Construction and evolution of an Escherichia coli strain relying on nonoxidative glycolysis for sugar catabolism

Proceedings of the National Academy of Sciences of the United States of America

Volumn 115, Issue 14, 2018, Pages 3538-3546

  Lin, Paul P ^a   Jaeger, Alec J ^a   Wu, Tung Yun ^a   Xu, Sharon C ^a   Lee, Abraxa S ^a   Gao, Fanke ^a   Chen, Po Wei ^a   Liao, James C ^b  

^a University of California   (United States)

^b INSTITUTE OF BIOLOGICAL CHEMISTRY   (Taiwan)

Author keywords

Escherichia coli; Evolution; Glycolysis; Metabolic engineering; Synthetic biology

Indexed keywords

ACETYL COENZYME A; GLUCOSE; GLYOXYLIC ACID; PYRUVIC ACID;

ANAEROBIC FERMENTATION; ARTICLE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL STRAIN; CARBON METABOLISM; CATABOLISM; CITRIC ACID CYCLE; CONTROLLED STUDY; ESCHERICHIA COLI; GENE DELETION; GENE MUTATION; GENE OVEREXPRESSION; GLUCONEOGENESIS; GLUCOSE METABOLISM; GLYCOLYSIS; NONHUMAN; PRIORITY JOURNAL; SUGAR CATABOLISM; CARBOHYDRATE METABOLISM; CLASSIFICATION; ENERGY METABOLISM; FERMENTATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLIC ENGINEERING; METABOLISM; MUTATION;

ACETYL COENZYME A; CARBOHYDRATE METABOLISM; ENERGY METABOLISM; ESCHERICHIA COLI; FERMENTATION; GLUCOSE; GLYCOLYSIS; METABOLIC ENGINEERING; MUTATION;

EID: 85044859974     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1802191115     Document Type: Article

References (34)

