and reveal potential therapeutic strategies for preserving epithelial architecture during inflammatory stress.

cell biology↗

bioRxiv2021

Assisted assembly of bacteriophage T7 core components for genome translocation across the bacterial envelope

In most bacteriophages, the genome transport across bacterial envelopes is carried out by the tail machinery. In Podoviridae viruses, where the tail is not long enough to traverse the bacterial wall, it has been postulated that viral core proteins are translocated and assembled into a tube within the periplasm. T7 bacteriophage, a member from the Podoviridae family, infects E. coli gram-negative bacteria. Despite extensive studies, the precise mechanism by which this virus translocates its genome remains unknown. Using cryo-electron microscopy, we have resolved the structure two different assemblies of the T7 bacteriophage DNA translocation complex, built by core proteins gp15 and gp16. Gp15 alone forms a partially folded hexamer, which is further assembled by interaction with gp16, resulting in a tubular structure with dimensions compatible with traversing the bacterial envelope and a channel that allows DNA passage. The structure of the gp15-gp16 complex also shows the location in gp16 of a canonical transglycosylase motif essential in the bacterial peptidoglycan layer degradation. Altogether these results allow us to propose a model for the assembly of the core translocation complex in the periplasm, which helps in the understanding at the molecular level of the mechanism involved in the T7 viral DNA release in the bacterial cytoplasm. SIGNIFICANCE STATEMENTT7 bacteriophage infects E. coli bacteria. During this process, the DNA transverses the bacterial cell wall, but the precise mechanism used by the virus remains unknown. Previous studies suggested that proteins found inside the viral capsid (core proteins) disassemble and reassemble in the bacterial periplasm to form a DNA translocation channel. In this article we solved by cryo-electron microscopy two different assemblies of the core proteins that reveal the steps followed by them to finally form a tube large enough to traverse the periplasm, as well as the location of the transglycosylase enzyme involved in peptidoglycan degradation. These findings confirm previously postulated hypothesis and make experimentally visible the mechanism of DNA transport trough the bacterial wall.

biophysics↗

bioRxiv2020

DeepEMhacer: a deep learning solution for cryo-EM volume post-processing

Cryo-EM maps are valuable sources of information for protein structure modeling. However, due to the loss of contrast at high frequencies, they generally need to be post-processed to improve their interpretability. Most popular approaches, based on B-factor correction, suffer from limitations. For instance, they ignore the heterogeneity in the map local quality that reconstructions tend to exhibit. Aiming to overcome these problems, we present DeepEMhancer, a deep learning approach designed to perform automatic post-processing of cryo-EM maps. Trained on a dataset of pairs of experimental maps and maps sharpened using their respective atomic models, DeepEMhancer has learned how to post-process experimental maps performing masking-like and sharpening-like operations in a single step. DeepEMhancer was evaluated on a testing set of 20 different experimental maps, showing its ability to obtain much cleaner and more detailed versions of the experimental maps. Additionally, we illustrated the benefits of DeepEMhancer on the structure of the SARS-CoV-2 RNA polymerase.

bioinformatics↗

bioRxiv2019

Systematics, biogeography and diversification of Scytalopus tapaculos (Rhinocryptidae), an enigmatic radiation of Neotropical montane birds

We studied the phylogeny, biogeography and diversification of suboscine birds in the genus Scytalopus (Rhinocryptidae), a widespread, speciose, and taxonomically challenging group of Neotropical birds. We analyzed nuclear (exons, regions flanking ultraconserved elements) and mitochondrial (ND2) DNA sequence data for a taxonomically and geographically comprehensive sample of specimens collected from Costa Rica to Patagonia and eastern Brazil. We found that Scytalopus is a monophyletic group sister to Eugralla, and consists of three main clades roughly distributed in (1) the Southern Andes, (2) eastern Brazil, and (3) the Tropical Andes and Central America. The clades from the Southern Andes and Eastern Brazil are sister to each other. Despite their confusing overall uniformity in plumage coloration, body shape and overall appearance, rates of species accumulation through time in Scytalopus since the origin of the clade in the Late Miocene are unusually high compared to those of other birds, suggesting rapid non-adaptive diversification in the group which we attribute to their limited dispersal abilities making them speciation-prone and their occurrence in a complex landscape with numerous barriers promoting allopatric differentiation. Divergence times among species and downturns in species accumulation rates in recent times suggest that most speciation events in Scytalopus predate climatic oscillations of the Pleistocene. Our analyses identified various cases of strong genetic structure within species and lack of monophyly of taxa, flagging populations which likely merit additional study to establish their taxonomic status. In particular, detailed analyses of species limits are due in S. parvirostris, S. latrans, S. speluncae, the S. atratus complex, and the Southern Andes clade.

evolutionary biology↗