Structure and function of SRP RNA

Summary

Principal Investigator: C Zwieb
Affiliation: University of Texas Health Center
Country: USA
Abstract: The objective of this research proposal is to advance the molecular understanding of the basic process of protein transport across biological membranes. Our particular focus is on the signal recognition particle (SRP) as it plays a central role in protein targeting and secretion. The SRP RNA is an essential component of every SRP and contains several conserved features of functional importance. The goal of our research is to understand the structural and functional role of this RNA in the human system. We will define those regions of the human SRP RNA which are involved in SRP-mediated protein secretion and SRP assembly by using a combination of site-directed mutagenesis, site-directed cross-linking, structure probing, comparative analyses, biochemical, and biophysical studies. The major topics to be investigated are: (1) Mechanisms that involve SRP RNA in SRP assembly, signal recognition, and protein translocation. Complexes will be reconstituted from recombinant components to study the formation of the SRP and translocation competence of secretory proteins. The effects of altered complexes on individual events in the SRP-cycle, such as signal peptide recognition, translation arrest, and release of the arrest, will be identified. (2) Structural and functional role of proteins SRP68 and SRP72 within the human SRP. The interactions of SRP RNA with SRP68 and SRP72 will be studied by systematic site-directed mutagenesis. RNA-protein neighborhoods will be determined by using site-directed photochemical cross-linking followed by the identification of the cross-linked nucleotides and amino acids. The data from these experiments will be viewed collectively and used to generate a three-dimensional molecular model of human SRP. (3) Biophysical characterization of the M-domain of SRP54 which binds to the SRP RNA helix 8 and the signal as well as of recombinant signal fusion protein derivatives (SFPs) manipulated to contain altered signal peptides. These studies will focus on the specific features of two critical interactions and define their dynamic relationship to SRP function.
Funding Period: 1995-01-01 - 2008-04-30
more information: NIH RePORT

Top Publications

  1. ncbi Identification of the RNA binding regions of SRP68/72 and SRP72 by systematic mutagenesis of human SRP RNA
    Jiaming Yin
    Department of Molecular Biology, University of Texas Health Science Center at Tyler, Tyler, Texas, USA
    RNA Biol 4:154-9. 2007
  2. ncbi Structural transitions of the RING1B C-terminal region upon binding the polycomb cbox domain
    Renjing Wang
    Department of Biochemistry, University of Texas Health Science Center at San Antonio, MSC 7760, 7703 Floyd Curl Drive, San Antonio, Texas 78229 3900, USA
    Biochemistry 47:8007-15. 2008
  3. ncbi A. fulgidus SRP54 M-domain
    Udayar Ilangovan
    Department of Biochemistry, Allied Health Building/Biochemistry, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA
    J Biomol NMR 41:241-8. 2008
  4. ncbi Identification of an RNA-binding domain in human SRP72
    Elena Iakhiaeva
    Department of Molecular Biology, The University of Texas Health Science Center at Tyler, 11937 US Highway 271, Tyler, TX 75708 3154, USA
    J Mol Biol 345:659-66. 2005
  5. ncbi Characterization of the SRP68/72 interface of human signal recognition particle by systematic site-directed mutagenesis
    Elena Iakhiaeva
    Department of Molecular Biology, University of Texas Health Science Center at Tyler, 75708, USA
    Protein Sci 18:2183-95. 2009
  6. ncbi Making the jump: new insights into the mechanism of trans-translation
    Jacek Wower
    Department of Animal Sciences, Auburn University, Auburn, AL 36849, USA
    J Biol 7:17. 2008
  7. ncbi The 5e motif of eukaryotic signal recognition particle RNA contains a conserved adenosine for the binding of SRP72
    Elena Iakhiaeva
    Department of Molecular Biology, University of Texas Health Science Center at Tyler, Tyler, Texas 75708 3154, USA
    RNA 14:1143-53. 2008
  8. ncbi Schistosoma mansoni: TGF-beta signaling pathways
    Philip T LoVerde
    Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229 3900, USA
    Exp Parasitol 117:304-17. 2007
  9. ncbi Protein SRP68 of human signal recognition particle: identification of the RNA and SRP72 binding domains
    Elena Iakhiaeva
    Department of Molecular Biology, University of Texas Health Science Center at Tyler, Tyler, Texas 75708 3154, USA
    Protein Sci 15:1290-302. 2006
  10. ncbi The tmRDB and SRPDB resources
    Ebbe Sloth Andersen
    Department of Molecular Biology, University of Aarhus, C F Moellers Alle, Building 139, 8000 Aarhus, Denmark
    Nucleic Acids Res 34:D163-8. 2006

Scientific Experts

  • C Zwieb
  • Jody Burks
  • Philip T LoVerde
  • Elena Iakhiaeva
  • Jacek Wower
  • Jiaming Yin
  • Andrew P Hinck
  • Magnus Alm Rosenblad
  • Udayar Ilangovan
  • Iwona K Wower
  • Cynthia S Hinck
  • Renjing Wang
  • Tore Samuelsson
  • Niels Larsen
  • Ebbe Sloth Andersen
  • Shakhawat H Bhuiyan
  • Patricia M Schwarz
  • Angela K Robinson
  • Eileen M Lafer
  • Olga N Pakhomova
  • Chongwoo A Kim
  • Virgil Schirf
  • Borries Demeler
  • Jeffrey T Hoyle
  • Elena Menichelli
  • Shakhawat Hossain Bhuiyan
  • Jesper Cairo Westergaard
  • Jan Gorodkin

