Bottom–Up Protocell Design: Gaining Insights in the Emergence of Complex Functions

  • Rafał Wieczorek
  • Michael C. Wamberg
  • Anders N. Albertsen
  • Philipp M. G. Löffler
  • Pierre-Alain Monnard
Chapter

Abstract

All contemporary living cells are a collection of self-assembled molecular elements that by themselves are non-living but through the creation of a network exhibit the emergent properties of self-maintenance, self-reproduction, and evolution. Protocells are chemical systems that should mimic cell behavior and their emergent properties through the interactions of their components. For a functional protocell designed bottom-up, three fundamental elements are required: a compartment, a reaction network, and an information system. Even if the functions of protocell components are very simplified compared to those of modern cells, realizing a system with true inter-connection and inter-dependence of all the functions should lead to emergent properties. However, none of the currently studied systems have yet reached the threshold level necessary to be considered alive. This chapter will discuss the on-going research that aims at creating artificial cells assembled from a collection of smaller components, i.e., protocell systems from bottom-up designs.

References

  1. Balazs AC, Epstein IR (2009) Chemistry. Emergent or just complex? Science 325(5948):1632–1634PubMedCrossRefGoogle Scholar
  2. Bedau MA, Parke EC (eds) (2009) The prospect of Protocells: moral and social implications of creating life in the laboratory. MIT Press, CambridgeGoogle Scholar
  3. Bersini H, Stano P, Luisi PL, Bedau M (2012) Philosophical and scientific perspectives on emergence. Synthese 185:165–169CrossRefGoogle Scholar
  4. Cape JL, Monnard PA, Boncella JM (2011) Prebiotically relevant mixed fatty acid vesicles support anionic solute encapsulation and photochemically catalyzed trans-membrane charge transport. Chem Sci 2(4):661–667CrossRefGoogle Scholar
  5. Cape JL, Edson JB, Spencer LP, DeClue MS, Ziock HJ, Maurer SE, Rasmussen S, Monnard PA, Boncella JM (2012) Phototriggered DNA phosphoramidate ligation in a tandem 5′-amine deprotection/3′-imidazole activated phosphate coupling reaction. Bioconjug Chem 23(10):2014–2019PubMedCrossRefGoogle Scholar
  6. Chakrabarti AC, Breaker RR, Joyce GF, Deamer DW (1994) Production of RNA by a polymerase protein encapsulated within phospholipid vesicles. J Mol Evol 39:555–559PubMedCrossRefGoogle Scholar
  7. Chen IA, Roberts RW, Szostak JW (2004) The emergence of competition between model protocells. Science 305(5689):1474–1476PubMedCrossRefGoogle Scholar
  8. Cleland CE, Chyba CF (2002) Defining life. Orig Life Evol Biosph 32(4):387–393PubMedCrossRefGoogle Scholar
  9. Cooper GJ, Kitson PJ, Winter R, Zagnoni M, Long DL, Cronin L (2011) Modular redox-active inorganic chemical cells: iCHELLs. Angew Chem Int Ed Engl 50(44):10373–10376PubMedCrossRefGoogle Scholar
  10. Crick FH (1968) The origin of the genetic code. J Mol Biol 38:367–379PubMedCrossRefGoogle Scholar
  11. DeClue MS, Monnard PA, Bailey JA, Maurer SE, Collis GE, Ziock HJ, Rasmussen S, Boncella JM (2009) Nucleobase mediated, photocatalytic vesicle formation from an ester precursor. J Am Chem Soc 131(3):931–933PubMedCrossRefGoogle Scholar
  12. Gilbert W (1986) Origin of life: the RNA world. Nature 319:618CrossRefGoogle Scholar
  13. Hanczyc MM, Fujikawa SM, Szostak JW (2003) Experimental models of primitive cellular compartments: encapsulation, growth, and division. Science 302(5645):618–622PubMedCrossRefGoogle Scholar
  14. Ishikawa K, Sato K, Shima Y, Urabe I, Yomo T (2004) Expression of a cascading genetic network within liposomes. FEBS Lett 576:387–390PubMedCrossRefGoogle Scholar
  15. Kita H, Matsuura T, Sunami T, Hosoda K, Ichihashi N, Tsukada K, Urabe I, Yomo T (2008) Replication of genetic information with self-encoded replicase in liposomes. ChemBioChem 9:2403–2410PubMedCrossRefGoogle Scholar
  16. Kumar RK, Li M, Olof SN, Patil AJ, Mann S (2013) Artificial cytoskeletal structures within enzymatically active bio-inorganic protocells. Small 9(3):357–362PubMedCrossRefGoogle Scholar
  17. Kuruma Y, Stano P, Ueda T, Luisi PL (2009) A synthetic biology approach to the construction of membrane proteins in semi-synthetic minimal cells. Biochim Biophys Acta 1788(2):567–574PubMedCrossRefGoogle Scholar
  18. Lazzerini-Ospri L, Stano P, Luisi P, Marangoni R (2012) Characterization of the emergent properties of a synthetic quasi-cellular system. BMC Bioinformatics 13(Suppl 4):S9PubMedCrossRefGoogle Scholar
  19. Li M, Green DC, Anderson JLR, Binks BP, Mann S (2011) In vitro gene expression and enzyme catalysis in bio-inorganic protocells. Chem Sci 2:1739–1745CrossRefGoogle Scholar
