Publications by authors named "Stephen A Peter"

4 Publications

  • Page 1 of 1

A Novel, Universally Active C-terminal Protein Degradation Signal Generated by Alternative Splicing.

J Mol Biol 2021 Apr 23;433(8):166890. Epub 2021 Feb 23.

Department of Biology, Technical University of Darmstadt, Darmstadt 64287, Germany. Electronic address:

Proteome integrity is crucial for cellular homeostasis and adaptation to stress conditions such as hypoxia. One mechanism for rapid adaptation of the proteome in response to changing environmental signals is alternative splicing. In addition to generating different protein isoforms, alternative splicing is also capable of controlling total protein levels by the regulated synthesis of non-productive mRNA isoforms. The hypoxia-induced isoform E of the tumor suppressor MAX is produced by retention and translation of the last intron. This leads to an alternative C-terminus that harbors a potent C-degron, the isoE degron. Strikingly, the isoE degron represents a universal protein degradation signal that is not only functional in mammalian cells, but also in yeast and even in bacteria. Essential for efficient protein decay is a conserved (F/W)xxW motif. Degradation of isoE tagged proteins is mediated by the proteasome in eukaryotes and Lon protease in bacteria. Thus, the isoE degron is a broadly applicable and highly efficient tool in protein analyses.
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http://dx.doi.org/10.1016/j.jmb.2021.166890DOI Listing
April 2021

H, C and N chemical shift assignment of the stem-loop 5a from the 5'-UTR of SARS-CoV-2.

Biomol NMR Assign 2021 04 23;15(1):203-211. Epub 2021 Jan 23.

Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany.

The SARS-CoV-2 (SCoV-2) virus is the causative agent of the ongoing COVID-19 pandemic. It contains a positive sense single-stranded RNA genome and belongs to the genus of Betacoronaviruses. The 5'- and 3'-genomic ends of the 30 kb SCoV-2 genome are potential antiviral drug targets. Major parts of these sequences are highly conserved among Betacoronaviruses and contain cis-acting RNA elements that affect RNA translation and replication. The 31 nucleotide (nt) long highly conserved stem-loop 5a (SL5a) is located within the 5'-untranslated region (5'-UTR) important for viral replication. SL5a features a U-rich asymmetric bulge and is capped with a 5'-UUUCGU-3' hexaloop, which is also found in stem-loop 5b (SL5b). We herein report the extensive H, C and N resonance assignment of SL5a as basis for in-depth structural studies by solution NMR spectroscopy.
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http://dx.doi.org/10.1007/s12104-021-10007-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7822759PMC
April 2021

Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy.

Nucleic Acids Res 2020 12;48(22):12415-12435

Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany.

The current pandemic situation caused by the Betacoronavirus SARS-CoV-2 (SCoV2) highlights the need for coordinated research to combat COVID-19. A particularly important aspect is the development of medication. In addition to viral proteins, structured RNA elements represent a potent alternative as drug targets. The search for drugs that target RNA requires their high-resolution structural characterization. Using nuclear magnetic resonance (NMR) spectroscopy, a worldwide consortium of NMR researchers aims to characterize potential RNA drug targets of SCoV2. Here, we report the characterization of 15 conserved RNA elements located at the 5' end, the ribosomal frameshift segment and the 3'-untranslated region (3'-UTR) of the SCoV2 genome, their large-scale production and NMR-based secondary structure determination. The NMR data are corroborated with secondary structure probing by DMS footprinting experiments. The close agreement of NMR secondary structure determination of isolated RNA elements with DMS footprinting and NMR performed on larger RNA regions shows that the secondary structure elements fold independently. The NMR data reported here provide the basis for NMR investigations of RNA function, RNA interactions with viral and host proteins and screening campaigns to identify potential RNA binders for pharmaceutical intervention.
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http://dx.doi.org/10.1093/nar/gkaa1013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7736788PMC
December 2020

Structural basis for the recognition of transiently structured AU-rich elements by Roquin.

Nucleic Acids Res 2020 07;48(13):7385-7403

Institute for Molecular Biosciences, Goethe University Frankfurt and Center for Biomolecular Magnetic Resonance (BMRZ), 60438 Frankfurt, Germany.

Adenylate/uridylate-rich elements (AREs) are the most common cis-regulatory elements in the 3'-untranslated region (UTR) of mRNAs, where they fine-tune turnover by mediating mRNA decay. They increase plasticity and efficacy of mRNA regulation and are recognized by several ARE-specific RNA-binding proteins (RBPs). Typically, AREs are short linear motifs with a high content of complementary A and U nucleotides and often occur in multiple copies. Although thermodynamically rather unstable, the high AU-content might enable transient secondary structure formation and modify mRNA regulation by RBPs. We have recently suggested that the immunoregulatory RBP Roquin recognizes folded AREs as constitutive decay elements (CDEs), resulting in shape-specific ARE-mediated mRNA degradation. However, the structural evidence for a CDE-like recognition of AREs by Roquin is still lacking. We here present structures of CDE-like folded AREs, both in their free and protein-bound form. Moreover, the AREs in the UCP3 3'-UTR are additionally bound by the canonical ARE-binding protein AUF1 in their linear form, adopting an alternative binding-interface compared to the recognition of their CDE structure by Roquin. Strikingly, our findings thus suggest that AREs can be recognized in multiple ways, allowing control over mRNA regulation by adapting distinct conformational states, thus providing differential accessibility to regulatory RBPs.
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http://dx.doi.org/10.1093/nar/gkaa465DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7367199PMC
July 2020