Transcriptome profiling of the endophyte Burkholderia phytofirmans PsJN indicates sensing of the plant environment and drought stress
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR864057.fastq.gz | Fastqsanger.gz | |||
| ERR864058.fastq.gz | Fastqsanger.gz | |||
| ERR864059.fastq.gz | Fastqsanger.gz | |||
| ERR864060.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:Whole transcriptome sequencing of B. phytofirmans PsJN colonizing potato (Solanum tuberosum L.) plants was used to analyze in planta gene activity and in the response of strain PsJN to plant stress in three different time points. The transcriptome of PsJN colonizing in vitro potato plants showed a broad array of functionalities encoded on the genome of strain PsJN. Our study indicates that endophytic B. phytofirmans PsJN cells are active inside plants. Moreover, the activity of strain PsJN is affected by plant drought stress, it senses plant stress signals and adjusts its gene expression accordingly.
2015-04-23 | E-MTAB-3524 | biostudies-arrayexpress
Project description:UnlabelledIt is widely accepted that bacterial endophytes actively colonize plants, interact with their host, and frequently show beneficial effects on plant growth and health. However, the mechanisms of plant-endophyte communication and bacterial adaption to the plant environment are still poorly understood. Here, whole-transcriptome sequencing of B. phytofirmans PsJN colonizing potato (Solanum tuberosum L.) plants was used to analyze in planta gene activity and the response of strain PsJN to plant stress. The transcriptome of PsJN colonizing in vitro potato plants showed a broad array of functionalities encoded in the genome of strain PsJN. Transcripts upregulated in response to plant drought stress were mainly involved in transcriptional regulation, cellular homeostasis, and the detoxification of reactive oxygen species, indicating an oxidative stress response in PsJN. Genes with modulated expression included genes for extracytoplasmatic function (ECF) group IV sigma factors. These cell surface signaling elements allow bacteria to sense changing environmental conditions and to adjust their metabolism accordingly. TaqMan quantitative PCR (TaqMan-qPCR) was performed to identify ECF sigma factors in PsJN that were activated in response to plant stress. Six ECF sigma factor genes were expressed in PsJN colonizing potato plants. The expression of one ECF sigma factor was upregulated whereas that of another one was downregulated in a plant genotype-specific manner when the plants were stressed. Collectively, our study results indicate that endophytic B. phytofirmans PsJN cells are active inside plants. Moreover, the activity of strain PsJN is affected by plant drought stress; it senses plant stress signals and adjusts its gene expression accordingly.ImportanceIn recent years, plant growth-promoting endophytes have received steadily growing interest as an inexpensive alternative to resource-consuming agrochemicals in sustainable agriculture. Even though promising effects are recurrently observed under controlled conditions, these are rarely reproducible in the field or show undesirably strong variations. Obviously, a better understanding of endophyte activities in plants and the influence of plant physiology on these activities is needed to develop more-successful application strategies. So far, research has focused mainly on analyzing the plant response to bacterial inoculants. This prompted us to study the gene expression of the endophyte Burkholderia phytofirmans PsJN in potato plants. We found that endophytic PsJN cells express a wide array of genes and pathways, pointing to high metabolic activity inside plants. Moreover, the strain senses changes in the plant physiology due to plant stress and adjusts its gene expression pattern to cope with and adapt to the altered conditions.
| S-EPMC4600099 | biostudies-literature
Project description:Plant growth promoting rhizobacteria (PGPR) induce positive effects in plants, such as increased growth or reduced stress susceptibility. The mechanisms behind PGPR/plant interaction are poorly understood, as most studies have described short- term responses on plants and only a few studies have analyzed plant molecular responses under PGPR colonization. Transcriptional profiles were determined by microarray analysis (Affymetrix ATH1 Genome Array) in Arabidopsis thaliana plants inoculated with the PGPR bacterial model Burkholderia phytofirmans PsJN
2013-05-31 | GSE47092 | GEO
Project description:Paraburkholderia phytofirmans PsJN DAP-Seq epigenomics
| PRJNA757850 | ENA
Project description:Plant growth promoting rhizobacteria (PGPR) induce positive effects in plants, such as increased growth or reduced stress susceptibility. The mechanisms behind PGPR/plant interaction are poorly understood, as most studies have described short- term responses on plants and only a few studies have analyzed plant molecular responses under PGPR colonization. Transcriptional profiles were determined by microarray analysis (Affymetrix ATH1 Genome Array) in Arabidopsis thaliana plants inoculated with the PGPR bacterial model Burkholderia phytofirmans PsJN Arabidopsis seeds were sown on square Petri dishes with half strength Murashige and Skoog medium (MS) 0.8% agar, and inoculated or not (control) with strain PsJN. To assess the effect of inactivated bacteria, an inoculum was heated at 95M-BM-0C for 20 min and then was used at the same dilution.Three biological replicates, consisting of ten plantlets of 13 days after sowing (DAS) each, for control and strain PsJN treatments, were used for global gene expression.
