Abstract
The capability of Escherichia coli to catabolize d-xylonate is a crucial component for building and optimizing the Dahms pathway. It relies on the inherent dehydratase and keto-acid aldolase activities of E. coli. Although the biochemical characteristics of these enzymes are known, their inherent expression regulation remains unclear. This knowledge is vital for the optimization of d-xylonate assimilation, especially in addressing the problem of d-xylonate accumulation, which hampers both cell growth and target product formation. In this report, molecular biology techniques and synthetic biology tools were combined to build a simple genetic switch controller for d-xylonate. First, quantitative and relative expression analysis of the gene clusters involved in d-xylonate catabolism were performed, revealing two d-xylonate-inducible operons, yagEF and yjhIHG. The 5′-flanking DNA sequence of these operons were then subjected to reporter gene assays which showed PyjhI to have low background activity and wide response range to d-xylonate. A PyjhI-driven synthetic genetic switch was then constructed containing feedback control to autoregulate d-xylonate accumulation and to activate the expression of the genes for 1,2,4-butanetriol (BTO) production. The genetic switch effectively reduced d-xylonate accumulation, which led to 31% BTO molar yield, the highest for direct microbial fermentation systems thus far. This genetic switch can be further modified and employed in the production of other compounds from d-xylose through the xylose oxidative pathway.
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References
Beisel CL, Afroz T (2016) Rethinking the hierarchy of sugar utilization in bacteria. J Bacteriol 198:374–376. https://doi.org/10.1128/JB.00890-15
Brouns SJJ, Walther J, Snijders APL, van de Werken HJG, Willemen HLDM, Worm P, de Vos MGJ, Andersson A, Lundgren M, Mazon HFM, van den Heuvel RHH, Nilsson P, Salmon L, de Vos WM, Wright PC, Bernander R, van der Oost J (2006) Identification of the missing links in prokaryotic pentose oxidation pathways: evidence for enzyme recruitment. J Biol Chem 281:27378–27388. https://doi.org/10.1074/jbc.M605549200
Cabulong RB, Valdehuesa KNG, Ramos KRM, Nisola GM, Lee W-K, Lee CR, Chung W-J (2017) Enhanced yield of ethylene glycol production from D-xylose by pathway optimization in Escherichia coli. Enzym Microb Technol 97:11–20. https://doi.org/10.1016/j.enzmictec.2016.10.020
Cabulong RB, Lee W-K, Bañares AB, Ramos KRM, Nisola GM, Valdehuesa KNG, Chung W-J (2018a) Engineering Escherichia coli for glycolic acid production from D-xylose through the Dahms pathway and glyoxylate bypass. Appl Microbiol Biotechnol 102:2179–2189. https://doi.org/10.1007/s00253-018-8744-8
Cabulong RB, Valdehuesa KNG, Bañares AB, Ramos KRM, Nisola GM, Lee W-K, Chung W-J (2018b) Improved cell growth and biosynthesis of glycolic acid by overexpression of membrane-bound pyridine nucleotide transhydrogenase. J Ind Microbiol Biotechnol 46:159–169. https://doi.org/10.1007/s10295-018-2117-2
Cao Y, Niu W, Guo J, Xian M, Liu H (2015) Biotechnological production of 1,2,4-butanetriol: an efficient process to synthesize energetic material precursor from renewable biomass. Sci Rep 5:18149. https://doi.org/10.1038/srep18149
Chen YY, Galloway KE, Smolke CD (2012) Synthetic biology: advancing biological frontiers by building synthetic systems. Genome Biol 13:240. https://doi.org/10.1186/gb-2012-13-2-240
Choi SY, Park SJ, Kim WJ, Yang JE, Lee H, Shin J, Lee SY (2016) One-step fermentative production of poly(lactate-co-glycolate) from carbohydrates in Escherichia coli. Nat Biotechnol 34:435–440. https://doi.org/10.1038/nbt.3485
