Arabidopsis: the original plant chassis organism

  • Cynthia K. Holland
  • Joseph M. Jez


Arabidopsis thaliana (thale cress) has a past, current, and future role in the era of synthetic biology. Arabidopsis is one of the most well-studied plants with a wealth of genomics, genetics, and biochemical resources available for the metabolic engineer and synthetic biologist. Here we discuss the tools and resources that enable the identification of target genes and pathways in Arabidopsis and heterologous expression in this model plant. While there are numerous examples of engineering Arabidopsis for decreased lignin, increased seed oil, increased vitamins, and environmental remediation, this plant has provided biochemical tools for introducing Arabidopsis genes, pathways, and/or regulatory elements into other plants and microorganisms. Arabidopsis is not a vegetative or oilseed crop, but it is as an excellent model chassis for proof-of-concept metabolic engineering and synthetic biology experiments in plants.


Arabidopsis thaliana Chassis organism Genome resources Metabolic engineering Plant biochemistry Synthetic biology 



The authors acknowledge support from the National Science Foundation (MCB-1614539 to JMJ and DGE-1143954 to CKH).

Author contribution statement

Both authors researched and wrote this review.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.


  1. Abdel-Ghany SE, Day I, Heuberger AL, Broeckling CD, Reddy ASN (2013) Metabolic engineering of Arabidopsis for butanetriol production using bacterial genes. Metab Eng 20:109–120CrossRefPubMedGoogle Scholar
  2. Adams JP, Adeli A, Hsu CY, Harkess RL, Page GP, Depamphilis CW, Schultz EB, Yuceer C (2012) Plant-based FRET biosensor discriminates environmental zinc levels. Plant Biotechnol J 10:207–216CrossRefPubMedGoogle Scholar
  3. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815CrossRefGoogle Scholar
  4. Atwell S, Huang YS, Vilhjálmsson BJ, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone AM, Hu TT, Jiang R, Muliyati NW, Zhang X, Amer MA, Baxter I, Brachi B, Chory J, Dean C, Debieu M, de Meaux J, Ecker JR, Faure N, Kniskern JM, Jones JD, Michael T, Nemri A, Roux F, Salt DE, Tang C, Todesco M, Traw MB, Weigel D, Marjoram P, Borevitz JO, Bergelson J, Nordborg M (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465:627–631CrossRefPubMedPubMedCentralGoogle Scholar
  5. Bonawitz ND, Chapple C (2013) Can genetic engineering of lignin deposition be accomplished without an unacceptable yield penalty? Curr Opin Biotechnol 24:336–343CrossRefPubMedGoogle Scholar
  6. Cahoon RE, Lutke WK, Cameron JC, Chen S, Lee SG, Rivard RS, Rea PA, Jez JM (2015) Adaptive engineering of phytochelatin-based heavy metal tolerance. J Biol Chem 290:17230–17321CrossRefGoogle Scholar
  7. Chu Y, Kwon T, Nam J (2014) Enzymatic and metabolic engineering for efficient production of syringing, sinapyl alcohol 4-O-glucoside, in Arabidopsis thaliana. Phytochemistry 102:55–63CrossRefPubMedGoogle Scholar
  8. Clough SJ, Bent AF (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16:735–743CrossRefPubMedGoogle Scholar
  9. Dong W, Stockwell VO, Goyer A (2015) Enhancement of thiamin content in Arabidopsis thaliana by metabolic engineering. Plant Cell Physiol 56:2285–2296CrossRefPubMedGoogle Scholar
  10. Ecker JR (2016) Epigenomic diversity in a global collection of Arabidopsis thaliana accessions. Cell 166:492–505CrossRefPubMedPubMedCentralGoogle Scholar
