PUBLICATIONS

Publications

1. Das, S., Naik, Y., Mishra, U., Ganguly, M., Dubey, B. N., Jana, S., and Mahanta, N.* (Year). Dimerization of MilM Is Essential for Catalyzing Pyridoxal-5′-Phosphate (PLP)–Dependent Cγ-Hydroxylation of L-Arginine During Mildiomycin Biosynthesis. (2026)

      Under consideration in ACS catalysis.

2. Das, S., Naik, Y., Mishra, U., Ganguly, M., Dubey, B. N., Jana, S., and Mahanta, N. (2026). Dimerization of MilM is essential for catalyzing the pyridoxal-5′-phosphate (PLP)–dependent Cγ-hydroxylation of L-arginine during mildiomycin biosynthesis. bioRxiv, 2026.02.25.707955. https://doi.org/10.64898/2026.02.25.707955

3. 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

4. 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. (2026)
   Antibiotic-induced negative hysteresis is a widespread envelope stress response in Gram-negative bacteria.
   Nature Communications (in press).

5. 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).

6. Rudin L., Roth N., Kneubühler J., Ahmad S., Dubey B. N., Bornstein M. M., Shyp V. (2023)
   Inhibitory effect of natural flavone luteolin on Streptococcus mutans biofilm formation.
   Microbiology Spectrum 11(5). American Society for Microbiology (ASM).
   https://doi.org/10.1128/spectrum.05223-22

7. Brüderlin M., Böhm R., Fadel F., Hiller S., Schirmer T.,* Dubey B. N. ** (2023)
   Structural features discriminating hybrid histidine kinase Rec domains from response regulator homologs.
   Nature Communications 14, 1002.    **Lead Corresponding authors
   https://doi.org/10.1038/s41467-023-36597-8

8. Dubey B. N.*, Shyp V., Fucile G., Sondermann H., Jenal U., Schirmer T. (2023)
   Mutant structure of metabolic switch protein in complex with monomeric c-di-GMP reveals a potential mechanism of protein-mediated ligand dimerization.
   Scientific Reports 13, 2727. (Corresponding author)
   https://doi.org/10.1038/s41598-023-29110-0

9. 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)
   https://doi.org/10.1038/s41564-020-00809-4
   — Faculty of 1000 “Recommended”
   — Featured in Hengge R., Nature Microbiology (2021):
   https://doi.org/10.1038/s41564-020-00842-3

10. Dubey B. N., Agustoni E., Böhm R., 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.
    PNAS 117(2), 1000–1008.
    https://doi.org/10.1073/pnas.1911427117

11. 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.
    https://doi.org/10.1038/s41467-020-14585-6

12. 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(13), 5275–5285.
    https://doi.org/10.1021/jacs.8b13023

13. 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 noncovalent domain cross-linking.
    Science Advances 2, e1600823.
    https://doi.org/10.1126/sciadv.1600823
    Faculty of 1000 evaluation:
    https://f1000.com/prime/726763649

14. 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.
    https://doi.org/10.1038/nature14473

15. Selvaraj M., Govindan A., Seshadri A., Dubey B. N., Varshney U., Vijayan M. (2013)
    Molecular flexibility of Mycobacterium tuberculosis ribosome recycling factor and its functional consequences.
    Journal of Biosciences 38, 845–855.
    https://doi.org/10.1007/s12038-013-9381-0

16. Ehsan A., Dubey B. N., Zhang S.-C., Gremer L., Dvorsky R., Moll J. M., Taha M. S., Schmitt L., Groth G., Nagel-Steger L., Piekorz R. P., Ahmadian M. R. (2013)
    Rho-kinase: Structure, regulation, (dys)function, and inhibition.
    Biological Chemistry 394(11), 1399–1410.
    https://doi.org/10.1515/hsz-2013-0181

17. Seshadri A., Dubey B. N., Weber M. H., Varshney U. (2009)
    Impact of rRNA methylations on ribosome recycling and fidelity of initiation in Escherichia coli.
    Molecular Microbiology 72(3), 795–808. (Cover article)
    https://doi.org/10.1111/j.1365-2958.2009.06685.x

18. Ranjan A., Sinha A. Y., Dubey B. N., Saikia A., Buragohain A. K., Ray S. K. (2008)
    Analysis of bacterial genomes reveals conserved patterns in dinucleotide abundance and codon usage.
    Current Science 94(2).
    http://www.jstor.org/stable/24101862

19. Dubey B. N., Buragohain A. K., Ray S. K. (2008)
    Positive correlation of bacterial genome GC% with anticodon diversity.
    IUP Journal of Biotechnology.
    https://iupindia.in/309/IJBT_Positive_Correlation_of_Bacterial39.html

Book Chapter

• Jaiswal M., Dubey B. N., Koessmeier K. T., Gremer L., Ahmadian M. R. (2011)
  Biochemical assay to characterize Rho GTPases.
  Methods in Molecular Biology, Vol. 827, pp. 37–58.
  https://doi.org/10.1007/978-1-61779-442-1_3
  (Impact Factor: 1.3)

Scientific Blog

• Behind the Paper – Nature Microbiology (2021)
  The Yin and Yang of bacterial growth and development: How two opposing signaling molecules, (p)ppGpp and c-di-GMP, cooperate to control growth and behaviour in Caulobacter crescentus.
  https://microbiologycommunity.nature.com/posts/the-yin-and-yang-of-bacterial-growth-and-development

Press release/news magazine

• How do molecular machines pass the ball?
  https://www.cssb-hamburg.de/news_amp_events/news/2023/how_do_molecular_machines_pass_the_ball/index_eng.html

• The power of two rings
  https://www.cssb-hamburg.de/news_amp_events/news/2023/the_power_of_two_rings/index_eng.html

• Inner clockwork sets the time for cell division in bacteria
  https://www.eurekalert.org/pub_releases/2020-02/uob-is021020.php

• PNAS Altmetric – Media coverage and news attention
  https://pnas.altmetric.com/details/73355184/news

• Bacterial second messenger switches enzyme into “reverse gear”
  https://www.sciencedaily.com/releases/2016/06/160616143403.htm