References
Antoniewicz, M.R., Kelleher, J.K., Stephanopoulos, G., 2006. Determination of confidence intervals of metabolic fluxes estimated from stable isotope measurements. Metab. Eng. 8, 324–337. doi: 10.1016/j.ymben.2006.01.004
Becker, J., Wittmann, C., 2012. Bio-based production of chemicals, materials and fuels - Corynebacterium glutamicum as versatile cell factory. Curr. Opin. Biotechnol. 23, 631-640. doi: 10.1016/j.copbio.2011.11.012
Bennett, B.D., Kimball, E.H., Gao, M., Osterhout, R., Van Dien, J.S. & Rabinowitz, J.D., 2009. Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat. Chem. Bio. 5, 593-599. doi: 10.1038/nchembio.186
Bierman, M., Logan, R., O’Brien, K., Seno, E.T., Rao, R.N., Schoner, B.E., 1992. Plasmid cloning vectors for the conjugal transfer of DNA from Escherichia coli to Streptomyces spp. Gene. 116, 43–49. doi: 10.1016/0378-1119(92)90627-2
Bojanowsa, K.R., Ruczaj, Z., Korszynka, D.S., Rafalski. A., 1973. Limiting reaction in activation of acylunits in biosynthesis of macrolide antibiotics. Antimicrob. Agents CH. 3, 162-167. doi: 10.1128/aac.3.2.162
Butler, M.S., 2008. Natural products to drugs: natural product-derived compounds in clinical trials. Nat. Prod. Rep. 25, 475–516. doi: 10.1039/b514294f
Chakraburtty, R., Bibb. M., 1997. The ppGpp synthetase gene(relA ) of Streptomyces coelicolor A3(2) play a conditional role I antibiotic production and morphological differentiation. J. Bacteriol. 18, 5854-5861. doi: 10.1128/jb.179.18.5854-5861.1997
Chan, Y.A., Podevels, A.M., Kevany, B.M., Thomas, G.M., 2009. Biosynthesis of polyketide synthase extender units. Nat. Prod. Rep. 1, 90–114. doi: 10.1039/B801658P
Cheah, Y.E., Young, J.D., 2018. Isotopically nonstationary metabolic flux analysis (INST-MFA): putting theory into practice. Curr. Opin. Biotechnol. 54, 80-87. doi: 10.1016/j.copbio.2018.02.013
Chen, Y., Deng, W., Wu, J., Qian, J., Chu, J., Zhuang, Y.P., Zhang, S.L., Liu, W., 2008. Genetic modulation of the overexpression of tailoring genes eryK and eryG leading to the improvement of erythromycin A purity and production in Saccharopolyspora erythraea fermentation. Appl. Environ. Microbiol. 74,1820–1828. doi: 10.1128/AEM.02770-07
Chen, Y., Huang, M.Z., Wang, Z.J., Chu, J., Zhuang, Y.P., Zhang, S.L., 2013. Controlling the feed rate of glucose and propanol for the enhancement of erythromycin production and exploration of propanol metabolism fate by quantitative metabolic flux analysis. Bioprocess Biosyst. Eng. 36, 1445-1453. doi:10.1007/s00449-013-0883-9
Chen, C.C., Hong, M., Chu, J., Huang, M.Z., Ouyang, L.M., Tian, X.W., Zhuang, Y.P., 2017. Blocking the flow of propionate into TCA cycle through a mutB knockout leads to a significant increase of erythromycin production by an industrial strain of Saccharopolyspora erythraea. Bioprocess Biosyst. Eng. 40, 201-209. doi: 10.1007/s00449-016-1687-5
Crown, S.B., Long, C.P., Antoniewicz, M.R., 2016. Optimal tracers for parallel labeling experiments and 13C metabolic flux analysis: A new precision and synergy scoring system. Metab. Eng. 38, 10-18. doi: 10.1016/j.ymben.2016.06.001
El-Enshasy, H.A., Mohamed, N.A., Farid, M.A., El-Diwany, A.I., 2008. Improvement of erythromycin production by Saccharopolyspora erythraea in molasses based medium through cultivation medium optimization. Bioresour. Technol. 99, 4263–4268. doi: 10.1016/j.biortech.2007.08.050
Fan, J., Ye, J.B., Kamphorst, J.J., Shlomi, T., Thompson, C.B. & Rabinowitz, J.D., 2014. Quantitative flux analysis reveals folate-dependent NADPH production. Nature. 510, 298-302. doi: 10.1038/nature13236
