laboratory bottles
Natural product biosynthesis | Microbial genetics | Targeted metagenomics

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.

mass spectrometer
Research
Natural product discovery

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.

Accessing Nature’s metabolic potential
bacteria

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.

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polytheonamide structure
Publications

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

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.]

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calvin
People
Lab Members
Michael F. Freeman

Michael F. Freeman
Principal Investigator
mffreema@umn.edu
CV:

Aman Imani

Aman Imani
BMBB Ph.D. Candidate
imani006@umn.edu

Aileen Lee

Aileen Lee
BMBB Ph.D. Candidate
leex9223@umn.edu

Kathryn Crone

Kathryn Crone
BMBB Ph.D. Candidate
crone011@umn.edu

Nisha Vishwanathan

Nisha Vishwanathan
Researcher I
vishw025@umn.edu

Sayuj Suresh

Sayuj Suresh
Undergraduate
sures082@umn.edu

Austin Cihak

Austin Cihak
Undergraduate
cihak010@umn.edu

Finn

Finn
Adorable Support Staff
scienceisruff@umn.edu


BMBB = Biochemistry, Molecular Biology, and Biophysics

Lab Alumni
2020Floris de WaalVisiting scholar
2016-2020Dr. Fredarla S. MillerBMBB graduate student
Current position: Manufacturing scientist
Beckman Coulter, Inc., Chaska, MN
2018-2019Chandler HellenbrandUndergraduate
2019Sarah Schmidt-DannertUndergraduate
2019Sumire KurosawaVisiting scholar
2019Chloé LopezVisiting scholar
2019Anna GlöckleVisiting scholar
2018-2019Alexander HutchensUndergraduate
2018Jakub MichalskiVisiting scholar
2016-2018Marissa QuijanoMaster's student
2017-2018Dr. Matthew R. JensenPost-doctoral associate
Current position: Tenure-track assistant professor
Chemistry department, Concordia University, St. Paul
2017-2018Luke BundayHigh school student
2017-2018Lucy ChenHigh school student
2016-2017Ryan BaerUndergraduate
2016-2017Dr. Keshav K. NepalPost-doctoral associate
Current position: Post-doctoral associate
University of Washington in St. Louis
2016-2017Kinsey PhilipsUndergraduate
2016-2017Jacob AndersonUndergraduate

