An in-silico approach to unravel the structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHPS): a critical enzyme for sennoside biosynthesis in Cassia angustifolia Vahl

Abstract

The laxative properties of senna are attributed to the presence of sennosides produced in the plant. The low production level of sennosides in the plant is an important impediment to their growing demand and utilization. Understanding biosynthetic pathways helps to engineer them in terms of enhanced production. The biosynthetic pathways of sennoside production in plants are not completely known yet. However, attempts to get information on genes and proteins engaged in it have been made which decode involvement of various pathways including shikimate pathway. 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHPS) is a key enzyme involved in sennosides production through the shikimate pathway. Unfortunately, there is no information available on proteomic characterization of DAHPS enzyme of senna (caDAHPS) resulting in lack of knowledge about its role. We for the first time characterized DAHPS enzyme of senna using in-silico analysis. To the best of our knowledge this is the first attempt to identify the coding sequence of caDAHPS by cloning and sequencing. We found Gln179, Arg175, Glu462, Glu302, Lys357 and His420 amino acids in the active site of caDAHPS through molecular docking. followed by molecular dynamic simulation. The amino acid residues, Lys182, Cys136, His460, Leu304, Gly333, Glu334, Pro183, Asp492 and Arg433 at the surface interact with PEP by van der Waals bonds imparting stability to the enzyme-substrate complex. Docking results were further validated by molecular dynamics. The presented in-silico analysis of caDAHPS will generate opportunities to engineer the sennoside biosynthesis in plants.

Communicated by Ramaswamy H. Sarma

Keywords:

• Senna
• sennoside
• 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase
• shikimic acid pathway
• molecular docking
• homology modeling

Acknowledgments

We acknowledge ScHeme Of Developing High quality research (SHODH), Education Department, Government of Gujarat, India for providing the research fellowship to J.P and Department of Biotechnology (DBT) for providing research fellowship to K.R. We are grateful for the facilities provided by the Director, ICAR-Directorate of Medicinal and Aromatic Plants Research, Boriavi, Anand, Gujarat, India and Indian Council of Agricultural research (ICAR), New Delhi to undertake the study. We appreciate the assistance provided by the Department of Biochemistry and Forensic Science, School of Sciences, Gujarat University in the preparation of this publication.

Authors’ contribution

K.T: Writing, molecular docking, and interaction analysis; J.P: Secondary structure prediction and retrieval of homology models; K.R: Preparation of figures; D.P: Writing, performing and analyzing molecular dynamic studies; N.R: Conceptualization, reviewed the manuscript; R.J: Data collection and reviewed the manuscript M.P: Supervision of the work and data analysis.

Disclosure statement

The authors declare no conflict of interest.

Additional information

Funding

This work was supported by the grant of SERB (Science and Engineering Research Board)-TARE (TAR/2019/000153), India.