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Designer promoter: an artwork of cis engineering

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Abstract

Advances in systematic computational biology and rapid elucidation of synergistic interplay between cis and trans factors governing transcriptional control have facilitated functional annotation of gene networks. The generation of data through deconstructive, reconstructive and database assisted promoter studies, and its integration to principles of synthetic engineering has started an era of designer promoters. Exploration of natural promoter architecture and the concept of cis engineering have not only enabled fine tuning of single or multiple transgene expression in response to perturbations in the chemical, physiological and environmental stimuli but also provided researchers with a unique answer to various problems in crop improvement in the form of bidirectional promoters.

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References

  • Alper H, Fischer C, Nevoigt E, Stephanopoulos G (2005) Tuning genetic control through promoter engineering. Proc Natl Acad Sci USA 102:12678–12683

    Article  PubMed  CAS  Google Scholar 

  • An G, Costa MA, Ha S-B (1990) Nopaline synthase promoter 1S wound inducible and auxin inducible. Plant Cell 2:25–33

    Article  Google Scholar 

  • Benfey PN, Chua N-H (1990) The cauliflower mosaic virus 35S promoter: combinatorial regulation of transcription in plants. Science 250:959–966

    Article  PubMed  CAS  Google Scholar 

  • Bhullar S, Chakravarthy S, Advani S, Datta S, Pental D, Burma PK (2003) Strategies for development of functionally equivalent promoters with minimum sequence homology for transgene expression in plants: cis-elements in a novel DNA context versus domain swapping. Plant Physiol 132:988–998

    Article  PubMed  CAS  Google Scholar 

  • Bhullar S, Datta S, Advani S, Chakravarthy S, Gautam T, Pental D, Burma PK (2007) Functional analysis of the cauliflower mosaic virus 35S promoter: re-evaluation of the role of subdomains B5, B4, and B2 in promoter activity. Plant Biotechnol J 5:696–708

    Article  PubMed  CAS  Google Scholar 

  • Bhullar S, Datta S, Burma PK (2010) Delayed trans-inactivation of synthetic domain A 35S promoters by “Tobacco 271 Locus” due to reduced sequence homology. Plant Mol Biol Rep 29:1–11

    Google Scholar 

  • Brusslan JA, Karlin-Neumann GA, Huang L, Tobin EM (1993) An Arabidopsis mutant with a reduced level of cab140 RNA is a result of cosuppression. Plant Cell 5:667–677

    Article  PubMed  CAS  Google Scholar 

  • Cazzonelli CI, Velten EJ (2008) In vivo characterization of plant promoter element interaction using synthetic promoters. Trans Res 17:437–457

    Article  CAS  Google Scholar 

  • Chaturvedi CP, Sawant SV, Kiran K, Mehrotra R, Lodhi N, Ansari SA, Tuli R (2006) Analysis of polarity in the expression from a multifactorial bidirectional promoter designed for high-level expression of transgenes in plants. J Biotechnol 123:1–12

    Article  PubMed  CAS  Google Scholar 

  • Chung S, Parish RW (2008) Combinatorial interactions of multiple cis-elements regulating the induction of the Arabidopsis XERO2 dehydrin gene by abscisic acid and cold. Plant J 54:15–29

    Article  PubMed  CAS  Google Scholar 

  • Comai L, Moran P, Maslyar D (1990) Novel and useful properties of a chimeric plant promoter combining CaMV 35S and MAS elements. Plant Mol Biol 15:373–381

    Article  PubMed  CAS  Google Scholar 

  • Coutu C, Brandle J, Brown D, Brown K, Miki B, Simmonds J, Hegedus DD (2007) pORE: a modular binary vector series suited for both monocot and dicot plant transformation. Trans Res 16:771–781

    Article  CAS  Google Scholar 

  • Dhadi SR, Krom N, Ramakrishna W (2009) Genome-wide comparative analysis of putative bidirectional promoters from rice, Arabidopsis and Populus. Gene 429:65–73

    Article  PubMed  CAS  Google Scholar 

  • Ellis JG, Llewellyn DJ, Walker JC, Dennis ES, Peacock WJ (1987) The ocs element: a 16 base pair palindrome essential for activity of the octopine synthase enhancer. EMBO J 6:3203–3208

