Background European beech (Fagus sylvatica L.) trees produce seeds irregularly; therefore, it is necessary to store beech seeds for forestation. Despite the acquisition of desiccation tolerance during development, beech seeds are classified as intermediate because they lose viability during long-term storage faster than typical orthodox seeds. In this study, beech seeds stored for short (3 years) or long (20 years) periods under optimal conditions and displaying 92 and 30% germination capacity, respectively, were compared. Results Aged seeds displayed increased membrane damage, manifested as electrolyte leakage and lipid peroxidation levels. Analyses have been based on embryonic axes, which contained higher levels of reactive oxygen species (ROS) and higher levels of protein-bound methionine sulfoxide (MetO) in aged seeds. Using label-free quantitative proteomics, 3,949 proteins were identified, of which 2,442 were reliably quantified pointing to 24 more abundant proteins and 35 less abundant proteins in beech seeds under long-term storage conditions. Functional analyses based on gene ontology annotations revealed that nucleic acid binding activity (molecular function), ribosome organization or biogenesis and transmembrane transport (cellular processes), translational proteins (protein class) and membranous anatomical entities (cellular compartment) were affected in aged seeds. To verify whether MetO, the oxidative posttranslational modification of proteins that can be reversed via the action of methionine sulfoxide reductase (Msr) enzymes, is involved in the aging of beech seeds, we identified and quantified 226 MetO-containing proteins, among which 9 and 19 exhibited significantly up- and downregulated MetO levels, respectively, in beech seeds under long-term storage conditions. Several Msr isoforms were identified and recognized as MsrA1-like, MsrA4, MsrB5 and MsrB5-like in beech seeds. Only MsrA1-like displayed decreased abundance in aged seeds. Conclusions We demonstrated that the loss of membrane integrity reflected in the elevated abundance of membrane proteins had a higher impact on seed aging progress than the MetO/Msr system. Proteome analyses enabled us to propose protein Sec61 and glyceraldehyde-3-phosphate dehydrogenase as potential longevity modulators in beech seeds.

Thaumatin-like proteins (TLPs, osmotins) form a protein family which shares a significant sequence homology to the sweet-tasting thaumatin from the plant Thaumatococcus daniellii. TLPs are not sweet-tasting and are involved in response to biotic stresses and developmental processes. Recently it has been shown using a proteomic approach that the tuber extract from Corydalis cava (Papaveraceae) contains a TLP protein. The aim of this work was to characterize the structure and expression of TLP from C. cava tubers. The results obtained using a PCR approach with degenerate primers demonstrated a coding sequence of a novel protein, named CcTLP1. It consists of 225 aa, has a predicted molecular weight of 24.2 kDa (NCBI GenBank accession no. KJ513303) and has 16 strictly conserved cysteine residues, which form 8 disulfide bridges and stabilize the 3D structure. CcTLP1 may be classified into class IX of plant TLPs. The highest CcTLP1 expression levels were shown by qPCR in the stem of the plant compared to other organs and in the medium-size plants compared to other growth phases. The results confirm that CcTLP1 is expressed during plant growth and development until flowering, with a possible defensive function against different stress conditions.

Sequence-deficient mitochondrial pre-mRNAs in African trypanosomes are substrates of a U-nucleotide-specific RNA editing reaction to generate translation-competent mRNAs. The reaction is catalyzed by a macromolecular protein complex termed the editosome. Editosomes execute RNA-chaperone activity to overcome the highly folded nature of pre-edited substrate mRNAs. The molecular basis for this activity is unknown. Here we test five of the OB-fold proteins of the Trypanosoma brucei editosome as candidates. We demonstrate that all proteins execute RNA-chaperone activity albeit to different degrees. We further show that the activities correlate to the surface areas of the proteins and we map the protein-induced RNA-structure changes using SHAPE-chemical probing. To provide a structural context for our findings we calculate a coarse-grained model of the editosome. The model has a shell-like structure: Structurally well-defined protein domains are separated from an outer shell of intrinsically disordered protein domains, which suggests a surface-driven mechanism for the chaperone activity.