  11. Engler C, Youles M, Gruetzner R (2014) A golden gate modular cloning toolbox for plants. ACS Synth Biol 3:839–843CrossRefPubMedGoogle Scholar
  12. EU Joint Research Centre (2006) Transgenic Arabidopsis thaliana for detection of explosives in the soil. Notification number: B/DK/06/01Google Scholar
  13. Ewing R, Poirot O, Claverie JM (1999–2000) Comparative analysis of the Arabidopsis and rice expressed sequence tag (EST) sets. In Silico Biol 1:197–213Google Scholar
  14. Farre G, Twyman RM, Christou P, Capell T, Zhu C (2015) Knowledge-driven approaches for engineering complex metabolic pathways in plants. Curr Opin Biotechnol 32:54–60CrossRefPubMedGoogle Scholar
  15. Fitzpatrick TB, Basset GJC, Borel P, Carrari F, DellaPenna D, Fraser PD, Hellmann H, Osorio S, Rothan C, Valpuesta V, Caris-Veyrat C, Fernie AR (2012) Vitamin deficiencies in humans: can plant science help? Plant Cell 24:395–414CrossRefPubMedPubMedCentralGoogle Scholar
  16. Gou JY, Felippes FF, Liu CJ, Weigel D, Wang JW (2011) Negative regulator of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor. Plant Cell 23:1512–1522CrossRefPubMedPubMedCentralGoogle Scholar
  17. Goyer A (2010) Thiamine in plants: aspects of its metabolism and functions. Phytochemistry 71:1615–1624CrossRefPubMedGoogle Scholar
  18. Hu Z, Ren Z, Lu C (2012) The phosphatidylcholine diacylglycerol cholinephosphotransferase is required for efficient hydroxy fatty acid accumulation in transgenic Arabidopsis. Plant Physiol 158:1944–1954CrossRefPubMedPubMedCentralGoogle Scholar
  19. Jez JM, Lee SG, Sherp AM (2016) The next green movement: plant biology for the environment and sustainability. Science 353:1241–1244CrossRefPubMedGoogle Scholar
  20. Johnston EJ, Rylott EL, Beynon E, Lorenz A, Chechik V, Bruce NC (2015) Monodehydroascorbate reductase mediates TNT toxicity in plants. Science 349:1072–1075CrossRefPubMedGoogle Scholar
  21. Katari MS, Nowicki SD, Aceituno FF, Nero D, Kelfer J, Thompson LP, Cabello JM, Davidson RS, Goldberg AP, Shasha DE, Coruzzi GM, Gutiérrez RA (2010) VirtualPlant: a software platform to support systems biology research. Plant Physiol 152:500–515CrossRefPubMedPubMedCentralGoogle Scholar
  22. Kawakatsu T, Huang SC, Jupe F, Sasaki E, Schmitz RJ, Urich MA, Castanon R, Nery JR, Barragan C, He Y, Chen H, Dubin M, Lee CR, Wang C, Bemm F, Becker C, O’Neil R, O’Malley RC, Quarless DX; 1001 Genomes Consortium, Schork NJ, Weigel D, Nordborg M, Ecker JR (2016) Epigenomic diversity in a global collection of Arabidopsis thaliana accessions. Cell 166:492–505CrossRefPubMedPubMedCentralGoogle Scholar
  23. Laibach F (1907) Zur Frage nach der Individualität der Chromosomen im Pflanzenreich. Bot Centbl Beihefte (I) 22:191–210Google Scholar
  24. Laibach F (1943) Arabidopsis thaliana(L.) Heynh. als objekt fur genetische und entwicklungsphysiologische untersuchungen. Bot Archiv 44:439–455Google Scholar
  25. Lange I, Poirier BC, Herron BK, Lange BM (2015) Comprehensive assessment of transcriptional regulation facilitates metabolic engineering of isoprenoid accumulation in Arabidopsis. Plant Physiol 169:1595–1606PubMedPubMedCentralGoogle Scholar
  26. Leonelli S (2007) Growing weed, producing knowledge: an epistemic history of Arabidopsis thaliana. Hist Phil Life Sci 29:193–224Google Scholar
  27. Li JF, Aach J, Norville JE, McCormack M, Zhang D, Bush J, Church GM, Sheen J (2013) Multiplex and homologous recombination-mediated plant genome editing via guide RNA/Cas9. Nature Biotech 31:688–691CrossRefGoogle Scholar
