Design and testing of a synthetic biology framework for genetic engineering of Corynebacterium glutamicum

Microbial Cell Factories

Volumn 11, Issue , 2012, Pages

  Ravasi, Pablo ^a,b   Peiru, Salvador ^a   Gramajo, Hugo ^a   Menzella, Hugo G ^a  

^a UNIVERSIDAD NACIONAL DE ROSARIO   (Argentina)

^b Geneg SRL   (Argentina)

Author keywords

Corynebacterium glutamicum; Metabolic engineering; Synthetic biology

Indexed keywords

BETA GALACTOSIDASE;

ARTICLE; BINDING SITE; CORYNEBACTERIUM GLUTAMICUM; GENE CLUSTER; GENE EXPRESSION; GENE SEQUENCE; GENETIC ENGINEERING; METABOLISM; NONHUMAN; OPERON; PLASMID; REPORTER GENE; SYNTHETIC BIOLOGY;

BINDING SITES; CORYNEBACTERIUM GLUTAMICUM; GENE DOSAGE; GENETIC ENGINEERING; GREEN FLUORESCENT PROTEINS; LUMINESCENT PROTEINS; MULTIGENE FAMILY; PLASMIDS; PROMOTER REGIONS, GENETIC; RECOMBINANT PROTEINS; RESEARCH DESIGN; RIBOSOMES;

BACTERIA (MICROORGANISMS); CORYNEBACTERIUM GLUTAMICUM; ESCHERICHIA COLI;

EID: 84868319444     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/1475-2859-11-147     Document Type: Article

References (51)

