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Reprogramming of root cells during nitrogen-fixing symbiosis entails dynamic polysome association of coding and non-coding RNAs

ABSTRACT: Reprogramming of root cells during nitrogen-fixing symbiosis entails dynamic polysome association of coding and non-coding RNAs

PROVIDER: PRJNA551664 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9636710_1.fastq.gz	Fastqsanger.gz
	SRR9636710_2.fastq.gz	Fastqsanger.gz
	SRR9636703_1.fastq.gz	Fastqsanger.gz
	SRR9636703_2.fastq.gz	Fastqsanger.gz
	SRR9636704_1.fastq.gz	Fastqsanger.gz

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Reprogramming of root cells during nitrogen-fixing symbiosis entails dynamic polysome association of coding and non-coding RNAs

Project description:Reprogramming of root cells during nitrogen-fixing symbiosis entails dynamic polysome association of coding and non-coding RNAs

| PRJNA560627 | ENA

Reprogramming of root cells during nitrogen-fixing symbiosis entails dynamic polysome association of coding and non-coding RNAs

Project description:GMUCT 2.0 data were analyzed to globally identify 5’ ends differentially accumulated in SKI3 RNAi roots as compared with GUS RNAi, as well as those that change in abundance in response to rhizobia SUPERKILLER3 (*SKI3),* a member of SKI complex that guides RNAs to the 3 to 5' exoribonuclease of the exosome complex. In the absence of a functional SKI complex to thread transcripts to the exosome, the bulk of the mRNAs that accumulate in the cytoplasm are diverted to the 5 -to-3 XRN4 pathway for degradation. We explored the function of *SKI3* during root nodule symbiosis using RNA interference to knockdown *SKI3* in *M. truncatula* hairy roots. To evaluate whether silencing of *SKI3* in *M. truncatula* roots altered RNA decay in response to rhizobia, we performed genome-wide mapping of uncapped and cleaved transcripts (GMUCT 2.0) on *GUS* RNA and *SKI3*RNAi roots. This method identifies products of miRNA or siRNA guided-endonucleolytic cleavage as well as decapped mRNAs by selecting for molecules with a free 5 monophosphate (5 P) (Willmann et al., 2014). GMUCT 2.0 data were analyzed to globally identify 5' ends differentially accumulated in *SKI3* RNAi roots as compared with *GUS* RNAi, as well as those that change in abundance in response to rhizobia.

2022-10-01 | GSE135920 | GEO

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

Project description: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.

2015-09-30 | GSE61377 | GEO

Reprogramming of root cells during nitrogen-fixing symbiosis entails dynamic polysome association of coding and non-coding RNAs

Project description:we compared changes in the transcriptome and the translatome of M. truncatula roots upon rhizobial infection using direct RNA-seq and Translating Ribosome Affinity Purification (TRAP) combined with RNA-seq (TRAP-seq), respectively. TRAP is a ribosome immunopurification approach that has been extensively used in plants and mammals to assess translational changes

2019-11-15 | GSE133510 | GEO

Molecular bases of strain-specific responses of Phaseolus vulgaris roots to symbiotic bacteria with different efficiency in nitrogen-fixing symbiosis

Project description:Some legume plants can establish a nitrogen-fixing symbiosis with rhizobia. Compatibilty between rhizobia and legumes is determined at species-specific level, but there are variations on the efficiency of the process determined by the capacity of the plant to select specific strains that are better partners in terms of the biological outcome. In this work we used a model system based in the coevolution of two genetic pools of common bean (Phaseolus vulgaris) with strains of R. etli that establish a more efficient interaction to study the transcriptional changes occurring in roots at an early time of the interaction.

2020-12-10 | GSE155568 | GEO

Gene profiling during symbiosis between the actinorhizal tree Casuarina glauca and the actinobacteria Frankia CcI3

Project description:Casuarina glauca 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 C. glauca. Symbiosis between C. glauca 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.

2011-04-07 | GSE24158 | 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

Gene profiling during symbiosis between the actinorhizal tree Casuarina glauca and the actinobacteria Frankia CcI3

2011-04-07 | E-GEOD-24158 | biostudies-arrayexpress

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

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

The small proteome of the nitrogen-fixing plant symbiont Sinorhizobium meliloti

Project description:The Alphaproteobacterium Sinorhizobium meliloti lives in soil and is capable of fixing molecular nitrogen in symbiosis with legume plants. In this work, the small proteome of S. meliloti strain 2011 was studied to uncover translation of both annotated and novel small open reading frame (sORF)-encoded proteins (SEPs).

2023-03-13 | PXD034931 | Pride

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