Engineering organisms resistant to viruses and horizontally transferred genetic elements

Isaacs, Farren J.; Ma, Natalie; Rinehart, Jesse; Hemez, Colin

Engineering organisms resistant to viruses and horizontally transferred genetic elements

Patent · 19 October 2021

OSTI ID:1859963

Isaacs, Farren J.; Ma, Natalie; Rinehart, Jesse; Hemez, Colin

Organisms resistant to horizontal gene transfer (HGT), and compositions and methods of use thereof are provided. The organisms are typically genomically recoded organisms (GRO), typically cells, having a genome in which at least one endogenous codon has been eliminated by reassignment of the codon to a synonymous or non-synonymous codon. The GRO typically include a recombinant expression construct for expression of at least one element of a ribosomal rescue pathway, typically lacking the eliminated codon. Typically, the disclosed cells are resistant to completed transfer and/or expression of a horizontally transferred genetic element (HTGE) from another organism compared a corresponding cell having a genome wherein the eliminated codon has not been eliminated. In some embodiments, the organism from which the HTGE is being transferred is a bacterium or a virus.

View Patent

Research Organization:: Yale Univ., New Haven, CT (United States)

Sponsoring Organization:: USDOE; Defense Advanced Research Projects Agency (DARPA); National Institutes of Health (NIH)

DOE Contract Number:: FG02-02ER63445

Assignee:: Yale University (New Haven, CT)

Patent Number(s):: 11,149,280

Application Number:: 17/107,555

OSTI ID:: 1859963

Country of Publication:: United States

Language:: English

References (169)

