Synthetic Promoter Engineering

  • M. Venter
  • F. C. Botha


Despite the rapid progress as a result of high-throughput platforms, computational assistance and emerging technologies such as virus induced gene silencing (VIGS) and RNA interference (RNAi), targeted control of transgene activity remains probably the major stumbling block in successful application of gene modification technology in plants. The widespread failure of using current conventional strategies to find and optimize the use of wild-type promoters to attain specific biotechnological applications in transgenic plants has fuelled rapid developments in the design and optimization of synthetic engineered promoters. This chapter analyses the current status of synthetic promoter design and development and highlights factors that are still limiting progress in this area. Synthetic promoters are undoubtedly powerful molecular tools and, with the flexibility of gene control that can be achieved through design strategies, there can be little doubt that this kind of promoter will contribute significantly to future biotechnology applications and elucidation of gene function in basic research.


Core Promoter Aryl Hydrocarbon Receptor Bidirectional Promoter Virus Induce Gene Silence Synthetic Promoter 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. Alper H, Fischer C, Nevoigt E, Stephanopoulos G (2005) Tuning genetic control through promoter engineering. Proc Natl Acad Sci USA 102:12678–12683PubMedCrossRefGoogle Scholar
  2. Amirsadeghi S, McDonald AE, Vanlerberghe GC (2007) A glucocorticoid-inducible gene expression system can cause growth defects in tobacco. Planta 226:453–463PubMedCrossRefGoogle Scholar
  3. An G, Costa MA, Ha SB (1990) Nopaline synthase promoter is wound inducible and auxin inducible. Plant Cell 2:225–233PubMedCrossRefGoogle Scholar
  4. Andersen SU, Cvitanich C, Hougaard BK, Roussis A, Grønlund M, Jensen DB, Frøkjaer LA, Jensen EO (2003) The glucocorticoid-inducible GVG system causes severe growth defects in both root and shoot of the model legume Lotus japonicus. Mol Plant Microbe Interact 16:1069–1076PubMedCrossRefGoogle Scholar
  5. Andrianantoandro, E. Basu S, Karig DK, Weiss R (2006) Synthetic biology: new engineering rules for an emerging discipline. Mol Systems Biol 2:2006.0028.
  6. Barfield DG, Pua EC (1991) Gene transfer in plants of Brassica juncea using Agrobacterium tumefaciens-mediated transformation. Plant Cell Rep 10:308–314CrossRefGoogle Scholar
  7. Barouki R, Coumoul X, Fernandez-Salguero PM (2007) The aryl hydrocarbon receptor, more than a xenobiotic-interacting protein. FEBS Lett 581:3608–3615PubMedCrossRefGoogle Scholar
  8. Barrera LO, Ren B (2006) The transcriptional regulatory code of eukaryotic cells – insights from genome-wide analysis of chromatin organization and transcription factor binding. Curr Opin Cell Biol 18:291–298PubMedCrossRefGoogle Scholar
  9. Barrett CL, Kim TY, Kim HU, Palsson BØ, Lee SY (2006) Systems biology as a foundation for genome-scale synthetic biology. Curr Opin Biotechnol 17:488–492PubMedCrossRefGoogle Scholar
  10. Beer MA, Tavazoie S (2004) Predicting gene expression from sequence. Cell 117:185–198PubMedCrossRefGoogle Scholar
  11. Benfey PN, Chua N-H (1990) The cauliflower mosaic virus 35S promoter: combinatorial regulation of transcription in plants. Science 250:959–966PubMedCrossRefGoogle Scholar
  12. Benfey PN, Ren L, Chua N-H (1990) Combinatorial and synergistic properties of CaMV 35S enhancer subdomains. EMBO J 9:1685–1696PubMedGoogle Scholar
  13. Bhattacharyya S, Dey N, Maiti IB (2002) Analysis of cis-sequence of subgenomic transcript promoter from the Figwort mosaic virus and comparison of promoter activity with the cauliflower mosaic virus promoters in monocot and dicot cells. Virus Res 90:47–62PubMedCrossRefGoogle Scholar