  28. Li Q, Song J, Peng S, Wang JP, Guan-Zheng Q, Sederoff RR, Chiang VL (2014) Plant biotechnology for lignocellulosic biofuel production. Plant Biotech J 12:1174–1192CrossRefGoogle Scholar
  29. Mao Y, Zhang H, Xu N, Zhang B, Gou F, Zhu JK (2013) Application of the CRISPR-Cas system for efficient genome engineering in plants. Mol Plant 6:2008–2011CrossRefPubMedPubMedCentralGoogle Scholar
  30. Martin C, Li J (2017) Medicine is not health care, food is health care: plant metabolic engineering, diet and human health. New Phytol 216:699–719CrossRefPubMedGoogle Scholar
  31. Meyerowitz EM (2001) Prehistory and history of Arabidopsis research. Plant Physiol 125:15–19CrossRefPubMedPubMedCentralGoogle Scholar
  32. Mintz-Oron S, Meir S, Malitsky S, Ruppin E, Aharoni A, Shlomi T (2012) Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity. Proc Natl Acad Sci USA 109:339–344CrossRefPubMedGoogle Scholar
  33. Napier JA, Haslam RP, Beaudoin F, Cahoon EB (2014) Understanding and manipulating plant lipid composition: metabolic engineering leads the way. Curr Opin Plant Biol 19:68–75CrossRefPubMedPubMedCentralGoogle Scholar
  34. Nour-Eldin HH, Andersen TG, Burow M, Madsen SR, Jorgensen ME, Olsen CE, Dreyer I, Hedrich R, Geiger D, Halkier BA (2012) NRT/PTR transporters are essential for translocation of glucosinolate defense compounds to seeds. Nature 488:531–534CrossRefPubMedGoogle Scholar
  35. Nour-Eldin HH, Madsen SR, Engelen S, Jørgensen ME, Olsen CE, Andersen JS, Seynnaeve D, Verhoye T, Fulawka R, Denolf P, Halkier BA (2017) Reduction of antinutritional glucosinolates in Brassica oilseeds by mutation of genes encoding transporters. Nature Biotech 35:377–382CrossRefGoogle Scholar
  36. O’Malley RC, Barragan CC, Ecker JR (2015) A user’s guide to the Arabidopsis T-DNA insertion mutant collections. Methods Mol Biol 1284:323–342CrossRefPubMedPubMedCentralGoogle Scholar
  37. Owen C, Patron NJ, Huang A, Osbourn A (2017) Harnessing plant metabolic diversity. Curr Opin Chem Biol 40:24–30CrossRefPubMedGoogle Scholar
  38. Peng R, Fu X, Tian Y, Zhao W, Zhu B, Xu J, Wang B, Wang L, Yao Q (2014) Metabolic engineering of Arabidopsis for remediation of different polycyclic aromatic hydrocarbons using a hybrid bacterial dioxygenase complex. Metab Eng 26:100–110CrossRefPubMedGoogle Scholar
  39. Petrie JR, Shrestha P, Zhou XR, Mansour MP, Liu Q, Belide S, Nichols PD, Singh SP (2012) Metabolic engineering plant seeds with fish oil-like levels of DHA. PLoS One 7:e49165CrossRefPubMedPubMedCentralGoogle Scholar
  40. Provart NJ, Alonso J, Assmann SM, Bergmann D, Brady SM, Brkljacic J, Browse J, Chapple C, Colot V, Cutler S, Dangl J, Ehrhardt D, Friesner JD, Frommer WB, Grotewold E, Meyerowitz E, Nemhauser J, Nordborg M, Pikaard C, Shanklin J, Somerville C, Stitt M, Torii KU, Waese J, Wagner, McCourt P (2015) 50 Years of Arabidopsis research: highlights and future directions. New Phytol 209:921–944CrossRefPubMedGoogle Scholar
  41. Purnick PE, Weiss R (2009) The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol 10:410–422CrossRefPubMedGoogle Scholar
  42. Robert SS, Singh SP, Zhou XR, Petrie JR, Blackburn SI, Mansour PM, Nichols PD, Liu Q, Green AG (2005) Metabolic engineering of Arabidopsis to produce nutritionally important DHA in seed oil. Funct Plant Biol 32:473–479CrossRefGoogle Scholar
  43. Ruiz-Lopez N, Haslam RP, Usher SL, Napier JA, Sayanova O (2013) Reconstitution of EPA and DHA biosynthesis in Arabidopsis: iterative metabolic engineering for the synthesis of nS3 LC-PUFAs in transgenic plants. Metab Eng 17:30–41CrossRefPubMedPubMedCentralGoogle Scholar
