Calcium-Dependent Lipopeptide Antibiotics against Drug-Resistant Pathogens Discovered via Host-Dependent Heterologous Expression of a Cloned Biosynthetic Gene Cluster.
Hung-En Lai, V Helen Woolner, Rory F Little, Ethan F Woolly, Robert A Keyzers, Jeremy G Owen
Author Information
Hung-En Lai: School of Biological Sciences, Victoria University of Wellington, 6012, Wellington, New Zealand.
V Helen Woolner: School of Biological Sciences, Victoria University of Wellington, 6012, Wellington, New Zealand.
Rory F Little: School of Biological Sciences, Victoria University of Wellington, 6012, Wellington, New Zealand.
Ethan F Woolly: School of Biological Sciences, Victoria University of Wellington, 6012, Wellington, New Zealand.
Robert A Keyzers: Maurice Wilkins Centre for Molecular Biodiscovery, 1010, Auckland, New Zealand.
Jeremy G Owen: School of Biological Sciences, Victoria University of Wellington, 6012, Wellington, New Zealand. ORCID
Historically, small molecules biosynthesised by bacteria have been an excellent source for antibacterial drugs. Today, however, the rediscovery of known compounds is a significant hurdle to developing new antimicrobials. Here we use a genome mining and synthetic biology approach to discover the ambocidins: calcium-dependent lipodepsipeptides that are active against drug-resistant Gram-positive pathogens. By cloning a silent biosynthetic gene cluster (the amb cluster) from Streptomyces ambofaciens ATCC 2387 and integrating this into the chromosome of Streptomyces avermitilis we induce expression of ambocidin A and B: two new N-hydroxyarginine-containing cyclic lipodepsipeptides active against drug-resistant Gram-positive pathogens. Using a panel of Streptomyces host strains, we show that the choice of heterologous host is critical for producing the biologically active compounds, and that inappropriate host choice leads to aberrant production inactive derivatives. We show that N-hydroxyarginine is the product of a heme-dependent oxygenase and that it enhances biological activity. Ambocidin A inhibits cell wall biosynthesis by binding to Lipid II at a different site than vancomycin. Furthermore, unlike daptomycin, ambocidin A retains potent antimicrobial activity in the presence of lung surfactant, giving it the potential to treat bacterial pneumonia. Our work expands the family of calcium-dependent lipopeptide antibiotics with a new member exhibiting a distinct mechanism of action.
N. Bionda, J. P. Pitteloud, P. Cudic, Future Med. Chem. 2013, 5, 1311–1330.
R. D. Arbeit, D. Maki, F. P. Tally, E. Campanaro, B. I. Eisenstein, and the Daptomycin 98-01 and 99-01 Investigators, Clin Infect Dis 2004, 38, 1673–1681.
V. G. Fowler Jr., H. W. Boucher, G. R. Corey, E. Abrutyn, A. W. Karchmer, M. E. Rupp, D. P. Levine, H. F. Chambers, F. P. Tally, G. A. Vigliani, C. H. Cabell, A. S. Link, I. DeMeyer, S. G. Filler, M. Zervos, P. Cook, J. Parsonnet, J. M. Bernstein, C. S. Price, G. N. Forrest, G. Fätkenheuer, M. Gareca, S. J. Rehm, H. R. Brodt, A. Tice, S. E. Cosgrove, N. Engl. J. Med. 2006, 355, 653–665.
V. Cafiso, T. Bertuccio, D. Spina, S. Purrello, F. Campanile, C. Di Pietro, M. Purrello, S. Stefani, PLoS One 2012, 7, e29573;
L. Cui, E. Tominaga, H. M. Neoh, K. Hiramatsu, Antimicrob. Agents Chemother. 2006, 50, 1079–1082;
J. B. Patel, L. A. Jevitt, J. Hageman, L. C. McDonald, F. C. Tenover, Clin. Infect. Dis. 2006, 42, 1652–1653.
D. Jung, A. Rozek, M. Okon, R. E. Hancock, Chem. Biol. 2004, 11, 949–957.
B. M. Hover, S.-H. Kim, M. Katz, Z. Charlop-Powers, J. G. Owen, M. A. Ternei, J. Maniko, A. B. Estrela, H. Molina, S. Park, D. S. Perlin, S. F. Brady, Nat Microbiol 2018, 3, 415–422.
