The adult mouse proteome Foster, Leonard J
Nature methods,
07/2022, Letnik:
19, Številka:
7
Journal Article
Recenzirano
Evidence for at least one protein product from 80% of all mouse genes is reported in a comprehensive proteomic analysis of 41 adult mouse tissues. Comparison of tissue profiles between mouse and ...human suggests that the fundamental biology of this important model organism is even more different from our own than we thought.
Interactomes are often measured using affinity purification-mass spectrometry (AP-MS) or yeast two-hybrid approaches, but these methods do not provide stoichiometric or temporal information. We ...combine quantitative proteomics and size-exclusion chromatography to map 291 coeluting complexes. This method allows mapping of an interactome to the same depth and accuracy as AP-MS with less work and without overexpression or tagging. The use of triplex labeling enables monitoring of interactome rearrangements.
Interactome studies are necessary to understand cellular processes and co-elution methods are well suited for the simultaneous and global exploration of the interactome, as well as the assessment of ...biological perturbations of the network. These methods rely on the fundamental idea that proteins from the same complex migrate together during fractionation. We review the different separation techniques along with the quantification and bioinformatic approaches used for co-elution methods and provide design considerations to choose between them.
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Highlights
•Co-elution stands out as a global interactome mapping method.•Benefits include all-to-all protein analysis and measurement of interactome perturbations.•Different separation, quantification and bioinformatic strategies are available.•Design considerations depend largely on system under study.
Understanding how proteins interact is crucial to understanding cellular processes. Among the available interactome mapping methods, co-elution stands out as a method that is simultaneous in nature and capable of identifying interactions between all the proteins detected in a sample. The general workflow in co-elution methods involves the mild extraction of protein complexes and their separation into several fractions, across which proteins bound together in the same complex will show similar co-elution profiles when analyzed appropriately. In this review we discuss the different separation, quantification and bioinformatic strategies used in co-elution studies, and the important considerations in designing these studies. The benefits of co-elution versus other methods makes it a valuable starting point when asking questions that involve the perturbation of the interactome.
Pesticide exposure and queen loss are considered to be major causes of honey bee colony mortality, yet little is known regarding the effects of regularly encountered agrochemicals on honey bee ...reproduction. Here, we present the results of a two-generational study using specialized cages to expose queens to commonly used insect growth disrupting pesticides (IGDs) via their retinue of worker bees. Under IGD exposure, we tracked queen performance and worker responses to queens, then the performance of the exposed queens’ offspring was assessed to identify patterns that may contribute to the long-term health and stability of a social insect colony. The positive control, novaluron, resulted in deformed larvae hatching from eggs laid by exposed queens, and methoxyfenozide, diflubenzuron, and novaluron caused a slight decrease in daily egg laying rates, but this was not reflected in the total egg production over the course of the experiment. Curiously, eggs laid by queens exposed to pyriproxyfen exhibited increased hatching rates, and those larvae developed into worker progeny with increased responsiveness to their queens. Additionally, pyriproxyfen and novaluron exposure affected the queen ovarian protein expression, with the overwhelming majority of differentially expressed proteins coming from the pyriproxyfen exposure. We discuss these results and the potential implications for honey bee reproduction and colony health.
Bees are the most important insect pollinators of the crops humans grow, and
, the Western honey bee, is the most commonly managed species for this purpose. In addition to providing agricultural ...services, the complex biology of honey bees has been the subject of scientific study since the 18th century, and the intricate behaviors of honey bees and ants, fellow hymenopterans, inspired much sociobiological inquest. Unfortunately, honey bees are constantly exposed to parasites, pathogens, and xenobiotics, all of which pose threats to their health. Despite our curiosity about and dependence on honey bees, defining the molecular mechanisms underlying their interactions with biotic and abiotic stressors has been challenging. The very aspects of their physiology and behavior that make them so important to agriculture also make them challenging to study, relative to canonical model organisms. However, because we rely on
so much for pollination, we must continue our efforts to understand what ails them. Here, we review major advancements in our knowledge of honey bee physiology, focusing on immunity and detoxification, and highlight some challenges that remain.
External perturbations, by forcing cells to adapt to a new environment, often elicit large‐scale changes in gene expression resulting in an altered proteome that improves the cell's fitness in the ...new conditions. Steady‐state levels of a proteome depend on transcription, the levels of transcripts, translation and protein degradation but system‐level contribution that each of these processes make to the final protein expression change has yet to be explored. We therefore applied a systems biology approach to characterize the regulation of protein expression during cellular differentiation using quantitative proteomics. As a general rule, it seems that protein expression during cellular differentiation is largely controlled by changes in the relative synthesis rate, whereas the relative degradation rate of the majority of proteins stays constant. In these data, we also observe that the proteins in defined sub‐structures of larger protein complexes tend to have highly correlated synthesis and degradation rates but that this does not necessarily extend to the holo‐complex. Finally, we provide strong evidence that the generally poor correlation observed between transcript and protein levels can fully be explained once the protein synthesis and degradation rates are taken into account.
