Biology subjects

Moon, K.-M.

Publications and source records attributed to Moon, K.-M..

9 recordsLinked to original sources

bioRxiv2026

Comparative Proteomics Across Tissues and Crop Agroecosystems Reveals Agricultural Stressor Responses in the Western Honey Bee

Maintaining honey bee health in crop production systems is increasingly difficult because worker bees encounter multiple chemical and biological pressures from pesticides and pathogens. How these field-realistic pressures affect molecular physiology across functionally distinct tissues remains poorly understood. Here, we tested whether tissue-resolved proteomics could separate stable tissue-specific patterns from crop-associated molecular changes. To do this, we profiled abdomen, gut, and head proteomes from honey bees collected across four Canadian crop ecosystems over two consecutive years, and integrated these data with pesticide-residue and pathogen-load measurements. Proteomic variation was structured by both tissue identity and crop environment. Tissue-specific proteomic profiles were characterized across samples, whereas crop-associated effects were detected in both years and were stronger in 2021, the second year of the study. Tissue-specific enrichment and network analyses linked the abdomen to lipid catabolism and ubiquitin-proteasome proteostasis, the gut to central carbon metabolism, membrane transport, vesicle trafficking, and cytoskeletal organization, and the head to neurosensory and mitochondrial functions, together with amino-sugar metabolism and vesicle-associated quality-control modules. Among the measured pesticide residues, boscalid was the most reproducible chemical correlate of proteomic variation, with the strongest signal in the gut. Cross-year validation associated boscalid exposure with reduced abundance of gut proteins involved in mitochondrial metabolism, protein quality control, vesicle trafficking, nutrient transport, and biosynthetic pathways. Additionally, integrated proteome-transcriptome-microbiome factor analysis further identified gut-centered components associated with measured stressor variables and linked protein-level variation to coordinated transcriptomic and microbial shifts. Independent-year validation showed that compact crop-associated protein signatures detected in 2020 were also present in 2021. Together, these results show that honey bee tissues maintain stable proteomic identities while showing tissue- and year-specific responses to pesticide and pathogen pressures encountered in crop ecosystems. The gut proteome may specifically provide a sensitive molecular indicator of pesticide-associated perturbation under field conditions.

bioinformatics↗

bioRxiv2024

Proteomic Investigation of Neurotrophic trans-Banglene Reveals Potential Link to Iron Homeostasis

In an effort to gain insight into cellular systems impacted by neurotrophic trans-banglene (t-BG), global proteomic profiling and Western blot analyses were employed. Expression level changes in response to t-BG treatment were compared to those observed with nerve growth factor (NGF), a natural neurotrophic protein and functional analog to t-BG. Findings from these studies did not point to direct interception of NGF/TrkA signaling by t-BG. Instead, significant alterations in iron-binding and iron-regulating proteins were observed. Intracellular iron measurements by FerroOrange indicate lower ferrous (Fe2+) iron levels in t-BG treated cells but not in NGF treated cells. These results highlight a potential connection between iron regulation and neurotrophic activity.

molecular biology↗

bioRxiv2022

Exit of spore dormancy transforms the yeast cytoplasm and the solubility of its proteome

The biophysical properties of the cytoplasm are major determinants of key cellular processes and adaptation. Many yeasts produce dormant spores that can withstand extreme conditions. We show that spores of Saccharomyces cerevisiae exhibit extraordinary biophysical properties, including a highly viscous and acidic cytosol. These conditions alter the solubility of more than 100 proteins such as metabolic enzymes that become more soluble as spores transit to active cell proliferation upon nutrient repletion. A key regulator of this transition is the heat shock protein Hsp42, which shows transient solubilization and phosphorylation, and is essential for the transformation of the cytoplasm during germination. Germinating spores therefore return to growth through the dissolution of protein assemblies, orchestrated in part by Hsp42 activity. The modulation of spores molecular properties are likely key adaptive features of their exceptional survival capacities.

cell biology↗

bioRxiv2022

Multiple viral protein genome-linked proteins compensate viral translation in +ssRNA virus infection

