Genetic-Metabolic Coupling for Targeted Metabolic Engineering

Cell Reports

Volumn 20, Issue 5, 2017, Pages 1029-1037

  Cardinale, Stefano ^a   Tueros, Felipe Gonzalo ^a   Sommer, Morten Otto Alexander ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

Fe S clusters; oxidative stress response; RNA biosensors; thiamine biosynthesis; transposon mutagenesis

Indexed keywords

THIAMINE; BACTERIAL PROTEIN; COCARBOXYLASE; ESCHERICHIA COLI PROTEIN; FERRIC UPTAKE REGULATING PROTEINS, BACTERIAL; OXYR PROTEIN, E COLI; REPRESSOR PROTEIN;

ARTICLE; BACTERIAL GENE; BACTERIAL GENETICS; BACTERIAL METABOLISM; BACTERIAL STRAIN; BIOSYNTHESIS; CONTROLLED STUDY; ESCHERICHIA COLI; GENE INACTIVATION; GENE LIBRARY; GENE TARGETING; HIGH THROUGHPUT SCREENING; METABOLIC ENGINEERING; METABOLITE; NONHUMAN; OPERON; OXIDATIVE STRESS; POPULATION DYNAMICS; PRIORITY JOURNAL; RELIABILITY; SIGNAL TRANSDUCTION; GENETICS; METABOLISM;

BACTERIAL PROTEINS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; METABOLIC ENGINEERING; REPRESSOR PROTEINS; THIAMINE PYROPHOSPHATE;

EID: 85026887490     PISSN: None     EISSN: 22111247     Source Type: Journal    
DOI: 10.1016/j.celrep.2017.07.015     Document Type: Article

References (36)

