Protein Acylation Affects the Artificial Biosynthetic Pathway for Pinosylvin Production in Engineered E. coli

ACS Chemical Biology

Volumn 13, Issue 5, 2018, Pages 1200-1208

  Xu, Jun Yu ^a,b,c   Xu, Ya ^c   Chu, Xiaohe ^a   Tan, Minjia ^b   Ye, Bang Ce ^a,c  

^a ZHEJIANG UNIVERSITY OF TECHNOLOGY   (China)

^b SHANGHAI INSTITUTE OF MATERIA MEDICA   (China)

^c EAST CHINA UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

LYSINE; MALONYL COENZYME A; PINOSYLVIN; PROTEOME; STILBENE; SYNTHETASE; ESCHERICHIA COLI PROTEIN; STILBENE DERIVATIVE;

ACYLATION; ARTICLE; BIOSYNTHESIS; CHEMICAL MODIFICATION; ESCHERICHIA COLI; MALONYLATION; METABOLIC ENGINEERING; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN PROCESSING; SYNTHETIC BIOLOGY; TRANSGENIC MICROORGANISM; GENETICS; METABOLISM;

ACYLATION; BIOSYNTHETIC PATHWAYS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; METABOLIC ENGINEERING; PROTEIN PROCESSING, POST-TRANSLATIONAL; STILBENES;

EID: 85047258589     PISSN: 15548929     EISSN: 15548937     Source Type: Journal    
DOI: 10.1021/acschembio.7b01068     Document Type: Article

References (47)

