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Advances in biochemical engineering/biotechnology
Mar 25, 2025;

The Amoeba Dictyostelium discoideum as Novel Production Host for Complex Substances.

Johann E Kufs, Christin Reimer, Lars Regestein
Author Information
  1. Johann E Kufs: Research Group Genome Engineering and Editing, Faculty of Technology, Bielefeld University, Bielefeld, Germany. johann.kufs@uni-bielefeld.de. ORCID
  2. Christin Reimer: Research Group Genome Engineering and Editing, Faculty of Technology, Bielefeld University, Bielefeld, Germany. ORCID
  3. Lars Regestein: Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (Leibniz-HKI), Jena, Germany. lars.regestein@leibniz-hki.de. ORCID
PMID: 40128388 DOI: 10.1007/10_2025_283

Abstract

In this chapter, we discuss the necessity of novel chassis organisms for the production of natural products to steer away from petrochemical approaches and the usage of common model organisms. We present the social amoeba Dictyostelium discoideum as a novel host for the production of complex organic substances and exploration of cryptic biosynthetic routes of secondary metabolites. We shed light on the genetic repertoire of the amoeba in terms of natural product biosyntheses and give an overview of growth characteristics, genetic engineering tools, and cultivation methodologies from shake flasks to stirred-tank bioreactors. Finally, an outlook is made on the perspective of D. discoideum as the chassis for biotechnological production and discovery of novel active substances.

Keywords

Active substances Amoebae Biosynthetic gene clusters Metabolic engineering Microbial cell factories Natural products Phytochemicals Synthetic biology

