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Volumn 115, Issue 3, 2018, Pages 661-672

Engineering Escherichia coli for malate production by integrating modular pathway characterization with CRISPRi-guided multiplexed metabolic tuning

Author keywords

CRISPRi; glyoxylate cycle; in vitro modular optimization; multiplexed combinatorial regulation

Indexed keywords

BIOSYNTHESIS; ESCHERICHIA COLI; GENE EXPRESSION; METABOLISM;

EID: 85034750457     PISSN: 00063592     EISSN: 10970290     Source Type: Journal    
DOI: 10.1002/bit.26486     Document Type: Article
Times cited : (82)

References (48)
  • 1
    • 79958716478 scopus 로고    scopus 로고
    • Biochemical characterisation of aconitase from Corynebacterium glutamicum
    • Baumgart, M., & Bott, M. (2011). Biochemical characterisation of aconitase from Corynebacterium glutamicum. Journal of Biotechnology, 154(2-3), 163–170.
    • (2011) Journal of Biotechnology , vol.154 , Issue.2-3 , pp. 163-170
    • Baumgart, M.1    Bott, M.2
  • 2
    • 85026636276 scopus 로고    scopus 로고
    • Strategies for terpenoid overproduction and new terpenoid discovery
    • Bian, G., Deng, Z., & Liu, T. (2017). Strategies for terpenoid overproduction and new terpenoid discovery. Current Opinion Biotechnology, 48, 234–241.
    • (2017) Current Opinion Biotechnology , vol.48 , pp. 234-241
    • Bian, G.1    Deng, Z.2    Liu, T.3
  • 3
    • 85019157109 scopus 로고    scopus 로고
    • Releasing the potential power of terpene synthases by a robust precursor supply platform
    • Bian, G., Han, Y., Hou, A., Yuan, Y., Liu, X., Deng, Z., & Liu, T. (2017). Releasing the potential power of terpene synthases by a robust precursor supply platform. Metabolic Engineering, 42, 1–8.
    • (2017) Metabolic Engineering , vol.42 , pp. 1-8
    • Bian, G.1    Han, Y.2    Hou, A.3    Yuan, Y.4    Liu, X.5    Deng, Z.6    Liu, T.7
  • 4
    • 85013371899 scopus 로고    scopus 로고
    • Engineering rTCA pathway and C4-dicarboxylate transporter for L-malic acid production
    • Chen, X., Wang, Y., Dong, X., Hu, G., & Liu, L. (2017). Engineering rTCA pathway and C4-dicarboxylate transporter for L-malic acid production. Applied Microbiology and Biotechnology, 101(10), 4041–4052.
    • (2017) Applied Microbiology and Biotechnology , vol.101 , Issue.10 , pp. 4041-4052
    • Chen, X.1    Wang, Y.2    Dong, X.3    Hu, G.4    Liu, L.5
  • 5
    • 84949803963 scopus 로고    scopus 로고
    • Modular optimization of multi-gene pathways for fumarate production
    • Chen, X., Zhu, P., & Liu, L. (2016). Modular optimization of multi-gene pathways for fumarate production. Metabolic Engineering, 33, 76–85.
    • (2016) Metabolic Engineering , vol.33 , pp. 76-85
    • Chen, X.1    Zhu, P.2    Liu, L.3
  • 6
    • 84963516758 scopus 로고    scopus 로고
    • One-step fermentative production of poly(lactate-co-glycolate) from carbohydrates in Escherichia coli
    • Choi, S. Y., Park, S. J., Kim, W. J., Yang, J. E., Lee, H., Shin, J., & Lee, S. Y. (2016). One-step fermentative production of poly(lactate-co-glycolate) from carbohydrates in Escherichia coli. Nature Biotechnology, 34(4), 435–442.
    • (2016) Nature Biotechnology , vol.34 , Issue.4 , pp. 435-442
    • Choi, S.Y.1    Park, S.J.2    Kim, W.J.3    Yang, J.E.4    Lee, H.5    Shin, J.6    Lee, S.Y.7
  • 7
    • 84973136613 scopus 로고    scopus 로고
    • Corynebacterium glutamicum metabolic engineering with CRISPR interference (CRISPRi)
    • Cleto, S., Jensen, J. V., Wendisch, V. F., & Lu, T. K. (2016). Corynebacterium glutamicum metabolic engineering with CRISPR interference (CRISPRi). ACS Synthetic Biology, 5(5), 375–385.
