|Fedorova, Maria - UNIV. OF MINNESOTA|
|Van DE Mortel, Judith - UNIV. OF MINNESOTA|
|Matsumoto, Peter - UNIV. OF MINNESOTA|
|Cho, Jennifer - INST. GENOMIC RES.|
|Town, Christopher - INST. GENOMIC RES.|
|Vandenbosch, Kathryn - UNIV. OF MINNESOTA|
|Gantt, J - UNIV. OF MINNESOTA|
Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 19, 2002
Publication Date: N/A
Interpretive Summary: Legume plants like alfalfa, pea, and soybean have the unique ability to make their own nitrogen fertilizer through a process called symbiotic nitrogen fixation. This occurs in small wart-like structures on roots known as root nodules. Root nodules form as the result of a symbiotic interaction with soil bacteria. The bacteria live in root nodules and convert nitrogen gas to ammonia fertilizer for the plant. The plant gives the bacteria sugars for energy and growth. Although a great deal is known about the bacterial genes involved in this process, much less is known about the plant genes involved. In this study we determined which plant genes are specifically activated in legume root nodules. Using the model plant Medicago truncatula, which is closely related to alfalfa, we applied bioinformatics (computer language and questions) to analyze the gene database for this species. Because the database is quite large, approximately 150,000 gene sequences, we could determine which plant genes occur only in symbiotic root nodules. This research is important because it is the first to complete the analysis of the entire complement of plant genes to occur only in root nodules. Information from this study has provided new fundamental insight into how root nodules form and how their function is controlled. Newly identified genes from this study may be a rich source of targets to improve through plant breeding.
Technical Abstract: The Medicago truncatula EST database (Gene Index) contains more than 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 Medicago truncatula forms symbiotic root nodules, unlike Arabidopsis thaliana, 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 2 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 show similarity to the pea ENOD3 gene and encode small systeine 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 comprised of five or more ESTs, while the results for those TCs containing fewer ESTs were variable.