RNA Catalysis in Model Protocell Vesicles
Abstract
We are engaged in a long-term effort to synthesize chemical systems capable of Darwinian evolution, based on the encapsulation of self-replicating nucleic acids in self-replicating membrane vesicles. Here, we address the issue of the compatibility of these two replicating systems. Fatty acids form vesicles that are able to grow and divide, but vesicles composed solely of fatty acids are incompatible with the folding and activity of most ribozymes, because low concentrations of divalent cations (e.g., Mg2+) cause fatty acids to precipitate. Furthermore, vesicles that grow and divide must be permeable to the cations and substrates required for internal metabolism. We used a mixture of myristoleic acid and its glycerol monoester to construct vesicles that were Mg2+-tolerant and found that Mg2+ cations can permeate the membrane and equilibrate within a few minutes. In vesicles encapsulating a hammerhead ribozyme, the addition of external Mg2+ led to the activation and self-cleavage of the ribozyme molecules. Vesicles composed of these amphiphiles grew spontaneously through osmotically driven competition between vesicles, and further modification of the membrane composition allowed growth following mixed micelle addition. Our results show that membranes made from simple amphiphiles can form vesicles that are stable enough to retain encapsulated RNAs in the presence of divalent cations, yet dynamic enough to grow spontaneously and allow the passage of Mg2+ and mononucleotides without specific macromolecular transporters. This combination of stability and dynamics is critical for building model protocells in the laboratory and may have been important for early cellular evolution.
Introduction
Materials and Methods
Results and Discussion
MA:GMM ratio | [MgCl2] tolerated, assayed by dye leakagea (mM) | [MgCl2] at turbidity changeb (mM) |
1:0 | 0.5 | 1 |
4:1 | 2 | 3 |
2:1 | 4 | 6 |
a Dye leakage was assessed <1 h after addition of MgCl2, and onset of leakage defined the maximum [MgCl2] tolerated.b Turbidity change was visible as a sudden increase in the opacity of the solution.
[MgCl2] (mM) | kunencapsulated (min-1) | kencapsulated (min-1) |
1 | 1.3 | 0.4 |
4 | 7.9 | 1.7 |
Conclusions
Supporting Information
Supporting Information Available
Terms & Conditions
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Acknowledgment
We are grateful to Pierre-Alain Monnard, Martin Hanczyc, Shelly Fujikawa, Sheref Mansy, Justin Ichida, Michael Sacerdote, James Carothers, and Andrej Luptak for valuable discussions. We thank Gary Ruvkun and Frederick Ausubel for the use of their microscopes. J.W.S. is an investigator of the Howard Hughes Medical Institute. I.A.C. was supported by the NIH Medical Scientist Training Program (#T32-GM07753) and an NIH Molecular Biophysics Training Grant (#T32-GM08313). This work was supported in part by a grant from the NASA Exobiology Program (EXB02-0031-0018).
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28Salehi-Ashtiani, K.; Szostak, J. W. Nature 2001, 414, 82– 84 DOI: 10.1038/35102081There is no corresponding record for this reference.
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29Chakrabarti, A. C.; Deamer, D. W. Biochim. Biophys. Acta 1992, 1111, 171– 177 DOI: 10.1016/0005-2736(92)90308-9There is no corresponding record for this reference.
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30Watanabe, M.; Konishi, M. Pfluegers Arch. 2001, 442, 35– 40 DOI: 10.1007/s00424000049930https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3MXjt1Cht7s%253D&md5=05e4e91baae923d50bcfd5f09b5f953aIntracellular calibration of the fluorescent Mg2+ indicator furaptra in rat ventricular myocytesWatanabe, Masaru; Konishi, MasatoPfluegers Archiv (2001), 442 (1), 35-40CODEN: PFLABK; ISSN:0031-6768. (Springer-Verlag)Single ventricular myocytes enzymically isolated from rat hearts were loaded with the Mg2+ indicator furaptra, and the relationship between the fluorescence ratio signal (R) and the intracellular free concn. of Mg2+ ([Mg2+]i) was studied in situ at 25°C. After the application of ionophores (ionomycin, monensin, nigericin and valinomycin), an immediate change in furaptra R was noted, followed by a slow change in R that reached a steady level in 2-4 h. The direction of the early change in R that accompanied rigor contraction was independent of the extracellular Mg2+ concn. ([Mg2+]o), and was consistent with the breakdown of ATP and release of bound Mg2+. The intracellular calibration curve was constructed from the steady levels of R obtained at various [Mg2+]o between 0 and 47 mM. The dissocn. const. of intracellular furaptra was estd. to be 5.3 mM, which was 44% higher than that detd. in salt solns. (3.7 mM). The basal [Mg2+]i of rat ventricular myocytes calcd. with the intracellular curve averaged 0.91 mM.
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31Fung, B. K.-K.; Stryer, L. Biochemistry 1978, 17, 5241– 5248 DOI: 10.1021/bi00617a025There is no corresponding record for this reference.