1. Clomburg JM, Gonzalez R (2010) Biofuel production in Escherichia coli: The role of metabolic engineering and synthetic biology. Appl Microbiol Biotechnol 86:419–434.
2. Felnagle EA, Chaubey A, Noey EL, Houk KN, Liao JC (2012) Engineering synthetic recursive pathways to generate non-natural small molecules. Nat Chem Biol 8: 518–526.
3. Pokusaeva K, Fitzgerald GF, van Sinderen D (2011) Carbohydrate metabolism in Bifidobacteria. Genes Nutr 6:285–306.
4. Kocharin K, Siewers V, Nielsen J (2013) Improved polyhydroxybutyrate production by Saccharomyces cerevisiae through the use of the phosphoketolase pathway. Biotechnol Bioeng 110:2216–2224.
5. de Jong BW, Shi S, Siewers V, Nielsen J (2014) Improved production of fatty acid ethyl esters in Saccharomyces cerevisiae through up-regulation of the ethanol degradation pathway and expression of the heterologous phosphoketolase pathway. Microb Cell Fact 13:39.
6. 2 emission. J Biosci Bioeng 103:262–269.
7. Bogorad IW, Lin T-S, Liao JC (2013) Synthetic non-oxidative glycolysis enables complete carbon conservation. Nature 502:693–697.
8. Schaaper RM (1988) Mechanisms of mutagenesis in the Escherichia coli mutator mutD5: Role of DNA mismatch repair. Proc Natl Acad Sci USA 85:8126–8130.
9. Seta FD, Boschi-Muller S, Vignais ML, Branlant G (1997) Characterization of Escherichia coli strains with gapA and gapB genes deleted. J Bacteriol 179:5218–5221.
10. Nakahigashi K, et al. (2009) Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism. Mol Syst Biol 5:306.
11. Grabar TB, Zhou S, Shanmugam KT, Yomano LP, Ingram LO (2006) Methylglyoxal bypass identified as source of chiral contamination in l(+) and d(-)-lactate fermen-tations by recombinant Escherichia coli. Biotechnol Lett 28:1527–1535.
12. Boschi-Muller S, Azza S, Pollastro D, Corbier C, Branlant G (1997) Comparative enzymatic properties of GapB-encoded erythrose-4-phosphate dehydrogenase of Escherichia coli and phosphorylating glyceraldehyde-3-phosphate dehydrogenase. J Biol Chem 272:15106–15112.
13. Maloy SR, Nunn WD (1982) Genetic regulation of the glyoxylate shunt in Escherichia coli K-12. J Bacteriol 149:173–180.
14. Shimada T, Fujita N, Yamamoto K, Ishihama A (2011) Novel roles of cAMP receptor protein (CRP) in regulation of transport and metabolism of carbon sources. PLoS One 6:e20081.
15. Nakano M, Ogasawara H, Shimada T, Yamamoto K, Ishihama A (2014) Involvement of cAMP-CRP in transcription activation and repression of the pck gene encoding PEP carboxykinase, the key enzyme of gluconeogenesis. FEMS Microbiol Lett 355: 93–99.
16. Kotlarz D, Garreau H, Buc H (1975) Regulation of the amount and of the activity of phosphofructokinases and pyruvate kinases in Escherichia coli. Biochim Biophys Acta 381:257–268.
17. Weisser P, Krämer R, Sahm H, Sprenger GA (1995) Functional expression of the glucose transporter of Zymomonas mobilis leads to restoration of glucose and fructose uptake in Escherichia coli mutants and provides evidence for its facilitator action. J Bacteriol 177:3351–3354.
18. Meyer D, Schneider-Fresenius C, Horlacher R, Peist R, Boos W (1997) Molecular characterization of glucokinase from Escherichia coli K-12. J Bacteriol 179:1298–1306.
19. Babul J, Guixé V (1983) Fructose bisphosphatase from Escherichia coli. Purification and characterization. Arch Biochem Biophys 225:944–949.
20. Hines JK, Fromm HJ, Honzatko RB (2006) Novel allosteric activation site in Escherichia coli fructose-1,6-bisphosphatase. J Biol Chem 281:18386–18393.
21. Steinsiek S, Bettenbrock K (2012) Glucose transport in Escherichia coli mutant strains with defects in sugar transport systems. J Bacteriol 194:5897–5908.
22. Quail MA, Guest JR (1995) Purification, characterization and mode of action of PdhR, the transcriptional repressor of the pdhR-aceEF-lpd operon of Escherichia coli. Mol Microbiol 15:519–529.
23. Zhang Z, et al. (2005) Functional interactions between the carbon and iron utilization regulators, Crp and Fur, in Escherichia coli. J Bacteriol 187:980–990.
24. Lee Y, Lafontaine Rivera JG, Liao JC (2014) Ensemble Modeling for robustness analysis in engineering non-native metabolic pathways. Metab Eng 25:63–71.
25. Dong T, Schellhorn HE (2009) Control of RpoS in global gene expression of Escherichia coli in minimal media. Mol Genet Genomics 281:19–33.
26. Avison MB, Horton RE, Walsh TR, Bennett PM (2001) Escherichia coli CreBC is a global regulator of gene expression that responds to growth in minimal media. J Biol Chem 276:26955–26961.
27. Oberto J (2010) FITBAR: A web tool for the robust prediction of prokaryotic regulons. BMC Bioinformatics 11:554.
28. Plumbridge J, Kolb A (1995) Nag repressor-operator interactions: Protein-DNA contacts cover more than two turns of the DNA helix. J Mol Biol 249:890–902.
29. Tracy BP, Jones SW, Fast AG, Indurthi DC, Papoutsakis ET (2012) Clostridia: The importance of their exceptional substrate and metabolite diversity for biofuel and biorefinery applications. Curr Opin Biotechnol 23:364–381.
30. 2-fixation pathways to support synthetic biology strategies for production of fuels and chemicals. Curr Opin Chem Eng 1:380–395.
31. Schramm M, Klybas V, Racker E (1958) Phosphorolytic cleavage of fructose-6-phosphate by fructose-6-phosphate phosphoketolase from Acetobacter xylinum. J Biol Chem 233:1283–1288.
32. Fandi KG, Ghazali HM, Yazid AM, Raha AR (2001) Purification and N-terminal amino acid sequence of fructose-6-phosphate phosphoketolase from Bifidobacterium longum BB536. Lett Appl Microbiol 32:235–239.
33. Meile L, Rohr LM, Geissmann TA, Herensperger M, Teuber M (2001) Characterization of the D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase gene (xfp) from Bifidobacterium lactis. J Bacteriol 183:2929–2936.
34. Liu L, et al. (2012) Phosphoketolase pathway for xylose catabolism in Clostridium acetobutylicum revealed by 13C metabolic flux analysis. J Bacteriol 194:5413–5422.