Chapter 3: Discovery, heterologous production, and characterization of a novel type
3.8 Codon optimized nucleotide sequence for GeoC
1 ATGTCTATTA GCATGAAAGC CCTGGTTTGT AATCTGGCAA AAAAACTGAG CGATTATGAA 61 AATATGAAAC GCATTGTGAA TCATCCGAGC AATTATATTA AAATTGGCAA CAAAACCATT 121 AATCCGTTTA ATGAACTGAG CCTGAGCCAT GGTCTGCCTG CACTGTGTGC ACTGTATGGT 181 GAACTGAGCG AACAGTATCC GGATGAAGGT TGGGATCTGC TGGGTCATCA GTATATGAAA 241 AAAATTGGCG AACAAATGAA TCAGCATGGT TTTCCGAGCC TGAGCATGTT TACCGGTCTG 301 GCAGGTATTG GTCTGGCAGC AGTTTGTCTG AGCAAAGGTG GTAAACGCTA TCAGAATTTC 361 ATTAGCACCA TTAATCAGGT GATTGAAGAA CGCATTGGCG AAATGATTGA ATATCTGAAA 421 CAGAAACCGT ATCCGAATAT GGATGATTAT GATGCAATTA GCGGTGTTGC AGGTATTGCA 481 AGCTATTGTC TGCTGTTTCC GCAAGAAATG AAAAAAAGCA TTACCCTGAT TCTGAAATAC 541 ATTATTGATC TGAGCCAGGA TAAACAAATG GAAGATATTA ATGTTCCGGG TTGGTATATT 601 CCTCCGATGA ATGCATTTAG CGATACCGAA CGTCGTAAAT GGCCGAGCGG TTTTTTTAAT 661 ATTGGTCTGA GTCATGGCAT TCCGGCACTG CTGATTGTTC TGTGTAATGC CAAAAAACTG 721 AATATTTATG TGCATGGCCA GGATGAATGT ATTCAGCGTA TTGCAGATTT TCTGATGAAA 781 TTTCAGATTA AAGATGAAAA TGGCAGCTAT TGGGGCACCC ATGTTAGCCT GGAAGAATAT 841 AAAAATGGCA GCGTGCTGAA TAAAGATACC CGTGATGCAT GGTGTTATGG TACACCGGGT 901 GTTGCATATA GCCTGCTGAT TGCAGGTAAA ACCCTGAATA ATCAGAGCTA TATTGATTGT 961 GCCGTGAGCG GTATGAAACT GGCAAGCAAA CGTCTGTATA ATATTTTTAG CCCGAGCTTT 1021 TGCCATGGAC TGAGCGGTGT TGCCTATATT TGCAATCGCT TTTATGAAGA AACCAATATT 1081 AGCGATTTTA AAGAAGCAGC CTGCAAACTG GTGGATGATA TTATCAAATT TTATAATGAA 1141 GAATTCCCGT TTGGCTTTAA AAATATTGAA GAAAGCGAAG GCAGCACCAA ATATTATGAT 1201 TATGTGGGTC TGATTGATGG CACCGCAGGT ATTCTGCTGA CCATTCTGGC AATTCAGAAT 1261 AGCAAAAAAA CCCCGTGGGA TTGTGCATTT CTGCTGAGCG AAGTTTAA
3.9 References
1. Delves-Broughton, J., Blackburn, P., Evans, R. J., and Hugenholtz, J. (1996) Applications of the bacteriocin, nisin, Antonie van Leeuwenhoek 69, 193-202.
2. Yeaman, M. R., and Yount, N. Y. (2003) Mechanisms of antimicrobial peptide action and resistance, Pharmacol Rev 55, 27-55.
3. Yount, N. Y., and Yeaman, M. R. (2005) Immunocontinuum: perspectives in antimicrobial peptide mechanisms of action and resistance, Protein Pept Lett 12, 49-67. 4. Hsu, S. T., Breukink, E., Tischenko, E., Lutters, M. A., de Kruijff, B., Kaptein, R.,
Bonvin, A. M., and van Nuland, N. A. (2004) The nisin-lipid II complex reveals a pyrophosphate cage that provides a blueprint for novel antibiotics, Nat Struct Mol Biol 11, 963-967.
5. Breukink, E., Wiedemann, I., van Kraaij, C., Kuipers, O. P., Sahl, H., and de Kruijff, B. (1999) Use of the cell wall precursor lipid II by a pore-forming peptide antibiotic, Science 286, 2361-2364.
6. Hasper, H. E., Kramer, N. E., Smith, J. L., Hillman, J. D., Zachariah, C., Kuipers, O. P., de Kruijff, B., and Breukink, E. (2006) A new mechanism of antibiotic action, Science 313, 1636-1637.
