Harry Noller

Harry Noller
Professor of MCD Biology
Robert L. Sinsheimer Prof. of Molecular Biology
Director, Center for Molecular Biology of RNA
A.B., University of California, Berkeley
Ph.D., University of Oregon
1965-66 Natl Inst of Health Postdoctoral Fellow,
MRC Laboratory of Molecular Biology, Cambridge
1966-68 Natl Inst of Health Postdoctoral Fellow, Inst of Molecular Biology, Univ of Geneva, Switzerland

Ribosome Structure and Function
Ribosomes are complex molecular machines that are responsible for carrying out protein synthesis – translation of the genetic code. Their structures are highly conserved, and fundamentally similar in all organisms. A major question is, why do ribosomes contain such large amounts of RNA (50-60% of their mass)? It has gradually become clear that ribosomal RNA itself is centrally involved in translation, and may be a relic of the RNA World, a period of early molecular evolution when it is proposed that RNA carried out the genomic and catalytic roles of DNA and protein.

The Noller laboratory studies ribosome structure and function using a wide range of approaches, including X-ray crystallography, chemical probing methods, molecular genetics, comparative sequence analysis, fluorescence resonance energy transfer (FRET), including the use of single-molecule methods.  The ultimate goal of these studies is to understand how the ribosome works at the molecular level: what are the moving parts of the machine, and how do they move in three dimensions to enable translation?

X-ray Crystal Structure of the Ribosome
We have recently solved the structure of the whole 70S ribosome from Thermus thermophilus at a resolution of 3.7 Angstroms. This has enabled us to describe all of the detailed molecular interactions of the ribosome, including ones involving the ribosomal RNAs, ribosomal proteins, tRNAs and mRNA. This provides a molecular basis for beginning to address the important functional questions. Our next goals for crystallography are to solve the structures of the ribosome trapped in different intermediate states of translation, including complexes containing elongation factors and other components.

Movement Inside the Translational Engine
On the basis of chemical footprinting results, we realized that the tRNAs move on the ribosome during the translocation step of protein synthesis in two steps: first they move at their acceptor CCA ends on the large ribosomal subunit, and then they move at their anticodon ends on the small subunit. We believe that both steps are catalyzed by the elongation factor EF-G, but the second step depends on GTP hydrolysis. We want to understand how the interactions between EF-G and the ribosomal machinery results in movement of the tRNAs and mRNA during translation. Clues from structural studies and from biochemical experiments implicate certain molecular features of ribosomal RNA (but also ribosomal proteins) in this movement. We are using chemical probing, FRET and mutational alteration of RNA and proteins to address these questions.

Functional Interactions of Translational Factors with the Ribosome
During protein synthesis, the ribosome interacts with initiation factors, elongation factors, release factors and ribosome recycling factor. Little is understood about their molecular interactions with the ribosome, and what they actually do to help the ribosome through the translational cycle. We are using chemical footprinting and directed hydroxyl radical probing to position the factors on the ribosome, and fluorescence methods to catch them in action. We are also attempting to crystallize complexes of the ribosome bound to the factors. Since most factor-catalyzed functions can be carried out by the ribosome itself under certain conditions, it is likely that these are all fundamentally mechanisms of the ribosome, whose rates and accuracy are increased by the factors.

RECENT PUBLICATIONS

 For a full list of publications, please follow this link.

Noller, H.F. 2013.  By Ribosome Possessed.  J. Biol. Chem. 288:24872-24885.

Zhou, J., Lancaster, L., Donohue, J.P. and Noller, H.F. 2013. Crystal Structures of EF-G-Ribosome Complexes Trapped in Intermediate States of Translocation. Science  340:1236086

Guo, Z. and Noller, H.F. 2012. Rotation of the head of the 30S ribosomal subunit during mRNA translocation. Proc Natl Acad Sci U S A 109:20391-20394.

Zhou J, Korostelev A, Lancaster L and Noller HF. 2012. Crystal structures of 70S ribosomes bound to release factors RF1, RF2 and RF3. Curr Opin Struct Biol. 2012 22:733-742

Qu, X., Lancaster, L., Noller, H.F., Bustamante, C. and Tinoco, I., Jr. 2012. Ribosomal protein S1 unwinds double-stranded RNA in multiple steps. Proc Natl Acad Sci U S A 109:14458-14463.

Zhou, J., Lancaster, L., Trakhanov, S. and Noller, H.F.  2011. Crystal Structure of Release Factor RF3 Trapped in the GTP state on a rotated conformation of the ribosome.  RNA 18:230-240.

Qu, X., Wen, J.D., Lancaster, L., Noller, H.F., Bustamante, C., and Tinoco, I., Jr.  2011. The ribosome uses two active mechanisms to unwind messenger RNA during translation. Nature 475: 118-121.

Zhu, J., Korostelev, A., Costantino, D.A., Donohue, J.P., Noller, H.F. and Kieft, J.S. 2011. Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome. Proc Natl Acad Sci USA 108:1839-1844.

Ermolenko, D.N. and Noller, H.F. 2011. mRNA Translocation Occurs During the Second Step of Ribosomal Intersubunit Rotation. Nat Struct Mol Biol 18:457-462.

Korostelev, A., Zhu, J., Asahara, H. and Noller, H.F. 2010. Recognition of the amber UAG stop codon by release factor RF1. EMBO J 29:2577-85.

Korostelev, A., Laurberg, M., and Noller, H.F. 2009. Multistart simulated annealing refinement of the crystal structure of the 70S ribosome. Proc Natl Acad Sci USA 106:18195-18200.

Cornish, P.V., Ermolenko, D.N., Staple, D.W., Hoang, L., Hickerson, R., Noller, H.F. and Ha, T. 2009. Following Movement of the L1 Stalk Between Three Functional States in Single Ribosomes. Proc Natl Acad Sci USA 106:2571-2576.

Korostelev, A., Asahara, H., Lancaster, L., Laurberg, M. Hirschi, A., Zhu, J., Trakhanov, S., Scott, W. and Noller, H.F. 2008. Crystal Structure of a Translation Termination Complex Formed with Release Factor RF2. Proc Natl Acad Sci USA 105:19684-19689.

Korostelev, A., Ermolenko, D.N. and Noller, H.F. 2008. Structural Dynamics of the Ribosome. Curr Opin Chem Biol 12:674-83

Lancaster, L., Lambert, N.J., Maklan, E.J., Horan, L.H and Noller, H.F. 2008. The sarcin-ricin loop of 23S rRNA is essential for assembly of the functional core of the 50S ribosomal subunit.  RNA 14:1-14.

Martick, M., Horan, L., Noller, H., and Scott, W.G. 2008.  A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNA.  Nature 454:899-903.

Laurberg, M., Asahara, H., Korostelev, A., Zhu, J., Trakhanov, S. and Noller, H.F. 2008. Structural basis for translation termination on the 70S ribosome. Nature 454:852-857.

Wen, J.D., Lancaster, L., Hodges, C., Zeri, A.C., Yoshimura, S.H., Noller, H.F., Bustamante, C., and Tinoco, I. 2008.  Following translation by single ribosomes one codon at a time.  Nature 452:598-603.

Cornish, P.V., Ermolenko, D.N., Noller, H.F., and Ha, T. 2008.  Spontaneous intersubunit rotation in single riboomes. Mol Cell 30:578-88.