Biology subjects

Pearce, C.

Publications and source records attributed to Pearce, C..

5 recordsLinked to original sources

bioRxiv2026

TGIF is a golgin-like protein required for Golgi structural maintenance and function in Toxoplasma gondii

The Golgi is an essential organelle that serves as a central hub for endomembrane trafficking. In the protozoan parasite Toxoplasma gondii, a single Golgi stack is essential for parasite survival; however, the molecular determinants governing Golgi structure and function remain poorly understood. Here, we characterize a Golgi-associated protein that is required for Golgi integrity and function, which we named Toxoplasma Golgi Integrity Factor (TGIF). Loss of TGIF disrupts parasite replication and natural egress and is lethal to the parasite. To investigate the impact of TGIF depletion on secretory protein trafficking, we adapted a fluorescence-based pulse-chase assay to monitor the synthesis and trafficking of microneme and rhoptry proteins. We found that loss of TGIF significantly impaired the synthesis and trafficking of microneme and rhoptry neck proteins, whereas trafficking of rhoptry bulb proteins was minimally affected. These findings suggest that rhoptry bulb proteins may traffic independently of canonical Golgi-dependent pathways. Collectively, our study provides new insight into the mechanisms of Golgi-mediated trafficking in T. gondii and identifies TGIF as a critical regulator of parasite secretory pathway organization and function.

cell biology↗

bioRxiv2023

A Modified BPaL Regimen for Tuberculosis Treatment replaces Linezolid with Inhaled Spectinamides

The Nix-TB clinical trial evaluated a new 6-month regimen containing three-oral- drugs; bedaquiline (B), pretomanid (Pa) and linezolid (L) (BPaL regimen) for treatment of tuberculosis (TB). This regimen achieved remarkable results as almost 90% of the multidrug resistant (MDR) or extensively drug resistant (XDR) TB participants were cured but many patients also developed severe adverse events (AEs). The AEs were associated with the long-term administration of the protein synthesis inhibitor linezolid. Spectinamide 1599 is also a protein synthesis inhibitor of Mycobacterium tuberculosis with an excellent safety profile but which lacks oral bioavailability. Here, we propose to replace L in the BPaL regimen with spectinamide (S) administered via inhalation and we demonstrate that inhaled spectinamide 1599, combined with BPa --BPaS regimen--has similar efficacy to that of BPaL regimen while simultaneously avoiding the L-associated AEs. The BPaL and BPaS regimens were compared in the BALB/c and C3HeB/FeJ murine chronic TB efficacy models. After 4-weeks of treatment, both regimens promoted equivalent bactericidal effect in both TB murine models. However, treatment with BPaL resulted in significant weight loss and the complete blood count suggested development of anemia. These effects were not similarly observed in mice treated with BPaS. BPaL and BPa, but no the BPaS treatment, also decreased myeloid to erythroid ratio suggesting the S in the BPaS regimen was able to recover this effect. Moreover, the BPaL also increased concentration of proinflammatory cytokines in bone marrow compared to mice receiving BPaS regimen. During therapy both regimens improved the lung lesion burden, reduced neutrophil and cytotoxic T cells counts while increased the number of B and helper and regulatory T cells. These combined data suggest that inhaled spectinamide 1599 combined with BPa is an effective TB regimen that avoids L-associated AEs. IMPORTANCETuberculosis (TB) is an airborne infectious disease that spreads via aerosols containing Mycobacterium tuberculosis (Mtb), the causative agent of TB. TB can be cured by administration of 3-4 drugs for 6-9 months but there are limited treatment options for patients infected with multidrug (MDR) and extensively resistant (XDR) strains of Mtb. BPaL is a new all-oral combination of drugs consisting of Bedaquiline (B), Pretomanid (Pa) and Linezolid (L). This regimen was able to cure [~]90% of MDR and XDR TB patients in clinical trials but many patients developed severe adverse events (AEs) associated to the long-term administration of linezolid. We evaluated a new regimen in which Linezolid in the BPaL regimen was replaced with inhaled spectinamide 1599. In the current study, we demonstrate that 4-weeks of treatment with inhaled spectinamide 1599 in combination with Bedaquiline and Pretomanid has equivalent efficacy to the BPaL drug combination and avoids the L-associated-AEs.

microbiology↗

bioRxiv2022

Dynamic regulation of inter-organelle communication by ubiquitylation controls skeletal muscle development and disease onset

