REFERENCES
Agostinetto, R., Rossi, M., Dawson, J., Lim, A., Simoneau, M.H.,
Boucher, C., Valldorf, B., Ross-Gillespie, A., Jardine, J.G., Sok, D.,
et al. (2022). Rapid cGMP manufacturing of COVID-19 monoclonal antibody
using stable CHO cell pools. Biotechnol. Bioeng. 119 , 663–666.
Al’abri, I.S., Haller, D.J., Li, Z., and Crook, N. (2022). Inducible
directed evolution of complex phenotypes in bacteria. Nucleic Acids Res.50 , E58.
Baden, L.R., El Sahly, H.M., Essink, B., Kotloff, K., Frey, S., Novak,
R., Diemert, D., Spector, S.A., Rouphael, N., Creech, C.B., et al.
(2021). Efficacy and Safety of the mRNA-1273 SARS-CoV-2 Vaccine. N.
Engl. J. Med. 384 , 403–416.
Badran, A.H., and Liu, D.R. (2015). In vivo continuous directed
evolution. Curr. Opin. Chem. Biol. 24 , 1–10.
Bae, D., Hyeon, H., Shin, E., Yeom, J.H., and Lee, K. (2023). Relaxed
Cleavage Specificity of Hyperactive Variants of Escherichia coli RNase E
on RNA I. J. Microbiol. 61 , 211–220.
Bai, Y., Liu, D., He, Q., Liu, J., Mao, Q., and Liang, Z. (2023).
Research progress on circular RNA vaccines. Front. Immunol. 13 ,
1–12.
Bernstein, J.A., Khodursky, A.B., Lin, P.H., Lin-Chao, S., and Cohen,
S.N. (2002). Global analysis of mRNA decay and abundance in Escherichia
coli at single-gene resolution using two-color fluorescent DNA
microarrays. Proc. Natl. Acad. Sci. U. S. A. 99 , 9697–9702.
Bolivar, F., Rodriguez, R.L., Greene, P.J., Betlach, M.C., Heyneker,
H.L., Boyer, H.W., Crosa, J.H., and Falkow, S. (1977). Construction and
characterization of new cloning vehicle. II. A multipurpose cloning
system. Gene 2 , 95–113.
Börner, J., Friedrich, T., Bartkuhn, M., and Klug, G. (2023).
Ribonuclease E strongly impacts bacterial adaptation to different growth
conditions. RNA Biol. 20 , 120–135.
Breda, L., Papp, T.E., Triebwasser, M.P., Yadegari, A., Fedorky, M.T.,
Tanaka, N., Abdulmalik, O., Pavani, G., Wang, Y., Grupp, S.A., et al.
(2023). In vivo hematopoietic stem cell modification by mRNA delivery.
Science 381 , 436–443.
Brown, A.J., Gibson, S.J., Hatton, D., Arnall, C.L., and James, D.C.
(2019). Whole synthetic pathway engineering of recombinant protein
production. Biotechnol. Bioeng. 116 , 375–387.
Callaghan, A.J., Marcaida, M.J., Stead, J.A., McDowall, K.J., Scott,
W.G., and Luisi, B.F. (2005). Structure of Escherichia coli RNase E
catalytic domain and implications for RNA turnover. Nature 437 ,
1187–1191.
Carlile, T.M., Martinez, N.M., Schaening, C., Su, A., Bell, T.A.,
Zinshteyn, B., and Gilbert, W. V. (2019). mRNA structure determines
modification by pseudouridine synthase 1. Nat. Chem. Biol. 15 ,
966.
Carter, A.D., Morris, C.E., and McAllister, W.T. (1981). Revised
transcription map of the late region of bacteriophage T7 DNA. J. Virol.37 , 636–642.
Delgado-Martín, J., and Velasco, L. (2021). An efficient dsRNA
constitutive expression system in Escherichia coli. Appl. Microbiol.
Biotechnol. 105 , 6381–6393.
Deviatkin, A.A., Simonov, R.A., Trutneva, K.A., Maznina, A.A., Soroka,
A.B., Kogan, A.A., Feoktistova, S.G., Khavina, E.M., Mityaeva, O.N., and
Volchkov, P.Y. (2023). Cap-Independent Circular mRNA Translation
Efficiency. Vaccines 11 , 1–12.
