Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily

Abstract

The nucleotide binding site (NBS) is a characteristic domain of many plant resistance gene products. An increasing number of NBS-encoding sequences are being identified through gene cloning, PCR amplification with degenerate primers, and genome sequencing projects. The NBS domain was analyzed from 14 known plant resistance genes and more than 400 homologs, representing 26 genera of monocotyledonous, dicotyle-donous and one coniferous species. Two distinct groups of diverse sequences were identified, indicating divergence during evolution and an ancient origin for these sequences. One group was comprised of sequences encoding an N-terminal domain with Toll/Interleukin-1 receptor homology (TIR), including the known resistance genes, N, M, L6, RPP1 and RPP5. Surprisingly, this group was entirely absent from monocot species in searches of both random genomic sequences and large collections of ESTs. A second group contained monocot and dicot sequences, including the known resistance genes, RPS2, RPM1, I2, Mi, Dm3, Pi-B, Xa1, RPP8, RPS5 and Prf. Amino acid signatures in the conserved motifs comprising the NBS domain clearly distinguished these two groups. The Arabidopsis genome is estimated to contain approximately 200 genes that encode related NBS motifs; TIR sequences were more abundant and outnumber non-TIR sequences threefold. The Arabidopsis NBS sequences currently in the databases are located in approximately 21 genomic clusters and 14 isolated loci. NBS-encoding sequences may be more prevalent in rice. The wide distribution of these sequences in the plant kingdom and their prevalence in the Arabidopsis and rice genomes indicate that they are ancient, diverse and common in plants. Sequence inferences suggest that these genes encode a novel class of nucleotide-binding proteins.

Molecular cloning of a coiled-coil-nucleotide-binding-site-leucine-rich repeat gene from pearl millet and its expression pattern in response to the downy mildew pathogen

“…(Fig 3). This was confirmed by inspecting the sequence of kinase 2 motif for the presence of tryptophan (W) at the C-terminus [11].…”

“…The sequence alignment of the deduced amino acids of RGA RGPM 301 contained the consensus sequence of kinase 1a, kinase 2, kinase 3a, GLPL and MHD motifs characteristic of most of the plant R-genes [28]. These domains and motifs which are highly conserved, assists in the prediction of R-genes to either TIR or non-TIR subclasses [11]. The BLASTp results revealed 73% identity with Oryza sativa Japonica NBSt1 (BAH20866.1) and Pit (AIR72965.1) which are CC-NB-LRR protein of non-TIR subclass.…”

“…The R-genes are broadly categorized as TIR NBS-LRR (TNL) and non-TIR NBS-LRR subclasses on the basis of the presence or absence of N-terminal Drosophila Toll and mammalian interleukin-1 receptor (TIR) region [10]. The TIR subclass is found in dicot species whereas the non-TIR subclass with a coiled-coil (CC) structure occurs among both the monocot and dicot plants [11,10]. The CC domain with a coiled-coil structure is implicated in specific interactions with other proteins and also facilitates dimerization [12].…”

Resistance gene analogues identified through the NBS-profiling method map close to major genes and QTL for disease resistance in apple

“…Five out of the nine unmapped markers had a distorted segregation in the progeny, which could explain why they could not be reliably mapped. The P-loop motif targeted by degenerate primers used for NBS-profiling is known to be highly conserved through different plant species (Meyers et al 1999). This is exemplified by the fact that, even though the primers were designed from R genes isolated in species not belonging to the Rosaceae family and PCR conditions were very specific, numerous bands could be obtained in apple that were putative RGAs.…”

Cloning and Characterization of Resistance GeneAnalogues (RGAs) from Piper Nigrum L. cv. SemongokAman and Piper Colubrinum Link

“…The P-loop in NBS domain of plant RGAs has been reported to interact directly with the phosphate of the bound nucleotides and has been well characterized for adenosine triphosphate (ATP) and guanosine triphosphate (GTP) binding proteins [38], [39], [40], [41], [42]. Mutations of key residues in the P-loop can led to partial loss of the resistance gene (N gene) function in tobacco [7].…”