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PMID: 12376622 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

Genome-wide identification of nodule-specific transcripts in the model legume Medicago truncatula.

Plant physiology ·Vol. 130 ·No. 2 ·2002-10-00 ·Pages 519-37

Fedorova M, van de Mortel J, Matsumoto PA, Cho J, Town CD, VandenBosch KA, Gantt JS, Vance CP

Abstract

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.

MeSH Terms
Agglutinins/genetics Amino Acid Sequence Blotting, Northern Calmodulin-Binding Proteins/genetics DNA, Complementary/chemistry,genetics Expressed Sequence Tags Genome, Plant Medicago/genetics Membrane Proteins/genetics Membrane Transport Proteins/genetics Metalloproteins/genetics Molecular Sequence Data Nucleobase Transport Proteins Oligonucleotide Array Sequence Analysis Plant Proteins/genetics Plant Roots/genetics Plant Structures/genetics,physiology RNA, Plant/genetics,metabolism Sequence Analysis, DNA Sequence Homology, Amino Acid Symbiosis/genetics Transcription, Genetic
Chemicals
Agglutinins Calmodulin-Binding Proteins DNA, Complementary MTN6 protein, Medicago truncatula Membrane Proteins Membrane Transport Proteins Metalloproteins Nucleobase Transport Proteins Plant Proteins RNA, Plant nodulin CBP protein, Cucumis sativus purine permease
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Fedorova Maria
Department of Agronomy and Plant Genetics, 1991 Upper Bedford Circle, University of Minnesota, St. Paul, MN 55108, USA.
van de Mortel Judith
Matsumoto Peter A
Cho Jennifer
Town Christopher D
VandenBosch Kathryn A
Gantt J Stephen
Vance Carroll P
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Article Info
Journal
Plant physiology
Abbr.
Plant Physiol
ISSN
0032-0889
DOI
10.1104/pp.006833
Published
2002-10-00
Pages
519-37
Language
English
Region
United States
NLM ID
0401224
PMCID
PMC166584
Subset
IM
Databases
GENBANK
AF494212, AF494213, AF494214, AF494215, AF494216, AF494217, AF494218, AF494219, AF494220
External Links
PubMed source DOI: 10.1104/pp.006833 PMC Full Text View journal details
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