Biology subjects

Godin, A.

Publications and source records attributed to Godin, A..

3 recordsLinked to original sources

bioRxiv2026

Structural basis for the ATP-dependence of omegasome biogenesis by DFCP1

Autophagosome formation begins at phosphatidylinositol 3-phosphate-enriched endoplasmic reticulum (ER) subdomains termed omegasomes. DFCP1/ZFYVE1 is recruited to omegasomes through its FYVE domains and has recently been shown to function as an ATPase involved in omegasome constriction and autophagosome biogenesis. However, the structural basis of DFCP1 ATPase activity and how nucleotide-dependent conformational states regulate omegasome dynamics remain unknown. Here, we determined the crystal structures of the DFCP1 ATPase domain in complex with either ADP or the non-hydrolyzable ATP analogue, AppNHp at near atomic resolution. We employed structure-guided mutagenesis to define residues required for DFCP1 function in cells. The structures reveal that the active site contains a trans-acting Arg271 finger coordinating the {psi}-phosphate and trans-acting His323 that stacks on the ATP adenine ring. ATP hydrolysis results in a conformational switch in the vicinity of Arg271, while contacts with His323 persist in the presence of ADP. Biochemical analyses of DFCP1 and its mutants show that DFCP1 forms ATP-dependent microdomains on membranes. Disruption of His323 and Arg271 uncouples nucleotide binding from ATP hydrolysis and alters the oligomeric state of the protein. Live-cell imaging of DFCP1 knockout cells reconstituted with wild-type or mutant DFCP1 further demonstrates that these biochemical defects translate into distinct omegasome phenotypes. Together, our data provides a structural-function framework for DFCP1 ATPase activity and reveals how distinct catalytic elements control omegasome dynamics in vivo. We propose that nucleotide-dependent assembly and hydrolysis-driven conformational changes enable DFCP1 to regulate omegasome formation and its progression toward autophagosome closure. Significance StatementDFCP1 organizes the ER subdomains known as omegasomes, which are sites of autophagosome biogenesis. DFCP1 is an ATPase whose catalytic activity is required for function, but the precise role of its ATPase activity is unknown. Crystal structures of the DFCP1 ATPase domain in the presence of a non-hydrolyzable ATP analogue and ADP reveal an Arg finger that operates in trans, such that dimerization is required for ATP hydrolysis, and ATP hydrolysis destabilizes dimers. Dimerization is also promoted by an adenine base-stacking interaction in trans with H323. These residues are important for DFCP1 clustering on membranes and omegasome constriction, clarifying that the role of ATP is to promote the dimerization of the ATPase domain and thereby control the organization of DFCP1 on membranes.

biochemistry↗

bioRxiv2025

Thermal and mechanical modalities converge in the noxious range

SummaryThere are competing theories on how nociceptive input is encoded by sensory fibers. That sensory modalities are exclusively conveyed by distinct populations of fibers is supported by ablation studies, indicating that TRPV1+and MrgprD+afferents selectively encode for heat and mechanical input, respectively. However, interpreting ablation results can be clouded by compensatory plasticity. Furthermore, a population-level parametric analysis of afferent response profiles to natural stimuliin vivois still scarce. Using functional imagingin vivoin mice, we found that most TRPV1+neurons responded to noxious heat, but not cooling. While none of them responded to innocuous mechanical input, about half were also sensitive to noxious mechanical stimuli. In contrast, 80% of MrgprD+neurons responded to noxious mechanical stimuli. Yet, 70% were also sensitive to noxious thermal stimuli. Of innocuous mechanosensitive MrgprD+neurons, <15% responded to innocuous warming and none to innocuous cooling. Polymodality in the innocuous thermal and mechanical range also occurred in <10% of all primary afferents. Acute silencing of TRPV1+or MrgprD+afferents inhibited both thermal and mechanical nociception. In contrast, ablation did not reproduce a combined loss of sensitivity, which appeared to be due to compensatory central disinhibition. Our findings reveal that modality separation dominates in the innocuous regime, while polymodality predominates in the noxious range.

neuroscience↗

bioRxiv2019

National HIV testing and diagnosis coverage in sub-Saharan Africa: a new modeling tool for estimating the \"first 90\" from program and survey data

AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSObjectiveC_ST_ABSHIV testing services (HTS) are a crucial component of national HIV responses. Learning ones HIV diagnosis is the entry point to accessing life-saving antiretroviral treatment and care. Recognizing the critical role of HTS, the Joint United Nations Programme on HIV/AIDS (UNAIDS) launched the 90-90-90 targets stipulating that by 2020, 90% of people living with HIV know their status, 90% of those who know their status receive antiretroviral therapy, and 90% of those on treatment have a suppressed viral load. Countries will need to regularly monitor progress on these three indicators. Estimating the proportion of people living with HIV who know their status (i.e., the "first 90"), however, is difficult. MethodsWe developed a mathematical model (henceforth referred to as "F90") that formally synthesizes population-based survey and HTS program data to estimate HIV status awareness over time. The proposed model uses country-specific HIV epidemic parameters from the standard UNAIDS Spectrum model to produce outputs that are consistent with other national HIV estimates. The F90 model provides estimates of HIV testing history, diagnosis rates, and knowledge of HIV status by age and sex. We validate the F90 model using both in-sample comparisons and out-of-sample predictions using data from three countries: Cote dIvoire, Malawi, and Mozambique. ResultsIn-sample comparisons suggest that the F90 model can accurately reproduce longitudinal sex-specific trends in HIV testing. Out-of-sample predictions of the fraction of PLHIV ever tested over a 4-to-6-year time horizon are also in good agreement with empirical survey estimates. Importantly, out-of-sample predictions of HIV knowledge are consistent (i.e., within 4% points) with those of the fully calibrated model in the three countries, when HTS program data are included. The F90 models predictions of knowledge of status are higher than available self-reported HIV awareness estimates, however, suggesting -in line with previous studies- that these self-reports are affected by non-disclosure of HIV status awareness. ConclusionKnowledge of HIV status is a key indicator to monitor progress, identify bottlenecks, and target HIV responses. The F90 model can help countries track progress towards their "first 90" by leveraging surveys of HIV testing behaviors and annual HTS program data.

epidemiology↗