Integrated proteomic and transcriptomic analyses reveal that the Rj4-mediated immunity network restricts soybean-rhizobia symbiosis
Related Experiment Video
Updated: Jan 12, 2026

Plant Promoter Analysis: Identification and Characterization of Root Nodule Specific Promoter in the Common Bean
Published on: December 23, 2017
Jia-He Gao1, Fang Tang2, Ya-Wen Wang1
1Key Laboratory of Grassland Resources of the Ministry of Education and Key Laboratory of Forage Cultivation, Processing and High-Efficiency Utilization of Ministry of Agriculture, College of Grassland Science, Inner Mongolia Agricultural University, No.29 Erdos Street, Saihan District, Hohhot, 010011, Inner Mongolia, China.
Abstract:
BACKGROUND: Legumes-rhizobia symbiosis has high specificity regulated by a specific class of genes, such as Rj4. Rj4 encodes a thaumatin-like protein belonging to the PR-5 family that restricts soybean from nodulation with many strains of Bradyrhizobium elkanii. How Rj4, a member of broad-spectrum resistance family, specifically regulates nodulation remains unclear. To uncover the molecular mechanism of Rj4, current study integrated transcriptome and proteome to analyze the downstream regulatory pathways and key genes mediated by Rj4, through investigating the gene expression and protein abundance in the roots of soybean BARC2 (Rj4/Rj4) after 0, 6 and 24 h post inoculation (hpi) with B. elkanii USDA61. RESULTS: The results showed that a total of 1660 differentially expressed genes (DEGs) and 2633 differentially abundance proteins (DAPs) were identified, in which resistance-related genes and symbiosis-related genes showed opposite expression trend. The key symbiosis-related genes, such as ENOD55, PUB1, and NFP, were up-regulated at 6 hpi but down-regulated at 24 hpi compared with control group. Conversely, the expression of most plant immunity related genes exhibited an initial decrease at 6 hpi followed by an increase at 24 hpi, suggested Rj4 restricted host plant from nodulation in early process through induction of plant immunity related genes and pathways. The key genes involved in plant immunity included pattern-triggered immunity (PTI)-related genes, such as pattern recognition receptors FLS2 and EFR, mitogen-activated protein kinases (MAPK) signaling pathway MPKs, calcium ion related genes CNGCs, CaMCML, and ROS related genes RBOH, as well as effector-triggered immunity (ETI) related resistance (R) genes RPM1 and Ptis, plant hormone signal transduction related genes JAZ and TGA, and flavonoid and isoflavonoid biosynthesis gene Cyps. We validated 8 DEGs via qRT-PCR, showing consistent trends with RNA-Seq (Spearman r > 0.9). CONCLUSIONS: These findings provide new insights into how plant immunity inhibits legume-rhizobial symbiosis in the Rj4-mediated regulatory network, and provide key candidate genes to study legume-rhizobial nodulation specificity for future research.
Related Concept Videos
The Roles of Bacteria and Fungi in Plant Nutrition
Inorganic Nitrogen Assimilation
Ribosome Profiling
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
RNA Interference
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
Gene Regulation in Microbial Communities: Quorum Sensing
Riboswitches
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...