SUMMARY RNA editing in African trypanosomes represents an RNA-processing reaction that generates functional mitochondrial transcripts from sequence-deficient pre-mRNAs. The reaction is catalyzed by a macromolecular protein complex known as the editosome. Editosomes have been demonstrated to execute RNA-chaperone activity to overcome the highly folded nature of pre-edited substrate mRNAs. The molecular basis of this activity is unknown. Here we test five OB-fold proteins of the editosome as potential candidates. We show that the different proteins interact by hetero-oligomerization and we demonstrate that all proteins execute RNA-chaperone activity. Activity differences correlate with the surface areas of the proteins and map predominantly to the intrinsically disordered subdomains of the polypeptides. To provide a structural context for our findings we present a coarse-grained model of the editosome. The model suggests that an inner core of catalytically active editosome components is separated from an outer shell of IDP-domains that act as RNA-remodeling sites.

Peroxiredoxins (PRDXs) are thioredoxin-family antioxidant enzymes that scavenge peroxides. PRDXs are abundantly expressed in tumor cells, and their inhibition emerges as a novel antitumor strategy. We had previously reported on the synthesis of the thiol-specific peptidomimetic, SK053, showing antitumor activity [1]. In this study we identified SK053 protein targets in human Burkitt’s lymphoma cell lines. To identify SK053 targets we have used biotin affinity probe labelling approach. PRDXs levels were assessed by qPCR, Western blotting and immunohistochemistry. To study the role of PRDX1 and PRDX2 in lymphoma cells, we have employed the shRNA-mediated knockdown. We identified dimeric peroxiredoxins as targets for SK053. SK053 triggered the formation of covalent PRDX dimers, accumulation of intracellular ROS, phosphorylation of ERK1/2 and AKT, cell cycle arrest and apoptosis. Based on site-directed mutagenesis and SK053 docking studies, we propose a mechanism of SK053-mediated PRDX crosslinking. Furthermore, we found that PRDX1 and PRDX2 are upregulated in lymphoma cell lines and in lymphoma cells isolated from patients. Combined genetic downregulation of PRDX1 and PRDX2 attenuated the proliferation and survival of lymphoma cells. Altogether, our results highlight the importance of peroxiredoxins for lymphoma cells and demonstrate that these antioxidant proteins are attractive therapeutic targets in Burkitt’s lymphoma.

Signal transducers and activators of transcription (STATs) facilitate action of cytokines, growth factors and pathogens. STAT activation is mediated by a highly conserved SH2 domain, which interacts with phosphotyrosine motifs for specific STAT-receptor contacts and STAT dimerization. The active dimers induce gene transcription in the nucleus by binding to a specific DNA-response element in the promoter of target genes. Abnormal activation of STAT signaling pathways is implicated in many human diseases, like cancer, inflammation and auto-immunity. Searches for STAT-targeting compounds, exploring the phosphotyrosine (pTyr)-SH2 interaction site, yielded many small molecules for STAT3 but sparsely for other STATs. However, many of these inhibitors seem not STAT3-specific, thereby questioning the present modeling and selection strategies of SH2 domain-based STAT inhibitors. We generated new 3D structure models for all human (h)STATs and developed a comparative in silico docking strategy to obtain further insight into STAT-SH2 cross-binding specificity of a selection of previously identified STAT3 inhibitors. Indeed, by primarily targeting the highly conserved pTyr-SH2 binding pocket the majority of these compounds exhibited similar binding affinity and tendency scores for all STATs. By comparative screening of a natural product library we provided initial proof for the possibility to identify STAT1 as well as STAT3-specific inhibitors, introducing the 'STAT-comparative binding affinity value' and 'ligand binding pose variation' as selection criteria. In silico screening of a multi-million clean leads (CL) compound library for binding of all STATs, likewise identified potential specific inhibitors for STAT1 and STAT3 after docking validation. Based on comparative virtual screening and docking validation, we developed a novel STAT inhibitor screening tool that allows identification of specific STAT1 and STAT3 inhibitory compounds. This could increase our understanding of the functional role of these STATs in different diseases and benefit the clinical need for more drugable STAT inhibitors with high specificity, potency and excellent bioavailability.