K. Blin, S. Shaw, M. H. Medema, T. Weber, Nucleic Acids Res. 2024, 52, D586–D589;
S. A. Kautsar, J. J. J. van der Hooft, D. de Ridder, M. H. Medema, Gigascience 2021, 10;
J. C. Navarro-Munoz, N. Selem-Mojica, M. W. Mullowney, S. A. Kautsar, J. H. Tryon, E. I. Parkinson, E. L. C. De Los Santos, M. Yeong, P. Cruz-Morales, S. Abubucker, A. Roeters, W. Lokhorst, A. Fernandez-Guerra, L. T. D. Cappelini, A. W. Goering, R. J. Thomson, W. W. Metcalf, N. L. Kelleher, F. Barona-Gomez, M. H. Medema, Nat. Chem. Biol. 2020, 16, 60–68.
A. Fullam, I. Letunic, T. S. B. Schmidt, Q. R. Ducarmon, N. Karcher, S. Khedkar, M. Kuhn, M. Larralde, O. M. Maistrenko, L. Malfertheiner, A. Milanese, J. F. M. Rodrigues, C. Sanchis-Lopez, C. Schudoma, D. Szklarczyk, S. Sunagawa, G. Zeller, J. Huerta-Cepas, C. von Mering, P. Bork, D. R. Mende, Nucleic Acids Res. 2023, 51, D760–D766;
P. A. Kitts, D. M. Church, F. Thibaud-Nissen, J. Choi, V. Hem, V. Sapojnikov, R. G. Smith, T. Tatusova, C. Xiang, A. Zherikov, M. DiCuccio, T. D. Murphy, K. D. Pruitt, A. Kimchi, Nucleic Acids Res. 2016, 44, D73–80;
S. Mukherjee, D. Stamatis, J. Bertsch, G. Ovchinnikova, J. C. Sundaramurthi, J. Lee, M. Kandimalla, I. A. Chen, N. C. Kyrpides, T. B. K. Reddy, Nucleic Acids Res. 2021, 49, D723–D733.
M. J. Bibb, Curr. Opin. Microbiol. 2005, 8, 208–215.
K. Blin, S. Shaw, H. E. Augustijn, Z. L. Reitz, F. Biermann, M. Alanjary, A. Fetter, B. R. Terlouw, W. W. Metcalf, E. J. N. Helfrich, G. P. van Wezel, M. H. Medema, T. Weber, Nucleic Acids Res. 2023, 51, W46–W50;
M. A. Skinnider, C. W. Johnston, M. Gunabalasingam, N. J. Merwin, A. M. Kieliszek, R. J. MacLellan, H. Li, M. R. M. Ranieri, A. L. H. Webster, M. P. T. Cao, A. Pfeifle, N. Spencer, Q. H. To, D. P. Wallace, C. A. Dejong, N. A. Magarvey, Nat. Commun. 2020, 11, 6058.
B. Enghiad, C. Huang, F. Guo, G. Jiang, B. Wang, S. K. Tabatabaei, T. A. Martin, H. Zhao, Nat. Commun. 2021, 12, 1171;
B. M. Hover, S. H. Kim, M. Katz, Z. Charlop-Powers, J. G. Owen, M. A. Ternei, J. Maniko, A. B. Estrela, H. Molina, S. Park, D. S. Perlin, S. F. Brady, Nat Microbiol 2018, 3, 415–422;
V. Libis, L. W. MacIntyre, R. Mehmood, L. Guerrero, M. A. Ternei, N. Antonovsky, J. Burian, Z. Wang, S. F. Brady, Nat. Commun. 2022, 13, 5256;
K. Yamanaka, K. A. Reynolds, R. D. Kersten, K. S. Ryan, D. J. Gonzalez, V. Nizet, P. C. Dorrestein, B. S. Moore, Proc. Natl. Acad. Sci. USA 2014, 111, 1957–1962.
C. Wu, Z. Shang, C. Lemetre, M. A. Ternei, S. F. Brady, J. Am. Chem. Soc. 2019, 141, 3910–3919.
R. H. Baltz, J Ind Microbiol Biotechnol 2021, 48.
K. Blin, S. Shaw, A. M. Kloosterman, Z. Charlop-Powers, G. P. van Wezel, M. H. Medema, T. Weber, Nucleic Acids Res. 2021, 49, W29–W35.