Generation of phospho-ubiquitin variants by orthogonal translation reveals codon skipping George, Susanna; Aguirre, Jacob D.; Spratt, Donald E. FEBS Letters, Vol. 590, Issue 10 https://doi.org/10.1002/1873-3468.12182	journal	May 2016
Effects of plasmid amplification and recombinant gene expression on the growth kinetics of recombinantE. coli Betenbaugh, Michael J.; Beaty, Christine; Dhurjati, Prasad Biotechnology and Bioengineering, Vol. 33, Issue 11 https://doi.org/10.1002/bit.260331110	journal	May 1989
Multiple Site-Selective Insertions of Noncanonical Amino Acids into Sequence-Repetitive Polypeptides Wu, I-Lin; Patterson, Melissa A.; Carpenter Desai, Holly E. ChemBioChem, Vol. 14, Issue 8 https://doi.org/10.1002/cbic.201300069	journal	April 2013
Transfer RNA Misidentification Scrambles Sense Codon Recoding Krishnakumar, Radha; Prat, Laure; Aerni, Hans-Rudolf ChemBioChem, Vol. 14, Issue 15 https://doi.org/10.1002/cbic.201300444	journal	September 2013
Exploring the Substrate Range of Wild-Type Aminoacyl-tRNA Synthetases Fan, Chenguang; Ho, Joanne M. L.; Chirathivat, Napon ChemBioChem, Vol. 15, Issue 12 https://doi.org/10.1002/cbic.201402083	journal	May 2014
Biological Applications of Expanded Genetic Codes Li, Xiang; Liu, Chang C. ChemBioChem, Vol. 15, Issue 16 https://doi.org/10.1002/cbic.201402159	journal	August 2014
Characterization of mutant spectra generated by a forward mutational assay for geneA of ?X174 from ENU-treated transgenic mouse embryonic cell line PX-2 Valentine, Carrie R.; Montgomery, Beverly A.; Miller, Scott G. Environmental and Molecular Mutagenesis, Vol. 39, Issue 1 https://doi.org/10.1002/em.10043	journal	January 2002
Complete Nucleotide Sequence of Birmingham IncPα Plasmids Pansegrau, Werner; Lanka, Erich; Barth, Peter T. Journal of Molecular Biology, Vol. 239, Issue 5 https://doi.org/10.1006/jmbi.1994.1404	journal	June 1994
Bacteriophage Mu genome sequence: analysis and comparison with Mu-like prophages in Haemophilus, Neisseria and Deinococcus Morgan, Gregory J.; Hatfull, Graham F.; Casjens, Sherwood Journal of Molecular Biology, Vol. 317, Issue 3 https://doi.org/10.1006/jmbi.2002.5437	journal	March 2002
Red Queen Dynamics of Protein Translation Krakauer, David C.; Jansen, Vincent A. A. Journal of Theoretical Biology, Vol. 218, Issue 1 https://doi.org/10.1006/jtbi.2002.3054	journal	September 2002
The E Site and Its Importance for Improving Accuracy and Preventing Frameshifts Pech, Markus; Vesper, Oliver; Yamamoto, Hiroshi Nucleic Acids and Molecular Biology, Vol. 24, p. 345-362 https://doi.org/10.1007/978-0-387-89382-2_16	book	October 2009
The frequency of transcriptional and translational errors at nonsense codons in the lacZ gene of Escherichia coli Rosenberger, R. F.; Hilton, J. MGG Molecular & General Genetics, Vol. 191, Issue 2 https://doi.org/10.1007/BF00334815	journal	August 1983
Synthesis and degradation of termination and premature-termination fragments of β-galactosidase in vitro and in vivo Manley, James L. Journal of Molecular Biology, Vol. 125, Issue 4 https://doi.org/10.1016/0022-2836(78)90308-X	journal	November 1978
λ N antitermination system: Functional analysis of phage interactions with the host NusA protein Schauer, Alan T.; Carver, Debra L.; Bigelow, Bradley Journal of Molecular Biology, Vol. 194, Issue 4 https://doi.org/10.1016/0022-2836(87)90245-2	journal	April 1987
Stages in phage R17 infection Paranchych, W.; Ainsworth, S. K.; Dick, A. J. Virology, Vol. 45, Issue 3 https://doi.org/10.1016/0042-6822(71)90176-0	journal	September 1971
An Mr 29 000 protein is essential for mini-F maintenance in E. coli Watson, L. A.; Phua, S. H.; Bergquist, P. L. Gene, Vol. 19, Issue 2 https://doi.org/10.1016/0378-1119(82)90003-8	journal	September 1982
Delineating the Site of Interaction on the pIII Protein of Filamentous Bacteriophage fd with the F-pilus of Escherichia coli Deng, Lih-Wen; Perham, Richard N. Journal of Molecular Biology, Vol. 319, Issue 3 https://doi.org/10.1016/S0022-2836(02)00260-7	journal	June 2002
Phage lambda gene Q antiterminator recognizes RNA polymerase near the promoter and accelerates it through a pause site Grayhack, E.; Yang, X.; Lau, L. Cell, Vol. 42, Issue 1 https://doi.org/10.1016/S0092-8674(85)80121-5	journal	August 1985
The probioticEscherichia colistrain Nissle 1917 interferes with invasion of human intestinal epithelial cells by different enteroinvasive bacterial pathogens Altenhoefer, Artur; Oswald, Sibylle; Sonnenborn, Ulrich FEMS Immunology & Medical Microbiology, Vol. 40, Issue 3 https://doi.org/10.1016/S0928-8244(03)00368-7	journal	April 2004
Engineering bacteria for bioremediation Pieper, Dietmar H.; Reineke, Walter Current Opinion in Biotechnology, Vol. 11, Issue 3 https://doi.org/10.1016/S0958-1669(00)00094-X	journal	June 2000
Genetically engineered probiotics Steidler, Lothar Best Practice & Research Clinical Gastroenterology, Vol. 17, Issue 5 https://doi.org/10.1016/S1521-6918(03)00072-6	journal	October 2003
Bifunctional transfer-messenger RNA Keiler, Kenneth C.; Ramadoss, Nitya S. Biochimie, Vol. 93, Issue 11 https://doi.org/10.1016/j.biochi.2011.05.029	journal	November 2011
Genome-scale genetic engineering in Escherichia coli Jeong, Jaehwan; Cho, Namjin; Jung, Daehee Biotechnology Advances, Vol. 31, Issue 6 https://doi.org/10.1016/j.biotechadv.2013.04.003	journal	November 2013
Residue-specific incorporation of non-canonical amino acids into proteins: recent developments and applications Johnson, Jeremiah A.; Lu, Ying Y.; Van Deventer, James A. Current Opinion in Chemical Biology, Vol. 14, Issue 6 https://doi.org/10.1016/j.cbpa.2010.09.013	journal	December 2010