  14. Bhullar S, Chakravarthy S, Advani S, Datta S, Pental D, Kumar Burma P (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 132:988–998PubMedCrossRefGoogle Scholar
  15. Bhullar S, Datta S, Advani S, Chakravarthy S, Gautam T, Pental D, Kumar Burma P (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 5:696–708PubMedCrossRefGoogle Scholar
  16. Blais A, Dynlacht BD (2005) Constructing transcriptional regulatory networks. Genes Dev 19:1499–1511PubMedCrossRefGoogle Scholar
  17. Böhner S, Gatz C (2001) Characterization of novel target promoters for the dexamethasone-inducible/tetracycline-repressible regulator TGV using luciferase and isopentenyl transferase as sensitive reporter genes. Mol Gen Genet 264:860–870PubMedCrossRefGoogle Scholar
  18. Buchler NE, Gerland U, Hwa T (2003) On schemes of combinatorial transcription logic. Proc Natl Acad Sci USA 100:5136–5141PubMedCrossRefGoogle Scholar
  19. Butler JEF, Kadonaga JT (2002) The RNA polymerase II core promoter: a key component in the regulation of gene expression. Genes Dev 16:2583–2592PubMedCrossRefGoogle Scholar
  20. Cazzonelli CI, Velten J (2008) In vivo characterization of plant promoter element interaction using synthetic promoters. Transgenic Res 17:437–457PubMedCrossRefGoogle Scholar
  21. Cazzonelli CI, McCallum EJ, Lee R, Ramón Botella J (2005) Characterization of a strong, constitutive mung bean (Vigna radiate L.) promoter with a complex mode of regulation in planta. Transgenic Res 14:941–967PubMedCrossRefGoogle Scholar
  22. 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 123:1–12PubMedCrossRefGoogle Scholar
  23. Chaturvedi CP, Lodhi N, Ansari SA, Tiwari S, Srivastava R, Sawant SV, Tuli R (2007) Mutated TATA-box/TATA binding protein complementation system for regulated transgene expression in tobacco. Plant J 50:917–925PubMedCrossRefGoogle Scholar
  24. Christensen AH, Sharrock RA, Quail PH (1992) Maize polyubiquitin genes: structure, thermal perturbation of expression and transcript splicing, and promoter activity following transfer to protoplasts by electroporation. Plant Mol Biol 18:675–689PubMedCrossRefGoogle Scholar
  25. Comai L, Moran P, Maslyar D (1990) Novel and useful properties of a chimeric plant promoter containing CaMV 35S and MAS elements. Plant Mol Biol 15:373–381PubMedCrossRefGoogle Scholar
  26. Cox RS III, Surette MG, Elowitz MB (2007) Programming gene expression with combinatorial promoters. Mol Systems Biol 3:145Google Scholar
  27. Craft J, Samalova M, Baroux C, Townley H, Martinez A, Jepson I, Tsiantis M, Moore I (2005) New pOp/LhG4 vectors for stringent glucocorticoid-dependent transgene expression in Arabidopsis. Plant J 41:899–918PubMedCrossRefGoogle Scholar
  28. Dean C, Jones J, Favreau M, Dunsmuir P, Bedbrook J (1988) Influence of flanking sequences on variability of expression levels of an introduced gene in transgenic tobacco plants. Nucleic Acids Res 16:9267–9283PubMedCrossRefGoogle Scholar
  29. De Wilde C, Van Houdt H, De Buck S, Angenon G, De Jaeger G, Depicker A (2000) Plants as bioreactors for protein production: avoiding the problem of transgene silencing. Plant Mol Biol 43:347–359PubMedCrossRefGoogle Scholar
  30. Drubin DA, Way JC, Silver PA (2007) Designing biological systems. Genes Dev 21:242–254PubMedCrossRefGoogle Scholar
  31. Ellis JG, Llewellyn DJ, Dennis ES, Peacock WJ (1987) Maize Adh1 promoter sequences control anaerobic regulation: addition of upstream promoter elements from constitutive genes is necessary for expression in tobacco EMBO J 6:11–16PubMedGoogle Scholar
  32. Elnitski L, Jin VX, Farnham PJ, Jones SJM (2006) Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Res 16:1455–1464PubMedCrossRefGoogle Scholar
