Danica Galonić Fujimori, PhD

Professor
Cellular Molecular Pharmacology
+1 415 514-0147

The Fujimori Lab investigates fundamental biological mechanisms to understand how misregulation leads to disease. Our focus is on modifications of cellular components by small molecule chemical tags, and the roles of these modifications in biological regulation.

Publications: 

Covalent labeling of a chromatin reader domain using proximity-reactive cyclic peptides.

Chemical science

Zhang MY, Yang H, Ortiz G, Trnka MJ, Petronikolou N, Burlingame AL, DeGrado WF, Fujimori DG

Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics.

Nature structural & molecular biology

Tsai K, Stojkovic V, Lee DJ, Young ID, Szal T, Klepacki D, Vázquez-Laslop N, Mankin AS, Fraser JS, Fujimori DG

Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance.

eLife

Tsai K, Stojkovic V, Noda-Garcia L, Young ID, Myasnikov AG, Kleinman J, Palla A, Floor SN, Frost A, Fraser JS, Tawfik DS, Fujimori DG

Domain cross-talk in regulation of histone modifications: Molecular mechanisms and targeting opportunities.

Current opinion in chemical biology

Longbotham JE, Zhang MY, Fujimori DG

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.

Nature

Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Huettenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ

Dissecting contributions of catalytic and reader domains in regulation of histone demethylation.

Methods in enzymology

Petronikolou N, Longbotham JE, Fujimori DG

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing.

bioRxiv : the preprint server for biology

Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Naing ZZC, Zhou Y, Peng S, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Shen W, Shi Y, Zhang Z, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Ramachandran R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Lin Y, Wankowicz SA, Bohn M, Trenker R, Young JM, Cavero D, Hiatt J, Roth T, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Agard D, Emerman M, Ruggero D, García-Sastre A, Jura N, von Zastrow M, Taunton J, Schwartz O, Vignuzzi M, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor S, Fraser JS, Gross J, Sali A, Kortemme T, Beltrao P, Shokat K, Shoichet BK, Krogan NJ

Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit.

Nucleic acids research

Stojkovic V, Myasnikov AG, Young ID, Frost A, Fraser JS, Fujimori DG

Extended Recognition of the Histone H3 Tail by Histone Demethylase KDM5A.

Biochemistry

Petronikolou N, Longbotham JE, Fujimori DG

cfr(B), cfr(C), and a New cfr-Like Gene, cfr(E), in Clostridium difficile Strains Recovered across Latin America.

Antimicrobial agents and chemotherapy

Stojkovic V, Ulate MF, Hidalgo-Villeda F, Aguilar E, Monge-Cascante C, Pizarro-Guajardo M, Tsai K, Tzoc E, Camorlinga M, Paredes-Sabja D, Quesada-Gómez C, Fujimori DG, Rodríguez C

Histone H3 binding to the PHD1 domain of histone demethylase KDM5A enables active site remodeling.

Nature communications

Longbotham JE, Chio CM, Dharmarajan V, Trnka MJ, Torres IO, Goswami D, Ruiz K, Burlingame AL, Griffin PR, Fujimori DG

miCLIP-MaPseq, a Substrate Identification Approach for Radical SAM RNA Methylating Enzymes.

Journal of the American Chemical Society

Stojkovic V, Chu T, Therizols G, Weinberg DE, Fujimori DG

Mutations in RNA methylating enzymes in disease.

Current opinion in chemical biology

Stojkovic V, Fujimori DG

Antibiotic resistance evolved via inactivation of a ribosomal RNA methylating enzyme.

Nucleic acids research

Stojkovic V, Noda-Garcia L, Tawfik DS, Fujimori DG

Editorial overview: Chemical genetics and epigenetics.

Current opinion in chemical biology

Fujimori DG, Conway SJ

Htm1p-Pdi1p is a folding-sensitive mannosidase that marks N-glycoproteins for ER-associated protein degradation.

Proceedings of the National Academy of Sciences of the United States of America

Liu YC, Fujimori DG, Weissman JS

Opposing Chromatin Signals Direct and Regulate the Activity of Lysine Demethylase 4C (KDM4C).

The Journal of biological chemistry

Pack LR, Yamamoto KR, Fujimori DG

Docking and Linking of Fragments To Discover Jumonji Histone Demethylase Inhibitors.

Journal of medicinal chemistry

Korczynska M, Le DD, Younger N, Gregori-Puigjané E, Tumber A, Krojer T, Velupillai S, Gileadi C, Nowak RP, Iwasa E, Pollock SB, Ortiz Torres I, Oppermann U, Shoichet BK, Fujimori DG

Functional coupling between writers, erasers and readers of histone and DNA methylation.

Current opinion in structural biology

Torres IO, Fujimori DG

Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes.

Journal of the American Society for Mass Spectrometry

Lu J, Trnka MJ, Roh SH, Robinson PJ, Shiau C, Fujimori DG, Chiu W, Burlingame AL, Guan S

Radical SAM-Mediated Methylation of Ribosomal RNA.

Methods in enzymology

Stojkovic V, Fujimori DG

Histone demethylase KDM5A is regulated by its reader domain through a positive-feedback mechanism.

