Engineering of an oleaginous bacterium for the production of fatty acids and fuels

Nature Chemical Biology

Volumn 15, Issue 7, 2019, Pages 721-729

  Kim, Hye Mi ^a   Chae, Tong Un ^a   Choi, So Young ^a   Kim, Won Jun ^a   Lee, Sang Yup ^a  

^a Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ACYL COENZYME A; ACYL COENZYME A DEHYDROGENASE; ALCOHOL DEHYDROGENASE; ALDEHYDE; ALDEHYDE DEHYDROGENASE; ALKANE 1 MONOOXYGENASE; FATTY ACID; FATTY ACID ESTER; FOLDASE; FUEL; GLUCOSE; HYDROCARBON; OXYGENASE; SYNTHETASE; TRIACYLGLYCEROL; TRIACYLGLYCEROL LIPASE; UNCLASSIFIED DRUG; ESTER;

ARTICLE; BACTERIAL STRAIN; BACTERIUM; BIOFUEL PRODUCTION; BIOMASS; FATTY ACID SYNTHESIS; FED BATCH CULTURE; FERMENTATION; METABOLIC ENGINEERING; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; RHODOCOCCUS OPACUS; BIOSYNTHESIS; CHEMISTRY; METABOLISM; RHODOCOCCUS;

ESTERS; FATTY ACIDS; HYDROCARBONS; METABOLIC ENGINEERING; RHODOCOCCUS;

EID: 85067878142     PISSN: 15524450     EISSN: 15524469     Source Type: Journal    
DOI: 10.1038/s41589-019-0295-5     Document Type: Article

References (45)

