SUMO-activated target traps (SATTs) enable the identification of a comprehensive E3-specific SUMO proteome

Ubiquitin and ubiquitin-like conjugation cascades consist of dedicated E1, E2, and E3 enzymes with E3s providing substrate specificity. Mass spectrometry-based approaches have enabled the identification of more than 6500 SUMO2/3 target proteins. The limited number of SUMO E3s provides the unique opportunity to systematically study E3 substrate wiring. We developed SUMO-activated target traps (SATTs) and systematically identified substrates for eight different SUMO E3s, PIAS1, PIAS2, PIAS3, PIAS4, NSMCE2, ZNF451, LAZSUL (ZNF451-3), and ZMIZ2. SATTs enabled us to identify 427 SUMO1 and 961 SUMO2/3 targets in an E3-specific manner. We found pronounced E3 substrate preference. Quantitative proteomics enabled us to measure substrate specificity of E3s, quantified using the SATT index. Furthermore, we developed the Polar SATTs web-based tool to browse the dataset in an interactive manner. Overall, we uncover E3-to-target wiring of 1388 SUMO substrates, highlighting unique and overlapping sets of substrates for eight different SUMO E3 ligases.

A staging table of Balkan crested newt embryonic development to serve as a baseline in evolutionary developmental studies

There is an increased interest in the evolution and development of newts from the genus Triturus because: (1) morphological differentiation among the nine constituent species largely corresponds to different ecological preferences, (2) hybridization between different species pairs has various evolutionary outcomes in terms of life history traits and morphology, and (3) the genus expresses a balanced lethal system that causes arrested growth and death of half of the embryos. These features provide natural experimental settings for molecular, morphological, and life-history studies. Therefore, we produce a staging table for the Balkan crested newt (T. ivanbureschi). We provide detailed descriptions of 34 embryonic stages based on easily observable and interpretable external morphological characters, to ensure reproducibility. Compared with previous staging tables for Triturus, we include a vastly increased sample size and provide high-resolution photographs in lateral, ventral, and dorsal view, complemented by videos of specific developmental periods, and accompanied by detailed explanations on how to delineate the specific stages. Our staging table will serve as a baseline in comparative studies on Triturus newts: an emerging model system in evolutionary and developmental studies.

Impact of three co-occurring physical ecosystem engineers on soil Collembola communities

The interplay between organisms with their abiotic environment may have profound effects within ecological networks, but are still poorly understood. Soil physical ecosystem engineers (EEs) modify the abiotic environment, thereby potentially affecting the distribution of other species, such as microarthropods. We focus on three co-occurring physical EEs (i.e. cattle, vegetation, macrodetritivore) known for their profound effect on soil properties (e.g. pore volume, microclimate, litter thickness). We determined their effects on Collembola community composition and life-form strategy (a proxy for vertical distribution in soil) in a European salt marsh. Soil cores were collected in grazed (compacted soil, under short and tall vegetation) and non-grazed areas (decompacted soil, under short and tall vegetation), their pore structure analysed using X-ray computed tomography, after which Collembola were extracted. Collembola species richness was lower in grazed sites, but abundances were not affected by soil compaction or vegetation height. Community composition differed between ungrazed sites with short vegetation and the other treatments, due to a greater dominance of epigeic Collembola and lower abundance of euedaphic species in this treatment. We found that the three co-occurring EEs and their interactions modify the physical environment of soil fauna, particularly through changes in soil porosity and availability of litter. This alters the relative abundance of Collembola life-forms, and thus the community composition within the soil. As Collembola are known to play a crucial role in decomposition processes, these compositional changes in litter and soil layers are expected to affect ecosystem processes and functioning.

Inducing mechanical self-healing in polymer glasses

Polymer glasses such as the plastics used in pipes, structural materials, and medical devices are ubiquitous in daily life. The nature of their low molecular mobility is still poorly understood and it leads to brittle mechanical behavior, damage, and fracture over time. It also prevents the design of self-healing mechanisms that expand the material's lifespan, as more commonly done in recent years for higher mobility amorphous polymers such as gels and rubbers. We demonstrate through numerical simulations that controlled oscillatory deformations enhance the local molecular mobility of glassy polymers without compromising their structural or mechanical stability. We apply this principle to increase the molecular mobility around the surface of a cylindrical crack, counterintuitively inducing fracture repair and recovering the mechanical properties of the pristine material. Our findings are a first step to establish a general physical mechanism of self-healing in glasses that may inspire the design and processing of new glassy materials.