Towards understanding the regulation of rubber biosynthesis: Insights into the initiator and elongator enzymes

Ankita Punetha, Jayaraman Muthukumaran, Anmol Jaywant Hemrom, Nagarajan Arumugam, Mannu Jayakanthan and Durai Sundar*

Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi 110016, India.

*Corresponding author. E-mail: sundar@dbeb.iitd.ac.in. Tel: +91-11-26591066. Fax: +91-11-26582282.

Accepted 7 January, 2010

   Abstract

Natural rubber is an important polymer produced by plants and made up of isoprene units derived from isopentenyl diphosphate (IPP). Although more than 2000 plant species are known to produce natural rubber, currently there are two important commercial sources, Hevea brasiliensis (the Brazilian rubber tree) and Parthenium argentatum Gray (guayule). Natural rubber biosynthesis requires three distinct biochemical processes such as (i) initiation, (ii) elongation and (iii) termination.  Computational analyses of the enzymes farnesyl diphosphate (FPP) synthase in P. argentatum and cis-prenyl transferase (CPT) in H. brasiliensis that play a vital role in initiation and elongation stages for biosynthesis of cis-1,4-polyisoprene has been undertaken in this study. Amino acid sequence comparisons of FPP synthase and CPT to their identified similar sequences were carried out to understand the evolutionary relationship among different species.  Homology modeling and binding pocket analysis aided in the understanding of structure-function relationship and enzyme-substrate interaction of FPP synthase and CPT.  The structural templates farnesyl diphosphate synthase (Source: Gallus gallus) [PDB ID: 1UBX] for FPP synthase and undecaprenyl diphosphate synthase (Source: Micrococcus luteus B-P 26) [PDB ID: 1F75] for CPT were selected for homology modeling. The Ramachandran plots were developed for modeled structures of FPP synthase and CPT, which showed 95.9 and 92.6% of amino acid residues occurring in favored regions.  These models were deposited into Protein Model Database [PMDB ID: PM0075218 and PM0075509].  The substrate and cofactor binding site residues of FPP synthase (R103, L149, A184, Y197, L211, H214, E223, T226, D332, K246, Y306, K313) and CPT (Y4, E7, R20, K21, G22, K154, K178, D193, E231, T232, R233) were identified by using binding pocket analysis, which is consistent with available X-ray crystal structure of both the templates. The computational analysis of initiation and elongation for cis-1,4-polyisoprene biosynthesis provided invaluable insights into the identification of putative initiation and elongation factors for FPP synthase and CPT.

Key words: Cis-prenyl transferase, deep view, errat, farnesyl diphosphate synthase, Hevea brasiliensis, MODELLER, Parthenium argentatum, protein model database.