Recent advances in the applications of promoter engineering for the optimization of metabolite biosynthesis

  • Ning Xu
  • Liang Wei
  • Jun LiuEmail author


Cell metabolism in living organisms is largely regulated at the transcriptional level, and the promoters are regarded as basic regulatory elements responsible for transcription initiation. Promoter engineering is an important technique to regulate gene expression and optimize metabolite biosynthesis in metabolic engineering and synthetic biology. The rational and precise control of gene expression in the multi-gene pathways can significantly affect the metabolic flux distribution and maximize the production of specific metabolites. Thus, many efforts have been made to identify natural promoters, construct inducible or hybrid promoters, and design artificial promoters for fine-tuning specific gene expression at the transcriptional level and improving production levels of the metabolites of interest. In this review, we will briefly introduce the architecture and function of both prokaryotic and eukaryotic promoters, and provide an overview of several major approaches for promoter engineering. The recent achievements and advances by promoter engineering for the optimization of metabolite biosynthetic pathways in multiple widely-used model microorganism, including Escherichia coli, Corynebacterium glutamicum and Saccharomyces cerevisiae, will also be extensively discussed.


Promoter Gene expression Pathway optimization 



This study was supported by the National Natural Science Foundation of China (No. 31500044 and No. 31801526), the Natural Science Foundation of Tianjin (No. 17JCQNJC09600, No. 17JCYBJC24000), the Tianjin Science and Technology Project (15PTCYSY00020), the Key Projects in the Tianjin Science and Technology Pillar Program (14ZCZDSY00058) and “Hundred Talents Program” of Chinese Academy of Sciences for Prof. Jun Liu.


  1. Alper H, Fischer C, Nevoigt E, Stephanopoulos G (2005) Tuning genetic control through promoter engineering. Proc Natl Acad Sci USA 102:12678–12683. CrossRefPubMedGoogle Scholar
  2. Asakura Y, Kimura E, Usuda Y, Kawahara Y, Matsui K, Osumi T, Nakamatsu T (2007) Altered metabolic flux due to deletion of odhA causes L-glutamate overproduction in Corynebacterium glutamicum. Appl Environ Microbiol 73:1308–1319. CrossRefPubMedGoogle Scholar
  3. Becker J, Zelder O, Hafner S, Schroder H, Wittmann C (2011) From zero to hero–design-based systems metabolic engineering of Corynebacterium glutamicum for L-lysine production. Metab Eng 13:159–168. CrossRefPubMedGoogle Scholar
  4. Biggs BW, De Paepe B, Santos CNS, De Mey M, Ajikumar PK (2014) Multivariate modular metabolic engineering for pathway and strain optimization. Curr Opin Biotech 29:156–162. CrossRefPubMedGoogle Scholar
  5. Blazeck J, Alper HS (2013) Promoter engineering: Recent advances in controlling transcription at the most fundamental level. Biotech J 8:46–58. CrossRefGoogle Scholar
  6. Blazeck J, Liu L, Redden H, Alper H (2011) Tuning gene expression in Yarrowia lipolytica by a hybrid promoter approach. Appl Environ Microbiol 77:7905–7914. CrossRefPubMedPubMedCentralGoogle Scholar
  7. Blazeck J, Garg R, Reed B, Alper HS (2012) Controlling promoter strength and regulation in Saccharomyces cerevisiae using synthetic hybrid promoters. Biotechnol Bioeng 109:2884–2895. CrossRefPubMedGoogle Scholar
