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Dipeptidyl peptidases 8 and 9 are intracellular N-terminal dipeptidyl peptidases (preferentially postproline) associated with pathophysiological roles in immune response and cancer biology. While the DPP family member DPP4 is extensively characterized in molecular terms as a validated therapeutic target of type II diabetes, experimental 3D structures and ligand-/substrate-binding modes of DPP8 and DPP9 have not been reported. In this study we describe crystal and molecular structures of human DPP8 (2.5 Å) and DPP9 (3.0 Å) unliganded and complexed with a noncanonical substrate and a small molecule inhibitor, respectively. Similar to DPP4, DPP8 and DPP9 molecules consist of one β-propeller and α/β hydrolase domain, forming a functional homodimer. However, they differ extensively in the ligand binding site structure. In intriguing contrast to DPP4, where liganded and unliganded forms are closely similar, ligand binding to DPP8/9 induces an extensive rearrangement at the active site through a disorder-order transition of a 26-residue loop segment, which partially folds into an α-helix (R-helix), including R160/133, a key residue for substrate binding. As vestiges of this helix are also seen in one of the copies of the unliganded form, conformational selection may contributes to ligand binding. Molecular dynamics simulations support increased flexibility of the R-helix in the unliganded state. Consistently, enzyme kinetics assays reveal a cooperative allosteric mechanism. DPP8 and DPP9 are closely similar and display few opportunities for targeted ligand design. However, extensive differences from DPP4 provide multiple cues for specific inhibitor design and development of the DPP family members as therapeutic targets or antitargets.

Caspases form a family of proteinases required for the initiation and execution phases of apoptosis. Distinct proapoptotic stimuli lead to activation of the initiator caspases-8 and -9, which in turn activate the common executioner caspases-3 and -7 by proteolytic cleavage. Whereas crystal structures of several active caspases have been reported, no three-dimensional structure of an uncleaved caspase zymogen is available so far. We have determined the 2.9-Å crystal structure of recombinant human C285A procaspase-7 and have elucidated the activation mechanism of caspases. The overall fold of the homodimeric procaspase-7 resembles that of the active tetrameric caspase-7. Each monomer is organized in two structured subdomains connected by partially flexible linkers, which asymmetrically occupy and block the central cavity, a typical feature of active caspases. This blockage is incompatible with a functional substrate binding site/active site. After proteolytic cleavage within the flexible linkers, the newly formed chain termini leave the cavity and fold outward to form stable structures. These conformational changes are associated with the formation of an intact active-site cleft. Therefore, this mechanism represents a formerly unknown type of proteinase zymogen activation.

RNA polymerase II sub unit RPB8 is an essential subunit that is highly conserved throughout eukaryotic evolution and is present hi all three types of nuclear RNA polymerases. We report the first high resolution structural insight into eukaryotic RNA polymerase architecture with the solution structure of RPB8 from Saccharomyces cerevisiae . It consists of an eight stranded, antiparallel β-barrel, four short helical regions and a large, unstructured omega-loop. The strands are connected in classic Greek-key fashion. The overall topology is unusual and contains a striking C2 rotational symmetry. Furthermore, it is most likely a novel associate of the oligonucleotide/oligosaccharide (OB) binding protein class.

