Tobias W. Giessen, PhD

Harvard Medical School 1822 Beacon Street, Apt 2 Department of Systems Biology and Brookline, MA 02445 Wyss Institute for Biologically Inspired Engineering 617-992-4972 200 Longwood Ave, WAB 436 Boston, MA 02115 617-432-6406 [email protected]

EDUCATION:

PhD (summa cum laude) in Chemistry, Philipps-University Marburg 08/2013

Diploma (equiv. to M.Sc.) in Chemistry, Philipps-University Marburg 03/2010

Erasmus exchange student, Imperial College London 09/2008 – 03/2009

Intermediate Diploma in Chemistry, Philipps-University Marburg 04/2007

Abitur, Helmholtz-Gymnasium Zweibrücken 03/2005

RESEARCH EXPERIENCE:

Postdoctoral research: Leopoldina Postdoctoral Fellow, Harvard Medical School and Research Fellow in Systems Biology, Wyss Institute for Biologically Inspired Since 09/2014 Engineering at Harvard (Supervisor: Professor Pamela A. Silver)

 Discovered over 900 new protein-based compartmentalization systems in and archaea

 Established the involvement of two newly discovered protein compartments in oxidative and nitrosative stress resistance

 Explored the role of protein compartments in anaerobic ammonium oxidation and the global cycle

 Engineered protein compartments to control macromolecular co-localization in vivo for the improved production of indigo

 Engineered protein compartments for the production of functional inorganic nanomaterials exemplified by antimicrobial silver nanoparticles

 Rationally engineered the encapsulation of heterologous cargo inside protein compartments for the creation of artificial organelles and nanoreactors

 Engineered yeast using protein compartments for increased production of alkaloid precursors

Research Fellow, Center for Synthetic , Philipps-University Marburg 09/2013 – 08/2014 (Supervisor: Professor Mohamed A. Marahiel) 1 Tobias W. Giessen, PhD

 Engineered nonribosomal peptide synthetase adenylation domains for the incorporation of unnatural amino acids into proteins and peptides

Doctoral research: Graduate student, Department of Chemistry, Philipps-University Marburg 05/2010 – 08/2013 (Supervisor: Professor Mohamed A. Marahiel)

 Thesis: Ribosome-independent biosynthesis of peptide natural products: nonribosomal peptide synthetases and cyclodipeptide synthases

HONORS AND AWARDS:

German National Academy of Sciences Leopoldina Prize for Young Scientists 9/2017 (awarded to two scientists every two years, prize money: 5,000 EUR)

Awarded a Gordon and Betty Moore Foundation grant 10/2016 (with Pamela Silver/Harvard and Bess Ward/Princeton)

German National Academy of Sciences Leopoldina postdoctoral scholarship; accepted 06/2014

German Research Foundation (DFG) postdoctoral scholarship; declined 04/2014

Erasmus Exchange Scholarship 09/2008

Member of the German National Merit Foundation 10/2007

GRANT FUNDING:

Gordon and Betty Moore Foundation (GBMF5506): USD 700,000 (co-principal investigator with Pamela Silver/Harvard and Bess Ward/Princeton)

German National Academy of Sciences Leopoldina (LPDS 2014-05): EUR 65,000 (postdoctoral scholarship)

CURRENT COLLABORATORS:

Bess Ward William J. Sinclair Professor of Geosciences, Chair Department of Geosciences, , USA Collaboration project: Exploring Nitrogen Cycling in the from the Macro to the Molecular Scale

Robert E. Campbell Professor of Chemistry, Department of Chemistry, University of Alberta, Canada Collaboration project: Encapsulins as light-activatable delivery devices and actuators for neuroscience

Bianxiao Cui Associate Professor of Chemistry, Department of Chemistry, Stanford University, USA Collaboration project: Encapsulins as genetically-encodable magnetic actuators to manipulate mechanosensitive ion channels in neurons

Yu Heng Lau Assistant Professor of Chemistry, Department of Chemistry, University of Sydney, Australia

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Tobias W. Giessen, PhD

Collaboration project: Modifying encapsulins using bioconjugation for applications in catalysis and drug delivery

Maofu Liao Assistant Professor of Cell Biology Department of Cell Biology, Harvard Medical School Collaboration project: Studying the structure and function of encapsulin nanocompartments using cryoEM

TEACHING AND MENTORING EXPERIENCE:

Simmons College, Center for Excellence in Teaching, Boston, MA 6/2017 Certificate course “Teaching Institute: Theory, Practice & Navigating STEM Higher Ed”

Harvard Medical School, Department of Systems Biology, Boston, MA Mentor/ Project supervisor for 4 students (2 undergraduate students and 2 2015-2017 Supervisor graduate student)

Philipps-University Marburg, Department of Chemistry, Marburg, Hessen Mentor/ iGEM advisor for Team Marburg 2014 Supervisor