In this study the effect of host changes and multiple passages on Pepino mosaic virus ( PepMV ) evolution was analysed. A population of a mild isolate of PepMV was used to generate five independent evolution lineages on three tomato cultivars, which differ in rate of appearance of symptoms and their severity during viral infection (Beta Lux, Moneymaker and Malinowy Ożarowski) and on Datura inoxia . Twenty serial passages were performed over a period of 217–220 days. Symptom severity was monitored along the entire experiment. After the last series of passages total RNAs from each lineage and host were isolated and the triple gene block 3 ( TGB3 ) and coat protein ( CP ) were amplified, cloned and 10 clones for each gene sequenced. Among the 400 clones for both genes, 143 individual mutations (61 synonymous and 82 nonsynonymous) were identified, with the largest number of nonsynonymous mutations being observed for the tomato cultivars Malinowy Ożarowski and Beta Lux. In two of the lineages evolving in the most susceptible variety of tomato (Beta Lux) necrotic changes in leaf blades appeared after 17 passages, leading to death of the plants. In these two lineages the mutation responsible for necrotic symptoms was K67E in TGB3 . The appearance of this convergent mutation in independently evolving lineages may suggest that selection in this experimental set up favours more aggressive PepMV variants. We found a positive association between the severity of symptoms and the amount of genetic variability contained on viral populations. Indeed, the severity of symptoms turned out to be a good predictor for several indices of molecular variability. In addition, mapping all observed mutations in CP and TGB3 protein structures revealed that most were located on the surface, indicating a possible implication in viral–viral or viral–host interactions.

Burkitt lymphoma is a fast-growing tumor derived from germinal center B cells. It is mainly treated with aggressive chemotherapy, therefore novel therapeutic approaches are needed due to treatment toxicity and developing resistance. Disturbance of red-ox homeostasis has recently emerged as an efficient antitumor strategy. Peroxiredoxins (PRDXs) are thioredoxin-family antioxidant enzymes that scavenge cellular peroxides and contribute to red-ox homeostasis. PRDXs are robustly expressed in various malignancies and critically involved in cell proliferation, differentiation and apoptosis. To elucidate potential role of PRDXs in lymphoma, we studied their expression level in B cell-derived primary lymphoma cells as well as in cell lines. We found that PRDX1 and PRDX2 are upregulated in tumor B cells as compared with normal counterparts. Concomitant knockdown of PRDX1 and PRDX2 significantly attenuated the growth rate of lymphoma cells. Furthermore, in human Burkitt lymphoma cell lines, we isolated dimeric 2-cysteine peroxiredoxins as targets for SK053, a novel thiol-specific small-molecule peptidomimetic with antitumor activity. We observed that treatment of lymphoma cells with SK053 triggers formation of covalent PRDX dimers, accumulation of intracellular reactive oxygen species, phosphorylation of ERK1/2 and AKT and leads to cell cycle arrest and apoptosis. Based on site-directed mutagenesis and modeling studies, we propose a mechanism of SK053-mediated PRDX crosslinking, involving double thioalkylation of active site cysteine residues. Altogether, our results suggest that peroxiredoxins are novel therapeutic targets in Burkitt lymphoma and provide the basis for new approaches to the treatment of this disease.

