Expanded genetic code for the engineering of ribosomally synthetized and post-translationally modified peptide natural products (RiPPs)

Current Opinion in Biotechnology

Volumn 24, Issue 4, 2013, Pages 591-598

  Budisa, Nediljko ^a  

^a TECHNISCHE UNIVERSITÄT BERLIN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

FUNCTIONAL SPACES; GENETIC CODE; MEMBRANE PERMEABILITY; NATURAL PRODUCTS; NON-CANONICAL AMINO ACIDS; POST-TRANSLATIONAL MODIFICATIONS; UNIQUE SEQUENCE;

CHEMICAL STABILITY; PEPTIDES;

AMINO ACIDS;

AMINO ACID DERIVATIVE; AMINO ACID TRANSFER RNA LIGASE; COUMARIN; CYANOBACTIN; LANTIBIOTIC; LICHENIDIN; NATURAL PRODUCT; NISIN; NONCANONICAL AMINO ACID; NONRIBOSOMAL PEPTIDE SYNTHETASE; PEPTIDE DERIVATIVE; PHOSPHOSERINE; POLYPEPTIDE ANTIBIOTIC AGENT; RIBOSOMALLY SYNTHESIZED PEPTIDE PRODUCT; RIBOSOME PROTEIN; SCAFFOLD PROTEIN; TRANSFER RNA; UNCLASSIFIED DRUG;

ANTIBACTERIAL ACTIVITY; ANTIBIOTIC RESISTANCE; CELL MEMBRANE PERMEABILITY; CYTOTOXICITY; DRUG BIOAVAILABILITY; DRUG DESIGN; DRUG SPECIFICITY; DRUG STABILITY; DRUG SYNTHESIS; GENETIC CODE; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROTEIN ENGINEERING; PROTEIN PROCESSING; PROTEIN SYNTHESIS; PROTEIN TARGETING; REVIEW; RIBOSOME; RISK BENEFIT ANALYSIS;

AMINO ACIDS; BACTERIA; BACTERIOCINS; BIOLOGICAL PRODUCTS; GENETIC CODE; GENETIC ENGINEERING; PEPTIDES; PROTEIN PROCESSING, POST-TRANSLATIONAL; RIBOSOMES;

EID: 84880964743     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2013.02.026     Document Type: Review

References (52)

