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Research Articles

Polyketide synthases (PKSs) of secondary metabolism: in silico identification and characterization in orchids

, , , ORCID Icon & ORCID Icon
Pages 5486-5498 | Received 02 Feb 2022, Accepted 09 Jun 2022, Published online: 23 Jun 2022

References

  • Austin, M. B., & Noel, J. P. (2003). The chalcone synthase superfamily of type III polyketide synthases. Natural Product Reports, 20(1), 79–110. https://doi.org/10.1039/b100917f
  • Awasthi, P., Jamwal, V. L., Kapoor, N., & Rasool, S. (2016). Homology modeling and docking study of chalcone synthase gene (CfCHS) from Coleus forskohlii. Cogent Biology, 2(1), 1175332. https://doi.org/10.1080/23312025.2016.1175332
  • Baerson, S. R., & Rimando, A. M. (2007). A Plethora of polyketides: Structures, biological activities, and enzymes. ACS Publications. https://doi.org/10.1021/bk-2007-0955.ch001
  • Bhavsar, B., Kalaria, R. K., & Patel, M. I. (2019). Molecular and in silico identification of chalcone synthase gene-2 (CHS-2) in sorghum (Sorghum bicolor L.) against anthracnose. International Journal of Chemical Studies, 7, 839–844.
  • Cai, J., Liu, X., Vanneste, K., Proost, S., Tsai, W.-C., Liu, K.-W., Chen, L.-J., He, Y., Xu, Q., Bian, C., Zheng, Z., Sun, F., Liu, W., Hsiao, Y.-Y., Pan, Z.-J., Hsu, C.-C., Yang, Y.-P., Hsu, Y.-C., Chuang, Y.-C., … Liu, Z.-J. (2015). The genome sequence of the orchid Phalaenopsis equestris. Nature Genetics, 47(1), 65–72. https://doi.org/10.1038/ng.3149
  • Cheniany, M., Ebrahimzadeh, H., & Masoudi-nejad, A. (2012). Expression of chalcone synthase influences flavonoid content and frequency of rhizogenesis in microshoots of Juglans regia L. Plant Cell, Tissue and Organ Culture (PCTOC), 109(1), 51–59. https://doi.org/10.1007/s11240-011-0072-y
  • Cuadra, P., Guajardo, J., Carrasco-Orellana, C., Stappung, Y., Fajardo, V., & Herrera, R. (2020). Differential expression after UV-B radiation and characterization of chalcone synthase from the Patagonian hairgrass Deschampsia antarctica. Phytochemistry, 169, 112179. https://doi.org/10.1016/j.phytochem.2019.112179
  • Dhaubhadel, S., Gijzen, M., Moy, P., & Farhangkhoee, M. (2007). Transcriptome analysis reveals a critical role of CHS7 and CHS8 genes for isoflavonoid synthesis in soybean seeds. Plant Physiology, 143(1), 326–338. https://doi.org/10.1104/pp.106.086306
  • Durbin, M. L., McCaig, B., & Clegg, M. T. (2000). Molecular evolution of the chalcone synthase multigene family in the morning glory genome. In J. J. Doyle & B. S. Gaut (Eds.), Plant molecular evolution (pp. 79–92). Springer. https://doi.org/10.1007/978-94-011-4221-2_4
  • Ekalu, A., & Habila, J. D. (2020). Flavonoids: Isolation, characterization, and health benefits. Beni-Suef University Journal of Basic and Applied Sciences, 9(1), 1–14. https://doi.org/10.1186/s43088-020-00065-9
  • Eom, S. H., & Hyun, T. K. (2016). Genome-wide identification and transcriptional expression analysis of chalcone synthase in flax (Linum usitatissimum L.). Gene Reports, 5, 51–56. https://doi.org/10.1016/j.genrep.2016.08.011
  • Feinbaum, R. L., & Ausubel, F. M. (1988). Transcriptional regulation of the Arabidopsis thaliana chalcone synthase gene. Molecular and Cellular Biology, 8(5), 1985–1992. https://doi.org/10.1128/mcb.8.5.1985-1992.1988
