Characterisation of a 3-hydroxypropionic acid-inducible system from Pseudomonas putida for orthogonal gene expression control in Escherichia coli and Cupriavidus necator

Scientific Reports

Volumn 7, Issue 1, 2017, Pages

  Hanko, Erik K R ^a   Minton, Nigel P ^a   Malys, Naglis ^a  

^a UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

HYDRACRYLIC ACID; LACTIC ACID;

ANALOGS AND DERIVATIVES; BACTERIAL GENE; BINDING SITE; CONSERVED SEQUENCE; CUPRIAVIDUS NECATOR; DRUG EFFECT; ESCHERICHIA COLI; FLUORESCENCE; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; KINETICS; METABOLISM; METABOLOME; MUTATION; NUCLEOTIDE MOTIF; NUCLEOTIDE SEQUENCE; PROMOTER REGION; PSEUDOMONAS PUTIDA; REPORTER GENE;

BASE SEQUENCE; BINDING SITES; CONSERVED SEQUENCE; CUPRIAVIDUS NECATOR; ESCHERICHIA COLI; FLUORESCENCE; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; GENES, REPORTER; KINETICS; LACTIC ACID; METABOLOME; MUTATION; NUCLEOTIDE MOTIFS; PROMOTER REGIONS, GENETIC; PSEUDOMONAS PUTIDA; TRANSCRIPTION, GENETIC;

EID: 85019213625     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/s41598-017-01850-w     Document Type: Article

References (63)

