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United States Department of Agriculture

Agricultural Research Service

Title: Global changes in the transcript and metabolic profiles during symbiotic nitrogen fixation in phosphorus-stressed common bean plants

item Hernandez, Georgina
item Valdes-lopez, Oswaldo
item Ramirez, Mario
item Goffard, Nicolas
item Weiller, Georg
item Aparicio-fabre, Rosaura
item Fuentes, Sara Isabel
item Erban, Alexander
item Kopka, Joachim
item Udvardi, Michael
item Vance, Carroll

Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/28/2009
Publication Date: 11/16/2009
Publication URL:
Citation: Hernandez, G., Valdes-Lopez, O., Ramirez, M., Goffard, N., Weiller, G., Aparicio-Fabre, R., Fuentes, S., Erban, A., Kopka, J., Udvardi, M.K., Vance, C.P. 2009. Global changes in the transcript and metabolic profiles during symbiotic nitrogen fixation in phosphorus-stressed common bean plants. Plant Physiology. 151(3):1221-1238.

Interpretive Summary: Common bean is one of the world's most important legumes used for human consumption. It is particularly important in developing countries of Central America and Africa. Symbiotic nitrogen fixation (SNF) by legume root nodules is the principal mechanism contributing nitrogen to common bean seed protein. Low soil phosphorus (P) is the primary nutrient that limits SNF in most parts of the world. In order to understand the root nodule genes that are involved in P-deficiency stress responses, we evaluated the expression of 2,000 genes in P-deficient and P-sufficient common bean root nodules. At least 448 genes showed differential expression. We also measured the change in metabolites in P-deficient and P-sufficient root nodules. Our experiments showed that P-deficient nodules were reduced in SNF, amino acid metabolism, and organic acids with a concomitant increase in sugars and the glycolytic pathway. Galactolipid synthesis increased in P-deficient roots and nodules thereby compensating for reduced available P. Phosphorus stress had a striking effect on global gene regulators known as transcription factors. Our results are important because they suggest that transcription factors could be targets for selection to improve common bean adaptation to P-deficiency.

Technical Abstract: Phosphorus (P) deficiency is widespread in regions where the common bean (Phaseolus vulgaris L.), the most important legume for human consumption, is produced and is perhaps the factor that most limits nitrogen (N) fixation. Global gene expression and metabolome approaches were used to investigate the responses of nodules from common bean plants inoculated with Rhizobium tropici CIAT899 grown under P-deficient and P-sufficient conditions. P-deficient inoculated plants showed drastic reduction in nodulation and nitrogenase activity as determined by acetylene reduction assay. Nodule transcript profiling was performed through hybridization of nylon filter arrays spotted with cDNAs, ca. 2,000 unigene set, from nodule and P-deficient root library. A total of 448 genes, representing different biological processes according to updated annotation using the UniProt Knowledgebase database, showed significant differential expression in response to P: 59% of these were induced in P-deficient nodules. The expression platform for transcription factor (TF) genes based in quantitative reverse transcriptase-polymerase chain reaction revealed that 37 TF genes were differentially expressed in P-deficient nodules, only one gene was repressed. Data from performed non-targeted metabolic profile indicated that amino acids and other N metabolites were decreased while organic and polyhydroxy acids were accumulated in P-deficient nodules. Bioinformatics analyses using MapMan and PathExpress software tools, customized to common bean, were utilized for the analysis of global changes in gene expression that affected overall metabolism. Glycolysis and glycerolipid metabolism, and starch and sucrose metabolism were identified among the pathways significantly induced or repressed in P-deficient nodules, respectively.

Last Modified: 06/23/2017
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