faculty

Assistant Professor of Chemistry
Ph.D., Stanford University

Biochemistry

Phone:  (734) 615 2867   
E-mail: kkarbst@umich.edu

Research Group

We use a combination of approaches - including biochemistry, mechanistic enzymology, biophysics, chemical biology, protein engineering and yeast genetics - to study eukaryotic ribosome assembly at the molecular level. Our ultimate goal is to understand the function of assembly factors, the order of events as well as the rationale for this order, aiming to delineate principles important for the assembly of other large RNA-protein complexes, such as the spliceosome or the signal recognition particle.

Ribosomes are large macromolecular machines that catalyze protein synthesis in all cells. Groundbreaking work in bacteria has provided insight into the order of binding of ribosomal proteins to ribosomal RNA (rRNA) and has given a structural and thermodynamic rationale for this order. However, in eukaryotic cells the assembly process is much more complex, requiring a macromolecular machinery of >170 proteins and >70 RNAs. While we know that this machinery is absolutely essential, we have little understanding of the function of the individual players. By taking a biochemical approach to study these proteins, which is complimented by in vivo work in the yeast S. cerevisiae, we are pioneering the study of macromolecular function of these proteins. To tackle this fascinating problem we have focused on subcomplexes and their functions. Specific available projects include:

1. Investigating the Fap7's ATPase Cycle Using FRET Experiments.

Fap7 is an essential ATPase, required for the final step of small subunit assembly. We have devised a biochemical system to study the function of this protein that indicates that ATP binding and hydrolysis is intricately linked to conformational changes in the protein. We want to use fluorescence resonance energy transfer (FRET) to further characterize these conformational changes in an effort to understand their function during ribosome assembly.

2. Discovering the Endonuclease that Separates Assembly of the Small and Large Subunits.

While eight endonucleolytic steps have been identified to be required for ribosome assembly only two endonucleases have been identified, and all other nucleases remain mysterious. Rcl1 has been suggested to be an endonuclease required for a crucial step in ribosome assembly. We have recently established a biochemical and genetic system to test this proposal.

3. Molecular Architecture of Ribosome Assembly Complexes.  

We have purified > 12 essential proteins required for ribosome assembly. We would like to test pair wise and higher order interactions between these proteins in order to understand how they interact to form the ribosome assembly complexes. This will then be used to further test the role of binding partners on the biochemical and enzymatic activities of our proteins.

AWARDS

• UM Biological Scholar (2006)
• Damon Runyon Postdoctoral Fellow (2003)
• Boehringer Ingelheim Predoctoral Fellow (1998)
• Heinrich Hertz Fellow (1997)

REPRESENTATIVE PUBLICATIONS

1. Karbstein, K. (in the press) Eukaryotic Ribosome Assembly. Wiley Encyclopedia of Chemical Biology

2. Todd, G.C. and Karbstein, K. (2007) RNA takes center stage. Biopolymers 87, 275-278.

3. Karbstein, K. (2007) GTPases in ribosome assembly. Biopolymers 87 1-11.

4. Karbstein, K., Lee, J. and Herschlag, D. (2007) Probing the Role of a Secondary Structure Element at the 5'- and 3'-Splice Sites in Group I Intron Self-splicing: The Tetrahymena   L-16 Sca I Ribozyme Reveals a New Role of the G^.U Pair in Self-splicing. Biochemistry 46, 4861-75 .

5. Karbstein, K., and Doudna, J. A. (2006) GTP-dependent Formation of a Ribonucleoprotein Subcomplex Required for Ribosome Biogenesis. Journal of Molecular Biology 356, 432-443.

6. Karbstein, K., Jonas, S. and Doudna, J. A. (2005) An essential GTPase promotes assembly of ribosomal processing complexes. Molecular Cell 20, 633-643. [Preview by Dutca & Culver Molecular Cell 20, 497-499.]

7. Karbstein, K., and Doudna, J. A. (2004) RNA: Primed for Packing? Chemistry & Biology 11, 149-151.

8. Karbstein, K., Tang, K. H. and Herschlag, D. (2004) A Base Triple in the Tetrahymena Group I Core Affects the Reaction Equilibrium via a Threshold Effect. RNA 10, 1730-1739.

9. Karbstein, K., and Herschlag, D. (2003) Extraordinarily Slow Binding of Guanosine to the Tetrahymena Group I Ribozyme: Implications for RNA Preorganization and Function. Proceedings of the National Academy of Sciences 100, 2300-2305.

10. Wang, S.L., Karbstein, K., Peracchi, A., Beigelman, L., and Herschlag, D. (1999) Identification of the Hammerhead Ribozyme Metal Ion Binding Site that Rescues the Deleterious Effect of a Cleavage Site Phosphorothioate. Biochemistry 38, 14363-14378.