Nucleotide-binding Site Proteins Research Articles

Comparative analysis, diversification, and functional validation of plant nucleotide-binding site domain genes

Nucleotide-binding site (NBS) domain genes are one of the superfamily of resistance genes involved in plant responses to pathogens. The current study identified 12,820 NBS-domain-containing genes across 34 species covering from mosses to monocots and dicots. These identified genes are classified into 168 classes with several novel domain architecture patterns encompassing significant diversity among plant species. Several classical (NBS, NBS-LRR, TIR-NBS, TIR-NBS-LRR, etc.) and species-specific structural patterns (TIR-NBS-TIR-Cupin_1-Cupin_1, TIR-NBS-Prenyltransf, Sugar_tr-NBS etc.) were discovered. We observed 603 orthogroups (OGs) with some core (most common orthogroups; OG0, OG1, OG2, etc.) and unique (highly specific to species; OG80, OG82, etc.) OGs with tandem duplications. The expression profiling presented the putative upregulation of OG2, OG6, and OG15 in different tissues under various biotic and abiotic stresses in susceptible and tolerant plants to cotton leaf curl disease (CLCuD). The genetic variation between susceptible (Coker 312) and tolerant (Mac7) Gossypium hirsutum accessions identified several unique variants in NBS genes of Mac7 (6583 variants) and Coker312 (5173 variants). The protein–ligand and proteins-protein interaction showed a strong interaction of some putative NBS proteins with ADP/ATP and different core proteins of the cotton leaf curl disease virus. The silencing of GaNBS (OG2) in resistant cotton through virus-induced gene silencing (VIGS) demonstrated its putative role in virus tittering. The presented study will be further helpful in understanding the plant adaptation mechanism.

Identification and characterization of genome-wide resistance gene analogs (RGAs) of durian (Durio zibethinus L.)

BackgroundDurian (Durio zibethinus L.) is a tropical fruit crop which is popular in Southeast Asia but recently gaining popularity in other parts of the world. In this study, we analyzed the resistance gene analogs (RGAs) of durian through mining of the currently available reference genome of its ‘Musang King’ cultivar (PRJNA400310). ResultsA total of 2586 RGAs were identified in the durian genome consisting of 47 nucleotide binding site proteins (NBS), 158 NBS-leucine rich repeat proteins (NL), 400 coiled-coil NBS-LRR (CNL), 72 toll/interleukin-1 receptor NBS-LRR (TNL), 54 coiled-coil NBS (CN), 10 toll/interleukin-1 receptor NBS (TN), 19 toll/interleukin-1 receptor with unknown domain (TX), 246 receptor-like proteins (RLP), 1,377 receptor-like kinases (RLK), 185 TM-CC, and 18 other NBS-containing proteins with other domains. These RGAs were functionally annotated and characterized via gene ontology (GO) analysis. Among the RGAs with the highest copies in durian genome include the putative disease resistance RPP13-like protein 1, disease resistance protein At4g27190, disease resistance protein RPS6, Probable disease resistance protein At4g27220, and putative disease resistance protein RGA3, while 35 RGAs were found to be novel. Phylogenetic analyses revealed that the genome-wide RGAs were broadly clustered into four major clades based on their domain classification. ConclusionTo our knowledge, this is the most comprehensive analysis of durian RGAs which provides a valuable resource for genetic, agronomic, and other biological research of this important tropical fruit crop.

Resistance Gene Analogs of Mango: Insights on Molecular Defenses and Evolutionary Dynamics

Mango is an economically important fruit crop largely cultivated in the tropics and, thus, is constantly challenged by a myriad of insect pests and diseases. However, no detailed analysis of its resistance gene analogs (RGAs) has been performed, which is a vital resource for plant breeding. Here, we analyzed the RGAs of mango via de novo assembly of transcriptomic sequences and mining of the recently published whole genome sequence (WGS). From the transcriptomic assembly, a core mango RGA database with 747 protein models was established. Meanwhile, 1,775 RGAs were identified in the mango WGS and classified based on conserved domains and motifs: 54 nucleotide binding site proteins (NBS), 107 NBS – leucine rich repeat proteins (NBSLRR), 242 coiled-coil NBS-LRR (CNL), 79 toll/interleukin-1 receptor NBS-LRR (TNL), 78 coiled-coil NBS (CN), 30 toll/interleukin-1 receptor NBS (TN), 45 toll/interleukin-1 receptor with unknown domain (TX), 133 receptor-like proteins (RLP), 917 receptor-like kinases (RLK), 83 transmembrane coiled-coil domain protein (TM-CC), and seven NBS-encoding proteins with other domains. The transcriptome- and genome-wide RGAs have been functionally wellannotated through gene ontology (GO) analysis, and their expression profiles across different mango varieties were also examined. Phylogenetic analyses of expressed and genome-wide RGAs suggest highly divergent functions of the RGAs, which were broadly clustered into 6 and 8 major clades, respectively, based on their domain classification. From the mango RGA transcripts, 134 unique EST-SSR (expressed sequence tags – simple sequence repeat) loci were identified and primers were designed targeting these potential markers. Moreover, comparative analysis of mango with other plant species revealed 65 species-specific RGA families (396 orthologous genes) and detected 1,005 RGA gene duplication events. To date, this is the most comprehensive analysis of mango RGAs, which also provide insights into the dynamic mangopest co-evolutionary arms race and offer a trove of markers for utilization in resistance breeding.

Genome-wide analysis of NBS-encoding disease resistance genes in Cucumis sativusand phylogenetic study of NBS-encoding genes in Cucurbitaceae crops

BackgroundPlant nucleotide-binding site (NBS)-leucine-rich repeat (LRR) proteins encoded by resistance genes play an important role in the responses of plants to various pathogens, including viruses, bacteria, fungi, and nematodes. In this study, a comprehensive analysis of NBS-encoding genes within the whole cucumber genome was performed, and the phylogenetic relationships of NBS-encoding resistance gene homologues (RGHs) belonging to six species in five genera of Cucurbitaceae crops were compared.ResultsCucumber has relatively few NBS-encoding genes. Nevertheless, cucumber maintains genes belonging to both Toll/interleukine-1 receptor (TIR) and CC (coiled-coil) families. Eight commonly conserved motifs have been established in these two families which support the grouping into TIR and CC families. Moreover, three additional conserved motifs, namely, CNBS-1, CNBS-2 and TNBS-1, have been identified in sequences from CC and TIR families. Analyses of exon/intron configurations revealed that some intron loss or gain events occurred during the structural evolution between the two families. Phylogenetic analyses revealed that gene duplication, sequence divergence, and gene loss were proposed as the major modes of evolution of NBS-encoding genes in Cucurbitaceae species. Compared with NBS-encoding sequences from the Arabidopsis thaliana genome, the remaining seven TIR familes of NBS proteins and RGHs from Cucurbitaceae species have been shown to be phylogenetically distinct from the TIR family of NBS-encoding genes in Arabidopsis, except for two subfamilies (TIR4 and TIR9). On the other hand, in the CC-NBS family, they grouped closely with the CC family of NBS-encoding genes in Arabidopsis. Thus, the NBS-encoding genes in Cucurbitaceae crops are shown to be ancient, and NBS-encoding gene expansions (especially the TIR family) may have occurred before the divergence of Cucurbitaceae and Arabidopsis.ConclusionThe results of this paper will provide a genomic framework for the further isolation of candidate disease resistance NBS-encoding genes in cucumber, and contribute to the understanding of the evolutionary mode of NBS-encoding genes in Cucurbitaceae crops.