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Pseudomonas strains associated with entomopathogenic nematodes

ABSTRACT: Pseudomonas protegens , Pseudomonas chlororaphis, Pseudomonas putida and Pseudomonas sp. strains associated with Steinernema entomopathogenic nematodes

PROVIDER: PRJEB64688 | ENA |

REPOSITORIES: ENA

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Determination of ErfA regulon by DAP-seq in several Pseudomonas species

Project description:ErfA is a transcription factor of Pseudomonas aeruginosa. We here define the genome-wide binding sites of ErfA by DAP-seq in Pseudomonas aeruginosa PAO1 and IHMA87, Pseudomonas chlororaphis PA23, Pseudomonas protegens CHA0 and Pseudomonas putida KT2440.

2019-12-20 | GSE137648 | GEO

Activated entomopathogenic nematode infective juveniles release lethal venom proteins

Project description:Entomopathogenic nematodes (EPNs) are unique parasitic nematodes due to their symbiosis with entomopathogenic bacteria and their ability to kill insect hosts quickly after infection. Although it has been widely believed that EPNs rely on their bacterial partners for killing insect hosts, compelling evidence from previous studies challenges this model. We developed an improved method of activating millions of Steinernema carpocapsae infective juveniles (IJs) in vitro to harvest excreted/secreted (ES) proteins for bioactivity tests and proteomics analysis. We found that a low dose of the ES proteins from early activated nematodes is lethal to Drosophila melanogaster adults within 2-6 hours. We analyzed the protein composition of this venom using mass spectrometry and identified 472 proteins. Many of these venom proteins share high homology with those of vertebrate-parasitic nematodes. Among many different families of proteins found in the venom, proteases and protease inhibitors are especially abundant. Some toxin-related proteins such as Shk domain-containing proteins were also detected. We further analyzed the transcriptomes of individual non-activated IJs and nematodes that were activated in vitro and in vivo, which revealed a dramatic shift in gene expression during IJ activation. By comparing the whole transcriptomes and the genes encoding venom proteins between the in vitro and in vivo activated nematodes, we confirmed that the in vitro activation is a good approximation of the in vivo process. In summary, our findings strongly support a new model that S. carpocapsae and likely other Steinernema EPNs have a more active role in contributing to the pathogenicity of the nematode-bacterium complex than simply relying on their symbiotic bacteria. Furthermore, we propose that EPNs are a good model system for investigating vertebrate- and human-parasitic nematodes, especially regarding the function of ES products.

2017-03-27 | GSE89961 | GEO

The Drosophila immune response towards entomopathogenic nematodes and their associated bacteria.

Project description:Entomopathogenic nematodes (EPNs) of the genera Heterorhabditis are obligate and lethal insect parasites. In recent years they have been used increasingly as biological control agents. These EPNs are symbiotically associated with bacteria of the genera Photorhabdus. The bacterial symbionts are essential to kill the host (within 24-48 hours) and digest its tissues to provide nutrients for themselves as well for expanding nematodes. Drosophila larvae are suitable insect hosts and part of the tripartite model system we used before to show the importance of haemolymph clotting and eicosanoids during the infection. We used the well-established tripartite model (Drosophila, nematodes, bacteria), DNA chips and bioinformatic tools to compare gene expression in non-infected and infected fly larvae. We focused on the early time point of nematode infection and therefore infected Drosophila larvae using H. bacteriophora harbouring GFP-labelled P. luminescens bacteria. Infected (GFP positive) larvae were collected 6 hours after infection.

2014-03-07 | E-MTAB-1542 | biostudies-arrayexpress

Steinernema carpocapsae Breton small RNA sequencing insect in vitro simulation system, from "The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle"

Project description:We report small RNA sequencing of the entomopathogenic nematode Steinernema carpocapsae. The nematodes were grown in liquid culture in homogenates of pig kidney/fat and infective juveniles were gathered. Then Galleria mellonella insect haemolymph was added to simulate insect infection, control nematodes weren't added haemolymph. Nematodes were collected after two hours after haemolymph addition.

2016-09-05 | GSE85256 | GEO

Hybrid assembly of the genome of the entomopathogenic nematode Steinernema carpocapsae identifies the X-chromosome.

