Article Figures & Data
Figures
- Figure 1.
Representation of the DNA Sequence of the Ler and Col-0 RPP5 Haplotypes.
The RPP5 homologs in Ler and Col-0 are named from A to J and are shown as boxes, with the direction of transcription indicated by arrow-heads. The hatched areas at the centromeric (left) and telomeric (right) ends indicate almost completely (96%) identical sequences. Asterisks indicate the positions of the open reading frame (ORF)-disrupting point mutations. Retroelement insertions are shown as black arrows (Ty1/Copia class) and as a hatched arrow (Ty3/Gypsy class). Similarity to a serine/threonine protein kinase pseudogene is shown as filled triangles; the two open triangles indicate sequences with similarity to a mitochondrial 5S rRNA gene.
- Figure 2.
Transcript Analysis of RPP5 Family Members in Ler and Col-0.
Poly(A)+ RNA gel blot analysis was conducted. Transcripts encoded by RPP5 and La-G are indicated, with approximate transcript sizes indicated in kilobases.
- Figure 3.
Sequence Exchange among the RPP5 Multigene Family.
Gene structures are represented with exons as wide rectangles; promoters and introns are shown as narrow rectangles. Sequence affiliations were inferred from runs of at least three consecutive IPSs, with each shown in a different color. Asterisks indicate the position of the ORF-disrupting mutations, and the black arrowheads indicate the locations of the retroelement insertions. Deletions within the genes are indicated by open triangles. The spaces in some homologs are created because other homologs carry duplications in that region. The numbers of LRRs in the homologs are shown at the right.
- Figure 4.
Model for the Evolutionary History of the RPP5 Multigene Family.
The RPP5 homologs are shown as rectangles, with the TIR domains (left, N-terminal) and LRR domains (right, C-terminal) as open rectangles, and the central NB-ARC domains as black rectangles. Open arrowheads indicate intron positions. All individual LRRs among the entire RPP5 family can be classified into eight different groups (A to H). These LRRs are thought to be derived from an RPP5 ancestor (top center) with eight progenitor LRRs (shown in red). A series of intragenic duplications may have led to an increase of these ancestral LRRs from eight to 13 LRRs (curved arrow and duplication in blue), to 17 LRRs (curved arrow and duplication in black), to 21 LRRs (curved arrow and duplication in green). The Ler RPP5 gene and the Col-0 homologs Col-F and Col-D have an identical LRR configuration with 21 LRRs. Most family members (most not shown), however, lack some of the ancestral duplications but carry other duplications and deletions in the LRR-encoded region; for example, Col-B carries two duplications (gray and yellow), and Col-A has undergone a deletion event (Δ). In Ler, the functional RPP5-1 allele with 25 LRRs was recovered (curved arrow and duplication in pink).
- Figure 5.
Dendrograms Showing Distance Relationships between Conceptual Protein Sequences of RPP5 Family Members from the Ler and Col-0 Haplotypes.
Sequence distance trees were calculated using the neighbor-joining algorithm. Relative branch lengths (0.05) are indicated by bars below the trees. La, Ler; Lu, Linum usitatissimum; Nt, Nicotiana tabacum; Ws, Arabidopsis thaliana land race Ws-0.
(A) Distance tree of entire gene products of the RPP5 family and other R proteins containing N-terminal TIR domains.
(B) Distance tree of TIR domains (residues 1 to 160 in RPP5) of the RPP5 family members and other R proteins.
(C) Distance tree of NB sites (residues 202 to 333 in RPP5) of the RPP5 family members.
(D) Distance tree of ARC domains (residues 334 to 518 in RPP5) of the RPP5 family members.
- Figure 6.
Conserved and Hypervariable Amino Acids among Members of the RPP5 Multigene Family.
The RPP5 protein sequence and its predicted TIR, NB-ARC, and LRR structures are shown as given in Parker et al. (1997). Intron-exon boundaries are indicated by diamonds, and exon numbers are indicated at the right. Predicted proteins of 12 full-length family members are aligned, including those of RPP5, La-B, La-C, La-G, La-I, and Col-A to Col-G. Residues shown in lowercase letters either are part of highly variable regions and cannot be aligned or, like the residues that constitute exon 8, are absent from most members. Conserved amino acids (black) are defined as at most one different residue among the compared members. Hypervariable amino acids (red) are defined as four or more different types of residues among the compared members. Other amino acids are moderately variable (two or three different types of residues among the compared members) and are shown in blue. Because LRR-encoded regions were missing from some of the members, limited sequence comparison of LRRs 5 to 8 (five members) and LRRs 16 to 19 (four members) was possible. As a consequence, the hypervariable residues in these LRRs are possibly underestimated. Conserved kinase motifs that constitute an NB pocket and conserved hydrophobic residues within the LRRs are shown in boldface letters. Predicted solvent-exposed residues (x in the xxLxLxx motif) are shown between vertical lines.
Tables
- Table 1.
Pairwise Ka/Ks Ratios in the Predicted Solvent-Exposed LRR Residues and Structural LRR Residues among the RPP5 Familya
RPP5 La-B La-C La-G La-I Col-A Col-B Col-C Col-D Col-Eb Col-F Col-Gb RPP5 × 0.9 1.3 2.8 3.0 1.5 2.5 1.8 2.0 — 2.5 — La-B 0.8 × 0.7 0.9 0.6 1.0 1.0 0.5 0.8 — 0.5 — La-C 0.7 0.6 × 1.4 1.3 2.8 1.1 1.0 0.9 — 1.0 — La-G 0.6 0.8 0.4 × 1.7 2.5 3.0 1.3 5.7 — 2.5 — La-I 0.9 0.6 0.6 0.4 × 4.2 4.4 0.9 5.8 — 2.2 — Col-A 0.6 0.6 0.6 0.3 0.8 × 4.7 1.8 6.6 — 4.1 — Col-B 0.7 0.6 0.6 0.4 0.6 0.6 × 1.4 3.2 — 1.8 — Col-C 1.1 0.5 0.7 0.7 0.8 0.8 0.8 × 1.1 — 1.2 — Col-D 0.9 0.6 0.6 0.4 0.5 0.7 0.4 0.7 × — 1.9 — Col-E b — — — — — — — — — × — 1.7 Col-F 0.9 0.5 0.7 0.4 0.6 0.8 0.4 0.6 1.4 — × — Col-G b — — — — — — — — — 0.5 — × -
↵a Solvent-exposed residues are shown above the diagonal, and structural residues are shown below the diagonal.
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↵b Col-E and Col-G are highly similar but significantly diverge in their LRR-encoded DNA sequences from the rest of the family; as a consequence, the Ka/Ks analysis did not produce meaningful results (denoted by dashes).
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