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Molecular Biology Reports

, Volume 39, Issue 9, pp 8925–8935 | Cite as

Bioinformatics study of the 3-hydroxy-3-methylglotaryl-coenzyme A reductase (HMGR) gene in Gramineae

  • Maryam Darabi
  • Ali Masoudi-Nejad
  • Ghorbanali Nemat-Zadeh
Article

Abstract

Isoprenoids or terpenoids are synthesized by two important units’ including dimethylallyl diphosphate and isopentenyl diphosphate (IPP). Plants use two different methods for formation of IPP, which is a cytosolic and a plastidial method. The 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR, EC 1.1.1.34) catalyzes the conversion of HMG-CoA to mevalonate, which is the first stage in the cytosolic pathway for biosynthesis of isoprenoid in plants. In this study, a total of fifty HMGR protein sequences from Gramineae and three animal samples including human, mouse and fruit fly were aligned and analyzed by computational tools to predict the protein properties, such as molecular mass, pI, signal peptide, transmembrane and conserved domains, secondary and spatial structures. Sequence comparison analysis revealed that there is high identity between plants and animals. Three catalytic regions including L domain, N domain and S domain were detected by structural modeling of HMGR. The tertiary structure model of Oryza sativa HMGR (Accession Number: NP_001063541) was further checked by PROCHECK algorithm, and showed that 90.3 % of the amino acid residues were located in the most favored regions in Ramachandran plot, indicating that the simulated three-dimensional structure was reliable. Phylogenetic analysis indicated that there is a relationship among species of Gramineae and other organisms. According to these results, HMGRs should be derived from a common ancestor.

Keywords

Bioinformatics Gramineae HMGR Mevalonate pathway (MVA) 

Abbreviations

CAS

Cycloartenol synthase

DMAPP

Dimethylallyl diphosphate

DXP

1-Deoxy-d-xylulose 5-phosphate

HMGR

3-Hydroxy-3-methylglutaryl coenzyme A reductase

IPP

Isopentenyl diphosphate

LAS

Lanosterol synthase

MEP

2C-methyl-d-erythritol 4-phosphate

MVA

Mevalonic acid

OSC

Oxidosqualene cyclase

UDP

Uridine diphosphate

UGT

(UDP)-dependent glycosyltransferases

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Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • Maryam Darabi
    • 1
  • Ali Masoudi-Nejad
    • 2
  • Ghorbanali Nemat-Zadeh
    • 3
  1. 1.Department of Agronomy and Plant Breeding Sciences, College of AboureihanUniversity of TehranTehranIran
  2. 2.Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and BiophysicsUniversity of TehranTehranIran
  3. 3.Department of Agronomy and Plant Breeding, College of Agronomy SciencesSari Agricultural Sciences and Natural Resources University (SANRU)MazandaranIran

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