The Central Dogma, One Molecule at a Time
Our general goal is to understand the biological functions of macromolecules in terms of their detailed molecular structure. Of particular interest are the molecular mechanisms by which those proteins and nucleic acids involved in the central dogma of molecular biology (DNA replication, transcription, translation and genetic recombination) achieve their biological function. Virtually all aspects of the maintenance, rearrangement and expression of information stored in the genome involve interactions between proteins and nucleic acids.
Our recent accomplishments have included the determination of the atomic structure of the 50S ribosomal subunit and its complexes with substrate, intermediate and product analogues as well as complexes with about two dozen antibiotics. These structures establish that the ribosome is a ribozyme, provide insights into the mechanism of peptide bond formation and show how several classes of antibiotics function. We are now obtaining structures of the 70S ribosome captured in various states and including protein factors. In the area of transcription, six structures of T7 RNA polymerase captured in various functional states show the structural basis of the transition from the initiation to elongation phase, which involves a large protein structural rearrangement. They explain the basis of promoter clearance, processivity of the elongation phase, translocation and strand separation. The structures of the CCA-adding enzyme captured in each state of CCA incorporation onto tRNA explain the enzyme’s specificity for nucleotide incorporation in the absence of a nucleic acid template. The structure of a recombination intermediate of γδ resolvase suggests that site specific recombination by this enzyme is achieved by subunit rotation. Insights into the structural basis of DNA replication are emerging from our structures of the Pol III DNA polymerase as well as that of the phage φ29 DNA polymerase in complexes with substrates and with the priming protein. Also, the first structures of the primasome containing the helicase and a fragment of the primase provide a model for primasome function.
Future directions will focus on the complex macromolecular assemblies that are the functional machines in these processes, including the ribosome and the replisome. For example, we wish to establish the atomic structures of the ribosome captured in the act of protein synthesis in each of its conformational states with elongation factors as well as interacting with the proteins involved in protein secretion. Likewise, a mechanistic understanding of replication and recombination will require structures of the assemblies in each step of their functioning. Hypotheses arising from these structures will be tested using site directed mutagenesis and biochemical studies to relate structure to function.
Liu, B., Hong, C., Huang, R.K., Yu, Z., Steitz, T.A. (2017). Structural basis of bacterial transcription activation. Science 358, 947-951. PubMed
Zuo, Y., Steitz, T.A. (2015). Crystal structures of the E. coli transcription initiation complexes with a complete bubble. Mol Cell 58(3), 534-540. PubMed
Lin, J., Gagnon, M.G., Bulkley, D., Steitz, T.A. (2015). Conformational changes of elongation factor G on the ribosome during tRNA translocation. Cell 160, 219-227.PubMed
Gagnon, M.G., Lin, J., Bulkley, D., Steitz, T.A. (2014). Crystal structure of elongation factor 4 bound to a clockwise ratcheted ribosome. Science 345, 684-687. PubMed
Lomakin, I., Steitz, T.A. (2013). The initiation of mammalian protein synthesis and mRNA scanning mechanism. Nature 500, 307-311. PubMed
Zuo, Y., Wang, Y., Steitz, T.A. (2013). The mechanism of E. coli RNA polymerase regulation by ppGpp is suggested by the structure of their complex. Mol Cell 50(3), 430-436. PubMed
Polikanov, Y.I., Blaha, G.M. Steitz, T.A. (2012). How Hibernation Factors RMF, HPF, and YfiA Turn Off Protein Synthesis Science 336, 915-918. PubMed
Itsathitphaisarn, O., Wing, R.A., Eliason, W.K., Wang, J., Steitz, T.A. (2012). The Hexameric Helicase DnaB Adopts a Nonplanar Conformation during Translocation. Cell 151, 267-277. PubMed
Gagnon, M.G., Seetharaman, S.V., Bulkley, D., Steitz, T.A. (2012). Structural basis for the rescue of stalled ribosomes: structure of YaeJ bound to the ribosome. Science 335, 1370-1372. PubMed
Mitton-Fry, R.M., DeGregorio, S.J., Wang, J., Steitz, T.A., Steitz, J.A. (2010). Poly(A) tail recognition by a viral RNA element through assembly of a triple helix. Science 330, 1244-1247. PubMed
Pan, B., Xiong, Y., Steitz, T.A. (2010). How the CCA-adding enzyme selects adenine over cytosine at position 76 of tRNA.Science 330, 937-940. PubMed
Seidelt, B., Innis, C.A., Wilson, D.N., Gartmann, M., Armache, J.P., Villa, E., Trabuco, L.G., Becker, T., Mielke, T., Schulten, K., Steitz, T.A., Beckmann, R. (2009). Structural insight into nascent polypeptide chain-mediated translational stalling.Science 326, 1412-1415. PubMed
Blaha, G., Stanley, R.E., Steitz, T.A. (2009). Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome. Science 325, 966-970. PubMed
Palioura, S., Sherrer, R.L., Steitz, T.A., Soll, D., Simonovic, M. (2009). The human SepSecS-tRNASec complex reveals the mechanism of selenocysteine formation. Science 325, 321-325. PubMed
Durniak, K.J., Bailey, S., Steitz, T.A. (2008). The structure of a transcribing T7 RNA polymerase in transition from initiation to elongation. Science 322, 553-557. PubMed
Bailey, S. Eliason, W.K., Steitz, T.A. (2007). Structure of hexameric DnaB helicase and its complex with a domain of DnaG primase. Science 318, 459-463. PubMed
Lomakin, I.B., Xiong, Y., Steitz, T.A. (2007). The crystal structure of yeast fatty acid synthase, a cellular machine with eight active sites working together. Cell 129, 319-332.PubMed
Bailey, S., Wing, R.A., Steitz, T.A. (2006). The structure of T. aquaticus DNA polymerase III is distinct from eukaryotic replicative DNA polymerases. Cell 126, 893-904. PubMed
Li, W., Kamtekar, S., Xiong, Y., Sarkis, G.J., Grindley, N.D.F., Steitz, T.A. (2005). Structure of a synaptic γδ resolvase tetramer covalently linked to two cleaved DNAs. Science 309, 1210-1215. PubMed
Tu, D., Blaha, G., Moore, P.B., Steitz, T.A. (2005). Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance. Cell121, 257-270. PubMed
Schmeing, T.M., Huang, K.S., Strobel, S.A., Steitz, T.A. (2005). An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA. Nature 438, 520-524. PubMed
A complete list of publications can be found HERE.