Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome of Frankia in nitrogen-fixing root-nodule symbiosis with Datisca glomerata

ABSTRACT: A transcriptome of Cluster II Frankia in nitrogen-fixing root-nodule symbiosis with the host plant, Datisca glomerata, was obtained by Illumina sequencing and mapping to the corresponding published genome (NCBI Bioproject PRJNA46257). Major metabolic pathways detected in Cluster II Frankia in symbiosis with Datisca glomerata were comparable to those described as up-regulated in the Frankia alni-Alnus glutinosa symbiosis (N Alloisio et al, MPMI 23(5):593-607, 2010): nitrogenase biosynthesis, tricarboxylic acid cycle, respiratory-chain related functions, oxidation protection, and terpenoid biosynthesis. These functions are consistent with the primary activities of Frankia in root nodules, e.g. to carry out the energetically-demanding fixation of atmospheric dinitrogen to ammonium, and to maintain internal reducing conditions. Expression of genes coding for amino-acid biosynthetic pathways, including arginine as reported previously (AM Berry et al. Funct Plant Biol 38, 645–652, 2011) was detected. A striking difference from other Frankia strains, revealed in the transcriptome of the Cluster II Frankia in symbiosis, was the expression of homologs of rhizobial nodulation genes, nodA, nodB and nodC.

ORGANISM(S): Frankia

PROVIDER: GSE61377 | GEO | 2015/09/30

SECONDARY ACCESSION(S): PRJNA260924

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Comparison of transcriptome between free-living and symbiotic cells of Frankia alni ACN14a

Project description:The actinobacteria Frankia alni is able to induce the formation of nodules on the root of a large spectrum of actinorhizal plants, where it converts dinitrogen to ammonia in exchange for plant photosynthates. In the present study, transcriptional analyses were performed on nitrogen-replete free-living cells and on Alnus glutinosa nodule bacteria, using whole genome microarrays. Distribution of nodule-induced genes on the genome was found to be mostly over regions with high synteny between three Frankia genomes, while nodule-repressed genes, which were mostly hypothetical and not conserved, were spread around the genome. Genes known to be related to symbiosis were highly induced: nif (nitrogenase), hup2 (hydrogenase uptake), suf (sulfur-iron cluster) and shc (hopanoids synthesis). The expression of genes involved in ammonium assimilation and transport was strongly modified suggesting that bacteria ammonium assimilation was limited. Genes involved in particular in transcriptional regulation, signalling processes, protein drug export, protein secretion, lipopolysaccharide and peptidoglycan biosynthesis that may play a role in symbiosis were also identified. We showed that this nodule transcriptome of Frankia was highly similar among phylogenetically distant plant families. To address gene expression changes of Frankia alni ACN in the symbiotic state, we compared transcript levels between young nodules formed on 4 species of trees (Alnus glutinosa, Alnus nepalensis, Myrica gale and Myrica rubra) and free-living cells grown in nitrogen-replete minimal medium. For A. glutinosa nodule and free-living cells, two sets of experiments (A and B) were performed in two different laboratories. Three biological replicates were preformed for each condition.

2010-09-12 | E-GEOD-18190 | biostudies-arrayexpress

Comparison of transcriptome between free-living and symbiotic cells of Frankia alni ACN14a

2010-09-12 | GSE18190 | GEO

Gene profiling during symbiosis between the actinorhizal tree Alnus glutinosa and the actinobacteria Frankia alni ACN14

Project description:Alnus glutinosa belongs to a family of angiosperms called actinorhizal plants because they can develop nitrogen-fixing nodules in association with the soil bacteria Frankia. The aim of this transcriptomic study was to get a global view of the plant symbiotic genetic program and to identify new key plant genes that control nodulation during symbiosis in A. glutinosa. Symbiosis between A. glutinosa and Frankia was obtained after inoculation of young plant with a concentrated culture of the bacteria. Inoculation was performed in a medium depleted in nitrogen which favors the induction of nitrogen fixing symbiosis. For this study we considered two stages of symbiosis: - an early stage where inoculated roots were harvested 7 days after inoculation with the bacteria and compared to two controls (non-inoculated roots grown with or without nitrogen and harvested at the same time) - a late stage where nodules (nitrogen-fixing specific organs) were harvested 21 days after inoculation and compared to non-inoculated roots harvested on the day of inoculation (which is our reference time 0d). Three biological replicates were used for each condition.

2011-04-11 | GSE24153 | GEO

Frankia coriariae exoproteomes

Project description:This project defines the exoproteome dynamics of Frankia coriariae, a nitrogen-fixing bacterium, in presence of three host plants. Frankia coriariae was treated with root exudates from compatible (Coriaria myrtifolia), incompatible (Alnus glutinosa) and non-actinorhizal (Cucumis melo) host plants.

2017-05-19 | PXD005980 | Pride

Gene profiling during symbiosis between the actinorhizal tree Alnus glutinosa and the actinobacteria Frankia alni ACN14

2011-04-11 | E-GEOD-24153 | biostudies-arrayexpress

Proteogenome of Frankia coriariae cells

Project description:This project contributes to define the proteome dynamics of Frankia coriariae, a nitrogen-fixing bacterium, in presence of three host plants. Frankia coriariae was treated with root exudates from compatible (Coriaria myrtifolia), incompatible (Alnus glutinosa) and non-actinorhizal (Cucumis melo) host plants.

2017-05-19 | PXD005979 | Pride

Transcription profiling of A. glutinosa roots growing with indirect contact with Frankia in nitrogen-free culture medium against A. glutinosa roots alone in nitrogen-free culture medium during 2 days

Project description:Experiment with 2 conditions: - Contactless : A. glutinosa alone in nitrogen-free culture medium during 2 days (reference condition). - Indirect : A. glutinosa in nitrogen-free culture medium containing the Frankia bacterium confined in a dialysis tube during 2 days.

2021-12-31 | E-MTAB-8936 | biostudies-arrayexpress

Transcription profiling of A. glutinosa roots growing with Frankia culture supernatant in nitrogen-free culture medium against A. glutinosa roots alone in nitrogen-free culture medium plus frankialess culture medium for 2 days

Project description:Experiment with 2 conditions: - BAP-PCM : A. glutinosa alone in nitrogen-free culture medium plus frankialess culture medium during 2 days (reference condition). - CN BAP-PCM : A. glutinosa in nitrogen-free culture medium with Frankia culture supernatant during 2 days.

2021-12-31 | E-MTAB-8937 | biostudies-arrayexpress

Expression data of Frankia CcI3 in plant root nodules under salt stress

Project description:Purpose: To compare RNASeq data of Frankia CcI3 in plants under salt stress. Casuarina glauca root nodules infected with Frankia CcI3 were exposed to either no salt or 100 mM NaCl for 21 days. RNA-seq analysis provided insight into how the sybiont responds to salt stress.

2019-12-02 | GSE60938 | GEO

Frankia

Project description:Transcriptome of Frankia in nitrogen-fixing root-nodule symbiosis with Datisca glomerata

| PRJNA260924 | ENA