Nanocellulose enhances the dispersion and toxicity of ZnO NPs to green algae Eremosphaera viridis

The widespread cellulose nanomaterials from industrial production and natural plant degradation inevitably lead to the accumulation of nanocellulose in aquatic environment. However, the effect of nanocellulose on the fate, transport...

Enhanced Plant–microbe Remediation of PCBs in Soil using Enzyme Modification Technique Combined with Molecular Docking and Molecular Dynamics

The study on the enhanced mechanisms of the enzymes involved in plant absorption, plant degradation, and microbial mineralization in the remediation of soils contaminated with polychlorinated biphenyls (PCBs) is of great significance for the application of plant-microbe combined remediation technique in PCB-contaminated soils. The present study first used a combination of molecular docking and molecular dynamics methods to calculate the effects of the plant absorption enzyme, plant degradation enzyme, and microbial mineralization enzyme on the PCBs in the soil environment. A multifunctional plant degradation enzyme was constructed with three functional roles of absorption, degradation, and mineralization using amino acid sequence recombination and site-directed mutagenesis to modify the template of plant degradation enzyme. Finally, using the Taguchi experimental design-assisted molecular dynamics simulation method, the suitable external environmental conditions of plant-microbe combined remediation of the PCB­-contaminated soil were determined. In total, six multifunctional plant degradation enzymes were designed, which exhibited a significantly improved efficiency of PCB degradation. In comparison to the complex of plant absorption enzyme, plant degradation enzyme, and microorganism mineralization enzyme (6QIM-3GZX-1B85), the six multifunctional plant degradation enzymes exhibited significantly higher efficiency (2.10–2.38 times) in degrading the PCBs, with a maximum of 2.69 times under suitable external environmental conditions.

Winter is coming – ecosystem-scale COS exchange during senescence of a deciduous forest

<p>The gross uptake of CO<sub>2</sub> on ecosystem level (GPP) can’t be measured directly, but has to be inferred from models or proxies. One of the newly emerged constrains on GPP is the trace gas carbonyl sulfide (COS). COS enters the plant leaf through the stomata and diffuses through the intercellular space, the cell wall, the plasma membrane and the cytosol like CO<sub>2</sub>. Within the cytosol, it is then catalyzed by the enzyme carbonic anhydrase (CA) in a one-way reaction to H<sub>2</sub>S and CO<sub>2</sub>. Basically, this one way flux would make COS a very promising tracer for GPP on ecosystem level, but there is growing evidence that plants are also capable of emitting COS. Mosses and even vascular plants that are under high stress like drought and fungal infection, have been reported to emit COS. Furthermore, a winter wheat field, that showed a good correlation between the CO<sub>2</sub> and COS ecosystem fluxes during the peak growing phase turned into a source for COS after going into senescence. This indicates that yet unknown COS emission processes likely related to plant degradation, could complicate the use of COS as a tracer for GPP.</p><p>Since the majority of studies have focused on measuring COS ecosystem fluxes during peak growing times or on evergreen forests, we seek to quantify the relationship between the ecosystem-scale exchange of CO<sub>2</sub> and COS of an ecosystem going into senescence.</p><p>Between September and November 2019 we deployed our quantum cascade laser (Aerodyne Research Inc., MA, USA) at a beech forest in Leinefelde, Germany to conduct eddy covariance measurements for COS, CO<sub>2</sub> and H<sub>2</sub>O. Our observations started when the beech forest was still green and in full leaf and ended when most of the trees had already shed their leaves. The ecosystem fluxes of COS and CO<sub>2</sub> concurrently decreased over the course of our campaign up to the point when we could not observe a net uptake of CO<sub>2</sub> anymore. We will further compare the GPP estimates resulting from classical flux partitioning and flux partitioning with the additional use of COS to determine if the model differences increase towards the end of the season.</p>

Global analysis of non-animal peroxidases provides insights into the evolution of this gene family in the green lineage

The non-animal peroxidases belong to a superfamily of oxidoreductases that reduce hydrogen peroxide and oxidize numerous substrates. Since their initial characterization in 1992, a number of studies have provided an understanding of the origin and evolution of this protein family. Here, we report a comprehensive evolutionary analysis of non-animal peroxidases using integrated in silico and biochemical approaches. Thanks to the availability of numerous genomic sequences from more than 2500 species belonging to 14 kingdoms together with expert and comprehensive annotation of peroxidase sequences that have been centralized in a dedicated database, we have been able to use phylogenetic reconstructions to increase our understanding of the evolutionary processes underlying the diversification of non-animal peroxidases. We analysed the distribution of all non-animal peroxidases in more than 200 eukaryotic organisms in silico. First, we show that the presence or absence of non-animal peroxidases correlates with the presence or absence of certain organelles or with specific biological processes. Examination of almost 2000 organisms determined that ascorbate peroxidases (APxs) and cytochrome c peroxidases (CcPs) are present in those containing chloroplasts and mitochondria, respectively. Plants, which contain both organelles, are an exception and contain only APxs without CcP. Class II peroxidases (CII Prxs) are only found in fungi with wood-decay and plant-degradation abilities. Class III peroxidases (CIII Prxs) are only found in streptophyte algae and land plants, and have been subjected to large family expansion. Biochemical activities of APx, CcP, and CIII Prx assessed using protein extracts from 30 different eukaryotic organisms support the distribution of the sequences resulting from our in silico analysis. The biochemical results confirmed both the presence and classification of the non-animal peroxidase encoding sequences.

Global analysis of non-animal peroxidases provides insights into the evolutionary basis of this gene family in green lineage

The non-animal peroxidases belong to a superfamily of oxidoreductases that reduce the hydrogen peroxide and oxidize numerous substrates. Since their initial characterization in 1992, several advances have provided an understanding into the origin and evolutionary history of this family of proteins. Here, we report for the first time an exhaustive evolutionary analysis of non-animal peroxidases using integrated in silico and biochemical strategies. Thanks to the availability of numerous genomic sequences from many species belonging to different kingdoms together with expert and exhaustive annotation of peroxidase sequences centralized in a dedicated database, we have deepened our understanding of the evolutionary process underlying non-animal peroxidases through phylogenetic reconstructions. We analysed the distribution of all non-animal peroxidases in more than 200 eukaryotic organisms in silico. First, we show that the presence or absence of non-animal peroxidases can be correlated with the presence or absence of certain organelles or with specific biological processes. Examining a wide range of organisms, we confirmed that ascorbate peroxidases (APx) and cytochromes c peroxidases (CcP) were detected respectively in chloroplast and mitochondria containing organisms. Plants, which contain both organelles, are an exception and contain only APxs without CcP. Class III peroxidases (CIII Prx) were only detected in plants and Class II peroxidases (CII Prx) in fungi related to wood decay and plant degradation.Moreover, we demonstrate that biochemical activities (APx, CcP and CIII Prx) assayed in protein extracts obtained from 30 different eukaryotic organisms strongly support the distribution of the sequences resulting from our in silico analysis. The biochemical results confirmed both the presence and classification of non-animal peroxidase encoding sequences.