Primary structural features of the S haplotype-specific F-box protein, SFB, in Prunus

Abstract

The gene SFB encodes an F-box protein that has appropriate S-haplotype-specific variation to be the pollen determinant in the S-RNase-based gametophytic self-incompatibility (GSI) reaction in Prunus (Rosaceae). To further characterize Prunus SFB, we cloned and sequenced four additional alleles from sweet cherry (P. avium), SFB 1 , SFB 2 , SFB 4 , and SFB 5 . These four alleles showed haplotype-specific sequence diversity similar to the other nine SFB alleles that have been cloned. In an amino acid alignment of Prunus SFBs, including the four newly cloned alleles, 121 out of the 384 sites were conserved and an additional 65 sites had only conservative replacements. Amino acid identity among the SFBs ranged from 66.0% to 82.5%. Based on normed variability indices (NVI), 34 of the non-conserved sites were considered to be highly variable. Most of the variable sites were located at the C-terminal region. A windowaveraged plot of NVI indicated that there were two variable and two hypervariable regions. These variable and hypervariable regions appeared to be hydrophilic or at least not strongly hydrophobic, which suggests that these regions may be exposed on the surface and function in the allele specificity of the GSI reaction. Evidence of positive selection was detected using maximum likelihood methods with sites under positive selection concentrated in the variable and hypervariable regions.

Molecular and Genetic Analyses of Four Nonfunctional S Haplotype Variants Derived from a Common Ancestral S Haplotype Identified in Sour Cherry (Prunus cerasus L.)

“…Conserved nucleotides are shown on a darkened background. The locations of the F-box motif-V1, V2, HVa and HVb (Ikeda et al 2004a), and Vn (Nunes et al 2006)-are indicated by solid boxes. The asterisks under the amino acid sequence indicate the five amino acid residues that differ between SFB 36a and SFB 36b .…”

“…These fosmid libraries were screened at 60°with a mixture of DIGdUTP-labeled S 6 -RNase and SFB 6 probes, as previously described (Ushijima et al 2001). The DIG-labeled S 6 -RNase and SFB 6 probes were obtained by PCR labeling using a PCR DIG probe synthesis kit (Roche) with Pru-C2 and PCE-R primers (Tao et al 1999;Yamane et al 2001) and SFB-C1F (Ikeda et al 2004a) and SFB-C4R primers (Yamane et al 2003c), respectively. The S haplotype of each positive fosmid clone was determined by PCR with the S-RNase consensus primer pair (Pru-C2 and PCE-R), which detects length differences for the second intron of the S-RNase.…”

“…The S haplotype of each positive fosmid clone was determined by PCR with the S-RNase consensus primer pair (Pru-C2 and PCE-R), which detects length differences for the second intron of the S-RNase. Positive clones were also checked for the presence of SFB using PCR with the SFB consensus primer pair (SFB-C1F and SFB-C2R) (Ikeda et al 2004a). S-RNase and SFB allele-specific primer pairs were also used to verify the S haplotypes.…”

Isolation and identification of new pollen-specific SFB genes in Japanese apricot (Prunus mume)

“…Based on amino acid sequence comparison, Ikeda et al (2004) first summarized the structural features for Prunus SFB alleles. In this study, the structures of the 5 new SFB alleles were similar to other Prunus SFB alleles.…”

“…After the first identification of S-RNase in the Solanaceae (McClure et al, 1989), a very good candidate gene for the pollen S gene, an SFB, was recently found in several species of Prunus in the Rosaceae, including sweet cherry (P. avium; Yamane et al, 2003a;Ikeda et al, 2004;Sonneveld et al, 2005;Vaughan et al, 2006), almond (P. dulcis; Ushijima et al, 2003Ushijima et al, , 2004Sutherland et al, 2008), Japanese apricot (P. mume; Entani et al, 2003;Yamane et al, 2003b), apricot (P. armeniaca; Romero et al, 2004;Vilanova et al, 2006;Wu et al, 2009), Japanese plum (P. salicina; Zhang et al, 2007), dwarf almond (P. tenella; Šurbanovski et al, 2007), and Chinese cherry (P. pseudocerasus; Huang et al, 2008;Gu et al, 2011).…”