Mentor/ Project supervisor for 8 rotation students (6 undergraduate students and 2 2010-2014 Supervisor graduate students) in the context of the combined lecture/lab course ‘The Biochemistry of Energy Metabolism and Expression of Genetic Information’ (15 133 00505) and the ‘Biochemistry Lab Course for Master Students’ (15 133 00555)

Lab Course Organized and taught the lab course for ‘The Biochemistry of Energy 2012-2013 Metabolism and Expression of Genetic Information’ (15 133 00505)

Lab Course Organized and taught the ‘Biochemistry Lab Course for Master Students’ 2010-2013 (15 133 00555)

Seminar Organized and taught ‘Bioanalytics for Graduate Students’ (15 133 00540) 2010-2013

SCIENTIFIC PRESENTATIONS:

Invited speaker: Institute for Applied Microbiology, RWTH Aachen University, Special Seminar Series, Aachen, Upcoming:

Germany 02/2018 Wyss Institute for Biologically Inspired Engineering, Scientific Retreat, Boston, USA Upcoming: 11/2017 Institute for Advanced Study, Technical University Munich, Moessbauer Symposium, Munich, 05/2017 Germany Department of Systems Biology, Harvard Medical School, Seminar Series, Boston, USA 05/2017 Department of Geosciences, Princeton University, Moore MMI seminar, Princeton, USA 12/2016 Wyss Institute for Biologically Inspired Engineering, Synthetic Biology Platform Meeting, 10/2016 Boston, USA Wyss Institute for Biologically Inspired Engineering, Scientific Retreat, Boston, USA 11/2015 Peptide Meeting Kleinwalsertal, Hirschegg, Austria 08/2012 NRPS/PKS Meeting, Lake Tahoe, USA 08/2010

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Tobias W. Giessen, PhD

PUBLICATIONS:

†corresponding author, *contributed equally

1. Riglar, D. T., Giessen, T. W., Baym, M., Kerns, S. J., Niederhuber, M. J., Bronson, R. T., Kotula, J. W., Gerber, G. K., Way, J. C. and Silver, P. A.† Long-term monitoring of inflammation in the mammalian gut using programmable commensal bacteria, Nature Biotechnology, 2017, 35, 653-658. 2. Giessen, T. W. and Silver, P. A.† Widespread distribution of encapsulin nanocompartments reveals functional diversity, Nature Microbiology., 2017, 2, 17029. 3. Giessen, T. W. and Silver, P. A.† Engineering carbon fixation with artificial protein organelles, Current Opinion in Biotechnology, 2017, 46, 42-50. 4. Liu, X., Lopez, P. A., Giessen, T. W., Giles, M., Way, J. C. and Silver, P. A.† Engineering genetically-encoded mineralization and magnetism via directed evolution, Scientific Reports, 2016, 6, 38019. 5. Giessen, T. W. and Silver, P. A.† A catalytic nanoreactor based on in vivo encapsulation of multiple enzymes in an engineered protein nanocompartment, ChemBioChem, 2016, 17, 1931-1935. 6. Giessen, T. W. and Silver, P. A.† Converting a natural protein compartment into a nanofactor for the size- constrained synthesis of antimicrobial silver nanoparticles, ACS Synthetic Biology, 2016, 5, 1497–1504. 7. Giessen, T. W.† Encapsulins: microbial nanocompartments with applications in biomedicine, nanobiotechnology and materials science, Current Opinion in Chemical Biology, 2016, 34, 1-10. 8. Giessen, T. W.† and Silver, P. A.† Encapsulation as a strategy for the design of biological compartmentalization, Journal of , 2015, 428, 916-927. 9. Giessen, T. W.† and Marahiel, M. A. Rational and combinatorial tailoring of bioactive cyclic 9dipeptides, Frontiers in. Microbiology, 2015, 6, 785. 10. Giessen, T. W.†, Altegoer, F., Nebel, A. J., Steinbach, R. M., Bange, G.† and Marahiel, M. A.† A synthetic adenylation-domain-based tRNA-aminoacylation catalyst, Angewandte Chemie International Edition, 2015, 54, 2492-2496. 11. Giessen, T. W.† and Marahiel, M. A.† The tRNA-Dependent Biosynthesis of Modified Cyclic Dipeptides, International Journal of Molecular Sciences, 2014, 15, 14610-14631. 12. Giessen, T. W., von Tesmar, A. M. and Marahiel, M. A.† A tRNA-dependent two enzyme pathway for the generation of singly an doubly methylated ditryptophan 2,5-diketopiperazines, Biochemistry, 2013, 52, 4274-4283. 13. Flühe, L., Burghaus, O., Wieckowski, B. M., Giessen, T. W., Linne, U. and Marahiel, M. A.† Two [4Fe-4S] cluster containing radical SAM enzyme SkfB catalyze thioether bond formation during the maturation of the sporulation killing factor, Journal of the American Chemical Society, 2013, 135, 959-962. 14. Giessen, T. W., von Tesmar, A. M. and Marahiel, M. A.† Insights into the generation of structural diversity in a tRNA-dependent pathway for highly modified bioactive cyclic dipeptides, Chemistry & Biology, 2013, 20, 828-838. 15. Bosello, M., Mielcarek, A., Giessen, T. W. and Marahiel, M. A.† An enzymatic pathway for the biosynthesis of the formylhydroxyornithine required for rhodochelin iron coordination, Biochemistry, 2012, 14, 3059-3066. 16. Giessen, T. W. and Marahiel, M. A.† Ribosome-independent biosynthesis of biologically active peptides: Application of synthetic biology to generate structural diversity, FEBS Letters, 2012, 586, 2065-2075. 17. Kraas, F. I., Giessen, T. W. and Marahiel, M. A.† Exploring the mechanism of lipid transfer during biosynthesis of the acidic lipopetide antibiotic CDA, FEBS Letters, 2012, 586, 283-288. 18. Giessen, T. W., Franke, K. B., Knappe, T. A., Kraas, F. J., Bosello, M., Xie, X., Linne, U. and Marahiel, M. A.† Isolation, structure elucidation and biosynthesis of an unusual hydroxamic acid ester-containing siderophore from Actinosynnema mirum, Journal of Natural Products, 2012, 75, 905-914. 19. Giessen, T. W., Kraas, F. I. and Marahiel, M. A.† A four-enzyme pathway for 3,5-dihydroxy-4- methylanthranilic acid formation and incorporation into the antitumor antibiotic sibiromycin, Biochemistry, 2011, 50, 5680-5692.