    • (2016) ACS Synthetic Biology , vol.5 , Issue.5 , pp. 375-385
    • Cleto, S.1    Jensen, J.V.2    Wendisch, V.F.3    Lu, T.K.4
  • 8
    • 84930971149 scopus 로고    scopus 로고
    • CRISPathBrick: modular combinatorial assembly of type II-A CRISPR arrays for dCas9-mediated multiplex transcriptional repression in E. coli
    • Cress, B. F., Toparlak, O. D., Guleria, S., Lebovich, M., Stieglitz, J. T., Englaender, J. A., … Koffas, M. A. (2015). CRISPathBrick: modular combinatorial assembly of type II-A CRISPR arrays for dCas9-mediated multiplex transcriptional repression in E. coli. ACS Synthetic Biology, 4(9), 987–1000.
    • (2015) ACS Synthetic Biology , vol.4 , Issue.9 , pp. 987-1000
    • Cress, B.F.1    Toparlak, O.D.2    Guleria, S.3    Lebovich, M.4    Stieglitz, J.T.5    Englaender, J.A.6    Koffas, M.A.7
  • 10
    • 84962429359 scopus 로고    scopus 로고
    • Towards repurposing the yeast peroxisome for compartmentalizing heterologous metabolic pathways
    • DeLoache, W. C., Russ, Z. N., & Dueber, J. E. (2016). Towards repurposing the yeast peroxisome for compartmentalizing heterologous metabolic pathways. Nature Communications, 7, 11152.
    • (2016) Nature Communications , vol.7 , pp. 11152
    • DeLoache, W.C.1    Russ, Z.N.2    Dueber, J.E.3
  • 11
    • 84877307101 scopus 로고    scopus 로고
    • Compartmentalizing metabolic pathways in organelles
    • DeLoache, W. C., & Dueber, J. E. (2013). Compartmentalizing metabolic pathways in organelles. Nature Biotechnology, 31(4), 320–321.
    • (2013) Nature Biotechnology , vol.31 , Issue.4 , pp. 320-321
    • DeLoache, W.C.1    Dueber, J.E.2
  • 12
    • 84945981218 scopus 로고    scopus 로고
    • In vivo kinetic analysis of the penicillin biosynthesis pathway using PAA stimulus response experiments
    • Deshmukh, A. T., Verheijen, P. J., Maleki Seifar, R., Heijnen, J. J., & van Gulik, W. M. (2015). In vivo kinetic analysis of the penicillin biosynthesis pathway using PAA stimulus response experiments. Metabolic Engineering, 32, 155–173.
    • (2015) Metabolic Engineering , vol.32 , pp. 155-173
    • Deshmukh, A.T.1    Verheijen, P.J.2    Maleki Seifar, R.3    Heijnen, J.J.4    van Gulik, W.M.5
  • 13
    • 84952639685 scopus 로고    scopus 로고
    • Beyond editing: Repurposing CRISPR-Cas9 for precision genome regulation and interrogation
    • Dominguez, A. A., Lim, W. A., & Qi, L. S. (2016). Beyond editing: Repurposing CRISPR-Cas9 for precision genome regulation and interrogation. Nature Reviews Molecular Cell Biology, 17(1), 5–15.
    • (2016) Nature Reviews Molecular Cell Biology , vol.17 , Issue.1 , pp. 5-15
    • Dominguez, A.A.1    Lim, W.A.2    Qi, L.S.3
  • 15
    • 84903144112 scopus 로고    scopus 로고
    • Correlation analysis of targeted proteins and metabolites to assess and engineer microbial isopentenol production
    • George, K. W., Chen, A., Jain, A., Batth, T. S., Baidoo, E. E., Wang, G., & Lee, T. S. (2014). Correlation analysis of targeted proteins and metabolites to assess and engineer microbial isopentenol production. Biotechnology and Bioengineering, 111(8), 1648–1658.