Hong, M., Huang, M.Z., Chu, J., Zhuang, Y.P., Zhang, S.L., 2016. Impacts of proline on the central metabolism of an industrial erythromycin-producing strain saccharopolyspora erythraea via13C labeling experiments. J. Biotechnol. 231,1-8. doi: 10.1016/j.jbiotec.2016.05.026
Hong, M., Mou, H., Liu, X.Y., Huang, M.Z., Chu, J., 2017.13C-assisted metabolomics analysis reveals the positive correlation between specific erythromycin production rate and intracellular propionyl-CoA pool size in Saccharopolyspora erythraea . Bioprocess Biosyst. Eng. 40, 1337-1348. doi: 10.1007/s00449-017-1792-0
Borodina, I., Siebring, J., Zhang, J., Smith, C.P., van Keulen, G., Dijkhuizen, L., Nielsen, J., 2008. Antibiotic Overproduction in Streptomyces coelicolor A3(2) Mediated by Phosphofructokinase Deletion. The J. Biol. Chem. 37, 25186 –25199. doi: 10.1074/jbc.M803105200
Koffas, M., Stephanopoulos, G., 2005. Strain improvement by metabolic engineering: lysine production as a case study for systems biology. Curr. Opin. Biotechnol. 16, 361–366. doi: 10.1016/j.copbio.2005.04.010
Jazmin, L.J., Xu, Y., Cheah Y.E., Adebiyi, A.O., Johnson, C.H., Young, J.D., 2017. Isotopically nonstationary 13C flux analysis of cyanobacterial isobutyraldehyde production. Metab. Eng. 42, 9-18. doi: 10.1016/j.ymben.2017.05.001
Li, Y.Y., Chang, X., Yu, W.B., Li, H., Ye, Z.Q., Yu, H., Liu, B.H., Zhang, Y., Zhang, S.L., Ye, B.C., Li, Y.X., 2013. Systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of S. erythraea E3 and NRRL23338 strains. Bmc Genomics. 14, 523. doi: 10.1186/1471-2164-14-523
Li, B., Qiu, B., Lee, D.S.M., Walton, Z.E., Ochocki, J.D., Mathew, L.K., Mancuso, A., Gade, T.P.F., Keith, B., Nissim, I. & Simon, M.C., 2014. Fructose-1,6-bisphosphatase opposes renal carcinoma progression. Nature. 513, 251-255. doi: 10.1038/nature13557
Liang, J.G., Chu, X.H., Xiong, Z.Q., Chu, J., Wang, Y.H., 2011. Oxygen uptake rate regulation during cell growth phase for improving avermectin B1a batch fermentation on a pilot scale (2 m3). Microbiol. Biotechnol. 27, 2639–2644. doi: 10.1007/s11274-011-0737-z
Liu, J., Chen, Y.F., Wang, W.W., Ren, M., Wu, P.P., Wang, Y.S., Li, C.R., Zhang, L.X., Wu, H., Weaver, D.T., Zhang, B.C., 2017. Engineering of an Lrp family regulator SACE_Lrp improves erythromycin production inSaccharopolyspora erythraea . Metab. Eng. 39, 29-37. doi: 10.1016/j.ymben.2016.10.012
Mashego, M.R., Rumbold, K., De Mey, M., Vandamme, E., Soetaert, W., Heijnen, J.J., 2007. Microbial metabolomics: past, present and future methodologies. Biotechnol. Lett. 1, 1–16. doi: 10.1007/s10529-006-9218-0
Matsushima, P., Broughton, M.C., Turne,r J.R., Baltz, R.H., 1994. Conjugal transfer of cosmid DNA from Escherichia coli to Saccharopolyspora spinosa: effects of chromosomal insertions on macrolide A83543 production. Gene. 146, 39–45. doi: 10.1016/0378-1119(94)90831-1
Mironov, V.A., Sergienko, O.V., Nastasyak, I.N., Danilenko, V. N., 2004. Biogenesis and regulation of biosynthesis of erythromycins inSaccharopolyspora erythraea . Appl. Biochem. Microbiol. 40, 531-541. doi: 10.1023/B:ABIM.0000046985.66328.7a
Mullen, A.R., Wheaton, W.W., Jin, E.S., Chen, P.H., Sullivan, L.B., Cheng, T.L, Yang, Y.F, Linehan, W. M., Chandel, N.S. & DeBerardinis, R.J., 2012. Reductive carboxylation supports growth in tumour cells with defective mitochondria. Nature. 481, 385-388. doi: 10.1038/nature10642
