The application of powerful promoters to enhance gene expression in industrial microorganisms

World Journal of Microbiology and Biotechnology

Volumn 33, Issue 2, 2017, Pages

  Zhou, Shenghu ^a   Du, Guocheng ^a,b   Kang, Zhen ^a,b   Li, Jianghua ^a   Chen, Jian ^a,b   Li, Huazhong ^a   Zhou, Jingwen ^a  

^a JIANGNAN UNIVERSITY   (China)

^b Synergetic Innovative Center of Food Safety and Nutrition   (China)

Author keywords

Combinatorial promoter; Dynamic regulation; Logic gate; Metabolic engineering; Promoter prediction; Static regulation; Synthetic biology

Indexed keywords

BIOLOGY; COMPUTER CIRCUITS; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENES; INDUSTRIAL CHEMICALS; LOGIC GATES; METABOLIC ENGINEERING; METABOLISM; TRANSCRIPTION;

COMBINATORIAL PROMOTER; DYNAMIC REGULATION; PROMOTER PREDICTION; STATIC REGULATION; SYNTHETIC BIOLOGY;

MICROORGANISMS;

ARCHAEON; BACTERIUM; EUKARYOTE; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENETICS; METABOLIC ENGINEERING; MICROBIOLOGY; PROCEDURES; PROMOTER REGION; SYNTHETIC BIOLOGY;

ARCHAEA; BACTERIA; EUKARYOTA; GENE EXPRESSION; GENE EXPRESSION REGULATION; INDUSTRIAL MICROBIOLOGY; METABOLIC ENGINEERING; PROMOTER REGIONS, GENETIC; SYNTHETIC BIOLOGY;

EID: 85007565910     PISSN: 09593993     EISSN: 15730972     Source Type: Journal    
DOI: 10.1007/s11274-016-2184-3     Document Type: Review

References (99)

