Abstract
Gene assembly in stichotrichous ciliates is an impressive computational process. They have a unique way of storing their genetic information in two fundamentally different forms within their two types of nuclei. Micronuclear genes are broken into blocks (called MDSs), with MDSs shuffled and separated by non-coding material; some of the MDSs may even be inverted. During gene assembly, all MDSs are sorted in the correct order to yield the transcription-able macronuclear gene. Based on the intramolecular model for gene assembly, we prove in this paper that gene assembly may be used in principle to solve computational problems. We prove that any given instance of the Hamiltonian path problem may be encoded in a suitable way in the form of an ‘artificial’ gene so that gene assembly is successful on that gene-like pattern if and only if the given problem has an affirmative answer.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Abbreviations
- MDS:
-
Macronuclear destined sequence
- HPP:
-
Hamiltonian path problem
References
Adleman LM (1994) Molecular computation of solutions to combinatorial problems. Science 226:1021–1024
Angeleska A, Jonoska N, Saito M, Landweber LF (2007) RNA-template guided DNA assembly. J Theor Biol 248:706–720. Elsevier
Ehrenfeucht A, Petre I, Prescott DM, Rozenberg G (2001a) String and graph reduction systems for gene assembly in ciliates. Math Struct Comput Sci 12:113–134
Ehrenfeucht A, Prescott DM, Rozenberg G (2001b) Computational aspects of gene (un)scrambling in ciliates. In: Landweber LF, Winfree E (eds) Evolution as computation. Springer, Berlin Heidelberg New York, pp 216–256
Ehrenfeucht A, Harju T, Petre I, Prescott DM, Rozenberg G (2003a) Computation in living cells: gene assembly in ciliates. Springer-Verlag Berlin Heidelberg, Germany
Ehrenfeucht A, Harju T, Petre I, Prescott DM, Rozenberg G (2003b) Formal systems for gene assembly in ciliates. Theoret Comput Sci 292:199–219
Harju T, Petre I, Rozenberg G (2004a) Gene assembly in ciliates: molecular operations. In: Păun Gh, Rozenberg G, Salomaa A (eds) Current trends in theoretical computer science. World Scientific, pp 527–542
Harju T, Petre I, Rozenberg G (2004b) Gene assembly in ciliates: formal frameworks. In: Păun Gh, Rozenberg G, Salomaa A (eds) Current trends in theoretical computer science. World Scientific, pp 543–558
Kari L, Landweber LF (1999) Computational power of gene rearrangement. In: Winfree E, Gifford DK (eds) Proceedings of DNA bases computers, V. American Mathematical Society, pp 207–216
Landweber LF, Kari L (1998) The evolution of cellular computing: nature’s solution to a computational problem. In: Proceedings of the 4th DIMACS meeting on DNA-based computers. Philadelphia, PA, pp 3–15
Landweber LF, Kari L (2002) Universal molecular computation in ciliates. In: Landweber LF, Winfree E (eds) Evolution as computation. Springer, Berlin Heidelberg New York
Nowacki M, Vijayan V, Zhou Y, Schotanus K, Doak TG, Landweber LF (2008) RNA-mediated epigenetic programming of a genome-rearrangement pathway. Nature 451:153–158. doi:10.1038/nature06452
Onolt-Ishdorj T, Petre I, Rogojin V (2007) Computational power of intramolecular gene assembly. Int J Found Comput Sci 18(5):1123–1136. World Scientific
Papadimitriou CH (1994) Computational complexity. Addison-Wesley
Prescott DM (1994) The DNA of ciliated protozoa. Microbiol Rev 58(2):233–267
Prescott DM, Rozenberg G (2002) How ciliates manipulate their own DNA – a splendid example of natural computing. Nat Comput 1:165–183
Prescott DM, Rozenberg G (2003) Encrypted genes and their reassembly in ciliates. In: Amos M (ed) Cellular computing. Oxford University Press, Oxford
Prescott DM, Ehrenfeucht A, Rozenberg G (2001) Molecular operations for DNA processing in hypotrichous ciliates. Eur J Protistol 37:241–260
Williams KR, Doak TG, Herrick G (2002) Telomere formation on macronuclear chromosomes of Oxytricha trifallax and O. fallax: alternatively processed regions have multiple telomere addition sites. BMC Genet 3. doi:10.1186/1471-2156-3-16
Acknowledgements
I. Petre gratefully acknowledges support by Academy of Finland, project 108421. A. Alhazov and V. Rogojin gratefully acknowledge support by Academy of Finland, project 203667, and support by Science and Technology Center in Ukraine, project 4032. V. Rogojin is on leave of absence from Institute of Mathematics and Computer Science of Academy of Sciences of Moldova.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Alhazov, A., Petre, I. & Rogojin, V. Solutions to computational problems through gene assembly. Nat Comput 7, 385–401 (2008). https://doi.org/10.1007/s11047-008-9074-z
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11047-008-9074-z