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First published online September 15, 2009; 10.1104/pp.109.143842

Plant Physiology 151:1221-1238 (2009)
© 2009 American Society of Plant Biologists

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Global Changes in the Transcript and Metabolic Profiles during Symbiotic Nitrogen Fixation in Phosphorus-Stressed Common Bean Plants1,[W],[OA]

Georgina Hernández*, Oswaldo Valdés-López, Mario Ramírez, Nicolas Goffard, Georg Weiller, Rosaura Aparicio-Fabre, Sara Isabel Fuentes, Alexander Erban, Joachim Kopka, Michael K. Udvardi and Carroll P. Vance

Centro de Ciencias Genómicas-Universidad Nacional Autónoma de México, 62209 Cuernavaca, Morelos, México (G.H., O.V.-L., M.R., R.A.-F., S.I.F.); Australian Research Council Centre of Excellence for Integrative Legume Research, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia (N.G., G.W.); Max Planck Institute for Molecular Plant Physiology, 14476 Golm, Germany (G.H., A.E., J.K.); Samuel Robert Noble Foundation, Ardmore, Oklahoma 73401 (M.K.U.); Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 (G.H., C.P.V.); and United States Department of Agriculture, Agricultural Research Service, Plant Science Research Unit, St. Paul, Minnesota 55108 (G.H., C.P.V.)

Phosphorus (P) deficiency is widespread in regions where the common bean (Phaseolus vulgaris), the most important legume for human consumption, is produced, and it is perhaps the factor that most limits nitrogen 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, approximately 4,000 unigene set, from the nodule and P-deficient root library. A total of 459 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 genes based in quantitative reverse transcriptase-polymerase chain reaction revealed that 37 transcription factor genes were differentially expressed in P-deficient nodules and only one gene was repressed. Data from nontargeted metabolic profiles indicated that amino acids and other nitrogen 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 Suc metabolism, were identified among the pathways significantly induced or repressed in P-deficient nodules, respectively.

1 This work was supported by the Dirección General de Asuntos del Personal Académico/Universidad Nacional Autónoma de México (grant no. PAPIIT: IN211607 and sabbatical fellowship to G.H.), by the U.S. Department of Agriculture, Agricultural Research Service (grant no. USDA–FAS MX161 to the University of Minnesota), by the German Academic Exchange Service (research stay fellowship to G.H.), and by the Consejo Nacional de Ciencia y Tecnología, México (studentship no. 200048 to O.V.-L.).

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Georgina Hernández (gina{at}ccg.unam.mx).

[W] The online version of this article contains Web-only data.

[OA] Open Access articles can be viewed online without a subscription.

www.plantphysiol.org/cgi/doi/10.1104/pp.109.143842

* Corresponding author; e-mail gina{at}ccg.unam.mx.

Received June 30, 2009; accepted September 8, 2009; published September 15, 2009.


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