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Karbstein, Katrin
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Karbstein, Katrin

Faculty Member
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Positions

  • 2017 - Associate Professor, Integrative Structural and Computational Biology (ISCB) , Scripps Research
  • 2017 - Associate Professor (Joint Appointment), Molecular Medicine , Scripps Research
  • 2013 - 2017 Associate Professor (Joint Appointment), Cell and Molecular Biology (CMB) , Scripps Research
  • 2012 - 2017 Associate Professor, Cancer Biology , Scripps Research
  • 2010 - 2012 Assistant Professor, Cancer Biology , Scripps Research
Dr. Karbstein studies the function of essential proteins involved in the assembly of the 40S ribosomal subunit using a variety of biochemical, genetic, kinetic and biophysical techniques.

Contact

  • kkarbst@scripps.edu

Websites

  • Katrin Karbstein, Ph.D.
  • Publications
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Publications

recent publications
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  • Publications without PubMed PMIDs

  • academic article

    • Huang, H., Karbstein, K. Assembly factors chaperone ribosomal RNA folding by isolating helical junctions that are prone to misfolding Proceedings of the National Academy of Sciences of the United States of America  2021 118  DOI:10.1073/pnas.2101164118  PMID:34135123  PMCID:PMC8237570
    • Rai, J., Parker, M. D., Huang, H., Choy, S., Ghalei, H., Johnson, M. C., Karbstein, K., Stroupe, M. E. An open interface in the pre-80S ribosome coordinated by ribosome assembly factors Tsr1 and Dim1 enables temporal regulation of Fap7 RNA  2020 27:221-233  DOI:10.1261/rna.077610.120  PMID:33219089  PMCID:PMC7812869
    • Huang, H., Ghalei, H., Karbstein, K. Quality control of 40S ribosome head assembly ensures scanning competence Journal of Cell Biology  2020 219  DOI:10.1083/jcb.202004161  PMID:33007085  PMCID:PMC7534925
    • Parker, M. D., Collins, J. C., Korona, B., Ghalei, H., Karbstein, K. A kinase-dependent checkpoint prevents escape of immature ribosomes into the translating pool PLoS Biology  2019 17  DOI:10.1371/journal.pbio.3000329; 10.1371/journal.pbio.3000329.r001; 10.1371/journal.pbio.3000329.r002; 10.1371/journal.pbio.3000329.r003; 10.1371/journal.pbio.3000329.r004; 10.1371/journal.pbio.3000329.r005; 10.1371/journal.pbio.3000329.r006  PMID:31834877  PMCID:PMC6934326
    • Yin, Z., Liu, X., Ariosa, A., Huang, H., Jin, M., Karbstein, K., Klionsky, D. J. Psp2, a novel regulator of autophagy that promotes autophagy-related protein translation Cell Research  2019 29:994-1008  DOI:10.1038/s41422-019-0246-4  PMID:31666677  PMCID:PMC6951345
    • Karbstein, K. Mitochondria teach ribosome assembly Science  2019 365:1077-1078  DOI:10.1162/science.aay7771  PMID:31515371
    • Khoshnevis, S., Liu, X., Dattolo, M. D., Karbstein, K. Rrp5 establishes a checkpoint for 60S assembly during 40S maturation RNA  2019 25:1164-1176  DOI:10.1261/rna.071225.119  PMID:31217256
    • Ferretti, M. B., Karbstein, K. Does functional specialization of ribosomes really exist? RNA  2019 25:521-538  DOI:10.1261/rna.069823.118  PMID:30733326  PMCID:PMC6467006
    • Karbstein, K. Responsible peer review ACS Chemical Biology  2018 13:3217-3218  DOI:10.1021/acschembio.8b01035
    • Collins, J. C., Ghalei, H., Doherty, J. R., Huang, H., Culver, R. N., Karbstein, K. Ribosome biogenesis factor Ltv1 chaperones the assembly of the small subunit head Journal of Cell Biology  2018 217:4141-4154  DOI:10.1083/jcb.201804163  PMID:30348748  PMCID:PMC6279377
    • Ferretti, M. B., Barre, J. L., Karbstein, K. Translational reprogramming provides a blueprint for cellular adaptation Cell Chemical Biology  2018 25:1372-1379  DOI:10.1016/j.chembiol.2018.08.003  PMID:30174311  PMCID:PMC6239892
    • Ferretti, M. B., Ghalei, H., Ward, E. A., Potts, E. L., Karbstein, K. Rps26 directs mRNA-specific translation by recognition of Kozak sequence elements Nature Structural & Molecular Biology  2017 24:700-707  DOI:10.1038/nsmb.3442  PMID:28759050
    • Johnson, M. C., Ghalei, H., Doxtader, K. A., Karbstein, K., Stroupe, M. E. Structural heterogeneity in pre-40S ribosomes Structure  2017 25:329-340  DOI:10.1016/j.str.2016.12.011  PMID:28111018  PMCID:PMC5314460
    • Ghalei, H., Trepreau, J., Collins, J. C., Bhaskaran, H., Strunk, B. S., Karbstein, K. The ATPase Fap7 tests the ability to carry our translocation-like conformational changes and releases Dim1 during 40S ribosome maturation Molecular Cell  2017 67:990-1000  DOI:10.1016/j.molcel.2017.08.007  PMID:28890337
    • Khoshnevis, S., Askenasy, I., Johnson, M. C., Dattolo, M. D., Young-Erdos, C. L., Stroupe, M. E., Karbstein, K. The DEAD-box protein Rok1 orchestrates 40S and 60S ribosome assembly by promoting the release of Rrp5 from pre-40S ribosomes to allow for 60S maturation PLoS Biology  2016 14  DOI:10.1371/journal.pbio.1002480  PMID:27280440  PMCID:PMC4900678
    • Karbstein, K. What will the future hold: RNP quality control and degradation RNA-a Publication of the RNA Society  2015 21:657-658  DOI:10.1261/rna.050658.115  PMID:25780179  PMCID:PMC4371321
    • Ghalei, H., Schaub, F. X., Doherty, J. R., Noguchi, Y., Roush, W. R., Cleveland, J. L., Stroupe, M. E., Karbstein, K. Hrr25/CK1 delta-directed release of Ltv1 from pre-40S ribosomes is necessary for ribosome assembly and cell growth Journal of Cell Biology  2015 208:745-759  DOI:10.1083/jcb.201409056  PMID:25778921  PMCID:PMC4362465
    • Tyagi, R., Shahani, N., Gorgen, L., Ferretti, M., Pryor, W., Chen, P. Y., Swarnkar, S., Worley, P. F., Karbstein, K., Snyder, S. H., Subramaniam, S. Rheb inhibits protein synthesis by activating the PERK-eIF2 alpha signaling cascade Cell Reports  2015 10:684-693  DOI:10.1016/j.celrep.2015.01.014  PMID:25660019  PMCID:PMC4524804