    PubMed  CAS  Google Scholar 

  • Ettwiller LM, Rung J, Birney E (2003) Discovering novel cis-regulatory motifs using functional networks. Genome Res 13:883–895

    Article  PubMed  CAS  Google Scholar 

  • Evrard A, Ndatimana T, Eulgem T (2009) FORCA, a promoter element that responds to crosstalk between defense and light signaling. BMC Plant Biol 9:1–13

    Article  Google Scholar 

  • Fang RX, Nagy F, Subramaniam S, Chua NH (1989) Multiple cis regulatory elements for maximal expression of the cauliflower mosaic virus 35S promoter in transgenic plants. Plant Cell 1:141–150

    Article  PubMed  CAS  Google Scholar 

  • Fauteux F, Strömvik MV (2009) Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae. BMC Plant Biol 9:126–136

    Article  PubMed  Google Scholar 

  • Frey PM, Scharer-Hernandez NG, Futterer J, Potrykus I, Puonti-Kaerlas J (2001) Simultaneous analysis of the bidirectional African cassava mosaic virus promoter activity using two different luciferase genes. Virus Genes 22:231–242

    Article  PubMed  CAS  Google Scholar 

  • Gatz C, Frohberg C, Wendenberg R (1992) Stringent repression and homogeneous depression by tetracyclin of a modified CaMV 35S promoter in intact transgenic tobacco plants. Plant J 2:397–404

    PubMed  CAS  Google Scholar 

  • Gilmartin PM, Sarokin L, Memelink J, Chua NH (1990) Molecular light switches for plant genes. Plant Cell 2:369–378

    Article  PubMed  CAS  Google Scholar 

  • Gowda S, Wu FC, Herman HB, Shepherd RJ (1989) Gene VI of figwort mosaic virus (caulimovirus group) functions in posttranscriptional expression of genes on the full-length RNA transcript. Proc Natl Acad Sci USA 86:9203–9207

    Article  PubMed  CAS  Google Scholar 

  • Gurr SJ, Rushton PJ (2005) Engineering plants with increased disease resistance: how are we going to express it? Trends Biotechnol 23:283–290

    Article  PubMed  CAS  Google Scholar 

  • Hammer K, Mijakovic I, Jensen PR (2006) Synthetic promoter libraries—tuning of gene expression. Trends Biotechnol 24:53–55

    Article  PubMed  CAS  Google Scholar 

  • Hehl R, Wingender E (2001) Database-assisted promoter analysis. Trends Plant Sci 6:251–255

    Article  PubMed  CAS  Google Scholar 

  • Heise A, Lippok B, Kirsch C, Hahlbrock K (2002) Two immediate-early pathogen-responsive members of the AtCMPG gene family in Arabidopsis thaliana and the W-box-containing elicitor-response element of AtCMPG1. Proc Natl Acad Sci USA 99:9049–9054

    Article  PubMed  CAS  Google Scholar 

  • Helden JA (2003) Regulatory sequence analysis tools. Nucl Aci Res 31:3593–3596

    Article  Google Scholar 

  • Higo K, Ugawa W, Iwamoto M, Korenaga T (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucl Aci Res 27:297–300

    Article  CAS  Google Scholar 

  • Istrail S, Davidson EH (2004) Logic functions of the genomic cis-regulatory code. Proc Natl Acad Sci USA 102:4954–4959

    Article  Google Scholar 

  • Ito M, Iwase M, Kodama H, Lavisse P, Komamine A, Nishihama R, Machida Y, Watanabea A (1998) A novel cis-acting element in promoters of plant B-type cyclin genes activates M phase–specific transcription. Plant Cell 10:331–341

    Article  PubMed  CAS  Google Scholar 

  • Jensen PR, Hammer K (1998) The sequence of spacers between the consensus sequences modulates the strength of prokaryotic promoters. Appl Environ Microbiol 64:82–87

    PubMed  CAS  Google Scholar 

  • Jiao Y, Lau ON, Deng XW (2007) Light-regulated transcriptional networks in higher plants. Nat Rev Genet 8:217–230

    Article  PubMed  CAS  Google Scholar 

  • Kamisugi Y, Cuming AC (2005) The evolution of the abscisic acid-response in land plants: comparative analysis of group 1 LEA gene expression in moss and cereals. Plant Mol Biol 59:723–737

