SCPL (serine carboxypeptidase-like) enzymes

From Purdue Genomics Database Facility

This work was supported by the National Science Foundation

Nicholas D. Bonawitz (nbonawit@purdue.edu) and Clint Chapple (chapple@purdue.edu)

Department of Biochemistry, Purdue University, West Lafayette, IN, USA.

Summary

Reactions catalyzed by some SCPL enzymes

Serine carboxypeptidases utilize a catalytic Ser-Asp-His triad to hydrolyze terminal peptide bonds during proteolysis^1,2. A number of serine carboxypeptidase-like (SCPL) enzymes have been identified in a wide range of organisms that contain the characteristic catalytic triad of serine carboxypeptidases, but function as acyltransferases or lyases rather than peptidases^3,4,5,6,7. For example, the Arabidopsis enzyme sinapoyl glucose:malate sinapoyl transferase (SMT), an SCPL enzyme, functions as an acyltransferase in the synthesis of sinapoyl malate⁵. Other characterized SCPL enzymes in Arabidopsis include SST, SCT, and SAT, which are involved in the biosynthesis of 1,2-disinapoyl glucose, sinapoyl choline, and sinapoylated anthocyanins, respectively^6,7. Interestingly, phylogenetic analysis of SCPL enzymes from a number of different species indicates that plants have undergone a major expansion of this protein family⁸. Whereas the human genome contains three SCPL enzymes, the Arabidopsis genome encodes more than 50. Since SCPL enzymes have been shown to act as acyltransferases (an important step in secondary metabolism) it has been suggested that they could play a role in generating the enormous diversity of secondary metabolites found in plants.

Our analysis of the Selaginella genome revealed that it encodes a large number of SCPL enzymes (though not as many as found in the Arabidopsis genome). We list the individual enzymes below, and show a phylogenetic tree at right containing the SCPL sequences from Selaginella, Arabiodopsis, and Physcomitrella. Previous comparison of the SCPL enzymes from Arabidopsis with those of animals and fungi resulted in their grouping into several distinct clades⁸. The very diverse clades I and II are found only in plants, while the smaller clade III is found in animals but not plants. Finally, clades IV, V, and VI are apparently ancient and are found in both animals and plants. Our phylogenetic analysis of the SCPL enzymes of the Selaginella genome reveals five groups of genes, which we have designated groups A through G. Interestingly, none of the SCPL enzymes cluster into clade I, indicating that this group of genes diversified in the angiosperms after their divergence from the rest of the plant kingdom. The great majority of the Selaginella SCPLs (groups A, B, and C below) are found in the plant specific clade II. The group B and group C genes in Selaginella are apparently orthologous to Arabidopsis genes, suggesting that the diversification of the these SCPL enzymes occurred early in plant evolution before the split between the lineages leading to Arabiodpsis and Selaginella. The Selaginella group A genes are similar to the genes found in clade I in that they have apparently diversified after the angiosperm/lycophyte split, but in this case the diversification was in the lineage leading to Selaginella rather than the lineage leading to Arabidopsis. The Selaginella group D and group E genes are found in clades IV and V, respectively, and are ancient genes found in animals as well as plants. Unexpectedly, we were unable to identify any homologs of Arabidopsis SCPL51 (clade VI) even after searching the Selaginella database with TBLASTN, despite the fact that this is an ancient enzyme found in animals as well as plants. This suggests at least initially that this gene was specifically lost in the lineage leading to Selaginella. Taken together, our results shed light on the diversification of the serine carboxypeptidase-like enzymes in plants, and suggests that group A SCPLs identified here could be involved in the synthesis of Selaginella-specific secondary metabolites.

List of Selaginella SCPL enzymes

Phylogenetic tree of SCPL enzymes from Arabiodpsis, Selaginella, and Physcomitrella

Group A

SCPLa1-1, SCPLa1-2

SCPLa2-1, SCPLa2-2

SCPLa3-1, SCPLa3-2

SCPLa4-1, SCPLa4-2

SCPLa5-1, SCPLa5-2

SCPLa6a-1, SCPLa6a-2, SCPLa6b-1, SCPLa6b-2

SCPLa7-1, SCPLa7-2

SCPLa8

Group B

SCPLb1-1, SCPLb1-2

SCPLb2-1, SCPLb2-2

Group C

SCPLc1-1, SCPLc1-2

SCPLc2-1, SCPLc2-2

SCPLc3-1, SCPLc3-2

SCPLc4-1, SCPLc4-2

Group D

SCPLd1-1, SCPLd1-2

Group E

SCPLe1-1, SCPLe1-2

SCPLe2-1, SCPLe2-2

References

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6. Shirley AM et al. Plant J 2001, 28: 83-94

7. Fraser CM et al. Plant Physiol 2007, 144: 1986-1999

8. Fraser CM et al. Plant Physiol 2005, 138: 1136-1148