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For: Javanpour AA, Liu CC. Evolving Small-Molecule Biosensors with Improved Performance and Reprogrammed Ligand Preference Using OrthoRep. ACS Synth Biol 2021;10:2705-2714. [PMID: 34597502 DOI: 10.1021/acssynbio.1c00316] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Number Cited by Other Article(s)
1
Pisera AO, Yu Y, Williams RL, Liu CC. Ultra-efficient Integration of Gene Libraries onto Yeast Cytosolic Plasmids. ACS Synth Biol 2025;14:1002-1008. [PMID: 40127237 DOI: 10.1021/acssynbio.4c00786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2025]
2
Chu W, Guo Y, Wu Y, Lv X, Li J, Liu L, Du G, Chen J, Liu Y. Enhancing Cellular and Enzymatic Properties Through In Vivo Continuous Evolution. Chembiochem 2024;25:e202400564. [PMID: 39248206 DOI: 10.1002/cbic.202400564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 09/08/2024] [Accepted: 09/09/2024] [Indexed: 09/10/2024]
3
Pham C, Stogios PJ, Savchenko A, Mahadevan R. Computation-guided transcription factor biosensor specificity engineering for adipic acid detection. Comput Struct Biotechnol J 2024;23:2211-2219. [PMID: 38817964 PMCID: PMC11137364 DOI: 10.1016/j.csbj.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 06/01/2024]  Open
4
Chacón M, Dixon N. Genetically encoded biosensors for the circular plastics bioeconomy. Metab Eng Commun 2024;19:e00255. [PMID: 39737114 PMCID: PMC11683335 DOI: 10.1016/j.mec.2024.e00255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 10/21/2024] [Accepted: 11/27/2024] [Indexed: 01/01/2025]  Open
5
Pisera A, Yu Y, Williams RL, Liu CC. Ultra-Efficient Integration of Gene Libraries onto Yeast Cytosolic Plasmids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.29.626108. [PMID: 39651169 PMCID: PMC11623697 DOI: 10.1101/2024.11.29.626108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2024]
6
Rix G, Williams RL, Hu VJ, Spinner H, Pisera A(O, Marks DS, Liu CC. Continuous evolution of user-defined genes at 1 million times the genomic mutation rate. Science 2024;386:eadm9073. [PMID: 39509492 PMCID: PMC11750425 DOI: 10.1126/science.adm9073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 09/10/2024] [Indexed: 11/15/2024]
7
Mengiste AA, McDonald JL, Nguyen Tran MT, Plank AV, Wilson RH, Butty VL, Shoulders MD. MutaT7GDE: A Single Chimera for the Targeted, Balanced, Efficient, and Processive Installation of All Possible Transition Mutations In Vivo. ACS Synth Biol 2024;13:2693-2701. [PMID: 39190860 DOI: 10.1021/acssynbio.4c00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
8
Van Gelder K, Lindner SN, Hanson AD, Zhou J. Strangers in a foreign land: 'Yeastizing' plant enzymes. Microb Biotechnol 2024;17:e14525. [PMID: 39222378 PMCID: PMC11368087 DOI: 10.1111/1751-7915.14525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 07/02/2024] [Indexed: 09/04/2024]  Open
9
Guan A, He Z, Wang X, Jia ZJ, Qin J. Engineering the next-generation synthetic cell factory driven by protein engineering. Biotechnol Adv 2024;73:108366. [PMID: 38663492 DOI: 10.1016/j.biotechadv.2024.108366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/21/2024] [Accepted: 04/22/2024] [Indexed: 05/09/2024]
10
Joshi SHN, Jenkins C, Ulaeto D, Gorochowski TE. Accelerating Genetic Sensor Development, Scale-up, and Deployment Using Synthetic Biology. BIODESIGN RESEARCH 2024;6:0037. [PMID: 38919711 PMCID: PMC11197468 DOI: 10.34133/bdr.0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/23/2024] [Indexed: 06/27/2024]  Open
11
Peng Q, Bao W, Geng B, Yang S. Biosensor-assisted CRISPRi high-throughput screening to identify genetic targets in Zymomonas mobilis for high d-lactate production. Synth Syst Biotechnol 2024;9:242-249. [PMID: 38390372 PMCID: PMC10883783 DOI: 10.1016/j.synbio.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/04/2024] [Accepted: 02/04/2024] [Indexed: 02/24/2024]  Open
12
Zeng M, Sarker B, Rondthaler SN, Vu V, Andrews LB. Identifying LasR Quorum Sensors with Improved Signal Specificity by Mapping the Sequence-Function Landscape. ACS Synth Biol 2024;13:568-589. [PMID: 38206199 DOI: 10.1021/acssynbio.3c00543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
13
Xi C, Diao J, Moon TS. Advances in ligand-specific biosensing for structurally similar molecules. Cell Syst 2023;14:1024-1043. [PMID: 38128482 PMCID: PMC10751988 DOI: 10.1016/j.cels.2023.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 08/23/2023] [Accepted: 10/19/2023] [Indexed: 12/23/2023]