    Article  PubMed  CAS  Google Scholar 

  • Kim Y-H, Bae JM, Huh G-H (2010) Transcriptional regulation of the cinnamyl alcohol dehydrogenase gene from sweet potato in response to plant developmental stage and environmental stress. Plant Cell Rep 29:779–791

    Article  PubMed  CAS  Google Scholar 

  • Kovalchuk N, Li M, Wittek F, Reid N, Singh R, Shirley N, Ismagul A, Eliby S, Johnson A, Milligan AS, Hrmova M, Langridge P, Lopato S (2010) Defensin promoters as potential tools for engineering disease resistance in cereal grains. Plant Biotechnol J 8:47–64

    Article  PubMed  CAS  Google Scholar 

  • Lam E, Lam YKP (1995) Binding site requirements and differential representation of TGA factors in nuclear ASF-1 activity. Nucl Acids Res 23:3778–3785

    Article  PubMed  CAS  Google Scholar 

  • Last DI, Bretteli RIS, Chamberlain DA, Chaudhary AM, Larkin PJ, Marsh EL, Peacock WJ, Dennis ES (1991) pEmu: an improved promoter for gene expression in cereal cells. Theo App Genet 81:581–588

    CAS  Google Scholar 

  • Leeuwen WV, RuttInk T, Borst-Vrenssen AWM, Plas LHWVD, Krol ARVD (2001) Characterization of position-induced spatial and temporal regulation of transgene promoter activity in plants. J Exp Bot 52:949–959

    Article  PubMed  Google Scholar 

  • Lescot M, Dehais P, Thijs G, Marchal K, Moreau Y, Peer YVD, Rouze P, Rombauts S (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucl Acids Res 30:325–327

    Article  PubMed  CAS  Google Scholar 

  • Li ZT, Jayasankar S, Gray DJ (2004) Bi-directional duplex promoters with duplicated enhancers significantly increase transgene expression in grape and tobacco. Transgenic Res 13:143–154

    Article  PubMed  CAS  Google Scholar 

  • Liu Z-B, Ulmasov T, Shi X, Hagen G, Guilfoyle TJ (1994) Soybean GH3 promoter contains multiple auxin-inducible elements. Plant Cell 6:645–657

    Article  PubMed  CAS  Google Scholar 

  • Logemann E, Hahlbrock K (2002) Crosstalk among stress responses in plants: pathogen defense overrides UV protection through an inversely regulated ACE_ACE type of light-responsive gene promoter unit. Proc Natl Acad Sci USA 99:2428–2432

    Article  PubMed  CAS  Google Scholar 

  • Maiti IB, Gowda S, Kiernan J, Ghosh SK (1997) Promoter/leader deletion analysis and plant expression vectors with the figwort mosaic virus (FMV) full length transcript (FLt) promoter containing single or double enhancer domains. Transgenic Res 6:143–156

    Article  PubMed  CAS  Google Scholar 

  • Matys V, Fricke E, Geffers R, ßling EG, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos D-U, Land S, Lewicki-Potapov B, Michael H, Munch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S, Wingender E (2003) TRANSFAC: transcriptional regulation, from patterns to profiles. Nucl Acids Res 31:374–378

    Article  PubMed  CAS  Google Scholar 

  • Mehrotra R, Mehrotra S (2010) Promoter activation by ACGT in response to salicylic and abscisic acids is differentially regulated by the spacing between two copies of the motif. J Plant Physiol 167:1214–1218

    Article  PubMed  CAS  Google Scholar 

  • Mehrotra R, Panwar J (2009) Dimerization of GT element interferes negatively with gene activation. J Genet 88:257–260

    Article  PubMed  CAS  Google Scholar 

  • Mehrotra R, Kiran K, Chaturvedi CP, Anjuman S, Lodhi N, Sawant S, Tuli R (2005) Effect of copy number and spacing of the ACGT and GT cis elements on transient expression of minimal promoter in plants. J Genet 84:183–187

    Article  PubMed  CAS  Google Scholar 

  • Meyer P, Saedler H (1996) Homology-dependent gene silencing in plants. Ann Rev Plant Physiol Plant Mol Biol 47:23–48