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petri dishes
Lab News
February 15, 2021
covid blue 2021
Aman's blog gets some UMN press, highlighting how one person's compassion and effort can make a difference.
covid blue 2021
February 2021
TMNT 2021
Nisha joins the Freeman Lab...Cowabunga!
TMNT 2021
January 16, 2021
among us 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.
among us 2021
May 12, 2020
kathryn prelim 2020
Kathryn easily clears her BMBB graduate board oral exam - congratulations, well done!
kathryn prelim 2020
May 8, 2020
freddie phd 2020
Freddie rocks her Ph.D. defense - We could not be more proud of you!
freddie phd 2020
April 2020
aman ta 2020
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!
aman ta 2020
February 7, 2020
holiday 2020
Another fun holiday potluck party for the Freeman lab to ring in the new year!
holiday 2020
February 3, 2020
de Waal 2020
Floris de Waal from Wageningen University joins our lab as a visiting scholar...Welkom!
de Waal 2020
October 2019
Sumire 2019
Sumire Kurosawa from the University of Tokyo joins our lab as a visiting scholar...Yōkoso (ようこそ)!
Sumire 2019
September 28, 2019
FSM Wedding 2019
Our warmest congratulations goes out to our very own Freddie on her and Nathan's beautiful wedding day!
FSM Wedding 2019
September 2019
New undergrads 2019
Undergraduates Sarah Schmidt-Dannert and Sayuj Suresh join the lab...welcome!!
New undergrads 2019
August 28, 2019
MN State Fair 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.
MN State Fair 2019
July 18, 2019
Freeman-Buller lab outing 2019
1st Annual Freeman-Buller joint lab outing at Great River Bluffs State Park.
Freeman-Buller lab outing 2019
May 27, 2019
Chloe Lopez joins lab
Chloé Lopez joins the Freeman lab as a Biotechnology Master's student from the University of Lille, France. Bienvenue Chloé!
Chloe Lopez joins lab
May 23, 2019
Aileen passes graduate board oral exams
Aileen Lee passes her graduate board oral exams to officially become a BMBB Ph.D. candidate...congrats Aileen!
Aileen passes graduate board oral exams
May 18, 2019
Freddie receives TA award
Freddie receives yet another award: The Outstanding Performance Award for Teaching Assistants. Next time leave some for the rest of us :^).
Freddie receives TA award
May 16, 2019
Aman passes graduate board oral exams
Aman Imani passes his graduate board oral exams to officially become a BMBB Ph.D. candidate...way to go Aman!
Aman passes graduate board oral exams
May 5-9, 2019
Copehagen presentation 2019
Aman and Aileen present posters at the Natural Products - Discovery, Biosynthesis and Application conference in Copehagen!
Copehagen presentation 2019
May 1, 2019
Freddie Miller Cyrus Barnum Teaching Award 2019
Freddie receives the Cyrus Barnum Teaching Award (and recognition of her ARCS fellowship) at the 2019 Bollum symposium dinner award ceremony!
Freddie Miller Cyrus Barnum Teaching Award 2019
May 2019
Chandler scholarships 2019
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!
Chandler scholarships 2019
February 2019
Kathryn Crone Joins 2019
Our team is growing! Welcome, Kathryn!
Kathryn Crone Joins 2019
January 27, 2019
Anna Glöckle 2019
Anna Glöckle from the Technische Universität München joins our lab as a visiting scholar...Willkommen!
Anna Glöckle 2019
January 19, 2019
Freeman Holiday Party 2019
Celebrating the new year with a new tradition? (Bizarro holiday ornaments!)
Freeman Holiday Party 2019
October 30, 2018
ARCS scholarship 2018
Freddie Miller is awarded a prestigious ARCS scholarship!
ARCS scholarship 2018
August 29, 2018
state fair 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.
state fair 2018
August 14, 2018
poster award 2018
Aileen Lee wins the coveted poster prize for natural products at the Society for Industrial Microbiology and Biotechnology Annual Meeting!
poster award 2018
August 1, 2018
new job 2018
Congratulations to Matthew Jensen for starting his new assistant professorship in the chemistry department at Concordia University, St. Paul!
new job 2018
July 2, 2018
polish exchange 2018
Jakub Michalski from Poznań University in Poland joins our lab for his summer scholarship. Witam Jakub!
polish exchange 2018
April 2, 2018
fellowship 2018
Chandler Hellenbrand is awarded a prestigious LSSURP fellowship to fund her summer research in our lab…way to go!
fellowship 2018
February 12, 2018
two new students 2018
Aileen Lee and Aman Imani join the Freeman Lab as BBMB Ph.D. Students. Finally! Our Korfball team is complete!
two new students 2018
December 15, 2017
holiday party 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.
holiday party 2017
October 27, 2017
Minnetonka Research 2017
Freddie and the Freeman Lab get a shout-out for their work helping high school students for Minnetonka Research.
Minnetonka Research 2017
September 2017
press borosin RiPP 2017
A little university press for our borosin RiPP family discovery!
press borosin RiPP 2017
August 31, 2017
lab air hockey tournament 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.
lab air hockey tournament 2017
August 23, 2017
spirit lake foray 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!
spirit lake foray 2017
May 05, 2017
escape room 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.
escape room 2017
May 03, 2017
Jacob Anderson 2017 Scholarship
Jacob Anderson awarded the prestigious Danielson Blake Family Scholarship…great job Jacob!
Jacob Anderson 2017 Scholarship
August 31, 2016
state fair 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.
state fair 2016
April 28, 2016
lab benches 2016
Renovations complete! It’s a brand new lab…
lab benches 2016
January 2016
origin story 2016
Every lab needs an origins story ...
origin story 2016
January 4, 2016
the beginning 2016
The saga begins…the Freeman Lab is born.
the beginning 2016

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Gortner Lab
Contact
Michael F. Freeman, Ph.D.

Assistant Professor
Department of Biochemistry, Molecular Biology, and Biophysics
& The BioTechnology Institute
College of Biological Sciences
1479 Gortner Ave
Room 244 Gortner Lab
Saint Paul, MN 55108
mffreema@umn.edu
OFFICE (+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.

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Freeman Lab carving