ARABIDOPSIS RESISTANCE GENES


RGenes Data in mySQL database
RGenes distribution over chromosomes
Sequence Alignment of NBS region
RGenes Phylogeny
NBS Domain Relationship in Arabidopsis Genome
NBS, P450, PK-LRR Clustering in Arabidopsis Genome
NBS, P450, PK-LRR clustering on the background of duplication events in Arabidopsis genome
HMM profiles of Arabidopsis NBS domain



DATABASE OF ARABIDOPSIS NBS-LRR-ENCODING
DISEASE RESISTANCE GENE HOMOLOGS.


       Genes encoding the NBS-LRR protein motifs comprise one of the most prevalent classes in plant genomes. To date, the only demonstrated function for these genes is in disease or pest resistance. However, NBS-LRR proteins may also be involved in other aspects of plant biology. These proteins are one of ~5 classes of plant resistance genes (reviewed in Baker et al., 1997; Bent et al., 1996).

       The NBS (nucleotide binding site) is a common protein motif in all organisms, occurs in numerous structural forms, and functions to bind ATP or GTP (Saraste et al., 1990; Walker et al., 1982). The domains within the NBS include a highly conserved "P-loop" that functions in phosphate binding, followed by additional conserved domains also involved in binding (Traut, 1994). This database focuses on the sub-class of NBS sequences which contain a characteristic set of conserved motifs (van der Biezen and Jones, 1998; Meyers et al., 1999).

       The LRR (leucine rich repeat) in the plant R-genes is of variable length. This database refers to only one class of LRRs found in plant R-genes - the 'cytoplasmic LRR' that is found in conjunction with the NBS. The LRR regions are typically 10-40+ repeats of a motif of ~24 amino acids that is highly variable; the core signature of this repeated motif is of the form

LxxLxxLxLxxLxx(N/C/T)x(x)LxxIPxx

(L = leucine or other aliphatic residues, and x = any residue; reviewed in Jones and Jones, 1997).

       One of our research goals is to define the different classes of NBS-LRR-encoding genes, and ultimately to determine the function of these genes and how they are related to defense. Sequence analysis of the complete Arabidopsis genome has identified more than 160 NBS-LRR - encoding genes (see also, Meyers et al., 1999). Approximately two-thirds of these genes also encode a "Toll-Interleukin homology" domain at the N-terminus of the predicted protein (the "TIR" class), while the remaining one-third encode a coiled-coil motif at the N-terminus (the "non-TIR" class). Phylogenetic analysis demonstrates that known resistance genes are present in most of the major clades.

       Candidate NBS-encoding sequences were selected from the Arabidopsis genomic sequence, starting with those sequences identified in Meyers et al., 1999. Additional and more diverse NBS-encoding sequences in the Arabidopsis genome were identified by BLAST and HMM/Pfam analysis. These sequences were then compared against the translated complete Arabidopsis genomic sequence by FASTA analysis (ktup=1). The twelve best matches for each gene (or all with a score of e-24 or better) were extracted from the MIPS database and compiled in a single file. Redundant sequences were removed. The complete non-redundant dataset of predicted protein sequences was placed into a mySQL database.

       This database contains all of the known NBS-LRR - encoding genes in Arabidopsis, as of December 14, 2000. With the completion of the genome, we are finalizing the data set - please check back, as we will post this data shortly. In addition, we are studying the expression patterns and transcript structure for these genes, and expect to add this information to the database in the coming months.


RGenes Data in mySQL database
RGenes distribution over chromosomes
Sequence Alignment of NBS region
RGenes Phylogeny
NBS Domain Relationship in Arabidopsis Genome
NBS, P450, PK-LRR Clustering in Arabidopsis Genome
NBS, P450, PK-LRR clustering on the background of duplication events in Arabidopsis genome
HMM profiles of Arabidopsis NBS domain

email: Blake Meyers
email: Alexander Kozik
email: Richard Michelmore

We are grateful to our undergraduate assistants Alyssa Griego (artwork with images), Elena Kochetkova (art of Tcl/Tk programming) and Garrick Ng (PHP wizard) for their contributions to the database of NBS-LRR sequences. Without their efforts, this database would not be possible.

Last modified, August 14 2001