Signal transducers and activators of transcription (STATs) are a family of proteins activated by different stimulating factors, including interferons, interleukins, growth factors and oncoproteins. Their role in many diseases has been proven, so there is a strong demand to find specific strategies for STAT inhibition. Our searches for specific STAT-targeting compounds focused on exploring the phosphotyrosine (pTyr) SH2 interaction area. Current selection strategies are insufficient, thus, we developed a new pipeline strategy. In this work we used our recently built 3D models for all human (h)STATs (1–4, 5A, 5B and 6). To select specific inhibitors for the STAT protein of interest, we designed and implemented a five step comparative virtual screening tool, which we named – CAVS (comparative approach for virtual screening). CAVS introduces the ‘comparative binding affinity value’ (CBAV) and ‘ligand binding pose variation’ (LBPV) as selection criteria to identify specific inhibitors of STATs. In a five-step approach, including pre-screen, primary filtering of inhibitors, re-screen, secondary filtering of inhibitors and graphical inspection and final selection, CAVS leads to selection of specific STAT inhibitory compounds. CAVS was tested on a small ligand library of 130000 natural products and 5.7 million of clean leads for the selection of STAT1 or STAT3-specific inhibitors. With the use of a designed set of Python scripts for data managing and filtering, CAVS allows to convert the comparative virtual screening procedure into an automatic pipeline and to effectively analyze virtual screening results from standard Surflex-Dock 2.6 output files. We also adapted CAVS as a general-purpose pipeline, which will allow adapting written code to different experiments and protein families in the future.

The macroalgae representing the cosmopolitan Ulva flexuosa Wulfen species have been found in inland water ecosystems of Europe since the mid-1800s. The presence of the Ulva genus in waters of inland salt marshes was explained by high salinity of water in such systems. However, Ulva flexuosa thalli were found in lakes and rivers having no supply from strongly mineralized sources, either of natural or anthropogenic origin. The study focused only on populations of Ulva flexuosa subsp. pilifera (Kutz.) M.J. Wynne and Ulva flexuosa subsp. paradoxa (C. Agardh) M.J. Wynne occurring in inland ecosystems isolated from seawater. The differentiation of inland U. flexuosa subsp. pilifera and subspecies paradoxa was assessed by using classical morphological data and molecular techniques. We found that only two subspecies of Ulva flexuosa Wulfen occur in inland water ecosystems of Poland. On the basis of the analysis combining morphological features with the ITS region and rbcL gene sequences, a small degree of differentiation of the two inland taxa was demonstrated. These two subspecies have high differentiation of the habitat niches. U. flexuosa subsp. paradoxa settled in habitats featuring high salinity levels, and the second subspecies pilifera occurred only in fresh waters.

BACKGROUNDThe voltage-sensitive sodium channel (VSSC) is a target for the pharmacological action of pyrethroids which are used in controlling pests, including those of agricultural importance. Among these is the pollen beetle (Meligethes aeneus F.) - the most serious pest of Brassica napus. Owing to the heavy use of pyrethroids, a widespread build-up of resistance has occurred. The main cause of pyrethroid insensitivity in M. aeneus is considered to be an increased oxidative metabolism; however, the additional mechanism of resistance associated with mutations in the VSSC might contribute to this phenomenon.RESULTSWe generated a VSSC 3D model to study the docking affinities of pyrethroids to their target site within the channel. Our goal was to identify the pyrethroids for which docking affinity scores were high and not affected by potential mutations in the VSSC. We found that the docking scores of cypermethrin are hardly influenced by the appearance of point mutations. Additionally, tau-fluvalinate, deltamethrin and bifenthrin are VSSC ligands with high affinity scores.CONCLUSIONSOur docking models suggest that point mutations in the VSSC binding pocket might affect the stability of ligand interactions and change the pattern of ligand docking locations, which might have a potential effect on VSSC gating properties.

Mitochondrial pre‐mRNAs in trypanosomatids undergo RNA editing to be converted into translatable mRNAs. The reaction is characterized by the insertion and deletion of uridine residues and is catalyzed by a macromolecular protein complex called the editosome. Despite intensive research, structural information for the majority of editosome proteins is still missing and no high resolution structure for the editosome exists. Here we present a comprehensive structural bioinformatics analysis of all proteins of the Trypanosoma brucei editosome. We specifically focus on the interplay between intrinsic order and disorder. According to computational predictions, editosome proteins involved in the basal reaction steps of the processing cycle are mostly ordered. By contrast, thirty percent of the amino acid content of the editosome is intrinsically disordered, which includes most prominently proteins with OB‐fold domains. Based on the data we suggest a functional model, in which the structurally disordered domains of the complex are correlated with the RNA binding and RNA unfolding activity of the T. brucei editosome.