    • de la Cruz, J., Karbstein, K., Woolford Jr., J. L. Functions of ribosomal proteins in assembly of eukaryotic ribosomes in vivo Annual Review of Biochemistry  2015 84:93-129  DOI:10.1146/annurev-biochem-060614-033917  PMID:25706898  PMCID:PMC4772166
    • Young, C. L., Khoshnevis, S., Karbstein, K. Cofactor-dependent specificity of a DEAD-box protein Proceedings of the National Academy of Sciences of the United States of America  2013 110:E2668-E2676  DOI:10.1073/pnas.1302577110  PMID:23630256  PMCID:PMC3718167
    • Karbstein, K. Quality control mechanisms during ribosome maturation Trends in Cell Biology  2013 23:242-250  DOI:10.1016/j.tcb.2013.01.004  PMID:23375955  PMCID:PMC3640646
    • Strunk, B. S., Novak, M. N., Young, C. L., Karbstein, K. A translation-like cycle is a quality control checkpoint for maturing 40s ribosome subunits Cell  2012 150:111-121  DOI:10.1016/j.cell.2012.04.044  PMID:22770215  PMCID:PMC3615461
    • Young, C., Karbstein, K. Analysis of cofactor effects on RNA helicases Methods in Enzymology  2012 511:213-237  DOI:10.1016/b978-0-12-396546-2.00010-3  PMID:22713322
    • Karbstein, K. Inside the 40s ribosome assembly machinery Current Opinion in Chemical Biology  2011 15:657-663  DOI:10.1016/j.cbpa.2011.07.023  PMID:21862385  PMCID:PMC3329787
    • Horn, D. M., Mason, S. L., Karbstein, K. Rcl1 protein, a novel nuclease for 18 S ribosomal RNA production Journal of Biological Chemistry  2011 286:34082-34087  DOI:10.1074/jbc.M111.268649  PMID:21849504  PMCID:PMC3190816
    • Strunk, B. S., Loucks, C. R., Su, M., Vashisth, H., Cheng, S. S., Schilling, J., Brooks, C. L., Karbstein, K., Skiniotis, G. Ribosome assembly factors prevent premature translation initiation by 40S assembly intermediates Science  2011 333:1449-1453  DOI:10.1126/science.1208245  PMID:21835981  PMCID:PMC3402165
    • Young, C. L., Karbstein, K. The roles of S1 RNA-binding domains in Rrp5's interactions with pre-rRNA RNA-a Publication of the RNA Society  2011 17:512-521  DOI:10.1261/rna.2458811  PMID:21233221  PMCID:PMC3039150
    • Woolls, H. A., Lamanna, A. C., Karbstein, K. Roles of Dim2 in ribosome assembly Journal of Biological Chemistry  2011 286:2578-2586  DOI:10.1074/jbc.M110.191494  PMID:21075849  PMCID:PMC3024753
    • Campbell, M. G., Karbstein, K. Protein-protein interactions within late pre-40S ribosomes PLoS One  2011 6:e16194  DOI:10.1371/journal.pone.0016194  PMID:21283762  PMCID:PMC3024409
    • Lamanna, A. C., Karbstein, K. An RNA conformational switch regulates pre-18S rRNA cleavage Journal of Molecular Biology  2011 405:3-17  DOI:10.1016/j.jmb.2010.09.064  PMID:20934433  PMCID:PMC3006654
    • Karbstein, K. Chaperoning ribosome assembly Journal of Cell Biology  2010 189:11-12  DOI:10.1083/jcb.201002102  PMID:20368615  PMCID:PMC2854375
    • Strunk, B. S., Karbstein, K. Powering through ribosome assembly RNA-a Publication of the RNA Society  2009 15:2083-2104  DOI:10.1261/rna.1792109  PMID:19850913  PMCID:PMC2779681
    • Lamanna, A. C., Karbstein, K. Nob1 binds the single-stranded cleavage site d at the 3 '-end of 18s rRNA with its pin domain Proceedings of the National Academy of Sciences of the United States of America  2009 106:14259-14264  DOI:10.1073/pnas.0905403106  PMID:19706509  PMCID:PMC2732849
    • Todd, G., Karbstein, K. RNA takes center stage Biopolymers  2007 87:275-278  DOI:10.1002/bip.20824  PMID:17688253
    • Karbstein, K. Role of GTPases in ribosome assembly Biopolymers  2007 87:1-11  DOI:10.1002/bip.20762  PMID:17514744
    • Coppola, B. P., Holl, M. M. B., Karbstein, K. Closing the gap between interdisciplinary research and disciplinary teaching ACS Chemical Biology  2007 2:518-520  DOI:10.1021/cb7001544  PMID:17708666
    • Karbstein, K., Lee, J., Herschlag, D. 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 ScaI ribozyme reveals a new role of the G.U pair in self-splicing Biochemistry  2007 46:4861-4875  DOI:10.1021/bi062169g  PMID:17385892  PMCID:PMC2597287
    • Karbstein, K., Doudna, J. A. GTP-dependent formation of a ribonucleoprotein subcomplex required for ribosome biogenesis Journal of Molecular Biology  2006 356:432-443  DOI:10.1016/j.jmb.2005.11.052  PMID:16376378
    • Karbstein, K., Jonas, S., Doudna, J. A. An essential GTpase promotes assembly of preribosomal RNA processing complexes Molecular Cell  2005 20:633-643  DOI:10.1016/j.molcel.2005.09.017  PMID:16307926
    • Karbstein, K., Tang, K. H., Herschlag, D. A base triple in the tetrahymena group i core affects the reaction equilibrium via a threshold effect RNA-a Publication of the RNA Society  2004 10:1730-1739  DOI:10.1261/rna.7118104  PMID:15496521  PMCID:PMC1370661
    • Karbstein, K., Doudna, J. A. RNA: Primed for packing? Chemistry & Biology  2004 11:149-151  DOI:10.1016/j.chembiol.2004.02.007  PMID:15123272
    • Karbstein, K., Herschlag, D. Extraordinarily slow binding of guanosine to the Tetrahymena group I ribozyme: Implications for RNA preorganization and function Proceedings of the National Academy of Sciences of the United States of America  2003 100:2300-2305  DOI:10.1073/pnas.252749799  PMID:12591943  PMCID:PMC151335
    • Karbstein, K., Carroll, K. S., Herschlag, D. Probing the Tetrahymena group I ribozyme reaction in both directions Biochemistry  2002 41:11171-11183  DOI:10.1021/bi0202631  PMID:12220182
    • Wang, S. L., Karbstein, K., Peracchi, A., Beigelman, L., Herschlag, D. Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate Biochemistry  1999 38:14363-14378  DOI:10.1021/bi9913202  PMID:10572011
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Research