1. Agar, J.N., Krebs, C., Frazzon, J., Huynh, B.H., Dean, D.R., Johnson, M.K., IscU as a scaffold for iron-sulfur cluster biosynthesis: sequential qssembly of [2Fe-2S] and [4Fe-4S] clusters in IscU. Biochemistry 39 (2000), 7856–7862.
2. Biedendieck, R., Malten, M., Barg, H., Bunk, B., Martens, J.H., Deery, E., Leech, H., Warren, M.J., Jahn, D., Metabolic engineering of cobalamin (vitamin B12) production in Bacillus megaterium. Microb. Biotechnol. 3 (2010), 24–37.
3. Bou-Abdallah, F., Lewin, A.C., Le Brun, N.E., Moore, G.R., Chasteen, N.D., Iron detoxification properties of Escherichia coli bacterioferritin. Attenuation of oxyradical chemistry. J. Biol. Chem. 277 (2002), 37064–37069.
4. Boyd, J.M., Pierik, A.J., Netz, D.J.A., Lill, R., Downs, D.M., Bacterial ApbC can bind and effectively transfer iron-sulfur clusters. Biochemistry 47 (2008), 8195–8202.
5. Chatterjee, A., Li, Y., Zhang, Y., Grove, T.L., Lee, M., Krebs, C., Booker, S.J., Begley, T.P., Ealick, S.E., Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily. Nat. Chem. Biol. 4 (2008), 758–765.
6. Chen, Y., Xu, D., Fan, L., Zhang, X., Tan, T., Manipulating multi-system of NADPH regulation in Escherichia coli for enhanced S-adenosylmethionine production. RSC Advances 5 (2015), 41103–41111.
7. Crack, J.C., Green, J., Thomson, A.J., Le Brun, N.E., Iron-sulfur clusters as biological sensors: the chemistry of reactions with molecular oxygen and nitric oxide. Acc. Chem. Res. 47 (2014), 3196–3205.
8. Depuydt, M., Leonard, S.E., Vertommen, D., Denoncin, K., Morsomme, P., Wahni, K., Messens, J., Carroll, K.S., Collet, J., A periplasmic reducing system protects single cysteine residues from oxidation. Science 326 (2009), 1109–1111.
9. Ding, H., Harrison, K., Lu, J., Thioredoxin reductase system mediates iron binding in IscA and iron delivery for the iron-sulfur cluster assembly in IscU. J. Biol. Chem. 280 (2005), 30432–30437.
10. Dougherty, M.J., Downs, D.M., A connection between iron-sulfur cluster metabolism and the biosynthesis of 4-amino-5-hydroxymethyl-2-methylpyrimidine pyrophosphate in Salmonella enterica. Microbiology 152 (2006), 2345–2353.
11. Fletcher, E., Krivoruchko, A., Nielsen, J., Industrial systems biology and its impact on synthetic biology of yeast cell factories. Biotechnol. Bioeng. 113 (2016), 1164–1170.
12. Frodyma, M., Rubio, A., Downs, D.M., Reduced flux through the purine biosynthetic pathway results in an increased requirement for coenzyme A in thiamine synthesis in Salmonella enterica serovar typhimurium. J. Bacteriol. 182 (2000), 236–240.
13. Genee, H.J., Bali, A.P., Petersen, S.D., Siedler, S., Bonde, M.T., Gronenberg, L.S., Kristensen, M., Harrison, S.J., Sommer, M.O.A., Functional mining of transporters using synthetic selections. Nat. Chem. Biol. 12 (2016), 1015–1022.
14. Georgiou, G., How to flip the (redox) switch. Cell 111 (2002), 607–610.
15. Giel, J.L., Nesbit, A.D., Mettert, E.L., Fleischhacker, A.S., Wanta, B.T., Kiley, P.J., Regulation of iron-sulphur cluster homeostasis through transcriptional control of the Isc pathway by [2Fe-2S]-IscR in Escherichia coli. Mol. Microbiol. 87 (2013), 478–492.
16. Gralnick, J.A., Downs, D.M., The YggX protein of Salmonella enterica is involved in Fe(II) trafficking and minimizes the DNA damage caused by hydroxyl radicals: residue CYS-7 is essential for YggX function. J. Biol. Chem. 278 (2003), 20708–20715.
17. Huang, da W., Sherman, B.T., Lempicki, R.A., Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4 (2009), 44–57.
18. Imlay, J.A., Transcription factors that defend bacteria against reactive oxygen species. Annu. Rev. Microbiol. 69 (2015), 93–108.
19. Imlay, J.A., Chin, S.M., Linn, S., Toxic DNA damage by hydrogen peroxide through the Fenton reaction in vivo and in vitro., 240, 1988, 640–642.
20. Jang, S., Imlay, J.A., Hydrogen peroxide inactivates the Escherichia coli Isc iron-sulphur assembly system, and OxyR induces the Suf system to compensate. Mol. Microbiol. 78 (2010), 1448–1467.
21. Keseler, I.M., Bonavides-Martínez, C., Collado-Vides, J., Gama-Castro, S., Gunsalus, R.P., Johnson, D.A., Krummenacker, M., Nolan, L.M., Paley, S., Paulsen, I.T., et al. EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res. 37 (2009), D464–D470.
22. Kitagawa, M., Ara, T., Arifuzzaman, M., Ioka-Nakamichi, T., Inamoto, E., Toyonaga, H., Mori, H., Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12 (2005), 291–299.
23. Koo, M.S., Lee, J.H., Rah, S.Y., Yeo, W.S., Lee, J.W., Lee, K.L., Koh, Y.S., Kang, S.O., Roe, J.H., A reducing system of the superoxide sensor SoxR in Escherichia coli. EMBO J. 22 (2003), 2614–2622.
24. Kriek, M., Martins, F., Leonardi, R., Fairhurst, S.A., Lowe, D.J., Roach, P.L., Thiazole synthase from Escherichia coli: an investigation of the substrates and purified protein required for activity in vitro. J. Biol. Chem. 282 (2007), 17413–17423.
25. Lechner, A., Brunk, E., Keasling, J., The need for integrated approaches in metabolic engineering. Cold Spring Harb Pespect Biol, 8, 2016, a023903.
26. Lee, J., Hiibel, S.R., Reardon, K.F., Wood, T.K., Identification of stress-related proteins in Escherichia coli using the pollutant cis-dichloroethylene. J. Appl. Microbiol. 108 (2010), 2088–2102.
27. Lin, Z., Xu, Z., Li, Y., Wang, Z., Chen, T., Zhao, X., Metabolic engineering of Escherichia coli for the production of riboflavin. Microb. Cell Fact., 13, 2014, 104.
28. Nam, H., Lewis, N.E., Lerman, J.A., Lee, D., Chang, R.L., Kim, D., Palsson, B.O., Network context and selection in the evolution to enzyme specificity. Science 337 (2012), 1101–1104.
29. Oh, J., Fung, E., Price, M.N., Dehal, P.S., Davis, R.W., Giaever, G., Nislow, C., Arkin, A.P., Deutschbauer, A., A universal TagModule collection for parallel genetic analysis of microorganisms. Nucleic Acids Res., 38, 2010, e146.
30. Otero, J.M., Nielsen, J., Industrial systems biology. Biotechnol. Bioeng. 105 (2010), 439–460.
31. Outten, F.W., Djaman, O., Storz, G., A suf operon requirement for Fe-S cluster assembly during iron starvation in Escherichia coli. Mol. Microbiol. 52 (2004), 861–872.
32. Seo, S.W., Kim, D., Latif, H., O'Brien, E.J., Szubin, R., Palsson, B.O., Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli. Nat. Commun., 5, 2014, 4910.
33. Seth, D., Hausladen, A., Wang, Y.J., Stamler, J.S., Endogenous protein S-nitrosylation in E. coli: regulation by OxyR. Science 336 (2012), 470–473.
34. Tatusova, T., Ciufo, S., Fedorov, B., O'Neill, K., Tolstoy, I., RefSeq microbial genomes database: new representation and annotation strategy. Nucleic Acids Res. 42 (2014), D553–D559.
35. Townshend, B., Kennedy, A.B., Xiang, J.S., Smolke, C.D., High-throughput cellular RNA device engineering. Nat. Methods 12 (2015), 989–994.
36. Wetmore, K.M., Price, M.N., Waters, R.J., Lamson, J.S., He, J., Hoover, C.A., Blow, M.J., Bristow, J., Butland, G., Arkin, A.P., Deutschbauer, A., Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons. MBio 6 (2015), e00306–e00315.