Genome Organization of More Than 300 Defensin-Like Genes in Arabidopsis  

Abstract

Defensins represent an ancient and diverse set of small, cysteine-rich, antimicrobial peptides in mammals, insects, and plants. According to published accounts, most species' genomes contain 15 to 50 defensins. Starting with a set of largely nodulespecific defensin-like sequences (DEFLs) from the model legume Medicago truncatula, we built motif models to search the nearcomplete Arabidopsis (Arabidopsis thaliana) genome. We identified 317 DEFLs, yet 80% were unannotated at The Arabidopsis Information Resource and had no prior evidence of expression. We demonstrate that many of these DEFL genes are clustered in the Arabidopsis genome and that individual clusters have evolved from successive rounds of gene duplication and divergent or purifying selection. Sequencing reverse transcription-PCR products from five DEFL clusters confirmed our gene predictions and verified expression. For four of the largest clusters of DEFLs, we present the first evidence of expression, most frequently in floral tissues. To determine the abundance of DEFLs in other plant families, we used our motif models to search The Institute for Genomic Research's gene indices and identified approximately 1,100 DEFLs. These expressed DEFLs were found mostly in reproductive tissues, consistent with our reverse transcription-PCR results. Sequence-based clustering of all identified DEFLs revealed separate tissue-or taxon-specific subgroups. Previously, we and others showed that more than 300 DEFL genes were expressed in M. truncatula nodules, organs not present in most plants. We have used this information to annotate the Arabidopsis genome and now provide evidence of a large DEFL superfamily present in expressed tissues of all sequenced plants.Organisms are constantly confronted with potentially pathogenic microorganisms. Yet, few encounters result in disease, due to the multilayered lines of defense each organism possesses. In vertebrates, adaptive immunity has long held center stage because of its ability to recognize almost any foreign antigen. The ancient innate immune system is equally important and provides a critical line of defense in vertebrates, invertebrates, plants, and insects (Thomma et al., 2002;Beutler, 2004;Bulet et al., 2004;Finlay and Hancock, 2004).In plants, innate immunity occurs via elaborate mechanisms (Dangl and Jones, 2001;Veronese et al., 2003). The plant cell wall serves as a barrier to microbial penetration. Antimicrobial compounds deter would-be invaders. Should penetration occur, recognition leads to the production of reactive oxygen intermediates, cell wall strengthening, activation of protein kinase pathways, and the production of signaling intermediates. Signaling events lead to localized responses such as a hypersensitive response (programmed cell death) or to the release of antimicrobial compounds. The plant is also immunized against unrelated pathogens via systemic acquired resistance (Delaney, 1997;Dong, 2001;Gozzo, 2003).Much attention has focused on the interaction of plant resistance genes (R-genes) and pathoge...

New trends in peptide-based anti-biofilm strategies: a review of recent achievements and bioinformatic approaches

“…One of the most used methods for AMP discovery is the analysis of homologs of known genes by comparing new sequences with sequences of biochemically characterized AMPs Pestana-Calsa and Calsa Jr. 2011), since the sequence segments with high identity tend to share structure and function. For example: an in silico search based on HMMs (Silverstein et al 2005) supported genome assignment of 317 defensin-like sequences in Arabidopsis thaliana; a novel cathelicidin-like AMP, designated cathelicidin-AM, was identified (Yan et al 2011) by mining the genome of panda using BLAST and the sequence of a dog cathelicidin; and the systematic mining of the Nasonia vitripennis genome (Tian et al 2010), using the tools BLASTP, translated BLAST nucleotide (TBLASTN) and ScanProsite (http://prosite.expasy.org/scanprosite/scanprosite-doc. html), has delivered a large and diverse peptidome AMP repertoire of defensins, abaecins, hymenoptaecins and tachystatins.…”

Defence mechanisms of Brassicaceae: implications for plant-insect interactions and potential for integrated pest management. A review

“…2 and 3), such interactions have to be studied on a case-by-case basis for a purposeful plant genotype selection, as pointed out for the diamondback moth in oilseed rape (Sarfraz et al, 2006(Sarfraz et al, , 2007. Promising biochemical traits other than glucosinolates have been pointed out by Silverstein and co-authors regarding defensins and smaller cysteine-rich peptides for the establishment of constitutive resistance against insect pests (Silverstein et al, 2005(Silverstein et al, , 2007. Trait selections in less important species, e.g.…”

Recent Advances in Legume-Microbe Interactions: Recognition, Defense Response, and Symbiosis from a Genomic Perspective

“…Like defensins, the CCPs could be characterized by a conserved signal peptide, a highly divergent mature peptide with the exception of conserved Cys residues, and tissuespecific expression. Using CCP motif models developed from M. truncatula and soybean, Silverstein et al (2005) identified .300 defensin-like genes in the Arabidopsis genome. Genome analyses revealed that plant defensins had many features of classical R genes including clustering and evolution by duplication and positive selection.…”

“…Silverstein et al (2005) Using the same approach, we identified M. truncatula and soybean cDNA contigs that were statistically overrepresented (P , 0.05) with ESTs from at least two different pathogen or rhizobia-inoculated libraries. Of the 4,588 contigs identified from soybean, 65% were specific to defense, 27% were specific to nodulation, and 8% were expressed during nodulation and defense.…”