Construction of polyketide overproducing Escherichia coli strains via synthetic antisense RNAs based on in silico fluxome analysis and comparative transcriptome analysis

Biotechnology Journal

Volumn 11, Issue 4, 2016, Pages 530-541

  Meng, Hai Lin ^a,b   Xiong, Zhi Qiang ^a   Song, Shu Jie ^a,c   Wang, Jianfeng ^a   Wang, Yong ^a  

^a INSTITUTE OF PLANT PHYSIOLOGY AND ECOLOGY   (China)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^c SHANGHAI OCEAN UNIVERSITY   (China)

Author keywords

Antisense RNA; Comparative transcriptome analysis; In silico fluxome analysis; Metabolic module interactions; Polyketides

Indexed keywords

BIOCHEMISTRY; BIOSYNTHESIS; BOTTLES; CELL ENGINEERING; ESCHERICHIA COLI; KETONES; METABOLISM; NUCLEIC ACIDS; RNA; STRAIN;

ANTISENSE RNA; FUNCTIONAL MODULES; IN-SILICO; METABOLIC PATHWAYS; NUCLEOTIDE METABOLISM; POLYKETIDES; POTENTIAL TARGETS; TRANSCRIPTOME ANALYSIS;

METABOLIC ENGINEERING;

6 DEOXYERYTHRONOLIDE B; COMPLEMENTARY RNA; POLYKETIDE; TRANSCRIPTOME; UNCLASSIFIED DRUG; 6-DEOXYERYTHRONOLIDE B; ANTIINFECTIVE AGENT; ERYTHROMYCIN; ESCHERICHIA COLI PROTEIN;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BIOSYNTHESIS; COMPARATIVE STUDY; COMPUTER MODEL; CONTROLLED STUDY; ESCHERICHIA COLI; GENOME ANALYSIS; IN SILICO FLUXOME ANALYSIS; METABOLIC ENGINEERING; METABOLISM; NONHUMAN; NUCLEOTIDE METABOLISM; PENTOSE PHOSPHATE CYCLE; PRIORITY JOURNAL; SYNTHETIC BIOLOGY; TRANSCRIPTOMICS; ANALOGS AND DERIVATIVES; COMPUTER SIMULATION; DOWN REGULATION; DRUG EFFECTS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; PROCEDURES;

ANTI-BACTERIAL AGENTS; COMPUTER SIMULATION; DOWN-REGULATION; ERYTHROMYCIN; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; METABOLIC ENGINEERING; PENTOSE PHOSPHATE PATHWAY; RNA, ANTISENSE;

EID: 84956687926     PISSN: 18606768     EISSN: 18607314     Source Type: Journal    
DOI: 10.1002/biot.201500351     Document Type: Article

References (46)

