Affiliations

• Center for RNA Biology
• Ohio State Biochemistry Program
• Cellular, Molecular, and Biochemical Sciences Program

Awards

• Fellow, American Association for the Advancement of Science
• Fellow, American Academy of Microbiology

Research Interests

Our group is interested in how the ribosome works. The ribosome is a large (~2.5 MDa), two-subunit, RNA-based machine that translates the genetic code in all organisms. In recent years, numerous structures of the ribosome and various ribosomal complexes have been determined by X-ray crystallography and cryo-electron microscopy. Today, a primary challenge is to understand how the ribosome moves and how such dynamics govern the various steps of translation. Since the ribosome is the most common target of natural antibiotics, gaining insight on ribosome function may contribute substantially to the development of new antibiotics.

We use a combination of genetic, molecular, and biochemical methods to study protein synthesis in bacteria. Examples of questions under investigation in the laboratory include: (1) Which features of mRNA tune the rate of initiation? (2) How do mechanisms of initiation compare in different phyla? (3) How do rRNA dynamics contribute to the mechanism of decoding (aminoacyl-tRNA selection)? (4) What roles do nonessential ribosome-associated GTPases play in the cell? (5) How do elements of precursor rRNA contribute to subunit assembly?

Recent publications: 

Alom, M.S., Arpin, D., Zhu, H., Hay, B.N., Foster, L.J., Ortega, J., and Fredrick, K. 2025. Protein bL38 facilitates incorporation of uL6 during assembly of the 50S subunit in Flavobacterium johnsoniae. Nucleic Acids Res. 53, gkaf120. 

Fakhretaha Aval, S., Seffouh, A., Moon, K-M., Foster, L.J., Ortega, J., and Fredrick, K. 2025. Role of the sarcin-ricin loop of 23S rRNA in biogenesis of the 50S subunit. RNA 31, 585-599. 

Gemler, B.T., Warner, B.R., Bundschuh, R. and Fredrick, K. 2024. Identification of leader-trailer helices of precursor ribosomal RNA in all phyla of bacteria and archaea. RNA 30, 1264-1276. 

Warner, B.R. and Fredrick, K. 2024. Contribution of an alternative 16S rRNA helix to biogenesis of the 30S subunit of the ribosome. RNA 30, 770-778. 

Naeem, F.M., Gemler, B.T., McNutt, Z.A., Bundschuh, R. and Fredrick, K. 2024. Analysis of programmed frameshifting during translation of prfB in Flavobacterium johnsoniae. RNA 30, 136-148.

Warner, B.R., Bundschuh, R. and Fredrick, K. 2023. Roles of the leader-trailer helix and antitermination complex in biogenesis of the 30S ribosomal subunit. Nucleic Acids Res. 51, 5242-5454.

McNutt, Z.A., Roy, B., Gemler, B.T., Shatoff, E.A., Moon, K-M., Foster, L.J., Bundschuh, R. and Fredrick, K. 2023. Ribosomes lacking bS21 gain function to regulate protein synthesis in Flavobacterium johnsoniae. Nucleic Acids Res. 51, 1927-1942.

McNutt, Z.A., Gandhi, M.D., Shatoff, E.A., Roy, B., Devaraj, A., Bundschuh, R. and Fredrick, K. 2021. Comparative analysis of anti-Shine-Dalgarno function in Flavobacterium johnsoniae and Escherichia coli. Front. Mol. Biosci. 8, 787388.

Shatoff, E.A., Gemler, B.T., Bundschuh, R. and Fredrick, K. 2021. Maturation of 23S rRNA includes removal of helix H1 in many bacteria. RNA Biol. 18(sup2), 856-865.

Jha, V., Roy, B., Jahagirdar, D., McNutt, Z.A., Shatoff, E.A., Boleratz, B.L., Watkins, D.E., Bundschuh, R., Basu, K., Ortega, J. and Fredrick, K. 2021. Structural basis of sequestration of the Anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome. Nucleic Acids Res. 49, 547-567.

Gibbs, M.R., Moon, K-M., Warner, B.R., Chen, M., Bundschuh, R., Foster, L.J., and Fredrick, K. 2020. Functional analysis of BipA in E. coli reveals the natural plasticity of 50S subunit assembly. J. Mol. Biol. 432, 5259-5275.

Chen, M. and Fredrick, K. 2020. RNA polymerase’s relationship with the ribosome: Not so physical, most of the time. J. Mol. Biol. 432, 3981-3986.

Baez, W.D., Roy, B., McNutt, Z.A., Shatoff, E.A., Chen, S., Bundschuh, R. and Fredrick, K. 2019. Global analysis of protein synthesis in Flavobacterium johnsoniae reveals the use of Kozak-like sequences in diverse bacteria. Nucleic Acids Res. 47, 10477-10488. 

Hoffer, E.D., Maehigashi, T., Fredrick, K*, and Dunham, C.M.* 2019. Ribosomal ambiguity (ram) mutations promote the open (off) to closed (on) transition and thereby increase miscoding. Nucleic Acids Res. 47, 1557-1563. (*co-corresponding authors)

Ying, L., Zhu, H., Shoji, S. and Fredrick, K. 2019. Roles of specific aminoglycoside-ribosome interactions in the inhibition of translation. RNA 25, 247-254.

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