1. Endy D. Foundations for engineering biology. Nature 2005, 438(7067):449-453. 10.1038/nature04342, 16306983.
2. Heinemann M, Panke S. Synthetic biology-putting engineering into biology. Bioinformatics 2006, 22(22):2790-2799. 10.1093/bioinformatics/btl469, 16954140.
3. Leonard E, Nielsen D, Solomon K, Prather KJ. Engineering microbes with synthetic biology frameworks. Trends Biotechnol 2008, 26(12):674-681. 10.1016/j.tibtech.2008.08.003, 18977048.
4. McDaniel R, Weiss R. Advances in synthetic biology: on the path from prototypes to applications. Curr Opin Biotechnol 2005, 16(4):476-483. 10.1016/j.copbio.2005.07.002, 16019200.
5. Nielsen J, Keasling JD. Synergies between synthetic biology and metabolic engineering. Nat Biotechnol 2011, 29(8):693-695. 10.1038/nbt.1937, 21822239.
6. Dellomonaco C, Fava F, Gonzalez R. The path to next generation biofuels: successes and challenges in the era of synthetic biology. Microb Cell Fact 2010, 9:3. 10.1186/1475-2859-9-3, 2817670, 20089184.
7. Huang HH, Camsund D, Lindblad P, Heidorn T. Design and characterization of molecular tools for a Synthetic Biology approach towards developing cyanobacterial biotechnology. Nucleic Acids Res 2010, 38(8):2577-2593. 10.1093/nar/gkq164, 2860132, 20236988.
8. Holatko J, Elisakova V, Prouza M, Sobotka M, Nesvera J, Patek M. Metabolic engineering of the L-valine biosynthesis pathway in Corynebacterium glutamicum using promoter activity modulation. J Biotechnol 2009, 139(3):203-210. 10.1016/j.jbiotec.2008.12.005, 19121344.
9. Kikuchi Y, Itaya H, Date M, Matsui K, Wu LF. TatABC overexpression improves Corynebacterium glutamicum Tat-dependent protein secretion. Appl Environ Microbiol 2009, 75(3):603-607. 10.1128/AEM.01874-08, 2632119, 19074606.
10. Nakashima N, Mitani Y, Tamura T. Actinomycetes as host cells for production of recombinant proteins. Microb Cell Fact 2005, 4(1):7. 10.1186/1475-2859-4-7, 1079934, 15788099.
11. Hermann T. Industrial production of amino acids by coryneform bacteria. J Biotechnol 2003, 104(1-3):155-172.
12. Shinfuku Y, Sorpitiporn N, Sono M, Furusawa C, Hirasawa T, Shimizu H. Development and experimental verification of a genome-scale metabolic model for Corynebacterium glutamicum. Microb Cell Fact 2009, 8:43. 10.1186/1475-2859-8-43, 2728707, 19646286.
13. Papagianni M. Recent advances in engineering the central carbon metabolism of industrially important bacteria. Microb Cell Fact 2012, 11(1):50. 10.1186/1475-2859-11-50, 3461431, 22545791.
14. Nesvera J, Patek M. Tools for genetic manipulations in Corynebacterium glutamicum and their applications. Appl Microbiol Biotechnol 2011, 90(5):1641-1654. 10.1007/s00253-011-3272-9, 21519933.
15. Kirchner O, Tauch A. Tools for genetic engineering in the amino acid-producing bacterium Corynebacterium glutamicum. J Biotechnol 2003, 104(1-3):287-299.
16. Knoppova M, Phensaijai M, Vesely M, Zemanova M, Nesvera J, Patek M. Plasmid vectors for testing in vivo promoter activities in Corynebacterium glutamicum and Rhodococcus erythropolis. Curr Microbiol 2007, 55(3):234-239. 10.1007/s00284-007-0106-1, 17657537.
17. Handbook of Corynebacterium glutamicum 2005, BocaRaton, FL: CRC Press, Eggeling L, Bott M.
18. Tauch A, Kirchner O, Loffler B, Gotker S, Puhler A, Kalinowski J. Efficient electrotransformation of corynebacterium diphtheriae with a mini-replicon derived from the Corynebacterium glutamicum plasmid pGA1. Curr Microbiol 2002, 45(5):362-367. 10.1007/s00284-002-3728-3, 12232668.
19. Cormack BP, Valdivia RH, Falkow S. FACS-optimized mutants of the green fluorescent protein (GFP). Gene 1996, 173(1 Spec No):33-38.
20. Date M, Yokoyama K, Umezawa Y, Matsui H, Kikuchi Y. Production of native-type Streptoverticillium mobaraense transglutaminase in Corynebacterium glutamicum. Appl Environ Microbiol 2003, 69(5):3011-3014. 10.1128/AEM.69.5.3011-3014.2003, 154552, 12732581.
21. Brabetz W, Liebl W, Schleifer KH. Studies on the utilization of lactose by Corynebacterium glutamicum, bearing the lactose operon of Escherichia coli. Arch Microbiol 1991, 155(6):607-612. 10.1007/BF00245357, 1953301.
22. Becker J, Zelder O, Hafner S, Schroder H, Wittmann C. From zero to hero-design-based systems metabolic engineering of Corynebacterium glutamicum for L-lysine production. Metab Eng 2011, 13(2):159-168. 10.1016/j.ymben.2011.01.003, 21241816.
23. Patek M, Nesvera J. Sigma factors and promoters in Corynebacterium glutamicum. J Biotechnol 2011, 154(2-3):101-113.
24. Shaner NC, Campbell RE, Steinbach PA, Giepmans BN, Palmer AE, Tsien RY. Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat Biotechnol 2004, 22(12):1567-1572. 10.1038/nbt1037, 15558047.
25. Tauch A, Gotker S, Puhler A, Kalinowski J, Thierbach G. The 27.8-kb R-plasmid pTET3 from Corynebacterium glutamicum encodes the aminoglycoside adenyltransferase gene cassette aadA9 and the regulated tetracycline efflux system Tet 33 flanked by active copies of the widespread insertion sequence IS6100. Plasmid 2002, 48(2):117-129. 10.1016/S0147-619X(02)00120-8, 12383729.
