Dr. Robert A. Zimmermann
Professor, Biochemistry and Molecular Biology
University of Massachusetts at Amherst
zimmermann@biochem.umass.edu

Ribosome assembly and function, Protein-RNA interactions, Protein synthesis

 
Background and Training

Ph.D.: Massachusetts Institute of Technology
Postdoctoral training: Harvard Medical School; University of Geneva
Honors: Helen Hay Whitney Foundation Fellowship; National Institutes of Health Research Career Development Award; University Faculty Fellowship, Distinguished Faculty Lectureship

Research Summary

The central interests of the Zimmermann laboratory are focused on the structure, function and evolution of ribosomes, the organelles that carry out protein synthesis in all living cells.

The long-term goal of our research is to obtain a detailed description of ligand-ribosome interactions during peptide bond formation and to explore the hypothesis that the ribosome is a dynamic entity whose moving parts promote translation. Although recent high-resolution cryo-EM and crystallographic images provide new insights into the mechanism of translation, these 'snapshots' do not explain how the ribosome interacts with its ligands or how structural changes in the ribosome facilitate this process. Our specific objectives are to define the structural and functional relationships between tRNA and the components of the peptidyl transferase center (PTC) and the exit site (E site) of the E. coli 50S ribosomal subunit, using chemical, biochemical and genetic approaches.

We are presently examining putative differences in the structural organization of the PTC of archaeal and (eu)bacterial ribosomes, as well as possible changes in the position of tRNA relative to 23S rRNA during peptidyl transfer, by qualitative and quantitative analysis of the pattern of short-range, photochemically-induced crosslinks to the PTC from the 3' nucleotide of tRNA at the P and A sites and a transition-state analog that spans both.

Crystallography and tRNA crosslinking have revealed that there is a protein, L27, at or near the PTC of the (eu)bacterial 50S ribosomal subunit, a region that is otherwise composed entirely of RNA. Moreover, deletion of L27 leads to severe defects in translation. We are assessing the functional role of L27 by investigating the effects of specific mutations on cell growth and ribosome activity.

Protein L1 and its associated RNA comprise a flexible and semi-autonomous domain within the 50S subunit that appears to promote the release of deacyated tRNA from the ribosome following peptide bond formation. To test this theory, we are investigating the ability of tRNA to interact with L1-RNA fragment complexes in vitro and the effects of specific mutations in L1 and the adjacent portions of the 23S rRNA on tRNA release in vivo.

Space-filling model of binding site for ribosomal protein S8 in 16S rRNA showing structural features important for protein-RNA interaction identified by nucleotide analog substitution
Representative Publications

Manuilov, A.V., Hixson, S,S,. and Zimmermann, R.A. (2007). Changes in the Orientation of tRNA and 23S rRNA at the Peptidyl Transferase Center of the Ribosome: Crosslinking of a Photoreactive Transition-State Analog, in preparation.

Manuilov, A.V., Hixson, S,S,. and Zimmermann, R.A. (2007). New Photoreactive Derivatives of tRNA for Probing the Peptidyl Transferase Center of the Ribosome, RNA 13, 793-800.

Nevskaya, N., Tishchenko, S., Volchkov, S., Kljashtorny, V., Nikonova. E., Nikonov, O., Nikulin, A., Piendl, W., Zimmermann, R., Garber, M., and Nikonov, S. (2006), New Insights into the Interaction of Ribosomal Protein L1 with RNA, J. Mol. Biol. 355, 747-759.

Maguire, B.A., Beniaminov, A.D. Ramu, P., Mankin, A.S. & Zimmermann, R.A. (2005), A Protein Component at the Heart of an RNA Machine: The Importance of Protein L27 for the Function of the Bacterial Ribosome, Molecular Cell 20, 427-435.

Lavrik, I.N., Sergiev, P.V., Bogdanov, A.A., Zimmermann, R. A. & Dontsova, O.A. (2004), Escherichia coliRibosomes as a Model for Testing New Photoactivated tRNA Analogs Containing 6-Thioguanosine Residues, Molecular Biology38, 937-944.

