The cellular pool of ribonucleic acids (RNAs) is immensely diverse and complex. During their biosynthesis, RNA molecules undergo a vast number of co- and posttranscriptional processing and modification steps, which require dedicated enzyme machinery.
One unique example of RNA processing is non-conventional splicing of RNAs, which is an essential step during transfer RNA (tRNA) maturation. tRNAs are transcribed as precursor transcripts (pre-tRNA) and are subjected to multiple posttranscriptional processing events before they can fulfil their function. Intron-containing pre-tRNAs undergo non-conventional splicing—a cytosolic, enzyme-catalysed processing reaction. The splicing of pre-tRNAs occurs in two steps: The intron is first excised by a splicing endonuclease and the resulting tRNA exon halves are ligated by tRNA ligase to form a fully matured functional tRNA. Because eukaryotic tRNA introns disrupt the anticodon stem-loop structure, the removal of these introns is an essential process.
In our lab, we aim to comprehend the structure and function of the eukaryotic tRNA splicing machinery. The mechanistic and structural insights will provide a comprehensive picture of how tRNA splicing enzymes function in the cell.
While there is a substantial understanding for the various RNA maturation and degradation pathways, much less attention has been given to RNA repair and quality control. RNA can be subjected to damage through non-enzymatic hydrolysis or the action of endonucleases. These RNA cleavage events can be “sealed” by RNA ligases, which catalyse the ligation via phosphodiester bonds. We aim to uncover new RNA repair and quality control pathways based on these enzymes.
Using an interdisciplinary approach from protein and RNA biochemistry to structural biology and yeast genetics, we analyse the machinery and mechanisms that maintain RNA integrity. We often start by in vitro reconstitution of enzyme complexes, to determine their structure-function relationships. Once we purified protein, we study it using x-ray crystallography, cryo-electron microscopy (cryo-EM) as well as biophysical and biochemical methods. We explore the cellular role of RNA processing enzymes in the yeast Saccharomyces cerevisiae
and mammalian cells.
Li W*, Crotty K*, Garrido Ruiz D, Voorhies M, Rivera C, Sil A, Mullins RD, Jacobson MP, Peschek J§
, Walter P§
(2021) Protomer alignment modulates specificity of RNA substrate recognition by Ire1
& Walter P§
(2019) tRNA ligase structure reveals kinetic competition between non-conventional mRNA splicing and mRNA decay
Li W, Okreglak V, Peschek J
, Kimmig P, Zubradt M, Weissman JS, Walter P (2018) Engineering ER-stress dependent non-conventional mRNA splicing
, Acosta-Alvear D, Mendez AS, Walter P (2015) A conformational RNA zipper promotes intron ejection during non-conventional XBP1 mRNA splicing
. EMBO Rep
Mainz A, Peschek J
, Stavropoulou M, Back KC, Bardiaux B, Asami S, Prade E, Peters C, Weinkauf S, Buchner J, Reif B (2015) The chaperone αB-crystallin uses different interfaces to capture an amorphous and an amyloid client. Nat Struct Mol Biol
Feige MJ, Gräwert MA, Marcinowski M, Hennig J, Behnke J, Ausländer D, Herold EM, Peschek J
, Castro CD, Flajnik M, Hendershot LM, Sattler M, Groll M, Buchner J (2014) The structural analysis of shark IgNAR antibodies reveals evolutionary principles of immunoglobulins. PNAS
, Braun N, Rohrberg J, Back KC, Kriehuber T, Kastenmüller A, Weinkauf S, Buchner J (2013) Regulated structural transitions unleash the chaperone activity of αB-crystallin. PNAS
Müller R, Gräwert MA, Kern T, Madl T, Peschek J
, Sattler M, Groll M, Buchner J (2013) High-resolution structures of the IgM Fc domains reveal principles of its hexamer formation. PNAS
Drazic A, Miura H, Peschek J
, Le Y, Bach NC, Kriehuber T, Winter J (2013) Methionine oxidation activates a transcription factor in response to oxidative stress. PNAS
Braun N, Zacharias M, Peschek J
, Kastenmüller A, Zou J, Hanzlik M, Haslbeck M, Rappsilber J, Buchner J, Weinkauf S (2011) Multiple molecular architectures of the eye lens chaperone αB-crystallin elucidated by a triple hybrid approach. PNAS
, Braun N, Franzmann TM, Georgalis Y, Haslbeck M, Weinkauf S, Buchner J (2009) The eye lens chaperone α-crystallin forms defined globular assemblies. PNAS
Reviews and Method Papers
Karagöz GE, Peschek J
, Walter P, Acosta-Alvear D (2019) In vitro
RNA Cleavage Assays to Characterize IRE1-dependent RNA Decay. Bio-protocol
Haslbeck M, Peschek
, Buchner J, Weinkauf S (2016) Structure and function of α-crystallins: Traversing from in vitro to in vivo. Biochim Biophys Acta
1860(1 Pt B):149-66. [Review]
Complete List of Publications