An improved SNAP-ADAR tool enables efficient RNA base editing to interfere with post-translational protein modification.

RNA base editing relies on the introduction of adenosine-to-inosine changes into target RNAs in a highly programmable manner in order to repair disease-causing mutations. Here, we propose that RNA base editing could be broadly applied to perturb protein function by removal of regulatory phosphorylation and acetylation sites. We demonstrate the feasibility on more than 70 sites in various signaling proteins and identify key determinants for high editing efficiency and potent down-stream effects.

Temperature influences desiccation resistance of bumble bees.

Ongoing climate change has increased temperatures and the frequency of droughts in many parts of the world, potentially intensifying the desiccation risk for insects. Because resisting desiccation becomes more difficult at higher temperatures and lower humidity, avoiding water loss is a key challenge facing terrestrial insects. However, few studies have examined the interactive effects of temperature and environmental humidity on desiccation resistance in insects.

Shared Features Underlying Compact Genomes and Extreme Habitat Use in Chironomid Midges.

Nonbiting midges (family Chironomidae) are found throughout the world in a diverse array of aquatic and terrestrial habitats, can often tolerate harsh conditions such as hypoxia or desiccation, and have consistently compact genomes. Yet we know little about the shared molecular basis for these attributes and how they have evolved across the family. Here, we address these questions by first creating high-quality, annotated reference assemblies for Tanytarsus gracilentus (subfamily Chironominae, tribe Tanytarsini) and Parochlus steinenii (subfamily Podonominae).

Doa10/MARCH6 architecture interconnects E3 ligase activity with lipid-binding transmembrane channel to regulate SQLE.

Transmembrane E3 ligases play crucial roles in homeostasis. Much protein and organelle quality control, and metabolic regulation, are determined by ER-resident MARCH6 E3 ligases, including Doa10 in yeast. Here, we present Doa10/MARCH6 structural analysis by cryo-EM and AlphaFold predictions, and a structure-based mutagenesis campaign.

Discovery of Ligands for TRIM58, a Novel Tissue-Selective E3 Ligase.

Redirecting E3 ligases to neo-substrates, leading to their proteasomal disassembly, known as targeted protein degradation (TPD), has emerged as a promising alternative to traditional, occupancy-driven pharmacology. Although the field has expanded tremendously over the past years, the choice of E3 ligases remains limited, with an almost exclusive focus on CRBN and VHL. Here, we report the discovery of novel ligands to the PRY-SPRY domain of TRIM58, a RING ligase that is specifically expressed in erythroid precursor cells.

A Pro-Fluorescent Ubiquitin-Based Probe to Monitor Cysteine-Based E3 Ligase Activity.

Protein post-translational modification with ubiquitin (Ub) is a versatile signal regulating almost all aspects of cell biology, and an increasing range of diseases is associated with impaired Ub modification. In this light, the Ub system offers an attractive, yet underexplored route to the development of novel targeted treatments. A promising strategy for small molecule intervention is posed by the final components of the enzymatic ubiquitination cascade, E3 ligases, as they determine the specificity of the protein ubiquitination pathway.

Reconstructing midge consumer-resource dynamics using carbon stable isotope signatures of archived specimens.

Population cycles can be caused by consumer-resource interactions. Confirming the role of consumer-resource interactions, however, can be challenging due to an absence of data for the resource candidate. For example, interactions between midge larvae and benthic algae likely govern the high-amplitude population fluctuations of Tanytarsus gracilentus in Lake Mývatn, Iceland, but there are no records of benthic resources concurrent with adult midge population counts.

Ecosystem engineering alters density-dependent feedbacks in an aquatic insect population.

Ecosystem engineers have large impacts on the communities in which they live, and these impacts may feed back to populations of engineers themselves. In this study, we assessed the effect of ecosystem engineering on density-dependent feedbacks for midges in Lake Mývatn, Iceland. The midge larvae reside in the sediment and build silk tubes that provide a substrate for algal growth, thereby elevating benthic primary production.

Transient top-down and bottom-up effects of resources pulsed to multiple trophic levels.

Pulsed fluxes of organisms across ecosystem boundaries can exert top-down and bottom-up effects in recipient food webs, through both direct effects on the subsidized trophic levels and indirect effects on other components of the system. While previous theoretical and empirical studies demonstrate the influence of allochthonous subsidies on bottom-up and top-down processes, understanding how these forces act in conjunction is still limited, particularly when an allochthonous resource can simultaneously subsidize multiple trophic levels. Using the Lake Mývatn region in Iceland as an example system of allochthony and its potential effects on multiple trophic levels, we analyzed a mathematical model to evaluate how pulsed subsidies of aquatic insects affect the dynamics of a soil-plant-arthropod food web.

Structural Basis and Evolution of Glycan Receptor Specificities within the Polyomavirus Family.

Asymptomatic infections with polyomaviruses in humans are common, but these small viruses can cause severe diseases in immunocompromised hosts. New Jersey polyomavirus (NJPyV) was identified via a muscle biopsy in an organ transplant recipient with systemic vasculitis, myositis, and retinal blindness, and human polyomavirus 12 (HPyV12) was detected in human liver tissue. The evolutionary origins and potential diseases are not well understood for either virus.

One-Step ARMS-PCR for the Detection of SNPs-Using the Example of the Gene.

In eukaryotes, cellular functions are tightly controlled by diverse post-translational modifications (PTMs) of proteins. One such PTM affecting many proteins is the deimination of arginine to citrulline. This process, called citrullination is catalyzed by a group of hydrolases called protein arginine deiminases (PADs), of which five isoforms have been identified.

Quantitative and qualitative assessment of pollen DNA metabarcoding using constructed species mixtures.

Pollen DNA metabarcoding-marker-based genetic identification of potentially mixed-species pollen samples-has applications across a variety of fields. While basic species-level pollen identification using standard DNA barcode markers is established, the extent to which metabarcoding (a) correctly assigns species identities to mixes (qualitative matching) and (b) generates sequence reads proportionally to their relative abundance in a sample (quantitative matching) is unclear, as these have not been assessed relative to known standards. We tested the quantitative and qualitative robustness of metabarcoding in constructed pollen mixtures varying in species richness (1-9 species), taxonomic relatedness (within genera to across class) and rarity (5%-100% of grains), using Illumina MiSeq with the markers rbcL and ITS2.