Prokaryotic viperins produce diverse antiviral molecules.
Ontology highlight
ABSTRACT:
SUBMITTER: Bernheim A
PROVIDER: S-EPMC7610908 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Discovery of the anti-phage activity of prokaryotic viperins
| PRJEB36546 | ENA
Project description:Viperin is an interferon-induced cellular protein conserved in animals. It was shown to inhibit the replication of multiple viruses by producing a ribonucleotide called 3’-deoxy-3’4’-didehydro-CTP (ddhCTP), which acts as a chain terminator for the viral RNA polymerase. Here we show that the eukaryotic viperin has originated from a clade of bacterial and archaeal proteins that protect against phage infection. Prokaryotic viperins (pVips) produce a set of modified ribonucleotides that include, in addition to ddhCTP, also ddhGTP and ddhUTP. We further provide evidence that pVips protect against T7 phage infection by inhibiting viral polymerase-dependent transcription, suggesting a conserved mechanism of action shared between pVips and the animal viperin. Our results unveil a potential repository of natural antiviral compounds produced by bacterial immune systems.
2020-08-24 | MTBLS1750 | MetaboLights
Project description:Animal cytoplasmic fatty acid synthase (FAS) represents a unique family of enzymes that are classically thought to be most closely related to fungal polyketide synthase (PKS). Recently, a widespread family of animal lipid metabolic enzymes has been described that bridges the gap between these two ubiquitous and important enzyme classes: the animal FAS-like PKSs (AFPKs). Although very similar in sequence to FAS enzymes that produce saturated lipids widely found in animals, AFPKs instead produce structurally diverse compounds that resemble bioactive polyketides. Little is known about the factors that bridge lipid and polyketide synthesis in the animals. Here, we describe the function of EcPKS2 from Elysia chlorotica, which synthesizes a complex polypropionate natural product found in this mollusc. EcPKS2 starter unit promiscuity potentially explains the high diversity of polyketides found in and among molluscan species. Biochemical comparison of EcPKS2 with the previously described EcPKS1 reveals molecular principles governing substrate selectivity that should apply to related enzymes encoded within the genomes of photosynthetic gastropods. Hybridization experiments combining EcPKS1 and EcPKS2 demonstrate the interactions between the ketoreductase and ketosynthase domains in governing the product outcomes. Overall, these findings enable an understanding of the molecular principles of structural diversity underlying the many molluscan polyketides likely produced by the diverse AFPK enzyme family.
| S-EPMC10515154 | biostudies-literature
Project description:BackgroundDufulin is a new antiviral agent that is highly effective against plant viruses and acts by activating systemic acquired resistance (SAR) in plants. In recent years, it has been used widely to prevent and control tobacco and rice viral diseases in China. However, its targets and mechanism of action are still poorly understood.Methodology/principal findingsHere, differential in-gel electrophoresis (DIGE) and classical two-dimensional electrophoresis (2-DE) techniques were combined with mass spectrometry (MS) to identify the target of Dufulin. More than 40 proteins were found to be differentially expressed (≥1.5 fold or ≤1.5 fold) upon Dufulin treatment in Nicotiana tabacum K(326). Based on annotations in the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, these proteins were found to be related to disease resistance. Directed acyclic graph (DAG) analysis of the various pathways demonstrated harpin binding protein-1 (HrBP1) as the target of action of Dufulin. Additionally, western blotting, semi-quantitative reverse transcription polymerase chain reaction (RT-PCR), and real time PCR analyses were also conducted to identify the specific mechanism of action of Dufulin. Our results show that activation of HrBP1 triggers the salicylic acid (SA) signaling pathway and thereby produces antiviral responses in the plant host. A protective assay based on lesion counting further confirmed the antiviral activity of Dufulin.ConclusionThis study identified HrBP1 as a target protein of Dufulin and that Dufulin can activate the SA signaling pathway to induce host plants to generate antiviral responses.
| S-EPMC3360678 | biostudies-literature
Project description:Eudicot leaves have astoundingly diverse shapes. The central problem addressed in this paper is the developmental origin of this diversity. To investigate this problem, we propose a computational model of leaf development that generalizes the largely conserved molecular program for the reference plants Arabidopsis thaliana, Cardamine hirsuta and Solanum lycopersicum. The model characterizes leaf development as a product of three interwoven processes: the patterning of serrations, lobes and/or leaflets on the leaf margin; the patterning of the vascular system; and the growth of the leaf blade spanning the main veins. The veins play a significant morphogenetic role as a local determinant of growth directions. We show that small variations of this model can produce diverse leaf shapes, from simple to lobed to compound. It is thus plausible that diverse shapes of eudicot leaves result from small variations of a common developmental program.
