* Equal contribution of authors, § Co-corresponding authors, † Corresponding author

31. Lee, AR,* Carter, RS,* Imani, AS, Dommaraju, SR, Hudson, GA, Mitchell, DA§, Freeman, MF§ (2024) Discovery of borosin catalytic strategies and function through bioinformatic profiling. ACS Chem. Biol. 19(5): 1116-11124. DOI: 10.1021/acschembio.4c00066.

30. Crone, KK,* Jomori, T*, Miller, FS, Gralnick, JA, Elias, MH, Freeman, MF† (2023) RiPP enzyme heterocomplex structure-guided discovery of a bacterial borosin α-N-methylated peptide natural product. RSC Chem. Biol. 4(10): 804-816. DOI: 10.1039/D3CB00093A.

29. Gupta, VK, Bakshi, U, Chang, D, Lee, AR, Davis III, JM, Chandrasekaran, S, Jin, Y-S, Freeman, MF, Sung, Jaeyun (2022) TaxiBGC: A taxonomy-guided approach for profiling experimentally characterized microbial biosynthetic gene clusters and secondary metabolite production potential in metagenomes. mSystems 7(6): 1-17. DOI: 10.1128/msystems.00925-22.

28. Imani, AS,* Lee, AR,* Vishwanathan, N, de Waal, F, Freeman, MF† (2022) Diverse protein architectures and α-N-methylation patterns define split borosin RiPP biosynthetic gene clusters. ACS Chem. Biol. 17(4): 908-917. DOI: 10.1021/acschembio.1c01002. 

27. Miller, FS*, Crone, KK*, Jensen, MR, Shaw, S, Harcombe, WR, Elias, MH§, Freeman, MF§ (2021) Conformational rearrangements enable iterative backbone N-methylation in RiPP biosynthesis, Nat. Comm. 12(1): 5355. DOI: 10.1038/s41467-021-25575-7.

26. Mataboro, E, Song, H, Chepkirui, C, Kaspar, H, Witte, L, Naismith, JH, Freeman, MF, Künzler, M (2021) Enzyme-mediated backbone N-methylation in ribosomally encoded peptides, Methods Enzymol. 656: 429-458. DOI: 10.1016/bs.mie.2021.04.014.

25. Jensen, MR, Freeman, MF† (2020) Structure and biosynthesis of proteusin RiPP natural products, Comprehensive Natural Products III, Elsevier Publishing Amsterdam, NL. Chapter 6(2): 88-118. DOI: 10.1016/B978-0-12-409547-2.14727-4.

24. Rust, M, Helfrich, EJN, Freeman, MF*, Nanudorn, P*, Field, CM, Rückert, C, Kündig, T, Page, MJ, Webb, VL, Kalinowski, J, Sunagawa, S, Piel, J (2020) A multiproducer microbiome generates chemical diversity in the marine sponge Mycale hentscheli, Proc. Natl. Acad. Sci. U.S.A. 117(17): 9508-9518. DOI: 10.1073/pnas.1919245117.

23. Bhushan, A, Egli, PJ, Peters, EE, Freeman, MF, Piel, J (2019) A genome mining- and synthetic biology-enabled production platform for highly complex polytheonamide-type cytotoxins. Nat. Chem. 11(10): 931-939. DOI: 10.1038/s41557-019-0323-9.

[Concentrates: Chem. Eng. News 2019 97(36)]

22. Quijano, MR*, Zach, C*, Miller, FS, Lee, AR, Imani, AS, Künzler, M§, Freeman, MF§ (2019) Distinct autocatalytic α-N-methylating precursors expand the borosin RiPP family of peptide natural products. J. Am. Chem. Soc., 141(24): 9637-9644. DOI: 10.1021/jacs.9b03690.

21. Helf, MJ, Freeman, MF, Piel, J (2019) Investigations into PoyH, a promiscuous protease from polytheonamide biosynthesis, J. Ind. Microbiol. Biotechnol. 46(3-4): 551-563. DOI: 10.1007/s10295-018-02129-3.

[Special issue: Natural product discovery and development in the genomic era 2019.]

20. Song, H, van der Velden, NS, Shiran, SL, Bleiziffer, P, Zach, C, Sieber, R, Imani, AS, Krausbeck, F, Aebi, M, Freeman, MF, Riniker, S§, Künzler, M§, Naismith, JH§ (2018) A molecular mechanism for the enzymatic methylation of nitrogen atoms within peptide bonds, Sci. Adv. 4(8): eaat2720. DOI: 10.1126/sciadv.aat2720.

19. Miller, FS, Freeman, MF† (2018) Impact of synthetic biology on secondary metabolite biosynthesis, Modern biocatalysis: Advances towards synthetic biological systems, RSC Publishing Cambridge, UK. Chapter 11(32): 287-320. DOI: 10.1039/9781788010450.

18. Freeman, MF† (2018) Cobalamin-dependent C-methyltransferases from marine microbes: accessibility via rhizobia expression, Methods Enzymol. 604: 259-286. DOI: 10.1016/bs.mie.2018.02.013.

17. Imani, AS, Freeman, MF† (2018) RiPPing apart the rules for peptide natural products, Syst. Synth. Biotechnol. 3(2): 81-82. DOI: 10.1016/j.synbio.2018.03.002.

16. van der Velden, NS, Kälin, N, Helf, MJ, Piel, J, Freeman, MF§, Künzler, M§ (2017) Autocatalytic backbone N-methylation in a family of ribosomal peptide natural products, Nat. Chem. Biol. 13(8): 833-835. DOI: 10.1038/nchembio.2393.

