High-resolution translatome analysis reveals cortical cell programs during early soybean nodulation
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ABSTRACT:
PROVIDER: PRJNA793175 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17382442.fastq.gz | Fastqsanger.gz | |||
| SRR17382443.fastq.gz | Fastqsanger.gz | |||
| SRR17382444.fastq.gz | Fastqsanger.gz | |||
| SRR17382445.fastq.gz | Fastqsanger.gz | |||
| SRR17382446.fastq.gz | Fastqsanger.gz |
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Project description:Nodule organogenesis in legumes is regulated temporally and spatially through gene networks. Genome-wide transcriptome, proteomic, and metabolomic analyses have been used previously to define the functional role of various plant genes in the nodulation process. However, while significant progress has been made, most of these studies have suffered from tissue dilution since only a few cells/root regions respond to rhizobial infection, with much of the root non-responsive. To partially overcome this issue, we adopted translating ribosome affinity purification (TRAP) to specifically monitor the response of the root cortex to rhizobial inoculation using a cortex-specific promoter. While previous studies have largely focused on the plant response within the root epidermis (e.g., root hairs) or within developing nodules, much less is known about the early responses within the root cortex, such as in relation to the development of the nodule primordium or growth of the infection thread. We focused on identifying genes specifically regulated during early nodule organogenesis using roots inoculated with Bradyrhizobium japonicum. A number of novel nodulation gene candidates were discovered, as well as soybean orthologs of nodulation genes previously reported in other legumes. The differential cortex expression of several genes was confirmed using a promoter-GUS analysis, and RNAi was used to investigate gene function. Notably, a number of differentially regulated genes involved in phytohormone signaling, including auxin, cytokinin, and gibberellic acid (GA), were also discovered, providing deep insight into phytohormone signaling during early nodule development.
| S-EPMC9048599 | biostudies-literature
Project description:The TRAP-seq process is dependent on the expression of a cell layer-specific His-FLAG-tagged ribosomal protein L18 (HF-GmRPL 18), which allows for the immunoprecipitation of ribosomes with their corresponding mRNA to produce tissue-specific translatomes (Zanetti et al., 2005; Castro‐Guerrero et al., 2016).To capture events occurring in the cortex during the early stages of infection and initial cortical cell divisions, we inoculated plants and performed a time-course collection of root samples at 72- and 96-hour post inoculation (hpi) followed by TRAP-seq. Immunoblot analysis indicated that an adequate amount of protein was present for immunoprecipitation. To study rhizobial-induced transcriptional changes in the cortex during early nodule development, we identified a soybean promoter (Glyma.18g53890, Figure 1B) expressed exclusively in the cortex cells using LCM (Kerk et al., 2003; Casson et al., 2008) followed by transcriptional analysis. The cortex-specific promoter was used to drive the expression of GmRPL18 in soybean hairy roots. To capture events occurring in the cortex during the early stages of infection and initial cortical cell divisions, we inoculated plants and performed a time-course collection of root samples at 72- and 96-hour post inoculation (hpi) followed by TRAP-seq. Immunoblot analysis indicated that an adequate amount of protein was present for immunoprecipitation (Figure 1C). Taken together, time-course cortex-specific TRAP-seq was established for studying of early nodule development in soybean.