  8. Burr T, Mitchell J, Kolb A, Minchin S, Busby S (2000) DNA sequence elements located immediately upstream of the – 10 hexamer in Escherichia coli promoters: a systematic study. Nucleic Acids Res 28:1864–1870CrossRefGoogle Scholar
  9. Butler JE, Kadonaga JT (2002) The RNA polymerase II core promoter: a key component in the regulation of gene expression. Gene Dev 16:2583–2592. CrossRefPubMedGoogle Scholar
  10. Chae TU, Choi SY, Kim JW, Ko YS, Lee SY (2017) Recent advances in systems metabolic engineering tools and strategies. Curr Opin Biotechnol 47:67–82. CrossRefPubMedGoogle Scholar
  11. Chen X et al (2018) DCEO biotechnology: tools to design, construct, evaluate, and optimize the metabolic pathway for biosynthesis of chemicals. Chem Rev 118:4–72. CrossRefGoogle Scholar
  12. Cox RS, Surette III, Elowitz MG MB (2007) Programming gene expression with combinatorial promoters. Mol Syst Biol 3:145. CrossRefPubMedPubMedCentralGoogle Scholar
  13. Dahl RH et al (2013) Engineering dynamic pathway regulation using stress-response promoters. Nat biotechnol 31:1039–1046. CrossRefPubMedGoogle Scholar
  14. de Boer HA, Comstock LJ, Vasser M (1983) The tac promoter: a functional hybrid derived from the trp and lac promoters. Proc Natl Acad Sci USA 80:21–25. CrossRefPubMedGoogle Scholar
  15. De Mey M, Maertens J, Lequeux GJ, Soetaert WK, Vandamme EJ (2007) Construction and model-based analysis of a promoter library for E. coli: an indispensable tool for metabolic engineering. BMC Biotechnol 7:34. CrossRefPubMedPubMedCentralGoogle Scholar
  16. De Mey M, Maertens J, Boogmans S, Soetaert WK, Vandamme EJ, Cunin R, Foulquie-Moreno MR (2010) Promoter knock-in: a novel rational method for the fine tuning of genes. BMC Biotechnol 10:26. CrossRefPubMedPubMedCentralGoogle Scholar
  17. Deaner M, Alper HS (2018) Promoter and terminator discovery and engineering synthetic biology. Metab Eng 162:21–44. CrossRefGoogle Scholar
  18. Dolfini D, Zambelli F, Pavesi G, Mantovani R (2009) A perspective of promoter architecture from the CCAAT box. Cell Cycle 8:4127–4137. CrossRefPubMedGoogle Scholar
  19. Dostalova H et al (2017) Assignment of sigma factors of RNA polymerase to promoters in Corynebacterium glutamicum. AMB Express 7:133. CrossRefPubMedPubMedCentralGoogle Scholar
  20. Du J, Shao Z, Zhao H (2011) Engineering microbial factories for synthesis of value-added products. J Ind Microbiol 38:873–890. CrossRefGoogle Scholar
  21. Du J, Yuan Y, Si T, Lian J, Zhao H (2012) Customized optimization of metabolic pathways by combinatorial transcriptional engineering. Nucleic Acids Res 40:e142. CrossRefPubMedPubMedCentralGoogle Scholar
  22. Engstrom MD, Pfleger BF (2017) Transcription control engineering and applications in synthetic biology. Synth Syst Biotechnol 2:176–191. CrossRefPubMedPubMedCentralGoogle Scholar
  23. Estrem ST, Ross W, Gaal T, Chen ZW, Niu W, Ebright RH, Gourse RL (1999) Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase alpha subunit. Gene Dev 13:2134–2147CrossRefGoogle Scholar
  24. Ferreira R, Teixeira PG, Gossing M, David F, Siewers V, Nielsen J (2018) Metabolic engineering of Saccharomyces cerevisiae for overproduction of triacylglycerols. Metab Eng Commun 6:22–27. CrossRefPubMedPubMedCentralGoogle Scholar
  25. Guarente L, Lalonde B, Gifford P, Alani E (1984) Distinctly regulated tandem upstream activation sites mediate catabolite repression of the CYC1 gene of S. cerevisiae. Cell 36:503–511CrossRefGoogle Scholar
