Biology subjects

Uezu, A.

Publications and source records attributed to Uezu, A..

5 recordsLinked to original sources

bioRxiv2025

Deep Learning-coupled Proximity Proteomics to Deconvolve Kinase Signaling In Vivo

Deconvolving the substrates of hundreds of kinases linked to phosphorylation networks driving cellular behavior is a fundamental, unresolved biological challenge, largely due to the poorly understood interplay of kinase selectivity and substrate proximity. We introduce KolossuS, a deep learning framework leveraging protein language models to decode kinase-substrate specificity. KolossuS achieves superior prediction accuracy and sensitivity across mammalian kinomes, enabling proteome-wide predictions and evolutionary insights. By integrating KolossuS with CRISPR-based proximity proteomics in vivo, we capture kinase-substrate recognition and spatial context, obviating prior limitations. We show this combined framework identifies kinase substrates associated with physiological states such as sleep, revealing both known and novel Sik3 substrates during sleep deprivation. This novel integrated computational-experimental approach promises to transform systematic investigations of kinase signaling in health and disease.

cell biology↗

bioRxiv2023

Identification of new ciliary signaling pathways in the brain and insights into neurological disorders

Primary cilia are conserved sensory hubs essential for signaling transduction and embryonic development. Ciliary dysfunction causes a variety of developmental syndromes with neurological features and cognitive impairment, whose basis mostly remains unknown. Despite connections to neural function, the primary cilium remains an overlooked organelle in the brain. Most neurons have a primary cilium; however, it is still unclear how this organelle modulates brain architecture and function, given the lack of any systemic dissection of neuronal ciliary signaling. Here, we present the first in vivo glance at the molecular composition of cilia in the mouse brain. We have adapted in vivo BioID (iBioID), targeting the biotin ligase BioID2 to primary cilia in neurons. We identified tissue-specific signaling networks enriched in neuronal cilia, including Eph/Ephrin and GABA receptor signaling pathways. Our iBioID ciliary network presents a wealth of neural ciliary hits that provides new insights into neurological disorders. Our findings are a promising first step in defining the fundamentals of ciliary signaling and their roles in shaping neural circuits and behavior. This work can be extended to pathological conditions of the brain, aiming to identify the molecular pathways disrupted in the brain cilium. Hence, finding novel therapeutic strategies will help uncover and leverage the therapeutic potential of the neuronal cilium.

neuroscience↗

bioRxiv2023

Ecological monitoring using Collembola metabarcoding with extremely low bycatch amplification.

Collembola are used widely to monitor soil health and functional parameters. Recent developments in high throughput sequencing (especially metabarcoding) have substantially increased their potential for these ends. Collembola are especially amenable to metabarcoding because of their small size, high abundance, and ubiquity in most habitat types. However, most Collembola sampling protocols collect a substantial and highly varied bycatch that can be a considerable impediment to metabarcoding, especially because of data lost to non-target species. We designed a primer set amplifying the D2 expansion segment of ribosomal DNA that is highly conserved across Collembola and successfully excludes from amplification nearly all other invertebrate taxa. We tested the diagnostic power of the primer set by clearly distinguishing Collembola communities between forest sites with differing habitat qualities in Sao Paulo State, Brazil. The oligos successfully amplified targets from all Collembola orders previously encountered in the sampling locations, with no non-target amplification, and also excluded the closely related Protura and Diplura. Alpha diversity (OTU count) and phylogenetic diversity was significantly higher in high quality habitats. Moreover, the beta diversity indices successfully differentiated high and low-quality habitats. This new addition to the biomonitoring toolbox greatly increases the accessibility of Collembola metabarcoding for various types of habitat assessments.

molecular biology↗

bioRxiv2022

Activation of Nedd4L Ubiquitin Ligase by FCHO2-generated Membrane Curvature

The C2-WW-HECT domain ubiquitin ligase Nedd4L regulates sorting in endocytosis by mediating ubiquitination of cargo molecules, such as the epithelial sodium channel (ENaC). Defects in ENaC ubiquitination cause Liddle syndrome, a hereditary hypertension. Nedd4L is catalytically autoinhibited by an intramolecular interaction between the C2 and HECT domains, but the activation mechanism is poorly understood. Here, we show that Nedd4L is activated by membranes sculpted by FCHO2, a Bin-Amphiphysin-Rsv (BAR) domain protein that regulates endocytosis. We found that FCHO2 was required for Nedd4L-mediated ubiquitination and endocytosis of ENaC. Nedd4L co-localized with FCHO2 at clathrin-coated pits where it likely became activated. Nedd4L was specifically recruited to and activated by the FCHO2 BAR domain exogenously expressed in cells. Furthermore, we reconstituted in vitro FCHO2-induced recruitment and activation of Nedd4L. Both the recruitment and activation were mediated by membrane curvature rather than protein-protein interactions. The Nedd4L C2 domain recognized a specific degree of membrane curvature that was generated by the FCHO2 BAR domain. Consequently, this curvature activated Nedd4L by relieving autoinhibition. Thus, we show for the first time a specific functionality (i.e., recruitment and activation of an enzyme regulating cargo sorting) of membrane curvature by a BAR domain protein.

cell biology↗

bioRxiv2021

Map7D2 and Map7D1 facilitate MT stabilization through distinct mechanisms to control cell motility and neurite outgrowth

Microtubule (MT) dynamics are modulated through the coordinated action of various MT-associated proteins (MAPs). However, the regulatory mechanisms underlying MT dynamics remain unclear. We show that the MAP7 family protein Map7D2 stabilizes MTs to control cell motility and neurite outgrowth. Map7D2 directly bound to MTs through its N-terminal half and stabilized MTs in vitro. Map7D2 localized prominently to the centrosome and partially on MTs in mouse N1-E115 neuronal cells, which expresses two of the four MAP7 family members, Map7D2 and Map7D1. Map7D2 loss decreased the resistance to the MT-destabilizing agent, nocodazole without affecting acetylated/detyrosinated stable MTs, suggesting that Map7D2 stabilizes MTs via direct binding. In addition, Map7D2 loss increased the rate of random cell migration and neurite outgrowth, presumably by disturbing the balance between MT stabilization and destabilization. Map7D1 exhibited similar subcellular localization and gene knock-down phenotypes to Map7D2. However, in contrast to Map7D2, Map7D1 was required for the maintenance of acetylated stable MTs. Taken together, our data suggest that Map7D2 and Map7D1 facilitate MT stabilization through distinct mechanisms in cell motility and neurite outgrowth.

cell biology↗