1. Zakeri, B., Lu, T. K., Synthetic biology of antimicrobial discovery. ACS Synth. Biol. 2013, 2, 358-372.
2. Pfeifer, B. A., Admiraal, S. J., Gramajo, H., Cane, D. E., Khosla, C., Biosynthesis of complex polyketides in a metabolically engineered strain of E. coli. Science 2001, 291, 1790-1792.
3. Zhang, H., Wang, Y., Wu, J., Skalina, K., Pfeifer, B. A., Complete biosynthesis of erythromycin A and designed analogs using E. coli as a heterologous host. Chem. Biol. 2010, 17, 1232-1240.
4. Pfeifer, B., Hu, Z., Licari, P., Khosla, C., Process and metabolic strategies for improved production of Escherichia coli-derived 6-deoxyerythronolide B. Appl. Environ. Microbiol. 2002, 68, 3287-3292.
5. Lau, J., Tran, C., Licari, P., Galazzo, J., Development of a high cell-density fed-batch bioprocess for the heterologous production of 6-deoxyerythronolide B in Escherichia coli. J. Biotechnol. 2004, 110, 95-103.
6. Zhang, H., Boghigian, B. A., Pfeifer, B. A., Investigating the role of native propionyl-CoA and methylmalonyl-CoA metabolism on heterologous polyketide production in Escherichia coli. Biotechnol. Bioeng. 2010, 105, 567-573.
7. Dayem, L. C., Carney, J. R., Santi, D. V., Pfeifer, B. A., Khosla, C., Kealey, J. T., Metabolic engineering of a methylmalonyl-CoA mutase-epimerase pathway for complex polyketide biosynthesis in Escherichia coli. Biochemistry 2002, 41, 5193-5201.
8. Boghigian, B. A., Zhang, H., Pfeifer, B. A., Multi-factorial engineering of heterologous polyketide production in Escherichia coli reveals complex pathway interactions. Biotechnol. Bioeng. 2011, 108, 1360-1371.
9. Kinoshita, K., Pfeifer, B. A., Khosla, C., Cane, D. E., Precursor-directed polyketide biosynthesis in Escherichia coli. Bioorg. Med. Chem. Lett. 2003, 13, 3701-3704.
10. Meng, H. L., Lu, Z. G., Wang, Y., Wang, X. N., Zhang, S. L., In silico improvement of heterologous biosynthesis of erythromycin precursor 6-deoxyerythronolide B in Escherichia coli. Biotechnol. Bioproc. E. 2011, 16, 445-456.
11. Zhang, F., Carothers, J. M., Keasling, J. D., Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat. Biotechnol. 2012, 30, 354-359.
12. Dahl, R. H., Zhang, F., Alonso-Gutierrez, J., Baidoo, E., et al., Engineering dynamic pathway regulation using stress-response promoters. Nat. Biotechnol. 2013, 31, 1039-1046.
13. Ip, K., Donoghue, N., Kim, M. K., Lun, D. S., Constraint-based modeling of heterologous pathways: Application and experimental demonstration for overproduction of fatty acids in Escherichia coli. Biotechnol. Bioeng. 2014, 111, 2056-2066.
14. Yang, Y., Lin, Y., Li, L., Linhardt, R. J., Yan, Y., Regulating malonyl-CoA metabolism via synthetic antisense RNAs for enhanced biosynthesis of natural products. Metab. Eng. 2015, 29, 217-226.
15. Na, D., Yoo, S. M., Chung, H., Park, H., Park, J. H., Lee, S. Y., Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nat. biotechnol. 2013, 31, 170-174.
16. Yoo, S. M., Na, D., Lee, S. Y., Design and use of synthetic regulatory small RNAs to control gene expression in Escherichia coli. Nat. Protoc. 2013, 8, 1694-1707.
17. Wu, J., Yu, O., Du, G., Zhou, J., Chen, J., Fine-tuning of the fatty acid pathway by synthetic antisense RNA for enhanced (2S)-naringenin production from L-tyrosine in Escherichia coli. Appl. Environ. Microbiol. 2014, 80, 7283-7292.
18. Kang, Z., Zhang, C., Zhang, J., Jin, P., et al., Small RNA regulators in bacteria: Powerful tools for metabolic engineering and synthetic biology. Appl. Microbiol. Biotechnol. 2014, 98, 3413-3424.
19. Boghigian, B. A., Lee, K., Pfeifer, B. A., Computational analysis of phenotypic space in heterologous polyketide biosynthesis-applications to Escherichia coli, Bacillus subtilis, and Saccharomyces cerevisiae. J. Theor. Biol. 2010, 262, 197-207.
20. Yang, J., Xiong, Z. Q., Song, S. J., Wang, J. F., Lv, H. J., Wang, Y., Improving heterologous polyketide production in Escherichia coli by transporter engineering. Appl. Microbiol. Biotechnol. 2015, 99, 8691-8700.
21. Sambrook, J., Russell, D. W., Molecular Cloning: A Laboratory Manual. New York: Cold Spring Harbor Laboratory Press 2001.
22. You, C., Zhang, X. Z., Zhang, Y. H., Simple cloning via direct transformation of PCR product (DNA Multimer) to Escherichia coli and Bacillus subtilis. Appl. Environ. Microbiol. 2012, 78, 1593-1595.
23. Becker, S. A., Feist, A. M., Mo, M. L., Hannum, G., Palsson, B. O., Herrgard, M. J., Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox. Nat. Protoc. 2007, 2, 727-738.