Chung CT, Niemela SL, Miller RH (1989) One-step preparation of competent Escherichia coli: transformation and storage of bacterial cells in the same solution. Proc Natl Acad Sci U S A 86:2172–2175
Dahms AS (1974) 3-Deoxy-D-pentulosonic acid aldolase and its role in a new pathway of D-xylose degradation. Biochem Biophys Res Comm 60:1433–1439. https://doi.org/10.1016/0006-291X(74)90358-1
Gao Q, Wang X, Hu S, Xu N, Jiang M, Ma C, Yang J, Xu S, Chen K, Ouyang P (2019) High-yield production of D-1,2,4-butanetriol from lignocellulose-derived xylose by using a synthetic enzyme cascade in a cell-free system. J Biotechnol 292:76–83. https://doi.org/10.1016/j.jbiotec.2019.01.004
Gibson DG, Young L, Chuang R-Y, Venter JC, Hutchison CA, Smith HO (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Meth 6:343–345. https://doi.org/10.1038/nmeth.1318
Görke B, Stülke J (2008) Carbon catabolite repression in bacteria: many ways to make the most out of nutrients. Nat Rev Microbiol 6:613–624. https://doi.org/10.1038/nrmicro1932
Green MR, Sambrook J (2012) Molecular cloning: a laboratory manual, 4th edn. Cold Spring Harbor Laboratory Press, New York
Hu S, Gao Q, Wang X, Yang J, Xu N, Chen K, Xu S, Ouyang P (2018) Efficient production of D-1,2,4-butanetriol from D-xylose by engineered Escherichia coli whole-cell biocatalysts. Front Chem Sci Eng 12:772–779. https://doi.org/10.1007/s11705-018-1731-x
Jiang Y, Liu W, Cheng T, Cao Y, Zhang R, Xian M (2015) Characterization of D-xylonate dehydratase YjhG from Escherichia coli. Bioengineered 6:227–232. https://doi.org/10.1080/21655979.2015.1040208
Kremers G-J, Goedhart J, van den Heuvel DJ, Gerritsen HC, Gadella TWJ (2007) Improved green and blue fluorescent proteins for expression in bacteria and mammalian cells. Biochemistry 46:3775–3783. https://doi.org/10.1021/bi0622874
Liu H, Lu T (2015) Autonomous production of 1,4-butanediol via a de novo biosynthesis pathway in engineered Escherichia coli. Metab Eng 29:135–141. https://doi.org/10.1016/j.ymben.2015.03.009
Liu H, Valdehuesa KNG, Nisola GM, Ramos KRM, Chung W-J (2012) High yield production of D-xylonic acid from D-xylose using engineered Escherichia coli. Bioresour Technol 115:244–248. https://doi.org/10.1016/j.biortech.2011.08.065
Liu H, Ramos KRM, Valdehuesa KNG, Nisola GM, Lee W-K, Chung W-J (2013) Biosynthesis of ethylene glycol in Escherichia coli. Appl Microbiol Biotechnol 97:3409–3417. https://doi.org/10.1007/s00253-012-4618-7
Pédelacq J-D, Cabantous S, Tran T, Terwilliger TC, Waldo GS (2006) Engineering and characterization of a superfolder green fluorescent protein. Nat Biotechnol 24:79–88. https://doi.org/10.1038/nbt1172
Radek A, Krumbach K, Gätgens J, Wendisch VF, Wiechert W, Bott M, Noack S, Marienhagen J (2014) Engineering of Corynebacterium glutamicum for minimized carbon loss during utilization of D-xylose containing substrates. J Biotechnol 192:156–160. https://doi.org/10.1016/j.jbiotec.2014.09.026
Reese MG (2001) Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput Chem 26:51–56. https://doi.org/10.1016/S0097-8485(01)00099-7
Salusjärvi L, Toivari M, Vehkomäki M-L, Koivistoinen O, Mojzita D, Niemelä K, Penttilä M, Ruohonen L (2017) Production of ethylene glycol or glycolic acid from D-xylose in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 14:127–113. https://doi.org/10.1007/s00253-017-8547-3
Shimada T, Yamazaki Y, Tanaka K, Ishihama A (2014) The whole set of constitutive promoters recognized by RNA polymerase RpoD holoenzyme of Escherichia coli. PLoS One 9:e90447. https://doi.org/10.1371/journal.pone.0090447
Shimada T, Momiyama E, Yamanaka Y, Watanabe H, Yamamoto K, Ishihama A (2017) Regulatory role of XynR (YagI) in catabolism of xylonate in Escherichia coli K-12. FEMS Microbiol Lett 364:2926. https://doi.org/10.1093/femsle/fnx220
