Experimental tools to reduce the burden of bacterial synthetic biology

Current Opinion in Systems Biology - Tập 28 - Trang 100393 - 2021
Alice Grob1,2, Roberto Di Blasi1,2, Francesca Ceroni1,2
1Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK
2Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK

Tài liệu tham khảo

Brophy, 2014, Principles of genetic circuit design, Nat Methods, 11, 508, 10.1038/nmeth.2926 Tan, 2009, Emergent bistability by a growth-modulating positive feedback circuit, Nat Chem Biol, 5, 842, 10.1038/nchembio.218 Cookson, 2011, Queueing up for enzymatic processing: correlated signaling through coupled degradation, Mol Syst Biol, 7, 561, 10.1038/msb.2011.94 Cardinale, 2012, Contextualizing context for synthetic biology - identifying causes of failure of synthetic biological systems, Biotechnol J, 7, 856, 10.1002/biot.201200085 Kim, 2020, Trade-offs between gene expression, growth and phenotypic diversity in microbial populations, Curr Opin Biotechnol, 62, 29, 10.1016/j.copbio.2019.08.004 Scott, 2010, Interdependence of cell growth and gene expression: origins and consequences, Science, 330, 1099, 10.1126/science.1192588 Borkowski, 2016, Overloaded and stressed: whole-cell considerations for bacterial synthetic biology, Curr Opin Microbiol, 33, 123, 10.1016/j.mib.2016.07.009 Brophy, 2014, Principles of genetic circuit design, Nat Methods, 11, 508, 10.1038/nmeth.2926 Shin, 2020, Programming Escherichia coli to function as a digital display, Mol Syst Biol, 16, 10.15252/msb.20199401 Lastiri-Pancardo, 2020, A quantitative method for proteome reallocation using minimal regulatory interventions, Nat Chem Biol, 16, 1026, 10.1038/s41589-020-0593-y Izard, 2015, A synthetic growth switch based on controlled expression of RNA polymerase, Mol Syst Biol, 11, 840, 10.15252/msb.20156382 Segall-Shapiro, 2014, A 'resource allocator' for transcription based on a highly fragmented T7 RNA polymerase, Mol Syst Biol, 10, 742, 10.15252/msb.20145299 Aleksashin, 2020, A fully orthogonal system for protein synthesis in bacterial cells, Nat Commun, 11, 1858, 10.1038/s41467-020-15756-1 Ceroni, 2015, Quantifying cellular capacity identifies gene expression designs with reduced burden, Nat Methods, 12, 415, 10.1038/nmeth.3339 Ceroni, 2018, Burden-driven feedback control of gene expression, Nat Methods, 15, 387, 10.1038/nmeth.4635 Huang, 2018, A quasi-integral controller for adaptation of genetic modules to variable ribosome demand, Nat Commun, 9, 5415, 10.1038/s41467-018-07899-z Darlington, 2018, Dynamic allocation of orthogonal ribosomes facilitates uncoupling of co-expressed genes, Nat Commun, 9, 695, 10.1038/s41467-018-02898-6 Karim, 2020, In vitro prototyping and rapid optimization of biosynthetic enzymes for cell design, Nat Chem Biol, 16, 912, 10.1038/s41589-020-0559-0 Moore, 2017, Cell-free synthetic biology for in vitro prototype engineering, Biochem Soc Trans, 45, 785, 10.1042/BST20170011 Elani, 2021, Interfacing living and synthetic cells as an emerging frontier in synthetic biology, Angew Chem Int Ed Engl, 60, 5602, 10.1002/anie.202006941 Nielsen, 2016, Genetic circuit design automation, Science, 352 Nikolados, 2019, Growth defects and loss-of-function in synthetic gene circuits, ACS Synth Biol, 8, 1231, 10.1021/acssynbio.8b00531 Liao, 2017, An integrative circuit-host modelling framework for predicting synthetic gene network behaviours, Nat Microbiol, 2, 1658, 10.1038/s41564-017-0022-5 Gorochowski, 2016, A minimal model of ribosome allocation dynamics captures trade-offs in expression between endogenous and synthetic genes, ACS Synth Biol, 5, 710, 10.1021/acssynbio.6b00040 Steel, 2019, Low-burden biological feedback controllers for near-perfect adaptation, ACS Synth Biol, 8, 2212, 10.1021/acssynbio.9b00125 Sarvari, 2021, A modelling framework linking resource-based stochastic translation to the optimal design of synthetic constructs, Biology (Basel), 10 Gorochowski, 2019, Absolute quantification of translational regulation and burden using combined sequencing approaches, Mol Syst Biol, 15, 10.15252/msb.20188719 Gilman, 2021, Statistical design of experiments for synthetic biology, ACS Synth Biol, 10, 1, 10.1021/acssynbio.0c00385 Cambray, 2018, Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in Escherichia coli, Nat Biotechnol, 36, 1005, 10.1038/nbt.4238 Borkowski, 2018, Cell-free prediction of protein expression costs for growing cells, Nat Commun, 9, 1457, 10.1038/s41467-018-03970-x Pasini, 2016, Using promoter libraries to reduce metabolic burden due to plasmid-encoded proteins in recombinant Escherichia coli, Nat Biotechnol, 33, 78 Dahl, 2013, Engineering dynamic pathway regulation using stress-response promoters, Nat Biotechnol, 31, 1039, 10.1038/nbt.2689 Zhang, 2018, Engineered dCas9 with reduced toxicity in bacteria: implications for genetic circuit design, Nucleic