Engineering Promoter Architecture in Oleaginous Yeast Yarrowia lipolytica

ACS Synthetic Biology

Volumn 5, Issue 3, 2016, Pages 213-223

  Shabbir Hussain, Murtaza ^a   Gambill, Lauren ^b   Smith, Spencer ^b   Blenner, Mark A ^a  

^a AMRL   (United States)

^b CLEMSON UNIVERSITY   (United States)

Author keywords

enhancers; oleate response elements; POX2; promoter; UAS; Yarrowia lipolytica

Indexed keywords

ACYL COENZYME A OXIDASE; FUNGAL ENZYME; OLEIC ACID; RNA POLYMERASE II; FUNGAL PROTEIN;

ARTICLE; DNA BASE COMPOSITION; DNA RESPONSIVE ELEMENT; DNA SEQUENCE; ENHANCER REGION; FUNGAL GENE; FUNGAL GENOME; GENE EXPRESSION; METABOLIC ENGINEERING; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN EXPRESSION; TANDEM REPEAT; TATA BOX; XPR2 GENE; YARROWIA LIPOLYTICA; GENETIC ENGINEERING; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE; PLASMID; REAL TIME POLYMERASE CHAIN REACTION; YARROWIA;

BASE SEQUENCE; ENHANCER ELEMENTS, GENETIC; FUNGAL PROTEINS; GENETIC ENGINEERING; PLASMIDS; REAL-TIME POLYMERASE CHAIN REACTION; RNA POLYMERASE II; TATA BOX; YARROWIA;

EID: 84961820300     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/acssynbio.5b00100     Document Type: Article

References (51)