    • (2014) Biotechnology and Bioengineering , vol.111 , Issue.8 , pp. 1648-1658
    • George, K.W.1    Chen, A.2    Jain, A.3    Batth, T.S.4    Baidoo, E.E.5    Wang, G.6    Lee, T.S.7
  • 16
    • 85016060109 scopus 로고    scopus 로고
    • Why batch effects matter in omics data, and how to avoid them
    • Goh, W. W. B., Wang, W., & Wong, L. (2017). Why batch effects matter in omics data, and how to avoid them. Trends Biotechnology, 35(6), 498–507.
    • (2017) Trends Biotechnology , vol.35 , Issue.6 , pp. 498-507
    • Goh, W.W.B.1    Wang, W.2    Wong, L.3
  • 17
    • 85014739781 scopus 로고    scopus 로고
    • Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit
    • Gupta, A., Reizman, I. M., Reisch, C. R., & Prather, K. L. (2017). Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit. Nature Biotechnology, 35(3), 273–279.
    • (2017) Nature Biotechnology , vol.35 , Issue.3 , pp. 273-279
    • Gupta, A.1    Reizman, I.M.2    Reisch, C.R.3    Prather, K.L.4
  • 18
    • 84989256943 scopus 로고    scopus 로고
    • Forward design of a complex enzyme cascade reaction
    • Hold, C., Billerbeck, S., & Panke, S. (2016). Forward design of a complex enzyme cascade reaction. Nature Communications, 7, 12971.
    • (2016) Nature Communications , vol.7 , pp. 12971
    • Hold, C.1    Billerbeck, S.2    Panke, S.3
  • 19
    • 41249084917 scopus 로고    scopus 로고
    • Combining metabolic engineering and metabolic evolution to develop nonrecombinant strains of Escherichia coli C that produce succinate and malate
    • Haupt, M. J., Svoronos, S. A., Zhang, X., Moore, J. C.#x0026; Shanmugam, K. T., Ingram, L. O.
    • Jantama, K., Haupt, M. J., Svoronos, S. A., Zhang, X., Moore, J. C., & Shanmugam, K. T., Ingram, L. O. (2008). Combining metabolic engineering and metabolic evolution to develop nonrecombinant strains of Escherichia coli C that produce succinate and malate. Biotechnology Bioengineering, 99(5), 1140–1153.
    • (2008) Biotechnology Bioengineering , vol.99 , Issue.5 , pp. 1140-1153
    • Jantama, K.1
  • 20
    • 84952682854 scopus 로고    scopus 로고
    • CRISPR/Cas9 advances engineering of microbial cell factories
    • Jakociunas, T., Jensen, M. K., & Keasling, J. D. (2016). CRISPR/Cas9 advances engineering of microbial cell factories. Metabolic Engineering, 34, 44–59.
    • (2016) Metabolic Engineering , vol.34 , pp. 44-59
    • Jakociunas, T.1    Jensen, M.K.2    Keasling, J.D.3
  • 21
    • 84986198285 scopus 로고    scopus 로고
    • CRISPR interference-guided balancing of a biosynthetic mevalonate pathway increases terpenoid production
    • Kim, S. K., Han, G. H., Seong, W., Kim, H., Kim, S. W., Lee, D. H., & Lee, S. G. (2016). CRISPR interference-guided balancing of a biosynthetic mevalonate pathway increases terpenoid production. Metabolic Engineering, 38, 228–240.
    • (2016) Metabolic Engineering , vol.38 , pp. 228-240
    • Kim, S.K.1    Han, G.H.2    Seong, W.3    Kim, H.4    Kim, S.W.5    Lee, D.H.6    Lee, S.G.7
  • 23
    • 84946476393 scopus 로고    scopus 로고
    • Real-time metabolome profiling of the metabolic switch between starvation and growth
    • Link, H., Fuhrer, T., Gerosa, L., Zamboni, N., & Sauer, U. (2015). Real-time metabolome profiling of the metabolic switch between starvation and growth. Nature Methods, 12(11), 1091–1097.