Viral protein genome-linked (VPg) protein plays an essential role in protein-primed replication of plus stranded RNA viruses. VPg is covalently linked to the 5 end of the viral RNA genome via a phosphodiester bond typically at a conserved amino acid. Whereas most viruses have a single VPg, some viruses encode multiple VPgs that are proposed to have redundant yet undefined roles in viral replication. Here, we use the dicistrovirus, cricket paralysis virus (CrPV), which encodes four non-identical copies of VPg, as a model to characterize the role of VPg copies in infection. Dicistroviruses encode two main open reading frames (ORFs) that are driven by distinct IRESs. We systematically generated single and combinatorial deletions and mutations of VPg1-4 within the CrPV infectious clone and monitored viral yield in Drosophila S2 cells. Deletion of one to three VPg copies progressively decreased viral yield and delayed viral replication, suggesting a threshold number of VPgs for productive infection. Mass spectrometry analysis of CrPV VPg-linked RNAs revealed viral RNA linkage to either a serine or threonine in VPg, from which mutations in all VPgs attenuated infection. Mutating serine 4 in a single VPg abolished viral infection, indicating a dominant-negative effect. Using viral minigenome reporters that monitor dicistrovirus 5 untranslated (UTR) and intergenic internal ribosome entry site (IRES) translation revealed a relationship between VPg copy number and the ratio of distinct IRES translation. We uncover a novel viral strategy whereby VPg copies in dicistrovirus genomes compensate for the relative IRES translation efficiencies to promote infection. ImportanceGenetic duplication is exceedingly rare in small RNA viral genomes as there is selective pressure to prevent RNA genomes from expanding. However, some small RNA viruses encode multiple copies of a viral protein, most notably an unusual viral protein that is linked to the viral RNA genome. Here, we investigate a family of viruses that contains multiple viral protein genome-linked proteins and reveal a novel viral strategy whereby viral protein copy number counterbalances differences in viral protein synthesis mechanisms.

microbiology↗

bioRxiv2022

Identification of unusually disulphide-bonded insulin forms using mass spectrometry and thermolysin cleavage

Insulin is an essential hormone made by the pancreatic beta-cells in the islets of Langerhans. Beta-cells produce more insulin protein than virtually all other cellular proteins combined. Dysfunction in the process of insulin synthesis can lead to disease, including rare forms of monogenic diabetes. Specifically, aberrant intra-insulin and inter-insulin disulphide bonds have been implicated in the pathology of type 1 diabetes and type 2 diabetes, respectively. In type 1 diabetes, misprocessed insulin isoforms may be neoepitopes that kick-start and/or exacerbate the auto-immune response. In type 2 diabetes, aberrant disulphides form insulin dimers that can clog the endoplasmic reticulum and contribute to beta cell dysfunction. To facilitate the study of novel and known insulin neoepitopes and dimers, we present an unbiased and rapid technique for identifying insulin disulphide patterns from pancreatic islet extracts. The basis of this method is the cleavage between insulins cysteine residues with the metalloprotease, thermolysin, and subsequent identification of cysteine containing fragments and their partner peptides by LC-MS/MS. Using this technique, we identify 6 aberrant disulphide bonded insulin species, including a previously described type 1 diabetes neoepitope, as well as inter-chain disulphide bonded insulin dimers. Furthermore, using the endoplasmic stress inducer, thapsigargin, we observe increased disulphide errors in a patient donor sample. This approach lays foundations to identify the scope and cause of aberrant insulin disulphide formation in health and disease.

molecular biology↗

bioRxiv2020

Proteomic analysis of metabolic pathways shows chloroplast-mitochondria cross-talk in a Cu-limited diatom

Diatoms are one of the most successful phytoplankton groups in our oceans, being responsible for over 20% of the Earths photosynthetic productivity. Their chimeric genomes have genes derived from red algae, green algae, bacteria and heterotrophs, resulting in multiple isoenzymes targeted to different cellular compartments with the potential for differential regulation under nutrient limitation. The resulting interactions between metabolic pathways are not yet fully understood. We previously showed how acclimation to Cu limitation enhanced susceptibility to overreduction of the photosynthetic electron transport chain and its reorganization to favor photoprotection over light-harvesting in the oceanic diatom Thalassiosira oceanica (Hippmann et al., 2017). In order to gain a better understanding of the overall metabolic changes that help alleviate the stress of Cu limitation, we have further analyzed the comprehensive proteomic datasets generated in that study to identify differentially expressed proteins involved in carbon, nitrogen and oxidative stress-related metabolic pathways. Metabolic pathway analysis showed integrated responses to Cu limitation. The up-regulation of ferredoxin (Fdx) was correlated with up-regulation of plastidial Fdx-dependent isoenzymes involved in nitrogen assimilation as well as enzymes involved in glutathione synthesis, thus integrating nitrogen uptake and metabolism with photosynthesis and oxidative stress resistance. The differential expression of glycolytic isoenzymes located in the chloroplast and mitochondria may enable them to channel both excess electrons and/or ATP between these compartments. Additional evidence for chloroplast-mitochondrial cross-talk is the increased expression of chloroplast and mitochondrial proteins involved in the proposed malate shunt under Cu limitation. One sentence summaryDiatoms adapt to Cu limitation by regulating their large repertoire of isoenzymes to channel electrons away from the chloroplast, enhance nitrogen uptake, and integrate the oxidative stress response. 123