    Article  CAS  Google Scholar 

  • Mijakovic I, Petranovic D, Jensen PR (2005) Tunable promoters in systems biology. Curr Opin Biotechnol 16:329–335

    Article  PubMed  CAS  Google Scholar 

  • Mitra A, Han J, Zhang ZJ, Mitra A (2009) The intergenic region of Arabidopsis thaliana cab1 and cab2 divergent genes functions as a bidirectional promoter. Planta 229:1015–1022

    Article  PubMed  CAS  Google Scholar 

  • Moore I, Samalova M, Kurup S (2006) Transactivated and chemically inducible gene expression in plants. The Plant J 45:651–683

    Article  CAS  Google Scholar 

  • Ni M, Cui D, Einstein J, Narasimhulu S, Vergara CE, Gelvin SB (1995) Strength and tissue specificity of chimeric promoter derived from octopine and manopine synthase gene. Plant J 7:661–676

    Article  CAS  Google Scholar 

  • Novina CD, Roy AL (1996) Core promoters and transcriptional control. Trends Genet 12:351–355

    Article  PubMed  CAS  Google Scholar 

  • Odell JT, Nagy F, Chua N-H (1985) Identification of DNA sequences required for activity of the cauliflower mosaic virus 35S promoter. Nature 313:810–812

    Article  PubMed  CAS  Google Scholar 

  • Ordiz MI, Barbas CF-III, Beachy RN (2002) Regulation of transgene expression in plants with polydactyl zinc finger transcription factors. Proc Natl Acad Sci USA 99:13290–13295

    Article  PubMed  CAS  Google Scholar 

  • Pelham HRB (1982) A regulatory upstream promoter element in the Drosophila Hsp 70 heat-shock gene. Cell 30:517–528

    Article  PubMed  CAS  Google Scholar 

  • Pietrzak M, Burri M, Herrero J-J, Mosbach K (1989) Transcriptional activity is inducible in the cauliflower mosaic virus 35S promoter engineered with the heat shock consensus sequence. FEBS Lett 249:311–315

    Article  CAS  Google Scholar 

  • Puente P, Wei N, Deng XW (1996) Combinatorial interplay of promoter elements constitutes the minimal determinants for light and developmental control of gene expression in Arabidopsis. EMBO J 15:3732–3743

    PubMed  CAS  Google Scholar 

  • Roberts GR, Garoosi GA, Koroleva O, Ito M, Laufs P, Leader DJ, Caddick MX, Doonan JH, Tomsett AB (2005) The alc-GR system. A modified alc gene switch designed for use in plant tissue culture. Plant Physiol 138:1259–1267

    Article  PubMed  CAS  Google Scholar 

  • Römer P, Recht S, Lahaye T (2009) A single plant resistance gene promoter engineered to recognize multiple TAL effectors from disparate pathogens. Proc Natl Acad Sci USA 106:20526–20531

    Article  PubMed  Google Scholar 

  • Rushton PJ, Reinstädler A, Lipka V, Lippok B, Somssich IE (2002) Synthetic plant promoters containing defined regulatory elements provide novel insights into pathogen- and wound-induced signaling. Plant Cell 14:749–762

    Article  PubMed  CAS  Google Scholar 

  • Saha D, Kumar V, Bhat SR, Srinivasan R (2010) Characterization of upstream sequences of the LOJ gene leads to identification of a novel enhancer element conferring lateral organ junction-specific expression in Arabidopsis thaliana. Plant Mol Biol Rep 28. doi:10.1007/s11105-010-0229-6

  • Sawant SV, Singh PK, Gupta SK, Madanala R, Tuli R (1999) Conserved nucleotide sequence in highly expressed genes in plants. J Genet 78:1–8

    Article  Google Scholar 

  • Sawant SV, Singh PK, Madanala R, Tuli R (2001) Designing of an artificial expression cassette for the high-level expression of transgenes in plants. Theor Appl Genet 102:635–644

    Article  CAS  Google Scholar 

  • Sawant S, Kiran K, Mehrotra R, Chaturvedi CP, Ansari SA, Singh P, Lodhi N, Tuli R (2005) A variety of synergistic and antagonistic interactions mediated by cis-acting DNA motifs regulate gene expression in plant cells and modulate stability of the transcription complex formed on a basal promoter. J Exp Bot 56:2345–2353

