Since the discovery of penicillin in the 1920s, natural products have had an unmistakable impact on our health and have inspired us with their intricate chemical structures and fascinating underlying metabolic pathways. Historically, biochemical and genetic studies in these systems have focused on free-living, fast growing terrestrial organisms due to technological and laboratory constraints. However, the past 10-15 years have seen an explosion of new DNA sequencing technologies and molecular biological techniques that have, for the first time, allowed genetic access to more subtle and intricate ecosystems. Our work focuses on the discovery and heterologous expression of pathways and genes involved in the biosynthesis of metabolites from unique microbial sources. We use cutting-edge and classical techniques in biochemistry, microbiology, metagenomics, and mass spectrometry to investigate unconventional peptide-based metabolites and pathways invoking radical-mediated chemistry. All in all, our research aims to tackle the exponentially expanding genomic universe for the discovery of new enzymology and therapeutics.
Peptide natural products comprise a diverse set of pharmaceutically relevant antibiotic, antiviral, immunosuppressive, nematicidal, and anti-cancer agents. Many of these pharmaceuticals harbor backbone α-N-methylations and macrocyclizations, since these tailorings significantly improve peptide pharmacokinetics due to increased structural rigidity, proteolytic resistance, and membrane permeability as seen in the blockbuster immunosuppressant cyclosporin A. We identified a new biosynthetic route to backbone α-N-methylated peptides through the co-discovery of the borosin peptide natural product family. While natural sources of N-methylated peptides have been known for over 100 years, they were never found to be made by the ribosome. Borosins originate from an enzyme synthesized by the ribosome that self-modifies its own backbone with multiple N-methylations to eventually produce the final metabolite. This unprecedented biocatalysis affords new routes to engineered N-methylated metabolites and we are actively pursuing genome mining and metabolite discovery platforms for new borosins from basidiomycete fungi.
Microorganisms communicate using the language of small molecule natural products. Amazingly, the vast majority of microorganisms on Earth (>99%!) are as-of-yet uncultivated, but represent the single largest untapped reservoir of unique biochemistry and new therapeutics. Thus, the discovery of new metabolites, pathways, and enzymatic transformations from these niche microbial sources demand heterologous expression in tractable hosts. We in the Freeman Lab are developing new techniques and expression systems to more effectively tap into Nature’s microbial ‘silent majority’. We have recently exploited unconventional rhizobia bacteria to express a class of radical-SAM enzymes otherwise unfit for expression in more traditional hosts such as E. coli. We are continuing to develop diverse microbial expression platforms tailored to cofactor and substrate restraints of pathways from intractable microbes. In addition, we are trying to develop community-synthesized natural products, where metabolic pathways are partitioned across multiple microbial hosts.
* Equal contribution of authors, § Co-corresponding authors, † Corresponding author
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.]
Michael F. FreemanPrincipal Investigatormffreema@umn.eduCV:
Takahiro JomoriPostdoctoral Fellowtjomori@umn.edu
Aman ImaniBMBB Ph.D. Candidateimani006@umn.edu
Aileen LeeBMBB Ph.D. Candidateleex9223@umn.edu
Kathryn CroneBMBB Ph.D. Candidatecrone011@umn.edu
Nisha VishwanathanResearcher Ivishw025@umn.edu
FinnAdorable Support Staffscienceisruff@umn.edu
BMBB = Biochemistry, Molecular Biology, and Biophysics
|2020||Floris de Waal||Visiting scholar|
|2016-2020||Dr. Fredarla S. Miller||BMBB graduate student
Current position: Manufacturing scientistBeckman Coulter, Inc., Chaska, MN
|2019||Sumire Kurosawa||Visiting scholar|
|2019||Chloé Lopez||Visiting scholar|
|2019||Anna Glöckle||Visiting scholar|
|2018||Jakub Michalski||Visiting scholar|
|2016-2018||Marissa Quijano||Master's student|
|2017-2018||Dr. Matthew R. Jensen||Post-doctoral associate
Current position: Tenure-track assistant professorChemistry department, Concordia University, St. Paul
|2017-2018||Luke Bunday||High school student|
|2017-2018||Lucy Chen||High school student|
|2016-2017||Dr. Keshav K. Nepal||Post-doctoral associate
Current position: Post-doctoral associateUniversity of Washington in St. Louis
|June 19 2021||
Good food and better company at the Freeman lab BBQ, with special guest alumni Freddie and Matt!
Our group keeps growing...Dr. Takahiro Jomori joins our lab as a postdoctoral fellow...Yōkoso (ようこそ)!
|February 15, 2021||
Aman's blog gets some UMN press, highlighting how one person's compassion and effort can make a difference.
Nisha joins the Freeman Lab...Cowabunga!
|January 16, 2021||
We all had fun at the (virtual) Freeman Lab holiday party. Despite what Aileen kept saying, I wasn't the Imposter every. single. time.
|May 12, 2020||
Kathryn easily clears her BMBB graduate board oral exam - congratulations, well done!
|May 8, 2020||
Freddie rocks her Ph.D. defense - We could not be more proud of you!
