Phylogenetic Analysis Guides Transporter Protein Deorphanization: A Case Study of the SLC25 Family of Mitochondrial Metabolite Transporters.

Homology search and phylogenetic analysis have commonly been used to annotate gene function, although they are prone to error. We hypothesize that the power of homology search in functional annotation depends on the coupling of sequence variation to functional diversification, and we herein focus on the SoLute Carrier (SLC25) family of mitochondrial metabolite transporters to survey this coupling in a family-wide manner. The SLC25 family is the largest family of mitochondrial metabolite transporters in eukaryotes that translocate ligands of different chemical properties, ranging from nucleotides, amino acids, carboxylic acids and cofactors, presenting adequate experimentally validated functional diversification in ligand transport. Here, we combine phylogenetic analysis to profile SLC25 transporters across common eukaryotic model organisms, from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, to Homo sapiens, and assess their sequence adaptations to the transported ligands within individual subfamilies. Using several recently studied and poorly characterized SLC25 transporters, we discuss the potentials and limitations of phylogenetic analysis in guiding functional characterization.

Integrating sensory ecology and predator-prey theory to understand animal responses to fire.

Fire regimes are changing dramatically worldwide due to climate change, habitat conversion, and the suppression of Indigenous landscape management. Although there has been extensive work on plant responses to fire, including their adaptations to withstand fire and long-term effects of fire on plant communities, less is known about animal responses to fire. Ecologists lack a conceptual framework for understanding behavioural responses to fire, which can hinder wildlife conservation and management. Here, we integrate cue-response sensory ecology and predator-prey theory to predict and explain variation in if, when and how animals react to approaching fire. Inspired by the literature on prey responses to predation risk, this framework considers both fire-naïve and fire-adapted animals and follows three key steps: vigilance, cue detection and response. We draw from theory on vigilance tradeoffs, signal detection, speed-accuracy tradeoffs, fear generalization, neophobia and adaptive dispersal. We discuss how evolutionary history with fire, but also other selective pressures, such as predation risk, should influence animal behavioural responses to fire. We conclude by providing guidance for empiricists and outlining potential conservation applications.

Fear generalization and behavioral responses to multiple dangers.

Animals often exhibit consistent-individual differences (CIDs) in boldness/fearfulness, typically studied in the context of predation risk. We focus here on fear generalization, where fear of one danger (e.g., predators) is correlated with fear of other dangers (e.g., humans, pathogens, moving vehicles, or fire). We discuss why fear generalization should be ecologically important, and why we expect fear to correlate across disparate dangers. CIDs in fear are well studied for some dangers in some taxa (e.g., human fear of pathogens), but not well studied for most dangers. Fear of some dangers has been found to correlate with general fearfulness, but some cases where we might expect correlated fears (e.g., between fear of humans, familiar predators, and exotic predators) are surprisingly understudied.

Road salt compromises functional morphology of larval gills in populations of an amphibian.

Across the planet, winter de-icing practices have caused secondary salinization of freshwater habitats. Many amphibians are vulnerable because of permeable skin and reliance on small ponds, where salinity can be high. Early developmental stages of amphibians are especially sensitive to salt, and larvae developing in salt-polluted environments must osmoregulate through ion exchange in gills. Though ionoregulation in amphibian gills is generally understood, the role of gill morphology remains poorly described. Yet gill structure should affect ionoregulatory capacity, for instance in terms of available surface area. As larval amphibian gills also play critical roles in gas exchange and foraging, changes in gill morphology from salt pollution potentially affect not only osmoregulation, but also respiration and feeding. Here, we used an exposure experiment to quantify salinity effects on larval gill morphology in wood frogs (Rana sylvatica). We measured a suite of morphological traits on gill tufts-where ionoregulation and gas exchange occur-and on gill filters used in feeding. Larvae raised in elevated salinity developed larger gill tufts but with lower surface area to volume ratio. Epithelial cells on these tufts were less circular but occurred at higher densities. Gill filters showed increased spacing, likely reducing feeding efficiency. Many morphological gill traits responded quadratically, suggesting that salinity might induce plasticity in gills at intermediate concentrations until energetic demands exceed plasticity. Together, these changes likely diminish ionoregulatory and respiratory functionality of gill tufts, and compromise feeding functionality of gill filters. Thus, a singular change in aquatic environment from a widespread pollutant appears to generate a suite of consequences via changes in gill morphology. Critically, these changes in traits likely compound the severity of fitness impacts in populations dwelling in salinized environments, whereby ionoregulatory energetic demands should increase respiratory and foraging demands, but in individuals who possess structures poorly adapted for these functions.

Encoding human serine phosphopeptides in bacteria for proteome-wide identification of phosphorylation-dependent interactions.

Post-translational phosphorylation is essential to human cellular processes, but the transient, heterogeneous nature of this modification complicates its study in native systems. We developed an approach to interrogate phosphorylation and its role in protein-protein interactions on a proteome-wide scale. We genetically encoded phosphoserine in recoded E. coli and generated a peptide-based heterologous representation of the human serine phosphoproteome. We designed a single-plasmid library encoding >100,000 human phosphopeptides and confirmed the site-specific incorporation of phosphoserine in >36,000 of these peptides. We then integrated our phosphopeptide library into an approach known as Hi-P to enable proteome-level screens for serine-phosphorylation-dependent human protein interactions. Using Hi-P, we found hundreds of known and potentially new phosphoserine-dependent interactors with 14-3-3 proteins and WW domains. These phosphosites retained important binding characteristics of the native human phosphoproteome, as determined by motif analysis and pull-downs using full-length phosphoproteins. This technology can be used to interrogate user-defined phosphoproteomes in any organism, tissue, or disease of interest.