Biology subjects

Foster, L. J.

Publications and source records attributed to Foster, L. J..

9 recordsLinked to original sources

bioRxiv2018

An atlas of protein-protein interactions across mammalian tissues

Cellular processes arise from the dynamic organization of proteins in networks of physical interactions. Mapping the complete network of biologically relevant protein-protein interactions, the interactome, has therefore been a central objective of high-throughput biology. Yet, because widely used methods for high-throughput interaction discovery rely on heterologous expression or genetically manipulated cell lines, the dynamics of protein interactions across physiological contexts are poorly understood. Here, we use a quantitative proteomic approach combining protein correlation profiling with stable isotope labelling of mammals (PCP SILAM) to map the interactomes of seven mouse tissues. The resulting maps provide the first proteome-scale survey of interactome dynamics across mammalian tissues, revealing over 27,000 unique interactions with an accuracy comparable to the highest-quality human screens. We identify systematic suppression of cross-talk between the evolutionarily ancient housekeeping interactome and younger, tissue-specific modules. Rewiring of protein interactions across tissues is widespread, and is poorly predicted by gene expression or coexpression. Rewired proteins are tightly regulated by multiple cellular mechanisms and implicated in disease. Our study opens up new avenues to uncover regulatory mechanisms that shape in vivo interactome responses to physiological and pathophysiological stimuli in mammalian systems.

systems biology↗

bioRxiv2018

Conditional interactions in literature-curated protein interaction databases

Databases of literature-curated protein-protein interactions (PPIs) are often used to interpret high-throughput interactome mapping studies and estimate error rates. These databases combine interactions across thousands of published studies and experimental techniques. Because the tendency for two proteins to interact depends on the local conditions, this heterogeneity of conditions means that only a subset of database PPIs are interacting during any given experiment. A typical use of these databases as gold standards in interactome mapping projects, however, assumes that PPIs included in the database are indeed interacting under the experimental conditions of the study. Using raw data from 20 co-fractionation experiments and six published interactomes, we demonstrate that this assumption is often false, with up to 55% of purported gold standard interactions showing no evidence of interaction, on average. We identify a subset of CORUM database complexes that do show consistent evidence of interaction in co-fractionation studies, and we use this subset as gold standards to dramatically improve interactome mapping as judged by the number of predicted interactions at a given error rate. We recommend using this CORUM subset as the gold standard set in future co-fractionation studies. More generally, we recommend using the subset of literature-curated PPIs that are specific to experimental conditions whenever possible.

bioinformatics↗

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↗

bioRxiv2018

Proteomic analysis of chemosensory organs in the honey bee parasite Varroa destructor: a comprehensive examination of the potential carriers for semiochemicals

The mite Varroa destructor is the major parasite of the honey bee and is responsible for great economical losses. The biochemical tools used by Varroa to detect semiochemicals produced by the host are still largely unknown. We have performed proteomic analysis on chemosensory organs of this species in order to identify putative soluble carriers for pheromones and other olfactory cues emitted by the host. In particular, we have analysed forelegs, mouthparts (palps, chelicera and hypostome) and the second pair of legs (as control tissue) in reproductive and phoretic stages of the Varroa life cycle. We identified 958 Varroa proteins, most of them common to organs and stages. Sequence analysis shows that four proteins can be assigned to the odorant-binding protein (OBP)-like class, which bear some similarity to insect OBPs, but so far are only reported in some Chelicerata. In addition, we have detected the presence of two proteins belonging to the Niemann-Pick family, type C2 (NPC2), which have been suggested to act as semiochemical carriers. This work contributes to elucidating the chemical communication systems in Varroa with the aim of understanding how detection of semiochemicals has evolved in terrestrial non-hexapod Arthropoda. Data are available via ProteomeXchange with identifier PXD008679.

zoology↗

bioRxiv2017

Results of follow-up experiments to "Odorant cues linked to social immunity induce lateralized antennal stimulation in honey bees (Apis mellifera L.)"

In 2017, we published the paper \"Odorant cues linked to social immunity induce lateralized antennal stimulation in honey bees (Apis mellifera L.)\" in Scientific Reports. Since then, we have performed three follow-up experiments which have either negative or contradictory results. Previously, we used electrophysiology to show that hygienic bees displayed significantly higher sensitivity to {beta}-ocimene when stimulated via their left antennae compared to their right. We repeated this assay using worker honey bees from a single hygienic colony and found, to our surprise, that the right antennae elicited higher sensitivity. We also previously attempted to identify a molecular basis for lateralization by using mass spectrometry-based proteomics to compare left and right antennal proteomes. Of the 1,845 proteins, none were differentially expressed. Here, we repeated this experiment but employed orthogonal peptide fractionation to increase proteome coverage to 3,114 proteins; however, still none were differentially expressed. Finally, we attempted to manipulate gene expression of a key antennal odorant binding protein linked to hygienic behaviour (OBP18) using RNA interference via antenna microinjection. We were not able to achieve long-lasting OBP18 knock-down, but comparing the proteomes of untreated, mock dsRNA-treated and OBP18 dsRNA-treated worker antennae revealed numerous off-target effects of the act of injecting alone. By openly reporting this data, we hope to set an example for information transparency.

molecular biology↗

bioRxiv2017

Death pheromones triggering hygienic behavior in honey bees (Apis mellifera L.)

