Genome engineering: unconventional biochemistry and food security

  • Vedpal Singh Malik
Review Article


Unprecedented technological advances in biology provide the tools to enhance plant productivity to meet world hunger. The genome sequences of thousands of organisms and their analyses is the blue print of their genome architecture which can now be further improved. New Nucleases offer the opportunity of modifying plant genomes in a way that was not possible only a while ago. Synthetic DNA and methodology of gene assembly further expand Synthetic biology and allow construction of metabolic pathways to produce valuable molecules in Novel hosts. The knowledge of Quorum Sensing (QS), could add to the successful use of biocontrol agents. The technology has no limitations, and excitements in biology will be exploited to meet future energy needs.


Metabolic engineering Biofuels Quorum sensing DNA sequencing Gene targeting 





DNA sequencing


Gene targeting


Metabolic engineering


Quorum sensing


Transcription activator-like effectors


Zinc fingers


  1. Barnes WM (2003) Ribocloning: DNA cloning and gene construction using PCR primers terminated with a ribonucleotide. In: Carl WD (ed) PCR Primer, vol 2. Spring Harbor Laboratory Press, Cold Spring Harbor, pp 441–449Google Scholar
  2. Bibikova B (2002) Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases. Genetics 161:1169–1178PubMedGoogle Scholar
  3. Bogdanove AJ, Voytas DF (2011) TAL effectors: customizable proteins for DNA targeting. Science 333:1843–1846PubMedCrossRefGoogle Scholar
  4. Brigham CJ, Kurosawa K, Rha C, Sinskey AJ (2011) J Microbial Biochem Technol S3:002Google Scholar
  5. Chung C, Ping G, Yu-Ching C, Shaw PD, Farrand SK (1998) Production of acyl-homoserine lactone: quorum-sensing signals by gram-negative plant-associated bacteria. MPMI 11:1119–1129CrossRefGoogle Scholar
  6. Cobb RE, Zhao H (2012) Direct cloning of large genomic sequences. Nat Biotechnol 30:405–406PubMedCrossRefGoogle Scholar
  7. Coggan KA, Wolfgang MC (2012) Global regulatory pathways and cross-talk control Pseudomonas aeruginosa environmental lifestyle and virulence phenotype. Curr Issues Mol Biol 14:47–70PubMedGoogle Scholar
  8. Crismani W, Girard C, Froger N, Pradillo M, Santos J, Chelysheva L, Copenhaver GP, Horlow C, Mercier R (2012) FANCM limits meiotic crossovers. Science 336:1588–1590PubMedCrossRefGoogle Scholar
  9. Ding D, Okamasa K, Yamane M, Tsutsumi C, Haraguchi T, Yamamoto M, Hiraoka Y (2012) Meiosis-specific noncoding RNA mediates robust pairing of homologous chromosomes in meiosis. Science 336:732–736PubMedCrossRefGoogle Scholar
  10. Ducat DC, Avelar-Rivas JA, Way JC, Silvera PA (2012) Rerouting carbon flux to enhance photosynthetic productivity. Appl Microbiol Biotechnol 78:2660–2668Google Scholar
  11. Ellis DI, Goodacre R (2012) Metabolomics-assisted synthetic biology. Curr Opin Biotechnol 23:22–28PubMedCrossRefGoogle Scholar
  12. Eriksson ME, Webb AR (2011) Plant cell responses to cold are all about timing. Curr Opin Plant Biol 14:731–737PubMedCrossRefGoogle Scholar
  13. 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 (2008) Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319:1215–1220PubMedCrossRefGoogle Scholar
  14. Gonzalez JE, Keshavan ND (2006) Messing with bacterial Quorum sensing. Microbiol Mol Biol Rev 70:859–875PubMedCrossRefGoogle Scholar
  15. Gonzalez A, Knight R (2012) Advancing analytical algorithms and pipelines for billions of microbial sequences. Curr Opin Biotechnol 23:64–71PubMedCrossRefGoogle Scholar