[News and Views: Nat. Chem. Biol. 2017 13: 821-822.]

[Highlight: Angew. Chem. Int. Ed. 2017 56: 13570-13572.]

15. Morinaka, BI, Verest, M, Freeman, MF, Gugger, M, Piel, J (2017) An orthogonal D2O-based induction system provides insights into D-amino acid pattern formation by radical S-adenosylmethionine peptide epimerases, Angew. Chem. Int. Ed. 56(3): 762-766. DOI: 10.1002/anie.201609469.

14. Freeman, MF§, Helf, MJ, Bhushan, A, Morinaka, BI, Piel, J§ (2017) Seven enzymes create extraordinary molecular complexity in an uncultivated bacterium, Nat. Chem. 9(4): 387-395. DOI: 10.1038/nchem.2666.

[Research Highlight: Nat. Chem. Biol. 2017 13: 129.]

[Leading Edge: Cell 2017 169: 373.]

13. Freeman, MF, Vagstad, AL, Piel, J (2016) Polytheonamide biosynthesis showcasing the metabolic potential of sponge-associated uncultivated 'Entotheonella', Curr. Opin. Chem. Biol. 31: 8-14. DOI: 10.1016/j.cbpa.2015.11.002.

12. Buller, AR, Freeman, MF, Schildbach, JF, Townsend, CA (2014) Exploring the role of conformational heterogeneity in cis-autoproteolytic activation of ThnT, Biochemistry 53(26): 4273-4281. DOI: 10.1021/bi500385d.

11. Morinaka, BI, Vagstad, AL, Helf, MJ, Gugger, M, Kegler, C, Freeman, MF, Bode, HB, Piel, J (2014) Radical S-adenosyl methionine epimerases: regioselective introduction of diverse D-amino acid patterns into peptide natural products, Angew. Chem. Int. Ed. 53(32): 8503-8507. DOI: 10.1002/anie.201400478.

10. Cai, X, Teta, R, Kohlhass, C, Crüsemann, M, Ueoka, R, Mangoni, A, Freeman, MF§, Piel, J§ (2013) Manipulation of regulatory genes reveals complexity and fidelity in hormaomycin biosynthesis, Chem. Biol. 20(6): 839-846. DOI: 10.1016/j.chembiol.2013.04.018.

9. Freeman, MF*, Gurgui, C*, Helf, MJ, Uria, AR, Oldham, NJ, Sahl, H-G, Matsunaga, S, Piel, J (2012) Metagenome mining reveals polytheonamides as posttranslationally modified ribosomal peptides, Science 338(6105): 387-390. DOI: 10.1126/science.1226121.

[Concentrates: Chem. Eng. News 2012 90(3): 26.]

[In Brief: Nat. Rev. Microbiol. 2012 10: 802.]

8. Buller, AR, Labonte, JW, Freeman, MF, Wright, NT, Schildbach, JF, Townsend, CA (2012) Autoproteolytic activation of ThnT results in structural reorganization necessary for substrate binding and catalysis, J. Mol. Biol. 422(4): 508-518. DOI: 10.1016/j.jmb.2012.06.012.

7. Labonte, JW, Kudo, F, Freeman, MF, Raber, ML, Townsend, CA (2012) Engineering the synthetic potential of β-lactam synthetase and the importance of catalytic group dynamics, MedChemComm. 3(8): 960-966. DOI: 10.1039/C2MD00305H.

6. Buller, AR, Freeman, MF, Wright, NT, Schildbach, JF, Townsend, CA (2011) Insights into cis-autoproteolysis reveal a reactive state formed through conformation rearrangement, Proc. Natl. Acad. Sci. U.S.A. 109(7): 2308-2313. DOI: 10.1073/pnas.1113633109.

5. Bodner, MJ, Li, R, Phelan, RM, Freeman, MF, Moshos, KA, Lloyd, E, Townsend, CA (2011) Definition of the common and divergent steps in carbapenem β-lactam antibiotic biosynthesis, ChemBioChem. 12(14): 2159-2165. DOI: 10.1002/cbic.201100366.

4. Gulder, TAM, Freeman, MF, Piel, J (2011) The catalytic diversity of multimodular polyketide synthases: natural product biosynthesis beyond textbook assembly rules, Top. Curr. Chem. Springer-Verlag Berlin Heidelberg: 1-53. DOI: 10.1007/128_2010_113.

3. Bodner, MJ, Phelan, R, Freeman, MF, Li, R, Townsend, CA (2010) Non-heme iron oxygenases generate natural structural diversity in carbapenem antibiotics, J. Am. Chem. Soc. 132(1): 12-13. DOI: 10.1021/ja907320n.

2. Raber, ML, Freeman, MF, Townsend, CA (2009) Dissection of the stepwise mechanism to β-lactam formation and elucidation of a rate-determining conformational change in β-lactam synthetase, J. Biol. Chem. 284(1): 207-217. DOI: 10.1074/jbc.M805390200.

1. Freeman, MF, Moshos, KA, Bodner, MJ, Li, R, Townsend, CA (2008) Four enzymes define the role of coenzyme A in thienamycin biosynthesis, Proc. Natl. Acad. Sci. U.S.A. 105(32): 11128-11133. DOI: 10.1073/pnas.0804500105.

[Research Highlight: ACS Chem. Biol. 2008 3(9): 522.]