References

  1. Skellam E (2019) Strategies for engineering natural product biosynthesis in fungi. Trends Biotechnol 37:416–427
  2. Han J, Jiang L, Zhang L, Quinn RJ, Liu X, Feng Y (2021) Peculiarities of meroterpenoids and their bioproduction. Appl Microbiol Biotechnol 105:3987–4003
  3. Brakhage AA (2013) Regulation of fungal secondary metabolism. Nat Rev Microbiol 11:21–32
  4. De La Lastra CA, Villegas I (2007) Resveratrol as an antioxidant and pro-oxidant agent: mechanisms and clinical implications. Biochem Soc Trans 35:1156–1160
  5. Watson S, Jüttner F (2019) Biological production of taste and odour compounds. In: Taste and odour in source and drinking water: causes, controls, and consequences. IWA Publishing, London, pp 63–112
  6. Reimer C (2022) Engineering of polyketide production routes in the amoeba Dictyostelium discoideum. Friedrich-Schiller-Universität Jena
  7. Harvey AL (2008) Natural products in drug discovery. Drug Discov Today 13:894–901
  8. Krespach MKC, Stroe MC, Netzker T, Rosin M, Zehner LM, Komor AJ, Beilmann JM, Krüger T, Scherlach K, Kniemeyer O et al (2023) Streptomyces polyketides mediate bacteria–fungi interactions across soil environments. Nat Microbiol 8:1348–1361
  9. Walsh CT, Gehring AM, Weinreb PH, Quadri LEN, Flugel RS (1997) Post-translational modification of polyketide and nonribosomal peptide synthases. Curr Opin Chem Biol 1:309–315
  10. Jullesson D, David F, Pfleger B, Nielsen J (2015) Impact of synthetic biology and metabolic engineering on industrial production of fine chemicals. Biotechnol Adv 33:1395–1402
  11. Gil R, Peretó J (2015) Small genomes and the difficulty to define minimal translation and metabolic machineries. Front Ecol Evol 3. https://doi.org/10.3389/fevo.2015.00123
  12. Kufs JE, Hoefgen S, Rautschek J, Bissell AU, Graf C, Fiedler J, Braga D, Regestein L, Rosenbaum MA, Thiele J et al (2020) Rational design of flavonoid production routes using combinatorial and precursor-directed biosynthesis. ACS Synth Biol 9:1823–1832
  13. Annesley SJ, Fisher PR (2009) Dictyostelium discoideum – a model for many reasons. Mol Cell Biochem 329:73–91
  14. Schilde C, Schaap P (2013) The Amoebozoa. Methods Mol Biol 983:1–15
  15. Bozzaro S (2019) The past, present and future of Dictyostelium as a model system. Int J Dev Biol 63:321–331
  16. Chen ZH, Schaap P (2016) Secreted cyclic di-GMP induces stalk cell differentiation in the eukaryote Dictyostelium discoideum. J Bacteriol 198:27–31
  17. Eichinger L, Pachebat JA, Glockner G, Rajandream MA, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K, Xu Q et al (2005) The genome of the social amoeba Dictyostelium discoideum. Nature 435:43–57
  18. Veltman DM, Akar G, Bosgraaf L, Van Haastert PJ (2009) A new set of small, extrachromosomal expression vectors for Dictyostelium discoideum. Plasmid 61:110–118
  19. Veltman DM, Keizer-Gunnink I, Haastert PJ (2009) An extrachromosomal, inducible expression system for Dictyostelium discoideum. Plasmid 61:119–125
  20. Zhu X, Ricci-Tam C, Hager ER, Sgro AE (2023) Self-cleaving peptides for expression of multiple genes in Dictyostelium discoideum. PLoS One 18:e0281211
  21. Reimer C, Kufs JE, Rautschek J, Regestein L, Valiante V, Hillmann F (2022) Engineering the amoeba Dictyostelium discoideum for biosynthesis of a cannabinoid precursor and other polyketides. Nat Biotechnol 40:751–758
  22. Hoefgen S, Lin J, Fricke J, Stroe MC, Mattern DJ, Kufs JE, Hortschansky P, Brakhage AA, Hoffmeister D, Valiante V (2018) Facile assembly and fluorescence-based screening method for heterologous expression of biosynthetic pathways in fungi. Metab Eng 48:44–51
  23. Faix J, Kreppel L, Shaulsky G, Schleicher M, Kimmel AR (2004) A rapid and efficient method to generate multiple gene disruptions in Dictyostelium discoideum using a single selectable marker and the Cre-loxP system. Nucleic Acids Res 32:e143
  24. Muramoto T, Iriki H, Watanabe J, Kawata T (2019) Recent advances in CRISPR/Cas9-mediated genome editing in Dictyostelium. Cells 8:46
  25. Sekine R, Kawata T, Muramoto T (2018) CRISPR/Cas9 mediated targeting of multiple genes in Dictyostelium. Sci Rep 8:8471
  26. Fey P, Dodson RJ, Basu S, Hartline EC, Chisholm RL (2019) dictyBase and the Dicty Stock Center (version 2.0) – a progress report. Int J Dev Biol 63:563–572
  27. Fey P, Dodson RJ, Basu S, Chisholm RL (2013) One stop shop for everything Dictyostelium: DictyBase and the Dicty Stock Center in 2012. Methods Mol Biol 983:59–92
  28. Zucko J, Skunca N, Curk T, Zupan B, Long PF, Cullum J, Kessin RH, Hranueli D (2007) Polyketide synthase genes and the natural products potential of Dictyostelium discoideum. Bioinformatics 23:2543–2549
  29. Morris HR, Taylor GW, Masento MS, Jermyn KA, Kay RR (1987) Chemical structure of the morphogen differentiation inducing factor from Dictyostelium discoideum. Nature 328:811–814
  30. Ghosh R, Chhabra A, Phatale PA, Samrat SK, Sharma J, Gosain A, Mohanty D, Saran S, Gokhale RS (2008) Dissecting the functional role of polyketide synthases in Dictyostelium discoideum: biosynthesis of the differentiation regulating factor 4-methyl-5-pentylbenzene-1,3-diol. J Biol Chem 283:11348–11354
