Insulation of a synthetic hydrogen metabolism circuit in bacteria

Journal of Biological Engineering

Volumn 4, Issue , 2010, Pages

  Agapakis, Christina M ^a   Ducat, Daniel C ^a,b   Boyle, Patrick M ^a   Wintermute, Edwin H ^a   Way, Jeffrey C ^b   Silver, Pamela A ^a,b  

^a HARVARD MEDICAL SCHOOL   (United States)

^b HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FERREDOXIN; HYDROGEN; IRON HYDROGENASE; IRON SULFUR PROTEIN; PYRUVATE SYNTHASE; SYNTHETIC HYDROGEN; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL METABOLISM; CELL METABOLISM; ELECTRON TRANSPORT; ESCHERICHIA COLI; GENE DELETION; HETEROLOGOUS EXPRESSION; METABOLIC ENGINEERING; NONHUMAN; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN LOCALIZATION; SIGNAL TRANSDUCTION;

ESCHERICHIA COLI;

EID: 78651486207     PISSN: None     EISSN: 17541611     Source Type: Journal    
DOI: 10.1186/1754-1611-4-3     Document Type: Article

References (54)

1. Marcus RA, Sutin N. Electron transfers in chemistry and biology. Biochim Biophys Acta 1985, 811:265-322.
2. Page CC, Moser CC, Chen X, Dutton PL. Natural engineering principles of electron tunnelling in biological oxidation-reduction. Nature 1999, 402:47-52. 10.1038/46972, 10573417.
3. Varadarajan R, Zewert TE, Gray HB, Boxer SG. Effects of buried ionizable amino acids on the reduction potential of recombinant myoglobin. Science 1989, 243:69-72. 10.1126/science.2563171, 2563171.
4. Lim W. The modular logic of signaling proteins: building allosteric switches from simple binding domains. Curr Opin Struct Biol 2002, 12:61-68. 10.1016/S0959-440X(02)00290-7, 11839491.
5. Gou P, Hanke GT, Kimata-Ariga Y, Standley DM, Kubo A, Taniguchi I, Nakamura H, Hase T. Higher order structure contributes to specific differences in redox potential and electron transfer efficiency of root and leaf ferredoxins. Biochemistry 2006, 45:14389-14396. 10.1021/bi061779d, 17128978.
6. Gilardi G, Fantuzzi A, Sadeghi SJ. Engineering and design in the bioelectrochemistry of metalloproteins. Curr Opin Struct Biol 2001, 11:491-499. 10.1016/S0959-440X(00)00238-4, 11495744.
7. Wong TS, Schwaneberg U. Protein engineering in bioelectrocatalysis. Current Opinion in Biotechnology 2003, 14:590-596. 10.1016/j.copbio.2003.09.008, 14662387.
8. Sadeghi SJ, Meharenna YT, Fantuzzi A, Valetti F, Gilardi G. Engineering artificial redox chains by molecular 'Lego'. Faraday Disc 2000, 116:135-153.
9. Bhalerao KD. Synthetic gene networks: the next wave in biotechnology?. Trends Biotechnol 2009, 27:368-374. 10.1016/j.tibtech.2009.03.003, 19409633.
10. Ghirardi ML, Posewitz MC, Maness PC, Dubini A, Yu J, Seibert M. Hydrogenases and Hydrogen Photoproduction in Oxygenic Photosynthetic Organisms. Annu Rev Plant Biol 2007, 58:71-91. 10.1146/annurev.arplant.58.032806.103848, 17150028.
11. Ye X, Wang Y, Hopkins RC, Adams MWW, Evans BR, Mielenz JR, Zhang Y-HP. Spontaneous High-Yield Production of Hydrogen from Cellulosic Materials and Water Catalyzed by Enzyme Cocktails. ChemSusChem 2009, 2:149-152. 10.1002/cssc.200900017, 19185036.
12. Aguirre de Carcer I, DiPasquale A, Rheingold AL, Heinekey DM. Active-site models for iron hydrogenases: reduction chemistry of dinuclear iron complexes. Inorganic chemistry 2006, 45:8000-8002. 10.1021/ic0610381, 16999394.
13. Yoshida A, Nishimura T, Kawaguchi H, Inui M, Yukawa H. Efficient induction of formate hydrogen lyase of aerobically grown Escherichia coli in a three-step biohydrogen production process. Appl Microbiol Biotechnol 2007, 74:754-760. 10.1007/s00253-006-0721-y, 17111135.
14. Maeda T, Sanchez-Torres V, Wood TK. Protein engineering of hydrogenase 3 to enhance hydrogen production. Appl Microbiol Biotechnol 2008, 79:77-86. 10.1007/s00253-008-1416-3, 18335216.
15. Akhtar M, Jones P. Engineering of a synthetic hydF-hydE-hydG-hydA operon for biohydrogen production. Anal Biochem 2008, 373:170-172. 10.1016/j.ab.2007.10.018, 17996187.
16. Laurinavichene TV, Tsygankov AA. H2 consumption by Escherichia coli coupled via hydrogenase 1 or hydrogenase 2 to different terminal electron acceptors. FEMS Microbiol Lett 2001, 202:121-124. 10.1111/j.1574-6968.2001.tb10790.x, 11506918.
