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First published online August 29, 2002; 10.1104/pp.006833

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Plant Physiol, October 2002, Vol. 130, pp. 519-537

Genome-Wide Identification of Nodule-Specific Transcripts in the Model Legume Medicago truncatula1

Maria Fedorova, Judith van de Mortel, Peter A. Matsumoto, Jennifer Cho, Christopher D. Town, Kathryn A. VandenBosch, J. Stephen Gantt, and Carroll P. Vance*

Departments of Agronomy and Plant Genetics, 1991 Upper Bedford Circle (M.F., J.v.d.M., P.A.M., C.P.V.) and Plant Biology, 1445 Gortner Avenue (K.A.V., J.S.G.), University of Minnesota, St. Paul, Minnesota 55108; United States Department of Agriculture-Agricultural Research Service, St. Paul, Minnesota 55108 (C.P.V.); and The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850 (J.C., C.D.T.)

The Medicago truncatula expressed sequence tag (EST) database (Gene Index) contains over 140,000 sequences from 30 cDNA libraries. This resource offers the possibility of identifying previously uncharacterized genes and assessing the frequency and tissue specificity of their expression in silico. Because M. truncatula forms symbiotic root nodules, unlike Arabidopsis, this is a particularly important approach in investigating genes specific to nodule development and function in legumes. Our analyses have revealed 340 putative gene products, or tentative consensus sequences (TCs), expressed solely in root nodules. These TCs were represented by two to 379 ESTs. Of these TCs, 3% appear to encode novel proteins, 57% encode proteins with a weak similarity to the GenBank accessions, and 40% encode proteins with strong similarity to the known proteins. Nodule-specific TCs were grouped into nine categories based on the predicted function of their protein products. Besides previously characterized nodulins, other examples of highly abundant nodule-specific transcripts include plantacyanin, agglutinin, embryo-specific protein, and purine permease. Six nodule-specific TCs encode calmodulin-like proteins that possess a unique cleavable transit sequence potentially targeting the protein into the peribacteroid space. Surprisingly, 114 nodule-specific TCs encode small Cys cluster proteins with a cleavable transit peptide. To determine the validity of the in silico analysis, expression of 91 putative nodule-specific TCs was analyzed by macroarray and RNA-blot hybridizations. Nodule-enhanced expression was confirmed experimentally for the TCs composed of five or more ESTs, whereas the results for those TCs containing fewer ESTs were variable.

1 This work was supported by the National Science Foundation (Plant Genome Project no. 9872664) and by the U.S. Department of Agriculture-Agricultural Research Service (grant no. CRIS 3640-21000-014-00D). This is a joint contribution of the U.S. Department of Agriculture-Agricultural Research Service and the Minnesota Agricultural Experimental Station Scientific Journal Series.

* Corresponding author; e-mail vance004{at}umn.edu; fax 651-649-5058.

© 2002 American Society of Plant Physiologists


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