1. Maston, G. A., Evans, S. K., and Green, M. R. (2006) Transcriptional regulatory elements in the human genome Annu. Rev. Genomics Hum. Genet. 7, 29-59 10.1146/annurev.genom.7.080505.115623
2. Venter, J. C., Adams, M. D., Myers, E. W., and Li, P. W. et al. 2001, The sequence of the human genome Science 291, 1304-1351 10.1126/science.1058040
3. Blazeck, J., Garg, R., Reed, B., and Alper, H. S. (2012) Controlling promoter strength and regulation in Saccharomyces cerevisiae using synthetic hybrid promoters Biotechnol. Bioeng. 109, 2884-2895 10.1002/bit.24552
4. Curran, K. A., Crook, N. C., Karim, A. S., and Gupta, A. (2014) Design of synthetic yeast promoters via tuning of nucleosome architecture Nat. Commun. 5, 4002 10.1038/ncomms5002
5. Nevoigt, E., Kohnke, J., Fischer, C. R., and Alper, H. et al. 2006, Engineering of promoter replacement cassettes for fine-tuning of gene expression in Saccharomyces cerevisiae Appl. Environ. Microbiol. 72, 5266-5273 10.1128/AEM.00530-06
6. Gaillardin, C. and Ribet, A. M. (1987) LEU2 directed expression of beta-galactosidase activity and phleomycin resistance in Yarrowia lipolytica Curr. Genet. 11, 369-375 10.1007/BF00378179
7. Mumberg, D., Muller, R., and Funk, M. (1995) Yeast vectors for the controlled expression of heterologous proteins in different genetic backgrounds Gene 156, 119-122 10.1016/0378-1119(95)00037-7
8. Schneider, J. C. and Guarente, L. (1991) Vectors for expression of cloned genes in yeast: regulation, overproduction, and underproduction Methods Enzymol. 194, 373-388 10.1016/0076-6879(91)94028-B
9. Caspeta, L. and Nielsen, J. (2013) Toward systems metabolic engineering of Aspergillus and Pichia species for the production of chemicals and biofuels Biotechnol. J. 8, 534-544 10.1002/biot.201200345
10. Goshima, T., Negi, K., Tsuji, M., and Inoue, H. et al. 2013, Ethanol fermentation from xylose by metabolically engineered strains of Kluyveromyces marxianus J. Biosci Bioeng 116, 551-554 10.1016/j.jbiosc.2013.05.010
11. Harner, N. K., Wen, X., Bajwa, P. K., and Austin, G. D. et al. 2015, Genetic improvement of native xylose-fermenting yeasts for ethanol production J. Ind. Microbiol. Biotechnol. 42, 1-20 10.1007/s10295-014-1535-z
12. Liu, L., Redden, H., and Alper, H. S. (2013) Frontiers of yeast metabolic engineering: diversifying beyond ethanol and Saccharomyces Curr. Opin. Biotechnol. 24, 1023-1030 10.1016/j.copbio.2013.03.005
13. Wu, S. G., He, L., Wang, Q., and Tang, Y. J. (2015) An ancient Chinese wisdom for metabolic engineering: Yin-Yang Microb. Cell Fact. 14, 39 10.1186/s12934-015-0219-3
14. Xu, P., Li, L., Zhang, F., and Stephanopoulos, G. et al. 2014, Improving fatty acids production by engineering dynamic pathway regulation and metabolic control Proc. Natl. Acad. Sci. U. S. A. 111, 11299-11304 10.1073/pnas.1406401111
15. Farmer, W. R. and Liao, J. C. (2000) Improving lycopene production in Escherichia coli by engineering metabolic control Nat. Biotechnol. 18, 533-537 10.1038/75398
16. Zhang, F. Z., Carothers, J. M., and Keasling, J. D. (2012) Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids Nat. Biotechnol. 30, 354-U166 10.1038/nbt.2149
17. Roy, P. K., Singh, H. D., Bhagat, S. D., and Baruah, J. N. (1979) Characterization of Hydrocarbon Emulsification and Solubilization Occurring during the Growth of Endomycopsis-Lipolytica on Hydrocarbons Biotechnol. Bioeng. 21, 955-974 10.1002/bit.260210604
18. Ruiz-Herrera, J. and Sentandreu, R. (2002) Different effectors of dimorphism in Yarrowia lipolytica Arch. Microbiol. 178, 477-483 10.1007/s00203-002-0478-3
19. Fickers, P., Benetti, P. H., Wache, Y., and Marty, A. et al. 2005, Hydrophobic substrate utilisation by the yeast Yarrowia lipolytica, and its potential applications FEMS Yeast Res. 5, 527-543 10.1016/j.femsyr.2004.09.004
20. Blazeck, J., Hill, A., Liu, L. Q., and Knight, R. et al. 2014, Harnessing Yarrowia lipolytica lipogenesis to create a platform for lipid and biofuel production Nat. Commun. 5, 3131 10.1038/ncomms4131
21. Qiao, K., Imam Abidi, S. H., Liu, H., and Zhang, H. et al. 2015, Engineering lipid overproduction in the oleaginous yeast Yarrowia lipolytica Metab. Eng. 29, 56-65 10.1016/j.ymben.2015.02.005
22. Beopoulos, A., Verbeke, J., Bordes, F., and Guicherd, M. et al. 2014, Metabolic engineering for ricinoleic acid production in the oleaginous yeast Yarrowia lipolytica Appl. Microbiol. Biotechnol. 98, 251-262 10.1007/s00253-013-5295-x
23. Xue, Z., Sharpe, P. L., Hong, S. P., and Yadav, N. S. et al. 2013, Production of omega-3 eicosapentaenoic acid by metabolic engineering of Yarrowia lipolytica Nat. Biotechnol. 31, 734-740 10.1038/nbt.2622
24. Anastassiadis, S., Aivasidis, A., and Wandrey, C. (2002) Citric acid production by Candida strains under intracellular nitrogen limitation Appl. Microbiol. Biotechnol. 60, 81-87 10.1007/s00253-002-1098-1
25. Fickers, P., Nicaud, J. M., Gaillardin, C., and Destain, J. et al. 2004, Carbon and nitrogen sources modulate lipase production in the yeast Yarrowia lipolytica J. Appl. Microbiol. 96, 742-749 10.1111/j.1365-2672.2004.02190.x
26. Zhou, J. W., Yin, X. X., Madzak, C., and Du, G. C. et al. 2012, Enhanced alpha-ketoglutarate production in Yarrowia lipolytica WSH-Z06 by alteration of the acetyl-CoA metabolism J. Biotechnol. 161, 257-264 10.1016/j.jbiotec.2012.05.025