17. Sawers RG. Formate and its role in hydrogen production in Escherichia coli. Biochem Soc Trans 2005, 33:42-46. 10.1042/BST0330042, 15667260.
18. King PW, Posewitz MC, Ghirardi ML, Seibert M. Functional studies of [FeFe] hydrogenase maturation in an Escherichia coli biosynthetic system. J Bacteriol 2006, 188:2163-2172. 10.1128/JB.188.6.2163-2172.2006, 1428129, 16513746.
19. Veit A, Akhtar M, Mizutani T, Jones PR. Constructing and testing the thermodynamic limits of synthetic NAD(P)H:H 2pathways. Microbial Biotechnology 2008, 1:382-394.
20. Akhtar M, Jones PR. Construction of a synthetic YdbK-dependent pyruvate:H2 pathway in Escherichia coli BL21(DE3). Metab Eng 2009, 11:139-147. 10.1016/j.ymben.2009.01.002, 19558967.
21. Richard DJ, Sawers G, Sargent F, McWalter L, Boxer DH. Transcriptional regulation in response to oxygen and nitrate of the operons encoding the [NiFe] hydrogenases 1 and 2 of Escherichia coli. Microbiology 1999, 145:2903-2912.
22. Skerker J, Perchuk B, Siryaporn A, Lubin E, Ashenberg O, Goulian M, Laub M. Rewiring the Specificity of Two-Component Signal Transduction Systems. Cell 2008, 133:1043-1054. 10.1016/j.cell.2008.04.040, 2453690, 18555780.
23. Akashi T, Matsumura T, Ideguchi T, Iwakiri K, Kawakatsu T, Taniguchi I, Hase T. Comparison of the electrostatic binding sites on the surface of ferredoxin for two ferredoxin-dependent enzymes, ferredoxin-NADP(+) reductase and sulfite reductase. J Biol Chem 1999, 274:29399-29405. 10.1074/jbc.274.41.29399, 10506201.
24. Peters JW, Lanzilotta WN, Lemon BJ, Seefeldt LC. X-ray crystal structure of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum to 1.8 angstrom resolution. Science 1998, 282:1853-1858. 10.1126/science.282.5395.1853, 9836629.
25. Long H, King P, Ghirardi M, Kim K. Hydrogenase/Ferredoxin Charge-Transfer Complexes: Effect of Hydrogenase Mutations on the Complex Association. The journal of physical chemistry 2009, 113:4060-4067.
26. Dueber JE, Wu GC, Malmirchegini GR, Moon TS, Petzold CJ, Ullal AV, Prather KLJ, Keasling JD. Synthetic protein scaffolds provide modular control over metabolic flux. Nat Biotechnol 2009, 27:753-759. 10.1038/nbt.1557, 19648908.
27. Guerrini O, Burlat B, Léger C, Guigliarelli B, Soucaille P, Girbal L. Characterization of Two 2[4Fe4S] Ferredoxins from Clostridium acetobutylicum. Curr Microbiol 2008, 56:261-267. 10.1007/s00284-007-9072-x, 18074176.
28. Pieulle L, Magro V, Hatchikian EC. Isolation and analysis of the gene encoding the pyruvate-ferredoxin oxidoreductase of Desulfovibrio africanus, production of the recombinant enzyme in Escherichia coli, and effect of carboxy-terminal deletions on its stability. Journal of Bacteriology 1997, 179:5684-5692. 179454, 9294422.
29. Phillips I, Silver P. A New Biobrick Assembly Strategy Designed for Facile Protein Engineering. dspace 2006,
30. Cironi P, Swinburne I, Silver P. Enhancement of Cell Type Specificity by Quantitative Modulation of a Chimeric Ligand. Journal of Biological Chemistry 2008, 283:8469-8476. 10.1074/jbc.M708502200, 2417160, 18230610.
31. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2006, 2:0008. 10.1038/msb4100050, 1681482, 16738554.
32. Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 1997, 18:2714-2723. 10.1002/elps.1150181505, 9504803.
33. Boxma B, de Graaf RM, Staay GW, van Alen TA, Ricard G, Gabaldón T, van Hoek AH, Moon-van der Staay SY, Koopman WJ, van Hellemond JJ, et al. An anaerobic mitochondrion that produces hydrogen. Nature 2005, 434:74-79. 10.1038/nature03343, 15744302.
34. Moulis JM, Davasse V. Probing the role of electrostatic forces in the interaction of Clostridium pasteurianum ferredoxin with its redox partners. Biochemistry 1995, 34:16781-16788. 10.1021/bi00051a028, 8527453.
35. Akhtar MK, Jones PR. Deletion of iscR stimulates recombinant clostridial Fe-Fe hydrogenase activity and H2-accumulation in Escherichia coli BL21(DE3). Appl Microbiol Biotechnol 2008, 78:853-862. 10.1007/s00253-008-1377-6, 18320190.