1. Lee, J. W., Na, D., Park, J. M., Lee, J., Choi, S., and Lee, S. Y. (2012) Systems metabolic engineering of microorganisms for natural and non-natural chemicals. Nat. Chem. Biol. 8, 536-546, 10.1038/nchembio.970
2. Nielsen, J. and Keasling, J. D. (2011) Synergies between synthetic biology and metabolic engineering. Nat. Biotechnol. 29, 693-695, 10.1038/nbt.1937
3. Seyedsayamdost, M. R. and Clardy, J. (2014) Natural products and synthetic biology. ACS Synth. Biol. 3, 745-747, 10.1021/sb400025p
4. Vickers, C. E., Blank, L. M., and Krömer, J. O. (2010) Grand Challenge Commentary: Chassis cells for industrial biochemical production. Nat. Chem. Biol. 6, 875-877, 10.1038/nchembio.484
5. Lee, S. Y. and Kim, H. U. (2015) Systems strategies for developing industrial microbial strains. Nat. Biotechnol. 33, 1061-1072, 10.1038/nbt.3365
6. Carbonellballestero, M., Garciaramallo, E., Montañez, R., Rodriguezcaso, C., and Macía, J. (2016) Dealing with the genetic load in bacterial synthetic biology circuits: convergences with the Ohm's law. Nucleic Acids Res. 44, 496-507, 10.1093/nar/gkv1280
7. Lynch, M. and Marinov, G. K. (2015) The bioenergetic costs of a gene. Proc. Natl. Acad. Sci. U. S. A. 112, 15690-15695, 10.1073/pnas.1514974112
8. Weiße, A. Y., Oyarzún, D. A., Danos, V., and Swain, P. S. (2015) Mechanistic links between cellular trade-offs, gene expression, and growth. Proc. Natl. Acad. Sci. U. S. A. 112, 1038-1047, 10.1073/pnas.1416533112
9. Borkowski, O., Ceroni, F., Stan, G. B., and Ellis, T. (2016) Overloaded and stressed: whole-cell considerations for bacterial synthetic biology. Curr. Opin. Microbiol. 33, 123-130, 10.1016/j.mib.2016.07.009
10. Krivoruchko, A., Zhang, Y., Siewers, V., Chen, Y., and Nielsen, J. (2015) Microbial acetyl-CoA metabolism and metabolic engineering. Metab. Eng. 28, 28-42, 10.1016/j.ymben.2014.11.009
11. Chong, J., Poutaraud, A., and Hugueney, P. (2009) Metabolism and roles of stilbenes in plants. Plant Sci. 177, 143-155, 10.1016/j.plantsci.2009.05.012
12. Meadows, A. L., Hawkins, K. M., Tsegaye, Y., Antipov, E., Kim, Y., Raetz, L., Dahl, R. H., Tai, A., Mahatdejkulmeadows, T., Lan, X. et al. (2016) Rewriting yeast central carbon metabolism for industrial isoprenoid production. Nature 537, 694-697, 10.1038/nature19769
13. Leonard, E., Yan, Y., Fowler, Z. L., Li, Z., Lim, C. G., Lim, K. H., and Koffas, M. A. G. (2008) Strain improvement of recombinant Escherichia coli for efficient production of plant flavonoids. Mol. Pharmaceutics 5, 257-265, 10.1021/mp7001472
14. van Rossum, H. M., Kozak, B. U., Pronk, J. T., and van Maris, A. J. (2016) Engineering cytosolic acetyl-coenzyme A supply in Saccharomyces cerevisiae: Pathway stoichiometry, free-energy conservation and redox-cofactor balancing. Metab. Eng. 36, 99-115, 10.1016/j.ymben.2016.03.006
15. Hong, K. K. and Nielsen, J. (2012) Metabolic engineering of Saccharomyces cerevisiae: a key cell factory platform for future biorefineries. Cell. Mol. Life Sci. 69, 2671-2690, 10.1007/s00018-012-0945-1
16. Menzies, K. J., Zhang, H., Katsyuba, E., and Auwerx, J. (2016) Protein acetylation in metabolism-metabolites and cofactors. Nat. Rev. Endocrinol. 12, 43-60, 10.1038/nrendo.2015.181
17. Choudhary, C., Weinert, B. T., Nishida, Y., Verdin, E., and Mann, M. (2014) The growing landscape of lysine acetylation links metabolism and cell signalling. Nat. Rev. Mol. Cell Biol. 15, 536-550, 10.1038/nrm3841
18. Choudhary, C., Kumar, C., Gnad, F., Nielsen, M. L., Rehman, M., Walther, T. C., Olsen, J. V., and Mann, M. (2009) Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 325, 834-840, 10.1126/science.1175371
19. Sabari, B. R., Zhang, D., Allis, C. D., and Zhao, Y. (2017) Metabolic regulation of gene expression through histone acylations. Nat. Rev. Mol. Cell Biol. 18, 90-101, 10.1038/nrm.2016.140
20. Xie, Z., Zhang, D., Chung, D., Tang, Z., Huang, H., Dai, L., Qi, S., Li, J., Colak, G., Yue, C. et al. (2016) Metabolic regulation of gene expression by histone lysine β-hydroxybutyrylation. Mol. Cell 62, 194-206, 10.1016/j.molcel.2016.03.036
21. Chen, Y., Sprung, R., Tang, Y., Ball, H., Sangras, B., Kim, S. C., Falck, J. R., Peng, J., Gu, W., and Zhao, Y. (2007) Lysine propionylation and butyrylation are novel post-translational modifications in histones. Mol. Cell. Proteomics 6, 812-819, 10.1074/mcp.M700021-MCP200
22. Tan, M., Luo, H., Lee, S., Jin, F., Yang, J. S., Montellier, E., Buchou, T., Cheng, Z., Rousseaux, S., Rajagopal, N. et al. (2011) Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 146, 1016-1028, 10.1016/j.cell.2011.08.008
23. Zhang, Z., Tan, M., Xie, Z., Dai, L., Chen, Y., and Zhao, T. (2011) Identification of lysine succinylation as a new post-translational modification. Nat. Chem. Biol. 7, 58-63, 10.1038/nchembio.495
24. Du, J., Zhou, Y., Su, X., Yu, J. J., Khan, S., Jiang, H., Kim, J., Woo, J., Kim, J. H., Choi, B. H. et al. (2011) Sirt5 is a NAD-dependent protein lysine demalonylase and desuccinylase. Science 334, 806-809, 10.1126/science.1207861
25. Tan, M., Peng, C., Anderson, K. A., Chhoy, P., Xie, Z., Dai, L., Park, J., Chen, Y., Huang, H., Zhang, Y. et al. (2014) Lysine glutarylation is a protein posttranslational modification regulated by SIRT5. Cell Metab. 19, 605-617, 10.1016/j.cmet.2014.03.014
