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RNA-Sequencing analysis of the Drosophila transcriptomic response to infection by entomopathogenic nematodes and their mutualistic bacteria

ABSTRACT: We report the application of next generation RNA sequencing to analyze the transcriptional response of Drosophila adult flies to infection by the insect pathogenic nematodes Heterorhabditis bacteriophora and their mutualistic bacteria Photorhabdus luminescens, either separately or together. We find that Heterorhabditis and Photorhabdus differentially modulate a large number of genes, many of which participate in metabolic functions, stress responses, repression of gene transcription and neuronal activities. We have also identified Drosophila genes with potential role in nematode recognition and others with putative anti-nematode properties. These findings generate novel insights into how the host immune function is shaped to respond against nematode parasites and their associated bacteria.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE61466 | GEO | 2015/09/12

REPOSITORIES: GEO

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RNA-Sequencing analysis of the Drosophila transcriptomic response to infection by entomopathogenic nematodes and their mutualistic bacteria

Project description:We report the application of next generation RNA sequencing to analyze the transcriptional response of Drosophila adult flies to infection by the insect pathogenic nematodes Heterorhabditis bacteriophora and their mutualistic bacteria Photorhabdus luminescens, either separately or together. We find that Heterorhabditis and Photorhabdus differentially modulate a large number of genes, many of which participate in metabolic functions, stress responses, repression of gene transcription and neuronal activities. We have also identified Drosophila genes with potential role in nematode recognition and others with putative anti-nematode properties. These findings generate novel insights into how the host immune function is shaped to respond against nematode parasites and their associated bacteria. Transcriptional profiles of Drosophila wild-type adult flies infected with Heterorhabditis bacteriophora carrying or lacking Photorhabdus or the bacteria alone were generated at 12 and 30 hours post infection using Illumina deep sequencing technology.

2015-09-12 | E-GEOD-61466 | biostudies-arrayexpress

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

Gene expression of a Photorhabdus M-form variant relative to the wild type P-form cells

2011-09-15 | GSE32088 | GEO

Transcriptionnal analysis of a Photorhabdus luminescens TT01 variant, named VAR*, which is a colonial and phenotypic variant displaying delayed pathogenicity in the insect, Spodoptera littoralis.

2010-10-13 | GSE24627 | GEO

Gene expression of a Photorhabdus M-form variant relative to the wild type P-form cells

Project description:Photorhabdus luminescens bacteria alternate lifestyles between its pathogenic insect host and its mutualistic nematode host. We found that Photorhabdus changes radically from the insect pathogenic form (P-form) to slow growing small cells when initiating mutualism (M-form). Here we characterize the gene expression of the M-form relative to the P-form. RNA was extracted from mid-exponential phase bacterial cultures of genetically locked P-form and M-form cells in LB media supplemented with 1 g/liter sodium pyruvate at 28 degree celcius. M-form gene expression was calculated relative to P-form. Three replicates were performed for each biological sample.

2011-09-14 | E-GEOD-32088 | biostudies-arrayexpress

Transcriptionnal analysis of a Photorhabdus luminescens TT01 variant, named VAR*, which is a colonial and phenotypic variant displaying delayed pathogenicity in the insect, Spodoptera littoralis.

Project description:Photorhabdus luminescens lives in a mutualistic association with entomopathogenic nematodes and is pathogenic for insects. Variants of Photorhabdus frequently arise. VAR* is a colonial and phenotypic variant displaying delayed pathogenicity in the insect, Spodoptera littoralis. In this study, we evaluated the role of transcriptomic modulation in determining the phenotypic variation and delayed pathogenicity of VAR* with respect to the corresponding wild-type form, TT01alpha. A P. luminescens microarray was used to determine changes in transcript profiles in the exponential and stationary phase growth phase of VAR* and TT01alpha grown in LB broth. Direct transcriptomic comparisons were carried out between VAR* and TT01alpha grown in LB broth. RNA were extracted from bacterial cells in the exponential growth phase (6-hour-old culture, 5 x 107 cfu/ml) and stationary phase (45-hour-old culture, 5 x 108 cfu/ml). Each microarray comparison (TT01alpha versus VAR* growth in exponential growth or stationary phase) included six slides, with three dye-swapping replicates. Each microarray comparison is done twice with two independant biological extractions (repbiol1 or 2).

2010-10-13 | E-GEOD-24627 | biostudies-arrayexpress

Small RNA directs symbiosis, virulence, and natural products biosynthesis in entomopathogenic bacteria

Project description:Rapid modulation of gene expression is a key feature for the success of bacteria, particularly for those that rapidly have to adapt to different niches. The lifecycles of Photorhabdus and Xenorhabdus involve a mutualistic association with nematodes as well as an entomopathogenic phase1,2, both of which rely on the production of numerous specialized metabolites (SMs) 3,4. Several regulators have been previously implicated in the regulation of SM production in these genera3,4. However, the molecular underpinnings regulating SM production and the role of small regulatory RNAs (sRNAs) in this process are unknown. Here we describe the mechanism underlying RNA-mediated control of SM synthesis. We show that the Hfq-dependent sRNA, ArcZ, is an essential requirement for SM production. We discovered that ArcZ directly base-pairs with the mRNA encoding HexA, a key repressor of SM genes. We further demonstrate that the ArcZ regulon is not restricted to SM production, but rather modulates up to ~15% of the transcriptional output in both Photorhabdus and Xenorhabdus. Together, our study shows that sRNAs are crucial for SM production in these species, reveals previously unknown targets for biosynthetic pathway manipulations, and offers a new tool for the (over)production, isolation and identification of unknown natural products.

2020-08-25 | PXD019095 | Pride

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

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

Project description:Drosophila melanogaster microbiome after infection with Steinernema nematodes

| PRJEB76541 | ENA

Small RNA directs symbiosis, virulence, and natural products biosynthesis in entomopathogenic bacteria

Project description:Rapid modulation of gene expression is a key feature for the success of bacteria, particularly for those that rapidly have to adapt to different niches. The lifecycles of Photorhabdus and Xenorhabdus involve a mutualistic association with nematodes as well as an entomopathogenic phase, both of which rely on the production of numerous specialized metabolites (SMs). Several regulators have been previously implicated in the regulation of SM production in these genera. However, the molecular mechanisms underlying the regulatory control of SM production, and especially the role of small regulatory RNAs, are unknown. Here we show that the Hfq-dependent small RNA, ArcZ, is required for SM production. We discovered that ArcZ directly base-pairs with the mRNA encoding HexA, a known repressor of SM production. We further demonstrate that the ArcZ regulon is not restricted to SM production, but rather modulates up to ~15% of the transcriptional output in both Photorhabdus and Xenorhabdus. Together, our study shows that small RNAs are key for SM production in these species, provides new targets for biosynthetic pathway manipulations, and offers a new tool for the (over-)production, isolation and identification of unknown natural products.

2019-08-01 | MSV000084163 | MassIVE

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