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34Vanderkooi, J. M.; Callis, J. B. Biochemistry 1974, 13, 4000– 4006 DOI: 10.1021/bi00716a028There is no corresponding record for this reference.
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35Schenkman, S.; Araujo, P. S.; Dijkman, R.; Quina, F. H.; Chaimovich, H. Biochim. Biophys. Acta 1981, 649, 633– 647 DOI: 10.1016/0005-2736(81)90168-1There is no corresponding record for this reference.
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36Blount, K. F.; Uhlenbeck, O. C. Biochem. Soc. Trans. 2002, 30, 1119– 1122 DOI: 10.1042/BST030111936https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XovF2it78%253D&md5=82ef535d1ee2899f59b12ff15ba5349dThe hammerhead ribozymeBlount, K. F.; Uhlenbeck, O. C.Biochemical Society Transactions (2002), 30 (6), 1119-1122CODEN: BCSTB5; ISSN:0300-5127. (Portland Press Ltd.)A review and discussion. The hammerhead ribozyme is a small RNA motif consisting of 3 helixes that intersect at a conserved core. When correctly folded, the hammerhead ribozyme stimulates nearly complete cleavage of the phosphodiester chain at a defined internal site to give 2',3'-cyclic and 5'-OH termini. The cleavage rate is ∼1 min-1 at 25°, pH 7.5, and increases proportionally with OH- concn. at pH 5-9. As the rate of non-catalyzed cleavage of RNA to form the same products is ∼10-6 min-1 under similar conditions, an important goal is to understand how the folded structure of this small ribozyme increases the rate of alk. cleavage 106-fold at this specific site.
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37Stage-Zimmermann, T. K.; Uhlenbeck, O. C. RNA 1998, 4, 875– 889 DOI: 10.1017/S1355838298980876There is no corresponding record for this reference.
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39Stage-Zimmermann, T. K.; Uhlenbeck, O. C. Nat. Struct. Biol. 2001, 8, 863– 867 DOI: 10.1038/nsb1001-863There is no corresponding record for this reference.
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41Diener, T. O. Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 9370– 9374 DOI: 10.1073/pnas.86.23.9370There is no corresponding record for this reference.
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42
Salehi-Ashtiani, K.; Szostak, J. W., unpublished data.
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43Khvorova, A.; Lescoute, A.; Westhof, E.; Jayasena, S. D. Nat. Struct. Biol. 2003, 10, 708– 712 DOI: 10.1038/nsb959There is no corresponding record for this reference.
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44Grubbs, R. D. Biometals 2002, 15, 251– 259 DOI: 10.1023/A:1016026831789There is no corresponding record for this reference.
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45Luptak, A.; Doudna, J. A. Nucleic Acids Res. 2004, 32, 2272– 2280 DOI: 10.1093/nar/gkh548There is no corresponding record for this reference.
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46Rangan, P.; Masquida, B.; Westhof, E.; Woodson, S. A. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 1574– 1579 DOI: 10.1073/pnas.0337743100There is no corresponding record for this reference.
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47Glasner, M. E.; Bergman, N. H.; Bartel, D. P. Biochemistry 2002, 41, 8103– 8112 DOI: 10.1021/bi012179bThere is no corresponding record for this reference.
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48Johnston, W. K.; Unrau, P. J.; Lawrence, M. S.; Glasner, M. E.; Bartel, D. P. Science 2001, 292, 1319– 1325 DOI: 10.1126/science.106078648https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3MXjvVGjsbg%253D&md5=eeea0406409405a19a4c50f77532d5ccRNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extensionJohnston, Wendy K.; Unrau, Peter J.; Lawrence, Michael S.; Glasner, Margaret E.; Bartel, David P.Science (Washington, DC, United States) (2001), 292 (5520), 1319-1325CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)The RNA world hypothesis regarding the early evolution of life relies on the premise that some RNA sequences can catalyze RNA replication. In support of this conjecture, we describe here an RNA mol. that catalyzes the type of polymn. needed for RNA replication. The ribozyme uses nucleoside triphosphates and the coding information of an RNA template to extend an RNA primer by the successive addn. of up to 14 nucleotides-more than a complete turn of an RNA helix. Its polymn. activity is general in terms of the sequence and the length of the primer and template RNAs, provided that the 3' terminus of the primer pairs with the template. Its polymn. is also quite accurate: when primers extended by 11 nucleotides were cloned and sequenced, 1088 of 1100 sequenced nucleotides matched the template.
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49Li, Y.; Breaker, R. R. J. Am. Chem. Soc. 1999, 121, 5364– 5372 DOI: 10.1021/ja990592pThere is no corresponding record for this reference.
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Standard curve for FRET signal prepared using 4:1 MA:GMM vesicles (Figure S1) and 2:1 MA:GMM vesicles (Figure S2). This material is available free of charge via the Internet at http://pubs.acs.org.
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