Oliynyk, M., Samborskyy, M., Lester, J.B., Mironenko, T., Scott, N., Dickens, S.,Haydock, S.F., Leadlay, P.F., 2007. Complete genome sequence of the erythromycin-producing bacterium Saccharopolyspora erythraea NRRL23338. Nat. Biotechnol. 25, 447–453. doi: 10.1038/nbt1297
Parekh, S., Vinci, V.A., Strobel, R.J., 2000. Improvement of microbial strains and fermentation processes. Appl. Microbiol. Biotechnol. 54, 287–301. doi: 10.1007/s002530000403
Reeves, A.R., Brikun, I.A., Cernota, W.H., Leach, B.I., Gonzalez, M.C., Weber, J.M., 2006. Effects of methylmalonyl-CoA mutase gene knockouts on erythromycin production in carbohydrate-based and oil-based fermentations of Saccharopolyspora erythraea. Ind. Microbiol. Biotechnol. 7, 600–609. doi: 10.1007/s10295-006-0094-3
Seifar, R.M., Ras, C., Deshmukh, A.T., Bekers, K.M., Suarez-Mendez, C.A., da Cruz, A.L.B., van Gulik, W.M., Heijnen, J.J., 2013. Quantitative analysis of intracellular coenzymes in Saccharomyces cerevisiae using ion pair reversed phase ultra high performance liquid chromatography tandem mass spectrometry. J Chromatogr A. 1311, 115–120. doi: 10.1016/j.chroma.2013.08.076
Wang, G., Wu, B.F., Zhao, J.F., Haringa, C., Xia, J.Y., Chu, J., Zhuang, Y.P., Zhang, S.L., Heijnen, J.J., van Gulik, W., Deshmukh, A.T., Noorman, H.J., 2018. Power Input Effects on Degeneration in Prolonged Penicillin Chemostat Cultures: A Systems Analysis at Flux, Residual Glucose, Metabolite and Transcript Levels. Biotechnol. Bioeng.115, 114-125. doi: 10.1002/bit.26447
Wang, Y., Wang, Y., Chu, J., Zhuang, Y., Zhang, L., Zhang, S., 2007. Improved production of erythromycin A by expression of a heterologous gene encoding S-adenosylmethionine synthetase. Appl. Microbiol. Biotechnol. 75, 837–842. doi: 10.1007/s00253-007-0894-z
Wright, J. A., Maeba, P., Sanwal, B.D., 1967. Allosteric regulation of the activity of citrate synthase of Escherichia coli by a-ketoglutarate. Biochem. Biophys. Res. Commun. 29, 34-38. doi: 10.1016/0006-291x(67)90536-0
Wu, J., Zhang, Q., Deng, W., Qian, J., Zhang, S., Liu, W., 2011. Toward improvement of erythromycin A production in an industrial Saccharopolyspora erythraea strain via facilitation of genetic manipulation with an artificial attB site for specific recombination. Appl. Environ. Microbiol. 77, 7508–7516. doi: 10.1128/AEM.06034-11
Wu, L., Mashego, M.R., van Dam, J.C., Proell, A.M., Vinke, J.L., Ras, C., van Winden, W.A., van Gulik, W.M., Heijnen, J.J., 2005. Quantitative analysis of the microbial metabolome by isotope dilution mass spectrometry using uniformly 13C-labeled cell extracts as internal standards. Anal. Biochem. 336, 164-171. doi: 10.1016/j.ab.2004.09.001
Young, J.D., Walther, J.L., Antoniewicz, M.R., Yoo, H., Stephanopoulos, G., 2008. An elementary metabolite unit (EMU) based method of isotopically nonstationary flux analysis. Biotechnol. Bioeng. 99, 686–699. doi: 10.1002/bit.21632
Young, J.D., 2014. INCA: a computational platform for isotopically non-stationary metabolic flux analysis. Bioinformatics. 30, 1333–1335. doi: 10.1093/bioinformatics/btu015
Zhang, Q., Chen, Y., Hong, M., Gao, Y., Chu, J., Zhuang, Y.P., Zhang, S.L., 2014. The dynamic regulation of nitrogen and phosphorus in the early phase of fermentation improves the erythromycin production by recombinant Saccharopolyspora erythraea strain. Bioresour. Bioprocess 1, 1–6. doi: 10.1186/s40643-014-0015-7
Zou, X., Hang, H.F., Chu, J., Zhuang, Y.P., Zhang, S.L., 2009. Enhancement of erythromycin A production with feeding available nitrogen sources in erythromycin biosynthesis phase. Bioresour. Technol. 100, 3358-3365. doi: 10.1016/j.biortech.2009.01.064