Biology subjects

Thibodeau, J.

Publications and source records attributed to Thibodeau, J..

5 recordsLinked to original sources

bioRxiv2026

An ancient receptor family illuminates the evolution of animal sensation

Animals use nervous systems to sense and respond to their environment. Yet single-celled organisms can also detect cues to execute diverse behaviors, suggesting that core components for animal sensation predate multicellularity and nervous systems. Here, we report that choanoflagellates, the closest living animal relatives, use an ancient sensory receptor family to detect bacterial prey. These receptors are related to transient receptor potential ion channels but are distinguished by WD40 domains, defining TRPW. TRPW1 detects specific bacterial lipids to modulate flagellar beating, providing a mechanism for attraction towards prey. TRPW emerged in early eukaryotes and reveals ancestral architectural and ligand-binding features that predate animal somatosensory receptors. In multicellular choanoflagellates, TRPW1 elicits collective responses, linking bacterial ecology to the evolution of receptors, sensory organelles, and multicellular life.

evolutionary biology↗

bioRxiv2025

A biotin ligation assay reveals a complex proxiome for HLA-A2 and implicates MIA3 in cell surface expression of MHC class I molecules

Antigen presentation via MHC class I molecules (MHC-Is) is a turning point in the establishment of immune responses to endogenous threats, such as viruses. From their synthesis to their cell surface display, MHC-Is travel to many compartments, including the ER, Golgi, and endosomes. They come close to a plethora of molecules, some of which regulate directly or indirectly their folding and trafficking. While many of these proteins are well characterized, such as those found in the peptide loading complex, others remain to be discovered. The proxiome can be studied using proximity labeling assays, such as BioID, which relies on a biotin ligase fused to a bait of interest that biotinylates lysine residues on nearby proteins. These modified targets can then be purified and identified by mass spectrometry. By fusing BioID to the HLA-A2 cytoplasmic tail, we have applied this technique to the MHC-I antigen and identified 209 potential specific interactors in HEK293 cells, including PDZD8 (LYVAC) and MIA3 (Tango1). We knocked out MIA3 in HEK293 cells and measured an increase in the expression of MHC-I molecules, suggesting a role for this vesicle budding protein in the regulation of MHC-I trafficking. Notably, MHC-I crosslinking identified targets that connect reverse signalling to diverse metabolic processes. Altogether, our results underscore the promise of HLA-coupled biotin ligases as a powerful approach to dissect antigen presentation pathways.

immunology↗

bioRxiv2024

A proximity ligation screen identifies SNAT2 as a novel target of the MARCH1 E3 ubiquitin ligase

E3 ubiquitin ligases are part of various families of proteins and include hundreds of members, which play key roles in all aspects of cell biology. They generally regulate the half-life of other proteins but can also modulate their cellular localization and functions. The MARCH family of ubiquitin ligases is composed of 11 members and two closely related proteins, MARCH1 and MARCH8, share similar targets, while being active in different cell types. Although they appear to target principally immune cell components, such as MHC class II molecules and the co-stimulatory molecule CD86, the repertory of their targets remains to be fully documented. Here, to further define the MARCH1s interactome, we adapted a proximity-dependent biotin identification (BioID)-based screening approach in live HEK293 cells. We transfected a fusion protein consisting of mouse MARCH1 linked to YFP at its N-terminus and to the biotin ligase of Aquifex aeolicus at its C-terminus. Upon transient overexpression of this construct in the presence of exogenous biotin, we could recover biotinylated proteins that are presumably found within 10nm of MARCH1. To help in the identification of bona fide down-regulated specific targets, we compared MARCH1s interactome with the one obtained using a ubiquitination-deficient MARCH1 mutant (MARCH1W104A). CD98 and CD71, two previously described targets of MARCH1, were identified in this screen. Of 16 other biotinylated proteins identified by semi-quantitative mass spectrometry, 10 were tested directly by flow cytometry to monitor their expression in the presence or absence of transfected MARCH1. The protein levels of five of these endogenous targets, CD29, CD112, NKCC1, CD147 and SNAT2, confirmed their negative regulation by MARCH1 in this system. SNAT2 was particularly sensitive to the presence of MARCH1 and was found to be ubiquitinated on Western blots following immunoprecipitation. Thus, BioID2 is an effective mean of characterizing the interactome of MARCH1 and the identification of SNAT2 suggests a role of this ubiquitin ligase in cellular metabolism.

immunology↗

bioRxiv2019

Invariant chain regulates endosomal fusion and maturation through the SNARE Vti1b

Invariant chain (Ii) is an important multifunctional player in the regulation of adaptive immune responses and is responsible for several cellular functions related to MHCI and MHCII antigen loading and antigen presentation. While regulating endosomal trafficking of MHCII and other proteins that bind to Ii, this molecule is able to influence the endosomal pathway delaying the maturation of endosomes to the late endosomal loading compartments. When expressed in cells Ii is found to increase endosomal size, but the mechanisms for this is not known. We used RNAi silencing to identify SNARE proteins controlling Ii induced increase of endosomal size and delay of the endosomal pathway. Ii was found to interact with the SNARE protein Vti1b. Vti1b localized at the contact sites of fusing Ii positive endosomes and a tailless Ii was able to relocate Vti1b to the plasma membrane. Furthermore, silencing Vti1b, abrogated the delay in endosomal maturation induced by Ii expression. In conclusion, Ii interacts with Vti1b and this interaction is fundamental for Ii-mediated alteration of the endosomal pathway. We propose that Ii, by interacting with SNAREs, in particular Vti1B in the biosynthetic pathway of antigen presenting cells, is able to assemble SNARE directed fusion partners in the early part of the endosomal pathway that lead to a slower endosomal maturation for efficient antigen processing and antigen loading.

cell biology↗

bioRxiv2018

Partially Overlapping Brain Networks for Singing and Cello Playing

1This research uses an MR-Compatible cello to compare functional brain activation during singing and cello playing within the same individuals to determine the extent to which arbitrary auditory-motor associations, like those required to play the cello, co-opt functional brain networks that evolved for singing. Musical instrument playing and singing both require highly specific associations between sounds and movements. However, vocal motor control is an evolutionarily old human trait and the auditory-motor associations used for singing are also used for speech and nonspeech vocalizations. This sets it apart from the arbitrary auditory-motor associations required to play musical instruments. The pitch range of the cello is similar to that of the human voice, but cello playing is completely independent of the vocal apparatus and can therefore be used to dissociate the auditory-vocal network from that of the auditory-motor network. While in the MR-Scanner, 11 expert cellists listened to and subsequently produced individual tones either by singing or cello playing. All participants were able to sing and play the target tones in tune (within 50Cents). We found that brain activity during cello playing directly overlaps with brain activity during singing in many areas within the auditory-vocal network. These include primary motor, dorsal pre-motor, and supplementary motor cortices, the primary and periprimary auditory cortices within the superior temporal gyrus including Heschls gyrus, anterior insula, anterior cingulate cortex, and intraparietal sulcus, and cerebellum but, notably, exclude the periaqueductal grey and basal ganglia. Second, we found that activity within the overlapping areas is positively correlated with, and therefore likely contributing to, both singing and playing in tune determined with performance measures. Third, we found that activity in auditory areas is functionally connected with activity in dorsal motor and pre-motor areas, and that the connectivity between them is positively correlated with good performance on this task. This functional connectivity suggests that the brain areas are working together to contribute to task performance and not just coincidently active. Last, our findings showed that cello playing may directly co-opt vocal areas (including larynx area of motor cortex), especially if musical training begins before age 7.

neuroscience↗