Designable DNA-binding Domains Enable Construction of Logic Circuits in Mammalian Cells

Overview

Journal Nat Chem Biol

Specialties Biochemistry
Biology
Chemistry

Date 2014 Jan 14

PMID 24413461

Citations 46

Authors

Rok Gaber

Tina Lebar

Andreja Majerle

Branko Ster

Andrej Dobnikar

Mojca Bencina

Roman Jerala

Affiliations

Soon will be listed here.

Abstract

Electronic computer circuits consisting of a large number of connected logic gates of the same type, such as NOR, can be easily fabricated and can implement any logic function. In contrast, designed genetic circuits must employ orthogonal information mediators owing to free diffusion within the cell. Combinatorial diversity and orthogonality can be provided by designable DNA- binding domains. Here, we employed the transcription activator-like repressors to optimize the construction of orthogonal functionally complete NOR gates to construct logic circuits. We used transient transfection to implement all 16 two-input logic functions from combinations of the same type of NOR gates within mammalian cells. Additionally, we present a genetic logic circuit where one input is used to select between an AND and OR function to process the data input using the same circuit. This demonstrates the potential of designable modular transcription factors for the construction of complex biological information-processing devices.

Citing Articles

The switch-liker's guide to plant synthetic gene circuits.

Lloyd J, Khan A, Lister R Plant J. 2025; 121(5):e70090.

PMID: 40052500 PMC: 11887007. DOI: 10.1111/tpj.70090.

Building the SynBio community in the Czech Republic from the bottom up: You get what you give.

Juracka S, Hrncirova B, Buryskova B, Georgiev D, Dvorak P Biotechnol Notes. 2024; 3:124-134.

PMID: 39416447 PMC: 11446354. DOI: 10.1016/j.biotno.2022.11.002.

Engineering signalling pathways in mammalian cells.

Leopold A, Verkhusha V Nat Biomed Eng. 2024; 8(12):1523-1539.

PMID: 39237709 PMC: 11852397. DOI: 10.1038/s41551-024-01237-z.

The art of designed coiled-coils for the regulation of mammalian cells.

Plaper T, Rihtar E, Ramuta T, Forstneric V, Jazbec V, Ivanovski F Cell Chem Biol. 2024; 31(8):1460-1472.

PMID: 38971158 PMC: 11335187. DOI: 10.1016/j.chembiol.2024.06.001.

Advancing programmable gene expression in plants using CRISPRi-based Boolean gates.

Nat Biotechnol. 2024; .

PMID: 38769425 DOI: 10.1038/s41587-024-02273-5.

References

Boch J, Scholze H, Schornack S, Landgraf A, Hahn S, Kay S . Breaking the code of DNA binding specificity of TAL-type III effectors. Science. 2009; 326(5959):1509-12. DOI: 10.1126/science.1178811. View

Bonnet J, Subsoontorn P, Endy D . Rewritable digital data storage in live cells via engineered control of recombination directionality. Proc Natl Acad Sci U S A. 2012; 109(23):8884-9. PMC: 3384180. DOI: 10.1073/pnas.1202344109. View

Andrianantoandro E, Basu S, Karig D, Weiss R . Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol. 2006; 2:2006.0028. PMC: 1681505. DOI: 10.1038/msb4100073. View

Elowitz M, Leibler S . A synthetic oscillatory network of transcriptional regulators. Nature. 2000; 403(6767):335-8. DOI: 10.1038/35002125. View

Fussenegger M, Morris R, Fux C, Rimann M, von Stockar B, Thompson C . Streptogramin-based gene regulation systems for mammalian cells. Nat Biotechnol. 2000; 18(11):1203-8. DOI: 10.1038/81208. View

Moscou M, Bogdanove A . A simple cipher governs DNA recognition by TAL effectors. Science. 2009; 326(5959):1501. DOI: 10.1126/science.1178817. View

Greber D, El-Baba M, Fussenegger M . Intronically encoded siRNAs improve dynamic range of mammalian gene regulation systems and toggle switch. Nucleic Acids Res. 2008; 36(16):e101. PMC: 2532736. DOI: 10.1093/nar/gkn443. View

Qi L, Larson M, Gilbert L, Doudna J, Weissman J, Arkin A . Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013; 152(5):1173-83. PMC: 3664290. DOI: 10.1016/j.cell.2013.02.022. View

Tamsir A, Tabor J, Voigt C . Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'. Nature. 2010; 469(7329):212-5. PMC: 3904220. DOI: 10.1038/nature09565. View

10.

Kramer B, Fischer C, Fussenegger M . BioLogic gates enable logical transcription control in mammalian cells. Biotechnol Bioeng. 2004; 87(4):478-84. DOI: 10.1002/bit.20142. View

11.

Regot S, Macia J, Conde N, Furukawa K, Kjellen J, Peeters T . Distributed biological computation with multicellular engineered networks. Nature. 2010; 469(7329):207-11. DOI: 10.1038/nature09679. View

12.

Lohmueller J, Armel T, Silver P . A tunable zinc finger-based framework for Boolean logic computation in mammalian cells. Nucleic Acids Res. 2012; 40(11):5180-7. PMC: 3367183. DOI: 10.1093/nar/gks142. View

13.

Garg A, Lohmueller J, Silver P, Armel T . Engineering synthetic TAL effectors with orthogonal target sites. Nucleic Acids Res. 2012; 40(15):7584-95. PMC: 3424557. DOI: 10.1093/nar/gks404. View

14.

Mali P, Aach J, Stranges P, Esvelt K, Moosburner M, Kosuri S . CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol. 2013; 31(9):833-8. PMC: 3818127. DOI: 10.1038/nbt.2675. View

15.

Ye H, Daoud-El Baba M, Peng R, Fussenegger M . A synthetic optogenetic transcription device enhances blood-glucose homeostasis in mice. Science. 2011; 332(6037):1565-8. DOI: 10.1126/science.1203535. View

16.

Tigges M, Marquez-Lago T, Stelling J, Fussenegger M . A tunable synthetic mammalian oscillator. Nature. 2009; 457(7227):309-12. DOI: 10.1038/nature07616. View

17.

Weber W, Fux C, Daoud-El Baba M, Keller B, Weber C, Kramer B . Macrolide-based transgene control in mammalian cells and mice. Nat Biotechnol. 2002; 20(9):901-7. DOI: 10.1038/nbt731. View

18.

cermak T, Doyle E, Christian M, Wang L, Zhang Y, Schmidt C . Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res. 2011; 39(12):e82. PMC: 3130291. DOI: 10.1093/nar/gkr218. View

19.

Maeder M, Linder S, Reyon D, Angstman J, Fu Y, Sander J . Robust, synergistic regulation of human gene expression using TALE activators. Nat Methods. 2013; 10(3):243-5. PMC: 3584229. DOI: 10.1038/nmeth.2366. View

20.

Siuti P, Yazbek J, Lu T . Synthetic circuits integrating logic and memory in living cells. Nat Biotechnol. 2013; 31(5):448-52. DOI: 10.1038/nbt.2510. View