    • (2015) Nature Methods , vol.12 , Issue.11 , pp. 1091-1097
    • Link, H.1    Fuhrer, T.2    Gerosa, L.3    Zamboni, N.4    Sauer, U.5
  • 24
    • 84920729162 scopus 로고    scopus 로고
    • Engineering an iterative polyketide pathway in Escherichia coli results in single-form alkene and alkane overproduction
    • Liu, Q., Wu, K., Cheng, Y., Lu, L., Xiao, E., Zhang, Y., … Liu, T. (2015). Engineering an iterative polyketide pathway in Escherichia coli results in single-form alkene and alkane overproduction. Metabolic Engineering, 28, 82–90.
    • (2015) Metabolic Engineering , vol.28 , pp. 82-90
    • Liu, Q.1    Wu, K.2    Cheng, Y.3    Lu, L.4    Xiao, E.5    Zhang, Y.6    Liu, T.7
  • 25
    • 84874652607 scopus 로고    scopus 로고
    • Biomimetic enzyme nanocomplexes and their use as antidotes and preventive measures for alcohol intoxication
    • … Lu, Y. F.
    • Liu, Y., Du, J., Yan, M., Lau, M. Y., Hu, J., Han, H., … Lu, Y. F. (2013). Biomimetic enzyme nanocomplexes and their use as antidotes and preventive measures for alcohol intoxication. Nature Nanotechnology, 8(3), 187–192.
    • (2013) Nature Nanotechnology , vol.8 , Issue.3 , pp. 187-192
    • Liu, Y.1    Du, J.2    Yan, M.3    Lau, M.Y.4    Hu, J.5    Han, H.6
  • 26
    • 84975795880 scopus 로고    scopus 로고
    • A dynamic pathway analysis approach reveals a limiting futile cycle in N-acetylglucosamine overproducing Bacillus subtilis
    • Liu, Y., Link, H., Liu, L., Du, G., Chen, J., & Sauer, U. (2016). A dynamic pathway analysis approach reveals a limiting futile cycle in N-acetylglucosamine overproducing Bacillus subtilis. Nature Communications, 7, 11933.
    • (2016) Nature Communications , vol.7 , pp. 11933
    • Liu, Y.1    Link, H.2    Liu, L.3    Du, G.4    Chen, J.5    Sauer, U.6
  • 27
    • 85018460890 scopus 로고    scopus 로고
    • In vitro reconstitution and optimization of the entire pathway to convert glucose into fatty acid
    • Liu, Z., Zhang, Y., Jia, X., Hu, M., Deng, Z., Xu, Y., & Liu, T. (2017). In vitro reconstitution and optimization of the entire pathway to convert glucose into fatty acid. ACS Synthetic Biology, 6(4), 701–709.
    • (2017) ACS Synthetic Biology , vol.6 , Issue.4 , pp. 701-709
    • Liu, Z.1    Zhang, Y.2    Jia, X.3    Hu, M.4    Deng, Z.5    Xu, Y.6    Liu, T.7
  • 28
    • 84926645319 scopus 로고    scopus 로고
    • Application of CRISPRi for prokaryotic metabolic engineering involving multiple genes, a case study: Controllable P(3HB-co-4HB) biosynthesis
    • Lv, L., Ren, Y. L., Chen, J. C., Wu, Q., & Chen, G. Q. (2015). Application of CRISPRi for prokaryotic metabolic engineering involving multiple genes, a case study: Controllable P(3HB-co-4HB) biosynthesis. Metabolic Engineering, 29, 160–168.
    • (2015) Metabolic Engineering , vol.29 , pp. 160-168
    • Lv, L.1    Ren, Y.L.2    Chen, J.C.3    Wu, Q.4    Chen, G.Q.5
  • 29
    • 44049083061 scopus 로고    scopus 로고
    • Metabolic engineering of Escherichia coli for the production of malic acid
    • Moon, S. Y., Hong, S. H., Kim, T. Y., & Lee, S. Y. (2008). Metabolic engineering of Escherichia coli for the production of malic acid. Biochemical Engineering Journal, 40(2), 312–320.
    • (2008) Biochemical Engineering Journal , vol.40 , Issue.2 , pp. 312-320
    • Moon, S.Y.1    Hong, S.H.2    Kim, T.Y.3    Lee, S.Y.4
  • 30
    • 84960460639 scopus 로고    scopus 로고
    • Engineering cellular metabolism
    • Nielsen, J., & Keasling, J. D. (2016). Engineering cellular metabolism. Cell, 164(6), 1185–1197.
