Biology subjects

Davis, R. B.

Publications and source records attributed to Davis, R. B..

6 recordsLinked to original sources

bioRxiv2025

Larger and polymorphic noctuid moths tend to show less inter-annual abundance variation in the canopy of a temperate forest

Inter-annual variation in insect abundance and seasonal phenology can be related to species traits such as body size, larval diet, overwintering stage, and colour variations. We sampled noctuid moths in the canopy of a forest in Western Poland using flight-interception traps during two vegetative seasons. We calculated inter-annual variation for 31 species, and date of peak abundance and length of the flight season for 18 species. We found that for the 23 species for which we had phylogenetic information, larger moths and those with adult colour variation showed less inter-annual abundance variation, which corroborates results of previous studies. We found no indication that phenological traits are associated with the tested species traits. However, species that can feed on the dominant broad-leaved tree in which the traps were placed (Quercus petraea) tended to have a later date of peak abundance than other species. To draw more robust conclusions, future research should encompass a longer time span and a broader range of species. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC="FIGDIR/small/643003v2_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@1ed537eorg.highwire.dtl.DTLVardef@494f5org.highwire.dtl.DTLVardef@cf7559org.highwire.dtl.DTLVardef@21495a_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2024

Protein Arginine Methylation of the Translation Initiation Factor eIF1A Increases Usage of a Near-cognate Start Codon

Protein arginine methylation has emerged as a key post-translational modification responsible for many facets of eukaryotic gene expression. To better understand the extent of this modification in cellular pathways, we carried out bioorthogonal methylation profiling in Saccharomyces cerevisiae to comprehensively identify the in vivo substrates of the major yeast protein arginine methyltransferase Hmt1. Gene ontology analysis of candidate substrates revealed an enrichment of proteins involved in the process of translation. We verified one such factor, eIF1A, by in vitro methylation. Three sites on eIF1A were found to be responsible for its methylation: R13, R14, and R62, with varied capacity by which each site contributed to the overall methylation capacity in vitro. To determine the role of methylation in eIF1A function, we used a battery of arginine-to-alanine substitution mutants to evaluate translation fidelity in these mutants. Our data show that substitution mutants at R13 and R14 in the N-terminal tail improved the fidelity of start codon recognition in an initiation fidelity assay. Overall, our data suggest that Hmt1-mediated methylation of eIF1A fine-tunes the fidelity of start codon recognition for proper translation initiation.

molecular biology↗

bioRxiv2023

Salinity plays a limited role in determining rates of size evolution in fishes globally across multiple scales

Substantial progress has been made to map biodiversity and its drivers across the planet at multiple scales, yet studies that quantify the evolutionary processes that underpin this biodiversity, and test their drivers at multiple scales, are comparatively rare. Studying most fish species, we quantify rates of body size evolution to test the role of fundamental salinity habitats in shaping rates of evolution at multiple scales. We also determine how four additional factors shape evolutionary rates. In up to 1710 comparisons studying over 27,000 ray-finned fish species, we compare rates of body size evolution between five salinity habits using 12 metrics. The comparisons span a molecular tree, supertrees, and ten scales of observation to test for robust patterns and reveal how patterns change with scale. Then, three approaches assess the role of three non-salinity factors on rates, and an alternative habitat scheme tests if lakes influence evolutionary rates. Rates of size evolution rarely differ consistently between salinity habitats; rate patterns are highly clade- and scale-dependent. One exception is freshwater-brackish fishes, which possess among the highest size rates of any salinity, and show higher rates than euryhaline fishes in most groupings studied at most scales, and verses marine, freshwater, and marine-brackish habitats at specific scales. Additionally, species richness had the greatest potential to predict phenotypic rates, followed by branch duration and absolute values of body size. Lacustrine environments were consistently associated with high rates of size evolution. We reveal the rate patterns that underpin global body size diversity for fishes, identifying factors that play a limited role in shaping rates of size evolution, such as salinity, and those such as species richness, age, and lake environments that consistently shape evolutionary rates across half of vertebrate diversity.

evolutionary biology↗

bioRxiv2023

Heterotypic interactions in the dilute phase can drive co-condensation of prion-like low-complexity domains of FET proteins and mammalian SWI/SNF complex

Prion-like domains (PLDs) are low-complexity protein sequences enriched within nucleic acid-binding proteins including those involved in transcription and RNA processing. PLDs of FUS and EWSR1 play key roles in recruiting chromatin remodeler mammalian SWI/SNF complex to oncogenic FET fusion protein condensates. Here, we show that disordered low-complexity domains of multiple SWI/SNF subunits are prion-like with a strong propensity to undergo intracellular phase separation. These PLDs engage in sequence-specific heterotypic interactions with the PLD of FUS in the dilute phase at sub-saturation conditions, leading to the formation of PLD co-condensates. In the dense phase, homotypic and heterotypic PLD interactions are highly cooperative, resulting in the co-mixing of individual PLD phases and forming spatially homogeneous co-condensates. Heterotypic PLD-mediated positive cooperativity in protein-protein interaction networks is likely to play key roles in the co-phase separation of mSWI/SNF complex with transcription factors containing homologous low-complexity domains.

biophysics↗

bioRxiv2021

FUS Oncofusion Protein Condensates Recruit mSWI/SNF Chromatin Remodelers via Heterotypic Interactions Between Prion-like Domains

Fusion transcription factors generated by genomic translocations are common drivers of several types of cancers including sarcomas and leukemias. Oncofusions of the FET (FUS, EWSR1, and TAF15) family of proteins result from fusion of the prion-like domain (PLD) of FET proteins to the DNA-binding domain (DBD) of certain transcription regulators and are implicated in aberrant transcriptional programs through interactions with chromatin remodelers. Here, we show that FUS-DDIT3, a FET oncofusion protein, undergoes PLD-mediated phase separation into liquid-like condensates. Nuclear FUS-DDIT3 condensates can recruit essential components of the global transcriptional machinery such as the chromatin remodeler SWI/SNF. The recruitment of mammalian SWI/SNF is driven by heterotypic PLD-PLD interactions between FUS-DDIT3 and core subunits of SWI/SNF, such as the catalytic component BRG1. Further experiments with single-molecule correlative force-fluorescence microscopy support a model wherein the fusion protein forms condensates on DNA surface and enrich BRG1 to activate transcription by ectopic chromatin remodeling. Similar PLD-driven co-condensation of mSWI/SNF with transcription factors can be employed by other oncogenic fusion proteins with a generic PLD-DBD domain architecture for global transcriptional reprogramming.

biophysics↗

bioRxiv2020

Sequence-encoded and Composition-dependent Protein-RNA Interactions Control Multiphasic Condensate Topologies

Multivalent protein-protein and protein-RNA interactions are the drivers of biological phase separation. Biomolecular condensates typically contain a dense network of multiple proteins and RNAs, and their competing molecular interactions play key roles in regulating the condensate composition and structure. Employing a ternary system comprising of a prion-like polypeptide (PLP), arginine-rich polypeptide (RRP), and RNA, we show that competition between the PLP and RNA for a single shared partner, the RRP, leads to RNA-induced demixing of PLP-RRP condensates into stable coexisting phases-homotypic PLP condensates and heterotypic RRP-RNA condensates. The morphology of these biphasic condensates (non-engulfing/ partial engulfing/ complete engulfing) is determined by the RNA-to-RRP stoichiometry and the hierarchy of intermolecular interactions, providing a glimpse of the broad range of multiphasic patterns that are accessible to these condensates. Our findings provide a minimal set of physical rules that govern the composition and spatial organization of multicomponent and multiphasic biomolecular condensates.

biophysics↗