  • Feng, Q., Gui-Gong, G., Yang, Z., Hui-Chun, X., Lan, J., Jun, S., & Zhi, C. (2015). Molecular cloning and expression profiling of a chalcone synthase gene from Lamiophlomis rotata. Journal of Genetics, 94(2), 193–205. https://doi.org/10.1007/s12041-015-0502-4
  • Ferrer, J. L., Jez, J. M., Bowman, M. E., Dixon, R. A., & Noel, J. P. (1999). Structure of chalcone synthase and the molecular basis of plant polyketide biosynthesis. Nature Structural Biology, 6(8), 775–784. https://doi.org/10.1038/11553
  • Flores-Sanchez, I. J., & Verpoorte, R. (2009). Plant polyketide synthases: A fascinating group of enzymes. Plant Physiology and Biochemistry: PPB, 47(3), 167–174. https://doi.org/10.1016/j.plaphy.2008.11.005
  • Goto-Yamamoto, N., Wan, G. H., Masaki, K., & Kobayashi, S. J. P. S. (2002). Structure and transcription of three chalcone synthase genes of grapevine (Vitis vinifera). Plant Science, 162(6), 867–872. https://doi.org/10.1016/S0168-9452(02)00042-0
  • Han, Y. Y., Ming, F., Wang, J. W., Ye, M. M., & Shen, D. L. (2005). A novel chalcone synthase gene from Phalaenopsis orchid that alters floral morphology in transgenic tobacco plants. Plant Molecular Biology Reporter, 23(2), 193–194. https://doi.org/10.1007/BF02772710
  • Han, Y. Y., Ming, F., Wang, W., Wang, J. W., Ye, M. M., & Shen, D. L. (2006a). Molecular evolution and functional specialization of chalcone synthase superfamily from Phalaenopsis orchid. Genetica, 128(1–3), 429–438. https://doi.org/10.1007/s10709-006-7668-x
  • Han, Y. Y., Ming, F., Wang, J. W., Wen, J. G., Ye, M. M., & Shen, D. L. (2006b). Cloning and characterization of a novel chalcone synthase gene from Phalaenopsis hybrida orchid flowers. Russian Journal of Plant Physiology, 53(2), 223–230. https://doi.org/10.1134/S1021443706020129
  • Han, Y., Ding, T., Su, B., & Jiang, H. (2016). Genome-wide identification, characterization and expression analysis of the chalcone synthase family in maize. International Journal of Molecular Sciences, 17(2), 161. https://doi.org/10.3390/ijms17020161
  • Han, Y., Cao, Y., Jiang, H., & Ding, T. (2017). Genome-wide dissection of the chalcone synthase gene family in Oryza sativa. Molecular Breeding, 37(10), 1–12. https://doi.org/10.1007/s11032-017-0721-x
  • Hertweck, C. (2009). The biosynthetic logic of polyketide diversity. Angewandte Chemie (International ed. in English), 48(26), 4688–4716. https://doi.org/10.1002/anie.200806121
  • Hrazdina, G., & Jensen, R. A. (1992). Spatial organization of enzymes in plant metabolic pathways. Annual Review of Plant Physiology and Plant Molecular Biology, 43(1), 241–267. https://doi.org/10.1146/annurev.pp.43.060192.001325
  • Hu, L., He, H., Zhu, C., Peng, X., Fu, J., He, X., Chen, X., Ouyang, L., Bian, J., & Liu, S. (2017). Genome-wide identification and phylogenetic analysis of the chalcone synthase gene family in rice. Journal of Plant Research, 130(1), 95–105. https://doi.org/10.1007/s10265-016-0871-7
  • Huang, L., Wang, H., Ye, H., Du, Z., Zhang, Y., Beerhues, L., & Liu, B. (2012). Differential expression of benzophenone synthase and chalcone synthase in Hypericum sampsonii. Natural Product Communications, 7(12), 1934578X1200701. https://doi.org/10.1177/1934578X1200701219