| S-EPMC5638099 | biostudies-literature
Project description:Infection with Ebola virus (EBOV) is responsible for hemorrhagic fever in humans with a high mortality rate. Combined efforts of prevention and therapeutic intervention are required to tackle highly variable RNA viruses, whose infections often lead to outbreaks. Here, we have screened the 2P2I3D chemical library using a nanoluciferase-based protein complementation assay (NPCA) and isolated two compounds that disrupt the interaction of the EBOV protein fragment VP35IID with the N-terminus of the dsRNA-binding proteins PKR and PACT, involved in IFN response and/or intrinsic immunity, respectively. The two compounds inhibited EBOV infection in cell culture as well as infection by measles virus (MV) independently of IFN induction. Consequently, we propose that the compounds are antiviral by restoring intrinsic immunity driven by PACT. Given that PACT is highly conserved across mammals, our data support further testing of the compounds in other species, as well as against other negative-sense RNA viruses.
| S-EPMC10573436 | biostudies-literature
Project description:The extent and role of horizontal gene transfer (HGT) in phytoplankton and, more broadly, eukaryotic evolution remain controversial topics. Recent studies substantiate the importance of HGT in modifying or expanding functions such as metal or reactive species detoxification and buttressing halotolerance. Yet, the potential of HGT to significantly alter the fate of species in a major eukaryotic assemblage remains to be established. We provide such an example for the ecologically important lineages encompassed by cryptophytes, rhizarians, alveolates, stramenopiles, and haptophytes ("CRASH" taxa). We describe robust evidence of prokaryotic HGTs in these taxa affecting functions such as polysaccharide biosynthesis. Numbers of HGTs range from 0.16 to 1.44% of CRASH species gene inventories, comparable to the ca. 1% prokaryote-derived HGTs found in the genomes of extremophilic red algae. Our results substantially expand the impact of HGT in eukaryotes and define a set of general principles for prokaryotic gene fixation in phytoplankton genomes.
| S-EPMC7190310 | biostudies-literature
Project description:The origins of human language remains a major question in evolutionary science. Unique to human language is the capacity to flexibly recombine a limited sound set into words and hierarchical sequences, generating endlessly new sentences. In contrast, sequence production of other animals appears limited, stunting meaning generation potential. However, studies have rarely quantified flexibility and structure of vocal sequence production across the whole repertoire. Here, we used such an approach to examine the structure of vocal sequences in chimpanzees, known to combine calls used singly into longer sequences. Focusing on the structure of vocal sequences, we analysed 4826 recordings of 46 wild adult chimpanzees from Taï National Park. Chimpanzees produced 390 unique vocal sequences. Most vocal units emitted singly were also emitted in two-unit sequences (bigrams), which in turn were embedded into three-unit sequences (trigrams). Bigrams showed positional and transitional regularities within trigrams with certain bigrams predictably occurring in either head or tail positions in trigrams, and predictably co-occurring with specific other units. From a purely structural perspective, the capacity to organize single units into structured sequences offers a versatile system potentially suitable for expansive meaning generation. Further research must show to what extent these structural sequences signal predictable meanings.
| S-EPMC9110424 | biostudies-literature
Project description:Nematode-trapping fungi are natural antagonists of nematodes. These predatory fungi are capable of switching their lifestyle from a saprophytic to predatory stage in the presence of nematodes by developing specialized trapping devices to capture and consume nematodes. The biochemical mechanisms of such predator-prey interaction have become increasingly studied given the potential application of nematode-trapping fungi as biocontrol agents, but the involved fungal metabolites remain underexplored. Here, we report a comprehensive liquid-chromatography mass spectrometry (LC-MS) metabolomics study on one hundred wild isolates of nematode-trapping fungi in three different species, Arthrobotrysoligospora, Arthrobotrys thaumasia, and Arthrobotrys musiformis. Molecular networking analysis revealed that the fungi were capable of producing thousands of metabolites, and such chemical diversity of metabolites was notably increased as the fungi switched lifestyle to the predatory stage. Structural annotations by tandem mass spectrometry revealed that those fungal metabolites belonged to various structural families, such as peptide, siderophore, fatty alcohol, and fatty acid amide, and their production exhibited species specificity. Several small peptides (<1.5 kDa) produced by A.musiformis in the predatory stage were found, with their partial amino acid sequences resolved by the tandem mass spectra. Four fungal metabolites (desferriferrichrome, linoleyl alcohol, nonadecanamide, and citicoline) that were significantly enriched in the predatory stage were identified and validated by chemical standards, and their bioactivities against nematode prey were assessed. The availability of the metabolomics datasets will facilitate comparative studies on the metabolites of nematode-trapping fungi in the future.
| S-EPMC7143726 | biostudies-literature
Project description:Scientific teams are increasingly diverse in discipline, international scope and demographics. Diversity has been found to be a driver of innovation but also can be a source of interpersonal friction. Drawing on a mixed-method study of 22 scientific working groups, this paper presents evidence that team diversity has a positive impact on scientific output (i.e., the number of journal papers and citations) through the mediation of the interdisciplinarity of the collaborative process, as evidenced by publishing in and citing more diverse sources. Ironically these factors also seem to be related to lower team member satisfaction and perceived effectiveness, countered by the gender balance of the team. Qualitative data suggests additional factors that facilitate collaboration, such as trust and leadership. Our findings have implications for team design and management, as team diversity seems beneficial, but the process of integration can be difficult and needs management to lead to a productive and innovative process.
| S-EPMC9707800 | biostudies-literature