Evolutionary Analysis of a Few Protein Superfamilies in Ocimum tenuiflorum

  • A. Gandhimathi
  • Nitish Sathyanarayanan
  • Meenakshi Iyer
  • Rachit Gupta
  • R. SowdhaminiEmail author
Part of the Compendium of Plant Genomes book series (CPG)


Phytochemicals in the form of secondary metabolites produced by plants have been used for therapeutic purposes, some of the well-known examples being artemisinin for treatment of malaria, vinblastine and vinblastine and vincristine for treatment of cancer. Plants produce several such secondary metabolites having anticancer, cardioprotectant, anti-inflammatory, antidiabetic, artificial sweetener, antimicrobial properties, and plants have evolved elaborate pathways to synthesize these complex biomolecules. Some of these molecules can be highly complex in their chemistry, and it is often impossible to synthesize them in the laboratory, while plants have evolved enzymes with a remarkable capacity to catalyze these reactions with chemo-, regio-, and stereospecificity. Understanding sequence and structural properties of plant enzymes involved in the synthesis of metabolites will help in deciphering the mechanism underlying the synthesis of these phytochemicals. In the present chapter, we describe a computational pipeline for identifying, validating, and analyzing the key components involved in the synthesis of terpenoids and a less studied class of proteases called rhomboids. A bioinformatic study of this nature will have wider implication as not only a tool to understand sequence and structure–function relationships of some of the well-studied metabolites and enzymes, to aid protein engineering for biotechnological utilization of these commercially valuable molecules.


  1. Abdallah I, Quax WJ (2017) A glimpse into the biosynthesis of terpenoids. KnE Life Sci 3(5):81–98CrossRefGoogle Scholar
  2. Afendi FM, Okada T, Yamazaki M, Hirai-Morita A, Nakamura Y, Nakamura K, Ikeda S, Takahashi H, Altaf-Ul-Amin M, Darusman LK, Saito K, Kanaya S (2012) KNApSAcK family databases: Integrated metabolite-plant species databases for multifaceted plant research. Plant Cell Physiol 53(2):1–12CrossRefGoogle Scholar
  3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410CrossRefGoogle Scholar
  4. Baerenfaller K, Hirsch-Hoffmann M, Svozil J, Hull R, Russenberger D, Bischof S, Baginsky S (2011) pep2pro: a new tool for comprehensive proteome data analysis to reveal information about organ-specific proteomes in Arabidopsis thaliana. Integrative Biology: Quantitative Biosciences from Nano to Macro 3(3), 225–237 Scholar
  5. Baldi P, Chauvint Y, Hunkapiller T, Mcclureii M (1994) Hidden Markov models of biological primary sequence information (multiple sequence alignments/protein modeling/adaptive algorithms/sequence Classification). Biochemistry 91:1059–1063Google Scholar
  6. Biegert A, Soding J (2009) Sequence context-specific profiles for homology searching. Proc Natl Acad Sci USA 106(10):3770–3775CrossRefGoogle Scholar
  7. Bohlmann J, Meyer-Gauen G, Croteau R (1998) Plant terpenoid synthases: molecular biology and phylogenetic analysis. Proc Natl Acad Sci USA 95(8):4126–4133CrossRefGoogle Scholar
  8. Boutanaev AM, Moses T, Zi J, Nelson DR, Mugford ST, Peters RJ, Osbourn A (2015) Investigation of terpene diversification across multiple sequenced plant genomes. Proc Natl Acad Sci USA 112(1):E81–E88CrossRefGoogle Scholar
  9. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST +: architecture and applications. BMC Bioinform 9:1–9Google Scholar
  10. Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P (2016) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucl Acids Res 44(D1):D471–D480CrossRefGoogle Scholar
  11. Chapple C (1998) Molecular-genetic analysis of plant cytochrome P450-dependent monooxygenases. Annu Rev Plant Physiol Plant Mol Biol 49:311–343CrossRefGoogle Scholar