  33. Fagard M, Vaucheret H (2000) (Trans) gene silencing in plants: how many mechanisms? Annu Rev Plant Physiol Plant Mol Biol 51:167–194PubMedCrossRefGoogle Scholar
  34. Fang R-X, Nagy F, Sivasubramaniam S, Chua N-H (1989) Multiple cis-regulatory elements for maximal expression of the cauliflower mosaic virus 35S promoter in transgenic plants. Plant Cell 1:141–150PubMedCrossRefGoogle Scholar
  35. Foster E, Hattori H, Labbe H, Ouellet T, Fobert PR, James LE, Iyer VN, Miki BL (1999) A tobacco cryptic constitutive promoter, tCUP, revealed by T-DNA tagging. Plant Mol Biol 41:45–55PubMedCrossRefGoogle Scholar
  36. Franck A, Guilley H, Jonard G, Richards K, Hirth L (1980) Nucleotide-sequence of cauliflower mosaic-virus DNA. Nucleic Acids Res 21:285–294Google Scholar
  37. François IEJA, Broekaert WF, Cammue BPA (2002) Different approaches for multi-transgene-stacking in plants. Plant Sci 163:281–295CrossRefGoogle Scholar
  38. Gatz C (1997) Chemical control of gene expression. Annu Rev Plant Physiol Plant Mol Biol 48:89–108PubMedCrossRefGoogle Scholar
  39. Gatz C, Lenk I (1998) Promoters that respond to chemical inducers. Trends Plant Sci 9:352–358CrossRefGoogle Scholar
  40. Geisler M, Kleczkowski LA, Karpinski S (2006) A universal algorithm for genome-wide in silico identification of biologically significant gene promoter putative cis-regulatory-elements; identification of new elements for reactive oxygen species and sucrose signaling in Arabidopsis. Plant J 45:384–398PubMedCrossRefGoogle Scholar
  41. Gilmartin PM, Sarokin L, Memelink J, Chua N-H (1990) Molecular light switches for plant genes. Plant Cell 2:369–378PubMedCrossRefGoogle Scholar
  42. Greber D, Fussenegger M (2007) Mammalian synthetic biology: engineering of sophisticated gene networks. J Biotechnol 130:329–345PubMedCrossRefGoogle Scholar
  43. Guerva-Garcia A, López-Bucio J, Herrera-Estrella L (1999) The mannopine synthase promoter contains vectorial cis-regulatory elements that act as enhancers and silencers. Mol Gen Genet 262:608–617CrossRefGoogle Scholar
  44. Guido NJ, Wang X, Adalsteinsson D, McMillen D, Hasty J, Cantor CR, Elston TC, Collins JJ (2006) A bottom-up approach to gene regulation. Nature 439:856–860PubMedCrossRefGoogle Scholar
  45. Guilfoyle TJ (1997) The structure of plant gene promoters. In: Setlow JK (ed) Genetic engineering. Plenum Press, New York, pp 15–47Google Scholar
  46. Guilfoyle TJ, Hagen G (1999) Potential use of hormone-responsive elements to control gene expression in plants. In: Reynolds PHS (ed) Inducible gene expression in plants. CABI Publishing, Wallingford, pp 219–236Google Scholar
  47. Guilley H, Dudley RK, Jonand G, Balazs E, Richards KE (1982) Transcription of cauliflower mosaic virus DNA: detection of promoter sequences and characterization of transcripts. Cell 30:763–773PubMedCrossRefGoogle Scholar
  48. Gurr SJ, Rushton PJ (2005) Engineering plants with increased disease resistance: how are we going to express it? Trends Biotechnol 23:283–290PubMedCrossRefGoogle Scholar
  49. Halpin C (2005) Gene stacking in transgenic plants – the challenge for 21st century plant biotechnology. Plant Biotechnol J 3:141–155PubMedCrossRefGoogle Scholar
  50. Hammer K, Mijakovic I, Jensen PR (2006) Synthetic promoter libraries - tuning of gene expression. Trends Biotechnol 24:53–55PubMedCrossRefGoogle Scholar
  51. Hehl R, Wingender E (2001) Database-assisted promoter analysis. Trends Plant Sci 6:251–255PubMedCrossRefGoogle Scholar
  52. Heintzman ND, Ren B (2007) The gateway to transcription: identifying, characterizing and understanding promoters in the eukaryotic genome. Cell Mol Life Sci 64:386–400PubMedCrossRefGoogle Scholar
  53. Hochheimer A, Tjan R (2003) Diversified transcription initiation complexes expand promoter selectivity and tissue-specific gene expression. Genes Dev 17:1309–1320PubMedCrossRefGoogle Scholar