    Article  PubMed  CAS  Google Scholar 

  • Schlabach MR, Hu JK, Li M, Elledge SJ (2010) Synthetic design of strong promoters. Proc Natl Acad Sci USA 107:2538–2543

    Article  PubMed  CAS  Google Scholar 

  • Sun Q, Gao F, Zhao F, Li K, Zhang J (2010) Identification of a new 130 bp cis-acting element in the TsVP1 promoter involved in the salt stress response from Thellungiella halophila. BMC Plant Biol 10:90–102

    Article  PubMed  Google Scholar 

  • Tittarelli A, Santiago M, Morales A, Meisel LA, Silva H (2009) Isolation and functional characterization of cold-regulated promoters, by digitally identifying peach fruit cold-induced genes from a large EST dataset. BMC Plant Biol 9:121–136

    Article  PubMed  Google Scholar 

  • Tiwari SB, Hagen G, Guilfoyle T (2003) The roles of auxin response factor domains in auxin-responsive transcription. Plant Cell 15:533–543

    Article  PubMed  CAS  Google Scholar 

  • Unger E, Cigan AM, Trimnell M, Xu RJ, Kendall T, Roth B, Albertsen M (2002) A chimeric ecdysone receptor facilitates methoxyfenozide-dependent restoration of male fertility in ms45 maize. Transgenic Res 11:455–465

    Article  PubMed  CAS  Google Scholar 

  • Vaucheret H, Béclin C, Fagard M (2001) Post-transcriptional gene silencing in plants. J Cell Sci 114:3083–3091

    PubMed  CAS  Google Scholar 

  • Venter M (2007) Synthetic promoters: genetic control through cis engineering. Trends Plant Sci 12:118–124

    Article  PubMed  CAS  Google Scholar 

  • Venter M, Botha FC (2010) Synthetic promoter engineering. Plant Develop Biol Biotechnol Persp 2(4):393–414

    Google Scholar 

  • Wassenegger M, Heimes S, Riedel L, Sänger HL (1994) RNA-directed de novo methylation of genomic sequences in plants. Cell 76:567–576

    Article  PubMed  CAS  Google Scholar 

  • Wray GA (1998) Promoter logic. Science 279:1871–1872

    Article  PubMed  CAS  Google Scholar 

  • Xie M, He Y, Gan S (2001) Bidirectionalization of polar promoters in plants. Nat Biotechnol 19:677–679

    Article  PubMed  CAS  Google Scholar 

  • Xu L, Ye R, Zheng Y, Wang Z, Zhou P, Lin Y, Li D (2010a) Isolation of the endosperm-specific LPAAT gene promoter from coconut (Cocos nucifera L.) and its functional analysis in transgenic rice plants. Plant Cell Rep 29:1061–1068

    Article  PubMed  CAS  Google Scholar 

  • Xu W, Yu Y, Ding J, Hua Z, Wang Y (2010b) Characterization of a novel stilbene synthase promoter involved in pathogen- and stress-inducible expression from Chinese wild Vitis pseudoreticulata. Planta 231:475–487

    Article  PubMed  CAS  Google Scholar 

  • Zavallo D, Bilbao ML, Hopp HE, Heinz R (2010) Isolation and functional characterization of two novel seed-specific promoters from sunflower (Helianthus annuus L.). Plant Cell Rep 29:239–248

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

RM is thankful to Department of science and Technolgy,Government of India for financial support under fast track scheme for young scientists.We are also thankful to the facilities provided by BITS, Pilani.

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  1. Department of Biological Sciences, BITS, Pilani, Rajasthan, 333-031, India

    Rajesh Mehrotra, Gauri Gupta, Riccha Sethi, Purva Bhalothia, Narayan Kumar & Sandhya Mehrotra

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  1. Rajesh Mehrotra
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  2. Gauri Gupta
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  3. Riccha Sethi
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  4. Purva Bhalothia
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Correspondence to Rajesh Mehrotra.

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Mehrotra, R., Gupta, G., Sethi, R. et al. Designer promoter: an artwork of cis engineering. Plant Mol Biol 75, 527–536 (2011). https://doi.org/10.1007/s11103-011-9755-3

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