  • Jez, J. M., Austin, M. B., Ferrer, J. L., Bowman, M. E., Schröder, J., & Noel, J. P. (2000). Structural control of polyketide formation in plant-specific polyketide synthases. Chemistry & Biology, 7(12), 919–930. https://doi.org/10.1016/S1074-5521(00)00041-7
  • Jucá, M. M., Cysne Filho, F. M. S., de Almeida, J. C., Mesquita, D. D. S., Barriga, J. R. D. M., Dias, K. C. F., Barbosa, T. M., Vasconcelos, L. C., Leal, L. K. A. M., Ribeiro, J. E., & Vasconcelos, S. M. M. (2020). Flavonoids: Biological activities and therapeutic potential. Natural Product Research, 34(5), 692–705. https://doi.org/10.1080/14786419.2018.1493588
  • Junghans, H., Dalkin, K., & Dixon, R. A. (1993). Stress responses in alfalfa (Medicago sativa L.). 15. Characterization and expression patterns of members of a subset of the chalcone synthase multigene family. Plant Molecular Biology, 22(2), 239–253. https://doi.org/10.1007/BF00014932
  • Junghanns, K. T., Kneusel, R. E., Baumert, A., Maier, W., Gröger, D., & Matern, U. (1995). Molecular cloning and heterologous expression of acridone synthase from elicited Ruta graveolens L. cell suspension cultures. Plant Molecular Biology, 27(4), 681–692. https://doi.org/10.1007/BF00020222
  • Kan, D., Zhao, D., & Duan, P. (2020). In silico identification of Capsicum type III polyketide synthase genes and expression patterns in Capsicum annuum. Open Life Sciences, 15(1), 753–762. https://doi.org/10.1515/biol-2020-0077
  • Kaur, R., Aslam, L., Kapoor, N., & Mahajan, R. (2020). Identification and comparative expression analysis of chalcone synthase, flavanone 3-hydroxylase and dihydroflavonol 4-reductase genes in wild pomegranate (Punica granatum L.) organs. Brazilian Journal of Botany, 43(4), 883–896. https://doi.org/10.1007/s40415-020-00648-x
  • Koduri, P. H., Gordon, G. S., Barker, E. I., Colpitts, C. C., Ashton, N. W., & Suh, D. Y. (2010). Genome-wide analysis of the chalcone synthase superfamily genes of Physcomitrella patens. Plant Molecular Biology, 72(3), 247–263. https://doi.org/10.1007/s11103-009-9565-z
  • Koes, R., Verweij, W., & Quattrocchio, F. (2005). Flavonoids: A colorful model for the regulation and evolution of biochemical pathways. Trends in Plant Science, 10(5), 236–242. https://doi.org/10.1016/j.tplants.2005.03.002
  • Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35(6), 1547–1549. https://doi.org/10.1093/molbev/msy096
  • Kumar, A., Sharma, M., Chaubey, S. N., & Kumar, A. (2020). Homology modeling and molecular dynamics based insights into Chalcone synthase and Chalcone isomerase in Phyllanthus emblica L. 3 Biotech, 10(8), 1–13. https://doi.org/10.1007/s13205-020-02367-2
  • Kuo, Y. T., Chao, Y. T., Chen, W. C., Shih, M. C., & Chang, S. B. (2019). Segmental and tandem chromosome duplications led to divergent evolution of the chalcone synthase gene family in Phalaenopsis orchids. Annals of Botany, 123(1), 69–77. https://doi.org/10.1093/aob/mcy136
  • Li, M., Cao, Y. T., Ye, S. R., Irshad, M., Pan, T. F., & Qiu, D. L. (2016). Isolation of CHS gene from Brunfelsia acuminata flowers and its regulation in anthocyanin biosysthesis. Molecules, 22(1), 44. https://doi.org/10.3390/molecules22010044
  • Liew, C. F., Goh, C. J., Loh, C. S., & Lim, S. H. (1998). Cloning and characterization of full-length cDNA clones encoding chalcone synthase from the orchid Bromheadia finlaysoniana. Plant Physiology and Biochemistry, 36(9), 647–656. https://doi.org/10.1016/S0981-9428(98)80013-2