Shu X, Shaner NC, Yarbrough CA, Tsien RY, Remington SJ (2006) Novel chromophores and buried charges control color in mFruits. Biochemistry 45:9639–9647. https://doi.org/10.1021/bi060773l
Solovyev VV, Salamov A (2011) Automatic annotation of microbial genomes and metagenomic sequences. In: Li RW (ed) Metagenomics and its applications in agriculture, biomedicine and environmental studies. Nova Science Publishers, New York, pp 61–78
Stephens C, Christen B, Fuchs T, Sundaram V, Watanabe K, Jenal U (2007) Genetic analysis of a novel pathway for D-xylose metabolism in Caulobacter crescentus. J Bacteriol 189:2181–2185. https://doi.org/10.1128/JB.01438-06
Sun L, Yang F, Sun H, Zhu T, Li X, Li Y, Xu Z, Zhang Y (2016) Synthetic pathway optimization for improved 1,2,4-butanetriol production. J Ind Microbiol Biotechnol 43:67–78. https://doi.org/10.1007/s10295-015-1693-7
Umarov RK, Solovyev VV (2017) Recognition of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks. PLoS One 12:e0171410. https://doi.org/10.1371/journal.pone.0171410
Valdehuesa KNG, Liu H, Ramos KRM, Park SJ, Nisola GM, Lee W-K, Chung W-J (2014) Direct bioconversion of D-xylose to 1,2,4-butanetriol in an engineered Escherichia coli. Process Biochem 49:25–32. https://doi.org/10.1016/j.procbio.2013.10.002
Valdehuesa KNG, Lee W-K, Ramos KRM, Cabulong RB, Choi J, Liu H, Nisola GM, Chung W-J (2015) Identification of aldehyde reductase catalyzing the terminal step for conversion of xylose to butanetriol in engineered Escherichia coli. Bioprocess Biosyst Eng 38:1761–1772. https://doi.org/10.1007/s00449-015-1417-4
Valdehuesa KNG, Ramos KRM, Nisola GM, Bañares AB, Cabulong RB, Lee W-K, Liu H, Chung W-J (2018) Everyone loves an underdog: metabolic engineering of the xylose oxidative pathway in recombinant microorganisms. Appl Microbiol Biotechnol 102:7703–7716. https://doi.org/10.1007/s00253-018-9186-z
Venayak N, Anesiadis N, Cluett WR, Mahadevan R (2015) Engineering metabolism through dynamic control. Curr Opin Biotechnol 34:142–152. https://doi.org/10.1016/j.copbio.2014.12.022
Vlahoviček K, Kaján L, Pangor S (2003) DNA analysis servers: plot.it, bend.it, model.it and IS. Nucl Acids Res 31:3686–3687. https://doi.org/10.1093/nar/gkg559
Wang X, Xu N, Hu S, Yang J, Gao Q, Xu S, Chen K, Ouyang P (2018) D-1,2,4-Butanetriol production from renewable biomass with optimization of synthetic pathway in engineered Escherichia coli. Bioresour Technol 250:406–412. https://doi.org/10.1016/j.biortech.2017.11.062
Weimberg R (1961) Pentose oxidation by Pseudomonas fragi. J Biol Chem 236:629–635
Xu P, Vansiri A, Bhan N, Koffas MAG (2012) ePathBrick: a synthetic biology platform for engineering metabolic pathways in E. coli. ACS Synth Biol 1:256–266. https://doi.org/10.1021/sb300016b
Zhang N, Wang J, Zhang Y, Gao H (2016) Metabolic pathway optimization for biosynthesis of 1,2,4-butanetriol from xylose by engineered Escherichia coli. Enzym Microb Technol 93-94:51–58. https://doi.org/10.1016/j.enzmictec.2016.07.007
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This work was supported by Korea Research Fellowship Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT (2015H1D3A1062172 and 2016R1C1B1013252) and by the Ministry of Education (2018R1D1A1B07043993).
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Bañares, A.B., Valdehuesa, K.N.G., Ramos, K.R.M. et al. Discovering a novel d-xylonate-responsive promoter: the PyjhI-driven genetic switch towards better 1,2,4-butanetriol production. Appl Microbiol Biotechnol 103, 8063–8074 (2019). https://doi.org/10.1007/s00253-019-10073-0
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DOI: https://doi.org/10.1007/s00253-019-10073-0