References
Abbott, E. P., Ianiri, G., Castoria, R., & Idnurm, A. (2013).
Overcoming recalcitrant transformation and gene manipulation inPucciniomycotina yeasts. Applied Microbiology and
Biotechnology , 97 (1), 283-295.
https://doi.org/10.1007/s00253-012-4561-7
Abdel-Mawgoud, A. M., Markham, K. A., Palmer, C. M., Liu, N.,
Stephanopoulos, G., & Alper, H. S. (2018). Metabolic engineering in the
host Yarrowia lipolytica. Metabolic Engineering , 50 ,
192-208. https://doi.org/10.1016/j.ymben.2018.07.016
Abe, I., Watanabe, T., & Noguchi, H. (2005). Chalcone synthase
superfamily of type III polyketide synthases from rhubarb Rheum
palmatum . Proceedings of the Japan Academy, Series B ,81 (10), 434-440. https://doi.org/10.2183/pjab.81.434
Athenstaedt, K. (2011). YALI0E32769g (DGA1) and YALI0E16797g (LRO1)
encode major triacylglycerol synthases of the oleaginous yeastYarrowia lipolytica . Biochimica et Biophysica Acta (BBA) -
Molecular and Cell Biology of Lipids , 1811 (10), 587-596.
https://doi.org/10.1016/j.bbalip.2011.07.004
Blazeck, J., Hill, A., Liu, L., Knight, R., Miller, J., Pan, A.,
Otoupal, P., & Alper, H. S. (2014). Harnessing Yarrowia lipolytica
lipogenesis to create a platform for lipid and biofuel production.Nature Communications , 5 (1), 3131.
https://doi.org/10.1038/ncomms4131
Cardenas, J., & Da Silva, N. A. (2014). Metabolic engineering ofSaccharomyces cerevisiae for the production of triacetic acid
lactone. Metabolic Engineering , 25 , 194-203.
https://doi.org/10.1016/j.ymben.2014.07.008
Cardenas, J., & Da Silva, N. A. (2016). Engineering cofactor and
transport mechanisms in Saccharomyces cerevisiae for enhanced
acetyl-CoA and polyketide biosynthesis. Metabolic Engineering ,36 , 80-89. https://doi.org/10.1016/j.ymben.2016.02.009
Chen, Y., Daviet, L., Schalk, M., Siewers, V., & Nielsen, J. (2013).
Establishing a platform cell factory through engineering of yeast
acetyl-CoA metabolism. Metabolic Engineering , 15 , 48-54.
https://doi.org/10.1016/j.ymben.2012.11.002
Chia, M., Schwartz, T. J., Shanks, B. H., & Dumesic, J. A. (2012).
Triacetic acid lactone as a potential biorenewable platform chemical.Green Chemistry , 14 (7), 1850-1853.
https://doi.org/10.1039/C2GC35343A
Coradetti, S. T., Pinel, D., Geiselman, G. M., Ito, M., Mondo, S. J.,
Reilly, M. C., Cheng, Y.-F., Bauer, S., Grigoriev, I. V., Gladden, J.
M., Simmons, B. A., Brem, R. B., Arkin, A. P., & Skerker, J. M. (2018).
Functional genomics of lipid metabolism in the oleaginous yeastRhodosporidium toruloides . eLife , 7 . Retrieved
2018/03//, from
Díaz, T., Fillet, S., Campoy, S., Vázquez, R., Viña, J., Murillo, J., &
Adrio, J. L. (2018). Combining evolutionary and metabolic engineering inRhodosporidium toruloides for lipid production with
non-detoxified wheat straw hydrolysates. Applied Microbiology and
Biotechnology , 102 (7), 3287-3300.
https://doi.org/10.1007/s00253-018-8810-2
Dinh, H. V., Suthers, P. F., Chan, S. H. J., Shen, Y., Xiao, T., Deewan,
A., Jagtap, S. S., Zhao, H., Rao, C. V., Rabinowitz, J. D., & Maranas,
C. D. (2019). A comprehensive genome-scale model forRhodosporidium toruloides IFO0880 accounting for functional
genomics and phenotypic data. Metabolic Engineering
Communications , 9 , e00101.