1. Grousseau, E., Lu, J., Gorret, N., Guillouet, S. E., & Sinskey, A. J. Isopropanol production with engineered Cupriavidus necator as bioproduction platform. Appl. Microbiol. Biotechnol. 98, 4277-4290 (2014
2. Latif, H., Zeidan, A. A., Nielsen, A. T., & Zengler, K. Trash to treasure: Production of biofuels and commodity chemicals via syngas fermenting microorganisms. Curr. Opin. Biotechnol. 27, 79-87 (2014
3. Clomburg, J. M., Crumbley, A. M., & Gonzalez, R. Industrial biomanufacturing: The future of chemical production. Science 355 (2017
4. Erickson, B., Nelson, & Winters, P. Perspective on opportunities in industrial biotechnology in renewable chemicals. Biotechnol. J 7, 176-185 (2012
5. Choi, S., Song, C. W., Shin, J. H., & Lee, S. Y. Biorefineries for the production of top building block chemicals and their derivatives. Metab. Eng. 28, 223-239 (2015
6. Becker, J., Lange, A., Fabarius, J., & Wittmann, C. Top value platform chemicals: Bio-based production of organic acids. Curr. Opin. Biotechnol. 36, 168-175 (2015
7. Valdehuesa, K. N. G., et al. Recent advances in the metabolic engineering of microorganisms for the production of 3-hydroxypropionic acid as C3 platform chemical. Appl. Microbiol. Biotechnol. 97, 3309-3321 (2013
8. Andreeben, B., Taylor, N., & Steinbüchel, A. Poly(3-hydroxypropionate): A promising alternative to fossil fuel-based materials. Appl. Environ. Microbiol. 80, 6574-6582 (2014
9. Rathnasingh, C., Raj, S. M., Jo, J. E., & Park, S. Development and evaluation of efficient recombinant Escherichia coli strains for the production of 3-hydroxypropionic acid from glycerol. Biotechnol. Bioeng. 104, 729-739 (2009
10. Zhou, S., Catherine, C., Rathnasingh, C., Somasundar, A., & Park, S. Production of 3-hydroxypropionic acid from glycerol by recombinant Pseudomonas denitrificans. Biotechnol. Bioeng. 110, 3177-3187 (2013
11. Burgé, G., et al. Diversity of Lactobacillus reuteri strains in converting glycerol into 3-hydroxypropionic acid. Appl. Biochem. Biotechnol. 177, 923-939 (2015
12. Chen, Y., Bao, J., Kim, I. K., Siewers, V., & Nielsen, J. Coupled incremental precursor and co-factor supply improves 3-hydroxypropionic acid production in Saccharomyces cerevisiae. Metab. Eng. 22, 104-109 (2014
13. Lan, E. I., et al. Metabolic engineering of cyanobacteria for photosynthetic 3-hydroxypropionic acid production from CO2 using Synechococcus elongatus PCC 7942. Metab. Eng. 31, 163-170 (2015
14. Zhao, L., Lin, J., Wang, H., Xie, J., & Wei, D. Development of a two-step process for production of 3-hydroxypropionic acid from glycerol using Klebsiella pneumoniae and Gluconobacter oxydans. Bioprocess Biosystems Eng 38, 2487-2495 (2015
15. Wang, Y., et al. Biosynthesis of platform chemical 3-hydroxypropionic acid (3-HP) directly from CO2 in cyanobacterium Synechocystis sp. PCC 6803. Metab. Eng. 34, 60-70 (2016
16. Chen, Z., et al. Metabolic engineering of Corynebacterium glutamicum for the production of 3-hydroxypropionic acid from glucose and xylose. Metab. Eng. 39, 151-158 (2017
17. Borodina, I., et al. Establishing a synthetic pathway for high-level production of 3-hydroxypropionic acid in Saccharomyces cerevisiae via β-alanine. Metab. Eng. 27, 57-64 (2015
18. Kim, K., Kim, S. K., Park, Y. C., & Seo, J. H. Enhanced production of 3-hydroxypropionic acid from glycerol by modulation of glycerol metabolism in recombinant Escherichia coli. Bioresour. Technol 156, 170-175 (2014
19. Rathnasingh, C., et al. Production of 3-hydroxypropionic acid via malonyl-CoA pathway using recombinant Escherichia coli strains. J. Biotechnol. 157, 633-640 (2012
20. Gokarn, R.R., et al In US8999700 (2015
21. Luo, H., et al. Production of 3-hydroxypropionic acid via the propionyl-CoA pathway using recombinant Escherichia coli strains. PLoS ONE 11 (2016
22. Li, Y., Wang, X., Ge, X., & Tian, P. High production of 3-hydroxypropionic acid in Klebsiella pneumoniae by systematic optimization of glycerol metabolism. Sci. Rep. 6 (2016
23. Chen, Y., & Nielsen, J. Biobased organic acids production by metabolically engineered microorganisms. Curr. Opin. Biotechnol. 37, 165-172 (2016
24. Zhou, S., Ainala, S.K., Seol, E., Nguyen, T.T., & Park, S. Inducible gene expression system by 3-hydroxypropionic acid. Biotechnol. Biofuels 8 (2015
25. Maddocks, S. E., & Oyston, P. C. F. Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins. Microbiology 154, 3609-3623 (2008
26. Oliver, P., Peralta-Gil, M., Tabche, M.L., & Merino, E. Molecular and structural considerations of TF-DNA binding for the generation of biologically meaningful and accurate phylogenetic footprinting analysis: The LysR-type transcriptional regulator family as a study model. BMC Genomics 17 (2016
27. MacLean, A. M., Anstey, M. I., & Finan, T. M. Binding site determinants for the LysR-type transcriptional regulator PcaQ in the legume endosymbiont Sinorhizobium meliloti. J. Bacteriol. 190, 1237-1246 (2008
28. Porrúa, O., et al. An A-tract at the AtzR binding site assists DNA binding, inducer-dependent repositioning and transcriptional activation of the PatzDEF promoter. Mol. Microbiol. 90, 72-87 (2013
29. Reen, F. J., Barret, M., Fargier, E., O?Muinneacháin, M., & O?Gara, F. Molecular evolution of LysR-type transcriptional regulation in Pseudomonas aeruginosa. Mol. Phylogen. Evol 66, 1041-1049 (2013