14
Tian R, Zhao R, Guo H, Yan K, Wang C, Lu C, Lv X, Li J, Liu L, Du G, Chen J, Liu Y. Engineered bacterial orthogonal DNA replication system for continuous evolution. Nat Chem Biol 2023;19:1504-1512. [PMID: 37443393 DOI: 10.1038/s41589-023-01387-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 06/16/2023] [Indexed: 07/15/2023]
15
Rix G, Williams RL, Spinner H, Hu VJ, Marks DS, Liu CC. Continuous evolution of user-defined genes at 1-million-times the genomic mutation rate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566922. [PMID: 38014077 PMCID: PMC10680746 DOI: 10.1101/2023.11.13.566922] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
16
Baugh AC, Momany C, Neidle EL. Versatility and Complexity: Common and Uncommon Facets of LysR-Type Transcriptional Regulators. Annu Rev Microbiol 2023;77:317-339. [PMID: 37285554 DOI: 10.1146/annurev-micro-050323-040543] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
17
Martin HG, Radivojevic T, Zucker J, Bouchard K, Sustarich J, Peisert S, Arnold D, Hillson N, Babnigg G, Marti JM, Mungall CJ, Beckham GT, Waldburger L, Carothers J, Sundaram S, Agarwal D, Simmons BA, Backman T, Banerjee D, Tanjore D, Ramakrishnan L, Singh A. Perspectives for self-driving labs in synthetic biology. Curr Opin Biotechnol 2023;79:102881. [PMID: 36603501 DOI: 10.1016/j.copbio.2022.102881] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/23/2022] [Accepted: 12/07/2022] [Indexed: 01/04/2023]
18
Volk MJ, Tran VG, Tan SI, Mishra S, Fatma Z, Boob A, Li H, Xue P, Martin TA, Zhao H. Metabolic Engineering: Methodologies and Applications. Chem Rev 2022;123:5521-5570. [PMID: 36584306 DOI: 10.1021/acs.chemrev.2c00403] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
19
Holland K, Blazeck J. High throughput mutagenesis and screening for yeast engineering. J Biol Eng 2022;16:37. [PMID: 36575525 PMCID: PMC9793380 DOI: 10.1186/s13036-022-00315-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/03/2022] [Indexed: 12/28/2022]  Open
20
Shin SM, Jha RK, Dale T. Tackling the Catch-22 Situation of Optimizing a Sensor and a Transporter System in a Whole-Cell Microbial Biosensor Design for an Anthropogenic Small Molecule. ACS Synth Biol 2022;11:3996-4008. [PMID: 36472954 DOI: 10.1021/acssynbio.2c00364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
21
d'Oelsnitz S, Love JD, Diaz DJ, Ellington AD. GroovDB: A Database of Ligand-Inducible Transcription Factors. ACS Synth Biol 2022;11:3534-3537. [PMID: 36178800 DOI: 10.1021/acssynbio.2c00382] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
22
Zou ZP, Yang Y, Wang J, Zhou Y, Ye BC. Coupling split-lux cassette with a toggle switch in bacteria for ultrasensitive blood markers detection in feces and urine. Biosens Bioelectron 2022;214:114520. [DOI: 10.1016/j.bios.2022.114520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/24/2022] [Accepted: 06/26/2022] [Indexed: 11/29/2022]
23
Andon JS, Lee B, Wang T. Enzyme directed evolution using genetically encodable biosensors. Org Biomol Chem 2022;20:5891-5906. [PMID: 35437559 DOI: 10.1039/d2ob00443g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
24
Pham C, Stogios PJ, Savchenko A, Mahadevan R. Advances in engineering and optimization of transcription factor-based biosensors for plug-and-play small molecule detection. Curr Opin Biotechnol 2022;76:102753. [PMID: 35872379 DOI: 10.1016/j.copbio.2022.102753] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/31/2022] [Accepted: 06/06/2022] [Indexed: 11/30/2022]
25
Molina RS, Rix G, Mengiste AA, Alvarez B, Seo D, Chen H, Hurtado J, Zhang Q, Donato García-García J, Heins ZJ, Almhjell PJ, Arnold FH, Khalil AS, Hanson AD, Dueber JE, Schaffer DV, Chen F, Kim S, Ángel Fernández L, Shoulders MD, Liu CC. In vivo hypermutation and continuous evolution. NATURE REVIEWS. METHODS PRIMERS 2022;2:37. [PMID: 37073402 PMCID: PMC10108624 DOI: 10.1038/s43586-022-00130-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
26
McLure RJ, Radford SE, Brockwell DJ. High-throughput directed evolution: a golden era for protein science. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2022.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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