Construction of a BioBrick™ compatible vector system for Rhodococcus

Plasmid

Volumn 90, Issue , 2017, Pages 1-4

  Ellinger, James ^a   Schmidt Dannert, Claudia ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

BioBrick ; Rhodococcus; Synthetic biology

Indexed keywords

GENUS; GRAM POSITIVE BACTERIUM; HETEROLOGOUS EXPRESSION; HUMAN; HUMAN CELL; NONHUMAN; PLASMID; PROMOTER REGION; RHODOCOCCUS OPACUS; SYNTHETIC BIOLOGY; CHEMISTRY; DRUG EFFECTS; ESCHERICHIA COLI; GENE EXPRESSION; GENE VECTOR; GENETIC ENGINEERING; GENETICS; METABOLISM; PROCEDURES; REPORTER GENE; RHODOCOCCUS;

ANTIINFECTIVE AGENT; ENHANCED GREEN FLUORESCENT PROTEIN; GREEN FLUORESCENT PROTEIN; KANAMYCIN; LAC REPRESSOR; RESTRICTION ENDONUCLEASE;

ANTI-BACTERIAL AGENTS; DNA RESTRICTION ENZYMES; ESCHERICHIA COLI; GENE EXPRESSION; GENES, REPORTER; GENETIC ENGINEERING; GENETIC VECTORS; GREEN FLUORESCENT PROTEINS; KANAMYCIN; LAC REPRESSORS; PLASMIDS; PROMOTER REGIONS, GENETIC; RHODOCOCCUS;

EID: 85011672165     PISSN: 0147619X     EISSN: 10959890     Source Type: Journal    
DOI: 10.1016/j.plasmid.2017.01.004     Document Type: Article

References (42)