  54. Hoheisel JD (2006) Microarray technology: beyond transcript profiling and genotype analysis. Nature Rev Genet 7:200–210PubMedCrossRefGoogle Scholar
  55. Holtorf S, Apel K, Bohlmann H (1995) Comparison of different constitutive and inducible promoters for the transgenes in Arabidopsis thaliana. Plant Mol Biol 29:637–646PubMedCrossRefGoogle Scholar
  56. Hull R, Covey SN, Dale P (2002) Genetically modified plants and the 35S promoter: assessing the risk and enhancing the debate. Microb Ecol Health Dis 12:1–5Google Scholar
  57. Istrail S, Davidson EH (2005) Logic functions of the genomic cis-regulatory code. Proc Natl Acad Sci USA 102:4954–4959PubMedCrossRefGoogle Scholar
  58. Janssens H, Hou S, Jaeger J, Kim A-R, Myasnikova E, Sharp D, Reinitz J (2006) Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene. Nature Genet 38:1159–1165PubMedCrossRefGoogle Scholar
  59. Jensen PR, Hammer K (1998) Artificial promoters for metabolic optimization. Biotechnol Bioeng 58:191–195PubMedCrossRefGoogle Scholar
  60. Kang H-G, Fang Y, Singh KB (1999) A glucocorticoid-inducible transcription system causes severe growth defects in Arabidopsis and induces defense-related genes. Plant J 20:127–133PubMedCrossRefGoogle Scholar
  61. Kay R, Chan A, Daly M, McPherson J (1987) Duplication of CaMV 35S promoter sequences creates a strong enhancer for plant genes. Science 236:1299–1302PubMedCrossRefGoogle Scholar
  62. Kodama S, Okada K, Inui H, Ohkawa H (2007) Aryl hydrocarbon receptor (AhR)-mediated reporter gene expression systems in transgenic tobacco plants. Planta 227:37–45PubMedCrossRefGoogle Scholar
  63. Kolchanov NA, Merkulova TI, Ignatieva EV, Ananko EA, Oshchepkov DY, Levitsky VG, Vasiliev GV, Klimova NV, Merkulov VM, Hodgman TC (2007) Combined experimental and computational approaches to study the regulatory elements in eukaryotic genes. Brief Bioinform 8:266–274PubMedCrossRefGoogle Scholar
  64. Kooter JM, Matzke MA, Meyer P (1999) Listening to the silent genes: transgene silencing, gene regulation and pathogen control. Trends Plant Sci 4:340–345PubMedCrossRefGoogle Scholar
  65. Lam E (1994) Analysis of the tissue-specific elements in the CaMV 35S promoter. In: Nover L (ed) Results and Problems in Cell Differentiation, Plant Promoters and Transcription Factors, vol 20. Springer, Berlin Heidelberg, pp 181–196Google Scholar
  66. Lessard PA, Kulaveerasingam H, York GM, Strong A, Sinskey AJ (2002) Manipulating gene expression for the metabolic engineering of plants. Metab Eng 4:67–79PubMedCrossRefGoogle Scholar
  67. Li ZT, Jayasankar S, Gray DJ (2004) Bi-directional duplex promoters with duplicated enhancers significantly increase transgene expression in grape and tobacco. Transgenic Res 13:143–154PubMedCrossRefGoogle Scholar
  68. Liu XJ, Prat S, Willmitzer L, Frommer WB (1990) Cis regulatory elements directing tuber-specific and sucrose-inducible expression of a chimeric class I patatin promoter/GUS–gene fusion. Mol Gen Genet 223:401–406PubMedCrossRefGoogle Scholar
  69. Maiti IB, Shepard RJ (1998) Isolation and expression analysis of peanut chlorotic streak caulimovirus (PCISV) full-length transcript (FLt) promoter in transgenic plants. Biochem Biophys Res Comm 244:440–444PubMedCrossRefGoogle Scholar
  70. Martinelli R, De Simone V (2005) Short and highly efficient synthetic promoters for melanoma-specific gene expression. FEBS Lett 579:153–156PubMedCrossRefGoogle Scholar
  71. Matzke MA, Matzke AJM (1998a) Position effects and epigenetic silencing of plant transgenes. Curr Opin Plant Biol 1:142–148PubMedCrossRefGoogle Scholar
  72. Matzke MA, Matzke AJM (1998b) Epigenetic silencing of plant transgenes as a consequence of diverse cellular defence responses. Cell Mol Life Sci 54:94–103PubMedCrossRefGoogle Scholar