Integrating Biological Redesign: Where Synthetic Biology Came From and Where It Needs to Go Way, Jeffrey C.; Collins, James J.; Keasling, Jay D. Cell, Vol. 157, Issue 1 https://doi.org/10.1016/j.cell.2014.02.039	journal	March 2014
Ribosome Excursions during mRNA Translocation Mediate Broad Branching of Frameshift Pathways Yan, Shannon; Wen, Jin-Der; Bustamante, Carlos Cell, Vol. 160, Issue 5 https://doi.org/10.1016/j.cell.2015.02.003	journal	February 2015
Genomic Recoding Broadly Obstructs the Propagation of Horizontally Transferred Genetic Elements Ma, Natalie Jing; Isaacs, Farren J. Cell Systems, Vol. 3, Issue 2 https://doi.org/10.1016/j.cels.2016.06.009	journal	August 2016
N -Acetyl lysyl-tRNA synthetases evolved by a CcdB-based selection possess N -acetyl lysine specificity in vitro and in vivo Umehara, Takuya; Kim, Jihyo; Lee, Sangsik FEBS Letters, Vol. 586, Issue 6 https://doi.org/10.1016/j.febslet.2012.01.029	journal	January 2012
Synthetic constructs in/for the environment: Managing the interplay between natural and engineered Biology Schmidt, Markus; de Lorenzo, Víctor FEBS Letters, Vol. 586, Issue 15 https://doi.org/10.1016/j.febslet.2012.02.022	journal	February 2012
Enhanced phosphoserine insertion during Escherichia coli protein synthesis via partial UAG codon reassignment and release factor 1 deletion Heinemann, Ilka U.; Rovner, Alexis J.; Aerni, Hans R. FEBS Letters, Vol. 586, Issue 20 https://doi.org/10.1016/j.febslet.2012.08.031	journal	September 2012
Near-cognate suppression of amber, opal and quadruplet codons competes with aminoacyl-tRNA ^Pyl for genetic code expansion O'Donoghue, Patrick; Prat, Laure; Heinemann, Ilka U. FEBS Letters, Vol. 586, Issue 21 https://doi.org/10.1016/j.febslet.2012.09.033	journal	October 2012
Environmentally Controlled Invasion of Cancer Cells by Engineered Bacteria Anderson, J. Christopher; Clarke, Elizabeth J.; Arkin, Adam P. Journal of Molecular Biology, Vol. 355, Issue 4 https://doi.org/10.1016/j.jmb.2005.10.076	journal	January 2006
An Enhanced System for Unnatural Amino Acid Mutagenesis in E. coli Young, Travis S.; Ahmad, Insha; Yin, Jun A. Journal of Molecular Biology, Vol. 395, Issue 2 https://doi.org/10.1016/j.jmb.2009.10.030	journal	January 2010
ArfA Recruits RF2 into Stalled Ribosomes Shimizu, Yoshihiro Journal of Molecular Biology, Vol. 423, Issue 4 https://doi.org/10.1016/j.jmb.2012.08.007	journal	November 2012
The role of alternative genetic codes in viral evolution and emergence Shackelton, Laura A.; Holmes, Edward C. Journal of Theoretical Biology, Vol. 254, Issue 1 https://doi.org/10.1016/j.jtbi.2008.05.024	journal	September 2008
Nascent polypeptide sequences that influence ribosome function Cruz-Vera, Luis Rogelio; Sachs, Matthew S.; Squires, Catherine L. Current Opinion in Microbiology, Vol. 14, Issue 2 https://doi.org/10.1016/j.mib.2011.01.011	journal	April 2011
Synthetic microbial communities Großkopf, Tobias; Soyer, Orkun S. Current Opinion in Microbiology, Vol. 18 https://doi.org/10.1016/j.mib.2014.02.002	journal	April 2014
Engineering microbial consortia: a new frontier in synthetic biology Brenner, Katie; You, Lingchong; Arnold, Frances H. Trends in Biotechnology, Vol. 26, Issue 9, p. 483-489 https://doi.org/10.1016/j.tibtech.2008.05.004	journal	September 2008
Exploring the costs of horizontal gene transfer Baltrus, David A. Trends in Ecology & Evolution, Vol. 28, Issue 8 https://doi.org/10.1016/j.tree.2013.04.002	journal	August 2013
Complete genome sequence of bacteriophage T5 Wang, Jianbin; Jiang, Yan; Vincent, Myriam Virology, Vol. 332, Issue 1 https://doi.org/10.1016/j.virol.2004.10.049	journal	February 2005
A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast Jaschke, Paul R.; Lieberman, Erica K.; Rodriguez, Jon Virology, Vol. 434, Issue 2 https://doi.org/10.1016/j.virol.2012.09.020	journal	December 2012
An RNA polymerase mutant with reduced accuracy of chain elongation Blank, A.; Gallant, Jonathan A.; Burgess, Richard R. Biochemistry, Vol. 25, Issue 20 https://doi.org/10.1021/bi00368a013	journal	October 1986
An Evolved Aminoacyl-tRNA Synthetase with Atypical Polysubstrate Specificity, Young, Douglas D.; Young, Travis S.; Jahnz, Michael Biochemistry, Vol. 50, Issue 11 https://doi.org/10.1021/bi101929e	journal	March 2011
Structural Basis of Improved Second-Generation 3-Nitro-tyrosine tRNA Synthetases Cooley, Richard B.; Feldman, Jessica L.; Driggers, Camden M. Biochemistry, Vol. 53, Issue 12 https://doi.org/10.1021/bi5001239	journal	March 2014
Generating Permissive Site-Specific Unnatural Aminoacyl-tRNA Synthetases Miyake-Stoner, Shigeki J.; Refakis, Christian A.; Hammill, Jared T. Biochemistry, Vol. 49, Issue 8 https://doi.org/10.1021/bi901947r	journal	March 2010
Addition of p-Azido-L-phenylalanine to the Genetic Code of Escherichia coli Chin, Jason W.; Santoro, Stephen W.; Martin, Andrew B. Journal of the American Chemical Society, Vol. 124, Issue 31, p. 9026-9027 https://doi.org/10.1021/ja027007w	journal	July 2002
A Genetically Encoded Infrared Probe Schultz, Kathryn C.; Supekova, Lubica; Ryu, Youngha Journal of the American Chemical Society, Vol. 128, Issue 43 https://doi.org/10.1021/ja0636690	journal	November 2006
Genetically Encoded Tetrazine Amino Acid Directs Rapid Site-Specific in Vivo Bioorthogonal Ligation with trans -Cyclooctenes Seitchik, Jason L.; Peeler, Jennifer C.; Taylor, Michael T. Journal of the American Chemical Society, Vol. 134, Issue 6 https://doi.org/10.1021/ja2109745	journal	February 2012