Eusocial insects live in teeming societies with thousands of their kin. In this crowded environment, workers combat disease by removing or burying their dead or diseased nestmates. For honey bees, we found that hygienic brood-removal behavior is triggered by two odorants - {beta}-ocimene and oleic acid - which are released from brood upon freeze-killing. {beta}-ocimene is a co-opted pheromone that normally signals larval food-begging, whereas oleic acid is a conserved necromone across arthropod taxa. Interestingly, the odorant blend can induce hygienic behavior more consistently than either odorant alone. We suggest that the volatile {beta}-ocimene flags hygienic workers attention, while oleic acid is the death cue, triggering removal. Bees with high hygienicity detect and remove brood with these odorants faster than bees with low hygienicity, and both molecules are strong ligands for hygienic behavior-associated odorant binding proteins (OBP16 and OBP18). Odorants that induce low levels of hygienic behavior, however, are weak ligands for these OBPs. We are therefore beginning to paint a picture of the molecular mechanism behind this complex behavior, using odorants associated with freeze-killed brood as a model.

animal behavior and cognition↗

bioRxiv2017

A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE)

BackgroundAn organisms protein interactome, or complete network of protein-protein interactions, defines the protein complexes that drive cellular processes. Techniques for studying protein complexes have traditionally applied targeted strategies such as yeast two-hybrid or affinity purification-mass spectrometry to assess protein interactions. However, given the vast number of protein complexes, more scalable methods are necessary to accelerate interaction discovery and to construct whole interactomes. We recently developed a complementary technique based on the use of protein correlation profiling (PCP) and stable isotope labeling in amino acids in cell culture (SILAC) to assess chromatographic co-elution as evidence of interacting proteins. Importantly, PCP-SILAC is also capable of measuring protein interactions simultaneously under multiple biological conditions, allowing the detection of treatment-specific changes to an interactome. Given the uniqueness and high dimensionality of co-elution data, new tools are needed to compare protein elution profiles, control false discovery rates, and construct an accurate interactome.\n\nResultsHere we describe a freely available bioinformatics pipeline, PrInCE, for the analysis of co-elution data. PrInCE is a modular, open-source library that is computationally inexpensive, able to use label and label-free data, and capable of detecting tens of thousands of protein-protein interactions. Using a machine learning approach, PrInCE offers greatly reduced run time, better performance, prediction of protein complexes, and greater ease of use over previous bioinformatics tools for co-elution data. PrInCE is implemented in Matlab (version R2015b). Source code and standalone executable programs for Windows and Mac OSX are available at https://github.com/fosterlab/PrInCE, where usage instructions can be found. An example dataset and output are also provided for testing purposes.\n\nConclusionsPrInCE is the first fast and easy-to-use data analysis pipeline that predicts interactomes and protein complexes from co-elution data. PrInCE allows researchers without bioinformatics proficiency to analyze high-throughput co-elution datasets.

bioinformatics↗

bioRxiv2017

A Varroa Destructor Protein Atlas Reveals Molecular Underpinnings Of Developmental Transitions And Sexual Differentiation

Varroa destructor is the most economically damaging honey bee pest, weakening colonies by simultaneously parasitizing bees and transmitting harmful viruses. Despite these impacts on honey bee health, surprisingly little is known about its fundamental molecular biology. Here we present a Varroa protein atlas crossing all major developmental stages (egg, protonymph, deutonymph and adult) for both male and female mites as a web-based interactive tool (http://foster.nce.ubc.ca/varroa/index.html). By intensity-based label-free quantitation, 1,433 proteins were differentially expressed across developmental stages, including two distinct viral polyproteins. Enzymes for processing carbohydrates and amino acids were among many of these differences as well as proteins involved in cuticle formation. Lipid transport involving vitellogenin was the most significantly enriched biological process in the foundress (reproductive female) and young mites. In addition, we found that 101 proteins were sexually regulated and functional enrichment analysis suggests that chromatin remodeling may be a key feature of sex determination. In a proteogenomic effort, we identified 519 protein-coding regions (169 of which were differentially expressed) supported by 1,464 peptides which were previously unannotated. Since this is a recurring trend with annotating genomes of non-model species, we analyzed their amino acid and nucleotide composition as well as their orthology to other species to suggest reasons why they may have been missed initially. Overall, this work provides a first-of-its-kind interrogation of the patterns of gene expression that govern the Varroa life cycle and the tools we have developed will support further research on this threatening honey bee pest.

developmental biology↗

bioRxiv2016

Odorant cues linked to social immunity induce lateralized antenna stimulation in honey bees (Apis mellifera L.)

Hygienic behaviour (HB) is a social immunity trait in honey bees (Apis mellifera L.) whereby workers detect, uncap and remove unhealthy brood, improving disease resistance in the colony. This is clearly economically valuable; however, the molecular mechanism behind it is not well understood. The freeze-killed brood (FKB) assay is the conventional method of HB selection, so we compared odour profiles of FKB and live brood. Surprisingly, we found that significantly more brood pheromone ({beta}-ocimene) was released from FKB. {beta}-ocimene abundance also positively correlated with HB, suggesting there could be a brood effect contributing to overall hygiene. We found that β ocimene stimulated worker antennae in a dose-dependent manner, with the left antennae responding significantly stronger than right antennae in hygienic bees, but not in non-hygienic bees. This suggests that HB depends not only on odour detection, but also lateralization of sensitivity. We also compared odour profiles of Varroa-infested brood to healthy brood and found an overall interactive effect between developmental stage and infestation, but specific odours did not drive these differences. Overall, the data we present here is an important foundation on which to build our understanding the molecular mechanism behind this complex behaviour.

biochemistry↗