  73. Mayo AE, Setty Y, Shavit S, Zaslaver A, Alon U (2006) Plasticity of the cis-regulatory input function of a gene. PLoS Biol 4:e45Google Scholar
  74. Mazarei M, Teplova I, Hajimorad MR, Stewart CN (2008) Pathogen phytosensing: plants to report plant pathogens. Sensors 8(4):2628–2641CrossRefGoogle Scholar
  75. Meyer P (2000) Transcriptional transgene silencing and chromatin components. Plant Mol Biol 43:221–234PubMedCrossRefGoogle Scholar
  76. Meyer P (2001) Chromatin remodelling. Curr Opin Plant Biol 4:457–462PubMedCrossRefGoogle Scholar
  77. Meyer P, Saedler H (1996) Homology dependent gene silencing in plants. Annu Rev Plant Physiol Plant Mol Biol 47:23–48PubMedCrossRefGoogle Scholar
  78. Mijakovic I, Petranovic D, Jensen PR (2005) Tunable promoters in systems biology. Curr Opin Biotechnol 16:329–335PubMedCrossRefGoogle Scholar
  79. Miksch G, Bettenworth F, Friehs K, Flaschel E, Saalbach A, Twellmann T, Nattkemper TW (2005) Libraries of synthetic-phase and stress promoters as a tool for fine-tuning of recombinant proteins in Escherichia coli. J Biotechnol 120:25–37PubMedCrossRefGoogle Scholar
  80. Mitsuhara I, Ugaki M, Hirochika H, Ohshima M, Murakami T, Gotoh Y, Katayose Y, Nakamura S, Honkura R, Nishimiya S, Ueno K, Mochizuki A, Tanimoto H, Tsugawa H, Otsuki Y, Ohashi Y (1996) Efficient promoter cassettes for enhanced expression of foreign genes in dicotyledonous and monocotyledonous plants. Plant Cell Physiol 37:49–59PubMedGoogle Scholar
  81. Moore I, Gälweiler L, Grosskopf D, Schell J, Palme K (1998) A transcription activation system for regulated gene expression in transgenic plants. Proc Natl Acad Sci USA 95:376–381PubMedCrossRefGoogle Scholar
  82. Moore I, Samalova M, Kurup S (2006) Transactivated and chemically inducible gene expression in plants. Plant J 45:651–683PubMedCrossRefGoogle Scholar
  83. Müller AE, Wassenegger M (2004) Control and silencing of transgene expression. In: Christou P, Klee H (eds) Handbook of Plant Biotechnology, vol 1. Wiley, Hoboken, NJ, pp 291–330Google Scholar
  84. Müller F, Demény MA, Tora L (2007) New problems in RNA polymerase II transcription initiation: matching the diversity of core promoters with a variety of promoter recognition factors. J Biol Chem 282:14685–14689PubMedCrossRefGoogle Scholar
  85. Murphy KF, Balazsi G, Collins JJ (2007) Combinatorial promoter design for engineering noisy gene expression. Proc Natl Acad Sci USA 104:12726–12731PubMedCrossRefGoogle Scholar
  86. Nguyen DH, D’haeseleer P (2006) Deciphering principles of transcription regulation in eukaryotic genomes. Mol Systems Biol 2:2006.0012Google Scholar
  87. Ni M, Cui D, Einstein J, Narasimhulu S, Vergara CE, Gelvin SB (1995) Strength and tissue specificity of chimeric promoters derived from octopine and manopine synthase genes. Plant J 7:661–676CrossRefGoogle Scholar
  88. Ni M, Cui D, Gelvin SB (1996) Sequence-specific interactions of wound-inducible nuclear factors with mannopine synthase 2′ promoter wound-responsive elements. Plant Mol Biol 30:77–96PubMedCrossRefGoogle Scholar
  89. Novina CD, Roy AL (1996) Core promoters and transcriptional control. Trends Genet 12:351–355PubMedCrossRefGoogle Scholar
  90. Odell JT, Nagy F, Chua N-H (1985) Identification of DNA sequences required for activity of the cauliflower mosaic virus 35S promoter. Nature 313:810–812PubMedCrossRefGoogle Scholar
  91. Ohl S, Hedrick SA, Chory J, Lamb CJ (1990) Functional properties of a phenylalanine ammonia-lyase promoter from Arabidopsis. Plant Cell 2:95–106CrossRefGoogle Scholar
  92. Orphanides G, Reinberg D (2002) A unified theory of gene expression. Cell 108:439–451PubMedCrossRefGoogle Scholar
