Biology subjects

Germain, M.

Publications and source records attributed to Germain, M..

14 recordsLinked to original sources

bioRxiv2025

Mitochondrial pull-out controls mitochondrial structure in response to mitochondrial activity

Mitochondrial networks undergo continuous remodeling through fusion and fission, processes that are essential for maintaining energy production and cellular homeostasis. Rapid elongation of the tip of mitochondrial tubules, a process termed dynamic tubulation, also participates in mitochondrial network formation. However, these mechanisms alone cannot fully account for the formation of highly interconnected mitochondrial networks that are required for rapid distribution of mitochondria material. Here, we identify a distinct type of dynamic tubulation, mitochondrial pull-outs characterized by the lateral extrusion from pre-existing mitochondrial tubules, as metabolically regulated determinants of mitochondrial network formation. Pull-outs are distinct from the tip elongation form of dynamic tubulation as they are modulated by the mitochondrial dynamins MFN1 and DRP1 and are stimulated by conditions favoring oxidative phosphorylation. Pull-outs also depend on mitochondrial actin polymerization and are required to increase mitochondrial connectivity and respiratory activity. Together, these findings establish mitochondrial pull-out as a metabolically sensitive mechanism that promotes mitochondrial network connectivity and links organelle architecture to cellular energy demands.

cell biology↗

bioRxiv2024

sRNA-mediated crosstalk between cell wall stress and galactose metabolism in Staphylococcus aureus

Staphylococcus aureus is an opportunistic pathogen responsible for a wide range of diseases in humans. During infections, this bacterium is exposed to various stresses that target its cell wall, such as oxidative or acid environments as well as various cell wall-acting antimicrobials. S. aureus has effective regulatory systems for responding to environmental stresses enabling the expression of factors necessary for its survival. Bacterial small RNAs (sRNAs) play a crucial role in this adaptation process. In this study, we show that RsaOI, an S. aureus sRNA, accumulates under acid stress conditions. This response is mediated via the two-component system VraSR, which is associated with the cell wall damage response. As a component of the VraSR regulon, RsaOI contributes to the survival of S. aureus under acid stress and affects its susceptibility to glycopeptide antibiotics. Our findings reveal that RsaOI targets lacABCDFEG operon, which encodes components of tagatose pathway, a unique mechanism responsible for galactose metabolism in S. aureus. By antisense base pairing near the ribosome-binding site of lacD, RsaOI inhibits the expression of this gene, encoding tagatose-6-phosphate aldolase. This regulation disrupts the tagatose pathway, impairing galactose utilization in S. aureus. These findings highlight the role of RsaOI in the mediation between cell wall stress responses and specific metabolic pathway.

microbiology↗

bioRxiv2024

TBC1D24 regulates mitochondria and endoplasmic reticulum-mitochondria contact sites

The RabGAP protein TBC1D24 is mutated in several neurological disorders including DOORS syndrome (Deafness, Onycho-Osteodystrophy, Mental Retardation, Seizures). Although TBC1D24 comprises two highly conserved domains -- the Tre2/Bub2/Cdc16 (TBC) domain and the TLDc domain -- both of which seem to play critical roles in cellular functions, its exact physiological function within the cell remains poorly understood. Here, we show that TBC1D24 affects mitochondrial structure and activity. Specifically, both primary fibroblasts from patients with TBC1D24 mutations and cells in which TBC1D24 has been knocked down exhibit fragmented mitochondria, decreased ATP production, and reduced mitochondrial membrane potential. Importantly, loss or mutation of TBC1D24 also alters sites of contact between the endoplasmic reticulum (ER) and mitochondria (ERMCS). These sites are vital for mitochondrial fusion and fission processes, which regulate mitochondrial dynamics and, consequently, mitochondrial activity. Altogether, our results uncover a new role for TBC1D24 in the regulation of mitochondrial functions and ERMCS which likely contribute to the neurological dysfunction present in affected patients.

