Applied Microbiology and Biotechnology

, Volume 93, Issue 5, pp 1853–1863 | Cite as

Available methods for assembling expression cassettes for synthetic biology

  • Tianwen Wang
  • Xingyuan Ma
  • Hu Zhu
  • Aitao Li
  • Guocheng Du
  • Jian Chen
Mini-Review
First Online:
Received:
Revised:
Accepted:

Abstract

Studies in the structural biology of the multicomponent protein complex, metabolic engineering, and synthetic biology frequently rely on the efficient over-expression of these subunits or enzymes in the same cell. As a first step, constructing the multiple expression cassettes will be a complicated and time-consuming job if the classic and conventional digestion and ligation based cloning method is used. Some more efficient methods have been developed, including (1) the employment of a multiple compatible plasmid expression system, (2) the rare-cutter-based design of vectors, (3) in vitro recombination (sequence and ligation independent cloning, the isothermally enzymatic assembly of DNA molecules in a single reaction), and (4) in vivo recombination using recombination-efficient yeast (in vivo assembly of overlapping fragments, reiterative recombination for the chromosome integration of foreign expression cassettes). In this review, we systematically introduce these available methods.

Keywords

Synthetic biology Simultaneous expression Pathway construction Yeast recombination Cre-loxP site-specific recombination Acembl system 
This is a preview of subscription content, log in to check access.

Notes

Acknowledgements

Grants from the National Science Foundation of China (31000054, 30873190) and the Fundamental Research Funds for the Central Universities (No. JUSRP10917) supported this research.