Project description:Entomopathogenic nematodes from the genus Steinernema are lethal insect parasites that quickly kill their insect hosts with the help of their symbiotic bacteria. Steinernema carpocapsae is one of the most studied entomopathogens due to its broad lethality to diverse insect species and its effective commercial use as a biological control agent for insect pests, as well as a genetic model for studying parasitism, pathogenesis, and symbiosis. In this study, we used long-reads from the Pacific Biosciences platform and BioNano Genomics Irys system to assemble the best genome of S. carpocapsae ALL strain to date, comprising 84.5 Mb in 16 scaffolds, with an N50 of 7.36Mb. The largest scaffold, with 20.9Mb, was identified as chromosome X based on sex-specific genome sequencing. The high level of contiguity allowed us to characterize gene density, repeat content, and GC content. RNA-seq data from 17 developmental stages, spanning from embryo to adult, were used to predict 30,957 gene models. Using this new genome, we performed a macrosyntenic analysis to Caenorhabditis elegans and Pristionchus pacificus and found S. carpocapsae’s chromosome X to be primarily orthologous to C. elegans’ and P. pacificus’ chromosome II and IV. We also investigated the expansion of protein families and gene expression differences between male and female stage nematodes. This new genome and more accurate set of annotations provide a foundation for new comparative genomic and gene expression studies within the Steinernema clade and across the Nematode phylum.

2019-03-06 | GSE127823 | GEO

Characterization of DkaiC mutants of Pseudomonas putida KT2440/2 and Pseudomonas protegens CHA0

Project description:KaiC is the central cog of the circadian clock in Cyanobacteria. Close homologs of this protein are widespread among bacteria not known to have a circadian physiology. The function, interaction network, and mechanism of action of these KaiC homologs are still largely unknown. Here, we focus on KaiC homologs found in environmental Pseudomonas species. We characterize experimentally the only KaiC homolog present in Pseudomonas putida KT2440 and Pseudomonas protegens CHA0. Through phenotypic assays and transcriptomics, we show that KaiC is involved in osmotic and oxidative stress resistance in P. putida and in biofilm production in both P. putida and P. protegens.

2023-01-04 | GSE221044 | GEO

2016-09-05 | E-GEOD-85256 | biostudies-arrayexpress

Low temperature exposure has immediate and lasting effects on the stress tolerance, chemotaxis and proteome of entomopathogenic nematodes

Project description:Entomopathogenic nematodes (EPN) such as Steinernema spp. and Heterorhabditis spp. are obligate parasites of insects and effective biocontrol agents. Infective juveniles (IJs) of Steinernema carpocapsae and Heterorhabditis megidis are distantly related and exhibit different foraging behaviours but utilise similar volatiles to find hosts. These IJs live in the soil year-round and are exposed to a range of temperatures and associated stressors. Here we attempt to understand how exposure to low temperatures, and the duration of this exposure, affects the behaviour and stress resistance of these IJs. S. carpocapsae and H. megidis have similar responses to many odorants upon emergence from their natal host. The chemotaxis of H. megidis at 20°C is generally enhanced after exposure to lower temperatures, whereas the chemotaxis of S. carpocapsae at 20°C tends to be inverted by exposure low temperatures. Exposure to temperatures below culture temperature affects the chemotaxis of H. megidis gradually, whereas S. carpocapsae behave in a binary manner. Brief exposure to 9°C causes the behaviour of S. carpocapsae IJs to be altered and increased their resistance to freezing and desiccation for weeks afterwards. Label free quantitative proteomics confirms that exposure to 9°C for 1 week elicits dramatic increases in chaperone proteins in S. carpocapsae IJs, which are retained at high levels for 2 weeks after their transfer to 20°C. The proteome of S. carpocapsae IJs exposed to 9°C for 1 week and subsequently transferred to 20°C for 2 weeks conforms closely to that of IJs kept at 9°C for 3 weeks. Thus, S. carpocapsae IJs display a high degree of plasticity, and their behaviour and stress resistance may be manipulated by brief controlled exposure to low temperatures.

2022-11-09 | PXD027609 | Pride

Drosophila melanogaster microbiome after infection with entomopathogenic nematodes (Steinernema spp.)

Project description:Drosophila melanogaster microbiome after infection with Steinernema nematodes

| PRJEB76541 | ENA

Secreted proteins from activated infective juveniles of the entomopathogenic nematode Steinernema capocapsae

Project description:The infective juveniles (IJs) of entomopathogenic nematodes such as Steinernema carpocapsae are the only stage in their life cycle that is free living before infecting new hosts. When the IJs enter the host, they activate and secrete proteins to modulate the host immune system. The secreted proteins are identified by mass spectrometry in this study.

2016-11-01 | MSV000080306 | MassIVE

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