In silico characterization and differential expression analysis of 1-deoxy-d-xylulose-5-phosphate reductoisomerase (DXR) of Centella asiatica

Aziz ZA, Davey MR, Power JB, Anthony P, Smith RM, Lowe KC (2007) Production of asiaticoside and madecassoside in Centella asiatica in vitro and in vivo. Biol Plant 51(1):34–42 Berendsen HJC, Van Der Spoel D, Van Drunen R (1995) GROMACS: a message-passing parallel molecular dynamics implementation. Comput Phys Commun 91:43–56 Campos N, Arró M, Ferrer A, Boronat A (2014) Determination of 3-hydroxy-3-methylglutaryl CoA reductase activity in plants. In: Rodríguez-Concepción M (ed) Methods in molecular biology manuel, plant isoprenoids: methods and protocols, pp 21–41 Carretero-Paulet L, Ahumada I, Cunillera N et al (2002) Expression and molecular analysis of the Arabidopsis DXR gene encoding1-deoxy-d-xylulose 5-phosphate reductoisomerase, the first committed enzyme of the 2-C-methyl-d-erythritol 4-phosphate pathway. Plant Physiol 129:1581–1591 Chen F, Ro DK, Petri J et al (2004) Characterization of a root-specific Arabidopsis terpene synthase responsible for the formation of the volatile monoterpene 1,8-cineole. Plant Physiol 135:1956–1966 Das AJ (2011) Review on nutritional, medicinal and pharmacological properties of Centella asiatica (Indian pennywort). J Biol Active Prod Nat 4:216–228 Dehury B, Patra MC, Maharana J, Sahu J, Sen P, Modi MK, Choudhury MD, Barooah M (2014) Structure-based computational study of two disease resistance gene homologues (Hm1and Hm2) in maize (Zea mays L.) with implications in plant-pathogen interactions. PLoS ONE 9(5):1–14 Devi K, Dehury B, Phukon M, Modi MK, Sen P (2015) Novel insights into the structure-function mechanism and tissue-specific expression profiling of full-length dxr gene from Cymbopogon winterianus. FEBS Open Bio 5:325–334 Eisenreich W, Rohdich F, Bacher A (2001) Deoxyxylulose phosphate pathway to terpenoids. Trends Plant Sci 6:1401–1426 Fukusak E, Takeno S, Bamba T et al (2004) Biosynthetic pathway for the C45 polyprenol, solanesol, in tobacco. Biosci Biotechnol Biochem 68:1988–1990 Gohil KJ, Patel JA, Gajjar AK (2010) Pharmacological Review on Centella asiatica: a potential herbal cure-all. Indian J Pharm Sci 72(5):546–556 Gong Y, Liao Z, Chen M et al (2005) Molecular cloning and characterization of a deoxy-d-xylulose 5-phosphate reductoisomerase gene from Ginkgo biloba. DNA Seq 16:111–121 Gupta P, Agarwal AV, Akhtar N, Sangwan RS, Singh SP, Trivedi PK (2013) Cloning and characterization of 2-C-methyl-D-erythritol-4-phosphate pathway genes for isoprenoid biosynthesis from Indian ginseng, Withania somnifera. Protoplasma 250:285–295 Hampel D, Mosandl A, Wu M (2005) Biosynthesis of mono and sesquiterpenes in carrot roots and leaves (Daucus carota L.): metabolic cross talk of cytosolic mevalonate and plastidial methylerythritol phosphate pathways. Phytochemistry 66:305–311 Howes MJR, Houghton P (2003) Plants used in Chinese and Indian traditional medicine for improvement of memory and cognitive function. Pharmacol Biochem Behav 75:513–527 Iorizzo M, Ellison S, Senalik D et al (2016) A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution. Nat Genet 48:657–666 James JT, Dubery IA (2009) Pentacyclic Triterpenoids from the Medicinal Herb, Centella asiatica (L.) Urban. Molecules 14:3922–3941 Jamil S, Nizami Q, Salam M (2007) Centella asiatica (Linn.) Urban: a review. Nat Prod Radiance 6:158–170 Kalita R, Patar L, Shasany AK, Modi MK, Sen P (2015) Molecular cloning, characterization and expression analysis of 3-hydroxy-3-methylglutaryl coenzyme A reductase gene from Centella asiatica L. Mol Biol Rep 42(9):1431–1439 Khemvong S, Suvachittanont W (2005) Molecular cloning and expression of a cDNA encoding 1-deoxy-d-xylulose-5-phosphate synthase from oil palm Elaeis guineensis Jcaq. Plant Sci 169:571–578 Kim OT, Kim MY, Hong MH, Ahn JC, Oh MH, Hwang B (2002) Production of triterpene glycosides from whole plant cultures of Centella asiatica (L.) Urban. Korea J Plant Biotechnol 29:275–279 Lange BM, Croteau RB (1999) Isoprenoid biosynthesis via a mevalonate-independent pathway in plants: cloning and heterologous expression of 1-deoxy-d-xylulose-5 phosphate reductoisomerase from peppermint. Arch Biochem Biophys 365:170–174 Laskowski RA, MacArthur MW, Thornton JM (2001) PROCHECK: validation of protein structure coordinates. In: Rossmann MG, Arnold E (eds) International tables of crystallography, volume F, crystallography of biological macro-molecules. Kluwer, Dordrecht, pp 722–725 Laskowski