27. Ryu, S., Labbe, N., and Trinh, C. T. (2015) Simultaneous saccharification and fermentation of cellulose in ionic liquid for efficient production of alpha-ketoglutaric acid by Yarrowia lipolytica Appl. Microbiol. Biotechnol. 99, 4237-4244 10.1007/s00253-015-6521-5
28. Matthaus, F., Ketelhot, M., Gatter, M., and Barth, G. (2014) Production of Lycopene in the Non-Carotenoid-Producing Yeast Yarrowia lipolytica Appl. Environ. Microb 80, 1660-1669 10.1128/AEM.03167-13
29. Lubliner, S., Keren, L., and Segal, E. (2013) Sequence features of yeast and human core promoters that are predictive of maximal promoter activity Nucleic Acids Res. 41, 5569-5581 10.1093/nar/gkt256
30. Weingarten-Gabbay, S. and Segal, E. (2014) The grammar of transcriptional regulation Hum. Genet. 133, 701-711 10.1007/s00439-013-1413-1
31. Madzak, C., Treton, B., and 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. Microb Biotech 2, 207-216
32. Blazeck, J., Liu, L., Redden, H., and Alper, H. (2011) Tuning gene expression in Yarrowia lipolytica by a hybrid promoter approach Appl. Environ. Microbiol. 77, 7905-7914 10.1128/AEM.05763-11
33. Blazeck, J., Reed, B., Garg, R., and Gerstner, R. et al. 2013, Generalizing a hybrid synthetic promoter approach in Yarrowia lipolytica Appl. Microbiol. Biotechnol. 97, 3037-3052 10.1007/s00253-012-4421-5
34. Madzak, C., Blanchin-Roland, S., Otero, R. R. C., and Gaillardin, C. (1999) Functional analysis of upstream regulating regions from the Yarrowia lipolytica XPR2 promoter Microbiology 145, 75-87 10.1099/13500872-145-1-75
35. Juretzek, T., Wang, H. J., Nicaud, J. M., Mauersberger, S., and Barth, G. (2000) Comparison of Promoters Suitable for Regulated Overexpression of Beta-Galactosidase in the Alkane-Utilizing Yeast Yarrowia lipolytica Biotechnol. Bioprocess Eng. 5, 320-326 10.1007/BF02942206
36. Nicaud, J. M., Madzak, C., van den Broek, P., and Gysler, C. et al. 2002, Protein expression and secretion in the yeast Yarrowia lipolytica FEMS Yeast Res. 2, 371-379 10.1016/S1567-1356(02)00082-X
37. Nthangeni, M. B., Urban, P., Pompon, D., and Smit, M. S. et al. 2004, The use of Yarrowia lipolytica for the expression of human cytochrome P450 CYP1A1 Yeast 21, 583-592 10.1002/yea.1127
38. Poopanitpan, N., Kobayashi, S., Fukuda, R., and Horiuchi, H. et al. 2010, An ortholog of farA of Aspergillus nidulans is implicated in the transcriptional activation of genes involved in fatty acid utilization in the yeast Yarrowia lipolytica Biochem. Biophys. Res. Commun. 402, 731-735 10.1016/j.bbrc.2010.10.096
39. Erb, I. and van Nimwegen, E. (2011) Transcription factor binding site positioning in yeast: proximal promoter motifs characterize TATA-less promoters PLoS One 6, e24279 10.1371/journal.pone.0024279
40. Singer, V. L., Wobbe, C. R., and Struhl, K. (1990) A Wide Variety of DNA-Sequences Can Functionally Replace a Yeast Tata Element for Transcriptional Activation Genes Dev. 4, 636-645 10.1101/gad.4.4.636
41. Mishra, A. K., Vanathi, P., and Bhargava, P. (2003) The transcriptional activator GAL4-VP16 regulates the intramolecular interactions of the TATA-binding protein J. Biosci. 28, 423-436 10.1007/BF02705117
42. Wobbe, C. R. and Struhl, K. (1990) Yeast and Human Tata-Binding Proteins Have Nearly Identical DNA-Sequence Requirements for Transcription Invitro Mol. Cell. Biol. 10, 3859-3867 10.1128/MCB.10.8.3859
43. Jiang, C. and Pugh, B. F. (2009) Nucleosome positioning and gene regulation: advances through genomics Nat. Rev. Genet. 10, 161-172 10.1038/nrg2522
44. Furter-Graves, E. M. and Hall, B. D. (1990) DNA sequence elements required for transcription initiation of the Schizosaccharomyces pombe ADH gene in Saccharomyces cerevisiae Mol. Gen. Genet. 223, 407-416 10.1007/BF00264447
45. Hahn, S., Hoar, E. T., and Guarente, L. (1985) Each of three "TATA elements" specifies a subset of the transcription initiation sites at the CYC-1 promoter of Saccharomyces cerevisiae Proc. Natl. Acad. Sci. U. S. A. 82, 8562-8566 10.1073/pnas.82.24.8562
46. Zhang, Z. and Dietrich, F. S. (2005) Mapping of transcription start sites in Saccharomyces cerevisiae using 5′ SAGE Nucleic Acids Res. 33, 2838-2851 10.1093/nar/gki583
47. Flagfeldt, D. B., Siewers, V., Huang, L., and Nielsen, J. (2009) Characterization of chromosomal integration sites for heterologous gene expression in Saccharomyces cerevisiae Yeast 26, 545-551 10.1002/yea.1705
48. Barth, G. and Gaillardin, C. (1996) Yarrowia lipolytica, in Non-conventional Yeasts in Biotechnology. A Handbook (Wolf, K., Ed.) pp 313-388, Springer, Berlin.
49. Yamane, T., Sakai, H., Nagahama, K., and Ogawa, T. et al. 2008, Dissection of centromeric DNA from yeast Yarrowia lipolytica and identification of protein-binding site required for plasmid transmission J. Biosci. Bioeng. 105, 571-578 10.1263/jbb.105.571
50. Li, M. Z. and Elledge, S. J. (2007) Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC Nat. Methods 4, 251-256 10.1038/nmeth1010
51. Kretzschmar, A., Otto, C., Holz, M., and Werner, S. et al. 2013, Increased homologous integration frequency in Yarrowia lipolytica strains defective in non-homologous end-joining Curr. Genet. 59, 63-72 10.1007/s00294-013-0389-7