Author

J. A. Nakamoto

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 4 Bioengineering· 1 Biophysics· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 5 Research Focus:protein folding & dynamics· 4 Organism:bacteria (other)· 3 Research Focus:cell type annotation· 3 Assay:proteomics· 3 Research Focus:cell signaling & trafficking· 2 Research Focus:host-pathogen & immune response· 2 Approach:biophysical modeling· 1

Frequent Co-Authors

G. C. Atkinson· 3 shared P. Milon· 3 shared T. Tenson· 3 shared V. Hauryliuk· 3 shared A. Garcia-Pino· 2 shared K. Ernits· 2 shared L. Shyrokova· 2 shared M. J. O. Johansson· 2 shared

Activity by Year

2019-2024 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 36 mutual co-author links

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3 shared papersMicrobiology

G. C. Atkinson

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Author profile →

6 papers

Recent·Most cited

A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis

H. Takada, H. Paternoga, K. Fujiwara, J. A. Nakamoto, E. N. Park, L. Dimitrova-Paternoga, B. Beckert, M. Saarma, T. Tenson, A. Buskirk, G. C. Atkinson, S. Chiba, D. N. Wilson, V. Hauryliuk

This study identifies YlmH as a novel RQC factor in B. subtilis, showing it can replace RqcP in polyalanine tail addition and is conserved in bacteria lacking RqcP.

bioRxiv · Mar 3, 2024 · PreprintMicrobiology

Mechanism of phage sensing and abortion by toxin-antitoxin-chaperone systems

T. Mets, T. Kurata, K. Ernits, M. J. O. Johansson, S. Z. Craig, G. M. Evora, J. A. Buttress, R. Odai, K. Coppieters't Wallant, J. A. Nakamoto, L. Shyrokova, A. A. Egorov, C. R. Doering, T. Brodiazhenko, M. T. Laub, , V. Hauryliuk

This study identifies and characterizes two Escherichia coli TAC systems that mediate antiphage defense by recognizing phage proteins and modifying mRNA to inhibit translation.

bioRxiv · Feb 24, 2024 · PreprintMicrobiology

The structural basis of hyperpromiscuity in a core combinatorial network of Type II toxin-antitoxin and related phage defence systems

K. Ernits, C. K. Saha, T. Brodiazhenko, B. Chouhan, A. Shenoy, J. J. Duque-Pedraza, V. Bojar, J. A. Nakamoto, T. Kurata, A. Egorov, L. Shyrokova, M. J. O. Johansson, T. Mets, A. Rustamova, J. Dzigurski, , G. C. Atkinson

The paper identifies a core combinatorial network of Type II toxin-antitoxin systems, reveals their structural basis for hyperpromiscuity, and validates new TA systems with functional annotations.

bioRxiv · Mar 22, 2023 · PreprintMicrobiology

(p)ppGpp inhibits 70S ribosome formation in Staphylococcus aureus by impeding GTPase-ribosome interactions

D. J. Bennison, J. A. Nakamoto, T. D. Craggs, P. Milon, J. B. Rafferty, R. M. Corrigan

This study shows (p)ppGpp inhibits 70S ribosome formation in Staphylococcus aureus by reducing RA-GTPase-ribosome interactions through inducing the OFF-state conformation.

bioRxiv · Jan 19, 2021 · PreprintMicrobiology

The complete, functional and dynamic cycle of the bacterial Initiation Factor 3

J. A. Nakamoto, R. Spurio, A. L. Konevega, A. Fabbretti, P. Milon

This study reveals the kinetic mechanisms and conformational changes of bacterial IF3 during translation initiation.

bioRxiv · Mar 16, 2019 · PreprintBiophysics

DNA aptamers for the recognition of HMGB1 from Plasmodium falciparum

D. F. Joseph, J. A. Nakamoto, O. A. Garcia Ruiz, K. Penaranda, A. E. Sanchez-Castro, P. S. Castillo, P. Milon

This study identifies HMGB1 as a potential biomarker for malaria and develops DNA aptamers for its detection, showing high binding affinity and specificity.

bioRxiv · Jan 23, 2019Bioengineering