Systemic inflammation presents a significant challenge to the long-term function of biohybrid implants. While endothelialisation of biohybrid implants has been shown to improve device hemocompatibility, its feasibility under the influence of patients' inflammatory status remains largely unexplored. To investigate this, we developed a controlled in vitro model which allows to study endothelial dysfunction under inflammatory stress. Endothelial cells were cultured on polydimethylsiloxane under physiological shear stress and exposed to lipopolysaccharide (LPS)-activated peripheral blood mononuclear cells (PBMCs), mimicking systemic inflammation at the blood-material interface. Endothelial morphology and confluence was assessed using immunohistochemistry and scanning electron microscopy. Leukocyte adhesion was evaluated directly as well as indirectly, using flow cytometry to analyse cell adhesion molecules. Quantitative PCR was used for gene expression analysis of inflammatory mediators. Notably, neither LPS nor PBMCs alone induced endothelial disruption under shear stress, whereas their combination significantly impaired endothelial confluence. Inflammatory activation led to substantial loss of endothelial confluence, increased leukocyte adhesion, and elevated expression of adhesion molecules ICAM-1, VCAM-1, and E-selectin. Gene expression analysis further highlighted the upregulation of inflammatory mediators, such as IL-6, IL-8, IL-10, and MCP-1. This study underscores the challenges of implementing endothelialisation in biohybrid devices, particularly in patients with systemic inflammation. By considering translational hurdles, this work contributes to the development of clinically viable biohybrid constructs and highlights the importance of considering inflammatory dynamics when designing next-generation implants.

The root-colonizing endophytic fungus Piriformospora indica promotes the root and shoot growth of its host plants. We show that the growth promotion of Arabidopsis thaliana leaves is abolished when the seedlings are grown on media with nitrogen (N) limitation. The fungus neither stimulated the total N content nor did it promote [sup.15]NO[sub.3] [sup.−] uptake from agar plates to the leaves of the host under N-sufficient or N-limiting conditions. However, when the roots were co-cultivated with [sup.15]N-labelled P. indica, more labels were detected in the leaves of N-starved host plants but not in plants supplied with sufficient N. Amino acid and primary metabolite profiles, as well as the expression analyses of N metabolite transporter genes suggest that the fungus alleviates the adaptation of its host from the N limitation condition. P. indica alters the expression of transporter genes, which participate in the relocation of NO[sub.3] [sup.−], NH[sub.4] [sup.+] and N metabolites from the roots to the leaves under N limitation. We propose that P. indica participates in the plant’s metabolomic adaptation against N limitation by delivering reduced N metabolites to the host, thus alleviating metabolic N starvation responses and reprogramming the expression of N metabolism-related genes.

Geminiviral single-stranded circular DNA genomes replicate in nuclei so that the progeny DNA has to cross both the nuclear envelope and the plasmodesmata for systemic spread within plant tissues. For intra- and intercellular transport, two proteins are required: a nuclear shuttle protein (NSP) and a movement protein (MP). New characteristics of ectopically produced Abutilon mosaic virus (AbMV) MP (MPAbMV), either authentically expressed or fused to a yellow fluorescent protein or epitope tags, respectively, were determined by localization studies in mammalian cell lines in comparison to plant cells. Wild-type MPAbMV and the distinct MPAbMV: reporter protein fusions appeared as curled threads throughout mammalian cells. Co-staining with cytoskeleton markers for actin, intermediate filaments, or microtubules identified these threads as re-organized microtubules. These were, however, not stabilized by the viral MP, as demonstrated by nocodazole treatment. The MP of a related bipartite New World begomovirus, Cleome leaf crumple virus (ClLCrV), resulted in the same intensified microtubule bundling, whereas that of a nanovirus did not. The C-terminal section of MPAbMV, i.e., the protein’s oligomerization domain, was dispensable for the effect. However, MP expression in plant cells did not affect the microtubules network. Since plant epidermal cells are quiescent whilst mammalian cells are proliferating, the replication-associated protein RepAbMV protein was then co-expressed with MPAbMV to induce cell progression into S-phase, thereby inducing distinct microtubule bundling without MP recruitment to the newly formed threads. Co-immunoprecipitation of MPAbMV in the presence of RepAbMV, followed by mass spectrometry identified potential novel MPAbMV-host interaction partners: the peptidyl-prolyl cis-trans isomerase NIMA-interacting 4 (Pin4) and stomatal cytokinesis defective 2 (SCD2) proteins. Possible roles of these putative interaction partners in the begomoviral life cycle and cytoskeletal association modes are discussed.

