Publications (since 1999)

PpASCL, a moss ortholog of anther-specific chalcone synthase-like enzymes, is a hydroxyalkylpyrone synthase involved in an  evolutionarily conserved sporopollenin biosynthesis pathway. Colpitts, C.C., Kim, S.S., Posehn, S.E., Jepson, C., Kim, S.Y., Wiedermann, G., Reski, R., Wee, A.G.H., Douglas, C.J., Suh, D.-Y. (2011) New Phytologist 192, 855-868

   Sporopollenin is the main constituent of the exine layer of spore and pollen walls. Recently, several Arabidopsis genes including PKSA, which encodes an anther-specific chalcone synthase-like enzyme (ASCL), have been shown to be involved in sporopollenin biosynthesis. The genome of the moss Physcomitrella contains putative orthologs of the Arabidopsis sporopollenin biosynthesis genes. Physcomitrella orthologs of Arabidopsis genes for sporopollenin biosynthesis were found to be expressed in the sporophyte generation. Similarly to Arabidopsis PKSA, PpASCL condenses hydroxyfatty acyl-CoA esters with malonyl-CoA and produces hydroxyalkyl -pyrones that probably serve as building blocks of sporopollenin. The ASCL-specific set of Gly-Gly-Ala residues modeled to be at the floor of the putative active site is proposed to serve as the opening of an acyl-binding tunnel of ASCL. These results suggest that ASCL functions together with other sporophyte-specific enzymes to provide polyhydroxylated precursors of sporopollenin in a pathway common to land plants.

POLYKETIDE SYNTHASE A and POLYKETIDE SYNTHASE B encode hydroxyalkyl -pyrone synthases required for pollen development and sporopollenin biosynthesis in Arabidopsis thaliana. Kim, S.S., Grienenberger, E., Lallemand, B., Colpitts, C.C., Kim, S.Y., Geoffroy, P., Heintz, D., Krahn, D., Kaiser, M., Kombrink, E., Heitz, T., Suh, D.-Y., Legrand, M., Douglas, C.J.  (2010) Plant Cell, 22, 4045-4066

Plant type III polyketide synthases (PKSs) catalyze the condensation of malonyl-CoA units with various CoA ester starter molecules to generate a diverse array of natural products. The fatty acyl-CoA esters synthesized by Arabidopsis thaliana ACYL-COA SYNTHETASE5 (ACOS5) are key intermediates in the biosynthesis of sporopollenin, the major constituent of exine in the outer pollen wall. By coexpression analysis, we identified two Arabidopsis PKS genes, POLYKETIDE SYNTHASE A (PKSA) and PKSB (also known as LAP6 and LAP5, respectively) that are tightly coexpressed with ACOS5. Recombinant PKSA and PKSB proteins generated tri-and tetraketide -pyrone compounds in vitro from a broad range of potential ACOS5-generated fatty acyl-CoA starter substrates by condensation with malonyl-CoA. Furthermore, substrate preference profile and kinetic analyses strongly suggested that in planta substrates for both enzymes are midchain- and -hydroxylated fatty acyl-CoAs (e.g., 12-hydroxyoctadecanoyl-CoA and 16-hydroxyhexadecanoyl-CoA), which are the products of sequential actions of anther-specific fatty acid hydroxylases and acyl-CoA synthetase. PKSA and PKSB are specifically and transiently expressed in tapetal cells during microspore development in Arabidopsis anthers. Mutants compromised in expression of the PKS genes displayed pollen exine layer defects, and a double pksa pksb mutant was completely male sterile, with no apparent exine. These results show that hydroxylated -pyrone polyketide compounds generated by the sequential action of ACOS5 and PKSA/B are potential and previously unknown sporopollenin precursors.