The contribution of transcription, protein synthesis and degradation rates to the control of protein expression during differentiation was analyzed using quantitative proteomics and transcriptomics data. Protein synthesis rate was identified as the main determinant of protein expression.
Synopsis
The contribution of transcription, protein synthesis and degradation rates to the control of protein expression during differentiation was analyzed using quantitative proteomics and transcriptomics data. Protein synthesis rate was identified as the main determinant of protein expression.
The lack of correlation usually observed between transcript and protein levels can be fully explained when correcting for the synthesis and degradation rates of the individual proteins.
Synthesis rates for individual proteins are extensively regulated, in contrast to degradation rates that mostly remain constant in response to differentiation.
The modularity of macromolecular complexes is maintained during synthesis and degradation of the complexes.
We present CFdb, a harmonized resource of interaction proteomics data from 411 co-fractionation mass spectrometry (CF-MS) datasets spanning 21,703 fractions. Meta-analysis of this resource charts ...protein abundance, phosphorylation, and interactions throughout the tree of life, including a reference map of the human interactome. We show how large-scale CF-MS data can enhance analyses of individual CF-MS datasets, and exemplify this strategy by mapping the honey bee interactome.
Co-fractionation mass spectrometry (CF-MS) has emerged as a powerful technique for interactome mapping. However, there is little consensus on optimal strategies for the design of CF-MS experiments or ...their computational analysis. Here, we reanalyzed a total of 206 CF-MS experiments to generate a uniformly processed resource containing over 11 million measurements of protein abundance. We used this resource to benchmark experimental designs for CF-MS studies and systematically optimize computational approaches to network inference. We then applied this optimized methodology to reconstruct a draft-quality human interactome by CF-MS and predict over 700,000 protein-protein interactions across 27 eukaryotic species or clades. Our work defines new resources to illuminate proteome organization over evolutionary timescales and establishes best practices for the design and analysis of CF-MS studies.
Extreme temperature exposure can reduce stored sperm viability within queen honey bees; however, little is known about how thermal stress may directly impact queen performance or other maternal ...quality metrics. Here, in a blind field trial, we recorded laying pattern, queen mass, and average callow worker mass before and after exposing queens to a cold temperature (4°C, 2 h), hot temperature (42°C, 2 h), and hive temperature (33°C, control). We measured sperm viability at experiment termination, and investigated potential vertical effects of maternal temperature stress on embryos using proteomics. We found that cold stress, but not heat stress, reduced stored sperm viability; however, we found no significant effect of temperature stress on any other recorded metrics (queen mass, average callow worker mass, laying patterns, the egg proteome, and queen spermathecal fluid proteome). Previously determined candidate heat and cold stress biomarkers were not differentially expressed in stressed queens, indicating that these markers only have short-term post-stress diagnostic utility. Combined with variable sperm viability responses to temperature stress reported in different studies, these data also suggest that there is substantial variation in temperature tolerance, with respect to impacts on fertility, amongst queens. Future research should aim to quantify the variation and heritability of temperature tolerance, particularly heat, in different populations of queens in an effort to promote queen resilience.
Recently, autophagy has been implicated as a host defense mechanism against intracellular pathogens. On the other hand, certain intracellular pathogens such as Leishmania can manipulate the host's ...autophagy to promote their survival. Our recent findings regarding the regulation of autophagy by Leishmania donovani indicate that this pathogen induces non-classical autophagy in infected macrophages, independent of regulation by the mammalian target of rapamycin complex 1. This suggests the fine-tuning of autophagy to optimally promote parasite survival, possibly by the sequestration or modulation of specific autophagosome-associated proteins. To investigate how Leishmania potentially manipulates the composition of host-cell autophagosomes, we undertook a quantitative proteomic study of the human monocytic cell line THP-1 following infection with L. donovani. We used stable isotope labeling by amino acid in cell culture and liquid chromatography-tandem mass spectrometry to compare expression profiles between autophagosomes isolated from THP-1 cells infected with L. donovani or treated with known autophagy inducers. Selected proteomic results were validated by Western blotting. In this study, we showed that L. donovani modulates the composition of macrophage autophagosomes during infection when compared to autophagosomes induced by either rapamycin (selective autophagy) or starvation (non-selective autophagy). Among 1787 proteins detected in Leishmania-induced autophagosomes, 146 were significantly modulated compared to the proteome of rapamycin-induced autophagosomes, while 57 were significantly modulated compared to starvation-induced autophagosomes. Strikingly, 23 Leishmania proteins were also detected in the proteome of Leishmania-induced autophagosomes. Together, our data provide the first comprehensive insight into the proteome dynamics of host autophagosomes in response to Leishmania infection and demonstrate the complex relations between the host and pathogen at the molecular level. A comprehensive analysis of the Leishmania-induced autophagosome proteome will be instrumental in the advancement of understanding leishmaniasis.
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