26. Dai, L., Peng, C., Montellier, E., Lu, Z., Chen, Y., Ishii, H., Debernardi, A., Buchou, T., Rousseaux, S., Jin, F. et al. (2014) Lysine 2-hydroxyisobutyrylation is a widely distributed active histone mark. Nat. Chem. Biol. 10, 365-370, 10.1038/nchembio.1497
27. Baeza, J., Smallegan, M. J., and Denu, J. M. (2016) Mechanisms and dynamics of protein acetylation in mitochondria. Trends Biochem. Sci. 41, 231-244, 10.1016/j.tibs.2015.12.006
28. Bernal, V., Castañocerezo, S., Gallegojara, J., Ecija-Conesa, é., de Diego, D. T., Iborra, J. L., and Cánovas, M. (2014) Regulation of bacterial physiology by lysine acetylation of proteins. New Biotechnol. 31, 586-595, 10.1016/j.nbt.2014.03.002
29. Hentchel, K. L. and Escalantesemerena, J. C. (2015) Acylation of biomolecules in prokaryotes: a widespread strategy for the control of biological function and metabolic stress. Microbiol. Mol. Biol. Rev. 79, 321-346, 10.1128/MMBR.00020-15
30. Ren, J., Sang, Y., Lu, J., and Yao, Y. F. (2017) Protein acetylation and its role in bacterial virulence. Trends Microbiol. 25, 768-779, 10.1016/j.tim.2017.04.001
31. van SummerenWesenhagen, P. V. and Marienhagen, J. (2015) Metabolic engineering of Escherichia coli for the synthesis of the plant polyphenol pinosylvin. Appl. Environ. Microbiol. 81, 840-849, 10.1128/AEM.02966-14
32. Colak, G., Pougovkina, O., Dai, L., Tan, M., te Brinke, H., Huang, H., Cheng, Z., Park, J., Wan, X., Liu, X. et al. (2015) Proteomic and biochemical studies of lysine malonylation suggest its malonic aciduria-associated regulatory role in mitochondrial function and fatty acid oxidation. Mol. Cell. Proteomics 14, 3056-3071, 10.1074/mcp.M115.048850
33. Qian, L., Nie, L., Chen, M., Liu, P., Zhu, J., Zhai, L., Tao, S., Cheng, Z., Zhao, Y., and Tan, M. (2016) Global profiling of protein lysine malonylation in Escherichia coli reveals its role in energy metabolism. J. Proteome Res. 15, 2060-2071, 10.1021/acs.jproteome.6b00264
34. Ritter, H. and Schulz, G. E. (2004) Structural basis for the entrance into the phenylpropanoid metabolism catalyzed by phenylalanine ammonia-lyase. Plant Cell 16, 3426-3436, 10.1105/tpc.104.025288
35. Conti, E., Stachelhaus, T., Marahiel, M. A., and Brick, P. (1997) Structural basis for the activation of phenylalanine in the non-ribosomal biosynthesis of gramicidin S. EMBO J. 16, 4174-4183, 10.1093/emboj/16.14.4174
36. Morita, H., Wanibuchi, K., Nii, H., Kato, R., Sugio, S., and Abe, I. (2010) Morita, H. et al. Structural basis for the one-pot formation of the diarylheptanoid scaffold by curcuminoid synthase from Oryza sativa. Proc. Natl. Acad. Sci. U. S. A. 107, 19778-19783, 10.1073/pnas.1011499107
37. Austin, M. B., Bowman, M. E., Ferrer, J. L., Schröder, J., and Noel, J. P. (2004) An aldol switch discovered in stilbene synthases mediates cyclization specificity of type III polyketide synthases. Chem. Biol. 11, 1179-1194, 10.1016/j.chembiol.2004.05.024
38. Xu, J. Y., Xu, Z., Zhou, Y., and Ye, B. C. (2016) Lysine malonylome may affect the central metabolism and erythromycin biosynthesis pathway in Saccharopolyspora erythraea. J. Proteome Res. 15, 1685-1701, 10.1021/acs.jproteome.6b00131
39. Ma, Y., Yang, M., Lin, X., Liu, X., Huang, H., and Ge, F. (2017) Malonylome analysis reveals the involvement of lysine malonylation in metabolism and photosynthesis in cyanobacteria. J. Proteome Res. 16, 2030-2043, 10.1021/acs.jproteome.7b00017
40. Xie, L., Wang, X., Zeng, J., Zhou, M., Duan, X., Li, Q., Zhang, Z., Luo, H., Pang, L., Li, W. et al. (2015) Proteome-wide lysine acetylation profiling of the human pathogen Mycobacterium tuberculosis. Int. J. Biochem. Cell Biol. 59, 193-202, 10.1016/j.biocel.2014.11.010
41. Rollié, S., Mangold, M., and Sundmacher, K. (2012) Designing biological systems: Systems engineering meets synthetic biology. Chem. Eng. Sci. 69, 1-29, 10.1016/j.ces.2011.10.068
42. Kim, E., Moore, B. S., and Yoon, Y. J. (2015) Reinvigorating natural product combinatorial biosynthesis with synthetic biology. Nat. Chem. Biol. 11, 649-659, 10.1038/nchembio.1893
43. Khalil, A. S. and Collins, J. J. (2010) Synthetic biology: applications come of age. Nat. Rev. Genet. 11, 367-379, 10.1038/nrg2775
44. Agapakis, C. M., Boyle, P. M., and Silver, P. A. (2012) Natural strategies for the spatial optimization of metabolism in synthetic biology. Nat. Chem. Biol. 8, 527-535, 10.1038/nchembio.975
45. Lynch, S. A. and Gill, R. T. (2012) Synthetic biology: New strategies for directing design. Metab. Eng. 14, 205-211, 10.1016/j.ymben.2011.12.007
46. Boersema, P. J., Raijmakers, R., Lemeer, S., Mohammed, S., and Heck, A. J. (2009) Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics. Nat. Protoc. 4, 484-494, 10.1038/nprot.2009.21
47. Bertram, R. M., Takemoto, J. K., Remsberg, C. M., Vegavilla, K. R., Sablani, S., and Davies, N. M. (2010) High-performance liquid chromatographic analysis: applications to nutraceutical content and urinary disposition of oxyresveratrol in rats. Biomed. Chromatogr. 24, 516-521, 10.1002/bmc.1320