cell biology↗

bioRxiv2024

Mitochondrial Dysfunction alters Early Endosome Distribution and Cargo Trafficking via ROS-Mediated Microtubule Reorganization

Mitochondria are essential for bioenergetic functions and various cellular processes, including differentiation and immunity, their dysfunction leading to several pathologies. While these pathologies have traditionally been associated with ATP deficits, mitochondrial dysfunction also leads to reactive oxygen species (ROS) generation, inflammation, and alterations the function of other organelles. While the negative impact of mitochondrial dysfunction on lysosomal activity has been established, the relationship between mitochondria and the rest of the endocytic compartment remains poorly understood. Here, we show that inhibiting mitochondrial activity through genetic and chemical approaches causes early endosome (EE) perinuclear aggregation and impairs cargo delivery to lysosomes. This impairment is due to altered microtubule architecture and centrosome dynamics, mediated by ROS. Antioxidants can rescue these EE defects, underlying the pivotal role of mitochondria in maintaining cellular activities through ROS regulation of microtubule networks. Our findings highlight the significance of mitochondria beyond ATP production, emphasizing their critical involvement in endocytic trafficking and cellular homeostasis. These insights emphasize mitochondrias critical involvement in cellular activities and suggest novel targets for therapies to mitigate the effects of mitochondrial dysfunction.

cell biology↗

bioRxiv2024

Early Detection of an Invasive Alien Plant (Phragmites australis) Using Unoccupied Aerial Vehicles and Artificial Intelligence

The combination of unoccupied aerial vehicles (UAVs) and artificial intelligence to map vegetation represents a promising new approach to improve the detection of invasive alien plant species (IAPS). The high spatial resolution achievable with UAVs and recent innovations in computer vision, especially with convolutional neural networks, suggest that early detection of IAPS could be possible, thus facilitating their management. In this study, we evaluated the suitability of this approach for mapping the location of common reed (Phragmites australis subsp. australis) within a national park located in southern Quebec, Canada. We collected data on six distinct dates during the growing season, covering environments with different levels of reed invasion. Overall, model performance was high for the different dates and zones, especially for recall (mean of 0.89). The results showed an increase in performance, reaching a peak following the appearance of the inflorescence in September (highest F1-score at 0.98). Furthermore, a decrease in spatial resolution negatively affected recall (18% decrease between a spatial resolution of 0.15 cm pixel-1 and 1.50 cm pixel-1) but did not have a strong impact on precision (2% decrease). Despite challenges associated with common reed mapping in a post-treatment monitoring context, the use of UAVs and deep learning shows great potential for IAPS detection when supported by a suitable dataset. Our results show that, from an operational point of view, this approach could be an effective tool for speeding up the work of biologists in the field and ensuring better management of IAPS.

ecology↗

bioRxiv2024

A genome wide search for non-additive allele effects identifies PSKH2 as involved in the variability of Factor V activity.

BackgroundFactor V (FV) is a key molecular player in the coagulation cascade. FV plasma levels have been associated with several human diseases, including thrombosis, bleeding and diabetic complications. So far, two genes have been robustly found through genome wide association analyses to contribute in the inter-individual variability of plasma FV levels: structural F5 gene and PLXDC2. MethodsWe used the underestimated Brown-Forsythe methodology implemented in the Quicktest software to search for non-additive genetic effects that could contribute to the inter-individual variability of FV plasma activity. QUICKTEST was applied to 4 independent GWAS studies (LURIC, MARTHA, MEGA and RETROVE) totaling 4,505 participants of European ancestry with measured FV plasma levels. Results obtained in the 4 cohorts were meta-analyzed using a fixed-effect model. Additional analyses involved exploring haplotype and genexgene interactions in downstream investigations. ResultsWe observed a genome-wide significant signal at PSKH2 locus, on chr8q21.3 with lead variant rs75463553 with no evidence for heterogeneity across cohorts (p = 0.518). Although rs75463553 did not show association with mean FV levels (p = 0.49), it demonstrated a robust significant (p = 8.4 10-9) association with the variance of FV plasma levels. Further analyses confirmed the reported association of PSKH2 with neutrophil biology and revealed that rs75463553 likely interact with two loci, GRIN2A and POM121L12, known for their involvement in smoking biology. ConclusionsThis comprehensive approach identifies the role of PSKH2 as a novel molecular player in the genetic regulation of FV, shedding light on the contribution of neutrophils to FV biology.