1. Alvarez, H.M., Steinbüchel, A., Triacylglycerols in prokaryotic microorganisms. Appl. Microbiol. Biotechnol. 60 (2002), 367–376.
2. Alvarez, H.M., Mayer, F., Fabritius, D., Steinbüchel, A., Formation of intracytoplasmic lipid inclusions by Rhodococcus opacus strain PD630. Arch. Microbiol. 165 (1996), 377–386.
3. Alvarez, H.M., Steinbüchel, A., Physiology, biochemistry, and molecular biology of triacylglycerol accumulation by Rhodococcus. Alvarez, H.M., (eds.) Biology of Rhodococcus Microbiology Monographs, 16, 2010, Springer, Berlin Heidelberg, 263–290.
4. Archer, J.A.C., Sinskey, A.J., The DNA sequence and minimal replicon of the Corynebacterium glutamicum plasmid pSR1: evidence of a common ancestry with plasmids from C. diphtheriae. J. Gen. Microbiol. 139 (1993), 1753–1759.
5. Bell, Philp, Aw, Christofi, The genus Rhodococcus. J. Appl. Microbiol. 85 (1998), 195–210.
6. Bi, C., Su, P., Müller, J., Yeh, Y.-C., Chhabra, S.R., Beller, H.R., Singer, S.W., Hillson, N.J., Development of a broad-host synthetic biology toolbox for Ralstonia eutropha and its application to engineering hydrocarbon biofuel production. Microb. Cell Factories, 12, 2013, 107.
7. Chartrain, M., Jackey, B., Taylor, C., Sandford, V., Gbewonyo, K., Lister, L., Dimichele, L., Hirsch, C., Heimbuch, B., Maxwell, C., Pascoe, D., Buckland, B., Greasham, R., Bioconversion of indene to cis (1S,2R) indandiol and trans (1R,2R) indandiol by Rhodococcus species. J. Ferment. Bioeng. 86 (1998), 550–558.
8. Chen, Y., Ding, Y., Yang, L., Yu, J., Liu, G., Wang, X., Zhang, S., Yu, D., Song, L., Zhang, H., Zhang, C., Huo, L., Huo, C., Wang, Y., Du, Y., Zhang, H., Zhang, P., Na, H., Xu, S., Zhu, Y., Xie, Z., He, T., Zhang, Y., Wang, G., Fan, Z., Yang, F., Liu, H., Wang, X., Zhang, X., Zhang, M.Q., Li, Y., Steinbüchel, A., Fujimoto, T., Cichello, S., Yu, J., Liu, P., Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630. Nucleic Acids Res. 42 (2014), 1052–1064.
9. Chen, J.H., Yeh, H.T., The seventh copy of IS1 in Escherichia coli W3110 belongs to the IS1 A (IS1E) type which is the only IS1 type that transposes from chromosome to plasmids. Proc. Natl. Sci. Counc. Repub. China B 21 (1997), 100–105.
10. Dong, L., Nakashima, N., Tamura, N., Tamura, T., Isolation and characterization of the Rhodococcus opacus thiostrepton-inducible genes tipAL and tipAS: application for recombinant protein expression in Rhodococcus. FEMS Microbiol. Lett. 237 (2004), 35–40.
11. Gouda, M.K., Omar, S.H., Aouad, L.M., Single cell oil production by Gordonia sp. DG using agro-industrial wastes. World J. Microbiol. Biotechnol. 24 (2008), 1703–1711.
12. Hetzler, S., Bröker, D., Steinbüchel, A., Saccharification of cellulose by recombinant Rhodococcus opacus PD630 strains. Appl. Environ. Microbiol. 79 (2013), 5159–5166.
13. Hetzler, S., Steinbüchel, A., Establishment of cellobiose utilization for lipid production in Rhodococcus opacus PD630. Appl. Environ. Microbiol. 79 (2013), 3122–31225.
14. Holder, J.W., Ulrich, J.C., DeBono, A.C., Godfrey, P.A., Desjardins, C.A., Zucker, J., Zeng, Q., Leach, A.L.B., Ghiviriga, I., Dancel, C., Abeel, T., Gevers, D., Kodira, C.D., Desany, B., Affourtit, J.P., Birren, B.W., Sinskey, A.J., Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development. PLoS Genet., 7, 2011, e1002219.
15. Kalscheuer, R., Arenskötter, M., Steinbüchel, A., Establishment of a gene transfer system for Rhodococcus opacus PD630 based on electroporation and its application for recombinant biosynthesis of poly(3-hydroxyalkanoic acids). Appl. Microbiol. Biotechnol. 52 (1999), 508–515.
16. Kang, M.-K., Lee, J., Um, Y., Lee, T.S., Bott, M., Park, S.J., Woo, H.M., Synthetic biology platform of CoryneBrick vectors for gene expression in Corynebacterium glutamicum and its application to xylose utilization. Appl. Microbiol. Biotechnol. 98 (2014), 5991–6002.
17. Kilbane, J.J. II, Metabolic Engineering to Develop a Pathway for the Selective Cleavage of Carbon-Nitrogen Bonds. 2006, Gas Technology Institute, 78–83, 10.2172/887496.
18. Knight, T.F., Idempotent vector design for standard assembly of BioBricks. Technical report. MIT Synthetic Biology Working Group Technical Reports, 2003 http://hdl.handle.net/1721.1/21168.
19. Knoppová, M., Phensaijai, M., Veselý, M., Zemanová, M., Nešvera, J., Pátek, M., Plasmid vectors for testing in vivo promoter activities in Corynebacterium glutamicum and Rhodococcus erythropolis. Curr. Microbiol. 55 (2007), 234–239.
20. Kosa, M., Ragauskas, A.J., Bioconversion of lignin model compounds with oleaginous Rhodococci. Appl. Microbiol. Biotechnol. 93 (2012), 891–900.
