Toward predictable universal genetic circuit design

Yuanli Gao, Baojun Wang

PDF(560 KB)
PDF(560 KB)
Quant. Biol. ›› 2024, Vol. 12 ›› Issue (2) : 225-229. DOI: 10.1002/qub2.48
COMMENTARY

Toward predictable universal genetic circuit design

Author information +
History +

Keywords

circuit predictability / genetic circuit design / host independent / part characterization / portability

Cite this article

Download citation ▾
Yuanli Gao, Baojun Wang. Toward predictable universal genetic circuit design. Quant. Biol., 2024, 12(2): 225‒229 https://doi.org/10.1002/qub2.48

References

[1]
Gao Y , Wang L , Wang B . Customizing cellular signal processing by synthetic multi-level regulatory circuits. Nat Commun. 2023; 14 (1): 8415.
[2]
Wang B , Buck M . Customizing cell signaling using engineered genetic logic circuits. Trends Microbiol. 2012; 20 (8): 376- 84.
[3]
Buson F , Gao Y , Wang B . Genetic parts and enabling tools for biocircuit design. ACS Synth Biol. 2024; 13 (3): 697- 713.
[4]
Xiang Y , Dalchau N , Wang B . Scaling up genetic circuit design for cellular computing: advances and prospects. Nat Comput. 2018; 17 (4): 833- 53.
[5]
Nielsen AAK , Der BS , Shin J , Vaidyanathan P , Paralanov V , Strychalski EA , et al. Genetic circuit design automation. Science. 2016; 352 (6281): aac7341.
[6]
Riglar DT , Silver PA . Engineering bacteria for diagnostic and therapeutic applications. Nat Rev Microbiol. 2018; 16 (4): 214- 25.
[7]
De Wannemaeker L , Bervoets I , De Mey M . Unlocking the bacterial domain for industrial biotechnology applications using universal parts and tools. Biotechnol Adv. 2022; 60: 108028.
[8]
Kushwaha M , Salis HM . A portable expression resource for engineering cross-species genetic circuits and pathways. Nat Commun. 2015; 6: 7832.
[9]
Qin C , Xu T , Zhao X , Zong Y , Zhang H , Lou C , et al. Functional predictability of universal gene circuits in diverse microbial hosts. Quant Biol. 2024: 1- 12.
CrossRef Google scholar
[10]
Huang BD , Groseclose TM , Wilson CJ . Transcriptional programming in a Bacteroides consortium. Nat Commun. 2022; 13: 3901.
[11]
Taketani M , Zhang J , Zhang S , Triassi A , Huang YJ , Griffith L , et al. Genetic circuit design automation for the gut resident species Bacteroides thetaiotaomicron. Nat Biotechnol. 2020; 38: 962- 9.
[12]
Liu B , Samaniego CC , Bennett MR , Franco E , Chappell J . A portable regulatory RNA array design enables tunable and complex regulation across diverse bacteria. Nat Commun. 2023; 14 (1): 5268.
[13]
Liu CC , Jewett MC , Chin JW , Voigt CA . Toward an orthogonal central dogma. Nat Chem Biol. 2018; 14 (2): 103- 6.
[14]
Lloyd JPB , Ly F , Gong P , Pflueger J , Swain T , Pflueger C , et al. Synthetic memory circuits for stable cell reprogramming in plants. Nat Biotechnol. 2022; 40 (12): 1862- 72.
[15]
Liu Y , Wan X , Wang B . Engineered CRISPRa enables programmable eukaryote-like gene activation in bacteria. Nat Commun. 2019; 10 (1): 3693.
[16]
Pinto D , Vecchione S , Wu H , Mauri M , Mascher T , Fritz G . Engineering orthogonal synthetic timer circuits based on extracytoplasmic function σ factors. Nucleic Acids Res. 2018; 46 (14): 7450- 64.
[17]
Topp S , Reynoso CMK , Seeliger JC , Goldlust IS , Desai SK , Murat D , et al. Synthetic riboswitches that induce gene expression in diverse bacterial species. Appl Environ Microbiol. 2010; 76 (23): 7881- 4.
[18]
Ma AT , Schmidt CM , Golden JW . Regulation of gene expression in diverse cyanobacterial species by using theophylline-responsive riboswitches. Appl Environ Microbiol. 2014; 80 (21): 6704- 13.
[19]
Gambill L , Staubus A , Mo K , Ameruoso A , Chappell J . A split ribozyme that links detection of a native RNA to orthogonal protein outputs. Nat Commun. 2023; 14 (1): 543.
[20]
Pinto F , Thornton EL , Wang B . An expanded library of orthogonal split inteins enables modular multi-peptide assemblies. Nat Commun. 2020; 11 (1): 1529.
[21]
Ho TYH , Shao A , Lu Z , Savilahti H , Menolascina F , Wang L , et al. A systematic approach to inserting split inteins for Boolean logic gate engineering and basal activity reduction. Nat Commun. 2021; 12 (1): 2200.
[22]
Wan X , Pinto F , Yu L , Wang B . Synthetic protein-binding DNA sponge as a tool to tune gene expression and mitigate protein toxicity. Nat Commun. 2020; 11 (1): 5961.
[23]
Green AA , Kim J , Ma D , Silver PA , Collins JJ , Yin P . Complex cellular logic computation using ribocomputing devices. Nature. 2017; 548 (7665): 117- 21.
[24]
Casini A , Christodoulou G , Freemont PS , Baldwin GS , Ellis T , MacDonald JT . R2oDNA Designer: computational design of biologically neutral synthetic DNA sequences. ACS Synth Biol. 2014; 3 (8): 525- 8.
[25]
Liu Q , Schumacher J , Wan X , Lou C , Wang B . Orthogonality and burdens of heterologous AND gate gene circuits in E. coli. ACS Synth Biol. 2018; 7 (2): 553- 64.
[26]
Pandi A , Diehl C , Yazdizadeh Kharrazi A , Scholz SA , Bobkova E , Faure L , et al. A versatile active learning workflow for optimization of genetic and metabolic networks. Nat Commun. 2022; 13 (1): 3876.
[27]
Gyorgy A , Menezes A , Arcak M . A blueprint for a synthetic genetic feedback optimizer. Nat Commun. 2023; 14 (1): 2554.

RIGHTS & PERMISSIONS

2024 2024 The Authors. Quantitative Biology published by John Wiley & Sons Australia, Ltd on behalf of Higher Education Press.
AI Summary AI Mindmap
PDF(560 KB)

Accesses

Citations

Detail

Sections
Recommended

/