1. Hoesl M.G., Budisa N. Recent advances in genetic code engineering in Escherichia coli. Curr Opin Biotechnol 2012, 23:751-757.
2. Budisa N. Engineering the Genetic Code 2006, Wiley-VCH, Weinheim.
3. Walsh G. Post-translational modifications of protein biopharmaceuticals. Drug Discov Today 2010, 15:773-780.
4. Bock A., Forchhammer K., Heider J., Leinfelder W., Sawers G., Veprek B., Zinoni F. Selenocysteine-the 21st amino acid. Mol Microbiol 1991, 5:515-520.
5. Srinivasan G., James C.M., Krzycki J.A. Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA. Science 2002, 296:1459-1462.
6. Macek B., Mann M., Olsen J.V. Global and site-specific quantitative phosphoproteomics: principles and applications. Ann Rev Pharm Toxicol 2009, 49:199-221.
7. Pilobello K.T., Mahal L.K. Deciphering the glycocode: the complexity and analytical challenge of glycomics. Curr Opin Chem Biol 2007, 11:300-305.
8. Yaffe M.B., Elia A.E.H. Phosphoserine/threonine-binding domains. Curr Opin Cell Biol 2001, 13:131-138.
9. Link A.J., Mock M.L., Tirrell D.A. Non-canonical amino acids in protein engineering. Curr Opin Biotechnol 2003, 14:603-609.
10. Budisa N. Prolegomena to future experimental efforts on genetic code engineering by expanding its amino acid repertoire. Angew Chem Int Ed Engl 2004, 43:6426-6463.
11. Gfeller D., Michielin O., Zoete V. SwissSidechain: a molecular and structural database of non-natural sidechains. Nucl Acids Res 2013, Epub 2012 October 26.
12. Merkel L., Beckmann H.S.G., Wittmann V., Budisa N. Efficient N-terminal glycoconjugation of proteins by the N-end rule. Chembiochem 2008, 9:1220-1224.
13. Plass T., Milles S., Koehler C., Schultz C., Lemke E.A. Genetically encoded copper-free click chemistry. Angew Chem Int Ed Engl 2011, 50:3878-3881.
14. Lepthien S., Merkel L., Budisa N. In vivo double and triple labeling of proteins using synthetic amino acids. Angew Chem Int Ed Engl 2010, 49:5446-5450.
15. Bruechner P., Koch D., Voigtmann U., Blechert S. Cross-metathesis of C-glycosides and peptides. Synth Commun 2007, 37:2757-2769.
16. Gauthier M.A., Klok H.A. Peptide/protein-polymer conjugates: synthetic strategies and design concepts. Chem Commun 2008, 23:2591-2611.
17. Wiltschi B., Budisa N. Natural history and experimental evolution of the genetic code. Appl Microbiol Biotechnol 2007, 74:739-753.
18. Budisa N., Minks C., Alefelder S., Wenger W., Dong F.M., Moroder L., Huber R. Toward the experimental codon reassignment in vivo: protein building with an expanded amino acid repertoire. FASEB J 1999, 13:41-51.
19. Young D.D., Young T.S., Jahnz M., Ahmad I., Spraggon G., Schultz P.G. An evolved aminoacyl-tRNA synthetase with atypical polysubstrate specificity. Biochemistry 2011, 50:1894-1900.
20. Furter R. Expansion of the genetic code: site-directed p-fluoro-phenylalanine incorporation in Escherichia coli. Protein Sci 1998, 7:419-426.
21. Wang L., Schultz P.G. A general approach for the generation of orthogonal tRNAs. Chem Biol 2001, 8:883-890.
22. Hoesl M.G., Budisa N. In vivo incorporation of multiple noncanonical amino acids into proteins. Angew Chem Int Ed Engl 2011, 50:2896-2902.
23. Hipolito C.J., Suga H. Ribosomal production and in vitro selection of natural product-like peptidomimetics: the FIT and RaPID systems. Curr Opin Chem Biol 2012, 16:196-203.
24. Josephson K., Hartman M.C.T., Szostak J.W. Ribosomal synthesis of unnatural peptides. J Am Chem Soc 2005, 127:11727-11735.
25. Forster A.C., Cornish V.W., Blacklow S.C. Pure translation display. Anal Biochem 2004, 333:358-364.
26. Levengood M.R., Knerr P.J., Oman T.J., van der Donk W.A. In vitro mutasynthesis of lantibiotic analogues containing nonproteinogenic amino acids. J Am Chem Soc 2009, 131:12024-12026.
27. Wang Q., Parrish A.R., Wang L. Expanding the genetic code for biological studies. Chem Biol 2009, 16:323-336.
28. Devos W.M., Kuipers O.P., Vandermeer J.R., Siezen R.J. Maturation pathway of Nisin and other lantibiotics-posttranslationally modified antimicrobial peptides exported by gram-positive bacteria. Mol Microbiol 1995, 17:427-437.