https://doi.org/10.1016/j.mec.2019.e00101
Dolan, S. K., & Welch, M. (2018). The Glyoxylate Shunt, 60 Years On.Annual Review of Microbiology , 72 (1), 309-330.
https://doi.org/10.1146/annurev-micro-090817-062257
Du, J., Shao, Z., & Zhao, H. (2011). Engineering microbial factories
for synthesis of value-added products. Journal of Industrial
Microbiology and Biotechnology , 38 (8), 873-890.
https://doi.org/10.1007/s10295-011-0970-3
Eckermann, S., Schröder, G., Schmidt, J., Strack, D., Edrada, R. A.,
Helariutta, Y., Elomaa, P., Kotilainen, M., Kilpeläinen, I., Proksch,
P., Teeri, T. H., & Schröder, J. (1998). New pathway to polyketides in
plants. Nature , 396 (6709), 387-390.
https://doi.org/10.1038/24652
Gerlt, J. A., Bouvier, J. T., Davidson, D. B., Imker, H. J., Sadkhin,
B., Slater, D. R., & Whalen, K. L. (2015). Enzyme Function
Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating
protein sequence similarity networks. Biochimica et Biophysica
Acta (BBA) - Proteins and Proteomics , 1854 (8), 1019-1037.
https://doi.org/10.1016/j.bbapap.2015.04.015
Gibson, D. G., Young, L., Chuang, R.-Y., Venter, J. C., Hutchison, C.
A., & Smith, H. O. (2009). Enzymatic assembly of DNA molecules up to
several hundred kilobases. Nature Methods , 6 (5), 343-345.
https://doi.org/10.1038/nmeth.1318
Jagtap, S. S., & Rao, C. V. (2018). Production of d-arabitol from
d-xylose by the oleaginous yeast Rhodosporidium toruloidesIFO0880. Applied Microbiology and Biotechnology , 102 (1),
143-151. https://doi.org/10.1007/s00253-017-8581-1
Jiao, X., Zhang, Y., Liu, X., Zhang, Q., Zhang, S., & Zhao, Z. K.
(2019). Developing a CRISPR/Cas9 System for Genome Editing in the
Basidiomycetous Yeast Rhodosporidium toruloides .Biotechnology Journal , 14 (7), 1900036.
https://doi.org/10.1002/biot.201900036
Keatinge-Clay, A. T. (2016). Stereocontrol within polyketide assembly
lines. Natural Product Reports , 33 (2), 141-149.
https://doi.org/10.1039/C5NP00092K
Kozak, B. U., van Rossum, H. M., Luttik, M. A., Akeroyd, M., Benjamin,
K. R., Wu, L., de Vries, S., Daran, J. M., Pronk, J. T., & van Maris,
A. J. (2014). Engineering acetyl coenzyme A supply: functional
expression of a bacterial pyruvate dehydrogenase complex in the cytosol
of Saccharomyces cerevisiae. mBio , 5 (5), e01696-01614.
https://doi.org/10.1128/mBio.01696-14
Lee, J. J., Chen, L., Cao, B., & Chen, W. N. (2016). EngineeringRhodosporidium toruloides with a membrane transporter facilitates
production and separation of carotenoids and lipids in a bi-phasic
culture. Appl Microbiol Biotechnol , 100 (2), 869-877.
https://doi.org/10.1007/s00253-015-7102-3
Li, Y., Qian, S., Dunn, R., & Cirino, P. C. (2018). EngineeringEscherichia coli to increase triacetic acid lactone (TAL)
production using an optimized TAL sensor-reporter system. J Ind
Microbiol Biotechnol , 45 (9), 789-793.