Transcription of an Expanded Genetic Alphabet Seo, Young Jun; Matsuda, Shigeo; Romesberg, Floyd E. Journal of the American Chemical Society, Vol. 131, Issue 14 https://doi.org/10.1021/ja9006996	journal	April 2009
Direct Mutagenesis of Thousands of Genomic Targets Using Microarray-Derived Oligonucleotides Bonde, Mads T.; Kosuri, Sriram; Genee, Hans J. ACS Synthetic Biology, Vol. 4, Issue 1 https://doi.org/10.1021/sb5001565	journal	June 2014
Lateral gene transfer and the nature of bacterial innovation Ochman, Howard; Lawrence, Jeffrey G.; Groisman, Eduardo A. Nature, Vol. 405, Issue 6784 https://doi.org/10.1038/35012500	journal	May 2000
Rewiring the keyboard: evolvability of the genetic code Knight, Robin D.; Freeland, Stephen J.; Landweber, Laura F. Nature Reviews Genetics, Vol. 2, Issue 1 https://doi.org/10.1038/35047500	journal	January 2001
Ribosome-mediated incorporation of a non-standard amino acid into a peptide through expansion of the genetic code Bain, J. D.; Switzer, Christopher; Chamberlin, Richard Nature, Vol. 356, Issue 6369, p. 537-539 https://doi.org/10.1038/356537a0	journal	April 1992
Determinants of translation efficiency and accuracy Gingold, Hila; Pilpel, Yitzhak Molecular Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1038/msb.2011.14	journal	January 2011
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants the Keio collection Baba, Tomoya; Ara, Takeshi; Hasegawa, Miki Molecular Systems Biology, Vol. 2, Article No. 2006.0008 https://doi.org/10.1038/msb4100050	journal	February 2006
Quality control by the ribosome following peptide bond formation Zaher, Hani S.; Green, Rachel Nature, Vol. 457, Issue 7226 https://doi.org/10.1038/nature07582	journal	December 2008
Programming cells by multiplex genome engineering and accelerated evolution Wang, Harris H.; Isaacs, Farren J.; Carr, Peter A. Nature, Vol. 460, Issue 7257, p. 894-898 https://doi.org/10.1038/nature08187	journal	July 2009
The anti-Shine–Dalgarno sequence drives translational pausing and codon choice in bacteria Li, Gene-Wei; Oh, Eugene; Weissman, Jonathan S. Nature, Vol. 484, Issue 7395 https://doi.org/10.1038/nature10965	journal	March 2012
Recoded organisms engineered to depend on synthetic amino acids Rovner, Alexis J.; Haimovich, Adrian D.; Katz, Spencer R. Nature, Vol. 518, Issue 7537 https://doi.org/10.1038/nature14095	journal	January 2015
Biocontainment of genetically modified organisms by synthetic protein design Mandell, Daniel J.; Lajoie, Marc J.; Mee, Michael T. Nature, Vol. 518, Issue 7537 https://doi.org/10.1038/nature14121	journal	January 2015
Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids Amiram, Miriam; Haimovich, Adrian D.; Fan, Chenguang Nature Biotechnology, Vol. 33, Issue 12 https://doi.org/10.1038/nbt.3372	journal	November 2015
Virus stalls Genzyme plant Bethencourt, Victor Nature Biotechnology, Vol. 27, Issue 8 https://doi.org/10.1038/nbt0809-681a	journal	August 2009
Functional gene transfer from intracellular bacteria to mammalian cells Grillot-Courvalin, Catherine; Goussard, Sylvie; Huetz, Frarnçois Nature Biotechnology, Vol. 16, Issue 9 https://doi.org/10.1038/nbt0998-862	journal	September 1998
Recombinant protein folding and misfolding in Escherichia coli Baneyx, François; Mujacic, Mirna Nature Biotechnology, Vol. 22, Issue 11 https://doi.org/10.1038/nbt1029	journal	November 2004
Programmable ligand-controlled riboregulators of eukaryotic gene expression Bayer, Travis S.; Smolke, Christina D. Nature Biotechnology, Vol. 23, Issue 3 https://doi.org/10.1038/nbt1069	journal	February 2005
Conditional Suicide System for Containment of Bacteria and Plasmids Molin, S.; Klemm, P.; Poulsen, L. K. Nature Biotechnology, Vol. 5, Issue 12 https://doi.org/10.1038/nbt1287-1315	journal	December 1987
Biological containment of genetically modified Lactococcus lactis for intestinal delivery of human interleukin 10 Steidler, Lothar; Neirynck, Sabine; Huyghebaert, Nathalie Nature Biotechnology, Vol. 21, Issue 7 https://doi.org/10.1038/nbt840	journal	June 2003
Engineered riboregulators enable post-transcriptional control of gene expression Isaacs, Farren J.; Dwyer, Daniel J.; Ding, Chunming Nature Biotechnology, Vol. 22, Issue 7 https://doi.org/10.1038/nbt986	journal	June 2004
Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness Hammerling, Michael J.; Ellefson, Jared W.; Boutz, Daniel R. Nature Chemical Biology, Vol. 10, Issue 3 https://doi.org/10.1038/nchembio.1450	journal	February 2014
RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites Johnson, David B. F.; Xu, Jianfeng; Shen, Zhouxin Nature Chemical Biology, Vol. 7, Issue 11 https://doi.org/10.1038/nchembio.657	journal	September 2011
Natural expansion of the genetic code Ambrogelly, Alexandre; Palioura, Sotiria; Söll, Dieter Nature Chemical Biology, Vol. 3, Issue 1 https://doi.org/10.1038/nchembio847	journal	December 2006
A flexible codon in genomically recoded Escherichia coli permits programmable protein phosphorylation Pirman, Natasha L.; Barber, Karl W.; Aerni, Hans R. Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms9130	journal	September 2015
Recombineering: a homologous recombination-based method of genetic engineering Sharan, Shyam K.; Thomason, Lynn C.; Kuznetsov, Sergey G. Nature Protocols, Vol. 4, Issue 2 https://doi.org/10.1038/nprot.2008.227	journal	January 2009
Precise manipulation of bacterial chromosomes by conjugative assembly genome engineering Ma, Natalie J.; Moonan, Daniel W.; Isaacs, Farren J. Nature Protocols, Vol. 9, Issue 10 https://doi.org/10.1038/nprot.2014.081	journal	September 2014