  31. Saito T, Taylor GW, Yang JC, Neuhaus D, Stetsenko D, Kato A, Kay RR (2006) Identification of new differentiation inducing factors from Dictyostelium discoideum. Biochim Biophys Acta 1760:754–761
  32. Günther M, Reimer C, Herbst R, Kufs JE, Rautschek J, Ueberschaar N, Zhang S, Peschel G, Reimer L, Regestein L et al (2022) Yellow polyketide pigment suppresses premature hatching in social amoeba. Proc Natl Acad Sci USA 119:e2116122119
  33. Kubohara Y, Kikuchi H (2019) Dictyostelium: an important source of structural and functional diversity in drug discovery. Cells 8:6
  34. Chen X, Köllner TG, Jia Q, Norris A, Santhanam B, Rabe P, Dickschat JS, Shaulsky G, Gershenzon J, Chen F (2016) Terpene synthase genes in eukaryotes beyond plants and fungi: occurrence in social amoebae. Proc Natl Acad Sci USA 113:12132
  35. Rabe P, Rinkel J, Nubbemeyer B, Köllner TG, Chen F, Dickschat JS (2016) Terpene cyclases from social amoebae. Angew Chem Int Ed Engl 55:15420–15423
  36. Kufs JE, Reimer C, Stallforth P, Hillmann F, Regestein L (2022) The potential of amoeba-based processes for natural product syntheses. Curr Opin Biotechnol 77:102766
  37. Abe I, Morita H (2010) Structure and function of the chalcone synthase superfamily of plant type III polyketide synthases. Nat Prod Rep 27:809–838
  38. Austin MB, Noel JP (2003) The chalcone synthase superfamily of type III polyketide synthases. Nat Prod Rep 20:79–110
  39. Austin MB, Saito T, Bowman ME, Haydock S, Kato A, Moore BS, Kay RR, Noel JP (2006) Biosynthesis of Dictyostelium discoideum differentiation-inducing factor by a hybrid type I fatty acid-type III polyketide synthase. Nat Chem Biol 2:494–502
  40. Carvalho Â, Hansen EH, Kayser O, Carlsen S, Stehle F (2017) Designing microorganisms for heterologous biosynthesis of cannabinoids. FEMS Yeast Res 17:fox037
  41. Klapper M, Götze S, Barnett R, Willing K, Stallforth P (2016) Bacterial alkaloids prevent amoebal predation. Angew Chem Int Ed Engl 55:8944–8947
  42. Barnett R, Stallforth P (2018) Natural products from social amoebae. Eur J Chem 24:4202–4214
  43. Tsuchiya HM, Drake JF, Jost JL, Fredrickson AG (1972) Predator-prey interactions of Dictyostelium discoideum and Escherichia coli in continuous culture. J Bacteriol 110:1147–1153
  44. Dunn JD, Bosmani C, Barisch C, Raykov L, Lefrancois LH, Cardenal-Munoz E, Lopez-Jimenez AT, Soldati T (1906) Eat Prey, Live: Dictyostelium discoideum as a model for cell-autonomous defenses. Front Immunol 2017:8
  45. Van Haastert PJ (2010) Chemotaxis: insights from the extending pseudopod. J Cell Sci 123:3031–3037
  46. Fey P, Kowal AS, Gaudet P, Pilcher KE, Chisholm RL (2007) Protocols for growth and development of Dictyostelium discoideum. Nat Protoc 2:1307–1316
  47. Han S-I, Friehs K, Flaschel E (2004) Improvement of a synthetic medium for Dictyostelium discoideum. Process Biochem 39:925–930
  48. Kufs JE, Reimer C, Steyer E, Valiante V, Hillmann F, Regestein L (2022) Scale-up of an amoeba-based process for the production of the cannabinoid precursor olivetolic acid. Microb Cell Factories 21:217
  49. Ullisch DA, Müller CA, Maibaum S, Kirchhoff J, Schiermeyer A, Schillberg S, Roberts JL, Treffenfeldt W, Büchs J (2012) Comprehensive characterization of two different Nicotiana tabacum cell lines leads to doubled GFP and HA protein production by media optimization. J Biosci Bioeng 113:242–248
  50. Meier K, Klöckner W, Bonhage B, Antonov E, Regestein L, Büchs J (2016) Correlation for the maximum oxygen transfer capacity in shake flasks for a wide range of operating conditions and for different culture media. Biochem Eng J 109:228–235
  51. Srinivas UK, Katz ER (1980) Oxygen utilization in Dictyostelium discoideum. FEMS Microbiol Lett 9:53–55
  52. Lattermann C, Funke M, Hansen S, Diederichs S, Büchs J (2014) Cross-section perimeter is a suitable parameter to describe the effects of different baffle geometries in shaken microtiter plates. J Biol Eng 8:18
  53. Han S-I, Friehs K, Flaschel E (2004) Cultivation of Dictyostelium discoideum on an improved synthetic medium in a conventional bioreactor. Process Biochem 39:585–589
  54. Keil T, Dittrich B, Lattermann C, Habicher T, Büchs J (2019) Polymer-based controlled-release fed-batch microtiter plate – diminishing the gap between early process development and production conditions. J Biol Eng 13:18
  55. Habicher T, Czotscher V, Klein T, Daub A, Keil T, Büchs J (2019) Glucose-containing polymer rings enable fed-batch operation in microtiter plates with parallel online measurement of scattered light, fluorescence, dissolved oxygen tension, and pH. Biotechnol Bioeng 116:2250–2262
  56. Hardy N, Augier F, Nienow AW, Béal C, Ben Chaabane F (2017) Scale-up agitation criteria for Trichoderma reesei fermentation. Chem Eng Sci 172:158–168
  57. Daub A, Böhm M, Delueg S, Mühlmann M, Schneider G, Büchs J (2014) Maximum stable drop size measurements indicate turbulence attenuation by aeration in a 3m aerated stirred tank. Biochem Eng J 86:24–32
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