Reference

  1. Aslanidis C, de Jong PJ (1990) Ligation-independent cloning of PCR products (LIC-PCR). Nucleic Acids Res 18(20):6069–6074CrossRefGoogle Scholar
  2. Aslanidis C, de Jong PJ, Schmitz G (1994) Minimal length requirement of the single-stranded tails for ligation-independent cloning (LIC) of PCR products. PCR Methods Appl 4(3):172–177Google Scholar
  3. Berger I, Fitzgerald DJ, Richmond TJ (2004) Baculovirus expression system for heterologous multiprotein complexes. Nat Biotechnol 22(12):1583–1587. doi: 10.1038/nbt1036 CrossRefGoogle Scholar
  4. Bieniossek C, Nie Y, Frey D, Olieric N, Schaffitzel C, Collinson I, Romier C, Berger P, Richmond TJ, Steinmetz MO, Berger I (2009) Automated unrestricted multigene recombineering for multiprotein complex production. Nat Methods 6(6):447–450. doi: 10.1038/nmeth.1326 CrossRefGoogle Scholar
  5. Busso D, Peleg Y, Heidebrecht T, Romier C, Jacobovitch Y, Dantes A, Salim L, Troesch E, Schuetz A, Heinemann U, Folkers GE, Geerlof A, Wilmanns M, Polewacz A, Quedenau C, Bussow K, Adamson R, Blagova E, Walton J, Cartwright JL, Bird LE, Owens RJ, Berrow NS, Wilson KS, Sussman JL, Perrakis A, Celie PH (2011) Expression of protein complexes using multiple Escherichia coli protein co-expression systems: a benchmarking study. J Struct Biol 175(2):159–170. doi: 10.1016/j.jsb.2011.03.004 CrossRefGoogle Scholar
  6. Carrera J, Rodrigo G, Jaramillo A (2009) Towards the automated engineering of a synthetic genome. Mol Biosyst 5(7):733–743. doi: 10.1039/b904400k CrossRefGoogle Scholar
  7. Cohen SN, Chang AC, Boyer HW, Helling RB (1973) Construction of biologically functional bacterial plasmids in vitro. Proc Natl Acad Sci U S A 70(11):3240–3244CrossRefGoogle Scholar
  8. Cowieson NP, Kobe B, Martin JL (2008) United we stand: combining structural methods. Curr Opin Struct Biol 18(5):617–622. doi: 10.1016/j.sbi.2008.07.004 CrossRefGoogle Scholar
  9. Dennis K, Srienc F, Bailey JE (1985) Ampicillin effects on five recombinant Escherichia coli strains: implications for selection pressure design. Biotechnol Bioeng 27(10):1490–1494. doi: 10.1002/bit.260271014 CrossRefGoogle Scholar
  10. Dymond JS, Richardson SM, Coombes CE, Babatz T, Muller H, Annaluru N, Blake WJ, Schwerzmann JW, Dai J, Lindstrom DL, Boeke AC, Gottschling DE, Chandrasegaran S, Bader JS, Boeke JD (2011) Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature 477(7365):471–476. doi: 10.1038/nature10403 CrossRefGoogle Scholar
  11. Fitzgerald DJ, Berger P, Schaffitzel C, Yamada K, Richmond TJ, Berger I (2006) Protein complex expression by using multigene baculoviral vectors. Nat Methods 3(12):1021–1032. doi: 10.1038/nmeth983 CrossRefGoogle Scholar
  12. Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, Stockwell TB, Brownley A, Thomas DW, Algire MA, Merryman C, Young L, Noskov VN, Glass JI, Venter JC, Hutchison CA, Smith HO (2008a) Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319(5867):1215–1220. doi: 10.1126/science.1151721 CrossRefGoogle Scholar
  13. Gibson DG, Benders GA, Axelrod KC, Zaveri J, Algire MA, Moodie M, Montague MG, Venter JC, Smith HO, Hutchison CA (2008b) One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome. Proc Natl Acad Sci U S A 105(51):20404–20409. doi: 10.1073/pnas.0811011106 CrossRefGoogle Scholar
  14. Gibson DG, Young L, Chuang RY, Venter JC, Hutchison CA 3rd, Smith HO (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6(5):343–345. doi: 10.1038/nmeth.1318 CrossRefGoogle Scholar
  15. Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA, Smith HO, Venter JC (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329(5987):52–56. doi: 10.1126/science.1190719 CrossRefGoogle Scholar
  16. Gunyuzlu PL, Hollis GF,Toyn JH (2001) Plasmid construction by linker-assisted homologous recombination in yeast. Biotechniques 31(6):1246, 1248, 1250Google Scholar
  17. Kaznessis YN (2007) Models for synthetic biology. BMC Syst Biol 1:47. doi: 10.1186/1752-0509-1-47 CrossRefGoogle Scholar
  18. Kim KJ, Kim HE, Lee KH, Han W, Yi MJ, Jeong J, Oh BH (2004) Two-promoter vector is highly efficient for overproduction of protein complexes. Protein Sci 13(6):1698–1703. doi: 10.1110/ps.04644504 CrossRefGoogle Scholar
  19. Krivoruchko A, Siewers V, Nielsen J (2011) Opportunities for yeast metabolic engineering: lessons from synthetic biology. Biotechnol J 6(3):262–276. doi: 10.1002/biot.201000308 CrossRefGoogle Scholar
  20. Lee JW, Kim TY, Jang YS, Choi S, Lee SY (2011) Systems metabolic engineering for chemicals and materials. Trends Biotechnol 29(8):370–378. doi: 10.1016/j.tibtech.2011.04.001 CrossRefGoogle Scholar
  21. Li MZ, Elledge SJ (2007) Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nat Methods 4(3):251–256. doi: 10.1038/nmeth1010 CrossRefGoogle Scholar
  22. Ma H, Kunes S, Schatz PJ, Botstein D (1987) Plasmid construction by homologous recombination in yeast. Gene 58(2–3):201–216CrossRefGoogle Scholar