  • Lijuan, C., Huiming, G., Yi, L., & Hongmei, C. (2015). Chalcone synthase EaCHS1 from Eupatorium adenophorum functions in salt stress tolerance in tobacco. Plant Cell Reports, 34(5), 885–894. https://doi.org/10.1007/s00299-015-1751-7
  • Lin, C. S., Chen, J. J., Chiu, C. C., Hsiao, H. C., Yang, C. J., Jin, X. H., Leebens, Mack, J., de Pamphilis, C. W., Huang, Y. T., Yang, L. H., Chang, W. J., Kui, L., Wong, G. K. S., Hu, J. M., Wang, W., & Shih, M. C. (2017). Concomitant loss of NDH complex-related genes within chloroplast and nuclear genomes in some orchids. The Plant Journal: For Cell and Molecular Biology, 90(5), 994–1006. https://doi.org/10.1111/tpj.13525
  • Liu, W., Xie, Y., Ma, J., Luo, X., Nie, P., Zuo, Z., Lahrmann, U., Zhao, Q., Zheng, Y., Zhao, Y., Xue, Y., & Ren, J. (2015). IBS: An illustrator for the presentation and visualization of biological sequences. Bioinformatics (Oxford, England), 31(20), 3359–3361. https://doi.org/10.1093/bioinformatics/btv362
  • Liu, X., Meng, X., Ye, J., Zhang, W., Chang, J., & Xu, F. (2018). Characterization of novel Chalcone synthase gene (CnCHS) from Chamaemelum nobile. Biotechnology(Faisalabad), 17(2), 54–61. https://doi.org/10.3923/biotech.2018.54.61
  • Lu, X., Zhou, W., & Gao, F. (2009). Cloning, characterization and localization of CHS gene from blood orange, Citrus sinensis (L.) Osbeck cv. Ruby. Molecular Biology Reports, 36(7), 1983–1990. https://doi.org/10.1007/s11033-008-9408-z
  • Ma, W., Wu, Y., Wu, M., Ren, Z., & Zhong, Y. (2015). Cloning, characterization and expression of chalcone synthase from medicinal plant Rhus chinensis. Journal of Plant Biochemistry and Biotechnology, 24(1), 18–24. https://doi.org/10.1007/s13562-013-0231-9
  • Mallika, V., Sivakumar, K. C., & Soniya, E. V. (2011). Evolutionary implications and physicochemical analyses of selected proteins of type III polyketide synthase family. Evolutionary Bioinformatics, 7, EBO.S6854–53. https://doi.org/10.4137/EBO.S6854
  • Morris, A. L., MacArthur, M. W., Hutchinson, E. G., & Thornton, J. M. (1992). Stereochemical quality of protein structure coordinates. Proteins: Structure, Function, and Bioinformatics, 12(4), 345–364. https://doi.org/10.1002/prot.340120407
  • Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods, 5(7), 621–628. https://doi.org/10.1038/nmeth.1226
  • Pandith, S. A., Ramazan, S., Khan, M. I., Reshi, Z. A., & Shah, M. A. (2020). Chalcone synthases (CHSs): The symbolic type III polyketide synthases. Planta, 251(1), 1–29. https://doi.org/10.1007/s00425-019-03307-y
  • Pitakdantham, W., Sutabutra, T., Chiemsombat, P., & Pitaksutheepong, C. (2010). Isolation and characterization of chalcone synthase gene isolated from Dendrobium Sonia Earsakul. Pakistan Journal of Biological Sciences: PJBS, 13(20), 1000–1005. https://doi.org/10.3923/pjbs.2010.1000.1005
  • Pothiraj, R., Ravikumar, M. J., Suthanthiram, B., Subbaraya, U., & Krishnamurthy, P. (2021). Genome-scale analyses of polyketide synthases in banana: Phylogenetics and expression profiling forecast their candidacy in specialized metabolism. Gene, 778, 145472. https://doi.org/10.1016/j.gene.2021.145472
  • Preisig-Müller, R., Gnau, P., & Kindl, H. (1995). The inducible 9, 10-dihydrophenanthrene pathway: Characterization and expression of bibenzyl synthase and S-adenosylhomocysteine hydrolase. Archives of Biochemistry and Biophysics, 317(1), 201–207. https://doi.org/10.1006/abbi.1995.1154