Species of Ulva (Ulvaceae, Chlorophyta) are relatively common macroalgae in most coastal areas. In this paper, we examine Ulva in inland aquatic ecosystems to determine relationships between the chemical parameters of the water and the Ulva taxa present. Two groups of samples of freshwater Ulva were selected from: (i) habitats with high salinity levels, and (ii) habitats with fresh or slightly saline waters. We showed that these two groups of Ulva, which occupy distinct habitats, represent two separate taxa. The first group represents Ulva flexuosa subsp. pilifera (Kützing) M.J. Wynne, which is very common and regularly encountered in fresh waters, but is equally well represented in slightly saline waters. The second is U. flexuosa subsp. paradoxa (C. Agardh) M.J. Wynne, which is less common, preferring mainly salt-wedge saline waters. We did not find both Ulva flexuosa subspecies together at any of the research sites.There were significant morphological differences between the Ulva flexuosa subspecies. Ulva flexuosa subsp. pilifera had longer and wider thalli and wider cells than those of subsp. paradoxa. Ulva flexuosa subsp. paradoxa cells were longer and of greater circumference than those of subsp. pilifera. Analyses of the rRNA ITS region and partial rbcL gene sequences demonstrated minor sequence variation within the two subspecies. The results of this study provide detailed information on the characteristics of limnic Ulva habitats and indicate the niches where such populations are likely to occur.

The pollen beetle (Meligethes aeneus F.) is the most devastating pest of oilseed rape (Brassica napus) and is controlled by pyrethroid insecticides. However, resistance to pyrethroids in Europe is becoming widespread and predominant. Pyrethroids target the voltage-sensitive sodium channel (VSSC), and mutations in VSSC may be responsible for pyrethroid insensitivity. Here, we analysed individual beetles that were resistant to esfenvalerate, a pyrethroid, from 14 populations that were collected from oilseed rape fields in Poland. We screened the VSSC domains that were presumed to directly interact with pyrethroids. We identified 18 heterozygous nucleic acid substitutions, amongst which six caused an amino acid change: N912S, G926S, I936V, R957G, F1538L and E1553G. Our analysis of the three-dimensional structure of these domains in VSSC revealed that some of these changes may slightly influence the protein structure and hence the docking efficiency of esfenvalerate. Therefore, these mutations may impact the susceptibility of the sodium channel to the action of this insecticide.

Signal transducers and activators of transcription (STATs) facilitate action of cytokines, growth factors and pathogens. STAT activation is mediated by a highly conserved SH2 domain, which interacts with phosphotyrosine (pTyr) motifs for specific STAT-receptor contacts and STAT dimerization. The active dimers induce gene transcription in the nucleus by binding to specific DNA-response elements of target genes. Abnormal activation of STAT signaling pathways is implicated in many human diseases, like cancer, inflammation and auto-immunity. STAT inhibitory strategies mostly focus on inhibiting STAT dimerization using small molecules identified by molecular modeling, virtual or library screening, or natural products. Searches for STAT-targeting compounds, exploring the pTyr-SH2 interaction area, yielded many small molecules for STAT3 but sparsely for other STATs. So far, no STAT-targeting drug is approved by the FDA. Moreover, many of these inhibitors do not seem STAT-specific, thereby questioning the present selection strategies of SH2 domain-based STAT inhibitors. This illustrates the need for better models, and screening and validation tools for more druggable STAT inhibitors with high specificity, potency and excellent bioavailability. Based on newly developed 3D structure models for all human (h)STATs, we propose a pipeline approach that combines comparative in silico docking of STAT-SH2 models with an in vitro STAT phosphorylation assay, as a novel tool to screen multi-million compound libraries and identify specific inhibitors for different STATs. Identification of specific and effective STAT inhibitory compounds could provide a tool to increase our understanding of their functional role in different diseases, and serve as therapeutic strategies in cancer, inflammation and auto-immunity.