Acids Res, 46, 11115 Wu, 2016, Metabolic burden: cornerstones in synthetic biology and metabolic engineering applications, Trends Biotechnol, 34, 652, 10.1016/j.tibtech.2016.02.010 He, 2014, Central metabolic responses to the overproduction of fatty acids in Escherichia coli based on 13C-metabolic flux analysis, Biotechnol Bioeng, 111, 575, 10.1002/bit.25124 Wang, 2020, How retroactivity affects the behavior of incoherent feedforward loops, iScience, 23, 101779, 10.1016/j.isci.2020.101779 Gyorgy, 2021, A practical step-by-step guide for quantifying retroactivity in gene networks, Methods Mol Biol, 2229, 293, 10.1007/978-1-0716-1032-9_14 Liu, 2018, Toward an orthogonal central dogma, Nat Chem Biol, 14, 103, 10.1038/nchembio.2554 Costello, 2021, Synthetic biological circuits within an orthogonal central dogma, Trends Biotechnol, 39, 59, 10.1016/j.tibtech.2020.05.013 Brodel, 2016, Engineering orthogonal dual transcription factors for multi-input synthetic promoters, Nat Commun, 7, 13858, 10.1038/ncomms13858 Cameron, 2014, Tunable protein degradation in bacteria, Nat Biotechnol, 32, 1276, 10.1038/nbt.3053 Orelle, 2015, Protein synthesis by ribosomes with tethered subunits, Nature, 524, 119, 10.1038/nature14862 Carlson, 2019, Engineered ribosomes with tethered subunits for expanding biological function, Nat Commun, 10, 3920, 10.1038/s41467-019-11427-y Aleksashin, 2019, Assembly and functionality of the ribosome with tethered subunits, Nat Commun, 10, 930, 10.1038/s41467-019-08892-w Schmied, 2018, Controlling orthogonal ribosome subunit interactions enables evolution of new function, Nature, 564, 444, 10.1038/s41586-018-0773-z Sachdeva, 2014, Concerted, rapid, quantitative, and site-specific dual labeling of proteins, J Am Chem Soc, 136, 7785, 10.1021/ja4129789 Darlington, 2020, Architectures for combined transcriptional and translational resource allocation controllers, Cell Syst, 11, 382, 10.1016/j.cels.2020.08.014 Darlington, 2018, Engineering translational resource allocation controllers: mechanistic models, design guidelines, and potential biological implementations, ACS Synth Biol, 7, 2485, 10.1021/acssynbio.8b00029 Muzzey, 2009, A systems-level analysis of perfect adaptation in yeast osmoregulation, Cell, 138, 160, 10.1016/j.cell.2009.04.047 El-Samad, 2002, Calcium homeostasis and parturient hypocalcemia: an integral feedback perspective, J Theor Biol, 214, 17, 10.1006/jtbi.2001.2422 Shopera, 2017, Decoupling resource-coupled gene expression in living cells, ACS Synth Biol, 6, 1596, 10.1021/acssynbio.7b00119 Aoki, 2019, A universal biomolecular integral feedback controller for robust perfect adaptation, Nature, 570, 533, 10.1038/s41586-019-1321-1 Briat, 2016, Antithetic integral feedback ensures robust perfect adaptation in noisy biomolecular networks, Cell Syst, 2, 133, 10.1016/j.cels.2016.02.010 Dragosits, 2012, A synthetic biology approach to self-regulatory recombinant protein production in Escherichia coli, J Biol Eng, 6, 2 Gupta, 2017, Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit, Nat Biotechnol, 35, 273, 10.1038/nbt.3796 Rugbjerg, 2018, Diverse genetic error modes constrain large-scale bio-based production, Nat Commun, 9, 787, 10.1038/s41467-018-03232-w Xiao, 2016, Exploiting nongenetic cell-to-cell variation for enhanced biosynthesis, Nat Chem Biol, 12, 339, 10.1038/nchembio.2046 Rugbjerg, 2018, Synthetic addiction extends the productive life time of engineered Escherichia coli populations, Proc Natl Acad Sci USA, 115, 2347, 10.1073/pnas.1718622115 D'Ambrosio, 2020, Regulatory control circuits for stabilizing long-term anabolic product formation in yeast, Metab Eng, 61, 369, 10.1016/j.ymben.2020.07.006 Rugbjerg, 2019, Overcoming genetic heterogeneity in industrial fermentations, Nat Biotechnol, 37, 869, 10.1038/s41587-019-0171-6 Charbonneau, 2020, Developing a new class of engineered live bacterial therapeutics to treat human diseases, Nat Commun, 11, 1738, 10.1038/s41467-020-15508-1 Renda, 2014, Engineering reduced evolutionary potential for synthetic biology, Mol Biosyst, 10, 1668, 10.1039/C3MB70606K Csorgo, 2012, Low-mutation-rate, reduced-genome Escherichia coli: an improved host for faithful maintenance of engineered genetic constructs, Microb Cell Factories, 11, 11, 10.1186/1475-2859-11-11 Burgard, 2016, Development of a commercial scale process for production of 1,4-butanediol from sugar, Curr Opin Biotechnol, 42, 118, 10.1016/j.copbio.2016.04.016 Tsoi, 2018, Metabolic division of labor in microbial systems, Proc Natl Acad Sci U S A, 115, 2526, 10.1073/pnas.1716888115 McCarty, 2019, Synthetic biology tools to engineer microbial communities for Biotechnology, Trends Biotechnol, 37, 181, 10.1016/j.tibtech.2018.11.002 Ledesma-Amaro, 2020, Editorial: synthetic biology-guided metabolic engineering, Front Bioeng Biotechnol, 8, 10.3389/fbioe.2020.00221