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Atlanta Cook

Co-workers:

Uma Jayachandran, Valdeko Kruusvee
Cook lab website

Structural biology of macromolecular complexes involved in RNA metabolism

Translation is the central process in biology during which genetic information encoded on mRNAs is read by the ribosome and polypeptides are synthesized. Extensive biochemical studies on prokaryotic ribosomes have given insights into the assembly of this machine, while structural studies have illuminated its workings during translation.

Eukaryotic ribosome biogenesis is vastly more complex than in prokaryotes, requiring more than 200 additional factors and proceeding through multiple cellular compartments. The process centers around the transcription of a long ribosomal RNA transcript in the nucleolus. Chemical modification of bases and the association of small subunit ribosomal proteins occur at this early stage. A series of RNA cleavage events then separates the pre- 40S and pre-60S particles, which exit the nucleus as almost fully assembled pre-ribosomal particles. These particles associate with late-acting biogenesis factors that also act as transport adaptors, mediating interactions with the nucleocytoplasmic transport machinery. Final maturation is completed in the cytoplasm where late-acting biogenesis factors are removed and the mature ribosomal particles can associate on mRNAs. Proteomic studies have generated parts lists of proteins involved in ribosome biogenesis in yeast and many of these proteins are conserved in mammals. Less clear is the order of individual events, particularly in late cytoplasmic maturation of ribosomal particles. Similarly, the roles of vertebrate-specific proteins in ribosome biogenesis are less well studied. I am interested in using structural and biochemical approaches to gain mechanistic insights into the function of ribosome biogenesis factors in yeast and mammalian cells.

Nuclear factors (NF) 90 and 45 form a heterodimeric complex (Fig. 1A) that is found in nucleoli of mammalian cells. Loss of NF90/NF45 leads to nucleolar rearrangements and a 60S ribosomal subunit synthesis defect. Our biochemical and structural studies on the dsRNA binding domains (dsRBDs) of NF90 show that this protein multimerises on dsRNA (Fig. 1B). The dsRBDs of NF90 recognise A-form dsRNA using shape and charge complementarity (Fig. 1C). In addition, we have found that these dsRBDs are able to make base-specific interactions, a mode of recognition that has previously been observed in the RNA modifying enzyme ADAR2. Consequently, NF90/NF45 heterodimers use both structure and sequence cues to recognise dsRNA are likely to form stable complexes at specific locations on highly structure RNA species (Fig. 1D).

Selected publications:

Jayachandran U, Grey H and Cook AG (2015) Nuclear Factor 90 uses an ADAR2-like binding mode to recognize specific bases in dsRNA Nucl. Acids Res. doi: 10.1093/nar/gkv1508

Wandrey F, Montellese C, Koó, K, Badertscher L, Bammert L, Cook AG, Zemp I, Horvath, P and Kutay U (2015) The NF45/NF90 heterodimer contributes to the biogenesis of 60S ribosomal subunits and influences nucleolar morphology. Mol. Cell. Biol. doi: 10.1128/MCB.00306-15

Hector RD, Burlacu E, Aitken S, Le Bihan T, Tuijtel M, Zaplatina A, Cook, AG and Granneman S (2014) Snapshots of pre-rRNA structural flexibility reveal eukaryotic 40S assembly dynamics at nucleotide resolution Nucleic Acids Res. doi: 10.1093/nar/gku815


 

1. (A) Overview of domain organization of NF90 and NF45. (B) Both full length NF90/NF45 complex and constructs
of the dsRBDs alone multimerise on dsRNA. (C) A co-crystal structure of NF90 tandem dsRBDs with dsRNA. (D)
Model of dsRNA binding.