https://doi.org/10.1007/s10295-018-2062-0
Lian, J., Si, T., Nair, N. U., & Zhao, H. (2014). Design and
construction of acetyl-CoA overproducing Saccharomyces cerevisiaestrains. Metabolic Engineering , 24 , 139-149.
https://doi.org/10.1016/j.ymben.2014.05.010
Lin, X., Wang, Y., Zhang, S., Zhu, Z., Zhou, Y. J., Yang, F., Sun, W.,
Wang, X., & Zhao, Z. K. (2014). Functional integration of multiple
genes into the genome of the oleaginous yeast Rhodosporidium
toruloides . FEMS Yeast Research , 14 (4), 547-555.
https://doi.org/10.1111/1567-1364.12140
Liu, D., Geiselman, G. M., Coradetti, S., Cheng, Y.-F., Kirby, J.,
Prahl, J.-P., Jacobson, O., Sundstrom, E. R., Tanjore, D., Skerker, J.
M., & Gladden, J. (2020). Exploiting nonionic surfactants to enhance
fatty alcohol production in Rhodosporidium toruloides .Biotechnology and Bioengineering , 117 (5), 1418-1425.
https://doi.org/10.1002/bit.27285
Liu, H., Marsafari, M., Wang, F., Deng, L., & Xu, P. (2019).
Engineering acetyl-CoA metabolic shortcut for eco-friendly production of
polyketides triacetic acid lactone in Yarrowia lipolytica .Metabolic Engineering , 56 , 60-68.
https://doi.org/10.1016/j.ymben.2019.08.017
Liu, J.-J., Zhang, G.-C., Kwak, S., Oh, E. J., Yun, E. J., Chomvong, K.,
Cate, J. H. D., & Jin, Y.-S. (2019). Overcoming the thermodynamic
equilibrium of an isomerization reaction through oxidoreductive
reactions for biotransformation. Nature Communications ,10 (1), 1356. https://doi.org/10.1038/s41467-019-09288-6
Liu, S., Zhang, M., Ren, Y., Jin, G., Tao, Y., Lyu, L., Zhao, Z. K., &
Yang, X. (2021). Engineering Rhodosporidium toruloides for
limonene production. Biotechnology for Biofuels , 14 (1),
243. https://doi.org/10.1186/s13068-021-02094-7
Liu, X., Zhang, Y., Liu, H., Jiao, X., Zhang, Q., Zhang, S., & Zhao, Z.
K. (2019). RNA interference in the oleaginous yeast Rhodosporidium
toruloides . FEMS Yeast Research , 19 (3).
https://doi.org/10.1093/femsyr/foz031
Lyu, L., Chu, Y., Zhang, S., Zhang, Y., Huang, Q., Wang, S., & Zhao, Z.
K. (2021). Engineering the Oleaginous Yeast Rhodosporidium
toruloides for Improved Resistance Against Inhibitors in Biomass
Hydrolysates. Frontiers in bioengineering and biotechnology ,9 , 768934-768934. https://doi.org/10.3389/fbioe.2021.768934
Markham, K. A., Palmer, C. M., Chwatko, M., Wagner, J. M., Murray, C.,
Vazquez, S., Swaminathan, A., Chakravarty, I., Lynd, N. A., & Alper, H.
S. (2018). Rewiring Yarrowia lipolytica toward triacetic acid
lactone for materials generation. Proceedings of the National
Academy of Sciences , 115 (9), 2096.
https://doi.org/10.1073/pnas.1721203115
Nora, L. C., Wehrs, M., Kim, J., Cheng, J.-F., Tarver, A., Simmons, B.