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Tobias W. Giessen, PhD

Manuscripts in preparation:

20. Giessen, T. W.*†, Altenburg, W. J.*, Rollins, N, Lau, YH and Silver, P. A.† Controlling in vivo cargo-loading of protein nanocompartments. 21. Giessen, T. W.*†, Lau, YH*, Altenburg, W. J. and Silver, P. A.† Protein co-localization, protection and catalysis using an engineered nanoreactor in yeast.

PATENT:

Giessen, T. W. and Silver, P. A. 2016. Methods and compositions relating to metal nanoparticles. U.S. Patent Application No. 62/333,946, filed 05/10/2016 (pending).

IMPACT OF SELECTED PUBLICATIONS:

Nature Microbiology, 2017: I carried out the first systematic analysis of the distribution and diversity of encapsulin protein organelles in bacterial and archaeal genomes using bioinformatics, phylogenetic analysis and biochemistry. I identified more than 900 new protein organelle systems in 15 bacterial and 2 archaeal phyla showing that some of these systems are involved in iron mineralization and redox metabolism, oxidative and nitrosative stress resistance and anaerobic ammonium oxidation, a process responsible for 30% of the nitrogen lost from the and thus an important part of the global . The widespread occurrence of protein-based organelles in prokaryotes demonstrates that many bacteria and archaea employ sophisticated compartmentalization mechanisms to spatially organize and regulate their metabolism and adapt to dynamic and often hostile environments. Current Opinion in Biotechnology, 2017: In this publication, I outline a strategy of how to improve photosynthetic efficiency in plants using engineered protein organelles. The major intelectual advance in this work is the proposal to use an encapsulin-based minimal CO2-fixing organelle to achieve this goal. By co-localizing RuBisCO and carbonic anhydrase inside encapsulins a three-gene system will be created with the aim of introducing it to plant chloroplasts in the future. A small percentage increase in photosynthetic efficiency in food crops will already be a major contribution towards slowing down climate change and decreasing food supply problems due to overpopulation. ACS Synthetic Biology, 2016: In a proof-of-principle study, I was able to engineer the first encapsulin system for the biological production of functional inorganic nanomaterials, in this case antimicrobial silver nanoparticles. One of the greatest challenges of the 21st century is to transition to the sustainable production of functional molecules and materials with synthetic biology and bioengineering approaches being some of the most promising startegies to achieve this goal. Angewandte Chemie International Edition, 2015: In this study, I was able to rationally engineer the first example of a non-ribosomal peptide synthetase adenylation domain able to load unnatural amino acids onto tRNAs which could then be used by the translational machinery and be incorporated into proteins or ribosomally produced bioactive peptides. This approach opens up the possibility to rationally increase the structural diversity of peptide-based natural products with the aim of tailoring and improving their bioactivities and of expanding their functional space. Chemistry & Biology, 2013: Here, I was able to discover and characterize a whole family of new antibacterial highly modified cyclic dipeptides based on a bioinformaitc genome mining approach. I discovered that these molecules are biosynthesized by tRNA-dependent enzymes distantly related to aminoacyl-tRNA synthetases and modified by a set of promiscuous tailoring enzymes. These enzymes and cyclic dipeptide scaffolds hold great promise for the rational or combinatorial generation of structural diversity which may result in new bioactive compounds with improved activities.

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