Ornithine decarboxylase (ODC) is the key enzyme in the polyamine biosynthetic pathway. ODC levels are controlled by polyamines through the induction of antizymes (AZs), small proteins that inhibit ODC and target it to proteasomal degradation without ubiquitination. Antizyme inhibitors (AZIN1 and AZIN2) are proteins homologous to ODC that bind to AZs and counteract their negative effect on ODC. Whereas ODC and AZIN1 are well-characterized proteins, little is known on the structure and stability of AZIN2, the lastly discovered member of this regulatory circuit. In this work we first analyzed structural aspects of AZIN2 by combining biochemical and computational approaches. We demonstrated that AZIN2, in contrast to ODC, does not form homodimers, although the predicted tertiary structure of the AZIN2 monomer was similar to that of ODC. Furthermore, we identified conserved residues in the antizyme-binding element, whose substitution drastically affected the capacity of AZIN2 to bind AZ1. On the other hand, we also found that AZIN2 is much more labile than ODC, but it is highly stabilized by its binding to AZs. Interestingly, the administration of the proteasome inhibitor MG132 caused differential effects on the three AZ-binding proteins, having no effect on ODC, preventing the degradation of AZIN1, but unexpectedly increasing the degradation of AZIN2. Inhibitors of the lysosomal function partially prevented the effect of MG132 on AZIN2. These results suggest that the degradation of AZIN2 could be also mediated by an alternative route to that of proteasome. These findings provide new relevant information on this unique regulatory mechanism of polyamine metabolism.

Recently, Pepino mosaic virus (PepMV) infections causing severe yellowing symptoms in tomato plants have been reported in glasshouse tomato crops. When studying this phenomenon in commercial glasshouses, two different types of yellowing symptoms, occurring in adjacent plants, were distinguished: interveinal leaf yellowing and yellow mosaics. After several weeks, the interveinal leaf yellowing symptoms gradually disappeared and the plant heads became green again, with yellow mosaic patterns on the leaves as an intermediate stage. The sequencing of multiple isolates causing interveinal leaf yellowing identified two point mutations, occurring in positions 155 and 166 of the coat protein (CP), as unique to the yellowing pathotype. Site-directed mutagenesis of infectious clones confirmed that both CP mutations are determinants of the interveinal leaf yellowing symptoms. Sequencing of CP clones from plants or plant parts with the yellow mosaic symptoms resulted in a mixture of wild-type and mutated sequences, whereas sequencing of CP clones from the green heads of recovered plants resulted in only wild-type sequences. Yellow mosaic symptoms could be reproduced by inoculation of an artificial 1:1 mixture of RNA transcripts from the wild-type and mutated infectious clones. These results show that the ratio of mutated versus wild-type sequences can determine the nature and severity of symptom development. The gradual recovery of the plants, which coincides with the disappearance of the yellowing mutations, suggests that selection pressure acts to the advantage of the wild-type virus. Experiments with wild-type and mutated infectious clones showed that reverse mutation events from mutant to wild-type occur and that the wild-type virus does not have a replicative advantage over the mutant. These results suggest that reverse mutation events occur, with subsequent selection pressure acting in favour of the wild-type virus in the growing plant parts, possibly related to a lower long-distance movement efficiency of the mutant.

Prototyping is an important phase during development of innovative solutions. Iterative design process and testing prototypes with users may highly improve the final result. Design Thinking methodology developed in Silicon Valley is widely recognized and used in many successful companies as a method to foster creativity and innovation. The paper presents selected case studies from Polish universities, where Design Thinking and prototyping have been introduced.