A semi-synthetic organism with an expanded genetic alphabet

Nature

Volumn 509, Issue 7500, 2014, Pages 385-388

  Malyshev, Denis A ^a   Dhami, Kirandeep ^a   Lavergne, Thomas ^a   Chen, Tingjian ^a   Dai, Nan ^b   Foster, Jeremy M ^b   Corrêa, Ivan R ^b   Romesberg, Floyd E ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b NEW ENGLAND BIOLABS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOSIDE TRIPHOSPHATE; NUCLEOTIDE;

ALGA; COLIFORM BACTERIUM; CYTOLOGY; ENZYME ACTIVITY; FUNCTIONAL ROLE; GENETIC ANALYSIS; GENETIC ENGINEERING; GENOMICS; PLASMID;

ARTICLE; BASE PAIRING; CONTROLLED STUDY; DNA REPAIR; ESCHERICHIA COLI; GENE EXPRESSION; GENE REPLICATION; GENETIC ANALYSIS; MACHINE; NONHUMAN; PLASMID; PRIORITY JOURNAL; UNNATURAL BASE PAIR;

ALGAL PROTEINS; BASE PAIRING; CULTURE MEDIA; DNA REPAIR; DNA REPLICATION; ESCHERICHIA COLI; GENETIC CODE; GENOMIC INSTABILITY; ISOQUINOLINES; NAPHTHALENES; NUCLEOTIDE TRANSPORT PROTEINS; NUCLEOTIDES; PLASMIDS; SYNTHETIC BIOLOGY; THIONES;

EID: 84900560301     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature13314     Document Type: Article

References (38)

