Structural plasticity of bacterial ESCRT-III protein PspA in higher-order assemblies.

Eukaryotic members of the endosome sorting complex required for transport-III (ESCRT-III) family have been shown to form diverse higher-order assemblies. The bacterial phage shock protein A (PspA) has been identified as a member of the ESCRT-III superfamily, and PspA homo-oligomerizes to form rod-shaped assemblies. As observed for eukaryotic ESCRT-III, PspA forms tubular assemblies of varying diameters. Using electron cryo-electron microscopy, we determined 61 Synechocystis PspA structures and observed in molecular detail how the structural plasticity of PspA rods is mediated by conformational changes at three hinge regions in the monomer and by the fixed and changing molecular contacts between protomers. Moreover, we reduced and increased the structural plasticity of PspA rods by removing the loop connecting helices α3/α4 and the addition of nucleotides, respectively. Based on our analysis of PspA-mediated membrane remodeling, we suggest that the observed mode of structural plasticity is a prerequisite for the biological function of ESCRT-III members.

ModEst: Accurate estimation of genome size from next generation sequencing data.

Accurate estimates of genome sizes are important parameters for both theoretical and practical biodiversity genomics. Here we present a fast, easy-to-implement and accurate method to estimate genome size from the number of bases sequenced and the mean sequencing depth. To estimate the latter, we take advantage of the fact that an accurate estimation of the Poisson distribution parameter lambda is possible from truncated data, restricted to the part of the sequencing depth distribution representing the true underlying distribution. With simulations we show that reasonable genome size estimates can be gained even from low-coverage (10×), highly discontinuous genome drafts. Comparison of estimates from a wide range of taxa and sequencing strategies with flow cytometry estimates of the same individuals showed a very good fit and suggested that both methods yield comparable, interchangeable results.

Genomic basis for drought resistance in European beech forests threatened by climate change.

In the course of global climate change, Central Europe is experiencing more frequent and prolonged periods of drought. The drought years 2018 and 2019 affected European beeches (Fagus sylvatica L.) differently: even in the same stand, drought-damaged trees neighboured healthy trees, suggesting that the genotype rather than the environment was responsible for this conspicuous pattern. We used this natural experiment to study the genomic basis of drought resistance with Pool-GWAS. Contrasting the extreme phenotypes identified 106 significantly associated single-nucleotide polymorphisms (SNPs) throughout the genome. Most annotated genes with associated SNPs (>70%) were previously implicated in the drought reaction of plants. Non-synonymous substitutions led either to a functional amino acid exchange or premature termination. An SNP assay with 70 loci allowed predicting drought phenotype in 98.6% of a validation sample of 92 trees. Drought resistance in European beech is a moderately polygenic trait that should respond well to natural selection, selective management, and breeding.

Climate change is having a serious impact on many ecosystems. In the summer of 2018 and 2019, around two thirds of European beech trees were damaged or killed by extreme drought. It is critical to keep these beech woods healthy, as they are central to the survival of over 6,000 other species of animals and plants. The level of damage caused by the drought varied between forests. However, not all the trees in each forest responded in the same way, with severely damaged trees often sitting next to fully healthy ones. This suggests that the genetic make-up of each tree determines how well it can adapt to drought rather than its local environment. To investigate this further, Pfenninger et al. studied the genome of over 400 European beech trees from the Hesse region in Germany. The samples came from pairs of neighbouring trees that had responded differently to the droughts. The analysis found more than 80 parts of the genome that differed between healthy and damaged trees. Pfenninger et al. then used this information to create a genetic test which can quickly and inexpensively predict how well an individual beech tree might survive in a drought. Applying this test to another 92 trees revealed that it can reliably detect which ones were healthy and which ones were damaged. Beech forests are typically managed by private owners, agencies or breeders that could use this genetic test to select and reproduce trees that are better adapted to drought. The goal now is to develop the test so that it can be used more widely to manage European beech trees and potentially other species.