Esquerré, T., Moisan, A., Chiapello, H., Arike, L., Vilu, R., Gaspin,
C., Cocaign-Bousquet, M., and Girbal, L. (2015). Genome-wide
investigation of mRNA lifetime determinants in Escherichia coli cells
cultured at different growth rates. BMC Genomics 16 , 1–13.
Esvelt, K.M., Carlson, J.C., and Liu, D.R. (2011). A system for the
continuous directed evolution of biomolecules. Nature 472 ,
499–503.
Fan, J., Sripada, S.A., Pham, D.N., Linova, M.Y., Woodley, J.M.,
Menegatti, S., Boi, C., and Carbonell, R.G. (2023). Purification of a
monoclonal antibody using a novel high-capacity multimodal cation
exchange nonwoven membrane. Sep. Purif. Technol. 317 , 123920.
Gan, L.M., Lagerström-Fermér, M., Carlsson, L.G., Arfvidsson, C.,
Egnell, A.C., Rudvik, A., Kjaer, M., Collén, A., Thompson, J.D., Joyal,
J., et al. (2019). Intradermal delivery of modified mRNA encoding VEGF-A
in patients with type 2 diabetes. Nat. Commun. 10 , 1–9.
Gholamalipour, Y., Karunanayake Mudiyanselage, A., and Martin, C.T.
(2018). NAR breakthrough article 3 end additions by T7 RNA polymerase
are RNA self-templated, distributive and diverse in character—-RNA-Seq
analyses. Nucleic Acids Res. 46 , 9253–9263.
Heyde, S.A.H., and Nørholm, M.H.H. (2021). Tailoring the evolution of
BL21(DE3) uncovers a key role for RNA stability in gene expression
toxicity. Nat. Commun. 21 , 1–9.
Jiang, Z., and Dalby, P.A. (2023). Challenges in scaling up AAV-based
gene therapy manufacturing. Trends Biotechnol. 41 , 1268–1281.
Joshi, S.H.N., Yong, C., and Gyorgy, A. (2022). Inducible plasmid copy
number control for synthetic biology in commonly used E. coli strains.
Nat. Commun. 13 .
Kime, L., Vincent, H.A., Gendoo, D.M.A., Jourdan, S.S., Fishwick,
C.W.G., Callaghan, A.J., and McDowall, K.J. (2015). The first
small-molecule inhibitors of members of the ribonuclease E family. Sci.
Rep. 5 , 8028.
Kis, Z., Kontoravdi, C., Shattock, R., and Shah, N. (2021). Resources,
production scales and time required for producing RNA vaccines for the
global pandemic demand. Vaccines 9 , 1–14.
Kram, K.E., and Finkel, S.E. (2015). Rich medium composition affects
Escherichia coli survival, glycation, and mutation frequency during
long-term batch culture. Appl. Environ. Microbiol. 81 ,
4442–4450.
Laalami, S., Zig, L., and Putzer, H. (2014). Initiation of mRNA decay in
bacteria. Cell. Mol. Life Sci. 71 , 1799–1828.
Lee, C., Kim, J., Shin, S.G., and Hwang, S. (2006). Absolute and
relative QPCR quantification of plasmid copy number in Escherichia coli.
J. Biotechnol. 123 , 273–280.
Leppek, K., Byeon, G.W., Kladwang, W., Wayment-Steele, H.K., Kerr, C.H.,
Xu, A.F., Kim, D.S., Topkar, V. V., Choe, C., Rothschild, D., et al.
(2022). Combinatorial optimization of mRNA structure, stability, and
translation for RNA-based therapeutics. Nat. Commun. 13 .
Lin‐Chao, S., Chen, W. ‐T, and Wong, T. ‐T (1992). High copy number of
the pUC plasmid results from a Rom/Rop‐suppressible point mutation in
RNA II. Mol. Microbiol. 6 , 3385–3393.
Liu, X., Zhang, Y., Zhou, S., Dain, L., Mei, L., and Zhu, G. (2022).
Circular RNA: An emerging frontier in RNA therapeutic targets, RNA
therapeutics, and mRNA vaccines. J. Control. Release 348 , 84–94.
Ma, Z.Z., Zhou, H., Wei, Y.L., Yan, S., and Shen, J. (2020). A novel
plasmid–Escherichia coli system produces large batch dsRNAs for insect
gene silencing. Pest Manag. Sci. 76 , 2505–2512.
Mairhofer, J., Wittwer, A., Cserjan-Puschmann, M., and Striedner, G.