2013-05-31 | E-GEOD-47092 | biostudies-arrayexpress
Project description:Plant defense responses to biotic stresses are complex biological processes, all governed by sophisticated molecular regulations. Induced systemic resistance (ISR) is one of these defense mechanisms where beneficial bacteria or fungi prime plants to resist pathogen or pest attacks. In ISR the defense arsenal in plants remains dormant and it is only triggered by the infection, allowing a rapid response and a better allocation of plant resources. We recently described that the well-known beneficial bacterium Paraburkholderia phytofirmans PsJN is able to reduce Arabidopsis thaliana susceptibility to Pseudomonas syringae Pst DC3000 through ISR. Nevertheless, the molecular networks governing this beneficial interaction remain unknown. To tackle this issue we analyzed the temporal changes in the transcriptome of PsJN-inoculated plants before and after the infection with Pst DC3000 strain. These data were used to perform a gene network analysis to identify highly connected transcription factors that may be acting as hubs in controlling this ISR response. Before the pathogen challenge, strain PsJN regulated 405 genes (corresponding to 1.5% of the analyzed genome). PsJN-inoculated plants presented a faster and stronger transcriptional response 1-hour post infection (hpi) compared with the non-inoculated plants, which presented the highest transcriptional changes 24 hpi. A principal component analysis showed that PsJN-induced plant responses to the pathogen could be differentiated from those induced by the sole pathogen. Forty-eight transcription factors were regulated by PsJN 1 hpi, and a system biology analysis revealed a network with 4 modules where LHY, WRKY28, MYB31 and RRTF1 are highly connected transcription factors, that can be acting as hub regulators in this interaction. These modules are related to Jasmonate, Ethylene, Salicylic acid and ROS pathways. Additionally, the down- and up-regulation of ANAC32 and ORA59, respectively, support an important role of PDF1.2. These results indicate that a rapid and specific response of PsJN-inoculated plants to this virulent pathogen could be the pivotal element in the protection mechanism. A role for specific transcriptional regulators in the orchestration of this complex molecular response is also proposed
2019-07-31 | GSE124475 | GEO
Project description:Two potato cultivars, Russet Burbank and Bionta, were inoculated with three different endophytes containing different AHL types. The impact of the endophytes to the different cultivars was measured by gene expression analysis with a customized microarray B. phytofirmans type strain PsJN was originally isolated as a contaminant from surface-sterilized, Glomus vesculiferum-infected onion roots (Nowak et al., 1998), whereas strain P6 RG6-12 was isolated from the rhizosphere of a grassland in the Netherlands (Salles et al., 2006). This strain was selected based on its similarity to strain PsJN based on 16S rRNA gene homology, and similar phenotypic features. Both strains were generally cultivated on King's medium (King et al., 1954). For the mutant AHL to the strain B. phytofirmans PsJN a quorum quenching approach as described by Wopperer et al., 2006 was employed. Plasmid pMLBAD-aiiA, which contains aiiA, the Bacillus sp. 240B1 lactonase gene, was transferred to B. phytofirmans PsJN by triparental mating as described by de Lorenzo and Timmis (1994). 2 cultivars, 3 endophytes
2010-05-19 | E-GEOD-12862 | biostudies-arrayexpress
Project description:Burkholderia phytofirmans overview
| PRJNA35961 | ENA
Project description:Paraburkholderia phytofirmans OLGA172 Genome sequencing
| PRJNA226249 | ENA
Project description:Gene Networks Underlying the Early Regulation of Paraburkholderia Phytofirmans Psjn-induced Systemic Resistance in Arabidopsis
| PRJNA512117 | ENA