A toolkit to enable hydrocarbon conversion in aqueous environments

Journal of Visualized Experiments

Volumn , Issue 68, 2012, Pages

  Brinkman, Eva K ^a   Schipper, Kira ^a   Bongaerts, Nadine ^a   Voges, Mathias J ^a   Abate, Alessandro ^b   Aljoscha Wahl, S ^a  

^a DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

^b DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

Author keywords

Alkane hydroxylase system; Alkane metabolism; BioBrick; Biochemistry; Bioengineering; Chemical engineering; Chemistry; Escherichia coli; Homologous interaction mapping; iGEM; Issue 68; Mathematical model; Microbiology; Oil remediation; Prefoldin; Resting cell assay; Synthetic biology

Indexed keywords

EID: 84868296580     PISSN: 1940087X     EISSN: None     Source Type: Journal    
DOI: 10.3791/4182     Document Type: Article

References (22)

1. Allen, E.W. Process water treatment in Canada's oil sands industry: I: Target pollutants and treatment objectives. J. Environ. Eng. Sci. 7, 123-138 (2008).
2. Alon, U. An Introduction to Systems Biology: Design Principles of Biological Circuits. CRC Press., (2007).
3. Center, O.P. Understanding Oil Spills and Oil Spill Response. (1999).
4. Cytoscape. An Open Source Platform for Complex Network Analysis and Visualization. http://www.cytoscape.org/ (2012).
5. Debreczeny, M.P. & Davies E.T. Non-Invasive Biomass Monitor with Wide Linear Range. http://www.buglab.com/docs/OnLineODMeasurement.pdf (2012).
6. Eichler, K., Buchet, A., Lemke, R., Kleber, H.P., & Mandrand-Berthelot, M.A. Identification and characterization of the caiF gene encoding a potential transcriptional activator of carnitine metabolism in Escherichia coli. J. Bacteriol. 178, 1248-1257 (1995).
7. Feng, L., Wang, W., Cheng, J., Ren, Y., Zhao, G., Gao, C., Tang, Y., Liu, X., Han, W., Peng, X., et al. Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir. Proc. Natl. Acad. Sci. U.S.A. 104 (13), 5602-5607 (2007).
8. Fujii, T., Narikawa, T., Takeda, K., & Kato, J. Biotransformation of various alkanes using the Escherichia coli expressing an alkane hydroxylase system from Gordonia sp. TF6. Biosci. Biotechnol. Biochem. 68 (10), 2171-2177 (2004).
9. iGEM. Registry of Standard Biological Parts. http://partsregistry.org/Main_Page (2012).
10. Kato, T., Miyanaga, A., Haruki, M., Imanaka, T., Morikawa, M., & Kanaya, S. Gene cloning of an alcohol dehydrogenase from thermophilic alkane-degrading Bacillus thermoleovorans B23. J. Biosci. Bioeng. 91 (1), 100-102 (2001).
11. Kato, T., Miyanaga, A., Kanaya, S., & Morikawa, M. Gene cloning and characterization of an aldehyde dehydrogenase from long-chain alkane-degrading Geobacillus thermoleovorans B23. Extremophiles. 14, 33-39 (2010).
12. Kieboom, J. & De Bont, J.A.M. Bacterial Stress Responses. Washington, D.C., ASM Press., (2000).
13. Kotte, O., Zaugg, J.B., & Heinemann, M. Bacterial adaptation through distributed sensing of metabolic fluxes. Mol Syst Biol. 6 355 (2010)
14. Kremling, A., Bettenbrock, K., & Gilles, E.D. Analysis of global control of Escherichia coli carbohydrate uptake. BMC Syst. Biol. 1, 42 (2007).
15. Li, L., Liu, X., Yang, W., Xu, F., Wang, W., Feng, L., Bartlam, M., Wang, L., & Rao, Z. Crystal structure of long-chain alkane monooxygenase (LadA) in complex with coenzyme FMN: unveiling the long-chain alkane hydroxylase. J. Mol. Biol. 376 (2), 453-465 (2008).
16. Lin, H.Y., Mathiszik, B., Xu, B., Enfors, S.O., & Neubauer, P. Determination of the maximum specific uptake capacities for glucose and oxygen in glucose-limited fed-batch cultivations of Escherichia coli. Biotechnol. Bioeng. 73 (5), 347-357 (2001).
17. Okochi, M., Kanie, K., Kurimoto, M., Yohda, M., & Honda, H. Overexpression of prefoldin from the hyperthermophilic archaeum Pyrococcus horikoshii OT3 endowed Escherichia coli with organic solvent tolerance. Appl. Microbiol. Biotechnol. 79 (3), 443-449 (2008).
18. Rehm, H.J. & Reiff, I. Mechanisms and occurrence of microbial oxidation of long-chain alkanes. Adv. Biochem. Eng. / Biotechnol. 19, 175-215 (1981).
19. Rojo, F. Degradation of alkanes by bacteria. Environ. Microbiol. 11 (10), 2477-2490 (2009).
20. STRING 9.0 Known and Predicted Protein-Protein Interactions. http://string-db.org/newstring_cgi/show_download_page.pl (2012).
21. Van Beilen, J.B., Panke, S., Lucchini, S., Franchini, A.G., Rothlisberger, M., & Witholt, B. Analysis of Pseudomonas putida alkane-degradation gene clusters and flanking insertion sequences: evolution and regulation of the alk genes. Microbiology. 147 (Pt. 6), 1621-1630 (2001).
22. Wang, L., Tang, Y., Wang, S., Liu, R.L., Liu, M.Z., Zhang, Y., Liang, F.L., & Feng, L. Isolation and characterization of a novel thermophilic Bacillus strain degrading long-chain n-alkanes. Extremophiles. 10 (4), 347-356 (2006).