genetics↗

bioRxiv2024

Extracellular matrix signals promotes actin-dependent mitochondrial elongation and activity

Mitochondria are crucial metabolic organelles that are regulated by both intracellular and extracellular cues. The extracellular matrix (ECM) is a key component of the cellular environment that controls cellular behavior and metabolic activity. Here, we determined how ECM signalling regulates mitochondrial structure and activity. To distinguish mitochondrial regulation from the general survival cues generated by the ECM, we used breast cancer-derived spheres (mammospheres) because of their ability to grow in suspension culture in the absence of ECM. Using this system, we demonstrate that the association of mammospheres with the ECM results in dramatic mitochondrial elongation, along with enhanced mitochondrial respiration and ATP production. This remodeling occurs independently of DRP1 activity, but relies on integrin signaling and actin polymerization. Therefore, our findings demonstrate that ECM-driven actin polymerization plays a crucial role in remodeling mitochondrial networks to promote OXPHOS, which represents a vital step for migrating cells to enhance cellular adhesion and facilitate cell growth.

cell biology↗

bioRxiv2023

Influence of Temperate Forest Autumn Leaf Phenology on Segmentation of Tree Species from UAV Imagery Using Deep Learning

Remote sensing of forests has become increasingly accessible with the use of unoccupied aerial vehicles (UAV), along with deep learning, allowing for repeated high-resolution imagery and the capturing of phenological changes at larger spatial and temporal scales. In temperate forests during autumn, leaf senescence occurs when leaves change colour and drop. However, the influence of leaf senescence in temperate forests on tree species segmentation using a Convolutional Neural Network (CNN) has not yet been evaluated. Here, we acquired high-resolution UAV imagery over a temperate forest in Quebec, Canada on seven occasions between May and October 2021. We segmented and labelled 23,000 tree crowns from 14 different classes to train and validate a CNN for each imagery acquisition. The CNN-based segmentation showed the highest F1-score (0.72) at the start of leaf colouring in early September and the lowest F1-score (0.61) at peak fall colouring in early October. The timing of the events occurring during senescence, such as leaf colouring and leaf fall, varied substantially between and within species and according to environmental conditions, leading to higher variability in the remotely sensed signal. Deciduous and evergreen tree species that presented distinctive and less temporally-variable traits between individuals were better classified. While tree segmentation in a heterogenous forest remains challenging, UAV imagery and deep learning show high potential in mapping tree species. Our results from a temperate forest with strong leaf colour changes during autumn senescence show that the best performance for tree species segmentation occurs at the onset of this colour change.

ecology↗

bioRxiv2023

Mitochondria- and ER-associated actin are required for mitochondrial fusion

Mitochondria play a crucial role in the regulation of cellular metabolism and signalling. Mitochondrial activity is modulated by the processes of mitochondrial fission and fusion, which are required to properly balance respiratory and metabolic functions, transfer material between mitochondria, and remove defective mitochondria. Mitochondrial fission occurs at sites of contact between the endoplasmic reticulum (ER) and mitochondria, and is dependent on the formation of actin filaments that drive mitochondrial constriction and the recruitment and activation of the dynamin-related GTPase fission protein DRP1. The requirement for mitochondria- and ER-associated actin filaments in mitochondrial fission remains unclear, and the role of actin in mitochondrial fusion remains entirely unexplored. Here we show that preventing the formation of actin filaments on either mitochondria or the ER disrupts both mitochondrial fission and fusion. We show that fusion but not fission is dependent on Arp2/3, whereas both fission and fusion are dependent on INF2 formin-dependent actin polymerization. We also show that mitochondria-associated actin marks fusion sites prior to the dynamin family GTPase fusion protein MFN2. Together, our work introduces a novel method for perturbing organelle-associated actin filaments, and demonstrates a previously unknown role for actin in mitochondrial fusion.

