Using synthetic biology to increase nitrogenase activity

Microbial Cell Factories

Volumn 15, Issue 1, 2016, Pages

  Li, Xin Xin ^a   Liu, Qi ^a   Liu, Xiao Meng ^a   Shi, Hao Wen ^a   Chen, San Feng ^a  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

Electron transporter; Fe S cluster assembly; Nitrogenase; Paenibacillus

Indexed keywords

NITROGENASE; PROTEIN KINASE FER; IRON SULFUR PROTEIN;

ARTICLE; CONTROLLED STUDY; ELECTRON TRANSPORT; ENZYME ACTIVITY; ESCHERICHIA COLI; FER GENE; FLDA GENE; GENE; GENE CLUSTER; KLEBSIELLA OXYTOCA; NIFFJ GENE; NIFQ GENE; NIFSU GENE; NIFWZM GENE; NONHUMAN; OPERON; PAENIBACILLUS; PFOAB GENE; PFOABFLDA GENE; PROMOTER REGION; SYNTHETIC BIOLOGY; BACTERIAL GENE; ENZYMOLOGY; GENETIC RECOMBINATION; GENETICS; KLEBSIELLA; METABOLISM; MULTIGENE FAMILY; PROCEDURES;

ELECTRON TRANSPORT; ESCHERICHIA COLI; GENES, BACTERIAL; IRON-SULFUR PROTEINS; KLEBSIELLA; MULTIGENE FAMILY; NITROGENASE; PAENIBACILLUS; RECOMBINATION, GENETIC; SYNTHETIC BIOLOGY;

EID: 84958280118     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/s12934-016-0442-6     Document Type: Article

References (38)