Rapid editing and evolution of bacterial genomes using libraries of synthetic DNA Gallagher, Ryan R.; Li, Zhe; Lewis, Aaron O. Nature Protocols, Vol. 9, Issue 10 https://doi.org/10.1038/nprot.2014.082	journal	September 2014
Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning Baranov, Pavel V.; Atkins, John F.; Yordanova, Martina M. Nature Reviews Genetics, Vol. 16, Issue 9 https://doi.org/10.1038/nrg3963	journal	August 2015
Designer proteins: applications of genetic code expansion in cell biology Davis, Lloyd; Chin, Jason W. Nature Reviews Molecular Cell Biology, Vol. 13, Issue 3 https://doi.org/10.1038/nrm3286	journal	February 2012
Surveillance pathways rescuing eukaryotic ribosomes lost in translation Graille, Marc; Séraphin, Bertrand Nature Reviews Molecular Cell Biology, Vol. 13, Issue 11 https://doi.org/10.1038/nrm3457	journal	October 2012
Horizontal gene transfer, genome innovation and evolution Gogarten, J. Peter; Townsend, Jeffrey P. Nature Reviews Microbiology, Vol. 3, Issue 9 https://doi.org/10.1038/nrmicro1204	journal	August 2005
Studying plasmid horizontal transfer in situ: a critical review Sørensen, Søren J.; Bailey, Mark; Hansen, Lars H. Nature Reviews Microbiology, Vol. 3, Issue 9 https://doi.org/10.1038/nrmicro1232	journal	September 2005
Mechanisms of, and Barriers to, Horizontal Gene Transfer between Bacteria Thomas, Christopher M.; Nielsen, Kaare M. Nature Reviews Microbiology, Vol. 3, Issue 9 https://doi.org/10.1038/nrmicro1234	journal	September 2005
Evolution and classification of the CRISPR–Cas systems Makarova, Kira S.; Haft, Daniel H.; Barrangou, Rodolphe Nature Reviews Microbiology, Vol. 9, Issue 6, p. 467-477 https://doi.org/10.1038/nrmicro2577	journal	May 2011
Mechanisms of ribosome rescue in bacteria Keiler, Kenneth C. Nature Reviews Microbiology, Vol. 13, Issue 5 https://doi.org/10.1038/nrmicro3438	journal	April 2015
Engineered ribosomes with tethered subunits for expanding biological function Carlson, Erik D.; d’Aquino, Anne E.; Kim, Do Soon Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-11427-y	journal	September 2019
Controlling orthogonal ribosome subunit interactions enables evolution of new function Schmied, Wolfgang H.; Tnimov, Zakir; Uttamapinant, Chayasith Nature, Vol. 564, Issue 7736 https://doi.org/10.1038/s41586-018-0773-z	journal	December 2018
Total synthesis of Escherichia coli with a recoded genome Fredens, Julius; Wang, Kaihang; de la Torre, Daniel Nature, Vol. 569, Issue 7757 https://doi.org/10.1038/s41586-019-1192-5	journal	May 2019
Viral contamination in biologic manufacture and implications for emerging therapies Barone, Paul W.; Wiebe, Michael E.; Leung, James C. Nature Biotechnology, Vol. 38, Issue 5 https://doi.org/10.1038/s41587-020-0507-2	journal	April 2020
Designing logical codon reassignment – Expanding the chemistry in biology Dumas, Anaëlle; Lercher, Lukas; Spicer, Christopher D. Chemical Science, Vol. 6, Issue 1 https://doi.org/10.1039/C4SC01534G	journal	January 2015
Enhancing the utility of unnatural amino acid synthetases by manipulating broad substrate specificity Stokes, Audrey L.; Miyake-Stoner, Shigeki J.; Peeler, Jennifer C. Molecular BioSystems, Vol. 5, Issue 9 https://doi.org/10.1039/b904032c	journal	January 2009
Compensatory adaptation to the deleterious effect of antibiotic resistance in Salmonella typhimurium : Adaptation to antibiotic resistance in Maisnier-Patin, Sophie; Berg, Otto G.; Liljas, Lars Molecular Microbiology, Vol. 46, Issue 2 https://doi.org/10.1046/j.1365-2958.2002.03173.x	journal	October 2002
Addition of the keto functional group to the genetic code of Escherichia coli Wang, L.; Zhang, Z.; Brock, A. Proceedings of the National Academy of Sciences, Vol. 100, Issue 1, p. 56-61 https://doi.org/10.1073/pnas.0234824100	journal	December 2002
Stop codons preceded by rare arginine codons are efficient determinants of SsrA tagging in Escherichia coli Hayes, Christopher S.; Bose, Baundauna; Sauer, Robert T. Proceedings of the National Academy of Sciences, Vol. 99, Issue 6 https://doi.org/10.1073/pnas.052707199	journal	March 2002
Regulated programmed lysis of recombinant Salmonella in host tissues to release protective antigens and confer biological containment Kong, W.; Wanda, S.-Y.; Zhang, X. Proceedings of the National Academy of Sciences, Vol. 105, Issue 27, p. 9361-9366 https://doi.org/10.1073/pnas.0803801105	journal	July 2008
Rapid evolution of stability and productivity at the origin of a microbial mutualism Hillesland, K. L.; Stahl, D. A. Proceedings of the National Academy of Sciences, Vol. 107, Issue 5 https://doi.org/10.1073/pnas.0908456107	journal	January 2010
Tracking, tuning, and terminating microbial physiology using synthetic riboregulators Callura, J. M.; Dwyer, D. J.; Isaacs, F. J. Proceedings of the National Academy of Sciences, Vol. 107, Issue 36 https://doi.org/10.1073/pnas.1009747107	journal	August 2010
High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides Ellis, H. M.; Yu, D.; DiTizio, T. Proceedings of the National Academy of Sciences, Vol. 98, Issue 12, p. 6742-6746 https://doi.org/10.1073/pnas.121164898	journal	May 2001
Programmable bacteria detect and record an environmental signal in the mammalian gut Kotula, Jonathan W.; Kerns, S. Jordan; Shaket, Lev A. Proceedings of the National Academy of Sciences, Vol. 111, Issue 13 https://doi.org/10.1073/pnas.1321321111	journal	March 2014
Intrinsic biocontainment: Multiplex genome safeguards combine transcriptional and recombinational control of essential yeast genes Cai, Yizhi; Agmon, Neta; Choi, Woo Jin Proceedings of the National Academy of Sciences, Vol. 112, Issue 6 https://doi.org/10.1073/pnas.1424704112	journal	January 2015
Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli Napolitano, Michael G.; Landon, Matthieu; Gregg, Christopher J. Proceedings of the National Academy of Sciences, Vol. 113, Issue 38 https://doi.org/10.1073/pnas.1605856113	journal	September 2016
Combination bacteriolytic therapy for the treatment of experimental tumors Dang, L. H.; Bettegowda, C.; Huso, D. L. Proceedings of the National Academy of Sciences, Vol. 98, Issue 26 https://doi.org/10.1073/pnas.251543698	journal	November 2001
Construction of Biologically Functional Bacterial Plasmids In Vitro Cohen, S. N.; Chang, A. C. Y.; Boyer, H. W. Proceedings of the National Academy of Sciences, Vol. 70, Issue 11 https://doi.org/10.1073/pnas.70.11.3240	journal	November 1973
The 3'-Terminal Sequence of Escherichia coli 16S Ribosomal RNA: Complementarity to Nonsense Triplets and Ribosome Binding Sites Shine, J.; Dalgarno, L. Proceedings of the National Academy of Sciences, Vol. 71, Issue 4 https://doi.org/10.1073/pnas.71.4.1342	journal	April 1974
Spectra of spontaneous mutations in Escherichia coli strains defective in mismatch correction: the nature of in vivo DNA replication errors. Schaaper, R. M.; Dunn, R. L. Proceedings of the National Academy of Sciences, Vol. 84, Issue 17 https://doi.org/10.1073/pnas.84.17.6220	journal	September 1987
Rates of spontaneous mutation among RNA viruses. Drake, J. W. Proceedings of the National Academy of Sciences, Vol. 90, Issue 9 https://doi.org/10.1073/pnas.90.9.4171	journal	May 1993
A new approach for containment of microorganisms: Dual control of streptavidin expression by antisense RNA and the T7 transcription system Szafranski, Przemyslaw; Mello, Charlene M.; Sano, Takeshi Proceedings of the National Academy of Sciences, Vol. 94, Issue 4 https://doi.org/10.1073/pnas.94.4.1059	journal	February 1997
C-terminal Extension of Truncated Recombinant Proteins in Escherichia coli with a 10Sa RNA Decapeptide Tu, Guo-Fen; Reid, Gavin E.; Zhang, Jian-Guo Journal of Biological Chemistry, Vol. 270, Issue 16 https://doi.org/10.1074/jbc.270.16.9322	journal	April 1995
The traY Gene Product and Integration Host Factor Stimulate Escherichia coli DNA Helicase I-catalyzed Nicking at the F Plasmid oriT Nelson, William C.; Howard, Michael T.; Sherman, Jonathan A. Journal of Biological Chemistry, Vol. 270, Issue 47 https://doi.org/10.1074/jbc.270.47.28374	journal	November 1995
Proteobacterial ArfA Peptides Are Synthesized from Non-stop Messenger RNAs Schaub, Ryan E.; Poole, Stephen J.; Garza-Sánchez, Fernando Journal of Biological Chemistry, Vol. 287, Issue 35 https://doi.org/10.1074/jbc.M112.374074	journal	July 2012
The Use of Live Attenuated Bacteria as a Delivery System for Heterologous Antigens Garmory, Helen S.; Leary, Sophie E. C.; Griffin, Kate F. Journal of Drug Targeting, Vol. 11, Issue 8-10 https://doi.org/10.1080/10611860410001670008	journal	January 2003
SsrA-mediated peptide tagging caused by rare codons and tRNA scarcity Roche, E. D. The EMBO Journal, Vol. 18, Issue 16 https://doi.org/10.1093/emboj/18.16.4579	journal	August 1999
Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements Lutz, R. Nucleic Acids Research, Vol. 25, Issue 6, p. 1203-1210 https://doi.org/10.1093/nar/25.6.1203	journal	March 1997
Recombineering with tolC as a Selectable/Counter-selectable Marker: remodeling the rRNA Operons of Escherichia coli DeVito, Joseph A. Nucleic Acids Research, Vol. 36, Issue 1 https://doi.org/10.1093/nar/gkm1084	journal	December 2007
YaeJ is a novel ribosome-associated protein in Escherichia coli that can hydrolyze peptidyl-tRNA on stalled ribosomes Handa, Y.; Inaho, N.; Nameki, N. Nucleic Acids Research, Vol. 39, Issue 5 https://doi.org/10.1093/nar/gkq1097	journal	November 2010
Codon reassignment in the Escherichia coli genetic code Mukai, T.; Hayashi, A.; Iraha, F. Nucleic Acids Research, Vol. 38, Issue 22 https://doi.org/10.1093/nar/gkq707	journal	August 2010
Enhanced multiplex genome engineering through co-operative oligonucleotide co-selection Carr, Peter A.; Wang, Harris H.; Sterling, Bram Nucleic Acids Research, Vol. 40, Issue 17 https://doi.org/10.1093/nar/gks455	journal	May 2012
Rational optimization of tolC as a powerful dual selectable marker for genome engineering Gregg, Christopher J.; Lajoie, Marc J.; Napolitano, Michael G. Nucleic Acids Research, Vol. 42, Issue 7 https://doi.org/10.1093/nar/gkt1374	journal	January 2014
Revealing the amino acid composition of proteins within an expanded genetic code Aerni, Hans R.; Shifman, Mark A.; Rogulina, Svetlana Nucleic Acids Research, Vol. 43, Issue 2 https://doi.org/10.1093/nar/gku1087	journal	November 2014
Multilayered genetic safeguards limit growth of microorganisms to defined environments Gallagher, Ryan R.; Patel, Jaymin R.; Interiano, Alexander L. Nucleic Acids Research, Vol. 43, Issue 3 https://doi.org/10.1093/nar/gku1378	journal	January 2015
Reassignment of a rare sense codon to a non-canonical amino acid in Escherichia coli Mukai, Takahito; Yamaguchi, Atsushi; Ohtake, Kazumasa Nucleic Acids Research, Vol. 43, Issue 16 https://doi.org/10.1093/nar/gkv787	journal	August 2015
Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use Atkins, John F.; Loughran, Gary; Bhatt, Pramod R. Nucleic Acids Research https://doi.org/10.1093/nar/gkw530	journal	July 2016
Large-scale recoding of a bacterial genome by iterative recombineering of synthetic DNA Lau, Yu Heng; Stirling, Finn; Kuo, James Nucleic Acids Research, Vol. 45, Issue 11 https://doi.org/10.1093/nar/gkx415	journal	May 2017
