Abstract
A schema is proposed by which the three-dimensional structure and temporal development of a biological organism might be encoded and implemented via a genetic “lookup table”. In the schema, diffusive morphogen gradients and/or the global concentration of a quickly diffusing signal index sets of kinase genes having promoters with logarithmically diminished affinity for the signal. Specificity of indexing is enhanced via concomitant expression of phosphatases undoing phosphorylation by “neighboring” kinases of greater affinity. Combinations of thus-selected kinases in turn jointly activate, via multiple phosphorylation, a particular enzyme from a virtual, multi-dimensional array thereof, at locations and times specified within the “lookup table”. In principle, such a scheme could be employed to specify arbitrary gross anatomy, surface pigmentation, and/or developmental sequencing, extending the burgeoning toolset of the nascent field of synthetic morphology. A model of two-dimensional surface coloration using this scheme is specified, and LabVIEW software for its exploration is described and made available.
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References
BindingDB, Skaggs School of Pharmacy and Pharmaceutical Sciences, UCSD, La Jolla, CA. http://bindingdb.org/bind/index.jsp Accessed 8 February 2011
Davies JA (2008) Synthetic morphology: prospects for engineered, self-constructing anatomies. J Anat 212:707–719
Gierer A, Meinhardt H (1972) A theory for biological pattern formation. Kybernetik 12:30–39
Goldbeter A, Koshland DE Jr (1981) An amplified sensitivity arising from covalent modification in biological systems. Proc Natl Acad Sci USA 78(11):6840–6844
Gregor T, Tank DW, Wieschaus EF, Bialek W (2007) Probing the limits to positional information. Cell 130(1):153–164
Kumar S, Gromiha M (2006) PINT: protein-protein interactions thermodynamic database. Nucleic Acids Res 34:D195–D198
Lisman JE (1985) A mechanism for memory storage insensitive to molecular turnover: A bistable autophosphorylating kinase. Proc Natl Acad Sci USA 82:3055–3057
Traut T (2007) Allosteric regulatory enzymes. Springer, Boston
Turing AM (1952) The chemical basis of morphogenesis. Philos Trans R Soc B-Biol Sci 237(641):37–72
Wolpert L (1994) Positional information and pattern formation in development. Dev Genet 15:485–490
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Reitz, F.B. A “lookup table” schema for synthetic biological patterning. Theory Biosci. 131, 43–47 (2012). https://doi.org/10.1007/s12064-012-0150-7
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DOI: https://doi.org/10.1007/s12064-012-0150-7