  16. Hamilton MD, Nuara AA, Gammon DB, Buller RM, Evans DH (2007) Duplex strand Henry joining reactions catalyzed by vaccinia virus DNA polymerase. Nucleic Acids Res 35:143–151PubMedCrossRefGoogle Scholar
  17. Hamra FK (2010) Gene targeting: enter the rat. Nature 467:161–163PubMedCrossRefGoogle Scholar
  18. Horswill AR, Stoodley P, Parsek MR (2007) The effect of the chemical, biological, and physical, environment on Quorum Sensing in structured microbial communities. Anal Bioanal Chem 387:371–380PubMedCrossRefGoogle Scholar
  19. Hsiao K (1993) Exonuclease III induced ligase-free directional subcloning of PCR products. Nucleic Acids Res 21:5528–5529PubMedCrossRefGoogle Scholar
  20. Kilian O, Christina SE, Benemann CSC, Niyogi KK, Vick B (2011) High-efficiency homologous recombination in the oil-producing alga Nannochloropsis sp. PNAS 108:21265–21269PubMedCrossRefGoogle Scholar
  21. Kurosawa K, Boccazzi P, de Almeida NM, Sinskey AJ (2010) High-cell-density batch fermentation of Rhodococcus opacus PD630 using a high glucose concentration for triacylglycerol production. J Biotechnol 147:212–218PubMedCrossRefGoogle Scholar
  22. Li MZ, Elledge SJ (2007) Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nat Methods 4:251–256PubMedCrossRefGoogle Scholar
  23. Li T, Liu B, Spalding MH, Weeks DP, Yang B (2012) High-efficiency TALEN-based gene editing produces disease-resistant rice. Nat Biotechnol 30:390–392PubMedCrossRefGoogle Scholar
  24. Lim E, Bowles D (2012) Plant production systems for bioactive small molecules. Curr Opin Biotechnol 23:271–277PubMedCrossRefGoogle Scholar
  25. Lusser M, Parisi C, Plan D, Rodríguez-Cerezo E (2012) Deployment of new biotechnologies in plant breeding. Nat New Biotechnol 30:231–239CrossRefGoogle Scholar
  26. Lutke-Eversloh T, Bahl H (2011) Metabolic engineering of Clostridium acetobutylicum: recent advances to improve butanol production. Curr Opin Biotechnol 22:634–647PubMedCrossRefGoogle Scholar
  27. Maeder ML (2008) Rapid “open-source” engineering of customized zinc-finger nucleases for highly effective gene modification. Mol Cell 31:294–298PubMedCrossRefGoogle Scholar
  28. Manrao EA, Derrington IM, Laszlo AH, Langford KW, Hopper MK, Gillgren N, Pavlenok M, Niederweis M, Gundlach JH (2012) Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nat Biotechnol 30:349–353PubMedCrossRefGoogle Scholar
  29. Mardis ER (2008) Next-generation DNA Sequencing methods. Ann Rev Genom Hum G 9:387–402CrossRefGoogle Scholar
  30. Marimuthu MP, Jolivet S, Ravi M, Pereira L, Davada JN, Cromer L, Wang L, Nogue F, Chan S, Siddiqi I, Mercier R (2011) Synthetic clonal reproduction through seeds. Science 331:876–878PubMedCrossRefGoogle Scholar
  31. Matthew B, Scholz MB, Lo C, Chain PSG (2012) Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr Opin Biotechnol 23:9–15CrossRefGoogle Scholar
  32. Miller MB, Bassler BL (2001) Quorum sensing in bacteria. In: Ornston LN, Ballows A, Gottesman S (eds) Annual Review of Microbiology 55. Palo Alto Annual reviewsGoogle Scholar
  33. Müller H, Westendorf C, Leitner E, Chernin L, Riedel K, Schmidt S, Eberl L, Berg G (2009) Quorum-sensing effects in the antagonistic rhizosphere bacterium Serratia plymuthica HRO-C48. Fems Microbiol Ecol 67:468–478PubMedCrossRefGoogle Scholar
  34. Muller H, Annaluru N, Schwerzmann JW, Richardson SM, Dymond JS, Cooper EM, Bader JS, Boeke JD, Chandrasegaran S (2012) Assembling large DNA segments in yeast. Methods Mol Biol 852:133–150PubMedCrossRefGoogle Scholar