Genome-wide analysis of the chalcone synthase superfamily genes of Physcomitrella patens. Koduri, P.K.H., Gordon, G.S., Barker, E.I., Colpitts, C.C., Ashton, N.W., Suh,  D.-Y. (2010) Plant Mol. Biol. 72, 247-263

The genome of the moss, P. patens, contains at least 17 putative CHS superfamily genes.PpCHS11 and probably also PpCHS9 encode non-CHS enzymes, while PpCHS10 appears to be an ortholog of plant genes encoding anther-specific CHS-like enzymes. The genomic locations of genes suggested that the superfamily expanded through tandem and segmental duplication events. Inferred exon-intron architectures and results from phylogenetic analysis showed that intron gain and loss occurred several times during evolution of this gene superfamily. More than a half of P. patens CHS genes are intronless, prompting speculation that CHS gene duplication via retrotransposition has occurred at least twice in the moss lineage. A surprisingly large number (as many as 13) of the moss CHS superfamily genes probably encode active CHS, and different light responsiveness observed with selected genes provide evidence for their differential regulation. Observed diversity within the moss CHS superfamily and amenability to gene manipulation make Physcomitrella a highly suitable model system for studying expansion and functional diversification of the plant CHS superfamily of genes.

Divergent evolution of the thiolase superfamily and chalcone synthase family. Jiang, C., Kim, S.Y., Suh, D.-Y. (2008)  Mol. Phylogenet. Evol. 49, 691-701

Enzymes of the thiolase superfamily catalyze the formation of carbon-carbon bond via Claisen condensation reaction. Thiolases and 3-hydroxyl-3-methylglutaryl-CoA synthase catalyze non-decarboxylative condensation reactions, whereas the condensing enzymes of fatty acid and polyketide synthases, 3-ketoacyl-CoA synthase, and chalcone synthase (CHS) and related enzymes catalyze decarboxylative condensation reactions. Detailed phylogenetic and structural analyses were carried out to propose a plausible evolutionary history for the thiolase superfamily that includes the emergence of decarboxylative condensing enzymes accompanied by a recruitment of the His in the Cys-His-His and Cys-His-Asn triads for a catalytic role during decarboxylative condensation. In addition, repeated gene birth-and-death and re-invention of non-CHS functions were suggested for the evolution of the CHS family in plants, and a moss CHS-like enzyme that is functionally similar to a cyanobacterial enzyme was identified as the most recent common ancestor to the plant CHS family.

Mutational analysis of conserved outer sphere arginine residues of chalcone synthase. Fukuma, K., Neuls, E.D.,   Ryberg, J. M., Suh, D.-Y., Sankawa, U. (2007) J. Biochem. 142, 731-739

Outer-shell effects of conserved, non-active site Arg residues of CHS and stilbene synthase were investigated to provide further insights into the structure-function relationship of these enzymes.

Cloning and characterization of chalcone synthase from the moss, Physcomitrella patens. Jiang, C., Schommer, C.K., Kim, S.Y., Suh, D.-Y. (2006) Phytochemistry 67, 2531-2540

The genome of the moss, P. patens contains a chs multigene family. Our bioinformative and biochemical analyses suggest the moss to be an archaeological dig for the study of evolution and functional divergence of the plant CHS superfamily. Taking advantage of the fact that P. patens is amenable to genetic manipulation, such studies are already underway in my laboratory.

Crystal structure of stilbene synthase from Arachis hypogaea. Shomura, Y.,  Torayama, I., Suh, D.-Y., Xiang, T.,  Kita, A., Sankawa, U., Miki, K. (2005) Proteins  60, 803-806

Stilbene synthase (STS) and CHS catalyze two different cyclization reactions of a common reaction intermediate. This paper reported the second crystal structure of STS, and confirmed the presence of a H-bond activated water molecule (aldol switch) at the STS active site. However, the aldol switch is not the sole factor distinguishing STS from CHS, and the cyclization reactions in CHS and STS are also modulated by stereo-control. By comparing the structures of STS and CHS, we identified a short stretch of amino acids (a1 region), which may contribute to stereo-control together with the 372GFGPG loop that we identified earlier.