Detail Information

Publications13

  1. ncbi Identification of the RNA binding regions of SRP68/72 and SRP72 by systematic mutagenesis of human SRP RNA
    Jiaming Yin
    Department of Molecular Biology, University of Texas Health Science Center at Tyler, Tyler, Texas, USA
    RNA Biol 4:154-9. 2007
    ..The data suggest that nucleotide residues throughout most of the large SRP domain are directly and/or indirectly engaged in the binding of SRP68. In contrast, SRP72 binds only to a portion of the 5ef region...
  2. ncbi Structural transitions of the RING1B C-terminal region upon binding the polycomb cbox domain
    Renjing Wang
    Department of Biochemistry, University of Texas Health Science Center at San Antonio, MSC 7760, 7703 Floyd Curl Drive, San Antonio, Texas 78229 3900, USA
    Biochemistry 47:8007-15. 2008
    ..The presence of flexible regions could allow C-RING1B to bind a variety of different factors, ultimately recruiting RING1B and its associated PcG proteins to different genomic loci...
  3. ncbi A. fulgidus SRP54 M-domain
    Udayar Ilangovan
    Department of Biochemistry, Allied Health Building/Biochemistry, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA
    J Biomol NMR 41:241-8. 2008
  4. ncbi Identification of an RNA-binding domain in human SRP72
    Elena Iakhiaeva
    Department of Molecular Biology, The University of Texas Health Science Center at Tyler, 11937 US Highway 271, Tyler, TX 75708 3154, USA
    J Mol Biol 345:659-66. 2005
    ..These identifications assign two important functions to a large portion of SRP72 and demonstrate the RNA-binding capacity of the protein...
  5. ncbi Characterization of the SRP68/72 interface of human signal recognition particle by systematic site-directed mutagenesis
    Elena Iakhiaeva
    Department of Molecular Biology, University of Texas Health Science Center at Tyler, 75708, USA
    Protein Sci 18:2183-95. 2009
    ....
  6. ncbi Making the jump: new insights into the mechanism of trans-translation
    Jacek Wower
    Department of Animal Sciences, Auburn University, Auburn, AL 36849, USA
    J Biol 7:17. 2008
    ..Although it is not yet understood how the ribosome gets from the 3' end of the truncated message onto the messenger portion of the tmRNA to add the tag, a recent study in BMC Biology has shed some light on this astonishing feat...
  7. ncbi The 5e motif of eukaryotic signal recognition particle RNA contains a conserved adenosine for the binding of SRP72
    Elena Iakhiaeva
    Department of Molecular Biology, University of Texas Health Science Center at Tyler, Tyler, Texas 75708 3154, USA
    RNA 14:1143-53. 2008
    ..The human 5ef RNA was remarkably resistant to ribonucleolytic attack suggesting that the 240-AUC-242 "loop" and its surrounding nucleotides form a peculiar compact structure recognized only by SRP72...
  8. ncbi Schistosoma mansoni: TGF-beta signaling pathways
    Philip T LoVerde
    Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229 3900, USA
    Exp Parasitol 117:304-17. 2007
    ..Studies on signaling in schistosomes opens a new era for investigation of host-parasite and male-female interactions...
  9. ncbi Protein SRP68 of human signal recognition particle: identification of the RNA and SRP72 binding domains
    Elena Iakhiaeva
    Department of Molecular Biology, University of Texas Health Science Center at Tyler, Tyler, Texas 75708 3154, USA
    Protein Sci 15:1290-302. 2006
    ..This portion of SRP72 was located within a predicted tandem array of four tetratricopeptide (TPR)-like motifs suggested to form a superhelical structure with a groove to accommodate the C-terminal region of SRP68...
  10. ncbi The tmRDB and SRPDB resources
    Ebbe Sloth Andersen
    Department of Molecular Biology, University of Aarhus, C F Moellers Alle, Building 139, 8000 Aarhus, Denmark
    Nucleic Acids Res 34:D163-8. 2006
    ..All alignments can be easily examined using a new exploratory browser. The databases provide links to high-resolution structures and serve as depositories for structures obtained by molecular modeling...
  11. ncbi Comparative 3-D modeling of tmRNA
    Jody Burks
    Department of Animal Sciences, Auburn University, Auburn, AL 36849, USA
    BMC Mol Biol 6:14. 2005
    ..Progress toward understanding the molecular mechanism of template switching, which constitutes an essential step in trans-translation, is hampered by our limited knowledge about the three-dimensional folding of tmRNA...
  12. ncbi A nomenclature for all signal recognition particle RNAs
    Christian Zwieb
    Department of Molecular Biology, The University of Texas Health Science Center at Tyler, 11937 US Highway 271, Tyler, TX 75708 3154, USA
    RNA 11:7-13. 2005
    ..In order to assist in the continuation of these studies, we propose an SRP RNA nomenclature applicable to the three divisions of life...
  13. ncbi Kinship in the SRP RNA family
    Magnus Alm Rosenblad
    Department of Cell and Molecular Biology, University of Gothenburg, Goteborg, Sweden
    RNA Biol 6:508-16. 2009
    ..Updates of the Rfam SRP RNA sequence collection are expected to benefit from the suggested groupings...