Zimmermann, R.A. (2003), The Double Life of Ribosomal Proteins, Cell 115, 130-132.

Nikulin, A., Eliseikina, I., Tishchenko, S., Nevskaya, N., Davydova, N., Platonova, O., Piendl, W., Selmer, M., Liljas, A., Drygin, D., Zimmermann, R., Garber, M. & Nikonov, S. (2003), Structure of the L1 Protuberance in the Ribosome, Nature Struct. Biol. 10, 104-108.

Kirillov, S.V., Wower, J., Hixson, S.S. and Zimmermann, R.A. (2002), Transit of tRNA through the Escherichia coli Ribosome: Cross-linking the 3' End of tRNA to Ribosomal Proteins at the P and E Sites, FEBS Lett. 514, 60-66.

Maguire, B.A., Manuilov, A.V. and Zimmermann, R.A. (2001), Differential Effects of Replacing Escherichia coli Ribosomal protein L27 with Its Homologue from Aquifex aeolicus , J. Bact . 183 , 6565-6572.

Maguire, B.A. and Zimmermann, R.A. (2001), The Ribosome in Focus. Cell 104, 813-816.

Drygin, D. and Zimmermann, R.A. (2000), Magnesium Ions Mediate Contacts between Phosphoryl Oxygens at Positions 2122 and 2176 of the 23S rRNA and Ribosomal Protein L1. RNA 6, 1714-1726.

Wower, J., Kirillov, S.V., Wower, I.K., Guven, S., Hixson, S.S. & Zimmermann, R.A. (2000), Transit of tRNA through the Escherichia coli Ribosome: Cross-linking of the 3' End of tRNA to Specific Nucleotides of the 23S Ribosomal RNA at the A, P and E Sites. J. Biol. Chem. 275, 37887-37894.

Zimmermann, R.A., Alimov, I., Uma, K., Wu, H., Wower, I., Nikonowicz, E.P., Drygin, D., Dong, P. & Jiang, L. (2000), How Ribosomal Proteins and rRNA Recognize One Another. In: The Ribosome: Structure, Function, Antibiotics, and Cellular Interactions (R.A. Garrett, S.R. Douthwaite, A. Liljas, A.T. Matheson, P.B. Moore & H.F. Noller, eds.), pp. 93-104. ASM Press, Washington, D.C.

Wower, I.K., Wower, J. and Zimmermann, R.A. (1998) Ribosomal Protein L27 Participates in Both 50S Subunit Assembly and the Peptidyl Transferase Reaction. J. Biol. Chem. 273, 19847-19852.

Zimmermann, R.A., Gait, M.J. and Moore, M.J. (1998) Incorporation of Modified Nucleotides into RNA for Studies on RNA Structure, Function and Intermolecular Interactions. In: Modification and Editing of RNA, pp. 59-84. (H. Grosjean & R. Benne, eds.). ASM Press, Washington, D.C.

Kalurachchi, K., Uma, K., Zimmermann, R.A. and Nikonowicz, E.P. (1997) Structural Features of the Binding Site for Ribosomal Protein S8 in Escherichia coli 16S rRNA Defined Using NMR Spectroscopy. Proc. Natl. Acad. Sci. USA 94, 2139-2144.

O’Connor, M., Thomas, C.L., Zimmermann, R.A. and Dahlberg, A.E. (1997) Decoding Fidelity at the Ribosomal A and P Sites: Influence of Mutations in Three Different Regions of the Decoding Domain in 16S rRNA. Nucleic Acids Res. 25, 1185-1193.

Rosen, K.V. and Zimmermann, R.A. (1997) Photoaffinity Labeling of 30S-Subunit Proteins S7 and S11 by 4-Thiouridine-substituted tRNAPhe Situated at the P Site of Escherichia coli Ribosomes. RNA 3, 1028-1036.