Badri Nath Dubey, PhD
Principal Investigator | Group Leader
Head of Structural Biology Lab
DBT-Ramalingaswami Faculty Fellow /Assi. Prof.
DBT-Ministry of Science & Technology, Government of India
Department of Biosciences and Bioengineering,
Indian Institute of Technology (IIT) Dharwad,
Chikkamalligwad, Dharwad 580011,
badrinathdubey@iitdh.ac.in,
Phone: +91-9935036314
Biography
Dr. Badri Nath Dubey is a DBT–Ramalingaswami Faculty Fellow/Assistant Professor in the Department of Biosciences and Bioengineering at IIT Dharwad, where he leads the Structural Biology Laboratory as Principal Investigator. Lab research focuses on the structural and molecular mechanisms of bacterial signaling, with a particular interest in exploiting bacterial survival pathways to address the global challenge of antimicrobial resistance (AMR).
Dr. Dubey began his research career at the Indian Institute of Science (IISc), Bangalore. He was awarded a BioStruct scholarship from government of Germany to pursue doctoral studies in Germany. He obtained his Ph.D. (Dr. rer. nat.) in Biochemistry and Molecular Biology from Heinrich-Heine University Düsseldorf, Germany. He subsequently carried out extensive postdoctoral and independent research at leading international institutions, including the Biozentrum, University of Basel, Switzerland, University of Bayreuth, Germany, Kiel University, Germany and the Centre for Structural Systems Biology (CSSB) at DESY, Hamburg. Prior to joining IIT Dharwad, he served as a Staff Scientist /Independent Scientist at CSSB–DESY.
Education and Training
Dr. rer. nat. (Ph.D.) in Biochemistry and Molecular Biology
International NRW Research School Biostruct
Institute of Biochemistry and Molecular Biology II,
Heinrich-Heine University Medical Center Düsseldorf, Germany
Master of Science in Molecular Biology and Biotechnology
Tezpur University (Central University), Assam, India
Bachelor of Science
University of Allahabad (Central University), India
Professional Appointments
2025 – Present
Principal Investigator and Group Leader
Head, Structural Biology Laboratory
DBT–Ramalingaswami Faculty Fellow / Assistant Professor
Department of Biosciences and Bioengineering,
Indian Institute of Technology (IIT) Dharwad, India
2021 – 2025
Staff Scientist / Independent Scientist
Centre for Structural Systems Biology (CSSB),
German Electron Synchrotron (DESY), Hamburg, Germany
2023
Guest Scientist
Zoological Institute, Kiel University, Kiel, Germany
2020 – 2021
Senior Scientist (Biochemistry)
University of Bayreuth, Bayreuth, Germany
2018 – 2019
Research Associate
Biozentrum, University of Basel, Basel, Switzerland
2012 – 2018
Postdoctoral Fellow
Biozentrum, University of Basel, Basel, Switzerland
2007 – 2008
Junior Research Fellow
Department of Microbiology and Cell Biology,
Indian Institute of Science, Bangalore, India
2024. DBT–Ramalingaswami Re-entry Fellowship, awarded by the Department of Biotechnology, Ministry of Science and Technology, Government of India
2023. Selected Speaker, CSSB Symposium, Hamburg, Germany
Talk: “Charting the Landscape of Infection: From Entry to Exit”
2012.Postdoctoral Fellowship, Max Planck Institute for Molecular Physiology, Dortmund, Germany
2011. Oral Presentation Award, Etter Early Career Award Symposium
American Crystallographic Association (ACA) Meeting, New Orleans, USA
2008–2012. Biostruct Ph.D. Scholarship, NRW Research School Biostruct, Düsseldorf, Germany
2008. Nomination for the Japanese Government Ph.D. Scholarship
2007. M. Sc. Scholarship, Department of Biotechnology (DBT),
Ministry of Science and Technology, Government of India
Dubey, B. N .,** Rezaei Adariani, S., Gremer, L., Dvorsky, R., Nie, Y., Amin, E., Moll, J. M., Zhang, S., Smits, S. H. J., Graewert, M. A., Willbold, D., Groth, G., Nagel, L., Pospich, S., Ahmadian, M. R*. (2026)
Structural and functional insights into the p160 Rho-associated coiled-coil-containing protein kinase ROCK.
Under consideration in Nature Communications.
**Lead Corresponding author
Buchholz F., Upterworth L. M., Tüffers L., Groth E., Haas K., Schütz D., Savietto-Scholz A., Batra A., Kirchoff L., Dubey B. N., Kalsdorf B., Rabe K., Lange C., Sondermann H., Rupp J., Bramkamp M., Roemhild R., Schulenburg H.
Antibiotic-induced negative hysteresis is a widespread envelope stress response in Gram-negative bacteria.
Nature Communications (In Press 2026).
Rudin L., Dubey B. N., Bornstein M. M., Shyp V. (2024)
Inhibitory effect of plant flavonoid cyanidin on oral microbial biofilm.
Microbiology Spectrum, American Society for Microbiology (ASM).
Brüderlin M., Böhm R., Fadel F., Hiller S., Schirmer T., Dubey B. N.* (2023)
Structural features discriminating hybrid histidine kinase receiver domains from response regulator homologs.
Nature Communications 14:1002.