  93. Padidam M (2003) Chemically regulated gene expression in plants. Curr Opin Plant Biol 6:169–177PubMedCrossRefGoogle Scholar
  94. 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 249:311–315CrossRefGoogle Scholar
  95. Pilpel Y, Sudarsanam P, Church GM (2001) Identifying regulatory networks by combinatorial analysis of promoter elements. Nature Genet 29:153–159PubMedCrossRefGoogle Scholar
  96. 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 15:3732–3743PubMedGoogle Scholar
  97. Reynolds PHS (1999) Inducible control of gene expression: an overview. In: Reynolds PHS (ed) Inducible gene expression in plants. CABI Publishing, Wallingford, pp 1–9Google Scholar
  98. Rhee SY, Dickerson J, Xu D (2006) Bioinformatics and its applications in plant biology. Annu Rev Plant Biol 57:335–360PubMedCrossRefGoogle Scholar
  99. Richards EJ, Elgin SCR (2002) Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects. Cell 108:489–500PubMedCrossRefGoogle Scholar
  100. Rud I, Jensen PR, Naterstad K, Axelsson L (2006) A synthetic promoter library for constitutive gene expression in Lactobacillus plantarum. Microbiology 152:1011–1019PubMedCrossRefGoogle Scholar
  101. Rushton PJ, Reinstadler 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 14:749–762PubMedCrossRefGoogle Scholar
  102. Samalova M, Brzobohaty B, Moore I (2005) pOp6/LhGR: a stringently regulated and highly responsive dexamethasone-inducible gene expression system for tobacco. Plant J 41:919–935PubMedCrossRefGoogle Scholar
  103. Sawant S, Singh PK, Gupta SK, Madanala R, Tuli R (1999) Conserved nucleotide sequences in highly expressed genes in plants. J Genet 78:123–131CrossRefGoogle Scholar
  104. Sawant S, 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 102:635–644CrossRefGoogle Scholar
  105. Sawant SV, 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 56:2345–2353PubMedCrossRefGoogle Scholar
  106. Schenk PM, Remans T, Sági L, Elliott AR, Dietzgen RG, Swennen R, Ebert PR, Grof CPL, Manners JM (2001) Promoters for pregenomic RNA of banana streak badnavirus are active for transgene expression in monocot and dicot plants. Plant Mol Biol 47:399–412PubMedCrossRefGoogle Scholar
  107. Schmid J, Doerner PW, Clouse SD, Dixon RA, Lanb CJ (1990) Developmental and environmental regulation of a bean chalcone synthase promoter in transgenic tobacco. Plant Cell 2:619–631PubMedCrossRefGoogle Scholar
  108. Schünmann PHD, Llewellyn DJ, Surin B, Boevink P, De Feyter RC, Waterhouse PM (2003) A suite of novel promoters and terminators for plant biotechnology. Funct Plant Biol 30:443–452CrossRefGoogle Scholar
  109. Schwechheimer C, Bevan M (1998) The regulation of transcription factor activity in plants. Trends Plant Sci 10:378–383CrossRefGoogle Scholar
  110. Singh KB (1998) Transcriptional regulation in plants: the importance of combinatorial control. Plant Physiol 118:1111–1120PubMedCrossRefGoogle Scholar
  111. Smale ST (2001) Core promoters: active contributors to combinatorial gene regulation. Genes Dev 15:2503–2508PubMedCrossRefGoogle Scholar
  112. Smale ST, Kadonaga JT (2003) The RNA polymerase II core promoter. Annu Rev Biochem 72:449–479PubMedCrossRefGoogle Scholar
  113. Sørensen SJ, Burmølle M, Hansen LH (2006) Making bio-sense of toxicity: new developments in whole-cell biosensors. Curr Opin Biotechnol 17:11–16PubMedCrossRefGoogle Scholar
  114. Tang W, Luo X, Sameuls V (2004) Regulated gene expression with promoters responding to inducers. Plant Sci 166:827–834CrossRefGoogle Scholar
  115. Tavva VS, Dinkins RD, Palli SR, Collins GB (2006) Development of a methoxyfenozide-responsive gene switch for applications in plants. Plant J 45:457–469PubMedCrossRefGoogle Scholar
  116. Taylor LE II, Dai Z, Decker SR, Brunecky R, Adney WS, Ding S-Y, Himmel ME (2008) Heterologous expression of glycosyl hydrolases in planta: a new departure for biofuels. Trends Biotechnol 26:413–424PubMedCrossRefGoogle Scholar