7. Brigham, M. F. (June 9, 2011) ImmuCell comments on status zero milk discard claim for mast out (R)., Available at http://www.reuters.com/article/2011/06/09/idUS120388+09-
Jun-2011+MW20110609.
8. Brigham, M. F. (2011) ImmuCell presents mast out product offering at World Animal Health Congress. World Health Congress 2011, Available at
http://finance.yahoo.com/news/ImmuCell-Presents-Mast-Out-R-iw-3929215384.html.
9. Chan, W. C., Bycroft, B. W., Lian, L. Y., and Roberts, G. C. K. (1989) Isolation and characterization of two degradation products derived from the peptide antibiotic nisin, FEBS Lett 252, 29-36.
10. Rollema, H. S., Kuipers, O. P., Both, P., de Vos, W. M., and Siezen, R. J. (1995) Improvement of solubility and stability of the antimicrobial peptide nisin by protein engineering, Appl Environ Microbiol 61, 2873-2878.
11. Rollema, H. S., Metzger, J. W., Both, P., Kuipers, O. P., and Siezen, R. J. (1996) Structure and biological activity of chemically modified nisin A species, Eur J Biochem 241, 716-722.
12. Lian, L. Y., Chan, W. C., Morley, S. D., Roberts, G. C., Bycroft, B. W., and Jackson, D. (1992) Solution structures of nisin A and its two major degradation products determined by n.m.r, Biochem J 283, 413-420.
13. Cruz, L., Garden, R. W., Kaiser, H. J., and Sweedler, J. V. (1996) Studies of the degradation products of nisin, a peptide antibiotic, using capillary electrophoresis with off-line mass spectrometry, J Chromatogr A 735, 375-385.
14. Olde Riekerink, R. G., Barkema, H. W., and Stryhn, H. (2007) The effect of season on somatic cell count and the incidence of clinical mastitis, J Dairy Sci 90, 1704-1715. 15. Knerr, P. J., Oman, T. J., Garcia De Gonzalo, C. V., Lupoli, T. J., Walker, S., and van der
Donk, W. A. (2012) Non-proteinogenic amino acids in lacticin 481 analogues result in more potent inhibition of peptidoglycan transglycosylation, ACS Chem Biol 7, 1791- 1795.
16. Chen, L., Walker, D., Sun, B., Hu, Y., Walker, S., and Kahne, D. (2003) Vancomycin analogues active against vanA-resistant strains inhibit bacterial transglycosylase without binding substrate, Proc Natl Acad Sci U S A 100, 5658-5663.
17. Oman, T. J., Lupoli, T. J., Wang, T. S., Kahne, D., Walker, S., and van der Donk, W. A. (2011) Haloduracin alpha binds the peptidoglycan precursor lipid II with 2:1 stoichiometry, J Am Chem Soc 133, 17544-17547.
18. Liu, W., Chan, A. S., Liu, H., Cochrane, S. A., and Vederas, J. C. (2011) Solid supported chemical syntheses of both components of the lantibiotic lacticin 3147, J Am Chem Soc 133, 14216-14219.
19. Feng, L., Wang, W., Cheng, J., Ren, Y., Zhao, G., Gao, C., Tang, Y., Liu, X., Han, W., Peng, X., Liu, R., and Wang, L. (2007) Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir, Proc Natl Acad Sci U S A 104, 5602-5607.
20. Marsh, A. J., O'Sullivan, O., Ross, R. P., Cotter, P. D., and Hill, C. (2010) In silico analysis highlights the frequency and diversity of type 1 lantibiotic gene clusters in genome sequenced bacteria, BMC Genomics 11, 679.
21. Zeigler, D. R. (2005) Application of a recN sequence similarity analysis to the identification of species within the bacterial genus Geobacillus, Int J Syst Evol Microbiol 55, 1171-1179.
22. Stein, T. (2008) Whole-cell matrix-assisted laser desorption/ionization mass spectrometry for rapid identification of bacteriocin/lantibiotic-producing bacteria, Rapid Commun Mass Spectrom 22, 1146-1152.
23. Engelke, G., Gutowski-Eckel, Z., Hammelmann, M., and Entian, K.-D. (1992) Biosynthesis of the lantibiotic nisin: genomic organization and membrane localization of the NisB protein, Appl Environ Microbiol 58, 3730-3743.
24. Shi, Y., Yang, X., Garg, N., and van der Donk, W. A. (2011) Production of lantipeptides in Escherichia coli, J Am Chem Soc 133, 2338-2341.
mutagenesis of rings A and B and by C-terminal truncation, Appl Environ Microbiol 73, 5809-5816.
26. Hasper, H. E., de Kruijff, B., and Breukink, E. (2004) Assembly and stability of nisin- lipid II pores, Biochemistry 43, 11567-11575.