  23. McArthur GHT, Fong SS (2010) Toward engineering synthetic microbial metabolism. J Biomed Biotechnol 2010:459760. doi: 10.1155/2010/459760 CrossRefGoogle Scholar
  24. Miyazaki K (2011) MEGAWHOP cloning: a method of creating random mutagenesis libraries via megaprimer PCR of whole plasmids. Methods Enzymol 498:399–406. doi: 10.1016/B978-0-12-385120-8.00017-6 Google Scholar
  25. Miyazaki K,Takenouchi M (2002) Creating random mutagenesis libraries using megaprimer PCR of whole plasmid. Biotechniques 33(5):1033–1034, 1036–1038Google Scholar
  26. Na D, Kim TY, Lee SY (2010) Construction and optimization of synthetic pathways in metabolic engineering. Curr Opin Microbiol 13(3):363–370. doi: 10.1016/j.mib.2010.02.004 CrossRefGoogle Scholar
  27. Nandagopal N, Elowitz MB (2011) Synthetic biology: integrated gene circuits. Science 333(6047):1244–1248. doi: 10.1126/science.1207084 CrossRefGoogle Scholar
  28. Perrakis A, Musacchio A, Cusack S, Petosa C (2011) Investigating a macromolecular complex: the toolkit of methods. J Struct Biol 175(2):106–112. doi: 10.1016/j.jsb.2011.05.014 CrossRefGoogle Scholar
  29. Portnoy VA, Bezdan D, Zengler K (2011) Adaptive laboratory evolution—harnessing the power of biology for metabolic engineering. Curr Opin Biotechnol 22(4):590–594. doi: 10.1016/j.copbio.2011.03.007 CrossRefGoogle Scholar
  30. Purnick PE, Weiss R (2009) The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol 10(6):410–422. doi: 10.1038/nrm2698 CrossRefGoogle Scholar
  31. Ramon A, Smith HO (2011) Single-step linker-based combinatorial assembly of promoter and gene cassettes for pathway engineering. Biotechnol Lett 33(3):549–555. doi: 10.1007/s10529-010-0455-x CrossRefGoogle Scholar
  32. Raymond CK, Pownder TA,Sexson SL (1999) General method for plasmid construction using homologous recombination. Biotechniques 26(1):134–138, 140–131.Google Scholar
  33. Scheich C, Kummel D, Soumailakakis D, Heinemann U, Bussow K (2007) Vectors for co-expression of an unrestricted number of proteins. Nucleic Acids Res 35(6):e43. doi: 10.1093/nar/gkm067 CrossRefGoogle Scholar
  34. Storici F, Durham CL, Gordenin DA, Resnick MA (2003) Chromosomal site-specific double-strand breaks are efficiently targeted for repair by oligonucleotides in yeast. Proc Natl Acad Sci U S A 100(25):14994–14999. doi: 10.1073/pnas.2036296100 CrossRefGoogle Scholar
  35. Tillett D, Neilan BA (1999) Enzyme-free cloning: a rapid method to clone PCR products independent of vector restriction enzyme sites. Nucleic Acids Res 27(19):e26CrossRefGoogle Scholar
  36. Vick JE, Johnson ET, Choudhary S, Bloch SE, Lopez-Gallego F, Srivastava P, Tikh IB, Wawrzyn GT, Schmidt-Dannert C (2011) Optimized compatible set of BioBrick vectors for metabolic pathway engineering. Appl Microbiol Biotechnol 92(6):1275–1286. doi: 10.1007/s00253-011-3633-4 CrossRefGoogle Scholar
  37. Wakamori M, Umehara T, Yokoyama S (2010) A series of bacterial co-expression vectors with rare-cutter recognition sequences. Protein Expr Purif 74(1):88–98. doi: 10.1016/j.pep.2010.06.016 CrossRefGoogle Scholar
  38. Wang TW, Zhu H, Ma XY, Zhang T, Ma YS, Wei DZ (2006) Mutant library construction in directed molecular evolution: casting a wider net. Mol Biotechnol 34(1):55–68. doi: 10.1385/MB:34:1:55 CrossRefGoogle Scholar
  39. Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, Church GM (2009) Programming cells by multiplex genome engineering and accelerated evolution. Nature 460(7257):894–898. doi: 10.1038/nature08187 CrossRefGoogle Scholar
  40. Wingler LM, Cornish VW (2011) Reiterative recombination for the in vivo assembly of libraries of multigene pathways. Proc Natl Acad Sci U S A 108(37):15135–15140. doi: 10.1073/pnas.1100507108 CrossRefGoogle Scholar
  41. Wladyka B, Puzia K, Dubin A (2005) Efficient co-expression of a recombinant staphopain A and its inhibitor staphostatin A in Escherichia coli. Biochem J 385(Pt 1):181–187. doi: 10.1042/BJ20040958 Google Scholar
  42. Yang W, Zhang L, Lu Z, Tao W, Zhai Z (2001) A new method for protein coexpression in Escherichia coli using two incompatible plasmids. Protein Expr Purif 22(3):472–478. doi: 10.1006/prep.2001.1453 CrossRefGoogle Scholar
  43. Yokoyama S (2003) Protein expression systems for structural genomics and proteomics. Curr Opin Chem Biol 7(1):39–43. doi: S1367593102000194 CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Tianwen Wang
    • 1
  • Xingyuan Ma
    • 2
  • Hu Zhu
    • 3
  • Aitao Li
    • 2
  • Guocheng Du
    • 1
  • Jian Chen
    • 1
  1. 1.State Key Laboratory of Food Science and TechnologyJiangnan UniversityWuxiChina
  2. 2.School of Biotechnology, and State Key Laboratory of Bioreactor EngineeringEast China University of Science and TechnologyShanghaiChina
  3. 3.Center for Bioengineering and BiotechnologyChina University of Petroleum (East China)QingdaoChina

Personalised recommendations