    • (2016) Cell , vol.164 , Issue.6 , pp. 1185-1197
    • Nielsen, J.1    Keasling, J.D.2
  • 31
    • 84963517324 scopus 로고    scopus 로고
    • A synthetic biochemistry module for production of bio-based chemicals from glucose
    • Opgenorth, P. H., Korman, T. P., & Bowie, J. U. (2016). A synthetic biochemistry module for production of bio-based chemicals from glucose. Nature Chemical Biology, 12(6), 393–395.
    • (2016) Nature Chemical Biology , vol.12 , Issue.6 , pp. 393-395
    • Opgenorth, P.H.1    Korman, T.P.2    Bowie, J.U.3
  • 33
    • 84874687019 scopus 로고    scopus 로고
    • Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression
    • Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P., & Lim, W. A. (2013). Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell, 152(5), 1173–1183.
    • (2013) Cell , vol.152 , Issue.5 , pp. 1173-1183
    • Qi, L.S.1    Larson, M.H.2    Gilbert, L.A.3    Doudna, J.A.4    Weissman, J.S.5    Arkin, A.P.6    Lim, W.A.7
  • 34
    • 84941129321 scopus 로고    scopus 로고
    • Modular pathway rewiring of Saccharomyces cerevisiae enables high-level production of L-ornithine
    • Qin, J., Zhou, Y. J., Krivoruchko, A., Huang, M., Liu, L., Khoomrung, S., … Nielsen, J. (2015). Modular pathway rewiring of Saccharomyces cerevisiae enables high-level production of L-ornithine. Nature Communications, 6, 8224.
    • (2015) Nature Communications , vol.6 , pp. 8224
    • Qin, J.1    Zhou, Y.J.2    Krivoruchko, A.3    Huang, M.4    Liu, L.5    Khoomrung, S.6    Nielsen, J.7
  • 35
    • 84880084177 scopus 로고    scopus 로고
    • Synthetic biology and metabolic engineering approaches to produce biofuels
    • Rabinovitch-Deere, C. A., Oliver, J. W., Rodriguez, G. M., & Atsumi, S. (2013). Synthetic biology and metabolic engineering approaches to produce biofuels. Chemical Reviews, 113(7), 4611–4632.
    • (2013) Chemical Reviews , vol.113 , Issue.7 , pp. 4611-4632
    • Rabinovitch-Deere, C.A.1    Oliver, J.W.2    Rodriguez, G.M.3    Atsumi, S.4
  • 36
    • 84937604735 scopus 로고    scopus 로고
    • The development and characterization of synthetic minimal yeast promoters
    • Redden, H., & Alper, H. S. (2015). The development and characterization of synthetic minimal yeast promoters. Nature Communications, 6, 7810.
    • (2015) Nature Communications , vol.6 , pp. 7810
    • Redden, H.1    Alper, H.S.2
  • 37
    • 85019538487 scopus 로고    scopus 로고
    • In vitro reconstitution guide for targeted synthetic metabolism of chemicals, nutraceuticals and drug precursors
    • Tan, G.-Y., Zhu, F., Deng, Z., & Liu, T. (2016). In vitro reconstitution guide for targeted synthetic metabolism of chemicals, nutraceuticals and drug precursors. Synthetic and Systems Biotechnology, 1(1), 25–33.
    • (2016) Synthetic and Systems Biotechnology , vol.1 , Issue.1 , pp. 25-33
    • Tan, G.-Y.1    Zhu, F.2    Deng, Z.3    Liu, T.4
  • 38
    • 84948109810 scopus 로고    scopus 로고
    • Limitation of thiamine pyrophosphate supply to growing Escherichia coli switches metabolism to efficient D-lactate formation
    • Tian, K. M., Niu, D. D., Liu, X. G., Prior, B. A., Zhou, L., Lu, F. P., … Wang, Z. X. (2016). Limitation of thiamine pyrophosphate supply to growing Escherichia coli switches metabolism to efficient D-lactate formation. Biotechnology and Bioengineering, 113(1), 182–188.