2022-03-21 | GSE192785 | GEO
Project description:Soybean (Glycine max) root nodulation is a symbiotic process that requires complex molecular and cellular coordination. The phloem plays a crucial role not only in nutrient transport but also in long-distance signaling that regulates nodulation. However, the molecular mechanisms underlying phloem-specific regulation during nodulation remain poorly characterized. Here, we developed a phloem-specific Translating Ribosome Affinity Purification sequencing (TRAP-seq) system to investigate the translational dynamics of phloem-associated genes during nodulation. Using a phloem-specific promoter (Glyma.01G040700) combined with the GAL4-UAS amplification system, we successfully captured the translatome of soybean root phloem at early (72 hours post-inoculation, hpi) and late (21 days post-inoculation, dpi) nodulation stages. Differential expression analysis revealed dynamic translational reprogramming, with 2,628 differentially expressed genes (DEGs) at 72 hpi and 8,422 DEGs at 21 dpi. Gene ontology and pathway enrichment analyses showed stage-specific regulatory shifts, including early activation of ethylene and defense pathways and late-stage enhancement of nutrient transport and vascular development. Transcription factor analysis identified GmbHLH121 as a key phloem-specific regulator of nodulation. Functional validation using RNAi knockdown and overexpression experiments demonstrated that GmbHLH121 negatively regulates nodule formation, likely acting downstream of or independently from early nodulation signaling pathways. Additionally, we uncovered dynamic regulation of cell wall-modifying enzymes (PME and PMEI) in the phloem, implicating their role in modulating plasmodesmata permeability and facilitating symplastic connectivity during nodulation. Our findings highlight the critical role of phloem-mediated translational regulation in coordinating root nodulation, emphasizing the phloem as an active regulatory hub for long-distance signaling and symbiotic efficiency. This study provides a foundational framework for future research on phloem-specific gene regulation and its impact on legume symbiosis.
2025-12-04 | GSE292049 | GEO
Project description:Employing translating ribosome affinity purification with RNA sequencing (TRAPseq) on cortical tissue to isolate astroglial-specific translatome from Aldh1l1-L10-GFP mice and examine sex (male + female) and age (postnatal days 1, 4, 7, 14, 35; adults (9 weeks)) dependent changes in the astroglial translatome.
2022-02-01 | GSE192490 | GEO
Project description:Phloem-Specific Translational Regulation of Soybean Nodulation
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Project description:Translatome profiling of cortical layer5a neurons using S100a10 bacTRAP mice
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Project description:Legumes interact with nodulating bacteria that convert atmospheric nitrogen into ammonia for plant use. This nitrogen fixation takes place within root nodules that form after infection of root hairs by compatible rhizobia. Using cDNA microarrays, we monitored gene expression in soybean (Glycine max) inoculated with the nodulating bacterium Bradyrhizobium japonicum 4, 8, and 16 days after inoculation (dai), time points that coincided with nodule development and the onset of nitrogen fixation. This experiment identified several thousand genes that were differentially expressed in response to B. japonicum inoculation. Expression of 27 genes was analyzed by qRT-PCR and their expression patterns mimicked the microarray results confirming integrity of analyses. The microarray results suggest that B. japonicum reduces plant defense responses during nodule development. In addition, the data revealed a high level of regulatory complexity (transcriptional, post-transcriptional, translational, post-translational) that is likely essential for development of the symbiosis and adjustment to an altered nutritional status. Keywords = symbiosis Keywords = nodulation Keywords = rhizobium Keywords = defense Keywords = ANOVA Keywords = plant Keywords: nodulating vs not nodulating
2008-02-05 | GSE10340 | GEO
Project description:Legumes interact with nodulating bacteria that convert atmospheric nitrogen into ammonia for plant use. This nitrogen fixation takes place within root nodules that form after infection of root hairs by compatible rhizobia. Using cDNA microarrays, we monitored gene expression in soybean (Glycine max) inoculated with the nodulating bacterium Bradyrhizobium japonicum 4, 8, and 16 days after inoculation (dai), time points that coincided with nodule development and the onset of nitrogen fixation. This experiment identified several thousand genes that were differentially expressed in response to B. japonicum inoculation. Expression of 27 genes was analyzed by qRT-PCR and their expression patterns mimicked the microarray results confirming integrity of analyses. The microarray results suggest that B. japonicum reduces plant defense responses during nodule development. In addition, the data revealed a high level of regulatory complexity (transcriptional, post-transcriptional, translational, post-translational) that is likely essential for development of the symbiosis and adjustment to an altered nutritional status. Keywords = symbiosis Keywords = nodulation Keywords = rhizobium Keywords = defense Keywords = ANOVA Keywords = plant loop design, 7 samples, 7 comparison, 2 technical repeats including dye swaps, 4 biological repeats
2008-02-04 | E-GEOD-10340 | biostudies-arrayexpress
Project description:Sex differences in the developmental patterns of the cortical astroglial cell translatome
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Project description:The translatome of adult cortical axons is regulated by learning in vivo
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