research overview

  • Unraveling Ribosome Assembly

    Ribosomes are large macromolecular machines that catalyze protein synthesis in all cells. In eukaryotic cells ribosome assembly requires a macromolecular machinery of >170 proteins and >70 RNAs. While we know that this machinery is absolutely essential for life, we have little understanding of the function of the individual players. To shed light on the function of these assembly factors, we use a combination of approaches – including biochemistry, mechanistic enzymology, yeast genetics, structural biology, and protein engineering. We have focused on assembly of the 40S subunit and have developed a recombinant system that recapitulates the final steps in assembly. This system now allows us to uncover new steps and dissect the role of individual proteins in these steps. 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 general principles important for the assembly of large RNA-protein complexes.

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Teaching

advisees

  • graduate advising relationship

    • Huang, Haina, Ph.D.  candidate, 2017 -
    • Parker, Melissa Danielle, Ph.D.  candidate, 2016 -
    • Salatino, Roberto Modesto, Ph.D.  candidate, 2018 -
    • Ferretti, Max, Ph.D.  candidate, 2013 - 2018
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Background

education and training

  • Ph.D. in Biochemistry, Stanford University 2003
  • Diploma in Biochemistry, Witten/Herdecke University 1998
  • Diploma in Chemistry, Ruhr University Bochum , (Voridplom) 1995
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Contact

full name

  • Katrin Karbstein

geographic location

  • Scripps Florida 
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Identity

ORCID iD

  • ORCID iD http://orcid.org/0000-0002-4034-1331

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