Abil Z, Ellefson JW, Gollihar JD, Watkins E, Ellington AD (2017) Compartmentalized partnered replication for the directed evolution of genetic parts and circuits. Nat Protoc 12(12):2493–2512. https://doi.org/10.1038/nprot.2017.119
Article PubMed PubMed Central CAS Google Scholar
Bansho Y, Ichihashi N, Kazuta Y, Matsuura T, Suzuki H, Yomo T (2012) Importance of parasite RNA species repression for prolonged translation-coupled RNA self-replication. Chem Biol 19(4):478–487. https://doi.org/10.1016/j.chembiol.2012.01.019
Article PubMed CAS Google Scholar
Baris Y, Taylor MRG, Aria V, Yeeles JTP (2022) Fast and efficient DNA replication with purified human proteins. Nature 606(7912):204–210. https://doi.org/10.1038/s41586-022-04759-1
Article PubMed CAS Google Scholar
Bartelt SM, Chervyachkova E, Ricken J, Wegner SV (2019) Mimicking adhesion in minimal synthetic cells. Adv Biosyst 3(6):e1800333. https://doi.org/10.1002/adbi.201800333
Blanken D, van Nies P, Danelon C (2019) Quantitative imaging of gene-expressing liposomes reveals rare favorable phenotypes. Phys Biol 16(4):045002. https://doi.org/10.1088/1478-3975/ab0c62
Boubakri H, de Septenville AL, Viguera E, Michel B (2010) The helicases DinG, Rep and UvrD cooperate to promote replication across transcription units in vivo. EMBO J 29(1):145–157. https://doi.org/10.1038/emboj.2009.308
Article PubMed CAS Google Scholar
Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, Wallace IM, Whitney JA, Weirauch MT, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pal C, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C (2010) The genetic landscape of a cell. Science 327(5964):425–431. https://doi.org/10.1126/science.1180823
Article PubMed PubMed Central CAS Google Scholar
Costanzo M, Baryshnikova A, Myers CL, Andrews B, Boone C (2011) Charting the genetic interaction map of a cell. Curr Opin Biotechnol 22(1):66–74. https://doi.org/10.1016/j.copbio.2010.11.001
Article PubMed CAS Google Scholar
Crick F (1970) Central dogma of molecular biology. Nature 227(5258):561–563. https://doi.org/10.1038/227561a0
Article PubMed CAS Google Scholar
Crick FH (1958) On protein synthesis. Symp Soc Exp Biol 12:8
Damiano L, Stano P (2020) On the “life-likeness” of synthetic cells. Front Bioeng Biotechnol 8:953. https://doi.org/10.3389/fbioe.2020.00953
Article PubMed PubMed Central Google Scholar
Danchin A (2021) Three overlooked key functional classes for building up minimal synthetic cells. Synth Biol (Oxf) 6(1):ysab010. https://doi.org/10.1093/synbio/ysab010
Fujiwara K, Katayama T, Nomura SM (2013) Cooperative working of bacterial chromosome replication proteins generated by a reconstituted protein expression system. Nucleic Acids Res 41(14):7176–7183. https://doi.org/10.1093/nar/gkt489
Article PubMed PubMed Central CAS Google Scholar
Garamella J, Garenne D, Noireaux V (2019) TXTL-based approach to synthetic cells. Methods Enzymol 617:217–239. https://doi.org/10.1016/bs.mie.2018.12.015
Article PubMed CAS Google Scholar
Gaut NJ, Adamala KP (2021) Reconstituting Natural cell elements in synthetic cells. Adv Biol (Weinh) 5(3):e2000188. https://doi.org/10.1002/adbi.202000188
Gopfrich K, Haller B, Staufer O, Dreher Y, Mersdorf U, Platzman I, Spatz JP (2019) One-pot assembly of complex giant unilamellar vesicle-based synthetic cells. ACS Synth Biol 8(5):937–947. https://doi.org/10.1021/acssynbio.9b00034
Article PubMed PubMed Central CAS Google Scholar
Guindani C, da Silva LC, Cao S, Ivanov T, Landfester K (2022) Synthetic cells: from simple bio-inspired modules to sophisticated integrated systems. Angew Chem Int Ed Engl 61(16):e202110855. https://doi.org/10.1002/anie.202110855
Article PubMed PubMed Central CAS Google Scholar
Hasebe T, Narita K, Hidaka S, Su’etsugu M (2018) Efficient arrangement of the replication fork trap for in vitro propagation of monomeric circular DNA in the Chromosome-replication cycle reaction. Life (Basel) 8(4). https://doi.org/10.3390/life8040043
Ichihashi N, Matsuura T, Kita H, Hosoda K, Sunami T, Tsukada K, Yomo T (2008) Importance of translation-replication balance for efficient replication by the self-encoded replicase. ChemBioChem 9(18):3023–3028. https://doi.org/10.1002/cbic.200800518
Article PubMed CAS Google Scholar
Ichihashi N, Usui K, Kazuta Y, Sunami T, Matsuura T, Yomo T (2013) Darwinian evolution in a translation-coupled RNA replication system within a cell-like compartment. Nat Commun 4:2494. https://doi.org/10.1038/ncomms3494
Article PubMed CAS Google Scholar
Jew K, Smith PEJ, So B, Kasman J, Oza JP, Black MW (2022) Characterizing and Improving pET Vectors for Cell-free Expression. Front Bioeng Biotechnol 10:895069. https://doi.org/10.3389/fbioe.2022.895069
Article PubMed PubMed Central Google Scholar