1. Rubio LM, Ludden PW. Biosynthesis of the iron-molybdenum cofactor of nitrogenase. Annu Rev Microbiol. 2008;62:93-111.
2. Hu Y, Ribbe MW. Biosynthesis of Nitrogenase FeMoco. Coord Chem Rev. 2011;255:1218-24.
3. Roberts GP, MacNeil T, MacNeil D, Brill WJ. Regulation and characterization of protein products coded by the nif (nitrogen fixation) genes of Klebsiella pneumoniae. J Bacteriol. 1979;136:267-79.
4. Arnold W, Rump A, Klipp W, Priefer UB, Puhler A. Nucleotide sequence of a 24,206-base-pair DNA fragment carrying the entire nitrogen fixation gene cluster of Klebsiella pneumoniae. J Mol Biol. 1988;203:715-38.
5. Setubal JC, dos Santos P, Goldman BS, Ertesvag H, Espin G, Rubio LM, Valla S, Almeida NF, Balasubramanian D, Cromes L, Curatti L, Du Z, Godsy E, Goodner B, Hellner-Burris K, Hernandez JA, Houmiel K, Imperial J, Kennedy C, Larson TJ, Latreille P, Ligon LS, Lu J, Maerk M, Miller NM, Norton S, O'Carroll IP, Paulsen I, Raulfs EC, Roemer R, Rosser J, Segura D, Slater S, Stricklin SL, Studholme DJ, Sun J, Viana CJ, Wallin E, Wang B, Wheeler C, Zhu H, Dean DR, Dixon R, Wood D. Genome sequence of Azotobacter vinelandii, an obligate aerobe specialized to support diverse anaerobic metabolic processes. J Bacteriol. 2009;191:4534-45.
6. Dos SP, Fang Z, Mason SW, Setubal JC, Dixon R. Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes. BMC Genom. 2012;13:162.
7. Masson-Boivin C, Giraud E, Perret X, Batut J. Establishing nitrogen-fixing symbiosis with legumes: how many rhizobium recipes? Trends Microbiol. 2009;17:458-66.
8. Boyd ES, Anbar AD, Miller S, Hamilton TL, Lavin M, Peters JW. A late methanogen origin for molybdenum-dependent nitrogenase. Geobiology. 2011;9:221-32.
9. Wang L, Zhang L, Liu Z, Zhao D, Liu X, Zhang B, Xie J, Hong Y, Li P, Chen S, Dixon R, Li J. A minimal nitrogen fixation gene cluster from Paenibacillus sp. WLY78 enables expression of active nitrogenase in Escherichia coli. PLoS Genet. 2013;9:e1003865.
10. 2-fixing Paenibacillus spp.: organization, evolution and expression of the nitrogen fixation genes. PLoS Genet. 2014;10:e1004231.
11. Dixon R, Cheng Q, Shen GF, Day A, Dowson-Day M. Nif gene transfer and expression in chloroplasts: prospects and problems. Netherlands: Springer; 1997. p. 193-203.
12. Dixon RA, Postgate JR. Genetic transfer of nitrogen fixation from Klebsiella pneumoniae to Escherichia coli. Nature. 1972;237:102-3.
13. Temme K, Zhao D, Voigt CA. Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. Proc Natl Acad Sci. 2012;109:7085-90.
14. Smanski MJ, Bhatia S, Zhao D, Park Y, Woodruff LBA, Giannoukos G, Ciulla D, Busby M, Calderon J, Nicol R, Gordon DB, Densmore D, Voigt CA. Functional optimization of gene clusters by combinatorial design and assembly. Nat Biotechnol. 2014;32:1241-9.
15. Wang X, Yang JG, Chen L, Wang JL, Cheng Q, Dixon R, Wang YP. Using synthetic biology to distinguish and overcome regulatory and functional barriers related to nitrogen fixation. PLoS One. 2013;8:e68677.
16. Ishiwa H, Shibahara H. New shuttle vectors for Escherichia coli and Bacillus subtilis. IV. The nucleotide sequence of pHY300PLK and some properties in relation to transformation. Jpn J Genet. 1986;61:515-28.
17. Johnson DC, Dean DR, Smith AD, Johnson MK. Structure, function, and formation of biological iron-sulfur clusters. Annu Rev Biochem. 2005;74:247-81.
18. Dixon R, Kahn D. Genetic regulation of biological nitrogen fixation. Nat Rev Microbiol. 2004;2:621-31.
19. Nieva-Gomez D, Roberts GP, Klevickis S, Brill WJ. Electron transport to nitrogenase in Klebsiella pneumoniae. Proc Natl Acad Sci. 1980;77:2555-8.
20. Hill S, Kavanagh EP. Roles of nifF and nifJ gene products in electron transport to nitrogenase in Klebsiella pneumoniae. J Bacteriol. 1980;141:470-5.
21. Ludden PW. Energetics and sources of energy for biological nitrogen fixation. Curr Topics Bioenerg. 1991;16:369-90.
22. Yoch DC. Electron-transport systems coupled to nitrogenase. A treatise on dinitrogen fixation. New York: Wiley; 1979. p. 605-52.
23. Deistung J, Cannon FC, Cannon MC, Hill S, Thorneley RN. Electron transfer to nitrogenase in Klebsiella pneumoniae. nifF gene cloned and the gene product, a flavodoxin, purified. Biochem J. 1985;231:743-53.
24. Roberts GP, MacNeil T, MacNeil D, Brill WJ. Regulation and characterization of protein products coded by the nif (nitrogen fixation) genes of Klebsiella pneumoniae. J Bacteriol. 1978;136:267-79.
25. MacNeil T, MacNeil D, Roberts GP, Supiano MA, Brill WJ. Fine-structure mapping and complementation analysis of nif (nitrogen fixation) genes in Klebsiella pneumoniae. J Bacteriol. 1978;136:253-66.
26. Gavini N, Tungtur S, Pulakat L. Peptidyl-prolyl cis/trans isomerase-independent functional NifH mutant of Azotobacter vinelandii. J Bacteriol. 2006;188:6020-5.
27. Achenbach LA, Genova EG. Transcriptional regulation of a second flavodoxin gene from Klebsiella pneumoniae. Gene. 1997;194:235-40.
28. Bakkes PJ, Biemann S, Bokel A, Eickholt M, Girhard M, Urlacher VB. Design and improvement of artificial redox modules by molecular fusion of flavodoxin and flavodoxin reductase from Escherichia coli. Sci Rep. 2015;5:12158.
29. Blaschkowski HP, Neuer G, Ludwig-Festl M, Knappe J. Routes of flavodoxin and ferredoxin reduction in Escherichia coli. CoA-acylating pyruvate: flavodoxin and NADPH: flavodoxin oxidoreductases participating in the activation of pyruvate formate-lyase. Eur J Biochem. 1982;123:563-9.
30. Bianchi V, Reichard P, Eliasson R, Pontis E, Krook M, Jornvall H, Haggard-Ljungquist E. Escherichia coli ferredoxin NADP + reductase: activation of E. coli anaerobic ribonucleotide reduction, cloning of the gene (fpr), and overexpression of the protein. J Bacteriol. 1993;175:1590-5.
31. McIver L, Leadbeater C, Campopiano DJ, Baxter RL, Daff SN, Chapman SK, Munro AW. Characterisation of flavodoxin NADP + oxidoreductase and flavodoxin; key components of electron transfer in Escherichia coli. Eur J Biochem. 1998;257:577-85.
32. Enkh-Amgalan J, Kawasaki H, Seki T. Molecular evolution of the nif gene cluster carrying nifI1 and nifI2 genes in the Gram-positive phototrophic bacterium Heliobacterium chlorum. Int J Syst Evol Microbiol. 2006;56:65-74.
33. Howard KS, McLean PA, Hansen FB, Lemley PV, Koblan KS, Orme-Johnson WH. Klebsiella pneumoniae nifM gene product is required for stabilization and activation of nitrogenase iron protein in Escherichia coli. J Biol Chem. 1986;261:772-8.
34. Imperial J, Ugalde RA, Shah VK, Brill WJ. Role of the nifQ gene product in the incorporation of molybdenum into nitrogenase in Klebsiella pneumoniae. J Bacteriol. 1984;158:187-94.
35. Oh CJ, Kim HB, Kim J, Kim WJ, Lee H, An CS. Organization of nif gene cluster in Frankia sp. EuIK1 strain, a symbiont of Elaeagnus umbellata. Arch Microbiol. 2012;194:29-34.
36. Welsh EA, Liberton M, Stockel J, Loh T, Elvitigala T, Wang C, Wollam A, Fulton RS, Clifton SW, Jacobs JM, Aurora R, Ghosh BK, Sherman LA, Smith RD, Wilson RK, Pakrasi HB. The genome of Cyanothece 51142, a unicellular diazotrophic cyanobacterium important in the marine nitrogen cycle. Proc Natl Acad Sci USA. 2008;105:15094-9.
37. Lake MW, Wuebbens MM, Rajagopalan KV, Schindelin H. Mechanism of ubiquitin activation revealed by the structure of a bacterial MoeB-MoaD complex. Nature. 2001;414:325-9.
38. Lehmann C, Begley TP, Ealick SE. Structure of the Escherichia coli ThiS-ThiF complex, a key component of the sulfur transfer system in thiamin biosynthesis. Biochemistry. 2006;45:11-9.