|Silverstein, Kevin - UNIV OF MINNESOTA|
|Moskal, Jr, William - INST GENOMIC RESEARCH|
|Wu, Hank - INST GENOMIC RESEARCH|
|Underwood, Beverly - INST GENOMIC RESEARCH|
|Town, Christopher - INST GENOMIC RESEARCH|
|Vandenbosch, Kathryn - UNIV OF MINNESOTA|
Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 21, 2007
Publication Date: July 2, 2007
Citation: Silverstein, K.A., Moskal, Jr, W.A., Wu, H.C., Underwood, B.A., Graham, M.A., Town, C.D., Vandenbosch, K.A. 2007. Small cysteine-rich peptides resembling antimicrobial peptides have been under-predicted in plants. Plant Journal. 51:262-280. Interpretive Summary: Plants use a variety of mechanisms to defend themselves against potential pathogen attack. The plant cell wall acts as an immediate barrier for pathogens. Plant signaling cascades allow the plant to target its own cells for destruction, preventing further spread of the pathogen. Antimicrobial compounds, like defensins, inhibit pathogen growth. Unlike typical resistance genes, defensins are important because they can provide broad-spectrum resistance to a variety of insect, bacterial and fungal pathogens. Until recently, most species were thought to have 15 to 50 defensins. However, their sequence diversity had made defensins difficult to identify using conventional methods. In previous work, we identified more than 300 defensin-like sequences from the model legume Medicago truncatula. These sequences provided a framework for identifying the key sequence signatures of defensins. Once the key signatures were identified, we could use bioinformatics to search sequence databases for these signatures. Using this approach, we identified approximately 13,000 plant genes encoding putative defensins and other antimicrobial proteins. These genes provide an arsenal of defense peptides that can be used by researchers and breeders to fight current and emerging pathogens.
Technical Abstract: Multicellular organisms produce small cysteine-rich anti-microbial peptides as an innate defense against pathogens. While defensins, a well-known class of such peptides, are common among eukaryotes, there are classes restricted to the plant kingdom. These include thionins, lipid transfer proteins, and snakins. In earlier work, we identified several divergent classes of small putatively secreted cysteine-rich peptides (CRPs) in legumes (Graham et al. Plant Physiol. 2004:135:1179-97). Here, we built sequence motif models for each of these classes of peptides, and iteratively searched four datasets for related sequences: the Arabidopsis thaliana and Medicago truncatula genomes, the comprehensive UniProt protein dataset, and the unigene sequences among all 33 plant gene indices at The Institute for Genomic Research. Using this search strategy, we identified ~13,000 plant genes encoding peptides with common features: (1) an N-terminal signal peptide, (2) a small divergent charged or polar mature peptide with conserved cysteines, (3) a similar intron/exon structure, (4) clustering in the Arabidopsis genome, and (5) over-representation in expressed sequences from reproductive structures of specific taxa. The identified genes include classes of defensins, thionins, lipid transfer proteins and snakins, plus other protease inhibitors, pollen allergens, and uncharacterized gene families. We estimate that these classes of genes account for ~3% of the Arabidopsis gene repertoire. Although many of the genes identified were not annotated in the latest genome releases (TIGR5, TAIR6), we were able to confirm expression via RT-PCR for the majority of the sequences we attempted. These findings highlight limitations in current annotation procedures for small divergent peptide classes.