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 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. A 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.

Propionate production from carbon monoxide by synthetic co-cultures of Acetobacterium wieringae spp. and propionigenic bacteria

Gas fermentation is a promising way for converting CO-rich gases to chemicals. We studied the use of synthetic co-cultures composed of carboxydotrophic and propionigenic bacteria to convert CO to propionate. So far isolated carboxydotrophs cannot directly ferment CO to propionate, and therefore this co-cultivation approach was investigated. Four distinct synthetic co-cultures were constructed, consisting of: Acetobacterium wieringae (DSM 1911T) and Pelobacter propionicus (DSM 2379T); Ac. wieringae (DSM 1911T) and Anaerotignum neopropionicum (DSM 3847T); Ac. wieringae strain JM and P. propionicus (DSM 2379T); Ac. wieringae strain JM and An. neopropionicum (DSM 3847T). Propionate was produced by all the co-cultures, with the highest titer (∼24 mM) measured in the co-culture composed of Ac. wieringae strain JM + An. neopropionicum, which also produced isovalerate (∼4 mM), butyrate (∼1 mM), and isobutyrate (0.3 mM). This co-culture was further studied using proteogenomics. As expected, enzymes involved in the Wood-Ljungdahl pathway in Ac. wieringae strain JM, which are responsible for the conversion of CO to ethanol and acetate, were detected; the proteome of An. neopropionicum confirmed the conversion of ethanol to propionate via the acrylate pathway. In addition, proteins related to amino acid metabolism and stress response were highly abundant during co-cultivation, which raises the hypothesis that amino acids are exchanged by the two microorganisms accompanied by isovalerate and isobutyrate production. This highlights the importance of explicitly looking at fortuitous microbial interactions during co-cultivation to fully understand co-cultures behavior. IMPORTANCE Syngas fermentation has great potential for the sustainable production of chemicals from wastes (via prior gasification) and flue gases containing CO/CO2. Research efforts need to be driven to expanding the product portfolio of gas fermentation, which is currently limited to mainly acetate and ethanol. This study provides the basis for a microbial process to produce propionate from CO using synthetic co-cultures composed of acetogenic and propionigenic bacteria and elucidates the metabolic pathways involved. Furthermore, based on proteomics results, we hypothesize that the two bacterial species engage in an interaction that results in amino acid exchange, which subsequently promotes isovalerate and isobutyrate production. These findings provide a new understanding of gas fermentation and a co-culturing strategy for expanding the product spectrum of microbial conversion of CO/CO2.

Effectiveness of sirolimus in a patient with a novel heterozygous FAS mutation leading to severe autoimmune lymphoproliferative syndrome

Here we report a patient with a novel mutation in the FAS gene associated with a severe phenotype of the autoimmune lymphoproliferative syndrome. FAS gene identified as a novel spontaneous somatic heterozygous missense mutation (c.857G > A, p.G286E) in exon 9, causing an amino acid exchange was identified using sequencing. Consequently, the treatment with sirolimus (1mg/d, blood concentration 5-15ng/L) was initiated. Subsequently, the patient’s platelet count and clinical condition improved rapidly. Moreover, our in vitro data showed that G286E could inhibit cell proliferation and induce apoptosis compared with the wild type. To sum up, these data indicated that defective apoptosis might contribute to the clinical phenotype of lymphoproliferation in FAS deficient patients. The polarization of DNT/Treg axis may be an operative target of the sirolimus application.

Mass Spectrometry Guided Discovery and Design of Novel Asperphenamate Analogs From Penicillium astrolabium Reveals an Extraordinary NRPS Flexibility

Asperphenamate is a small peptide natural product that has gained much interest due to its antitumor activity. In the recent years numerous bioactive synthetic asperphenamate analogs have been reported, whereas only a handful of natural analogs either of microbial or plant origin has been discovered. Herein we describe a UHPLC-HRMS/MS and amino acid supplement approach for discovery and design of novel asperphenamate analogs. Chemical analysis of Penicillium astrolabium, a prolific producer of asperphenamate, revealed three previously described and two novel asperphenamate analogs produced in significant amounts, suggesting a potential for biosynthesis of further asperphenamate analogs by varying the amino acid availability. Subsequent growth on proteogenic and non-proteogenic amino acid enriched media, revealed a series of novel asperphenamate analogs, including single or double amino acid exchange, as well as benzoic acid exchange for nicotinic acid, with the latter observed from a natural source for the first time. In total, 22 new asperphenamate analogs were characterized by HRMS/MS, with one additionally confirmed by isolation and NMR structure elucidation. This study indicates an extraordinary nonribosomal peptide synthetase (NRPS) flexibility based on substrate availability, and therefore the potential for manipulating and designing novel peptide natural products in filamentous fungi.

Single amino acid exchange in ACTIN2 confers increased tolerance to oxidative stress in Arabidopsis der1-3 mutant

Single-point mutation in the ACTIN2 gene of der1-3 mutant revealed that ACTIN2 is an essential actin isovariant required for root hair tip growth, and leads to shorter, thinner and more randomly oriented actin filaments in comparison to wild-type C24 genotype. Actin cytoskeleton has been linked to plant defence against oxidative stress, but it is not clear how altered structural organization and dynamics of actin filaments may help plants to cope with oxidative stress. In this study, we characterized seed germination, root growth, plant biomass, actin organization and antioxidant activity of der1-3 mutant under oxidative stress induced by paraquat and H2O2. Under these conditions, plant growth was better in der1-3 mutant, while actin cytoskeleton in der1-3 carrying pro35S::GFP:FABD2 construct showed lower bundling rate and higher dynamicity. Biochemical analyses documented lower degree of lipid peroxidation, elevated capacity to decompose superoxide and hydrogen peroxide. These results support the view that der1-3 mutant is more resistant to oxidative stress. Single amino acid exchange in mutated ACTIN2 protein (Cys to Arg at the position 97) is topologically exposed to the protein surface and we propose that this might alter protein post-translational modifications and/or protein-protein interactions, leading to enhanced tolerance of der1-3 mutant against oxidative stress.

Work horse strain Clostridioides difficile 630Δerm is oblivious to its anaerobic lifestyle

The laboratory reference strain 630Δerm of the anaerobic human pathogen Clostridioides difficile is characterized by a remarkable high oxygen tolerance. We show that an amino acid exchange in the DNA binding domain of the hydrogen peroxide sensor PerR results in a constitutive derepression of PerR-controlled genes and thus in an oxidative stress response even under anaerobic conditions. This questions the model status, strain 630Δerm claims in C. difficile research.