  • Reimold, U., Kröger, M., Kreuzaler, F., & Hahlbrock, K. (1983). Coding and 3' non-coding nucleotide sequence of chalcone synthase mRNA and assignment of amino acid sequence of the enzyme. The EMBO Journal, 2(10), 1801–1805. https://doi.org/10.1002/j.1460-2075.1983.tb01661.x
  • Samappito, S., Page, J., Schmidt, J., De-Eknamkul, W., & Kutchan, T. M. (2002). Molecular characterization of root-specific chalcone synthases from Cassia alata. Planta, 216(1), 64–71. https://doi.org/10.1007/s00425-002-0872-8
  • Schnee, S., Viret, O., & Gindro, K. (2008). Role of stilbenes in the resistance of grapevine to powdery mildew. Physiological and Molecular Plant Pathology, 72(4–6), 128–133. https://doi.org/10.1016/j.pmpp.2008.07.002
  • Sharma, A., Shahzad, B., Rehman, A., Bhardwaj, R., Landi, M., & Zheng, B. (2019). Response of phenylpropanoid pathway and the role of polyphenols in plants under abiotic stress. Molecules, 24(13), 2452. https://doi.org/10.3390/molecules24132452
  • Singh, K., Kumar, A., Kajal, M., & Singh, B. (2019). Characterization and expression analysis of chalcone synthase and chalcone isomerase genes in Phyllanthus emblica (L.). Journal of Plant Biochemistry and Biotechnology, 28(1), 105–113. https://doi.org/10.1007/s13562-018-0467-5
  • Singh, N., & Kumaria, S. (2020). Molecular cloning and characterization of chalcone synthase gene from Coelogyne ovalis Lindl. and its stress-dependent expression. Gene, 762, 145104. https://doi.org/10.1016/j.gene.2020.145104
  • Singh, N., & Kumaria, S. (2021). Deciphering the role of stress elicitors on the differential modulation of chalcone synthase gene and subsequent production of secondary metabolites in micropropagated Coelogyne ovalis Lindl., a therapeutically important medicinal orchid. South African Journal of Botany, 140, 336–348. https://doi.org/10.1016/j.sajb.2020.06.019
  • Su, X., Sun, X., Cheng, X., Wang, Y., Abdullah, M., Li, M., Li, D., Gao, J., Cai, Y., & Lin, Y. (2017). Comparative genomic analysis of the PKS genes in five species and expression analysis in upland cotton. PeerJ, 5, e3974. https://doi.org/10.7717/peerj.3974
  • Suh, D. Y., Fukuma, K., Kagami, J., Yamazaki, Y., Shibuya, M., Ebizuka, Y., & Sankawa, U. (2000). Identification of amino acid residues important in the cyclization reactions of chalcone and stilbene synthases. Biochemical Journal, 350(1), 229–235. https://doi.org/10.1042/bj3500229
  • Sun, W., Meng, X., Liang, L., Jiang, W., Huang, Y., He, J., Hu, H., Almqvist, J., Gao, X., & Wang, L. (2015). Molecular and biochemical analysis of chalcone synthase from Freesia hybrid in flavonoid biosynthetic pathway. PLoS One, 10(3), e0119054. https://doi.org/10.1371/journal.pone.0119054
  • Tai, D., Tian, J., Zhang, J., Song, T., & Yao, Y. (2014). A Malus crabapple chalcone synthase gene, McCHS, regulates red petal color and flavonoid biosynthesis. PLoS One, 9(10), e110570. https://doi.org/10.1371/journal.pone.0110570
  • Tropf, S., Lanz, T., Rensing, S. A., Schröder, J., & Schröder, G. (1994). Evidence that stilbene synthases have developed from chalcone synthases several times in the course of evolution. Journal of Molecular Evolution, 38(6), 610–618. https://doi.org/10.1007/BF00175881