  44. Sayanova O, Ruiz-Lopez N, Haslam RP, Napier JA (2012) The role of ∆6-desaturase acyl-carrier specificity in the efficient synthesis of long-chain polyunsaturated fatty acids in transgenic plants. Plant Biotech J 10:195–206CrossRefGoogle Scholar
  45. Shockey J, Mason C, Gilbert M, Cao H, Li X, Cahoon E, Dyer J (2015) Development and analysis of a highly flexible multi-gene expression system for metabolic engineering in Arabidopsis seeds and other plant tissues. Plant Mol Biol 89:113–126CrossRefPubMedGoogle Scholar
  46. Tzin V, Malitsky S, Ben Zvi MM, Bedair M, Sumner L, Aharoni A, Galili G (2012) Expression of a bacterial feedback-insensitive 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase of the shikimate pathway in Arabidopsis elucidates potential metabolic bottlenecks between primary and secondary metabolism. New Phytol 194:430–439CrossRefPubMedGoogle Scholar
  47. van Erp H, Kelly AA, Menard G, Eastmond PJ (2014) Multigene engineering of triacylglycerol metabolism boosts seed oil content in Arabidopsis. Plant Physiol 165:30–36CrossRefPubMedPubMedCentralGoogle Scholar
  48. Vanhercke T, Tahchy AE, Liu Q, Zhou XR, Shrestha P, Divi UK, Ral JP, Mansour MP, Nichols PD, James CN, Horn PJ, Chapman KD, Beaudoin F, Ruiz-Lopez N, Larkin PJ, de Feyter RC, Singh SP, Petrie JR (2014) Metabolic engineering of biomass for high energy density: oilseed-like triacylglycerol yields from plant leaves. Plant Biotech J 12:231–239CrossRefGoogle Scholar
  49. Vanholme R, Cesarino I, Rataj K, Xiao Y, Sundin L, Goeminne G, Kim H, Cross J, Morreel K, Araujo P, Welsh L, Haustraete J, McClellan C, Vanholme B, Ralph J, Simpson GG, Halpin C, Boerjan W (2013) Caffeoyl shikimate esterase (CSE) is an enzyme in the lignin biosynthetic pathway in Arabidopsis. Science 341:1103–1106CrossRefPubMedGoogle Scholar
  50. Weber AP, Brautigam A (2013) The role of membrane transport in metabolic engineering of plant primary metabolism. Curr Opin Biotechnol 24:256–262CrossRefPubMedGoogle Scholar
  51. Wood AJ, Lo TW, Zeitler B, Pickle CS, Ralston EJ, Lee AH, Amora R, Miller JC, Leung E, Meng X, Zhang L, Rebar EJ, Gregory PD, Urnov FD, Meyer BJ (2011) Targeted genome editing across species using ZFNs and TALENs. Science 333:307CrossRefPubMedPubMedCentralGoogle Scholar
  52. Yang Y, Munz J, Cass C, Zienkiewicz A, Kong Q, Ma W, Sanjaya, Sedbrook J, Benning C (2015) Ectopic expression of WRINKLED1affects fatty acid homeostasis in Brachypodium distachyon vegetative tissues. Plant Physiol 169:1836–1847CrossRefPubMedPubMedCentralGoogle Scholar
  53. Yuan L, Grotewold E (2015) Metabolic engineering to enhance the value of plants as green factories. Metab Eng 27:83–91CrossRefPubMedGoogle Scholar
  54. Yurchenko O, Shockey JM, Gidda SK, Silver MI, Chapman KD, Mullen RT, Dyer JM (2017) Engineering the production of conjugated fatty acids in Arabidopsis thaliana leaves. Plant Biotech J 15:1010–1023CrossRefGoogle Scholar
  55. Zhang S (2017) Whatever happened to the glowing plant Kickstarter? The Atlantic, April 20. Genomes Consortium (2016) 1135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell 166:481–491Google Scholar
  56. Zhang K, Bhuiya MW, Pazo JR, Miao Y, Kim H, Ralph J, Liu CJ (2012) An engineered monolignol 4-O-methyltransferase depresses lignin biosynthesis and confers novel metabolic capability in Arabidopsis. Plant Cell 24:3135–3152CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of BiologyWashington University in St. LouisSt. LouisUSA

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