Wellcome Centre for Cell Biology

Atlanta Cook

Structural biology of macromolecular complexes in RNA metabolism and transcriptional silencing

Photo of Atlanta Cook

Atlanta Cook is a Senior Research Fellow funded by the Wellcome Trust. Her group studies the mechanistic basis of post-transcriptional control of gene expression using biochemical and structural approaches.

Atlanta did her PhD on mechanistic studies of protein kinases with Dame Prof. Louise Johnson in Oxford. She joined the laboratory of Elena Conti in 2004 to work on the structural basis of tRNA export at the EMBL in Heidelberg. She completed this work after moving with the Conti laboratory to the MPI for Biochemistry in Martinsried near Munich. She started her group in Edinburgh in 2011, funded by an MRC Career Development Award. In 2017 she was awarded an Early Career Researcher prize from the British Crystallographic Association.

Lab members

Atika Hasaini, Uma Jayachandran, Aleksandra Kasprowicz (Ola), James Le Cornu, David MacLeod, Alexander Will and Sophie Winterbourne

Cook lab website

Structural biology of macromolecular complexes in RNA metabolism and transcriptional silencing

The expression of individual genes is controlled at the levels of mRNA transcription and also post-transcriptionally, by processes such as splicing, localization, modification or editing, and degradation. To gain a mechanistic understanding of these processes it is important to understand the interactions between the individual players, including both protein and nucleic acid components, at the molecular level. We have used structural approaches to tackle mechanistic questions about how protein-RNA interactions can control RNA maturation and RNA editing and how transcriptional repressors are recruited to methylated DNA. By combining structural studies with biochemical, biophysical and cell-based functional assays we can gain powerful insights into these molecular processes.

Recently, we solved a crystal structure of a yeast RNA binding protein, Ssd1, that is important in cell wall biogenesis. It is thought that Ssd1 functions by repressing translation of cognate transcripts. Using CRAC, we found that Ssd1 binds to specific sequences in the 5’UTRs of a small set of transcripts, several of which encode proteins required for cell wall biogenesis. This suggests that Ssd1 functions by blocking ribosome scanning along 5’UTRs. The structure of Ssd1 shows that it has a classical fold of an RNase II family nuclease. However, RNA degradation activity has been lost by two mechanisms. First, the catalytic residues have been altered during evolution. Second, a channel that, in active enzymes, allows RNA substrates to funnel into the active site has been blocked. We propose that Ssd1 has evolved a new RNA interacting surface.

Illustration of Atlanta Cook's research

A. The structure of Ssd1 (middle) compared with the structure of DIS3L2 (left), where RNA is bound, shows the different RNA binding sites. Domains of Ssd1 are marked in blue (cold shock domain 1, CSD1), cyan (CSD2), green (RNase II-like) and pink (S1). The Ssd1-specific insert is shown in the domain overview (below) and structure in orange. The yellow lollipops are phosphorylation sites. RNA travels down the central channel of DIS3L2 while Ssd1 binds a sequence-specific motif (purple) on the outside of the CSD domains. Two segments of the Ssd1 structure are shown in black – these block the active site funnel. A cartoon overview of the Ssd1-specific structures is shown on the right.

B. Four sets of point mutations were tested for RNA binding by electrophoretic mobility shift assay (left). Mutations to the side and top of the CSDs block binding to RNA. This is further demonstrated by fluorescence anisotropy assays (middle). Phenotypic assays in yeast show that mutations that prevent RNA binding have a cell wall stress phenotype.

Selected publications

Bayne R.A., Jayachandran U., Kasprowicz A., Bresson S., Tollervey D., Wallace E.W.J., Cook A.G. (2021) Yeast Ssd1 is a non-enzymatic member of the RNase II family with an alternative RNA recognition interface. Nucleic Acids Research, DOI: 10.1093/nar/gkab615.

Pantier R., Chhatbar K., Quante T., Skourti-Stathaki K., Cholewa-Waclaw J., Alston G., Alexander-Howden B., Lee H.Y., Cook A.G., C Spruijt C.G., Vermeulen M., Selfridge J., and Bird A. (2021) SALL4 controls cell fate in response to DNA base composition. Mol Cell 81:845-858.e8.

Ballou E.R., Cook A.G. and Wallace E.W.J. (2020) Repeated evolution of inactive pseudonucleases in a fungal branch of the Dis3/RNase II family of nucleases. Mol. Biol. Evol. doi:10.1093/molbev/msaa324