microbiology↗

bioRxiv2020

Frequent assembly of chimeric complexes in the protein interaction network of an interspecies hybrid

Hybrids between species often show extreme phenotypes, including some that take place at the molecular level. In this study, we investigated the phenotypes of an interspecies diploid hybrid in terms of protein-protein interactions inferred from protein correlation profiling. We used two yeast species, Saccharomyces cerevisiae and Saccharomyces uvarum, which are interfertile, but yet have proteins diverged enough to be differentiated using mass spectrometry. Most of the protein-protein interactions are similar between hybrid and parents, and are consistent with the assembly of chimeric complexes, which we validated using an orthogonal approach for prefoldin complex. We also identify instances of altered protein-protein interactions in the hybrid, for instance in complexes related to proteostasis and in mitochondrial protein complexes. Overall, this study uncovers likely frequent occurrence of chimeric protein complexes with few exceptions, which may result from incompatibilities or imbalances between the parental proteins.

evolutionary biology↗

bioRxiv2020

The parasite Schistocephalus solidus secretes proteins with putative host manipulation functions

BackgroundManipulative parasites are thought to liberate molecules in their external environment acting as manipulation factors with biological functions implicated in their hosts physiological and behavioural alterations. These manipulation factors are part of a complex mixture called the secretome. While the secretomes of various parasites have been described, there is very little data for a putative manipulative parasite. It is necessary to study the molecular interaction between a manipulative parasite and its host to better understand how such alterations evolve. MethodsHere, we used proteomics to characterize the secretome of a model cestode with a complex life cycle based on trophic transmission. We studied Schistocephalus solidus during the life stage in which behavioural changes take place in its obligatory intermediate fish host, the threespine stickleback (Gasterosteus aculeatus). We produced a novel genome sequence and assembly of S. solidus to improve protein coding gene prediction and annotation for this parasite. We then described the whole worms proteome and its secretome during fish host infection using LC-MS/MS. ResultsA total of 2 290 proteins were detected in the proteome of S. solidus, and 30 additional proteins were detected specifically in the secretome. We found that the secretome contains proteases, proteins with neural and immune functions, as well as proteins involved in cell communication. We detected Receptor-type tyrosine-protein phosphatases, which were reported in other parasitic systems to be manipulation factors. We also detected 12 S. solidus-specific proteins in the secretome that may play important roles in host-parasite interactions. ConclusionsOur results suggest that S. solidus liberates molecules with putative host manipulation functions in the host and that many of them are species specific.

genomics↗

bioRxiv2018

IRES-mediated ribosome repositioning directs translation of a +1 overlapping ORF that enhances viral pathogenicity

RNA structures can interact with the ribosome to alter translational reading frame maintenance and promote recoding that result in alternative protein products. Here, we show that the internal ribosome entry site (IRES) from the dicistrovirus Cricket paralysis virus drives translation of the 0-frame viral polyprotein and an overlapping +1 open reading frame, called ORFx, via a novel mechanism whereby a subset of ribosomes recruited to the IRES bypasses downstream to resume translation at the +1-frame 13th non-AUG codon. A mutant of CrPV containing a stop codon in the +1 frame ORFx sequence, yet synonymous in the 0-frame, is attenuated compared to wild-type virus in a Drosophila infection model, indicating the importance of +1 ORFx expression in promoting viral pathogenesis. This work demonstrates a novel programmed IRES-mediated recoding strategy to increase viral coding capacity and impact virus infection, highlighting the diversity of RNA-driven translation initiation mechanisms in eukaryotes.

biochemistry↗