  26. Hartner FS, Ruth C, Langenegger D, Johnson SN, Hyka P, Lin-Cereghino GP, Lin-Cereghino J, Kovar K, Cregg JM, Glieder A (2008) Promoter library designed for fine-tuned gene expression in Pichia pastoris. Nucleic Acids Res 36:e76. CrossRefPubMedPubMedCentralGoogle Scholar
  27. Hernandez-Garcia CM, Finer JJ (2014) Identification and validation of promoters and cis-acting regulatory elements. Plant Sci 217–218:109–119. CrossRefPubMedGoogle Scholar
  28. Hwang HJ, Lee SY, Lee PC (2018) Engineering and application of synthetic nar promoter for fine-tuning the expression of metabolic pathway genes in Escherichia coli. Biotechnol Biofuels 11:103. CrossRefPubMedPubMedCentralGoogle Scholar
  29. Jayaram N, Usvyat D, AC RM (2016) Evaluating tools for transcription factor binding site prediction. BMC Bioinformatics 17:1298. CrossRefGoogle Scholar
  30. Jensen PR, Hammer K (1998) The sequence of spacers between the consensus sequences modulates the strength of prokaryotic promoters. Appl Environ Microbiol 64:82–87PubMedPubMedCentralGoogle Scholar
  31. Jeppsson M, Johansson B, Jensen PR, Hahn-Hagerdal B, Gorwa-Grauslund MF (2003) The level of glucose-6-phosphate dehydrogenase activity strongly influences xylose fermentation and inhibitor sensitivity in recombinant Saccharomyces cerevisiae strains. Yeast 20:1263–1272. CrossRefPubMedGoogle Scholar
  32. Jeschek M, Gerngross D, Panke S (2016) Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort. Nat Commun 7:11163. CrossRefPubMedPubMedCentralGoogle Scholar
  33. Kanhere A, Bansal M (2005) Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes. Nucleic Acids Res 33:3165–3175. CrossRefPubMedPubMedCentralGoogle Scholar
  34. Keasling JD (2012) Synthetic biology and the development of tools for metabolic engineering. Metab Eng 14:189–195. CrossRefPubMedGoogle Scholar
  35. Kiryu H, Oshima T, Asai K (2005) Extracting relations between promoter sequences and their strengths from microarray data. Bioinformatics 21:1062–1068. CrossRefPubMedGoogle Scholar
  36. Kosuri S et al (2013) Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Proc Natl Acad Sci USA 110:14024–14029. CrossRefPubMedGoogle Scholar
  37. Lee JW, Kim TY, Jang YS, Choi S, Lee SY (2011) Systems metabolic engineering for chemicals and materials. Trends Biotechnol 29:370–378. CrossRefPubMedGoogle Scholar
  38. Lee JW, Na D, Park JM, Lee J, Choi S, Lee SY (2012) Systems metabolic engineering of microorganisms for natural and non-natural chemicals. Nat Chem Biol 8:536–546. CrossRefPubMedGoogle Scholar
  39. Lee JY, Na YA, Kim E, Lee HS, Kim P (2016) The Actinobacterium Corynebacterium glutamicum, an Industrial Workhorse. J Microbiol Biotechnol 26:807–822. CrossRefPubMedGoogle Scholar
  40. Lubliner S, Keren L, Segal E (2013) Sequence features of yeast and human core promoters that are predictive of maximal promoter activity. Nucleic Acids Res 41:5569–5581. CrossRefPubMedPubMedCentralGoogle Scholar
  41. McCullum EO, Williams BA, Zhang J, Chaput JC (2010) Random mutagenesis by error-prone PCR. Methods Mol Biol 634:103–109. CrossRefPubMedGoogle Scholar
  42. Mitchell JE, Zheng D, Busby SJ, Minchin SD (2003) Identification and analysis of ‘extended—10’ promoters in Escherichia coli. Nucleic Acids Res 31:4689–4695CrossRefGoogle Scholar
  43. Murphy KF, Balazsi G, Collins JJ (2007) Combinatorial promoter design for engineering noisy gene expression. Proc Natl Acad Sci USA 104:12726–12731. CrossRefPubMedGoogle Scholar