  12. Chen F, Tholl D, Bohlmann J, Pichersky E (2011) The family of terpene synthases in plants: a mid-size family of genes for specialized metabolism that is highly diversified throughout the kingdom. Plant J 66(1):212–229CrossRefGoogle Scholar
  13. Degenhardt J, Köllner TG, Gershenzon J (2009) Monoterpene and sesquiterpene synthases and the origin of terpene skeletal diversity in plants. Phytochemistry 70(15–16):1621–1637CrossRefGoogle Scholar
  14. Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14(9):755–763CrossRefGoogle Scholar
  15. Farnsworth NR (1988) Screening plants for new medicines. In: Wilson EO, Peter FM (eds) Biodiversity. National Academies Press, Washington, D.C.Google Scholar
  16. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17(6):368–376CrossRefGoogle Scholar
  17. Fox NK, Brenner SE, Chandonia JM (2014) SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures. Nucleic Acids Res 42(D1):D304–D309. Scholar
  18. García-Lorenzo M, Sjödin A, Jansson S, Funk C (2006) Protease gene families in Populus and Arabidopsis. BMC Plant Biol 6:1–24CrossRefGoogle Scholar
  19. Gertz EM, Yu Y-K, Agarwala R, Schäffer AA, Altschul SF (2006) Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST. BMC Biol 4:41CrossRefGoogle Scholar
  20. Gotoh O (1992) Substrate recognition sites in cytochrome P450 family 2 (CYP2) proteins inferred from comparative analyses of amino acid and coding nucleotide sequences. J Biol Chem 267(1):83–90PubMedGoogle Scholar
  21. Gotoh O (2012) Evolution of cytochrome P450 genes from the viewpoint of genome informatics. Biol Pharm Bull 812(356):812–817CrossRefGoogle Scholar
  22. Hofmann K (1993) TMBASE-A database of membrane spanning protein segments. Biol Chem Hoppe-Seyler 374, 166. Retrieved from
  23. Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Zimmermann P (2008) Genevestigator V3: A Reference Expression Database for the Meta-Analysis of Transcriptomes. Adv Bioinform. Scholar
  24. Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292:195–202CrossRefGoogle Scholar
  25. Käll L, Krogh A, Sonnhammer EL (2004) A combined transmembrane topology and signal peptide prediction method. J Mol Biol 338(5):1027–1036CrossRefGoogle Scholar
  26. Kampranis SC, Ioannidis D, Purvis A, Mahrez W, Ninga E, Katerelos NA, Anssour S, Dunwell JM, Degenhardt J, Makris AM, Goodenough PW, Johnson CB (2007) Rational conversion of substrate and product specificity in a Salvia monoterpene synthase: Structural insights into the evolution of terpene synthase function. Plant Cell 19(6):1994–2005CrossRefGoogle Scholar
  27. Kanaoka MM, Urban S, Freeman M, Okada K (2005) An Arabidopsis Rhomboid homolog is an intramembrane protease in plants. FEBS Letters. Scholar
  28. Kmiec-Wisniewska B, Krumpe K, Urantowka A, Sakamoto W, Pratje E, Janska H (2008) Plant mitochondrial rhomboid, AtRBL12, has different substrate specificity from its yeast counterpart. Plant Mol Biol 68(1–2):159–171CrossRefGoogle Scholar
  29. Knopf RR, Adam Z (2012) Rhomboid proteases in plants - still in square one? Physiol Plant 145(1):41–51CrossRefGoogle Scholar
  30. Kong DX, Guo MY, Xiao ZH, Chen LL, Zhang HY (2011) Historical variation of structural novelty in a natural product library. Chem Biodivers 8(11):1968–1977CrossRefGoogle Scholar
  31. Koonin EV, Makarova KS, Rogozin IB, Davidovic L, Letellier MC, Pellegrini L (2003) The rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers. Genome Biol 4(3):R19CrossRefGoogle Scholar
  32. Lemberg MK, Freeman M (2007) Functional and evolutionary implications of enhanced genomic analysis of rhomboid intramembrane proteases. Genome Res 17(11):1634–1646CrossRefGoogle Scholar
  33. Lemberg MK, Menendez J, Misik A, Garcia M, Koth CM, Freeman M (2005) Mechanism of intramembrane proteolysis investigated with purified rhomboid proteases. EMBO J 24(3):464–472CrossRefGoogle Scholar
  34. Li Q, Zhang N, Zhang L, Ma H (2015) Differential evolution of members of the rhomboid gene family with conservative and divergent patterns. New Phytol 206(1):368–380CrossRefGoogle Scholar