  117. Tokusumi Y, Ma Y, Song X, Jacobson RH, Takada S (2007) The new core promoter element XCPE1 (X Core Promoter Element 1) directs activator-, mediator-, and TATA-binding protein-dependant but TFIID-independent RNA polymerase II transcription from TATA-less promoters. Mol Cell Biol 27:1844–1858PubMedCrossRefGoogle Scholar
  118. Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Régnier M, Simonis N, Sinha S, Thijs G, Van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnol 23:137–144CrossRefGoogle Scholar
  119. Tornøe J, Kusk P, Johansen TE, Jensen PR (2002) Generation of a synthetic mammalian promoter library by modification of sequences spacing transcription factor binding sites. Gene 297:21–32PubMedCrossRefGoogle Scholar
  120. Tyo KE, Alper HS, Stephanopoulos GN (2007) Expanding the metabolic engineering toolbox: more options to engineer cells. Trends Biotechnol 25:132–137PubMedCrossRefGoogle Scholar
  121. Van Leeuwen W, Ruttink T, Borst-Vrenssen AWM, Van der Plas LHW, Van der Krol AR (2001) Characterization of position-induced spatial and temporal regulation of transgene promoter activity in plants. J Exp Bot 52:949–959PubMedCrossRefGoogle Scholar
  122. Venter M (2007) Synthetic promoters: genetic control through cis engineering. Trends Plant Sci 12:118–124PubMedCrossRefGoogle Scholar
  123. Vision TJ, McLysaght A (2004) Computational tools and resources in plant genome informatics. In: Christou P, Klee H (eds) Handbook of Plant Biotechnology, vol 1. Wiley, Hoboken, NJ, pp 201–228Google Scholar
  124. Wang R, Zhou X, Wang X (2003) Chemically regulated expression systems and their applications in transgenic plants. Transgenic Res 12:529–540PubMedCrossRefGoogle Scholar
  125. Wasserman WW, Sandelin A (2004) Applied bioinformatics for the identification of regulatory elements. Nature Rev Genet 5:276–287PubMedCrossRefGoogle Scholar
  126. Weber W, Fussenegger M (2006) Pharmacologic transgene control systems for gene therapy. J Gene Med 8:535–556PubMedCrossRefGoogle Scholar
  127. Werner T, Fessele S, Maier H, Nelson PJ (2003) Computer modelling of promoter organisation as a tool to study transcriptional coregulation. FASEB J 17:1228–1237PubMedCrossRefGoogle Scholar
  128. Xiao K, Zhang C, Harrison M, Wang Z-Y (2005) Isolation and characterization of a novel plant promoter that directs strong constitutive expression of transgenes in plants. Mol Breed 15:221–231CrossRefGoogle Scholar
  129. Xie M, He Y, Gan S (2001) Bidirectionalization of polar promoters in plants. Nature Biotechnol 19:677–679CrossRefGoogle Scholar
  130. Yew NS (2005) Controlling the kinetics of transgene expression by plasmid design. Adv Drug Deliver Rev 57:769–780CrossRefGoogle Scholar
  131. Yoshida K, Shinmyo A (2000) Transgene expression systems in plant, a natural bioreactor. J Biosci Bioeng 90:353–362PubMedGoogle Scholar
  132. Zhou Q, Wong WH (2004) CisModule: de novo discovery of cis-regulatory modules by hierarchical mixture modelling. Proc Natl Acad Sci USA 101:12114–12119PubMedCrossRefGoogle Scholar
  133. Zhu Q, Song B, Zhang C, Ou Y, Xie C, Liu J (2008) Construction and functional characteristics of tuber-specific and cold-inducible chimeric promoters in potato. Plant Cell Rep 27:47–55PubMedCrossRefGoogle Scholar
  134. Zuo J, Chua N-H (2000) Chemical-inducible systems for regulated expression of plant genes. Curr Opin Biotechnol 11:146–151PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  1. 1.Department of GeneticsStellenbosch UniversityMatielandSouth Africa
  2. 2.BSESIndooroopillyAustralia
  3. 3.Institute for Plant BiotechnologyStellenbosch UniversityMatielandSouth Africa

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