Disease Resistance Gene Analogs (RGAs) in Plants

Abstract

Plants have developed effective mechanisms to recognize and respond to infections caused by pathogens. Plant resistance gene analogs (RGAs), as resistance (R) gene candidates, have conserved domains and motifs that play specific roles in pathogens' resistance. Well-known RGAs are nucleotide binding site leucine rich repeats, receptor like kinases, and receptor like proteins. Others include pentatricopeptide repeats and apoplastic peroxidases. RGAs can be detected using bioinformatics tools based on their conserved structural features. Thousands of RGAs have been identified from sequenced plant genomes. High-density genome-wide RGA genetic maps are useful for designing diagnostic markers and identifying quantitative trait loci (QTL) or markers associated with plant disease resistance. This review focuses on recent advances in structures and mechanisms of RGAs, and their identification from sequenced genomes using bioinformatics tools. Applications in enhancing fine mapping and cloning of plant disease resistance genes are also discussed.

Keywords: disease resistance gene; gene mining; nucleotide binding site leucine rich repeat (NBS-LRR); pentatricopeptide repeats (PPRs); receptor like kinase (RLK); receptor like protein (RLP); resistance gene analog (RGA); small RNA (sRNA).

Figure 1

Schematic representation of common structures of four major plant R proteins. Motifs are depicted as colored boxes and labeled under the domain names. Note: the domain lengths are not drawn to scale for ease of visualization. (A) Typical domain dissection for TNL and CNL proteins. Only highly conserved motifs are illustrated; (B) Domain structures for RLKs and RLPs. The kinase domain is absent in RLPs. Other common domains utilized in our genome-wide identification pipeline are labeled above the colored boxes. TIR: Toll/interleukin-1 receptor; NB: nucleotide-binding site; ARC: abbreviated from Apaf-1, R proteins and CED-4; CC: coiled-coil; SP: signal peptide; TM: transmembrane; LRR: leucine-rich repeats.

Figure 2

Intracellular signaling mechanisms of RGAs in plant defense. RIN4, PBS1, Pto and EDS1 are targeted and modified by numerous effectors and, as a result, their corresponding TNL or CNL will detect the modification to initiate ETI responses [162,163,164]. TIR-TIR interactions occur between RPS4 and RRS1 to further activate defense genes [169]. Flg22, a bacterial PAMP, activates FLS2 and BAK1 RLKs to initiate the MAP kinase cascade that triggers PTI/MTI responses [170]. MAP kinase cascade signaling can be interrupted by pathogenic effectors. When MPK4 is compromised, SUMM2 will not be inactivated and will initiate PCD [165]. Effector Avr4 is recognized by Cf-4 RLP to initiate MAP kinase cascade and ROS production while simultaneously increasing calcium levels in the cytosol [171]. Upon Erysiphe cruciferarum infection, RPW8.2 can translocate from the Golgi to the extrahaustorial membrane where the fungal haustorium has penetrated to activate the downstream signaling of PCD [172,173]. Under normal conditions, NBS-LRR transcripts derived from the PHAS locus are regulated through transcript degradation by miRNAs [174]. Such miRNAs include, among others, miR1510, miR1507, miR2109, miR482/2118, miR5668, miR5376, miR172 and miR5041 [174,175,176]. Single arrows may indicate multi-step processes.

Figure 3

A common procedure for identification and characterization of plant RGAs.

Figure 4

Phylogenetic analysis of RGAs in plants. The protein sequences of 63 RGAs or cloned R-genes from eleven plant species were selected for this analysis using MEGA 6 [258]. The protein sequences were aligned using the Muscle algorithm, and then clustered using the neighbor-joining algorithm with the p-distance model, pairwise deletion for gaps or missing data treatment, and 500 bootstrap replicates. The phylogenetic tree consists of two large clades (Clades I and II), representing the NBS-LRR class and the RLK/RLP class of proteins, respectively. Clade I may be divided into two sub-groups (Clades Ia and Ib), containing TNL and CNL proteins, respectively, while Clade Ib may be further split into several diverged CNL clusters. The bootstrap values are labelled on branches.