(2015). Preventing T7 RNA polymerase read-through transcription-A
synthetic termination signal capable of improving bioprocess stability.
ACS Synth. Biol. 4 , 265–273.
Mardle, C.E., Goddard, L.R., Spelman, B.C., Atkins, H.S., Butt, L.E.,
Cox, P.A., Gowers, D.M., Vincent, H.A., and Callaghan, A.J. (2020).
Identification and analysis of novel small molecule inhibitors of RNase
E: Implications for antibacterial targeting and regulation of RNase E.
Biochem. Biophys. Reports 23 .
Mauger, D.M., Joseph Cabral, B., Presnyak, V., Su, S. V., Reid, D.W.,
Goodman, B., Link, K., Khatwani, N., Reynders, J., Moore, M.J., et al.
(2019). mRNA structure regulates protein expression through changes in
functional half-life. Proc. Natl. Acad. Sci. U. S. A. 116 ,
24075–24083.
McElwain, L., Phair, K., Kealey, C., and Brady, D. (2022). Current
trends in biopharmaceuticals production in Escherichia coli. Biotechnol.
Lett. 44 , 917–931.
Miroux, B., and Walker, J.E. (1996). Over-production of proteins in
Escherichia coli: Mutant hosts that allow synthesis of some membrane
proteins and globular proteins at high levels. J. Mol. Biol. 260 ,
289–298.
Mohanty, B.K., and Kushner, S.R. (2019). New Insights into the
Relationship between tRNA Processing and Polyadenylation in Escherichia
coli. Trends Genet. 35 , 434–445.
Mohanty, B.K., and Kushner, S.R. (2022). Regulation of mRNA decay in E.
coli. Crit. Rev. Biochem. Mol. Biol. 57 , 48–72.
Nelissen, F.H.T., Leunissen, E.H.P., Van De Laar, L., Tessari, M., Heus,
H.A., and Wijmenga, S.S. (2012). Fast production of homogeneous
recombinant RNA-towards large-scale production of RNA. Nucleic Acids
Res. 40 .
Nwokeoji, A.O., Kilby, P.M., Portwood, D.E., and Dickman, M.J. (2016).
RNASwift: A rapid, versatile RNA extraction method free from phenol and
chloroform. Anal. Biochem. 512 , 36–46.
Ouranidis, A., Vavilis, T., Mandala, E., Davidopoulou, C., Stamoula, E.,
Markopoulou, C.K., Karagianni, A., and Kachrimanis, K. (2022).
Manufacturing under Pharma 4 . 0 Principles. 1–31.
Pertzev, A. V., and Nicholson, A.W. (2006). Characterization of RNA
sequence determinants and antideterminants of processing reactivity for
a minimal substrate of Escherichia coli ribonuclease III. Nucleic Acids
Res. 34 , 3708–3721.
Plank, T.D.M., Whitehurst, J.T., and Kieft, J.S. (2013). Cell type
specificity and structural determinants of IRES activity from the 5′
leaders of different HIV-1 transcripts. Nucleic Acids Res. 41 ,
6698–6714.
Ponchon, L., and Dardel, F. (2011). Large scale expression and
purification of recombinant RNA in Escherichia coli. Methods 54 ,
267–273.
Ponchon, L., Beauvais, G., Nonin-Lecomte, S., and Dardel, F. (2009). A
generic protocol for the expression and purification of recombinant RNA
in Escherichia coli using a tRNA scaffold. Nat. Protoc. 4 ,
947–959.
Ponchon, L., Catala, M., Seijo, B., El Khouri, M., Dardel, F.,
Nonin-Lecomte, S., and Tisné, C. (2013). Co-expression of RNA-protein
complexes in Escherichia coli and applications to RNA biology. Nucleic
Acids Res. 41 , e150.
Pontrelli, S., Chiu, T.Y., Lan, E.I., Chen, F.Y.H., Chang, P., and Liao,
J.C. (2018). Escherichia coli as a host for metabolic engineering.
Metab. Eng. 50 , 16–46.
Qin, C., Xiang, Y., Liu, J., Zhang, R., Liu, Z., Li, T., Sun, Z.,
Ouyang, X., Zong, Y., Zhang, H.M., et al. (2023). Precise programming of
multigene expression stoichiometry in mammalian cells by a modular and
programmable transcriptional system. Nat. Commun. 2023 141 14 ,
1–10.