1. Stephanopoulos, G. Challenges in engineering microbes for biofuels production. Science 315, 801–804 (2007). DOI: 10.1126/science.1139612
2. Choi, Y. J. & Lee, S. Y. Microbial production of short-chain alkanes. Nature 502, 571–574 (2013). DOI: 10.1038/nature12536
3. Peralta-Yahya, P. P., Zhang, F. Z., del Cardayre, S. B. & Keasling, J. D. Microbial engineering for the production of advanced biofuels. Nature 488, 320–328 (2012). DOI: 10.1038/nature11478
4. Peralta-Yahya, P. P. & Keasling, J. D. Advanced biofuel production in microbes. Biotechnol. J. 5, 147–162 (2010). DOI: 10.1002/biot.200900220
5. Lee, S. Y., Kim, H. M. & Cheon, S. Metabolic engineering for the production of hydrocarbon fuels. Curr. Opin. Biotechnol. 33, 15–22 (2015). DOI: 10.1016/j.copbio.2014.09.008
6. Certik, M. & Shimizu, S. Biosynthesis and regulation of microbial polyunsaturated fatty acid production. J. Biosci. Bioeng. 87, 1–14 (1999). DOI: 10.1016/S1389-1723(99)80001-2
7. Tee, T. W., Chowdhury, A., Maranas, C. D. & Shanks, J. V. Systems metabolic engineering design: fatty acid production as an emerging case study. Biotechnol. Bioeng. 111, 849–857 (2014). DOI: 10.1002/bit.25205
8. Lu, X., Vora, H. & Khosla, C. Overproduction of free fatty acids in E. coli: implications for biodiesel production. Metab. Eng. 10, 333–339 (2008). DOI: 10.1016/j.ymben.2008.08.006
9. Xu, P., Gu, Q., Wang, W., Wong, L., Bower, A. G., Collins, C. H. & Koffas, M. A. Modular optimization of multi-gene pathways for fatty acids production in E. coli. Nat. Commun. 4, 1409 (2013). DOI: 10.1038/ncomms2425
10. Xiao, Y., Bowen, C. H., Liu, D. & Zhang, F. Exploiting nongenetic cell-to-cell variation for enhanced biosynthesis. Nat. Chem. Biol. 12, 339–344 (2016). DOI: 10.1038/nchembio.2046
11. Zhou, Y. J. et al. Production of fatty acid-derived oleochemicals and biofuels by synthetic yeast cell factories. Nat. Commun. 7, 11709 (2016). DOI: 10.1038/ncomms11709
12. Ruffing, A. M. Improved free fatty acid production in cyanobacteria with Synechococcus sp. PCC 7002 as Host. Front. Bioeng. Biotechnol. 2, 17 (2016).
13. Qiao, K., Wasylenko, T. M., Zhou, K., Xu, P. & Stephanopoulos, G. Lipid production in Yarrowia lipolytica is maximized by engineering cytosolic redox metabolism. Nat. Biotechnol. 35, 173–177 (2017). DOI: 10.1038/nbt.3763
14. Blazeck, J. et al. Harnessing Yarrowia lipolytica lipogenesis to create a platform for lipid and biofuel production. Nat. Commun. 5, 3131 (2014). DOI: 10.1038/ncomms4131
15. Xua, P., Qiaoa, K., Ahna, W. S. & Stephanopoulos, G. Engineering Yarrowia lipolytica as a platform for synthesis of drop-in transportation fuels and oleochemicals. Proc. Natl Acad. Sci. USA 113, 10848–10853 (2016). DOI: 10.1073/pnas.1607295113
16. Amaro, R. L., Dulermo, R., Niehus, X. & Nicaud, J. M. Combining metabolic engineering and process optimization to improve production and secretion of fatty acids. Metab. Eng. 38, 38–46 (2016). DOI: 10.1016/j.ymben.2016.06.004
17. Kurosawa, K., Boccazzi, P., de Almeida, N. M. & Sinskey, A. J. High-cell-density batch fermentation of Rhodococcus opacus PD630 using a high glucose concentration for triacylglycerol production. J. Biotechnol. 147, 212–218 (2010). DOI: 10.1016/j.jbiotec.2010.04.003
18. Alvarez, H. M., Kalscheuer, R. & Steinbüchel, A. Accumulation and mobilization of storage lipids by Rhodococcus opacus PD630 and Rhodococcus ruber NCIMB 40126. Appl. Microbiol. Biotechnol. 54, 218–223 (2000). DOI: 10.1007/s002530000395
19. Tucker, D. L., Tucker, N. & Conway, T. Gene expression profiling of the pH response in Escherichia coli. J. Bacteriol. 23, 6551–6558 (2002). DOI: 10.1128/JB.184.23.6551-6558.2002
20. Alvarez, H. M., Silva, R. A., Herrero, M., Hernández, M. A. & Villalba, M. S. Metabolism of triacylglycerols in Rhodococcus species: insights from physiology and molecular genetics. J. Mol. Biochem. 2, 69–78 (2012).
21. Gupta, R., Gupta, N. & Rathi, P. Bacterial lipases: an overview of production, purification and biochemical properties. Appl. Microbiol. Biotechnol. 64, 763–781 (2004). DOI: 10.1007/s00253-004-1568-8
22. Parish, T., Mahenthiralingam, E., Draper, P., Davis, E. O. & Colston, M. J. Regulation of the inducible acetamidase gene of Mycobacterium smegmatis. Microbiology 143, 2267–2276 (1997). DOI: 10.1099/00221287-143-7-2267
23. Chen, Y. et al. Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630. Nucleic Acids Res. 42, 1052–1064 (2014). DOI: 10.1093/nar/gkt932