29. Velasquez J.E., van der Donk W.A. Genome mining for ribosomally synthesized natural products. Curr Opin Chem Biol 2011, 15:11-21.
30. Marahiel M.A. Working outside the protein-synthesis rules: insights into non-ribosomal peptide synthesis. J Pept Sci 2009, 15:799-807.
31. Arnison P.G., Bibb M.J., Bierbaum G., Bowers A.A., Bugni T.S., Bulaj G., Camarero J.A., Campopiano D.J., Challis G.L., Clardy J., Cotter P.D., et al. Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat Prod Rep 2013, 30:108-160.
32. Weber T., Marahiel M.A. Exploring the domain structure of modular nonribosomal peptide synthetases. Structure 2001, 9:R3-R9.
33. Walsh C.T., Chen H.W., Keating T.A., Hubbard B.K., Losey H.C., Luo L.S., Marshall C.G., Miller D.A., Patel H.M. Tailoring enzymes that modify nonribosomal peptides during and after chain elongation on NRPS assembly lines. Curr Opin Chem Biol 2001, 5:525-534.
34. McIntosh J.A., Donia M.S., Schmidt E.W. Ribosomal peptide natural products: bridging the ribosomal and nonribosomal worlds. Nat Prod Rep 2009, 26:537-559.
35. Dawson M.J. The lantibiotics, an underexploited class of natural products with broad potential. Chim Oggi-Chem Today 2006, 24:25-27.
36. Knerr P.J., van der Donk W.A. Discovery, biosynthesis, and engineering of lantipeptides. Annu Rev Biochem 2012, 81:479-505.
37. Zhang Q., Yu Y., Velasquez J.E., van der Donk W.A. Evolution of lanthipeptide synthetases. Proc Natl Acad Sci U S A 2012, 109:18361-18366.
38. Lubelski J., Rink R., Khusainov R., Moll G.N., Kuipers O.P. Biosynthesis, immunity, regulation, mode of action and engineering of the model lantibiotic nisin. Cell Mol Life Sci 2008, 65:455-476.
39. Willey J.M., van der Donk W.A. Lantibiotics: peptides of diverse structure and function. Annu Rev Microbiol 2007, 61:477-501.
40. Hackenberger C.P.R., Schwarzer D. Chemoselective ligation and modification strategies for peptides and proteins. Angew Chem Int Ed Engl 2008, 47:10030-10074.
41. Sletten E.M., Bertozzi C.R. Bioorthogonal chemistry: fishing for selectivity in a sea of functionality. Angew Chem Int Ed Engl 2009, 48:6974-6998.
42. Oldach F., Al Toma R., Kuthning A., Caetano T., Mendo S., Budisa N., Sussmuth R.D. Congeneric lantibiotics from ribosomal in vivo peptide synthesis with noncanonical amino acids. Angew Chem Int Ed Engl 2012, 51:415-418.
43. Tianero M.D.B., Donia M.S., Young T.S., Schultz P.G., Schmidt E.W. Ribosomal route to small-molecule diversity. J Am Chem Soc 2012, 134:418-425.
44. Dischinger J., Josten M., Szekat C., Sahl H.G., Bierbaum G. Production of the novel two-peptide lantibiotic lichenicidin by Bacillus licheniformis DSM 13. PLoS ONE 2009, 4.
45. Begley M., Cotter P.D., Hill C., Ross R.P. Identification of a novel two-peptide lantibiotic, lichenicidin, following rational genome mining for LanM proteins. Appl Environ Microbiol 2009, 75:5451-5460.
46. Caetano T., Krawczyk J.M., Mosker E., Sussmuth R.D., Mendo S. Heterologous expression, biosynthesis, and mutagenesis of Type II lantibiotics from Bacillus licheniformis in Escherichia coli. Chem Biol 2011, 18:90-100.
47. Shenkarev Z.O., Finkina E.I., Nurmukhamedova E.K., Balandin S.V., Mineev K.S., Nadezhdin K.D., Yakimenko Z.A., Tagaev A.A., Temirov Y.V., Arseniev A.S., Ovchinnikova T.V. Isolation, Structure elucidation, and synergistic antibacterial activity of a novel two-component lantibiotic lichenicidin from Bacillus licheniformis VK21. Biochemistry 2010, 49:6462-6472.
48. Donia M.S., Ravel J., Schmidt E.W. A global assembly line for cyanobactins. Nat Chem Biol 2008, 4:341-343.
49. Sivonen K., Leikoski N., Fewer D.P., Jokela J. Cyanobactins-ribosomal cyclic peptides produced by cyanobacteria. Appl Microbiol Biotechnol 2010, 86:1213-1225.
50. Young T.S., Schultz P.G. Beyond the canonical 20 amino acids: expanding the genetic lexicon. J Biol Chem 2010, 285:11039-11044.
51. Cotter P.D., Ross R.P., Hill C. Bacteriocins-a viable alternative to antibiotics?. Nat Rev Microbiol 2013, 11:95-105.
52. Liu W.S.R., Wang Y.S., Wan W. Synthesis of proteins with defined posttranslational modifications using the genetic noncanonical amino acid incorporation approach. Mol Biosyst 2011, 7:38-47.