1. Adams BL, Carter KK, Guo M et al (2014) Evolved quorum sensing regulator, LsrR, for altered switching functions. ACS Synth Biol 3:210–219
2. Ajikumar PK, Xiao WH, Tyo KEJ et al (2010) Isoprenoid pathway optimization for taxol precursor overproduction in Escherichia coli. Science 330:70–74
3. Alper H, Fischer C, Nevoigt E et al (2005) Tuning genetic control through promoter engineering. P Natl Acad Sci USA 102:12678–12683
4. Amit R (2012) Towards synthetic gene circuits with enhancers: biology’s multi-input integrators. In: Subcell biochem. Springer, pp 3–20
5. Anderson JC, Voigt CA, Arkin AP (2007) Environmental signal integration by a modular AND gate. Mol Syst Biol 3:133
6. Anesiadis N, Cluett WR, Mahadevan R (2008) Dynamic metabolic engineering for increasing bioprocess productivity. Metab Eng 10:255–266
7. Atsumi S, Hanai T, Liao JC (2008) Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 451:86–89
8. Baez A, Majdalani N, Shiloach J (2014) Production of recombinant protein by a novel oxygen-induced system in Escherichia coli. Microb Cell Fact 13:50
9. Binder D, Gruenberger A, Loeschcke A et al (2014) Light-responsive control of bacterial gene expression: precise triggering of the lac promoter activity using photocaged IPTG. Integr Bio-UK 6:755–765
10. Blazeck J, Alper HS (2013) Promoter engineering: Recent advances in controlling transcription at the most fundamental level. Biotech J 8:46–58
11. Blazeck J, Liu L, Redden H et al (2011) Tuning gene expression in Yarrowia lipolytica by a hybrid promoter approach. Appl Environ Microb 77:7905–7914
12. Blazeck J, Garg R, Reed B et al (2012) Controlling promoter strength and regulation in Saccharomyces cerevisiae using synthetic hybrid promoters. Biotechnol Bioeng 109:2884–2895
13. Brockman IM, Prather KLJ (2015) Dynamic metabolic engineering: new strategies for developing responsive cell factories. Biotech J 10:1360–1369
14. Cox RS, Surette MG, Elowitz MB (2007) Programming gene expression with combinatorial promoters. Mol Syst Biol 3:145
15. De Mey M, Maertens J, Lequeux GJ et al (2007) Construction and model-based analysis of a promoter library for E. coli: an indispensable tool for metabolic engineering. Bmc Biotechnol 7:34
16. Dehli T, Solem C, Jensen PR (2012) Tunable promoters in synthetic and systems biology. In: Subcell biochem. Springer, pp 181–201
17. Dreos R, Ambrosini G, Perier RC et al (2015) The eukaryotic promoter database: expansion of EPDnew and new promoter analysis tools. Nucleic Acids Res 43:D92–D96
18. Dueber JE, Wu GC, Malmirchegini GR et al (2009) Synthetic protein scaffolds provide modular control over metabolic flux. Nat Biotechnol 27:753–759
19. Fassler JS, Gussin GN (1996) Promoters and basal transcription machinery in eubacteria and eukaryotes: concepts, definitions, and analogies. Methods Enzymol 273:3–29
20. Foster PL (2000) Adaptive mutation: implications for evolution. Bioessays 22:1067–1074
21. Fowler ZL, Gikandi WW, Koffas MAG (2009) Increased malonyl coenzyme A biosynthesis by tuning the Escherichia coli metabolic network and its application to flavanone production. Appl Environ Microbiol 75:5831–5839
22. Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M et al (2008) RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and textpresso navigation. Nucleic Acids Res 36:D120–D124
23. Goodman DB, Church GM, Kosuri S (2013) Causes and effects of N-terminal codon bias in bacterial genes. Science 342:475–479
24. Gralla JD (1996) Activation and repression of E. coli promoters. Curr Opin Genet Dev 6:526–530
25. Green AA, Silver PA, Collins JJ et al (2014) Toehold switches: de-novo-designed regulators of gene expression. Cell 159:1–15
26. Grohmann D, Werner F (2011) Recent advances in the understanding of archaeal transcription. Curr Opin Microbiol 14:328–334
27. Hahn S, Young ET (2011) Transcriptional regulation in Saccharomyces cerevisiae: transcription factor regulation and function, mechanisms of initiation, and roles of activators and coactivators. Genetics 189:705–736
28. Hammer K, Mijakovic I, Jensen PR (2006) Synthetic promoter libraries—tuning of gene expression. Trends Biotechnol 24:53–55
29. Hu Y, Wan H, Li J et al (2015) Enhanced production of l-sorbose in an industrial Gluconobacter oxydans strain by identification of a strong promoter based on proteomics analysis. J Ind Microbiol Biot 42:1039–1047
30. Ingolia NT, Murray AW (2007) Positive-feedback loops as a flexible biological module. Curr biol 17:668–677
31. Iyer S, Karig DK, Norred SE et al (2013) Multi-input regulation and logic with T7 promoters in cells and cell-free systems. PLoS One 8:e78442
32. Jaini S, Lyubetskaya A, Gomes A et al (2014) Transcription factor binding site mapping using ChIP-SEq. Microbiol Spectr 2:1–21
33. Jensen PR, Hammer K (1998a) Artificial promoters for metabolic optimization. Biotechnol Bioeng 58:191–195