24. Kranen, E., Detzel, C., Weber, T. & Jose, J. Autodisplay for the co-expression of lipase and foldase on the surface of E. coli: washing with designer bugs. Microb. Cell. Fact. 13, 19 (2014). DOI: 10.1186/1475-2859-13-19
25. Steen, E. J. et al. Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature 463, 559–562 (2010). DOI: 10.1038/nature08721
26. Holland-Staley, C. A., Lee, K., Clark, D. P. & Cunningham, P. R. Aerobic activity of Escherichia coli alcohol dehydrogenase is determined by a single amino acid. J. Bacteriol. 182, 6049–6054 (2000). DOI: 10.1128/JB.182.21.6049-6054.2000
27. Barney, B. M., Wahlen, B. D., Garner, E., Wei, J. S. & Seefeldt, L. C. Differences in substrate specificities of five bacterial wax ester synthases. Appl. Environ. Microb. 78, 5734–5745 (2012). DOI: 10.1128/AEM.00534-12
28. Stöveken, T., Kalscheuer, R., Malkus, U., Reichelt, R. & Steinbüchel, A. The wax ester synthase/acyl coenzyme A:diacylglycerol acyltransferase from Acinetobacter sp. strain ADP1: characterization of a novel type of acyltransferase. J. Bacteriol. 187, 1369–1376 (2005). DOI: 10.1128/JB.187.4.1369-1376.2005
29. Na, D., Lee, S. & Lee, D. Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with desired expression levels in prokaryotes. BMC Syst. Biol. 4, 71 (2010). DOI: 10.1186/1752-0509-4-71
30. Schirmer, A., Rude, M. A., Li, X. Z., Popova, E. & del Cardayre, S. B. Microbial biosynthesis of alkanes. Science 329, 559–562 (2010). DOI: 10.1126/science.1187936
31. Harger, M. et al. Expanding the product profile of a microbial alkane biosynthetic pathway. ACS Synth. Biol. 2, 59–62 (2013). DOI: 10.1021/sb300061x
32. Lui, R. et al. Metabolic engineering of fatty acyl-ACP reductase-dependent pathway to improve fatty alcohol production in Escherichia coli. Metab. Eng. 22, 10–21 (2014). DOI: 10.1016/j.ymben.2013.12.004
33. Holder, J. W. et al. Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development. PLoS Genet. 7, 9 (2011). DOI: 10.1371/journal.pgen.1002219
34. Jamshidi, N. & Palsson, B. Ø. Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets. BMC Syst. Biol. 1, 26 (2007). DOI: 10.1186/1752-0509-1-26
35. Lee, S. Y. & Kim, H. U. Systems strategies for developing industrial microbial strains. Nat. Biotechnol. 33, 1061–1072 (2015). DOI: 10.1038/nbt.3365
36. Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343–345 (2009). DOI: 10.1038/nmeth.1318
37. Hänisch, J., Wältermann, M., Robenek, H. & Steinbüchel, A. The Ralstonia eutropha H16 phasin PhaP1 is targeted to intracellular triacylglycerol inclusions in Rhodococcus opacus PD630 and Mycobacterium smegmatis mc2155, and provides an anchor to target other proteins. Microbiology 152, 3271–3280 (2006). DOI: 10.1099/mic.0.28969-0
38. Park, S. H. et al. Metabolic engineering of Corynebacterium glutamicum for l-arginine production. Nat. Commun. 5, 4618 (2014). DOI: 10.1038/ncomms5618
39. Kalscheuer, R., Arenskotter, M. & Steinbüchel, A. Establishment of a gene transfer system for Rhodococcus opacus PD630 based on electroporation and its application for recombinant biosynthesis of poly(3-hydroxyalkanoic acids). Appl. Microbiol. Biotechnol. 52, 508–515 (1999). DOI: 10.1007/s002530051553
40. Waltermann, M., Luftmann, H., Baumeister, D., Kalscheuer, R. & Steinbüchel, A. Rhodococcus opacus strain PD630 as a new source of high-value single-cell oil? Isolation and characterization of triacylglycerols and other storage lipids. Microbiology 146, 1143–1149 (2000). DOI: 10.1099/00221287-146-5-1143
41. Cai, S. F. et al. Identification of the haloarchaeal phasin (PhaP) that functions in polyhydroxyalkanoate accumulation and granule formation in Haloferax mediterranei. Appl. Environ. Microb. 78, 1946–1952 (2012). DOI: 10.1128/AEM.07114-11
42. Tian, J. M. et al. Analysis of transient polyhydroxybutyrate production in Wautersia eutropha H16 by quantitative Western analysis and transmission electron microscopy. J. Bacteriol. 187, 3825–3832 (2005). DOI: 10.1128/JB.187.11.3825-3832.2005
43. Weber, T. et al. antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res. 43, 237–243 (2015). DOI: 10.1093/nar/gkv437
44. Kumar, N. & Skolnick, J. EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes. Bioinformatics 28, 2687–2688 (2012). DOI: 10.1093/bioinformatics/bts510
45. King, Z. A. et al. BiGG Models: a platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Res. 4, 515–525 (2015).