26. Radford AJ, Hodgson AL. Construction and characterization of a Mycobacterium-Escherichia coli shuttle vector. Plasmid 1991, 25(2):149-153. 10.1016/0147-619X(91)90029-V, 1857754.
27. Tauch A, Bischoff N, Brune I, Kalinowski J. Insights into the genetic organization of the Corynebacterium diphtheriae erythromycin resistance plasmid pNG2 deduced from its complete nucleotide sequence. Plasmid 2003, 49(1):63-74. 10.1016/S0147-619X(02)00115-4, 12584002.
28. Serwold-Davis TM, Groman N, Rabin M. Transformation of Corynebacterium diphtheriae, Corynebacterium ulcerans, Corynebacterium glutamicum, and Escherichia coli with the C. diphtheriae plasmid pNG2. Proc Natl Acad Sci USA 1987, 84(14):4964-4968. 10.1073/pnas.84.14.4964, 305227, 3110777.
29. Tauch A, Puhler A, Kalinowski J, Thierbach G. Plasmids in Corynebacterium glutamicum and their molecular classification by comparative genomics. J Biotechnol 2003, 104(1-3):27-40.
30. Shetty RP, Endy D, Knight TF. Engineering BioBrick vectors from BioBrick parts. J Biol Eng 2008, 2:5. 10.1186/1754-1611-2-5, 2373286, 18410688.
31. Puigbo P, Guzman E, Romeu A, Garcia-Vallve S. OPTIMIZER: a web server for optimizing the codon usage of DNA sequences. Nucleic Acids Res 2007, 35(Web Server issue):W126-W131. 1933141, 17439967.
32. Menzella HG. Comparison of two codon optimization strategies to enhance recombinant protein production in Escherichia coli. Microb Cell Fact 2011, 10:15. 10.1186/1475-2859-10-15, 3056764, 21371320.
33. Reisinger SJ, Patel KG, Santi DV. Total synthesis of multi-kilobase DNA sequences from oligonucleotides. Nat Protoc 2006, 1(6):2596-2603.
34. Menzella HG, Reid R, Carney JR, Chandran SS, Reisinger SJ, Patel KG, Hopwood DA, Santi DV. Combinatorial polyketide biosynthesis by de novo design and rearrangement of modular polyketide synthase genes. Nat Biotechnol 2005, 23(9):1171-1176. 10.1038/nbt1128, 16116420.
35. Menzella HG, Carney JR, Santi DV. Rational design and assembly of synthetic trimodular polyketide synthases. Chem Biol 2007, 14(2):143-151. 10.1016/j.chembiol.2006.12.002, 17317568.
36. Sarrion-Perdigones A, Falconi EE, Zandalinas SI, Juarez P, Fernandez-del-Carmen A, Granell A, Orzaez D. GoldenBraid: an iterative cloning system for standardized assembly of reusable genetic modules. PLoS One 2011, 6(7):e21622. 10.1371/journal.pone.0021622, 3131274, 21750718.
37. Shetty R, Lizarazo M, Rettberg R, Knight TF. Assembly of BioBrick standard biological parts using three antibiotic assembly. Methods Enzymol 2011, 498:311-326.
38. Norville JE, Derda R, Gupta S, Drinkwater KA, Belcher AM, Leschziner AE, Knight TF. Introduction of customized inserts for s-treamlined assembly and optimization of BioBrick synthetic genetic circuits. J Biol Eng 2010, 4:17. 10.1186/1754-1611-4-17, 3022552, 21172029.
39. Eikmanns BJ, Kleinertz E, Liebl W, Sahm H. A family of Corynebacterium glutamicum/Escherichia coli shuttle vectors for cloning, controlled gene expression, and promoter probing. Gene 1991, 102(1):93-98. 10.1016/0378-1119(91)90545-M, 1864513.
40. Brune I, Werner H, Huser AT, Kalinowski J, Puhler A, Tauch A. The DtxR protein acting as dual transcriptional regulator directs a global regulatory network involved in iron metabolism of Corynebacterium glutamicum. BMC Genomics 2006, 7:21. 10.1186/1471-2164-7-21, 1382209, 16469103.
41. Menzella HG, Ceccarelli EA, Gramajo HC. Novel escherichia coli strain allows efficient recombinant protein production using lactose as inducer. Biotechnol Bioeng 2003, 82(7):809-817. 10.1002/bit.10630, 12701147.
42. Basu S, Gerchman Y, Collins CH, Arnold FH, Weiss R. A synthetic multicellular system for programmed pattern formation. Nature 2005, 434(7037):1130-1134. 10.1038/nature03461, 15858574.
43. Pfleger BF, Pitera DJ, Smolke CD, Keasling JD. Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat Biotechnol 2006, 24(8):1027-1032. 10.1038/nbt1226, 16845378.
44. Salis HM, Mirsky EA, Voigt CA. Automated design of synthetic ribosome binding sites to control protein expression. Nat Biotechnol 2009, 27(10):946-950. 10.1038/nbt.1568, 2782888, 19801975.
45. Agnew DEaPBF Optimization of synthetic operons using libraries of post-transcriptional regulatory elements. Strain Engineering: Methods and Protocols 2011, 99-111. Williams JA, Agnew DEaPBF.
46. Porcar M. Beyond directed evolution: Darwinian selection as a tool for synthetic biology. Syst Synth Biol 2010, 4(1):1-6. 10.1007/s11693-009-9045-4, 2816224,2816224, 19821059.
47. Anand R, Rai N, Thattai M. Promoter reliability in modular transcriptional networks. Methods Enzymol 2011, 497:31-49.
48. Hanahan D. Techniques for transformation of E. coli. DNA Cloning A Practical Approach 1985, 109-135. Oxford: IRL Press, Glover DM.
49. Maniatis T, Fritsch EF, Sambrook J. Molecular cloning: A Laboratory Manual 1982, Cold Spring Harbor. New York: Cold Spring Harbor Laboratory, Cold Spring Harbor.
50. Molecular cloning: a laboratory manual. Cold Spring Harbor 1989, New York: Cold SpringHarbor Press, Sambrook J, Fritsch EF, Maniatis T, Second.
51. Shaner NC, Steinbach PA, Tsien RY. A guide to choosing fluorescent proteins. Nat Methods 2005, 2(12):905-909. 10.1038/nmeth819, 16299475.