RA, McArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 26:283–291 Liao Z, Chen R, Chen M, Yang C, Wang Q, Gong Y (2007) A new 1-deoxy-d-xylulose5-phosphate reductoisomerase gene encoding the committed step enzyme in the MEP pathway from Rauvolfia verticillata. Z Naturforsch 62:296–304 Lindahl E, Hess B, Van Der Spoel D (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7:306–317 Liu J, Xu Y, Liang L, Wei J (2015) Molecular cloning, characterization and expression analysis of the gene encoding 1-deoxy-d-xylulose 5-phosphate reductoisomerase from Aquilaria sinensis (Lour.) Gilg. J Genet 94:239–249 Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2[-Delta DeltaC(T)] method. Methods 25:402–408 Luo J, Wang Y, Zhang JN (2014) Cloning and tissue-specific expression analysis of conserved fragments of DXR gene from Angelica sinensis. Chin Tradit Herb Drugs 45:1907–1913 Maharana J, Vats A, Gautam S et al (2017) POP1 might be recruiting its type-Ia interface for NLRP3-mediated PYD-PYD interaction: Insights from MD simulation. J Mol Recognit 30:1–10 Mathur S, Verma RK, Gupta MM, Ram M, Sharma S, Kumar S (2001) Screening of genetic resources of the medicinal-vegetable plant Centella asiatica for herb and asiaticoside yields under shaded and full sunlight conditions. J Hortic Sci Biotechnol 75:551–554 Meulenbeld GJ, Wujastyk D (2001) Studies on Indian medical history this is a scholarly work. The historical narrative is most interesting. The Scientific and Medical Network, Motilal Banarsidass Publishing, New Dehli Murkin AS, Manning KA, Kholodar SA (2014) Mechanism and inhibition of 1-deoxy-d-xylulose-5-phosphate reductoisomerase. Bioorg Chem 57:171–185 Nun YS, Sharkey TD, Suvachittanont W (2008) Molecular cloning and characterization of two cDNAs encoding 1-deoxy-d-xylulose 5-phosphate reductoisomerase from Hevea brasiliensis. J Plant Physiol 165:991–1002 Orhan IE (2012) Centella asiatica (L.) urban: from traditional medicine to modern medicine with neuroprotective potential. Evid Based Complement Alternat Med 12:946259 Pal S, Shasany A (2014) Centella asiatica 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) mRNA, complete cds. Accession number: JQ965955 Reuter K, Sanderbrand S, Jomaa H (2002) Crystal structure of 1-deoxy-d-xylulose-5-phosphate reductoisomerase, a crucial enzyme in the non-mevalonate pathway of isoprenoid biosynthesis. J Biol Chem 277:5378–5384 Saitou N, Nei M (1987) The Neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425 Sharma E, Pandey S, Gaur AK (2016) In silico characterization and differential expression pattern analysis of conserved HMG CoA reductase domain isolated from Aconitum balfourii Stapf. 3 Biotech 6:89 Takahashi S, Kuzuyama T, Watanabe H, Seto H (1998) A 1-deoxy-d-xylulose 5-phosphate reductoisomerase catalyzing the formation of 2-C-methyl-d-erythritol 4-phosphate in an alternative non-mevalonate pathway for terpenoid biosynthesis. Proc Natl Acad Sci USA 95:9879–9884 Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis Version 6.0. Mol Biol Evol 30:2725–2729 Tong Y, Su P, Zhao Y (2015) Molecular cloning and characterization of DXS and DXR Genes in the terpenoid biosynthetic pathway of Tripterygium wilfordii. Int J Mol Sci 16:25516–25535 Van Der Spoel D, Lindahl E, Hess B et al (2005) GROMACS: fast, flexible, and free. J Comput Chem 26:1701–1718 Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35:407–410 Wu GS, Robertson DH, Brooks CL, Michal V (2003) Detailed analysis of grid based molecular docking: a case study of CDOCKER-A CHARMm-based MDdocking algorithm. J Comput Chem 24:1549–1562 Yan X, Zhang I, Zhang J et al (2009) Molecular characterization and expression of 1-deoxy-d-xylulose5-phosphate reductoisomerase (DXR) gene from Salvia miltiorrhiza. Acta Physiol Plant 31:1015–1022 Yang J, Adhikari NM, Liu H et al (2012a) Characterization and functional analysis of the genes encoding 1-deoxy-d-xylulose-5-phosphate reductoisomerase and 1-deoxy-d-xylulose-5-phosphate synthase, the two enzymes in the MEP pathway, from Amomum villosum Lour. Mol Biol Rep 39:8287–8296 Yang J, Nath M, Adhikari HL et al (2012b) Characterization and functional analysis of the genes encoding 1-deoxy-d-xylulose-5-phosphate reductoisomerase and 1-deoxy-d-xylulose-5-phosphate synthase, the two enzymes in the MEP pathway, from Amomum villosum Lour. Mol Biol Rep 39:8287–8296 Yao H, Gong Y, Zuo K et al (2008) Molecular cloning, expression profiling and functional analysis of a DXR gene encoding1-deoxy-d-xylulose 5-phosphate reductoisomerase from Camptotheca acuminate. J Plant Physiol 165:203–213