Project Leader:Eugene Valkov
Department:Biochemistry - Izaurralde
Assistant: Maria GölzSibylle Patheiger
Phone:+49 7071 601-1352, +49 7071 601-1351
Fax:+49 7071 601-1353
Staff:Alphabetical List

Introduction

The life cycle of an mRNA molecule begins with transcription and after it is translated into protein the mRNA is degraded. The cell has evolved finely tuned mechanisms to balance the protein levels and this balance is the outcome of the rates of processes of mRNA synthesis and decay. Although many critical players in mRNA decay mechanisms have been identified and structural domains characterized the mechanisms are still not understood.

Our research focus is on the structural characterization of the mRNA degradation machinery and how decay factors interface mechanistically with other post-transcriptional processes such as translational repression and regulation.

We use X-ray crystallography to determine high-resolution structures of key domains and interactions with peptides in conjunction with studies of dynamics using small angle X-ray scattering (SAXS) and mass spectrometry. Structural studies are supported by analysis of affinity and kinetics of molecular interactions using latest biophysical platforms such as isothermal titration calorimetry, microscale thermophoresis, switchSENSE as well as classical methods such as thin-layer chromatography and gel-based enzyme assays.

We have established protocols using latest methods in recombinant production and reconstitution of large multisubunit complexes and we study the architecture of these complexes using single particle analysis from electron microscopy images, initially by negative staining. In the immediate future, the principal direction of the structural efforts will be toward obtaining high-resolution structural information with latest cryoEM techniques using a state-of-the-art 200 keV Talos Arctica cryoelectron microscope equipped with a phase plate and a Falcon 3 direct electron detector. For cryoEM work, we have a dedicated facility equipped with all the necessary peripheral equipment for cryoEM workflow including automated grid plungers and glow dischargers. A 120 keV Tecnai G2 Spirit microscope equipped with a cryoholder and a Gatan CCD camera is also available for screening and negative stain work. For computationally-demanding cryoEM data processing workflow we have access to 1200 CPU cluster, over a petabyte of storage capacity as well as individual multi-GPU workstations.

Integrated structural and biochemical studies of the composition, architecture and dynamics of multisubunit complexes rather than individual proteins or domains is essential in order to advance our mechanistic understanding of the complicated, multifaceted networks of interactions and events that regulate and control the fates of cellular mRNAs. A key strength of the department is a close synergy between structural biochemists and molecular and cell biologists. This supportive, interdisciplinary and highly collaborative research environment allows us to rapidly build a complete picture of the biological mechanism under investigation in vitro, in silico and in vivo.

# Equal contribution; * Co-corresponding author 

 

2017

GIGYF1/2 proteins use auxiliary sequences to selectively bind to 4EHP and repress target mRNA expression. Genes & Development. 31, 1147-1161. PMID: 28698298
Peter D, Weber R, Sandmeir F, Wohlbold L, Helms S, Bawankar P, Valkov E*, Igreja C, Izaurralde E.

Mille viae in eukaryotic mRNA decapping. Current Opinion in Structural Biology. 47, 40-51. PMID: 28591671
Valkov E, Jonas S, Weichenrieder O.

 

2016

The Structures of eIF4E-eIF4G Complexes Reveal an Extended Interface to Regulate Translation Initiation. Molecular Cell. 64, 467-479. PMID: 27773676
Grüner S, Peter D, Weber R, Wohlbold L, Chung MY, Weichenrieder O, Valkov E, Igreja C, Izaurralde E.

Structure of the Dcp2-Dcp1 mRNA-decapping complex in the activated conformation. Nature Structural & Molecular Biology. 23, 574-9. PMID: 27183195
Valkov E#, Muthukumar S#, Chang CT#, Jonas S, Weichenrieder O, Izaurralde E.

Distinct modes of recruitment of the CCR4-NOT complex by Drosophila and vertebrate Nanos. EMBO Journal. 35, 974-90. PMID: 26968986
Raisch T, Bhandari D, Sabath K, Helms S, Valkov E, Weichenrieder O, Izaurralde E.

 

2015

Structural Characterization of the Chaetomium thermophilum TREX-2 Complex and its Interaction with the mRNA Nuclear Export Factor Mex67:Mtr2. Structure. 23, 1246-57. PMID: 26051714
Dimitrova L#, Valkov E#, Aibara S#, Flemming D, McLaughlin SH, Hurt E, Stewart M.

The principal mRNA nuclear export factor NXF1:NXT1 forms a symmetric binding platform that facilitates export of retroviral CTE-RNA. Nucleic Acids Research. 43, 1883-93. PMID: 25628361
Aibara S, Katahira J, Valkov E, Stewart M.

Domain organization within the nuclear export factor Mex67:Mtr2 generates an extended mRNA binding surface. Nucleic Acids Research. 43: 1927-36. PMID: 25618852
Aibara S, Valkov E, Lamers M, Stewart M.

 

2014

Structural basis for Pan3 binding to Pan2 and its function in mRNA recruitment and deadenylation. EMBO Journal. 33, 1514-26. PMID: 24872509
Wolf J#, Valkov E#, Allen MD, Meineke B, Gordiyenko Y, McLaughlin SH, Olsen TM, Robinson CV, Bycroft M, Stewart M, Passmore LA.