36. Yonekura-Sakakibara K, Onda Y, Ashikari T, Tanaka Y, Kusumi T, Hase T. Analysis of reductant supply systems for ferredoxin-dependent sulfite reductase in photosynthetic and nonphotosynthetic organs of maize. Plant Physiol 2000, 122:887-894. 10.1104/pp.122.3.887, 58925, 10712553.
37. McCord JM. The evolution of free radicals and oxidative stress. Am J Med 2000, 108:652-659. 10.1016/S0002-9343(00)00412-5, 10856414.
38. Zarrinpar A, Park SH, Lim WA. Optimization of specificity in a cellular protein interaction network by negative selection. Nature 2003, 426:676-680. 10.1038/nature02178, 14668868.
39. Chang CH, King PW, Ghirardi ML, Kim K. Atomic resolution modeling of the ferredoxin:[FeFe] hydrogenase complex from Chlamydomonas reinhardtii. Biophys J 2007, 93:3034-3045. 10.1529/biophysj.107.108589, 2025642, 17660315.
40. Long H, Chang CH, King PW, Ghirardi ML, Kim K. Brownian Dynamics and Molecular Dynamics Study of the Association between Hydrogenase and Ferredoxin from Chlamydomonas reinhardtii. Biophysical Journal 2008, 95:3753-3766. 10.1529/biophysj.107.127548, 2553122, 18621810.
41. Aliverti A, Zanetti G. A three-domain iron-sulfur flavoprotein obtained through gene fusion of ferredoxin and ferredoxin-NADP+ reductase from spinach leaves. Biochemistry 1997, 36:14771-14777. 10.1021/bi971791t, 9398197.
42. Krishnamurthy VM, Semetey V, Bracher PJ, Shen N, Whitesides GM. Dependence of effective molarity on linker length for an intramolecular protein-ligand system. J Am Chem Soc 2007, 129:1312-1320. 10.1021/ja066780e, 2535942, 17263415.
43. Bashor CJ, Helman NC, Yan S, Lim WA. Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics. Science 2008, 319:1539-1543. 10.1126/science.1151153, 18339942.
44. Park SH, Zarrinpar A, Lim WA. Rewiring MAP kinase pathways using alternative scaffold assembly mechanisms. Science 2003, 299:1061-1064. 10.1126/science.1076979, 12511654.
45. Uyeda K, Rabinowitz JC. Pyruvate-ferredoxin oxidoreductase. IV. Studies on the reaction mechanism. J Biol Chem 1971, 246:3120-3125.
46. Pieulle L, Charon MH, Bianco P, Bonicel J, Pétillot Y, Hatchikian EC. Structural and kinetic studies of the pyruvate-ferredoxin oxidoreductase/ferredoxin complex from Desulfovibrio africanus. Eur J Biochem 1999, 264:500-508. 10.1046/j.1432-1327.1999.00648.x, 10491097.
47. Forster AC, Church GM. Towards synthesis of a minimal cell. Mol Syst Biol 2006, 2:45. 10.1038/msb4100090, 1681520, 16924266.
48. Maeda, Sanchez-Torres, Wood. Enhanced hydrogen production from glucose by metabolically engineered Escherichia coli. Appl Microbiol Biotechnol 2007, 77:879-890. 10.1007/s00253-007-1217-0, 17938909.
49. Cournac L, Guedeney G, Peltier G, Vignais PM. Sustained photoevolution of molecular hydrogen in a mutant of Synechocystis sp. strain PCC 6803 deficient in the type I NADPH-dehydrogenase complex. J Bacteriol 2004, 186:1737-1746. 10.1128/JB.186.6.1737-1746.2003, 355973, 14996805.
50. Melis A, Zhang L, Forestier M, Ghirardi ML, Seibert M. Sustained photobiological hydrogen gas production upon reversible inactivation of oxygen evolution in the green alga Chlamydomonas reinhardtii. Plant Physiol 2000, 122:127-136. 10.1104/pp.122.1.127, 58851, 10631256.
51. Zhu Y, Eiteman MA, Altman R, Altman E. High Glycolytic Flux Improves Pyruvate Production by a Metabolically Engineered Escherichia coli Strain. Appl Environ Microbiol 2008, 74:6649-6655. 10.1128/AEM.01610-08, 2576684, 18806005.
52. Penfold DW, Sargent F, Macaskie LE. Inactivation of the Escherichia coli K-12 twin-arginine translocation system promotes increased hydrogen production. FEMS Microbiol Lett 2006, 262:135-137. 10.1111/j.1574-6968.2006.00333.x, 16923067.
53. Andrianantoandro E, Basu S, Karig D, Weiss R. Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol 2006, 2. 2006.0028, 10.1038/msb4100073, 1681505, 16738572.
54. Binda C, Coda A, Aliverti A, Zanetti G, Mattevi A. Structure of the mutant E92K of [2Fe-2S] ferredoxin I from Spinacia oleracea at 1.7 A resolution. Acta Crystallogr D Biol Crystallogr 1998, 54:1353-1358. 10.1107/S0907444998005137, 10089511.