34. Jensen PR, Hammer K (1998b) The sequence of spacers between the consensus sequences modulates the strength of prokaryotic promoters. Appl Environ Microbiol 64:82–87
35. Jun SH, Reichlen MJ, Tajiri M et al (2011) Archaeal RNA polymerase and transcription regulation. Crit Rev Biochem Mol Biol 46:27–40
36. Kanhere A, Bansal M (2005) Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes. Nucleic Acids Res 33:3165–3175
37. Karr EA (2014) Transcription regulation in the third domain. In: Sariaslani S, Gadd GM (eds) Advances in applied microbiology, vol 89. Elsevier Academic Press Inc, San Diego, pp 101–133. doi:10.1016/b978-0-12-800259-9.00003-2
38. Keren L, Zackay O, Lotan-Pompan M et al (2013) Promoters maintain their relative activity levels under different growth conditions. Mol Syst Biol 9:701
39. Kim JN, Jeong Y, Yoo JS et al (2015a) Genome-scale analysis reveals a role for NdgR in the thiol oxidative stress response in Streptomyces coelicolor. Bmc Genom 16:116
40. Kim S, Lee K, Bae S-J et al (2015b) Promoters inducible by aromatic amino acids and gamma-aminobutyrate (GABA) for metabolic engineering applications in Saccharomyces cerevisiae. Appl Microbiol Biot 99:2705–2714
41. Kobayashi H, Kærn M, Araki M et al (2004) Programmable cells: interfacing natural and engineered gene networks. P Nat Acad Sci USA 101:8414–8419
42. Kodym A, Afza R (2003) Physical and chemical mutagenesis. Methods Mol Biol Plant Func Genom 236:189–204
43. Leavitt JM, Alper HS (2015) Advances and current limitations in transcript-level control of gene expression. Curr Opin Biotech 34:98–104
44. 2 production in a hyperthermophilic archaeon. Appl Microbiol Biot 99:4085–4092
45. Li S, Wang J, Li X et al (2015) Genome-wide identification and evaluation of constitutive promoters in streptomycetes. Microb Cell Fact 14:172–172
46. Liu T, Vora H, Khosla C (2010) Quantitative analysis and engineering of fatty acid biosynthesis in E. coli. Metab Eng 12:378–386
47. Lu CF, Jeffries T (2007) Shuffling of promoters for multiple genes to optimize xylose fermentation in an engineered Saccharomyces cerevisiae strain. Appl Environ Microb 73:6072–6077
48. Luo Y, Zhang L, Barton KW et al (2015) Systematic identification of a panel of strong constitutive promoters from streptomyces albus. ACS Synth Biol 4:1001–1010
49. Madar D, Dekel E, Bren A et al (2013) Promoter activity dynamics in the lag phase of Escherichia coli. BMC Syst Biol 7:136
50. Madzak C, Treton B, Blanchin-Roland S (2000) Strong hybrid promoters and integrative expression/secretion vectors for quasi-constitutive expression of heterologous proteins in the yeast Yarrowia lipolytica. J Mol Microbiol Biotechnol 2:207–216
51. Mardis ER (2007) ChIP-seq: welcome to the new frontier. Nat Methods 4:613–614
52. McGettigan PA (2013) Transcriptomics in the RNA-seq era. Curr Opin Chem Biol 17:4–11
53. McWhinnie RL, Nano FE (2014) Synthetic promoters functional in Francisella novicida and Escherichia coli. Appl Environ Microb 80:226–234
54. Mendoza-Vargas A, Olvera L, Olvera M et al (2009) Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli. PLoS One 4:e7526
55. Murphy KF, Balázsi G, Collins JJ (2007) Combinatorial promoter design for engineering noisy gene expression. P Nat Acad Sci USA 104:12726–12731
56. Myers KS, Yan HH, Ong IM et al (2013) Genome-scale analysis of Escherichia coli FNR reveals complex features of transcription factor binding. PLoS Genet 9:e1003565
57. Nair TM, Kulkarni B (1994) On the consensus structure within the E. coli promoters. Biophys Chem 48:383–393
58. Nakashima N, Tamura T, Good L (2006) Paired termini stabilize antisense RNAs and enhance conditional gene silencing in Escherichia coli. Nucleic Acids Res 34:e138
59. Nakashima N, Akita H, Hoshino T (2014) Establishment of a novel gene expression method, BICES (biomass-inducible chromosome-based expression system), and its application to the production of 2,3-butanediol and acetoin. Metab Eng 25:204–214
60. Nelson JD, Denisenko O, Bomsztyk K (2006) Protocol for the fast chromatin immunoprecipitation (ChIP) method. Nat Protocols 1:179–185
61. Oneill LP, Turner BM (1996) Immunoprecipitation of chromatin. RNA Polymerase A Factors Pt B 274:189–197
62. Pestka S, Daugherty BL, Jung V et al (1984) Anti-mRNA: specific inhibition of translation of single mRNA molecules. P Nat Acad Sci USA 81:7525–7528
63. Pisithkul T, Patel NM, Amador-Noguez D (2015) Post-translational modifications as key regulators of bacterial metabolic fluxes. Curr Opini Microbiol 24:29–37
64. Qi LS, Larson MH, Gilbert LA et al (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152:1173–1183
65. Qureshi SA, Jackson SP (1998) Sequence-specific DNA binding by the S. shibatae TFIIB homolog, TFB, and its effect on promoter strength. Mol Cell 1:389–400
66. Redden H, Alper HS (2015) The development and characterization of synthetic minimal yeast promoters. Nat Commun 6:7810
67. Roy AL, Singer DS (2015) Core promoters in transcription: old problem, new insights. Trends Biochem Sci 40:165–171