30. Michener, J. K., Thodey, K., Liang, J. C., & Smolke, C. D. Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways. Metab. Eng. 14, 212-222 (2012
31. Rogers, J. K., & Church, G. M. Genetically encoded sensors enable real-time observation of metabolite production. Proc. Natl. Acad. Sci. USA 113, 2388-2393 (2016
32. Rogers, J. K., et al. Synthetic biosensors for precise gene control and real-time monitoring of metabolites. Nucleic Acids Res 43, 7648-7660 (2015
33. Zhang, J., Jensen, M. K., & Keasling, J. D. Development of biosensors and their application in metabolic engineering. Curr. Opin. Chem. Biol. 28, 1-8 (2015
34. Zhang, F., Carothers, J. M., & Keasling, J. D. Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat. Biotechnol. 30, 354-359 (2012
35. Dietrich, J. A., Shis, D. L., Alikhani, A., & Keasling, J. D. Transcription factor-based screens and synthetic selections for microbial small-molecule biosynthesis. ACS Synth. Biol 2, 47-58 (2013
36. Eggeling, L., Bott, M., & Marienhagen, J. Novel screening methods-biosensors. Curr. Opin. Biotechnol. 35, 30-36 (2015
37. Qian, S., & Cirino, P. C. Using metabolite-responsive gene regulators to improve microbial biosynthesis. Curr. Opin. Chem. Eng. 14, 93-102 (2016
38. Mahr, R., et al. Biosensor-driven adaptive laboratory evolution of L-valine production in Corynebacterium glutamicum. Metab. Eng. 32, 184-194 (2015
39. Fang, M., et al. Intermediate-sensor assisted push-pull strategy and its application in heterologous deoxyviolacein production in Escherichia coli. Metab. Eng. 33, 41-51 (2016
40. Dos Santos, V. A. P. M., Heim, S., Moore, E. R. B., Strätz, M., & Timmis, K. N. Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440. Environ. Microbiol. 6, 1264-1286 (2004
41. Kovach, M. E., Phillips, R. W., Elzer, P. H., Roop I, R. M., & Peterson, K. M. pBBR1MCS: A broad-host-range cloning vector. BioTechniques 16 (1994
42. Heap, J. T., Pennington, O. J., Cartman, S. T., & Minton, N. P. A modular system for Clostridium shuttle plasmids. J. Microbiol. Methods 78, 79-85 (2009
43. Campbell, R. E., et al. A monomeric red fluorescent protein. Proc. Natl. Acad. Sci. USA 99, 7877-7882 (2002
44. Bi, C., et al. Development of a broad-host synthetic biology toolbox for Ralstonia eutropha and its application to engineering hydrocarbon biofuel production. Microb. Cell Fact. 12 (2013
45. Hughes, J. R., et al. Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences. Proc. Natl. Acad. Sci. USA 102, 9830-9835 (2005
46. Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31, 3406-3415 (2003
47. Hoffmann, J., & Altenbuchner, J. Functional characterization of the mannitol promoter of Pseudomonas fluorescens DSM 50106 and its application for a mannitol-inducible expression system for Pseudomonas putida KT2440. PLoS ONE 10 (2015
48. Parsek, M. R., Shinabarger, D. L., Rothmel, R. K., & Chakrabarty, A. M. Roles of CatR and cis, cis-muconate in activation of the catBC operon, which is involved in benzoate degradation in Pseudomonas putida. J. Bacteriol. 174, 7798-7806 (1992
49. Jiang, X., Meng, X., & Xian, M. Biosynthetic pathways for 3-hydroxypropionic acid production. Appl. Microbiol. Biotechnol. 82, 995-1003 (2009
50. Van Der Meer, J. R., & Belkin, S. Where microbiology meets microengineering: Design and applications of reporter bacteria. Nature Rev. Microbiol. 8, 511-522 (2010
51. Blattner, F. R., et al. The complete genome sequence of Escherichia coli K-12. Science 277, 1453-1462 (1997
52. Jensen, K. F. The Escherichia coli K-12 ?wild types? W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels. J. Bacteriol. 175, 3401-3407 (1993
53. Schlegel, H. G., Kaltwasser, H., & Gottschalk, G. Ein Submersverfahren zur Kultur wasserstoffoxydierender Bakterien: Wachstumsphysiologische Untersuchungen. Archiv für Mikrobiologie 38, 209-222 (1961
54. Sambrook, J., Fritsch, E. F., & Maniatis, T. Molecular cloning: a laboratory manual (Cold Spring Harbor Laboratory Press, New York, 1989
55. Ausubel, F. M., et al. Current Protocols in Molecular Biology (John Wiley, & Sons, 2003
56. Orosz, A., Boros, I., & Venetianer, P. Analysis of the complex transcription termination region of the Escherichia coli rrnB gene. Eur. J. Biochem. 201, 653-659 (1991
57. Pfeiffer, D., & Jendrossek, D. Interaction between poly(3-hydroxybutyrate) granule-associated proteins as revealed by two-hybrid analysis and identification of a new phasin in Ralstonia eutropha H16. Microbiology 157, 2795-2807 (2011
58. Sheng, L., Kovács, K., Winzer, K., Zhang, Y., & Minton, N. P. Development and implementation of rapid metabolic engineering tools for chemical and fuel production in Geobacillus thermoglucosidasius NCIMB 11955. Biotechnol. Biofuels 10 (2017
59. Sievers, F., et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7 (2011
60. Goujon, M., et al. A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res 38, W695-W699 (2010
61. Crooks, G. E., Hon, G., Chandonia, J. M., & Brenner, S. E. WebLogo: A sequence logo generator. Genome Res. 14, 1188-1190 (2004
62. Solovyev, V., & Salamov, A. In Metagenomics and its Applications in Agriculture, Biomedicine and Environmental Studies 62-78 (2011
63. Reese, M. G. Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput. Chem. 26, 51-56 (2001