Ubiquitin-proteasome system (UPS) dysfunction is associated with the pathology of a wide range of human diseases including myopathies and muscular atrophy. However, the mechanistic understanding of specific components on the regulation of protein turnover during development and disease progression in skeletal muscle is unclear. Mutations in KLHL40, an E3 ubiquitin ligase cullin3 (CUL3) substrate-specific adapter protein result in a severe form of congenital nemaline myopathy, but the events that initiate the pathology and the mechanism through which it becomes pervasive, remains poorly understood. To characterize the KLHL40-regulated ubiquitin modified proteome during skeletal muscle development and disease onset, we used global, quantitative mass spectrometry-based ubiquitylome and global proteome analyses of klhl40 mutant zebrafish during disease progression. Global proteomics during skeletal muscle development revealed extensive remodeling of functional modules linked with sarcomere formation, energy and biosynthetic metabolic processes and vesicle trafficking. Combined analysis of klh40 mutant muscle proteome and ubiquitylome identified thin filament proteins, metabolic enzymes and ER-Golgi vesicle trafficking pathway proteins regulated by ubiquitylation during muscle development. Our studies identified a role for KLHL40 as a negative regulator of ER-Golgi anterograde trafficking through ubiquitin-mediated protein degradation of secretion associated Ras related GTPase1a (Sar1a). In KLHL40 deficient muscle, defects in ER exit site vesicle formation alter Golgi compartment and downstream transport of extracellular cargo proteins, resulting in structural and functional abnormalities. Our work reveals that the muscle proteome is dynamically fine-tuned by ubiquitylation to regulate skeletal muscle development and uncovers new disease mechanisms for therapeutic development in patients. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/501000v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1950696org.highwire.dtl.DTLVardef@e37313org.highwire.dtl.DTLVardef@9804a6org.highwire.dtl.DTLVardef@59527f_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2021

MONTE enables serial immunopeptidome, ubiquitylome, proteome, phosphoproteome, acetylome analyses of sample-limited tissues

Serial multiomic analyses of proteome, phosphoproteome and acetylome provides functional insights into disease pathology and drug effects while conserving precious human material. To date, ubiquitylome and HLA peptidome analyses have required separate samples for parallel processing each using distinct protocols. Here we present MONTE, a highly-sensitive multi-omic native tissue enrichment workflow that enables serial, deepscale analysis of HLA-I and HLA-II immunopeptidome, ubiquitylome, proteome, phosphoproteome and acetylome from the same tissue samples. We demonstrate the capabilities of MONTE in a proof-of-concept study of primary patient lung adenocarcinoma(LUAD) tumors. Depth of coverage and quantitative precision at each of the omes is not compromised by serialization, and the addition of HLA immunopeptidomics enables identification of putative immunotherapeutic targets such as cancer/testis antigens and neoantigens. MONTE can provide insights into disease-specific changes in antigen presentation, protein expression, protein degradation, cell signaling, cross-talk and epigenetic pathways involved in disease pathology and treatment.

cancer biology↗

bioRxiv2019

Glacial runoff promotes deep burial of sulfur cycling-associated microorganisms in marine sediments

Marine fjords with active glacier outlets are hot spots for organic matter burial in the sediments and subsequent microbial mineralization, and will be increasingly important as climate warming causes more rapid glacial melt. Here, we investigated controls on microbial community assembly in sub-arctic glacier-influenced (GI) and non-glacier-influenced (NGI) marine sediments in the Godth[a]bsfjord region, south-western Greenland. We used a correlative approach integrating 16S rRNA gene and dissimilatory sulfite reductase (dsrB) amplicon sequence data over six meters of depth with biogeochemistry, sulfur-cycling activities, and sediment ages. GI sediments were characterized by comparably high sedimentation rates and had young sediment ages of <500 years even at 6 m sediment depth. In contrast, NGI stations reached ages of approximately 10,000 years at these depths. Sediment age-depth relationships, sulfate reduction rates, and C/N ratios were strongly correlated with differences in microbial community composition between GI and NGI sediments, indicating that age and diagenetic state were key drivers of microbial community assembly in subsurface sediments. Similar bacterial and archaeal communities were present in the surface sediments of all stations, whereas only in GI sediments were many surface taxa also abundant through the whole sediment core. The relative abundance of these taxa, including diverse Desulfobacteraceae members, correlated positively with sulfate reduction rates, indicating their active contributions to sulfur-cycling processes. In contrast, other surface community members, such as Desulfatiglans, Atribacteria and Chloroflexi, survived the slow sediment burial at NGI stations and dominated in the deepest sediment layers. These taxa are typical for the energy-limited marine deep biosphere and their relative abundances correlated positively with sediment age. In conclusion, our data suggests that high rates of sediment accumulation caused by glacier runoff and associated changes in biogeochemistry, promote persistence of sulfur-cycling activity and burial of a larger fraction of the surface microbial community into the deep subsurface.\n\nContribution to the Field StatementIn most coastal marine sediments organic matter turnover and total energy flux are highest at the surface and decrease significantly with increasing sediment depth, causing depth-dependent changes in the microbial community composition. Glacial runoff in arctic and subarctic fjords alters the composition of the microbial community at the surface, mainly due to different availabilities of organic matter and metals. Here we show that glacial runoff also modifies microbial community assembly with sediment depth. Sediment age was a key driver of microbial community composition in six-meter-long marine sediment cores from the Godth[a]bsfjord region, south-western Greenland. High sedimentation rates at glacier-influenced sediment stations enabled a complex community of sulfur-cycling-associated microorganisms to continuously thrive at high relative abundances from the surface into the sediment subsurface. These communities consisted of putative fermenters, sulfate reducers and sulfur oxidizers, which likely depended on high metal concentrations in the relatively young, glacier-influenced sediments. In non-glacier-influenced sediments with lower sedimentation rates, these sulfur-cycling-associated microorganisms were only present near the surface. With increasing sediment depth these surface microorganisms were largely replaced by other surface microorganisms that positively correlated with sediment age and belong to known taxa of the energy-limited, marine deep biosphere.

microbiology↗