24. Schellenberger, J., Que, R., Fleming, R. M., Thiele, I., et al., Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox v2.0. Nat. Protoc. 2011, 6, 1290-1307.
25. Orth, J. D., Conrad, T. M., Na, J., Lerman, J. A., et al., A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011. Mol. Syst. Biol. 2011, 7, 535.
26. Orth, J. D., Thiele, I., Palsson, B. O., What is flux balance analysis. Nat. Biotechnol. 2010, 28, 245-248.
27. Thiele, I., Jamshidi, N., Fleming, R. M., Palsson, B. O., Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: A knowledge base, its mathematical formulation, and its functional characterization. PLoS Comput. Biol. 2009, 5, e1000312.
28. Mao, L., Verwoerd, W. S., Model-driven elucidation of the inherent capacity of Geobacter sulfurreducens for electricity generation. J. Biol. Eng. 2013, 7, 14.
29. Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., et al., Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000, 25, 25-29.
30. Feist, A. M., Henry, C. S., Reed, J. L., Krummenacker, M., et al., A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol. Syst. Biol. 2007, 3, 121.
31. Gonzalez-Lergier, J., Broadbelt, L. J., Hatzimanikatis, V., Analysis of the maximum theoretical yield for the synthesis of erythromycin precursors in Escherichia coli. Biotechnol. Bioeng. 2006, 95, 638-644.
32. Zhang, H., Wang, Y., Boghigian, B., Pfeifer, B. A., Probing the heterologous metabolism supporting 6-deoxyerythronolide B biosynthesis in Escherichia coli. Microb. Biotechnol. 2009, 2, 390-394.
33. Wang, Y., Boghigian, B. A., Pfeifer, B. A., Improving heterologous polyketide production in Escherichia coli by overexpression of an S-adenosylmethionine synthetase gene. Appl. Microbiol. Biotechnol. 2007, 77, 367-373.
34. George, K. W., Chen, A., Jain, A., Batth, T. S., et al., Correlation analysis of targeted proteins and metabolites to assess and engineer microbial isopentenol production. Biotechnol. Bioeng. 2014, 111, 1648-1658.
35. Park, J. H., Lee, K. H., Kim, T. Y., Lee, S. Y., Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation. Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 7797-7802.
36. Lee, K. H., Park, J. H., Kim, T. Y., Kim, H. U., Lee, S. Y., Systems metabolic engineering of Escherichia coli for L-threonine production. Mol. Syst. Biol. 2007, 3, 149.
37. Song, B. G., Kim, T. K., Jung, Y. M., Lee, Y. H., Modulation of talA gene in pentose phosphate pathway for overproduction of poly-beta-hydroxybutyrate in transformant Escherichia coli harboring phbCAB operon. J. Biosci. Bioeng. 2006, 102, 237-240.
38. Sprenger, G. A., Schorken, U., Sprenger, G., Sahm, H., Transaldolase B of Escherichia coli K-12: Cloning of its gene, talB, and characterization of the enzyme from recombinant strains. J. Bacteriol. 1995, 177, 5930-5936.
39. Zhao, J., Baba, T., Mori, H., Shimizu, K., Effect of zwf gene knockout on the metabolism of Escherichia coli grown on glucose or acetate. Metab. Eng. 2004, 6, 164-174.
40. Zhao, J., Baba, T., Mori, H., Shimizu, K., Global metabolic response of Escherichia coli to gnd or zwf gene-knockout, based on 13C-labeling experiments and the measurement of enzyme activities. Appl. Microbiol. Biotechnol. 2004, 64, 91-98.
41. Farmer, W. R., Liao, J. C., Precursor balancing for metabolic engineering of lycopene production in Escherichia coli. Biotechnol. Prog. 2001, 17, 57-61.
42. Murli, S., Kennedy, J., Dayem, L. C., Carney, J. R., Kealey, J. T., Metabolic engineering of Escherichia coli for improved 6-deoxyerythronolide B production. J. Ind. Microbiol. Biotechnol. 2003, 30, 500-509.
43. Wang, Y., Pfeifer, B. A., 6-deoxyerythronolide B production through chromosomal localization of the deoxyerythronolide B synthase genes in E. coli. Metab. Eng. 2008, 10, 33-38.
44. Phue, J. N., Lee, S. J., Kaufman, J. B., Negrete, A., Shiloach, J., Acetate accumulation through alternative metabolic pathways in ackA (-) pta (-) poxB (-) triple mutant in E. coli B (BL21). Biotechnol. lett. 2010, 32, 1897-1903.
45. Lee, W. H., Chin, Y. W., Han, N. S., Kim, M. D., Seo, J. H., Enhanced production of GDP-L-fucose by overexpression of NADPH regenerator in recombinant Escherichia coli. Appl. Microbiol. Biotechnol. 2011, 91, 967-976.
46. Textor, S., Wendisch, V. F., De Graaf, A. A., Muller, U., et al., Propionate oxidation in Escherichia coli: Evidence for operation of a methylcitrate cycle in bacteria. Arch. Microbiol. 1997, 168, 428-436.