  20. Ludlow RF, Otto S (2008) Systems chemistry. Chem Soc Rev 37(1):101–108PubMedCrossRefGoogle Scholar
  21. Luisi PL (1998) About various definitions of life. Orig Life Evol Biosph 4–6:613–622CrossRefGoogle Scholar
  22. Luisi PL, Ferri F, Stano P (2006) Approaches to semi-synthetic minimal cells: a review. Naturwissenschaften 93:1–13PubMedCrossRefGoogle Scholar
  23. Mann S (2012) Systems of creation: the emergence of life from nonliving matter. Acc Chem Res 45(12):2131–2141PubMedCrossRefGoogle Scholar
  24. Mann S (2013) The origins of life: old problems, new chemistries. Angew Chem Int Ed Engl 52(1):155–162PubMedCrossRefGoogle Scholar
  25. Mansy SS, Schrum JP, Krishnamurthy M, Tobé S, Treco DA, Szostak JW (2008) Template-directed synthesis of a genetic polymer in a model protocell. Nature 454(7200):122–125PubMedCrossRefGoogle Scholar
  26. Maurer SE, DeClue MS, Albertsen AN, Dörr M, Kuiper DS, Ziock H, Rasmussen S, Boncella JM, Monnard PA (2011) Interactions between catalysts and amphiphilic structures and their implications for a protocell model. ChemPhysChem 12(4):828–835PubMedCrossRefGoogle Scholar
  27. Miras HN, Yan J, Long DL, Cronin L (2012) Engineering polyoxometalates with emergent properties. Chem Soc Rev 41(22):7403–7430PubMedCrossRefGoogle Scholar
  28. Monnard PA (2003) Liposome-entrapped polymerases as models for microscale/nanoscale bioreactors. J Membr Biol 191(2):87–97PubMedCrossRefGoogle Scholar
  29. Monnard PA, Deamer DW (2002) Membrane self-assembly processes: steps toward the first cellular life. Anat Rec 268(3):196–207PubMedCrossRefGoogle Scholar
  30. Noireaux V, Libchaber A (2004) A vesicle bioreactor as a step toward an artificial cell assembly. In: Proceedings of the national academy of sciences of the United States of America, vol 101(51). pp 17669–17674Google Scholar
  31. Nomura SM, Tsumoto K, Hamada T, Akiyoshi K, Nakatani Y, Yoshikawa K (2003) Gene expression within cell-sized lipid vesicles. ChemBioChem 4(11):1172–1175PubMedCrossRefGoogle Scholar
  32. Oberholzer T, Albrizio M, Luisi PL (1995) Polymerase chain reaction in liposomes. Chem Biol 2:677–682PubMedCrossRefGoogle Scholar
  33. Oberholzer T, Nierhaus KH, Luisi PL (1999) Protein expression in liposomes. Biochem Biophys Res Commun 261:238–241PubMedCrossRefGoogle Scholar
  34. Orgel LE (1968) Evolution of the genetic apparatus. J Mol Biol 38:381–393PubMedCrossRefGoogle Scholar
  35. Pasparakis G, Krasnogor N, Cronin L, Davis BG, Alexander C (2010) Controlled polymer synthesis–from biomimicry towards synthetic biology. Chem Soc Rev 39(1):286–300PubMedCrossRefGoogle Scholar
  36. Pohorille A, Deamer D (2002) Artificial cells: prospects for biotechnology. Trends Biotechnol 20(3):123–128PubMedCrossRefGoogle Scholar
  37. Pradeep CP, Misdrahi MF, Li FY, Zhang J, Xu L, Long DL, Liu T, Cronin L (2009) Synthesis of modular “inorganic-organic-inorganic” polyoxometalates and their assembly into vesicles. Angew Chem Int Ed Engl 48(44):8309–8313. http://onlinelibrary.wiley.com/doi/10.1002/anie.200903070/abstract Google Scholar
  38. Rasmussen S, Chen L, Nilsson M, Abe S (2003) Bridging nonliving and living matter. Artif Life 9(3):269–316PubMedCrossRefGoogle Scholar
  39. Rasmussen S, Chen L, Deamer DW, Krakauer DC, Packard NH, Stadler PF, Bedau MA (2004) Transitions from nonliving to living matter. Science 303:963–965PubMedCrossRefGoogle Scholar
  40. Stano P, Carrara P, Kuruma Y, de Souza TP, Luisi PL (2011) Compartmentalized reactions as a case of soft-matter biotechnology: synthesis of proteins and nucleic acids inside lipid vesicles. J Mater Chem 21(47):18887–18902CrossRefGoogle Scholar
  41. Szostak JW, Bartel DP, Luisi PL (2001) Synthesizing life. Nature 409(6818):387–390PubMedCrossRefGoogle Scholar
  42. Walde P, Goto A, Monnard PA, Wessicken M, Luisi PL (1994) Oparin’s reactions revisited: enzymic synthesis of poly (adenylic acid) in micelles and self-reproducing vesicles. J Am Chem Soc 116(17):7541–7547CrossRefGoogle Scholar
  43. Woese CR (1967) The genetic code: The molecular basis for genetic expression. Harper & Row, New YorkGoogle Scholar
  44. Yu W, Sato K, Wakabayashi M, Nakatshi T, Ko-Mitamura EP, Shima Y, Urabe I, Yomo T (2001) Synthesis of functional protein in liposome. J Biosci Bioeng 92:590–593PubMedGoogle Scholar
  45. Zhu TF, Szostak JW (2009) Coupled growth and division of model protocell membranes. J Am Chem Soc 131(15):5705–5713PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Rafał Wieczorek
    • 1
  • Michael C. Wamberg
    • 1
  • Anders N. Albertsen
    • 1
  • Philipp M. G. Löffler
    • 1
  • Pierre-Alain Monnard
    • 1
  1. 1.Center of Fundamental Living Technology (FLinT), Department of Physics, Chemistry and PharmacyUniversity of Southern DenmarkOdense MDenmark

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