Antigenic prenylated peptide conjugates and polyclonal antibodies to detect protein prenylation. Liu, X.-h., Suh, D.-Y., Call, J., Prestwich, G.D. (2004) Bioconjugate Chem. 15, 270-277

Oxidosqualene cyclase inhibitors as antimicrobial agents. Hinshaw, J.C., Suh, D.-Y., Garnier, P.,  Buckner, F.S., Eastman, R.T., Matsuda, S.P.T., Joubert, B.M., Coppens, I., Joiner, K.A., Merali, S., Nash, T.E., Prestwich, G.D.  (2003) J. Med. Chem. 46(20), 4240-4243

Bifunctional activities of valerophenone synthase in hop (Humulus lupulus L.). Okada, Y., Yamazaki, Y., Suh, D.-Y.,  Sankawa, U., Ito, K.(2001)  J. Am. Soc. Brew. Chem. 59, 163-166  

Diverse chalcone synthase superfamily enzymes from the most primitive vascular plant, Psilotum nudum.  Yamazaki, Y., Suh, D.-Y., Sitthithaworn, W., Ishiguro, K., Kobayashi, Y., Shibuya, M., Ebizuka, Y., Sankawa, U. (2001) Planta 214, 75-84

Geranylgeranyl diphosphate synthase from Scoparia dulcis. Plastid localization and conversion to a farnesyl diphosphate synthase by mutagenesis. Sitthithaworn, W., Kojima, N., Viroonchatapan, E., Suh, D.-Y., Iwanami, N., Hayashi, T., Noji, M., Saito, K., Niwa, Y., Sankawa, U. (2001) Chem. Pharm. Bull. 49, 197-202

Evidence for catalytic cystein-histidine dyad in chalcone synthase. Suh, D.-Y., Fukuma, K., Kagami, J., Sankawa, U. (2000) Biochem. Biophys. Res. Commun. 275, 725-730

Identification of amino acid residues important in the cyclization reactions of chalcone and stilbene synthases. Suh, D.-Y.,  Fukuma, K., Kagami, J., Yamazaki, Y., Shibuya, M., Ebizuka, Y., Sankawa, U. (2000) Biochem. J. 350, 229-235

Geranylgeranyl diphosphate synthases from Scoparia dulcis and Croton sublyratus. cDNA cloning, functional expression, and conversion to a farnesyl diphosphate synthase. Kojima, N., Sitthithaworn, W., Viroonchatapan, E., Suh, D.-Y., Iwanami, N., Hayashi, T., Sankawa, U. (2000) Chem. Pharm. Bull. 48, 1101-1103

Chalcone and stilbene synthases expressed in eucaryotes exhibit reduced cross-reactivity in vitro. Suh, D.-Y., Kagami, J., Fukuma, K., Iwanami, N., Yamazaki, Y., Yurimoto, H., Sakai, Y., Kato, N., Shibuya, M., Ebizuka, Y., Sankawa, U. (2000) Chem. Pharm. Bull. 48, 1051-1054

Cross-reaction of chalcone synthase and stilbene synthase overexpressed in Escherichia coli.  Yamaguchi, T.,  Kurosaki, F., Suh, D.-Y., Sankawa, U., Nishioka, M., Akiyama, T., Shibuya, M., Ebizuka, Y. (1999) FEBS Lett. 260, 457-461

Different inhibitory effects of 5-S-glutathionyl- L-alanyl-L-dopa (5-S-GA-L-D) analogues on autophosphorylation and substrate phosphorylation of Src protein tyrosine kinase. Zheng, Z.-B., Nagai, S., Iwanami, N., Suh, D.-Y., Kobayashi, A., Hijikata, M., Natori, S., Sankawa, U. (1999) Chem. Pharm. Bull. 47, 136-137