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.

[TOP]

polytheonamide structure
Publications

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

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§, Kuenzler, 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: 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, Kaelin, N, Helf, MJ, Piel, J, Freeman, MF§, Kuenzler, 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. Engl. 2017 56: 2-5.]

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. Engl. 56: 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: 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, Cruesemann, 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, HG, Matsunaga, S, Piel, J (2012) Metagenome mining reveals polytheonamides as posttranslationally modified ribosomal peptides, Science 338: 387-390. DOI: 10.1126/science.1226121.
[Concentrates: Chem. Eng. News 2012 90(3): 26.]

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: 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 DOI: 10.1007/128_2010_113: 1-53.

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.]

[TOP]

calvin
People
Lab Members
Michael F. Freeman

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

Freddie Miller

Freddie Miller
BMBB Ph.D. Candidate
mill5007@umn.edu

Aman Imani

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

Aileen Lee

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

Kathryn Crone

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

Marissa Quijano

Marissa Quijano
MicE Masters Candidate
quija015@umn.edu

Chandler Hellenbrand

Chandler Hellenbrand
Undergraduate
helle309@umn.edu

Alexander Hutchens

Alexander Hutchens
Undergraduate
hutch422@umn.edu

Finn

Finn
Adorable Support Staff
scienceisruff@umn.edu


BMBB = Biochemistry, Molecular Biology, and Biophysics
MicE = Microbial Engineering

Lab Alumni
2019Anna GlöckleVisiting scholar
2018Jakub MichalskiVisiting scholar
2017-2018Dr. Matthew 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 Kumar NepalPost-doctoral associate
Current position: Post-doctoral associate
University of Washington in St. Louis
2016-2017Kinsey PhilipsUndergraduate
2016-2017Jacob AndersonUndergraduate

[TOP]

petri dishes
Lab News
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

[TOP]

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.

[TOP]

Freeman Lab carving