Aman receives not one, but two TA awards: The Cyrus Barnum Teaching Award and The CBS Outstanding Performance Award for Teaching Assistants...way to go!
|February 7, 2020||
Another fun holiday potluck party for the Freeman lab to ring in the new year!
|February 3, 2020||
Floris de Waal from Wageningen University joins our lab as a visiting scholar...Welkom!
Sumire Kurosawa from the University of Tokyo joins our lab as a visiting scholar...Yōkoso (ようこそ)!
|September 28, 2019||
Our warmest congratulations goes out to our very own Freddie on her and Nathan's beautiful wedding day!
Undergraduates Sarah Schmidt-Dannert and Sayuj Suresh join the lab...welcome!!
|August 28, 2019||
Another day filled with barn animals and too much food at the Minnesota State Fair. Grueling battles at our 4th Annual air hockey tournament...Final results: Mike 1st, Aman 2nd, Freddie 3rd.
|July 18, 2019||
1st Annual Freeman-Buller joint lab outing at Great River Bluffs State Park.
|May 27, 2019||
Chloé Lopez joins the Freeman lab as a Biotechnology Master's student from the University of Lille, France. Bienvenue Chloé!
|May 23, 2019||
Aileen Lee passes her graduate board oral exams to officially become a BMBB Ph.D. candidate...congrats Aileen!
|May 18, 2019||
Freddie receives yet another award: The Outstanding Performance Award for Teaching Assistants. Next time leave some for the rest of us :^).
|May 16, 2019||
Aman Imani passes his graduate board oral exams to officially become a BMBB Ph.D. candidate...way to go Aman!
|May 5-9, 2019||
Aman and Aileen present posters at the Natural Products - Discovery, Biosynthesis and Application conference in Copehagen!
|May 1, 2019||
Freddie receives the Cyrus Barnum Teaching Award (and recognition of her ARCS fellowship) at the 2019 Bollum symposium dinner award ceremony!
Chandler Hellenbrand was awarded the Juliamarie Andreen Grilly Undergraduate Research Scholarship in Molecular Biology and the Monica Tsang and James Weatherbee Merit Scholarship in Biology!
Our team is growing! Welcome, Kathryn!
|January 27, 2019||
Anna Glöckle from the Technische Universität München joins our lab as a visiting scholar...Willkommen!
|January 19, 2019||
Celebrating the new year with a new tradition? (Bizarro holiday ornaments!)
|October 30, 2018||
Freddie Miller is awarded a prestigious ARCS scholarship!
|August 29, 2018||
Everyone is still stunned that Freddie was edged out of the standings at the annual State Fair air hockey tourney... Final results: Mike 1st, Aman 2nd, Matt 3rd.
|August 14, 2018||
Aileen Lee wins the coveted poster prize for natural products at the Society for Industrial Microbiology and Biotechnology Annual Meeting!
|August 1, 2018||
Congratulations to Matthew Jensen for starting his new assistant professorship in the chemistry department at Concordia University, St. Paul!
|July 2, 2018||
Jakub Michalski from Poznań University in Poland joins our lab for his summer scholarship. Witam Jakub!
|April 2, 2018||
Chandler Hellenbrand is awarded a prestigious LSSURP fellowship to fund her summer research in our lab…way to go!
|February 12, 2018||
Aileen Lee and Aman Imani join the Freeman Lab as BBMB Ph.D. Students. Finally! Our Korfball team is complete!
|December 15, 2017||
Jingle gels! Jingle gels! Running DNA. Oh what fun are aldehydes and laying crystal trays...Hey!...too much fun and glühwein at The Freeman Lab Holiday Party.
|October 27, 2017||
Freddie and the Freeman Lab get a shout-out for their work helping high school students for Minnetonka Research.
A little university press for our borosin RiPP family discovery!
|August 31, 2017||
Second Freeman Lab state fair outing. The Second Freeman Lab Annual Air Hockey Tournament! Results: 1st place: Mike (they are not letting me win, I swear), 2nd place: Aman, 3rd place: Freddie.
|August 23, 2017||
Hip, Hip, Foray! First mushroom collection trip to Cloquet Forestry Research Station and Spirit Lake with collaborator Bob Blanchette and his lab. We’re walking on water…it’s a bog!
|May 05, 2017||
Freeman Lab outing to Escape MN! Question: How many scientists does it take to escape from Doctor K’s Lethal Injection Room? Answer: We have no idea.
|May 03, 2017||
Jacob Anderson awarded the prestigious Danielson Blake Family Scholarship…great job Jacob!
|August 31, 2016||
First Freeman Lab state fair outing. Also instituting the First Freeman Lab Annual Air Hockey Tournament! Results: 1st place: Mike (naturally!), 2nd place: Freddie, 3rd place: Aman.
|April 28, 2016||
Renovations complete! It’s a brand new lab…
Every lab needs an origins story ...
|January 4, 2016||
The saga begins…the Freeman Lab is born.
Assistant Professor Department of Biochemistry, Molecular Biology, and Biophysics& The BioTechnology InstituteCollege of Biological Sciences1479 Gortner AveRoom 244 Gortner LabSaint Paul, MN email@example.comOFFICE (+1) 612-624-8575 LAB (+1) 612-625-4017
We are always looking for highly motivated students and researchers!
If you are interested in our work, please send me your CV and a detailed description of your research experience and your specific interests in our group.