Joyce GF, Szostak JW (2018) Protocells and RNA self-replication. Cold Spring Harb Perspect Biol 10(9). https://doi.org/10.1101/cshperspect.a034801
Kita H, Matsuura T, Sunami T, Hosoda K, Ichihashi N, Tsukada K, Urabe I, Yomo T (2008) Replication of genetic information with self-encoded replicase in liposomes. ChemBioChem 9(15):2403–2410. https://doi.org/10.1002/cbic.200800360
Article PubMed CAS Google Scholar
Kuzmin E, VanderSluis B, Wang W, Tan G, Deshpande R, Chen Y, Usaj M, Balint A, Mattiazzi Usaj M, van Leeuwen J, Koch EN, Pons C, Dagilis AJ, Pryszlak M, Wang JZY, Hanchard J, Riggi M, Xu K, Heydari H, San Luis BJ, Shuteriqi E, Zhu H, Van Dyk N, Sharifpoor S, Costanzo M, Loewith R, Caudy A, Bolnick D, Brown GW, Andrews BJ, Boone C, Myers CL (2018) Systematic analysis of complex genetic interactions. Science 360(6386). https://doi.org/10.1126/science.aao1729
Lang KS, Merrikh H (2018) The Clash of macromolecular titans: replication-transcription conflicts in bacteria. Annu Rev Microbiol 72:71–88. https://doi.org/10.1146/annurev-micro-090817-062514
Article PubMed PubMed Central CAS Google Scholar
Lavickova B, Maerkl SJ (2019) A Simple, robust, and low-cost method to produce the PURE cell-free system. ACS Synth Biol 8(2):455–462. https://doi.org/10.1021/acssynbio.8b00427
Article PubMed CAS Google Scholar
Leela JK, Raghunathan N, Gowrishankar J (2021) Topoisomerase I essentiality, DnaA-independent chromosomal replication, and transcription-replication conflict in Escherichia coli. J Bacteriol 203(17):e0019521. https://doi.org/10.1128/JB.00195-21
Lewis JS, Jergic S, Dixon NE (2016) The E. coli DNA replication fork. Enzymes 39:31–88. https://doi.org/10.1016/bs.enz.2016.04.001
Article PubMed CAS Google Scholar
Libicher K, Hornberger R, Heymann M, Mutschler H (2020) In vitro self-replication and multicistronic expression of large synthetic genomes. Nat Commun 11(1):904. https://doi.org/10.1038/s41467-020-14694-2
Article PubMed PubMed Central CAS Google Scholar
Liu B, Alberts BM (1995) Head-on collision between a DNA replication apparatus and RNA polymerase transcription complex. Science 267(5201):1131–1137. https://doi.org/10.1126/science.7855590
Article PubMed CAS Google Scholar
Matsushita-Ishiodori Y, Hanczyc MM, Wang A, Szostak JW, Yomo T (2019) Using imaging flow cytometry to quantify and optimize giant vesicle production by water-in-oil emulsion transfer methods. Langmuir 35(6):2375–2382. https://doi.org/10.1021/acs.langmuir.8b03635
Article PubMed CAS Google Scholar
Merrikh H, Zhang Y, Grossman AD, Wang JD (2012) Replication-transcription conflicts in bacteria. Nat Rev Microbiol 10(7):449–458. https://doi.org/10.1038/nrmicro2800
Article PubMed PubMed Central CAS Google Scholar
Monachino E, Jergic S, Lewis JS, Xu ZQ, Lo ATY, O’Shea VL, Berger JM, Dixon NE, van Oijen AM (2020) A primase-induced conformational switch controls the stability of the bacterial replisome. Mol Cell 79(1):140–154 e7. https://doi.org/10.1016/j.molcel.2020.04.037
Mukai T, Yoneji T, Yamada K, Fujita H, Nara S, Su’etsugu M, (2020) Overcoming the challenges of megabase-sized plasmid construction in Escherichia coli. ACS Synth Biol 9(6):1315–1327. https://doi.org/10.1021/acssynbio.0c00008
Article PubMed CAS Google Scholar
Nara S, Su’etsugu M (2021) In vitro amplification of whole large plasmids via transposon-mediated oriC insertion. Biotechniques 71(4):528–533. https://doi.org/10.2144/btn-2021-0068
Article PubMed CAS Google Scholar
Noireaux V, Liu AP (2020) The new age of cell-free biology. Annu Rev Biomed Eng 22:51–77. https://doi.org/10.1146/annurev-bioeng-092019-111110
Article PubMed CAS Google Scholar
Olivi L, Berger M, Creyghton RNP, De Franceschi N, Dekker C, Mulder BM, Claassens NJ, Ten Wolde PR, van der Oost J (2021) Towards a synthetic cell cycle. Nat Commun 12(1):4531. https://doi.org/10.1038/s41467-021-24772-8
Article PubMed PubMed Central CAS Google Scholar
Ragheb M, Merrikh H (2019) The enigmatic role of Mfd in replication-transcription conflicts in bacteria. DNA Repair (amst) 81:102659. https://doi.org/10.1016/j.dnarep.2019.102659
Romantseva E, Strychalski EA (2020) CELL-FREE (Comparable Engineered Living Lysates for Research Education and Entrepreneurship) Workshop Report. Special Publication (NIST SP), National Institute of Standards and Technology, Gaithersburg. https://doi.org/10.6028/NIST.SP.1500-13
Sakatani Y, Ichihashi N, Kazuta Y, Yomo T (2015) A transcription and translation-coupled DNA replication system using rolling-circle replication. Sci Rep 5:10404. https://doi.org/10.1038/srep10404
Article PubMed PubMed Central Google Scholar
Sato W, Zajkowski T, Moser F, Adamala KP (2022) Synthetic cells in biomedical applications. Wiley Interdiscip Rev Nanomed Nanobiotechnol 14(2):e1761. https://doi.org/10.1002/wnan.1761
留言 (0)