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

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An Erratum to this article was published on 03 April 2015

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.

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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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Authors and Affiliations

  1. Department of Agronomy and Plant Breeding Sciences, College of Aboureihan, University of Tehran, Tehran, Iran

    Maryam Darabi

  2. Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran

    Ali Masoudi-Nejad

  3. Department of Agronomy and Plant Breeding, College of Agronomy Sciences, Sari Agricultural Sciences and Natural Resources University (SANRU), Mazandaran, Iran

    Ghorbanali Nemat-Zadeh

Authors
  1. Maryam Darabi
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  2. Ali Masoudi-Nejad
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  3. Ghorbanali Nemat-Zadeh
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Correspondence to Maryam Darabi.

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An erratum to this article is available at http://dx.doi.org/10.1007/s11033-015-3872-z.

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Darabi, M., Masoudi-Nejad, A. & Nemat-Zadeh, G. Bioinformatics study of the 3-hydroxy-3-methylglotaryl-coenzyme A reductase (HMGR) gene in Gramineae. Mol Biol Rep 39, 8925–8935 (2012). https://doi.org/10.1007/s11033-012-1761-2

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