Qin, S., Tang, X., Chen, Y., Chen, K., Fan, N., Xiao, W., Zheng, Q., Li,
G., Teng, Y., Wu, M., et al. (2022). mRNA-based therapeutics: powerful
and versatile tools to combat diseases. Signal Transduct. Target. Ther.7 .
Qu, L., Yi, Z., Shen, Y., Lin, L., Chen, F., Xu, Y., Wu, Z., Tang, H.,
Zhang, X., Tian, F., et al. (2022). Circular RNA vaccines against
SARS-CoV-2 and emerging variants. Cell 185 , 1728-1744.e16.
Radoš, D., Donati, S., Lempp, M., Rapp, J., and Link, H. (2022).
Homeostasis of the biosynthetic E. coli metabolome. IScience 25 ,
104503.
Richards, J., and Belasco, J.G. (2023). Graded impact of obstacle size
on scanning by RNase E. Nucleic Acids Res. 51 , 1364–1374.
Rosa, S.S., Prazeres, D.M.F., Azevedo, A.M., and Marques, M.P.C. (2021).
mRNA vaccines manufacturing: Challenges and bottlenecks. Vaccine39 , 2190–2200.
Rostain, W., Shen, S., Cordero, T., Rodrigo, G., and Jaramillo, A.
(2020). Engineering a Circular Riboregulator in Escherichia coli.
BioDesign Res. 2020 , 1–9.
Rouches, M. V., Xu, Y., Cortes, L.B.G., and Lambert, G. (2022). A
plasmid system with tunable copy number. Nat. Commun. 13 , 1–12.
Roux, C., Etienne, T.A., Hajnsdorf, E., Ropers, D., Carpousis, A.J.,
Cocaign-Bousquet, M., and Girbal, L. (2022). The essential role of mRNA
degradation in understanding and engineering E. coli metabolism.
Biotechnol. Adv. 54 , 107805.
Sripada, S.A., Chu, W., Williams, T.I., Teten, M.A., Mosley, B.J.,
Carbonell, R.G., Lenhoff, A.M., Cramer, S.M., Bill, J., Yigzaw, Y., et
al. (2022). Towards continuous mAb purification: Clearance of host cell
proteins from CHO cell culture harvests via “flow-through affinity
chromatography” using peptide-based adsorbents. Biotechnol. Bioeng.119 , 1873–1889.
Vavilis, T., Stamoula, E., Ainatzoglou, A., Sachinidis, A., Lamprinou,
M., Dardalas, I., and Vizirianakis, I.S. (2023). mRNA in the Context of
Protein Replacement Therapy. Pharmaceutics 15 , 1–19.
Viegas, S.C., Apura, P., Martínez-García, E., De Lorenzo, V., and
Arraiano, C.M. (2018). Modulating Heterologous Gene Expression with
Portable mRNA-Stabilizing 5′-UTR Sequences. ACS Synth. Biol. 7 ,
2177–2188.
Wesselhoeft, R.A., Kowalski, P.S., and Anderson, D.G. (2018).
Engineering circular RNA for potent and stable translation in eukaryotic
cells. Nat. Commun. 9 , 1–10.
Whitley, J., Zwolinski, C., Denis, C., Maughan, M., Hayles, L., Clarke,
D., Snare, M., Liao, H., Chiou, S., Marmura, T., et al. (2022).
Development of mRNA manufacturing for vaccines and therapeutics: mRNA
platform requirements and development of a scalable production process
to support early phase clinical trials. Transl. Res. 242 , 38–55.
Yang, D., Pricilia, C., Prabowo, S., Eun, H., Park, S.Y., Cho, I.J.,
Jiao, S., and Lee, S.Y. (2021). Escherichia coli as a platform microbial
host for systems metabolic engineering. Essays Biochem. 65 ,
225–246.
Zhang, H., Zhang, L., Lin, A., Xu, C., Li, Z., Liu, K., Liu, B., Ma, X.,
Zhao, F., Jiang, H., et al. (2023). Algorithm for optimized mRNA design
improves stability and immunogenicity. Nature 621 , 396–403.
Zhang, Q., Ma, D., Wu, F., Standage-Beier, K., Chen, X., Wu, K., Green,
A.A., and Wang, X. (2021). Predictable control of RNA lifetime using
engineered degradation-tuning RNAs. Nat. Chem. Biol. 17 ,
828–836.