  • Vadivel, A. K. A., Krysiak, K., Tian, G., & Dhaubhadel, S. (2018). Genome-wide identification and localization of chalcone synthase family in soybean (Glycine max [L] Merr). BMC Plant Biology, 18(1), 13. https://doi.org/10.1186/s12870-018-1569-x
  • Wang, W. K., Schaal, B. A., Chiou, Y. M., Murakami, N., Ge, X. J., Huang, C. C., & Chiang, T. Y. (2007). Diverse selective modes among orthologs/paralogs of the chalcone synthase (Chs) gene family of Arabidopsis thaliana and its relative A. halleri ssp. gemmifera. Molecular Phylogenetics and Evolution, 44(2), 503–520. https://doi.org/10.1016/j.ympev.2007.05.006
  • Wang, Y., Dou, Y., Wang, R., Guan, X., Hu, Z., & Zheng, J. (2017). Molecular characterization and functional analysis of chalcone synthase from Syringa oblata Lindl. in the flavonoid biosynthetic pathway. Gene, 635, 16–23. https://doi.org/10.1016/j.gene.2017.09.002
  • Winkel-Shirley, B. (2001). Flavonoid biosynthesis. A colorful model for genetics, biochemistry, cell biology, and biotechnology. Plant Physiology, 126(2), 485–493. https://doi.org/10.1104/pp.126.2.485
  • Wu, X., Zhang, S., Liu, X., Shang, J., Zhang, A., Zhu, Z., & Zha, D. (2020). Chalcone synthase (CHS) family members analysis from eggplant (Solanum melongena L.) in the flavonoid biosynthetic pathway and expression patterns in response to heat stress. PLoS One, 15(4), e0226537. https://doi.org/10.1371/journal.pone.0226537
  • Xu, F., Cheng, S., Cheng, S., Wang, Y., & Du, H. (2007). Time course of expression of chalcone synthase gene in Ginkgo biloba. Zhi wu Sheng li yu Fen zi Sheng wu Xue Xue Bao = Journal of Plant Physiology and Molecular Biology, 33(4), 309–317.
  • Yao, X., Wang, T., Wang, H., Liu, H., Liu, S., Zhao, Q., Chen, K., & Zhang, P. (2019). Identification, characterization and expression analysis of the chalcone synthase family in the Antarctic moss Pohlia nutans. Antarctic Science, 31(1), 23–33. https://doi.org/10.1017/S0954102018000470
  • Yu, O., & Jez, J. M. (2008). Nature's assembly line: Biosynthesis of simple phenylpropanoids and polyketides. The Plant Journal: For Cell and Molecular Biology, 54(4), 750–762. https://doi.org/10.1111/j.1365-313X.2008.03436.x
  • Zhang, G.-Q., Xu, Q., Bian, C., Tsai, W.-C., Yeh, C.-M., Liu, K.-W., Yoshida, K., Zhang, L.-S., Chang, S.-B., Chen, F., Shi, Y., Su, Y.-Y., Zhang, Y.-Q., Chen, L.-J., Yin, Y., Lin, M., Huang, H., Deng, H., Wang, Z.-W., … Liu, Z.-J. (2016). The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution. Scientific Reports, 6, 19029. https://doi.org/10.1038/srep19029
  • Zhang, G.-Q., Liu, K.-W., Li, Z., Lohaus, R., Hsiao, Y.-Y., Niu, S.-C., Wang, J.-Y., Lin, Y.-C., Xu, Q., Chen, L.-J., Yoshida, K., Fujiwara, S., Wang, Z.-W., Zhang, Y.-Q., Mitsuda, N., Wang, M., Liu, G.-H., Pecoraro, L., Huang, H.-X., … Liu, Z.-J. (2017). The Apostasia genome and the evolution of orchids. Nature, 549(7672), 379–383. https://doi.org/10.1038/nature23897
  • Zhou, B., Wang, Y., Zhan, Y., Li, Y., & Kawabata, S. (2013). Chalcone synthase family genes have redundant roles in anthocyanin biosynthesis and in response to blue/UV-A light in turnip (Brassica rapa; Brassicaceae). American Journal of Botany, 100(12), 2458–2467. https://doi.org/10.3732/ajb.1300305

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