cell biology↗

bioRxiv2021

DRP1 regulates endoplasmic reticulum sheets to control mitochondrial DNA replication and segregation

Mitochondria are multi-faceted organelles crucial for cellular homeostasis that contain their own genome. Mitochondrial DNA (mtDNA) replication is a spatially regulated process essential for the maintenance of mitochondrial function, its defect causing mitochondrial diseases. mtDNA replication occurs at endoplasmic reticulum (ER)-mitochondria contact sites and is affected by mitochondrial dynamics: the absence of mitochondrial fusion is associated with mtDNA depletion whereas loss of mitochondrial fission causes the aggregation of mtDNA within abnormal structures termed mitobulbs. Here, we show that contact sites between mitochondria and ER sheets, the ER structure associated with protein synthesis, regulate mtDNA replication and distribution within mitochondrial networks. DRP1 loss or mutation leads to modified ER sheets and alters the interaction between ER sheets and mitochondria, disrupting RRBP1-SYNJ2BP interaction. Importantly, mtDNA distribution and replication were rescued by promoting ER sheets-mitochondria contact sites. Our work identifies the role of ER sheet-mitochondria contact sites in regulating mtDNA replication and distribution.

cell biology↗

bioRxiv2021

Mitochondrial fission is required for proper nucleoid distribution within mitochondrial networks

Mitochondrial DNA (mtDNA) maintenance is essential to sustain a functionally healthy population of mitochondria within cells. Proper mtDNA replication and distribution within mitochondrial networks are essential to maintain mitochondrial homeostasis. However, the fundamental basis of mtDNA segregation and distribution within mitochondrial networks is still unclear. To address these questions, we developed an algorithm, Mitomate tracker to unravel the global distribution of nucleoids within mitochondria. Using this tool, we decipher the semi-regular spacing of nucleoids across mitochondrial networks. Furthermore, we show that mitochondrial fission actively regulates mtDNA distribution by controlling the distribution of nucleoids within mitochondrial networks. Specifically, we found that primary cells bearing disease-associated mutations in the fission proteins DRP1 and MYH14 show altered nucleoid distribution, and acute enrichment of enlarged nucleoids near the nucleus. Further analysis suggests that the altered nucleoid distribution observed in the fission mutants is the result of both changes in network structure and nucleoid density. Thus, our study provides novel insights into the role of mitochondria fission in nucleoid distribution and the understanding of diseases caused by fission defects. Significance statementMutation or deletion of mitochondrial DNA (mtDNA) is associated with a large number of human diseases. However, the mechanisms controlling mtDNA replication and segregation are still poorly understood. Here, we have developed a new computational method to quantify the distribution of nucleoids (mtDNA with associated proteins) and define how nucleoid distribution is affected by changes in mitochondrial network structure. We demonstrate that mitochondrial fission is required for the proper distribution of nucleoids across mitochondrial networks, cells from patients with fission defects showing irregular nucleoid distribution and perinuclear accumulation. Nonetheless, each fission mutant behaved in a distinct manner, indicating a complex relationship between mitochondrial dynamics and nucleoid distribution.

cell biology↗

bioRxiv2020

Mitochondria-Derived Vesicles prevent inflammation by controlling the inclusion of mitochondrial proteins into extracellular vesicles