  35. Munns R, James RA, Xu B, Athman A, Conn SJ, Jordans C, Byrt CS, Hare RA, Tyerman SD, Tester M, Plett D, Gilliham M (2012) Wheat grain yield on saline soils is improved by an ancestral Na+ transporter gene. Nat Biotechnol 30:360–364PubMedCrossRefGoogle Scholar
  36. Porteus MH, Baltimore D (2003) Chimeric nucleases stimulate gene targeting in human cells. Science 300:763–765PubMedCrossRefGoogle Scholar
  37. Ro DK, Paradise EM, Ouellet M, Fisher KJ (2006) Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440:940–943PubMedCrossRefGoogle Scholar
  38. Sander JD (2011) Selection-free zinc-finger-nuclease engineering by context-dependent assembly. Nat Methods 8:67–71PubMedCrossRefGoogle Scholar
  39. Sanjana NE, Cong L, Shou Y, Cunniff MM, Feng G, Zhang F (2012) A transcription activator-like effector toolbox for genome engineering. Nat Protocols 7:171–192CrossRefGoogle Scholar
  40. Schirmer A, Rude MA, Li X, Popova E, Cardayre SB (2010) Microbial biosynthesis of alkanes. Science 329:559–562PubMedCrossRefGoogle Scholar
  41. Scott SA, Davey MP, Dennis JS, Horst I, Howe CJ, Lea-Smith DJ, Smith AG (2010) Biodiesel from algae: challenges and prospects. Curr Opin Biotechnol 2193:277–286CrossRefGoogle Scholar
  42. Shendure JH (2008) Next-generation DNA sequencing. Nat Biotechnol 26:1135–1145PubMedCrossRefGoogle Scholar
  43. Siddiqi I, Marimuthu MP, Ravi M (2009) Molecular approaches for the fixation of plant hybrid vigor. Biotechnol J 4:342–347PubMedCrossRefGoogle Scholar
  44. Steen EJ, Kang Y, Bokinsky G, Hu Z, Schirmer A, McClure A, delCardayre SB, Keasling JD (2010) Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature 463:559–562PubMedCrossRefGoogle Scholar
  45. Szczebara FM, Chandelier C, Villeret C, Masurel A, Bourot S, Duport C, Blanchard S, Groisillier A, Testet E, Costaglioli P, Cauet G, Degryse E, Balbuena D, Winter J, Achstetter J, Spagnoli R, Pompon D, Dumas B (2003) Biosynthesis of hydrocortisone from a simple carbon source in yeast. Nat Biotechnol 21:143–149PubMedCrossRefGoogle Scholar
  46. Webb S (2011) Genome editing goes global. Biotechniques 51:371–373PubMedGoogle Scholar
  47. Wijffels RH, Barbosa MJ (2010) An outlook on Microalgal biofuels (BF). Science 329:796–799PubMedCrossRefGoogle Scholar
  48. Ye VM, Bhatia SK (2012) Metabolic engineering for the production of clinically important molecules: omega-3 fatty acids, artemisinin, and taxol. Biotechnol J 1:20–33CrossRefGoogle Scholar
  49. Zerbino DR, Paten B, Haussler D (2012) Integrating genomes. Science 336:179–182PubMedCrossRefGoogle Scholar
  50. Zhang F, Rodriguez S, Keasling JD (2011) Metabolic engineering of microbial pathways for advanced biofuels (BF) production. Curr Opin Biotechnol 22:775–783PubMedCrossRefGoogle Scholar
  51. Zhang F, Carothers JM, Keasling JD (2012a) Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat Biotechnol 30:354–359CrossRefGoogle Scholar
  52. Zhang Y, Werling U, Edelmann W (2012b) SLiCE: a novel bacterial cell extract-based DNA cloning method. Nucleic Acids Res 1:1–10Google Scholar
  53. Zhu B, Cai G, Hall EO, Freeman GJ (2007) In-Fusion TM assembly: seamless engineering of multidomain fusion proteins, modular vectors, and mutations. Biotechniques 43:354–359PubMedCrossRefGoogle Scholar
  54. Zhu Q, Xue Z, Yadav N, Damude H et al (2010) Metabolic engineering of an oleaginous yeast for the production of omega-3 fatty acids. In: Cohen Z, Ratledge C (eds) Single cell oil, 2nd edn. ACOS Press, Urbana, pp 51–73Google Scholar

Copyright information

© Society for Plant Biochemistry and Biotechnology 2012

Authors and Affiliations

  1. 1.USDARiverdaleUSA

Personalised recommendations