In addition to vaccines, the World Health Organization sees novel medications as an urgent matter to fight the ongoing COVID-19 pandemic. One possible strategy is to identify target proteins, for which a perturbation by an existing compound is likely to benefit COVID-19 patients. In order to contribute to this effort, we present GuiltyTargets-COVID-19 ( https://guiltytargets-covid.eu/ ), a machine learning supported web tool to identify novel candidate drug targets. Using six bulk and three single cell RNA-Seq datasets, together with a lung tissue specific protein-protein interaction network, we demonstrate that GuiltyTargets-COVID-19 is capable of (i) prioritizing meaningful target candidates and assessing their druggability, (ii) unraveling their linkage to known disease mechanisms, (iii) mapping ligands from the ChEMBL database to the identified targets, and (iv) pointing out potential side effects in the case that the mapped ligands correspond to approved drugs. Our example analyses identified 4 potential drug targets from the datasets: AKT3 from both the bulk and single cell RNA-Seq data as well as AKT2, MLKL, and MAPK11 in the single cell experiments. Altogether, we believe that our web tool will facilitate future target identification and drug development for COVID-19, notably in a cell type and tissue specific manner.

Systemic inflammation presents a significant challenge to the long-term function of biohybrid implants. While endothelialisation of biohybrid implants has been shown to improve device hemocompatibility, its feasibility under the influence of patients’ inflammatory status remains largely unexplored. To investigate this, we developed a controlled in vitro model which allows to study endothelial dysfunction under inflammatory stress. Endothelial cells were cultured on polydimethylsiloxane under physiological shear stress and exposed to lipopolysaccharide (LPS)-activated peripheral blood mononuclear cells (PBMCs), simulating inflammatory conditions. Endothelial morphology and confluence was assessed using immunohistochemistry and scanning electron microscopy. Leukocyte adhesion was evaluated directly as well as indirectly, using flow cytometry to analyse cell adhesion molecules. Quantitative PCR was used for gene expression analysis of inflammatory mediators. Notably, neither LPS nor PBMCs alone induced endothelial disruption, whereas their combination significantly impaired endothelial confluence: Inflammatory activation led to substantial loss of endothelial confluence, increased leukocyte adhesion, and elevated expression of adhesion molecules ICAM-1, VCAM-1, and E-selectin. Gene expression analysis highlights the upregulation of inflammatory mediators, such as IL-6, IL-8, IL-10, and MCP-1. This study underscores the challenges of implementing endothelialisation in biohybrid devices, particularly in patients with systemic inflammation. By considering translational hurdles, this work contributes to the development of clinically viable biohybrid constructs and highlights the importance of considering inflammatory dynamics when designing next-generation implants.

Plants share their habitats with a multitude of different microbes. This close vicinity promoted the evolution of inter-organismic interactions between plants and many different microorganisms that provide mutual growth benefits both to the plant and the microbial partner. The symbiosis of Arabidopsis thaliana with the beneficial root colonizing endophyte Serendipita indica represents a well-studied system. Co-colonization of Arabidopsis roots with S. indica significantly promotes plant growth. Due to the notable phenotypic alterations of fungus-infected root systems, the involvement of a reprogramming of plant hormone levels, especially that of indole-3-acetic acid, has been suggested earlier. However, until now, the molecular mechanism by which S. indica promotes plant growth remains largely unknown. This study used comprehensive transcriptomics, metabolomics, reverse genetics, and life cell imaging to reveal the intricacies of auxin-related processes that affect root growth in the symbiosis between A. thaliana and S. indica. Our experiments revealed the essential role of tightly controlled auxin conjugation in the plant-fungus interaction. It particularly highlighted the importance of two GRETCHEN HAGEN 3 (GH3) genes, GH3.5 and GH3.17, for the fungus infection-triggered stimulation of biomass production, thus broadening our knowledge about the function of GH3s in plants. Furthermore, we provide evidence for the transcriptional alteration of the PIN2 auxin transporter gene in roots of Arabidopsis seedlings infected with S. indica and demonstrate that this transcriptional adjustment affects auxin signaling in roots, which results in increased plant growth.Competing Interest StatementThe authors have declared no competing interest.