    • (2016) Biotechnology and Bioengineering , vol.113 , Issue.1 , pp. 182-188
    • Tian, K.M.1    Niu, D.D.2    Liu, X.G.3    Prior, B.A.4    Zhou, L.5    Lu, F.P.6    Wang, Z.X.7
  • 40
    • 84940840437 scopus 로고    scopus 로고
    • Enhancing flavonoid production by systematically tuning the central metabolic pathways based on a CRISPR interference system in Escherichia coli
    • Wu, J., Du, G., Chen, J., & Zhou, J. (2015). Enhancing flavonoid production by systematically tuning the central metabolic pathways based on a CRISPR interference system in Escherichia coli. Scientific reports, 5, 13477.
    • (2015) Scientific reports , vol.5 , pp. 13477
    • Wu, J.1    Du, G.2    Chen, J.3    Zhou, J.4
  • 41
    • 84868263016 scopus 로고    scopus 로고
    • EPathBrick: A synthetic biology platform for engineering metabolic pathways in E. coli
    • Xu, P., Vansiri, A., Bhan, N., & Koffas, M. A. G. (2012). EPathBrick: A synthetic biology platform for engineering metabolic pathways in E. coli. ACS Synthetic Biology, 1(7), 256–266.
    • (2012) ACS Synthetic Biology , vol.1 , Issue.7 , pp. 256-266
    • Xu, P.1    Vansiri, A.2    Bhan, N.3    Koffas, M.A.G.4
  • 42
    • 84944237408 scopus 로고    scopus 로고
    • Effects of heterologous expression of phosphoenolpyruvate carboxykinase and phosphoenolpyruvate carboxylase on organic acid production in Aspergillus carbonarius
    • Yang, L., Lubeck, M., & Lubeck, P. S. (2015). Effects of heterologous expression of phosphoenolpyruvate carboxykinase and phosphoenolpyruvate carboxylase on organic acid production in Aspergillus carbonarius. Journal of Industrial Microbiology and Biotechnology, 42(11), 1533–1545.
    • (2015) Journal of Industrial Microbiology and Biotechnology , vol.42 , Issue.11 , pp. 1533-1545
    • Yang, L.1    Lubeck, M.2    Lubeck, P.S.3
  • 45
    • 84926646130 scopus 로고    scopus 로고
    • Distributing a metabolic pathway among a microbial consortium enhances production of natural products
    • Zhou, K., Qiao, K., Edgar, S., & Stephanopoulos, G. (2015). Distributing a metabolic pathway among a microbial consortium enhances production of natural products. Nature Biotechnology, 33(4), 377–383.
    • (2015) Nature Biotechnology , vol.33 , Issue.4 , pp. 377-383
    • Zhou, K.1    Qiao, K.2    Edgar, S.3    Stephanopoulos, G.4
  • 47
    • 84863116515 scopus 로고    scopus 로고
    • Modular pathway engineering of diterpenoid synthases and the mevalonic acid pathway for miltiradiene production
    • … Zhao, Z. K.
    • Zhou, Y. J., Gao, W., Rong, Q., Jin, G., Chu, H., Liu, W., … Zhao, Z. K. (2012). Modular pathway engineering of diterpenoid synthases and the mevalonic acid pathway for miltiradiene production. Journal of the American Chemical Society, 134(6), 3234–3241.
    • (2012) Journal of the American Chemical Society , vol.134 , Issue.6 , pp. 3234-3241
    • Zhou, Y.J.1    Gao, W.2    Rong, Q.3    Jin, G.4    Chu, H.5    Liu, W.6
  • 48
    • 84901617508 scopus 로고    scopus 로고
    • In vitro reconstitution of mevalonate pathway and targeted engineering of farnesene overproduction in Escherichia coli
    • Zhu F, Zhong X, Hu M, Lu L, Deng Z, Liu T. 2014. In vitro reconstitution of mevalonate pathway and targeted engineering of farnesene overproduction in Escherichia coli. Biotechnology and Bioengineering, 111(7):1396–405.
    • (2014) Biotechnology and Bioengineering , vol.111 , Issue.7 , pp. 1396-1405
    • Zhu, F.1    Zhong, X.2    Hu, M.3    Lu, L.4    Deng, Z.5    Liu, T.6


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