Most cells constitutively secrete mitochondrial DNA and proteins in extracellular vesicles (EVs), small vesicles that allow the transfer of material between cells. While under pro-inflammatory conditions, this mitochondrial content can further enhance inflammation, its role in the absence of inflammation remains elusive. Here, we demonstrate that cells actively prevent the packaging of pro-inflammatory, oxidized mitochondrial proteins into EVs. Importantly, the distinction between material to be included into EVs and damaged mitochondrial content to be excluded was dependent on their selective targeting to one of two distinct Mitochondria-Derived Vesicles (MDVs) pathways, MDVs being small vesicles carrying material between mitochondria and other organelles. Sorting nexin 9 (Snx9)-dependent MDVs were required to target mitochondrial proteins into EVs, while the Parkinsons disease related protein Parkin blocked this process by targeting damaged mitochondrial content to lysosomes. Our results thus provide important insight into the interplay between mitochondrial quality control mechanisms and mitochondria driven immune responses.

cell biology↗

bioRxiv2018

OPTIMIR, a novel algorithm for integrating available genome-wide genotype data into miRNA sequence alignment analysis.

Next-generation sequencing is an increasingly popular and efficient approach to characterize the full set of microRNAs (miRNAs) present in human biosamples. MiRNAs detection and quantification still remain a challenge as they can undergo different post transcriptional modifications and might harbor genetic variations (polymiRs) that may impact on the alignment step. We present a novel algorithm, OPTIMIR, that incorporates biological knowledge on miRNA editing and genome-wide genotype data available in the processed samples to improve alignment accuracy. OPTIMIR was applied to 391 human plasma samples that had been typed with genome-wide genotyping arrays. OPTIMIR was able to detect genotyping errors, suggested the existence of novel miRNAs and highlighted the allelic imbalance expression of polymiRs in heterozygous carriers. OPTIMIR is written in python, and freely available on the GENMED website (http://www.genmed.fr/index.php/fr/) and on Github (github.com/FlorianThibord/OptimiR).

bioinformatics↗

bioRxiv2018

Genetic determinants of risk and survival in pulmonary arterial hypertension

BackgroundPulmonary arterial hypertension (PAH) is a rare disorder leading to premature death. Rare genetic variants contribute to disease etiology but the contribution of common genetic variation to disease risk and outcome remains poorly characterized.\n\nMethodsWe performed two separate genome-wide association studies of PAH using data across 11,744 European-ancestry individuals (including 2,085 patients), one with genotypes from 5,895 whole genome sequences and another with genotyping array data from 5,849 further samples. Cross-validation of loci reaching genome-wide significance was sought by meta-analysis. We functionally annotated associated variants and tested associations with duration of survival.\n\nFindingsA locus at HLA-DPA1/DPB1 within the class II major histocompatibility (MHC) region and a second near SOX17 were significantly associated with PAH. The SOX17 locus contained two independent signals associated with PAH. Functional and epigenomic data indicate that the risk variants near SOX17 alter gene regulation via an enhancer active in endothelial cells. PAH risk variants determined haplotype-specific enhancer activity and CRISPR-inhibition of the enhancer reduced SOX17 expression. Analysis of median survival showed that PAH patients with two copies of the HLA-DPA1/DPB1 risk variant had a two-fold difference (>16 years versus 8 years), compared to patients homozygous for the alternative allele.\n\nInterpretationWe have found that common genetic variation at loci in HLA-DPA1/DPB1 and an enhancer near SOX17 are associated with PAH. Impairment of Sox17 function may be more common in PAH than suggested by rare mutations in SOX17. Allelic variation at HLA-DPB1 stratifies PAH patients for survival following diagnosis, with implications for future therapeutic trial design.\n\nFundingUK NIHR, BHF, UK MRC, Dinosaur Trust, NIH/NHLBI, ERS, EMBO, Wellcome Trust, EU, AHA, ACClinPharm, Netherlands CVRI, Dutch Heart Foundation, Dutch Federation of UMC, Netherlands OHRD and RNAS, German DFG, German BMBF, APH Paris, Inserm, Universite Paris-Sud, and French ANR.

genetics↗