  44. Nevoigt E, Kohnke J, Fischer CR, Alper H, Stahl U, Stephanopoulos G (2006) Engineering of promoter replacement cassettes for fine-tuning of gene expression in Saccharomyces cerevisiae. Appl Environ Microbiol 72:5266–5273. CrossRefPubMedPubMedCentralGoogle Scholar
  45. Nevoigt E, Fischer C, Mucha O, Matthaus F, Stahl U, Stephanopoulos G (2007) Engineering promoter regulation. Biotechnol Bioeng 96:550–558. CrossRefPubMedGoogle Scholar
  46. Paget MS, Helmann JD (2003) The sigma70 family of sigma factors. Genome Biol 4:203CrossRefGoogle Scholar
  47. Partow S, Siewers V, Bjorn S, Nielsen J, Maury J (2010) Characterization of different promoters for designing a new expression vector in Saccharomyces cerevisiae. Yeast 27:955–964. CrossRefPubMedGoogle Scholar
  48. Patek M, Nesvera J (2011) Sigma factors and promoters in Corynebacterium glutamicum. J Biotechnol 154:101–113. CrossRefPubMedGoogle Scholar
  49. Patek M, Holatko J, Busche T, Kalinowski J, Nesvera J (2013) Corynebacterium glutamicum promoters: a practical approach. Microb Biotechnol 6:103–117. CrossRefPubMedPubMedCentralGoogle Scholar
  50. Portela RMC, Vogl T, Kniely C, Fischer JE, Oliveira R, Glieder A (2017) Synthetic core promoters as universal parts for fine-tuning expression in different yeast species. ACS Synth Biol 6:471–484. CrossRefGoogle Scholar
  51. Pothoulakis G, Ellis T (2018) Construction of hybrid regulated mother-specific yeast promoters for inducible differential gene expression. PloS ONE 13:e0194588. CrossRefPubMedPubMedCentralGoogle Scholar
  52. Raman K, Chandra N (2009) Flux balance analysis of biological systems: applications and challenges. Brief Bioinform 10:435–449. CrossRefPubMedGoogle Scholar
  53. Rangel-Chavez C, Galan-Vasquez E, Martinez-Antonio A (2017) Consensus architecture of promoters and transcription units in Escherichia coli: design principles for synthetic biology. Mol Biosyst 13:665–676. CrossRefPubMedGoogle Scholar
  54. Redden H, Alper HS (2015) The development and characterization of synthetic minimal yeast promoters. Nat Commun 6:7810. CrossRefPubMedPubMedCentralGoogle Scholar
  55. Redden H, Morse N, Alper HS (2015) The synthetic biology toolbox for tuning gene expression in yeast. FEMS Yeast Res 15.
  56. Ross W, Aiyar SE, Salomon J, Gourse RL (1998) Escherichia coli promoters with UP elements of different strengths: modular structure of bacterial promoters. J Bacteriol 180:5375–5383PubMedPubMedCentralGoogle Scholar
  57. Rud I, Jensen PR, Naterstad K, Axelsson L (2006) A synthetic promoter library for constitutive gene expression in Lactobacillus plantarum. Microbiology 152:1011–1019. CrossRefPubMedGoogle Scholar
  58. Seizl M, Hartmann H, Hoeg F, Kurth F, Martin DE, Soding J, Cramer P (2011) A conserved GA element in TATA-less RNA polymerase II promoters. PloS ONE 6:e27595. CrossRefPubMedPubMedCentralGoogle Scholar
  59. Shen HJ, Hu JJ, Li XR, Liu JZ (2015) Engineering of Escherichia coli for lycopene production through promoter engineering. Curr Pharm Biotechnol 16:1094–1103. CrossRefPubMedGoogle Scholar
  60. Siegl T, Tokovenko B, Myronovskyi M, Luzhetskyy A (2013) Design, construction and characterisation of a synthetic promoter library for fine-tuned gene expression in actinomycetes. Metab Eng 19:98–106. CrossRefPubMedGoogle Scholar
  61. Solovyev VV, Shahmuradov IA, Salamov AA (2010) Identification of promoter regions and regulatory sites. Methods Mol Biol 674:57–83. CrossRefPubMedGoogle Scholar