  35. Marchler-Bauer A, Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY, Bryant SH (2002) CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucl Acids Res 30(1):281–283CrossRefGoogle Scholar
  36. Martin VJ, Pitera DJ, Withers ST, Newman JD, Keasling JD (2003) Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat Biotechnol 21:796–802CrossRefGoogle Scholar
  37. Mayer U, Nüsslein-Volhard C (1988) A group of genes required for pattern formation in the ventral ectoderm of the Drosophila embryo. Genes Dev 2(11):1496–1511CrossRefGoogle Scholar
  38. Nebert DW, Nelson DR, Coon MJ, Estabrook RW, Feyereisen R, Fujii-Kuriyama Y, Gonzalez FJ, Guengerich FP, Gunsalus IC, Johnson EF et al (1991) The P450 superfamily: update on new sequences, gene mapping, and recommended nomenclature. DNA Cell Biol 10(1):1–14CrossRefGoogle Scholar
  39. Nelson DR (2009) The cytochrome p450 homepage. Hum Genom 4(1):59–65Google Scholar
  40. Pazouki L, Niinemets Ü (2016) Multi-substrate terpene synthases: their occurrence and physiological significance. Front Plant Sci 7:1019CrossRefGoogle Scholar
  41. Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T et al (2013) A large-scale evaluation of computational protein function prediction. Nat Meth 10(3):221–227CrossRefGoogle Scholar
  42. Rambaut A (2009). FigTree. Tree Figure Drawing Tool. http://Tree.Bio.Ed.Ac.Uk/Software/Figtree/
  43. Schuler MA (1996) The role of cytochrome P450 monooxygenases in plant-insect interactions. Plant Physiol 112(4):1411–1419CrossRefGoogle Scholar
  44. Sonnhammer EL, Eddy SR, Birney E, Bateman A, Durbin R (1998) Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucl Acids Res 26(1):320–322CrossRefGoogle Scholar
  45. Stevenson LG, Strisovsky K, Clemmer KM, Bhatt S, Freeman M, Rather PN (2007) Rhomboid protease AarA mediates quorum-sensing in Providencia stuartii by activating TatA of the twin-arginine translocase. Proc Natl Acad Sci 104(3):1003–1008CrossRefGoogle Scholar
  46. Tholl D (2006) Terpene synthases and the regulation, diversity and biological roles of terpene metabolism. Curr Opin Plant Biol 9(3):297–304CrossRefGoogle Scholar
  47. Thompson EP, Llewellyn Smith SG, Glover BJ (2012) An arabidopsis rhomboid protease has roles in the chloroplast and in flower development. J Exp Bot 63(10):3559–3570CrossRefGoogle Scholar
  48. Tripathi LP, Sowdhamini R (2006) Cross genome comparisons of serine proteases in arabidopsis and rice. BMC Genom 7:1–31CrossRefGoogle Scholar
  49. Upadhyay AK, Chacko AR, Gandhimathi A, Ghosh P, Harini K, Joseph AP, Joshi AG (2015) Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties. BMC Plant Biol 15(1):1–20CrossRefGoogle Scholar
  50. Urban S, Freeman M (2003) Substrate specificity of rhomboid intramembrane proteases is governed by helix-breaking residues in the substrate transmembrane domain. Mol Cell 11(6):1425–1434CrossRefGoogle Scholar
  51. Urban S, Lee JR, Freeman M (2001) Drosophila rhomboid-1 defines a family of putative intramembrane serine oroteases. Cell 107(2):173–182CrossRefGoogle Scholar
  52. Wasserman JD, Urban S, Freeman M (2000) A family of rhomboid-like genes : Drosophila Rhomboid-1 and Roughoid/ Rhomboid-3 cooperate to activate EGF receptor signaling. Genes Dev 14(13):1651–1663PubMedPubMedCentralGoogle Scholar
  53. Zhang Z, Schäffer AA, Miller W, Madden TL, Lipman DJ, Koonin EV, Altschul SF (1998) Protein sequence similarity searches using patterns as seeds. Nucl Acids Res 26(17):3986–3990CrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  • A. Gandhimathi
    • 1
  • Nitish Sathyanarayanan
    • 1
  • Meenakshi Iyer
    • 1
  • Rachit Gupta
    • 1
    • 2
  • R. Sowdhamini
    • 1
    Email author
  1. 1.National Centre for Biological SciencesBangaloreIndia
  2. 2.Institute of Chemical TechnologyMumbaiIndia

Personalised recommendations