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

Abstract

Type III polyketide synthases (PKSs) catalyse the formation of an array of polyketides with diverse structures that play an important role in secondary metabolism in plants. This group of enzymes is encoded by a multigene family, the Type III polyketide synthase (PKS) gene family. Vast reserves of secondary metabolites in orchids make these plants suitable candidates for research in the area. In this study, genome-wide searches lead to the identification of five PeqPKS, eight DcaPKS and six AshPKS genes in Phalaenopsis equestris, Dendrobium catenatum and Apostasia shenzhenica, respectively. All the members showed the presence of two characteristic conserved domains (Chal_sti_synt_N and Chal_sti_synt_C) and were generally localised in the cytoplasm. The phylogenetic analysis led to the classification of these proteins into two groups: CHS (chalcone synthase (CHS) and non-CHS. A single protein in P. equestris and two proteins each in D. catenatum and A. shenzhenica clustered within the CHS clade. The majority of the genes exhibited similar structural patterns with a single intron. Expression profiling revealed the tissue-specific expression of these genes with high expression in reproductive tissues for most genes. A number of stress-responsive cis-regulatory elements were predicted, noteworthy amongst these are, ABRE and CGTCA that are chiefly responsible for responding to abscisic acid and methyl jasmonate, respectively. Our study provides a reference framework for future studies involving functional elucidation of PKS genes and biotechnological production of polyketides.

Communicated by Ramaswamy H. Sarma

Highlights

• Identification of five PeqPKS, eight DcaPKS and six AshPKS genes in Phalaenopsis equestris, Dendrobium catenatum and Apostasia shenzhenica based on genome-wide analysis

• Presence of characteristic conserved domains (Chal_sti_synt_N, Chal_sti_synt_C) with cytological localisation

• Phylogenetic clustering into two groups, CHS chalcone synthase (CHS) and non-CHS

• Expression profiling revealing high expression in reproductive tissues

• Prediction of stress-responsive cis-regulatory elements like ABRE and CGTCA

Keywords:

• Chalcone synthase
• polyketides
• secondary metabolism
• orchids

Disclosure statement

The authors do not have any conflicts to declare.

Ethics approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Author’s contribution

SVP and JKS conceptualized the work. AK and DG performed the analysis and prepared the original draft. SVP, JKS and VGY critically reviewed and edited the draft. All the authors have read and approved the final version.

Availability of data and material

All the data collected and analysed in this study has been included in the main body of the article.

Additional information

Funding

INSPIRE Fellowship from Department of Science and Technology (DST) for AK (File No. DST/INSPIRE/03/2021/002638). Senior Research Fellowship from Council of Scientific and Industrial Research for DG (File No. 09/135(0809)/2018-EMR-I). Partial financial support from Department of Science and Technology, Government of India under Promotion of University Research and Scientific Excellence (PURSE) grant scheme.