  62. Tirosh I, Berman J, Barkai N (2007) The pattern and evolution of yeast promoter bendability. Trends Genet 23:318–321. CrossRefPubMedGoogle Scholar
  63. Todeschini AL, Georges A, Veitia RA (2014) Transcription factors: specific DNA binding and specific gene regulation. Trends Genet 30:211–219. CrossRefPubMedGoogle Scholar
  64. Troein C, Ahren D, Krogh M, Peterson C (2007) Is transcriptional regulation of metabolic pathways an optimal strategy for fitness? PloS one 2:e855. CrossRefPubMedPubMedCentralGoogle Scholar
  65. Tyo KE, Nevoigt E, Stephanopoulos G (2011) Directed evolution of promoters and tandem gene arrays for customizing RNA synthesis rates and regulation. Methods Enzymol 497:135–155. CrossRefPubMedGoogle Scholar
  66. Vasicova P, Patek M, Nesvera J, Sahm H, Eikmanns B (1999) Analysis of the Corynebacterium glutamicum dapA promoter. J Bacteriol 181:6188–6191PubMedPubMedCentralGoogle Scholar
  67. Wang W, Li X, Wang J, Xiang S, Feng X, Yang K (2013) An engineered strong promoter for Streptomycetes. Appl Environ Microbiol 79:4484–4492. CrossRefPubMedPubMedCentralGoogle Scholar
  68. Wei L, Xu N, Wang Y, Zhou W, Han G, Ma Y, Liu J (2018) Promoter library-based module combination (PLMC) technology for optimization of threonine biosynthesis in Corynebacterium glutamicum. Appl Microbiol Biotechnol 102:4117–4130. CrossRefPubMedGoogle Scholar
  69. Wu J, Liu P, Fan Y, Bao H, Du G, Zhou J, Chen J (2013) Multivariate modular metabolic engineering of Escherichia coli to produce resveratrol from L-tyrosine. J Biotechnol 167:404–411. CrossRefPubMedGoogle Scholar
  70. Xu P, Wang W, Li L, Bhan N, Zhang F, Koffas MA (2014) Design and kinetic analysis of a hybrid promoter-regulator system for malonyl-CoA sensing in Escherichia coli. ACS Chem Biol 9:451–458. CrossRefPubMedGoogle Scholar
  71. Yadav VG, De Mey M, Lim CG, Ajikumar PK, Stephanopoulos G (2012) The future of metabolic engineering and synthetic biology: towards a systematic practice. Metab Eng 14:233–241. CrossRefPubMedPubMedCentralGoogle Scholar
  72. Yang L, Wang J, Lv Y, Hao D, Zuo Y, Li X, Jiang W (2014) Characterization of TATA-containing genes and TATA-less genes in S. cerevisiae by network topologies and biological properties. Genomics 104:562–571. CrossRefPubMedGoogle Scholar
  73. Yang S, Liu Q, Zhang Y, Du G, Chen J, Kang Z (2018) Construction and characterization of broad-spectrum promoters for synthetic biology. ACS Synth Biol 7:287–291. CrossRefPubMedGoogle Scholar
  74. Yim SS, An SJ, Kang M, Lee J, Jeong KJ (2013) Isolation of fully synthetic promoters for high-level gene expression in Corynebacterium glutamicum. Biotechnol Bioeng 110:2959–2969. CrossRefPubMedGoogle Scholar
  75. Yuan LZ, Rouviere PE, Larossa RA, Suh W (2006) Chromosomal promoter replacement of the isoprenoid pathway for enhancing carotenoid production in E. coli. Metab Eng 8:79–90. CrossRefPubMedGoogle Scholar
  76. Zhang GL, Cao Q, Liu JZ, Liu BY, Li J, Li C (2015) Refactoring -amyrin synthesis in Saccharomyces cerevisiae. Aiche J 61:3172–3179. CrossRefGoogle Scholar

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© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjinPeople’s Republic of China
  2. 2.Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjinPeople’s Republic of China
  3. 3.University of Chinese Academy of SciencesBeijingPeople’s Republic of China

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