Lead corresponding author
Dubey B. N.*, Shyp V., Fucile G., Sondermann H., Jenal U., Schirmer T. (2023)
Mutant structure of a metabolic switch protein in complex with monomeric c-di-GMP reveals a potential mechanism of protein-mediated ligand dimerization.
Scientific Reports 13:2727.
Lead corresponding author
Rudin L., Roth N., Kneubühler J., Dubey B. N., Bornstein M. M., Shyp V. (2023)
Inhibitory effect of natural flavone luteolin on Streptococcus mutans biofilm formation.
Microbiology Spectrum 10(5). (American Microbiology Society).
Shyp V.& , Dubey B. N.& , Böhm R., Nesper J., Hiller S., Schirmer T., Jenal U. (2021)
Reciprocal growth control by competitive binding of nucleotide second messengers to a metabolic switch in Caulobacter crescentus.
Nature Microbiology 6:59–72.
Equal first authors; F1000 Recommended
Dubey B. N.¹, Agustoni E.¹, Böhm R.¹, Kaczmarczyk A., Mangia F., von Arx C., Jenal U., Hiller S., Plaza-Menacho I., Schirmer T. (2020)
Hybrid histidine kinase activation by cyclic di-GMP-mediated domain liberation.
Proceedings of the National Academy of Sciences USA 117:1000–1008.
¹Equal first authors
Kaczmarczyk A., Hempel A. M., von Arx C., Böhm R., Dubey B. N., Nesper J., Schirmer T., Hiller S., Jenal U. (2020)
Precise transcription timing by a second messenger drives a bacterial G1/S cell cycle transition.
Nature Communications 11:816.
Stampfli A. R., Goncharenko K. V., Meury M., Dubey B. N., Schirmer T., Seebeck F. P. (2019)
An alternative active-site architecture for O₂ activation in the ergothioneine biosynthetic enzyme EgtB.
Journal of the American Chemical Society 141:5275–5285.
Dubey B. N., Lori C., Ozaki S., Fucile G., Plaza-Menacho I., Jenal U., Schirmer T. (2016)
Cyclic di-GMP mediates a histidine kinase/phosphatase switch by non-covalent domain cross-linking.
Science Advances 2:e1600823.
Evaluated by F1000
Lori C., Ozaki S., Steiner S., Böhm R., Abel S., Dubey B. N., Schirmer T., Hiller S., Jenal U. (2015)
Cyclic di-GMP acts as a cell-cycle oscillator to drive chromosome replication.
Nature 523:236–239.
Editorial and Guest Editorship
Invited Guest Editor, Frontiers in Cell and Developmental Biology
Research Topic: Exploring the mechanisms of second messenger signaling in mycobacteria: novel approaches to address antimicrobial resistance, biofilm formation, persistence, and drug resistance
Editorial Board / Reviewing Activities
Nature portfolio journals
Research in Microbiology (Elsevier)
Life Science Alliance
(An open-access journal published jointly by EMBO Press, Rockefeller University Press, and Cold Spring Harbor Laboratory Press)
Interdisciplinary Science: Computational Life Sciences
PLOS ONE
MDPI
CSSB Symposium, Hamburg, Germany
Speaker
Uncovering molecular mechanisms of bacterial signal transduction
Centre for Structural Systems Biology (DESY)
International Symposium on Structural Biology for Drug Discovery, SwissFEL/SLS
Paul Scherrer Institute, Villigen, Switzerland
EMBO–EMBL Conference: New Approaches and Concepts in Microbiology
Rhine–Knee Regional Meeting on X-ray Crystallography of Biomacromolecules
Oral presentation
Sensing the second messengers: Mechanistic insights into c-di-GMP and ppGpp signaling
International Union of Crystallography (IUCr) Congress
Hyderabad, India — Poster presentation
European Crystallographic Association Meeting (ECM-30)
Basel, Switzerland — Poster presentation
5th Murnau Conference on Structural Biology
Focus: Signal Transduction — Poster presentation
American Crystallographic Association Meeting
New Orleans, USA — Oral presentation (Etter Early Career Award Symposium)
American Crystallographic Association
National Centre for Biological Sciences (NCBS–TIFR), Bangalore
Molecular mechanisms of second messenger signaling in bacteria and implications for next-generation antibiotics
National Centre for Biological Sciences
Tata Institute of Fundamental Research (TIFR), Mumbai
Understanding the ‘brain’ behind bacterial success: Magic molecules controlling signaling circuits
Tata Institute of Fundamental Research
Central Drug Research Institute (CDRI), Lucknow
Understanding the molecular logic of bacterial survival signaling
Central Drug Research Institute
University of Bayreuth, Germany
Colloquium on Molecular Biosciences (BZMB)
Sensing second messengers: Mechanistic insights into c-di-GMP and ppGpp signaling
University of Bayreuth
LeadXpro / PSI, Villigen, Switzerland
How do second messengers control bifunctional hybrid histidine kinases at the molecular level?
LeadXpro
Max Planck Institute of Biochemistry, Martinsried, Germany
Structural insights into ROCK kinase architecture
Max Planck Institute of Biochemistry
International Institute of Molecular and Cell Biology, Warsaw, Poland
Crystal structure and biophysical properties of ROCK-HR1
International Institute of Molecular and Cell Biology