A., Magnuson, J., Harmon-Smith, M., Silva-Rocha, R., Gladden, J. M.,
Mukhopadhyay, A., Skerker, J. M., & Kirby, J. (2019). A toolset of
constitutive promoters for metabolic engineering of Rhodosporidium
toruloides . Microbial Cell Factories , 18 (1), 117.
https://doi.org/10.1186/s12934-019-1167-0
Otoupal, P. B., Ito, M., Arkin, A. P., Magnuson, J. K., Gladden, J. M.,
& Skerker, J. M. (2019). Multiplexed CRISPR-Cas9-Based Genome Editing
of Rhodosporidium toruloides . mSphere , 4 (2).
https://doi.org/10.1128/mSphere.00099-19
Park, Y.-K., Nicaud, J.-M., & Ledesma-Amaro, R. (2018). The Engineering
Potential of Rhodosporidium toruloides as a Workhorse for
Biotechnological Applications. Trends in Biotechnology ,36 (3), 304-317.
https://doi.org/10.1016/j.tibtech.2017.10.013
Pomraning, K. R., Collett, J. R., Kim, J., Panisko, E. A., Culley, D.
E., Dai, Z., Deng, S., Hofstad, B. A., Butcher, M. G., & Magnuson, J.
K. (2019). Transcriptomic analysis of the oleaginous yeastLipomyces starkeyi during lipid accumulation on enzymatically
treated corn stover hydrolysate. Biotechnology for Biofuels ,12 (1), 162. https://doi.org/10.1186/s13068-019-1510-z
Robinson, J. A. (1991). Polyketide synthase complexes: their structure
and function in antibiotic biosynthesis. Philosophical
transactions of the Royal Society of London. Series B, Biological
sciences , 332 (1263), 107-114.
https://doi.org/10.1098/rstb.1991.0038
Saunders, L. P., Bowman, M. J., Mertens, J. A., Da Silva, N. A., &
Hector, R. E. (2015). Triacetic acid lactone production in industrialSaccharomyces yeast strains. J Ind Microbiol Biotechnol ,42 (5), 711-721. https://doi.org/10.1007/s10295-015-1596-7
Schultz, J. C., Cao, M., Mejia, A., & Zhao, H. (2021). CUT&RUN
Identifies Centromeric DNA Regions of Rhodotorula toruloidesIFO0880. FEMS Yeast Research , foab066.
https://doi.org/10.1093/femsyr/foab066
Schultz, J. C., Cao, M., & Zhao, H. (2019). Development of a
CRISPR/Cas9 system for high efficiency multiplexed gene deletion inRhodosporidium toruloides . Biotechnology and
Bioengineering , 116 (8), 2103-2109.
https://doi.org/10.1002/bit.27001
Shao, Z., Zhao, H., & Zhao, H. (2009). DNA assembler, an in vivo
genetic method for rapid construction of biochemical pathways.Nucleic acids research , 37 (2), e16-e16.
https://doi.org/10.1093/nar/gkn991
Sun, L., Lee, J. W., Yook, S., Lane, S., Sun, Z., Kim, S. R., & Jin,
Y.-S. (2021). Complete and efficient conversion of plant cell wall
hemicellulose into high-value bioproducts by engineered yeast.Nature Communications , 12 (1), 4975.
https://doi.org/10.1038/s41467-021-25241-y
Tang, S.-Y., Qian, S., Akinterinwa, O., Frei, C. S., Gredell, J. A., &
Cirino, P. C. (2013). Screening for Enhanced Triacetic Acid Lactone
Production by Recombinant Escherichia coli Expressing a Designed
Triacetic Acid Lactone Reporter. Journal of the American Chemical
Society , 135 (27), 10099-10103.
https://doi.org/10.1021/ja402654z
Vorapreeda, T., Thammarongtham, C., Cheevadhanarak, S., & Laoteng, K.
(2012). Alternative routes of acetyl-CoA synthesis identified by
comparative genomic analysis: involvement in the lipid production of
oleaginous yeast and fungi. Microbiology , 158 (1), 217-228.
https://doi.org/10.1099/mic.0.051946-0
Wang, G.-Y., Zhang, Y., Chi, Z., Liu, G.-L., Wang, Z.-P., & Chi, Z.-M.
