Phylogenetic diversification of glycogen synthase kinase 3/SHAGGY-like kinase genes in plants

Abstract

Background: The glycogen synthase kinase 3 (GSK3)/SHAGGY-like kinases (GSKs) are non-receptor serine/threonine protein kinases that are involved in a variety of biological processes. In contrast to the two members of the GSK3 family in mammals, plants appear to have a much larger set of divergent GSK genes. Plant GSKs are encoded by a multigene family; analysis of the Arabidopsis genome revealed the existence of 10 GSK genes that fall into four major groups. Here we characterized the structure of Arabidopsis and rice GSK genes and conducted the first broad phylogenetic analysis of the plant GSK gene family, covering a taxonomically diverse array of algal and land plant sequences.

Results: We found that the structure of GSK genes is generally conserved in Arabidopsis and rice, although we documented examples of exon expansion and intron loss. Our phylogenetic analyses of 139 sequences revealed four major clades of GSK genes that correspond to the four subgroups initially recognized in Arabidopsis. ESTs from basal angiosperms were represented in all four major clades; GSK homologs from the basal angiosperm Persea americana (avocado) appeared in all four clades. Gymnosperm sequences occurred in clades I, III, and IV, and a sequence of the red alga Porphyra was sister to all green plant sequences.

Conclusion: Our results indicate that (1) the plant-specific GSK gene lineage was established early in the history of green plants, (2) plant GSKs began to diversify prior to the origin of extant seed plants, (3) three of the four major clades of GSKs present in Arabidopsis and rice were established early in the evolutionary history of extant seed plants, and (4) diversification into four major clades (as initially reported in Arabidopsis) occurred either just prior to the origin of the angiosperms or very early in angiosperm history.

Figure 1

The gene structure of ten Arabidopsis and nine rice GSK3/SHAGGY-like kinase genes. The positions of the introns within the coding region are mostly conserved among Arabidopsis and rice GSK genes, except AtSK12, AtSK21, AtSK31, AtSK32, and Os10g37740, which either lack an intron or an exon or have additional exons. Open triangles indicate the absence of an intron. Closed triangles indicate additional exons. Boxes of identical color among sequences represent exons of the same approximate size and relative position.

Figure 2

Pattern of nucleotide substitution in the coding regions of the plant GSK homologs based on the comparison of 116 sequences. The x-axis (site) was constructed based on 4-bp intervals.

Figure 3

Pattern of amino acid substitution in the coding regions of the plant GSK proteins based on the comparison of 116 sequences. The x-axis (site) was constructed based on 4-aa intervals.

Figure 4

Mean number of inferred nucleotide substitutions by codon position based on the comparison of 139 GSK homologs. Subsets of the full data set are based on the results of the phylogenetic analysis of GSKs (green plants, moss, clade I, clade II, clade III, clade IV) or represent well-recognized organismal groups (angiosperms, monocots).

Figure 5

Phylogenetic tree resulting from analysis of nucleotides using Support Weighting with jackknife values from non-weighted analysis. Orange labels indicate GSK homologs from Arabidopsis, and blue labels designate rice sequences. GSK homologs from FGP ESTs are labeled in red. Pinus ESTs are labeled in green.

Figure 6

Strict consensus tree of 17 most parsimonious trees (length = 11641; CI = 0.1522; RI = 0.5789) of GSK3/SHAGGY-like kinase homologs from plants, animals, protists, and fungi based on sequence alignment of the 1044 nucleotides encoding the catalytic domain and part of the 3' end of the sequences. Numbers above the branches are bootstrap values; only values over 50% are indicated. Numbers below the branches are posterior probabilities from the Bayesian analysis; only values over 0.90 are indicated. Orange labels indicate GSK homologs from Arabidopsis, and blue labels designate rice sequences. GSK homologs from FGP ESTs are labeled in red. Pinus ESTs are labeled in green.

Figure 7

50% majority rule consensus tree of 77 most parsimonious trees (length = 2156; CI = 0.4935; RI = 0.7532) of GSK3/SHAGGY-like kinase proteins from plants, animals, protists, and fungi based on sequence alignment of the 348 amino acids of the catalytic domain and part of the C terminus. Numbers above the branches are bootstrap values; only values over 50% are indicated. Arrows on the nodes indicated the collapsed braches in the strict consensus tree. Orange labels indicate GSK proteins from Arabidopsis, and blue labels designate rice proteins. GSK proteins inferred from FGP ESTs are labeled in red, and those from Pinus ESTs are labeled in green.