B. Aigle, X. Pang, B. Decaris, P. Leblond, J. Bacteriol. 2005, 187, 2491–2500;
L. Laureti, L. Song, S. Huang, C. Corre, P. Leblond, G. L. Challis, B. Aigle, Proc. Natl. Acad. Sci. USA 2011, 108, 6258–6263;
B. Aigle, S. Lautru, D. Spiteller, J. S. Dickschat, G. L. Challis, P. Leblond, J. L. Pernodet, J. Ind. Microbiol. Biotechnol. 2014, 41, 251–263.
T. Kieser, M. J. Bibb, M. J. Buttner, K. F. Chater, D. A. Hopwood, Practical Streptomyces Genetics, John Innes Foundation,, Norwich, 2000.
B. C. Covington, F. Xu, M. R. Seyedsayamdost, Annu. Rev. Biochem. 2021, 90, 763–788.
M. Liang, L. Liu, F. Xu, X. Zeng, R. Wang, J. Yang, W. Wang, L. Karthik, J. Liu, Z. Yang, G. Zhu, S. Wang, L. Bai, Y. Tong, X. Liu, M. Wu, L. X. Zhang, G. Y. Tan, Nucleic Acids Res. 2022, 50, 3581–3592.
M. Komatsu, K. Komatsu, H. Koiwai, Y. Yamada, I. Kozone, M. Izumikawa, J. Hashimoto, M. Takagi, S. Omura, K. Shin-ya, D. E. Cane, H. Ikeda, ACS Synth. Biol. 2013, 2, 384–396.
M. Myronovskyi, B. Rosenkranzer, S. Nadmid, P. Pujic, P. Normand, A. Luzhetskyy, Metab. Eng. 2018, 49, 316–324.
J. P. Gomez-Escribano, M. J. Bibb, Microb. Biotechnol. 2011, 4, 207–215.
H. R. Pyeon, H. J. Nah, S. H. Kang, S. S. Choi, E. S. Kim, Microb. Cell Fact. 2017, 16, 96.
S. Vijayasarathy, P. Prasad, L. J. Fremlin, R. Ratnayake, A. A. Salim, Z. Khalil, R. J. Capon, J. Nat. Prod. 2016, 79, 421–427.
Z. Wang, B. Koirala, Y. Hernandez, M. Zimmerman, S. F. Brady, Science 2022, 376, 991–996;
T. Schneider, K. Gries, M. Josten, I. Wiedemann, S. Pelzer, H. Labischinski, H. G. Sahl, Antimicrob. Agents Chemother. 2009, 53, 1610–1618.
E. V. K. Ledger, S. Mesnage, A. M. Edwards, Nat. Commun. 2022, 13, 2041;
J. A. Silverman, L. I. Mortin, A. D. Vanpraagh, T. Li, J. Alder, J. Infect. Dis. 2005, 191, 2149–2152.
F. Wang, W. H. Zhang, J. Zhao, W. J. Kang, S. Wang, B. Yu, H. X. Pan, G. L. Tang, J. Am. Chem. Soc. 2020, 142, 5996–6000.
Y. Zhang, T. M. Pham, C. Kayrouz, K. S. Ju, J. Am. Chem. Soc. 2022, 144, 9634–9644.
A. Nemoto, Y. Hoshino, K. Yazawa, A. Ando, Y. Mikami, H. Komaki, Y. Tanaka, U. Grafe, J Antibiot (Tokyo) 2002, 55, 593–597.
J. P. Jang, G. J. Hwang, M. C. Kwon, I. J. Ryoo, M. Jang, S. Takahashi, S. K. Ko, H. Osada, J. H. Jang, J. S. Ahn, J. Nat. Prod. 2018, 81, 806–810.
C. Makris, J. R. Carmichael, H. Zhou, A. Butler, ACS Chem. Biol. 2022, 17, 3140–3147.
Grants
RDF-VUW160/Royal Society Te Apārangi
RTVU1908/Ministry for Business Innovation and Employment
UOAX2010/Ministry for Business Innovation and Employment