A dual lethal system to enhance containment of recombinant micro-organisms Torres, Begoña; Jaenecke, Susanne; Timmis, Kenneth N. Microbiology, Vol. 149, Issue 12 https://doi.org/10.1099/mic.0.26618-0	journal	December 2003
Programmed cell death in bacteria: proteic plasmid stabilization systems Jensen, Rasmus Bugge; Gerdes, Kenn Molecular Microbiology, Vol. 17, Issue 2 https://doi.org/10.1111/j.1365-2958.1995.mmi_17020205.x	journal	July 1995
Ribosome rescue: tmRNA tagging activity and capacity in Escherichia coli : tmRNA tagging in Moore, Sean D.; Sauer, Robert T. Molecular Microbiology, Vol. 58, Issue 2 https://doi.org/10.1111/j.1365-2958.2005.04832.x	journal	September 2005
Reduced action of polypeptide release factors induces mRNA cleavage and tmRNA tagging at stop codons in Escherichia coli Li, Xia; Yokota, Teruaki; Ito, Koichi Molecular Microbiology, Vol. 63, Issue 1 https://doi.org/10.1111/j.1365-2958.2006.05498.x	journal	January 2007
Ribosome rescue by Escherichia coli ArfA (YhdL) in the absence of trans-translation system: Ribosome rescue by E. coli ArfA (YhdL) Chadani, Yuhei; Ono, Katsuhiko; Ozawa, Shin-ichiro Molecular Microbiology, Vol. 78, Issue 4 https://doi.org/10.1111/j.1365-2958.2010.07375.x	journal	September 2010
tmRNA regulates synthesis of the ArfA ribosome rescue factor: tmRNA regulates ArfA synthesis Garza-Sánchez, Fernando; Schaub, Ryan E.; Janssen, Brian D. Molecular Microbiology, Vol. 80, Issue 5 https://doi.org/10.1111/j.1365-2958.2011.07638.x	journal	March 2011
Plasmid addiction systems: perspectives and applications in biotechnology Kroll, Jens; Klinter, Stefan; Schneider, Cornelia Microbial Biotechnology, Vol. 3, Issue 6 https://doi.org/10.1111/j.1751-7915.2010.00170.x	journal	April 2010
Virus Attenuation by Genome-Scale Changes in Codon Pair Bias Coleman, J. R.; Papamichail, D.; Skiena, S. Science, Vol. 320, Issue 5884 https://doi.org/10.1126/science.1155761	journal	June 2008
Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement Isaacs, Farren J.; Carr, Peter A.; Wang, Harris H. Science, Vol. 333, Issue 6040, p. 348-353 https://doi.org/10.1126/science.1205822	journal	July 2011
Expanding the Genetic Code of Escherichia coli with Phosphoserine Park, H.-S.; Hohn, M. J.; Umehara, T. Science, Vol. 333, Issue 6046, p. 1151-1154 https://doi.org/10.1126/science.1207203	journal	August 2011
Genomically Recoded Organisms Expand Biological Functions Lajoie, M. J.; Rovner, A. J.; Goodman, D. B. Science, Vol. 342, Issue 6156, p. 357-360 https://doi.org/10.1126/science.1241459	journal	October 2013
Probing the Limits of Genetic Recoding in Essential Genes Lajoie, M. J.; Kosuri, S.; Mosberg, J. A. Science, Vol. 342, Issue 6156 https://doi.org/10.1126/science.1241460	journal	October 2013
Stop codon reassignments in the wild Ivanova, N. N.; Schwientek, P.; Tripp, H. J. Science, Vol. 344, Issue 6186, p. 909-913 https://doi.org/10.1126/science.1250691	journal	May 2014
Role of a Peptide Tagging System in Degradation of Proteins Synthesized from Damaged Messenger RNA Keiler, K. C.; Waller, P. R. H.; Sauer, R. T. Science, Vol. 271, Issue 5251 https://doi.org/10.1126/science.271.5251.990	journal	February 1996
A persistent untranslated sequence within bacteriophage T4 DNA topoisomerase gene 60 Huang, W.; Ao, S.; Casjens, S. Science, Vol. 239, Issue 4843 https://doi.org/10.1126/science.2830666	journal	February 1988
Inactivation of antibiotics and the dissemination of resistance genes Davies, J. Science, Vol. 264, Issue 5157 https://doi.org/10.1126/science.8153624	journal	April 1994
Design, synthesis, and testing toward a 57-codon genome Ostrov, N.; Landon, M.; Guell, M. Science, Vol. 353, Issue 6301 https://doi.org/10.1126/science.aaf3639	journal	August 2016
Design of a synthetic yeast genome Richardson, Sarah M.; Mitchell, Leslie A.; Stracquadanio, Giovanni Science, Vol. 355, Issue 6329 https://doi.org/10.1126/science.aaf4557	journal	March 2017
The Genome Project-Write Boeke, J. D.; Church, G.; Hessel, A. Science, Vol. 353, Issue 6295 https://doi.org/10.1126/science.aaf6850	journal	June 2016
Dual System To Reinforce Biological Containment of Recombinant Bacteria Designed for Rhizoremediation Ronchel, M. C.; Ramos, J. L. Applied and Environmental Microbiology, Vol. 67, Issue 6 https://doi.org/10.1128/AEM.67.6.2649-2656.2001	journal	June 2001
Evidence-Based Biosafety: a Review of the Principles and Effectiveness of Microbiological Containment Measures Kimman, Tjeerd G.; Smit, Eric; Klein, Michèl R. Clinical Microbiology Reviews, Vol. 21, Issue 3 https://doi.org/10.1128/CMR.00014-08	journal	July 2008
Efficient Decoding of the UAG Triplet as a Full-Fledged Sense Codon Enhances the Growth of a prfA-Deficient Strain of Escherichia coli Ohtake, K.; Sato, A.; Mukai, T. Journal of Bacteriology, Vol. 194, Issue 10 https://doi.org/10.1128/JB.00195-12	journal	March 2012
Resolving Nonstop Translation Complexes Is a Matter of Life or Death Keiler, K. C.; Feaga, H. A. Journal of Bacteriology, Vol. 196, Issue 12 https://doi.org/10.1128/JB.01490-14	journal	April 2014
Efficiency of the pTF-FC2 pas Poison-Antidote Stability System in Escherichia coli Is Affected by the Host Strain, and Antidote Degradation Requires the Lon Protease Smith, Anthony S. G.; Rawlings, Douglas E. Journal of Bacteriology, Vol. 180, Issue 20 https://doi.org/10.1128/JB.180.20.5458-5462.1998	journal	October 1998
Influenza A Virus Attenuation by Codon Deoptimization of the NS Gene for Vaccine Development Nogales, A.; Baker, S. F.; Ortiz-Riano, E. Journal of Virology, Vol. 88, Issue 18 https://doi.org/10.1128/JVI.01565-14	journal	June 2014