1. Malyshev, D. A. et al. Efficient and sequence-independent replication of DNA containing a third base pair establishes a functional six-letter genetic alphabet. Proc. Natl Acad. Sci. USA 109, 12005-12010 (2012).
2. Yang, Z., Chen, F., Alvarado, J. B. & Benner, S. A. Amplification, mutation, and sequencing of a six-letter synthetic genetic system. J. Am. Chem. Soc. 133, 15105-15112 (2011).
3. Yamashige, R. et al. Highly specific unnatural base pair systemsas a third base pair for PCR amplification. Nucleic Acids Res. 40, 2793-2806 (2012).
4. Seo, Y. J., Malyshev, D. A., Lavergne, T., Ordoukhanian, P. & Romesberg, F. E. Site-specific labeling of DNA and RNA using an efficiently replicated and transcribed class of unnatural base pairs. J. Am. Chem. Soc. 133, 19878-19888 (2011).
5. Seo, Y. J., Matsuda, S. & Romesberg, F. E. Transcription of an expanded genetic alphabet. J. Am. Chem. Soc. 131, 5046-5047 (2009).
6. Betz, K. et al. Structural insights into DNA replication without hydrogen bonds. J. Am. Chem. Soc. 135, 18637-18643 (2013).
7. Betz, K. et al. KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry. Nature Chem. Biol. 8, 612-614 (2012).
8. Wu, Y., Fa, M., Tae, E. L., Schultz, P. G. & Romesberg, F. E. Enzymatic phosphorylation of unnatural nucleosides. J. Am. Chem. Soc. 124, 14626-14630 (2002).
9. Yan, H. & Tsai, M. D. Nucleoside monophosphate kinases: structure, mechanism, and substrate specificity. Adv. Enzymol. 73, 103-134 (1999).
10. Winkler, H. H.& Neuhaus, H. E. Non-mitochondrial ATP transport. Trends Biochem. Sci. 24, 64-68 (1999).
11. Amiri, H., Karlberg, O. & Andersson, S. G. Deep origin of plastid/parasite ATP/ADP translocases. J. Mol. Evol. 56, 137-150 (2003).
12. Hatch, T. P., Al-Hossainy, E. & Silverman, J. A. Adenine nucleotide and lysine transport in Chlamydia psittaci. J. Bacteriol. 150, 662-670 (1982).
13. Winkler, H. H. Rickettsial permeability: anADP-ATP transport system. J. Biol. Chem. 251, 389-396 (1976).
14. Horn, M.&Wagner, M. Bacterial endosymbionts of free-livingamoebae. J. Eukaryot. Microbiol. 51, 509-514 (2004).
15. Haferkamp, I. et al. Tappingthe nucleotide pool of thehost:novel nucleotide carrier proteins of Protochlamydia amoebophila. Mol. Microbiol. 60, 1534-1545 (2006).
16. Miroux, B. & Walker, J. E. 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 (1996).
17. Haferkamp, I.&Linka, N.Functional expressionandcharacterisationofmembrane transport proteins. Plant Biol. 14, 675-690 (2012).
18. Ast, M. et al. Diatom plastids depend on nucleotide import from the cytosol. Proc. Natl Acad. Sci. USA 106, 3621-3626 (2009).
19. Baba, T. et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2, 2006.0008 (2006).
20. Lavergne, T., Malyshev, D. A. & Romesberg, F. E. Major groove substituents and polymerase recognition of a class of predominantly hydrophobic unnatural base pairs. Chemistry 18, 1231-1239 (2012).
21. Seo, Y. J., Hwang, G. T., Ordoukhanian, P. & Romesberg, F. E. Optimization of an unnatural base pair toward natural-like replication. J. Am. Chem. Soc. 131, 3246-3252 (2009).
22. Li, L. et al.Natural-like replication of an unnatural base pair for the expansion of the genetic alphabet and biotechnology applications. J.Am. Chem. Soc. 136, 826-829 (2014).
23. Tomizawa, J. & Selzer, G. Initiation of DNA synthesis in Escherichia coli. Annu. Rev. Biochem. 48, 999-1034 (1979).
24. Allen, J. M. et al. Roles of DNA polymerase I in leading and lagging-strand replication defined by a high-resolution mutation footprint of ColE1 plasmid replication. Nucleic Acids Res. 39, 7020-7033 (2011).
25. Hashimoto, H. et al. Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA. Nature 506, 391-395 (2013).
26. Malyshev, D. A., Seo, Y. J., Ordoukhanian, P. & Romesberg, F. E. PCR with an expanded genetic alphabet. J. Am. Chem. Soc. 131, 14620-14621 (2009).
27. Hirao, I. et al. An unnatural hydrophobic base pair system: site-specific incorporation of nucleotide analogs into DNA and RNA. Nature Methods 3, 729-735 (2006).
28. Goodman, M. F. Error-prone repair DNA polymerases in prokaryotes and eukaryotes. Annu. Rev. Biochem. 71, 17-50 (2002).
29. Quan, J. & Tian, J. Circular polymerase extension cloning for high-throughput cloning of complex and combinatorial DNA libraries. Nature Protocols 6, 242-251 (2011).
30. Ludwig, J. & Eckstein, F. Rapid and efficient synthesis of nucleoside 59-0-(1-thiotriphosphates), 59-triphosphates and 2',39-cyclophosphorothioates using 2-chloro-4H-1,3,2-benzodioxaphosphorin-4-one. J. Org. Chem. 54, 631-635 (1989).
31. Alpert, A. & Shukla, A. Precipitation of Large, High-Abundance Proteins from Serumwith Organic Solvents in ABRF 2003: Translating Biology using Proteomics and Functional Genomics Poster no. P111-W http://www.abrf.org/Other/ ABRFMeetings/ABRF2003/Alpert.pdf (2003).
32. Kubitschek, H. E. & Friske, J. A. Determination of bacterial cell volume with the Coulter Counter. J. Bacteriol. 168, 1466-1467 (1986).
33. Yanes, O., Tautenhahn, R., Patti, G. J. & Siuzdak, G. Expanding coverage of the metabolomefor globalmetabolite profiling. Anal. Chem. 83, 2152-2161 (2011).
34. Seidman, C. E., Struhl, K., Sheen, J. & Jessen, T. Introduction of plasmid DNA into cells. Curr. Prot. Mol. Biol. Chapter 1, Unit 1.8 (2001).
35. Knab, S., Mushak, T. M., Schmitz-Esser, S., Horn, M. & Haferkamp, I. Nucleotide parasitism by Simkania negevensis (Chlamydiae). J. Bacteriol. 193, 225-235 (2011).
36. Audia, J. P. & Winkler, H. H. Study of the five Rickettsia prowazekii proteins annotated as ATP/ADP translocases (Tlc): Only Tlc1 transports ATP/ADP, while Tlc4 and Tlc5 transport other ribonucleotides. J. Bacteriol. 188, 6261-6268 (2006).
37. Hofer, A., Ekanem, J. T.&Thelander, L. Allosteric regulation of Trypanosomabrucei ribonucleotide reductase studied in vitro and in vivo. J. Biol. Chem. 273, 34098-34104 (1998).
38. Reijenga, J. C., Wes, J. H. & van Dongen, C. A. M. Comparison of methanol and perchloric acid extraction procedures for analysis of nucleotides by isotachophoresis. J. Chromatogr. B Biomed. Sci. Appl. 374, 162-169 (1986).