(2015). Role of pyruvate carboxylase in accumulation of intracellular
lipid of the oleaginous yeast Yarrowia lipolytica ACA-DC 50109.Applied Microbiology and Biotechnology , 99 (4), 1637-1645.
https://doi.org/10.1007/s00253-014-6236-z
Wang, Y., Lin, X., Zhang, S., Sun, W., Ma, S., & Zhao, Z. K. (2016).
Cloning and evaluation of different constitutive promoters in the
oleaginous yeast Rhodosporidium toruloides. Yeast , 33 (3),
99-106. https://doi.org/https://doi.org/10.1002/yea.3145
Wen, Z., Zhang, S., Odoh, C. K., Jin, M., & Zhao, Z. K. (2020).Rhodosporidium toruloides - A potential red yeast chassis for
lipids and beyond. FEMS Yeast Research , 20 (5).
https://doi.org/10.1093/femsyr/foaa038
Xie, D., Shao, Z., Achkar, J., Zha, W., Frost, J. W., & Zhao, H.
(2006). Microbial synthesis of triacetic acid lactone.Biotechnology and Bioengineering , 93 (4), 727-736.
https://doi.org/10.1002/bit.20759
Xu, P., Ranganathan, S., Fowler, Z. L., Maranas, C. D., & Koffas, M. A.
G. (2011). Genome-scale metabolic network modeling results in minimal
interventions that cooperatively force carbon flux towards malonyl-CoA.Metabolic Engineering , 13 (5), 578-587.
https://doi.org/10.1016/j.ymben.2011.06.008
Yu, J., Landberg, J., Shavarebi, F., Bilanchone, V., Okerlund, A.,
Wanninayake, U., Zhao, L., Kraus, G., & Sandmeyer, S. (2018).
Bioengineering triacetic acid lactone production in Yarrowia
lipolytica for pogostone synthesis. Biotechnology and
Bioengineering , 115 (9), 2383-2388.
https://doi.org/10.1002/bit.26733
Zha, W., Rubin-Pitel, S. B., Shao, Z., & Zhao, H. (2009). Improving
cellular malonyl-CoA level in Escherichia coli via metabolic
engineering. Metabolic Engineering , 11 (3), 192-198.
https://doi.org/10.1016/j.ymben.2009.01.005
Zha, W., Shao, Z., Frost, J. W., & Zhao, H. (2004). Rational pathway
engineering of type I fatty acid synthase allows the biosynthesis of
triacetic acid lactone from D-glucose in vivo. Journal of the
American Chemical Society , 126 (14), 4534-4535.
https://doi.org/10.1021/ja0317271
Zhang, S., Skerker, J. M., Rutter, C. D., Maurer, M. J., Arkin, A. P.,
& Rao, C. V. (2016). Engineering Rhodosporidium toruloides for
increased lipid production. Biotechnology and Bioengineering ,113 (5), 1056-1066. https://doi.org/10.1002/bit.25864
Zhang, X.-K., Nie, M.-Y., Chen, J., Wei, L.-J., & Hua, Q. (2019).
Multicopy integrants of crt genes and co-expression of AMP deaminase
improve lycopene production in Yarrowia lipolytica . Journal
of Biotechnology , 289 , 46-54.
https://doi.org/10.1016/j.jbiotec.2018.11.009
Zhang, Y., Peng, J., Zhao, H., & Shi, S. (2021). Engineering oleaginous
yeast Rhodotorula toruloides for overproduction of fatty acid
ethyl esters. Biotechnology for Biofuels , 14 (1), 115.
https://doi.org/10.1186/s13068-021-01965-3
Zhu, Z., Zhang, S., Liu, H., Shen, H., Lin, X., Yang, F., Zhou, Y. J.,
Jin, G., Ye, M., Zou, H., & Zhao, Z. K. (2012). A multi-omic map of the
lipid-producing yeast Rhodosporidium toruloides . Nature
Communications , 3 (1), 1112.
https://doi.org/10.1038/ncomms2112
Table 1. List of plasmids and strains.