68. Rytter JV, Helmark S, Chen J et al (2014) Synthetic promoter libraries for Corynebacterium glutamicum. Appl Microbiol Biot 98:2617–2623
69. Saecker RM, Record MT, Dehaseth PL (2011) Mechanism of bacterial transcription initiation: RNA polymerase-promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis. J Mol Biol 412:754–771
70. Salis HM, Mirsky EA, Voigt CA (2009) Automated design of synthetic ribosome binding sites to control protein expression. Nat Biotechnol 27:946–950
71. Schaerli Y, Gili M, Isalan M (2014) A split intein T7 RNA polymerase for transcriptional AND-logic. Nucleic Acids Res 42:12322–12328
72. Schujman GE, Paoletti L, Grossman AD et al (2003) FapR, a bacterial transcription factor involved in global regulation of membrane lipid biosynthesis. Dev Cell 4:663–672
73. Seo SW, Yang J-S, Kim I et al (2013) Predictive design of mRNA translation initiation region to control prokaryotic translation efficiency. Metab Eng 15:67–74
74. Shiroguchi K, Jia TZ, Sims PA et al (2012) Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes. P Natl Acad Sci USA 109:1347–1352
75. Siegl T, Tokovenko B, Myronovskyi M et al (2013) Design, construction and characterisation of a synthetic promoter library for fine-tuned gene expression in actinomycetes. Metab Eng 19:98–106
76. Sierro N, Makita Y, de Hoon M et al (2008) DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res 36:D93–D96
77. Singh V (2014) Recent advances and opportunities in synthetic logic gates engineering in living cells. Syst Synth Biol 8:271–282
78. Singh AK, Sad K, Singh SK et al (2014) Regulation of gene expression at low temperature: role of cold-inducible promoters. Microbiology 160:1291–1296
79. Solovyev VV, Shahmuradov IA (2003) PromH: promoters identification using orthologous genomic sequences. Nucleic Acids Res 31:3540–3545
80. Soppa J (1999) Transcription initiation in Archaea: facts, factors and future aspects. Mol Microbiol 31:1295–1305
81. Sun JG, Han ZY, Ge XZ et al (2014) Distinct promoters affect pyrroloquinoline quinone production in recombinant Escherichia coli and Klebsiella pneumoniae. Curr Microbiol 69:451–456
82. Teo WS, Chang MW (2014) Development and characterization of AND-gate dynamic controllers with a modular synthetic GAL1 core promoter in Saccharomyces cerevisiae. Biotechnol Bioeng 111:144–151
83. Venayak N, Anesiadis N, Cluett WR et al (2015) Engineering metabolism through dynamic control. Curr Opin Biotech 34:142–152
84. Wang J, Ai X, Mei H et al (2013) High-throughput identification of promoters and screening of highly active promoter-5′-UTR DNA region with different characteristics from Bacillus thuringiensis. PLoS One 8:e62960
85. West RW Jr, Neve RL, Rodriguez RL (1979) Construction and characterization of E. coli promoter-probe plasmid vectors. I. Cloning of promoter-containing DNA fragments. Gene 7:271–288
86. Williams T, Averesch N, Winter G et al (2015) Quorum-sensing linked RNA interference for dynamic metabolic pathway control in Saccharomyces cerevisiae. Metab Eng 29:124–134
87. Wright BE (2004) Stress-directed adaptive mutations and evolution. Mol Microbiol 52:643–650
88. Wu JJ, Du GC, Zhou JW et al (2013a) Metabolic engineering of Escherichia coli for (2S)-pinocembrin production from glucose by a modular metabolic strategy. Metab Eng 16:48–55
89. Wu JJ, Liu PR, Fan YM et al (2013b) Multivariate modular metabolic engineering of Escherichia coli to produce resveratrol from l-tyrosine. J Biotechnol 167:404–411
90. Wu JJ, Zhou TT, Du GC et al (2014) Modular optimization of heterologous pathways for de novo synthesis of (2S)-naringenin in Escherichia coli. PloS One 9:e101492
91. Xu P, Ranganathan S, Fowler ZL et al (2011) Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA. Metab Eng 13:578–587
92. Xu P, Gu Q, Wang W et al (2013) Modular optimization of multi-gene pathways for fatty acids production in E. coli. Nat Commun 4:1409
93. Xu P, Li LY, Zhang FM et al (2014a) Improving fatty acids production by engineering dynamic pathway regulation and metabolic control. P Nat Acad Sci USA 111:11299–11304
94. Xu P, Wang WY, Li LY et al (2014b) Design and kinetic analysis of a hybrid promoter-regulator system for malonyl-CoA sensing in Escherichia coli. Acs Chem Biol 9:451–458
95. Yim SS, An SJ, Kang M et al (2013) Isolation of fully synthetic promoters for high-level gene expression in Corynebacterium glutamicum. Biotechnol Bioeng 110:2959–2969
96. Zaslaver A, Bren A, Ronen M et al (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Meth 3:623–628
97. Zhang F, Carothers JM, Keasling JD (2012) Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat Biotechnol 30:354–359
98. Zhang X, Zhang XF, Li HP et al (2014) Atmospheric and room temperature plasma (ARTP) as a new powerful mutagenesis tool. Appl Microbiol Biot 98:5387–5396
99. Zhou JW, Du GC, Chen J (2014) Novel fermentation processes for manufacturing plant natural products. Curr Opin Biotech 25:17–23