27. Wiedemann, I., Breukink, E., van Kraaij, C., Kuipers, O. P., Bierbaum, G., de Kruijff, B., and Sahl, H. G. (2001) Specific binding of nisin to the peptidoglycan precursor lipid II combines pore formation and inhibition of cell wall biosynthesis for potent antibiotic activity, J Biol Chem 276, 1772-1779.
28. Brötz, H., and Sahl, H. G. (2000) New insights into the mechanism of action of lantibiotics--diverse biological effects by binding to the same molecular target, J Antimicrob Chemother 46, 1-6.
29. Oman, T. J., and van der Donk, W. A. (2009) Insights into the Mode of Action of the Two-Peptide Lantibiotic Haloduracin, ACS Chem Biol 4, 865-874.
30. Field, D., Connor, P. M., Cotter, P. D., Hill, C., and Ross, R. P. (2008) The generation of nisin variants with enhanced activity against specific gram-positive pathogens, Mol Microbiol 69, 218-230.
31. Garg, N., Tang, W., Goto, Y., Nair, S. K., and van der Donk, W. A. (2012) Lantibiotics from Geobacillus thermodenitrificans, Proc Natl Acad Sci U S A 109, 5241-5246.
32. Ross, A. C., Liu, H., Pattabiraman, V. R., and Vederas, J. C. (2010) Synthesis of the lantibiotic lactocin S using peptide cyclizations on solid phase, J Am Chem Soc 132, 462- 463.
33. Li, B., Sher, D., Kelly, L., Shi, Y., Huang, K., Knerr, P. J., Joewono, I., Rusch, D., Chisholm, S. W., and van der Donk, W. A. (2010) Catalytic promiscuity in the biosynthesis of cyclic peptide secondary metabolites in planktonic marine cyanobacteria, Proc Natl Acad Sci U S A 107, 10430-10435.
34. Challis, G. L. (2008) Genome mining for novel natural product discovery, J Med Chem 51, 2618-2628.
35. Velásquez, J. E., and van der Donk, W. A. (2011) Genome mining for ribosomally synthesized natural products, Curr Opin Chem Biol 15, 11-21.
36. Kersten, R. D., Yang, Y.-L., Xu, Y., Cimermancic, P., Nam, S.-J., Fenical, W., Fischbach, M. A., Moore, B. S., and Dorrestein, P. C. (2011) A mass spectrometry– guided genome mining approach for natural product peptidogenomics, Nat Chem Biol 7, 794-802.
37. Dischinger, J., Josten, M., Szekat, C., Sahl, H. G., and Bierbaum, G. (2009) Production of the novel two-peptide lantibiotic lichenicidin by Bacillus licheniformis DSM 13, PLoS One 4, e6788.
38. Goto, Y., Li, B., Claesen, J., Shi, Y., Bibb, M. J., and van der Donk, W. A. (2010) Discovery of unique lanthionine synthetases reveals new mechanistic and evolutionary insights, PLoS Biol 8, e1000339.
39. Begley, M., Cotter, P. D., Hill, C., and Ross, R. P. (2009) Identification of a novel two- peptide lantibiotic, lichenicidin, following rational genome mining for LanM proteins, Appl Environ Microbiol 75, 5451-5460.
40. McClerren, A. L., Cooper, L. E., Quan, C., Thomas, P. M., Kelleher, N. L., and van der Donk, W. A. (2006) Discovery and in vitro biosynthesis of haloduracin, a two-component lantibiotic, Proc Natl Acad Sci U S A 103, 17243-17248.
41. Lawton, E. M., Cotter, P. D., Hill, C., and Ross, R. P. (2007) Identification of a novel two-peptide lantibiotic, Haloduracin, produced by the alkaliphile Bacillus halodurans C- 125, FEMS Microbiol Lett 267, 64-71.
42. Wang, H., Fewer, D. P., and Sivonen, K. (2011) Genome mining demonstrates the widespread occurrence of gene clusters encoding bacteriocins in cyanobacteria, PLoS One 6, e22384.
43. Kabuki, T., Uenishi, H., Seto, Y., Yoshioka, T., and Nakajima, H. (2009) A unique lantibiotic, thermophilin 1277, containing a disulfide bridge and two thioether bridges, J Appl Microbiol 106, 853-862.
44. Brötz, H., Josten, M., Wiedemann, I., Schneider, U., Götz, F., Bierbaum, G., and Sahl, H.-G. (1998) Role of lipid-bound peptidoglycan precursors in the formation of pores by nisin, epidermin and other lantibiotics, Mol Microbiol 30, 317-327.
45. Gut, I. M., Prouty, A. M., Ballard, J. D., van der Donk, W. A., and Blanke, S. R. (2008) Inhibition of Bacillus anthracis spore outgrowth by nisin, Antimicrob Agents Chemother 52, 4281-4288.