Development of efficient suicide mechanisms for biological containment of bacteria Knudsen, S. M.; Karlström, O. H. Applied and Environmental Microbiology, Vol. 57, Issue 1 https://doi.org/10.1128/aem.57.1.85-92.1991	journal	January 1991
A substrate-dependent biological containment system for Pseudomonas putida based on the Escherichia coli gef gene Jensen, L. B.; Ramos, J. L.; Kaneva, Z. Applied and Environmental Microbiology, Vol. 59, Issue 11 https://doi.org/10.1128/aem.59.11.3713-3717.1993	journal	November 1993
Isolation and Characterization of a Glucosamine-Requiring Mutant of Escherichia coli K-12 Defective in Glucosamine-6-Phosphate Synthetase Wu, H. C.; Wu, T. C. Journal of Bacteriology, Vol. 105, Issue 2 https://doi.org/10.1128/jb.105.2.455-466.1971	journal	January 1971
Inhibition of Formation of Escherichia coli Mating Pairs by f1 and MS2 Bacteriophages as Determined with a Coulter Counter Ou, Jonathan T. Journal of Bacteriology, Vol. 114, Issue 3 https://doi.org/10.1128/jb.114.3.1108-1115.1973	journal	January 1973
Structure of an Escherichia coli tRNA operon containing linked genes for arginine, histidine, leucine, and proline tRNAs. Hsu, L. M.; Klee, H. J.; Zagorski, J. Journal of Bacteriology, Vol. 158, Issue 3 https://doi.org/10.1128/jb.158.3.934-942.1984	journal	January 1984
Synthetic Fatty Acids Prevent Plasmid-Mediated Horizontal Gene Transfer Getino, María; Sanabria-Ríos, David J.; Fernández-López, Raúl mBio, Vol. 6, Issue 5 https://doi.org/10.1128/mBio.01032-15	journal	September 2015
Transfer ribonucleic acid-mediated suppression of termination codons in Escherichia coli. Eggertsson, G.; Söll, D. Microbiological Reviews, Vol. 52, Issue 3 https://doi.org/10.1128/mr.52.3.354-374.1988	journal	January 1988
Biology of DNA restriction. Bickle, T. A.; Krüger, D. H. Microbiological Reviews, Vol. 57, Issue 2 https://doi.org/10.1128/mr.57.2.434-450.1993	journal	January 1993
Analysis of the sequence and gene products of the transfer region of the F sex factor. Frost, L. S.; Ippen-Ihler, K.; Skurray, R. A. Microbiological Reviews, Vol. 58, Issue 2 https://doi.org/10.1128/mr.58.2.162-210.1994	journal	January 1994
Expanding and Reprogramming the Genetic Code of Cells and Animals Chin, Jason W. Annual Review of Biochemistry, Vol. 83, Issue 1 https://doi.org/10.1146/annurev-biochem-060713-035737	journal	June 2014
Toxin-Antitoxin Systems in Bacteria and Archaea Yamaguchi, Yoshihiro; Park, Jung-Ho; Inouye, Masayori Annual Review of Genetics, Vol. 45, Issue 1 https://doi.org/10.1146/annurev-genet-110410-132412	journal	December 2011
Evolutionary Implications of Horizontal Gene Transfer Syvanen, Michael Annual Review of Genetics, Vol. 46, Issue 1 https://doi.org/10.1146/annurev-genet-110711-155529	journal	December 2012
Adding New Chemistries to the Genetic Code Liu, Chang C.; Schultz, Peter G. Annual Review of Biochemistry, Vol. 79, Issue 1, p. 413-444 https://doi.org/10.1146/annurev.biochem.052308.105824	journal	June 2010
Incompatibility Group P Plasmids: Genetics, Evolution, and Use in Genetic Manipulation Thomas, C. M.; Smith, C. A. Annual Review of Microbiology, Vol. 41, Issue 1 https://doi.org/10.1146/annurev.mi.41.100187.000453	journal	October 1987
Translation initiation region sequence preferences in Escherichia coli Vimberg, Vladimir; Tats, Age; Remm, Maido BMC Molecular Biology, Vol. 8, Issue 1 https://doi.org/10.1186/1471-2199-8-100	journal	January 2007
SsrA-mediated trans-translation plays a role in mRNA quality control by facilitating degradation of truncated mRNAs Yamamoto, Y. RNA, Vol. 9, Issue 4 https://doi.org/10.1261/rna.2174803	journal	April 2003
Kinetic basis for global loss of fidelity arising from mismatches in the P-site codon:anticodon helix Zaher, H. S.; Green, R. RNA, Vol. 16, Issue 10 https://doi.org/10.1261/rna.2241810	journal	August 2010
trans-translation-mediated tight regulation of the expression of the alternative ribosome-rescue factor ArfA in Escherichia coli Chadani, Yuhei; Matsumoto, Emi; Aso, Hiroaki Genes & Genetic Systems, Vol. 86, Issue 3 https://doi.org/10.1266/ggs.86.151	journal	January 2011
The Distinction Between Recoding and Codon Reassignment Atkins, John F.; Baranov, Pavel V. Genetics, Vol. 185, Issue 4 https://doi.org/10.1534/genetics.110.119016	journal	August 2010
Preparing synthetic biology for the world Moe-Behrens, Gerd H. G.; Davis, Rene; Haynes, Karmella A. Frontiers in Microbiology, Vol. 4 https://doi.org/10.3389/fmicb.2013.00005	journal	January 2013
Ends of the line for tmRNA-SmpB Hudson, Corey M.; Lau, Britney Y.; Williams, Kelly P. Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00421	journal	August 2014
A second eukaryotic group with mitochondrion-encoded tmRNA: In silico identification and experimental confirmation Hafez, Mohamed; Burger, Gertraud; Steinberg, Sergey V. RNA Biology, Vol. 10, Issue 7 https://doi.org/10.4161/rna.25376	journal	July 2013
Organisms with alternative genetic codes resolve unassigned codons via mistranslation and ribosomal rescue Ma, Natalie Jing; Hemez, Colin F.; Barber, Karl W. eLife, Vol. 7 https://doi.org/10.7554/eLife.34878	journal	October 2018

Similar Records

Organisms with alternative genetic codes resolve unassigned codons via mistranslation and ribosomal rescue

Journal Article · 2018 · eLife · OSTI ID:1479816

Engineering organisms resistant to viruses and horizontally transferred genetic elements

Citation Formats

References (169)

Similar Records

Related Subjects