Nature communications

Torres IO, Kuchenbecker KM, Nnadi CI, Fletterick RJ, Kelly MJ, Fujimori DG

Product binding enforces the genomic specificity of a yeast polycomb repressive complex.

Cell

Dumesic PA, Homer CM, Moresco JJ, Pack LR, Shanle EK, Coyle SM, Strahl BD, Fujimori DG, Yates JR, Madhani HD

Radical SAM-mediated methylation reactions.

Current opinion in chemical biology

Fujimori DG

Reconstitution of nucleosome demethylation and catalytic properties of a Jumonji histone demethylase.

Chemistry & biology

Shiau C, Trnka MJ, Bozicevic A, Ortiz Torres I, Al-Sady B, Burlingame AL, Narlikar GJ, Fujimori DG

Site-specific and regiospecific installation of methylarginine analogues into recombinant histones and insights into effector protein binding.

Journal of the American Chemical Society

Le DD, Cortesi AT, Myers SA, Burlingame AL, Fujimori DG

Covalent Intermediate in the Catalytic Mechanism of the Radical S-Adenosyl-l-methionine Methyl Synthase RlmN Trapped by Mutagenesis

J Am Chem Soc

McCusker KP, Medzihradszky KF, Shiver AL, Nichols RJ, Yan F, Maltby DA, Gross CA, Fujimori DG.

Covalent intermediate in the catalytic mechanism of the radical S-adenosyl-L-methionine methyl synthase RlmN trapped by mutagenesis.

Journal of the American Chemical Society

McCusker KP, Medzihradszky KF, Shiver AL, Nichols RJ, Yan F, Maltby DA, Gross CA, Fujimori DG

Protein and nucleic acid methylating enzymes: mechanisms and regulation.

Current opinion in chemical biology

Le DD, Fujimori DG

RNA methylation by radical SAM enzymes RlmN and Cfr proceeds via methylene transfer and hydride shift.

Proceedings of the National Academy of Sciences of the United States of America

Yan F, Fujimori DG

A novel enzymatic rearrangement.

Chemistry & biology

Fujimori DG

RlmN and Cfr are radical SAM enzymes involved in methylation of ribosomal RNA.

Journal of the American Chemical Society

Yan F, LaMarre JM, Röhrich R, Wiesner J, Jomaa H, Mankin AS, Fujimori DG

Structural analysis of an open active site conformation of nonheme iron halogenase CytC3.

Journal of the American Chemical Society

Wong C, Fujimori DG, Walsh CT, Drennan CL

Hypoxia sensing goes gauche.

Nature chemical biology

Fujimori DG

Halogenation strategies in natural product biosynthesis.

Chemistry & biology

Neumann CS, Fujimori DG, Walsh CT

CD and MCD of CytC3 and taurine dioxygenase: role of the facial triad in alpha-KG-dependent oxygenases.

Journal of the American Chemical Society

Neidig ML, Brown CD, Light KM, Fujimori DG, Nolan EM, Price JC, Barr EW, Bollinger JM, Krebs C, Walsh CT, Solomon EI

Spectroscopic evidence for a high-spin Br-Fe(IV)-oxo intermediate in the alpha-ketoglutarate-dependent halogenase CytC3 from Streptomyces.

Journal of the American Chemical Society

Fujimori DG, Barr EW, Matthews ML, Koch GM, Yonce JR, Walsh CT, Bollinger JM, Krebs C, Riggs-Gelasco PJ

Cloning and characterization of the biosynthetic gene cluster for kutznerides.

Proceedings of the National Academy of Sciences of the United States of America

Fujimori DG, Hrvatin S, Neumann CS, Strieker M, Marahiel MA, Walsh CT

What's new in enzymatic halogenations.

Current opinion in chemical biology

Fujimori DG, Walsh CT

Characterization of the aminocarboxycyclopropane-forming enzyme CmaC.

Biochemistry

Kelly WL, Boyne MT, Yeh E, Vosburg DA, Galonic DP, Kelleher NL, Walsh CT

Two interconverting Fe(IV) intermediates in aliphatic chlorination by the halogenase CytC3.

Nature chemical biology

Galonic DP, Barr EW, Walsh CT, Bollinger JM, Krebs C

Enzymatic generation of the antimetabolite gamma,gamma-dichloroaminobutyrate by NRPS and mononuclear iron halogenase action in a streptomycete.

Chemistry & biology

Ueki M, Galonic DP, Vaillancourt FH, Garneau-Tsodikova S, Yeh E, Vosburg DA, Schroeder FC, Osada H, Walsh CT

Site-selective conjugation of thiols with aziridine-2-carboxylic acid-containing peptides.

Journal of the American Chemical Society

Galonic DP, van der Donk WA, Gin DY

Selenocysteine derivatives for chemoselective ligations.

Chembiochem : a European journal of chemical biology

Gieselman MD, Zhu Y, Zhou H, Galonic D, van der Donk WA

J Serb Chem Soc

Model Study of Epothilone Synthesis: An Alternative Synthetic Approach to the C1-C7 fragment

Lalic G, Galonic D, Matovic R, Saicic RN

Tetrahedron

Alkylation of Carbonyl Compounds in the TiCl4-promoted Reaction of Trimethylsilyl Enol Ethers with Epoxides

Lalic G, Petrovski Z, Galonic DP, Matovic R, Saicic RN