21. Kurosawa, K., Wewetzer, S.J., Sinskey, A.J., Engineering xylose metabolism in triacylglycerol-producing Rhodococcus opacus for lignocellulosic fuel production. Biotechnol. Biofuels, 6, 2013, 134.
22. Martínková, L., Uhnáková, B., Pátek, M., Nešvera, J., Křen, V., Biodegradation potential of the genus Rhodococcus. Environ. Int. 35 (2009), 162–177.
23. Murin, C.D., Segal, K., Bryksin, A., Matsumura, I., Expression vectors for the engineering of genes and genomes in Acinetobacter baylyi ADP1. Appl. Environ. Microbiol. 78 (2011), 280–283.
24. Nakashima, N., Tamura, T., A novel system for expressing recombinant proteins over a wide temperature range from 4 to 35 °C. Biotechnol. Bioeng. 86 (2004), 136–148.
25. Pinto, F., Pacheco, C.C., Oliveira, P., Montagud, A., Landels, A., Couto, N., Wright, P.C., Urchueguía, J.F., Tamagnini, P., Improving a Synechocystis-based photoautotrophic chassis through systematic genome mapping and validation of neutral sites. DNA Res. 22 (2015), 425–437.
26. Pósfai G, Plunkett G, Fehér T, Frisch D, Keil GM, Umenhoffer K, Kolisnychenko V, Stahl B, Sharma SS, Arruda M de, Burland V, Harcum SW, Blattner FR. 2006. Emergent properties of reduced-genome Escherichia coli. Science 312:1044–1046.
27. Prather, K.L.J., Edmonds, M.C., Herod, J.W., Identification and characterization of IS1 transposition in plasmid amplification mutants of E. coli clones producing DNA vaccines. Appl. Microbiol. Biotechnol. 73 (2006), 815–826.
28. Radeck, J., Kraft, K., Bartels, J., Cikovic, T., Dürr, F., Emenegger, J., Kelterborn, S., Sauer, C., Fritz, G., Gebhard, S., Mascher, T., The Bacillus BioBrick Box: generation and evaluation of essential genetic building blocks for standardized work with Bacillus subtilis. J. Biol. Eng., 7, 2013, 29.
29. Ravasi, P., Peiru, S., Gramajo, H., Menzella, H.G., Design and testing of a synthetic biology framework for genetic engineering of Corynebacterium glutamicum. Microb. Cell Factories 11 (2012), 1–11.
30. Schmidt-Dannert, C., Umeno, D., Arnold, F.H., Molecular breeding of carotenoid biosynthetic pathways. Nat. Biotechnol. 18 (2000), 750–753.
31. Shao, Z., Dick, W.a., Behki, R.m., An improved Escherichia coli-Rhodococcus shuttle vector and plasmid transformation in Rhodococcus spp. using electroporation. Lett. Appl. Microbiol. 21 (1995), 261–266.
32. Sorg, R.A., Kuipers, O.P., Veening, J.-W., Gene expression platform for synthetic biology in the human pathogen Streptococcus pneumoniae. ACS Synth. Biol. 4 (2015), 228–239.
33. Thastrup, O., Tullin, S., Poulsen, L.K., Bjørn, S.P., Novel variants of green fluorescent protein, GFP. International Application published under the Patent Cooperation Treaty (PCT). International Publication Number WO97/11094, 1997.
34. Tikh, I.B., Held, M., Schmidt-Dannert, C., BioBrickTM compatible vector system for protein expression in Rhodobacter sphaeroides. Appl. Microbiol. Biotechnol. 98 (2014), 3111–3119.
35. Tsuji, N., Honda, K., Wada, M., Okano, K., Ohtake, H., Isolation and characterization of a thermotolerant ene reductase from Geobacillus sp. 30 and its heterologous expression in Rhodococcus opacus. Appl. Microbiol. Biotechnol. 98 (2014), 5925–5935.
36. Van der Geize, R., Dijkhuizen, L., Harnessing the catabolic diversity of rhodococci for environmental and biotechnological applications. Curr. Opin. Microbiol. 7 (2004), 255–261.
37. Veselý, M., Pátek, M., Nešvera, J., Čejková, A., Masák, J., Jirků, V., Host-vector system for phenol-degrading Rhodococcus erythropolis based on Corynebacterium plasmids. Appl. Microbiol. Biotechnol. 61 (2003), 523–527.
38. Vick, J., Johnson, E., Choudhary, S., Bloch, S., Lopez-Gallego, F., Srivastava, P., Tikh, I., Wawrzyn, G., Schmidt-Dannert, C., Optimized compatible set of BioBrick™ vectors for metabolic pathway engineering. Appl. Microbiol. Biotechnol. 92 (2011), 1275–1286.
39. Wang, B., Rezenom, Y.H., Cho, K.-C., Tran, J.L., Lee, D.G., Russell, D.H., Gill, J.J., Young, R., Chu, K.-H., Cultivation of lipid-producing bacteria with lignocellulosic biomass: effects of inhibitory compounds of lignocellulosic hydrolysates. Bioresour. Technol. 161 (2014), 162–170.
40. Xiong, X., Wang, X., Chen, S., Engineering of a xylose metabolic pathway in Rhodococcus strains. Appl. Environ. Microbiol. 78 (2012), 5483–5491.
41. Yoneda, A., Henson, W.R., Goldner, N.K., Park, K.J., Forsberg, K.J., Kim, S.J., Pesesky, M.W., Foston, M., Dantas, G., Moon, T.S., Comparative transcriptomics elucidates adaptive phenol tolerance and utilization in lipid-accumulating Rhodococcus opacus PD630. Nucleic Acids Res. 44 (2016), 2240–2254.
42. Yoshihama, M., Higashiro, K., Rao, E.A., Akedo, M., Shanabruch, W.G., Follettie, M.T., Walker, G.C., Sinskey, A.J., Cloning vector system for Corynebacterium glutamicum. J. Bacteriol. 162 (1985), 591–597.