CIISB Research Highlights Archive

Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions.

Daniel N. Wilson Research Group

Significance

Ribosomes are the protein synthesizing machines of the cell. Recent advances in cryo-EM have led to the determination of structures from a variety of species, including bacterial 70S and eukaryotic 80S ribosomes as well as mitoribosomes from eukaryotic mitochondria, however, to date high resolution structures of plastid 70S ribosomes have been lacking. Here we present a cryo-EM structure of the spinach chloroplast 70S ribosome, with an average resolution of 5.4 Å for the small 30S subunit and 3.6 Å for the large 50S ribosomal subunit. The structure reveals the location of the plastid-specific ribosomal proteins (RPs) PSRP1, PSRP4, PSRP5 and PSRP6 as well as the numerous plastid-specific extensions of the RPs. We discover many features by which the plastid-specific extensions stabilize the ribosome via establishing additional interactions with surrounding ribosomal RNA and RPs. Moreover, we identify a large conglomerate of plastid-specific protein mass adjacent to the tunnel exit site that could facilitate interaction of the chloroplast ribosome with the thylakoid membrane and the protein-targeting machinery. Comparing the Escherichia coli 70S ribosome with that of the spinach chloroplast ribosome provides detailed insight into the co-evolution of RP and rRNA.

Graf, M.; Arenz, S.; Huter, P.; Dönhöfer, A.; Nováček, J. & Wilson D. N.: Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions. Nucleic Acids Research 45, 2887-2896, doi:10.1093/nar/gkw1272 (2017).

The virus structure of deformed wing virus of honeybees determined by cryo-electron microscopy. (A) Surface of the virus is rainbow-colored according to its distance from the particle center. (B) Cartoon representation of structure of the P-domain that decorates deformed wing virus surface is rainbow-colored from residue 260 in blue to 416 in red. The background shows image of the deformed wing virus particles from electron microscope.

Pavel Plevka Research Group

Significance

Honey bee populations in Europe and North America have been decreasing since the 1950s. Deformed wing virus (DWV), which is undergoing a worldwide epidemic, causes the deaths of individual honey bees and collapse of whole colonies. Three-dimensional structures of DWV determined at different conditions shows that the virus surface is decorated with protruding globular extensions of capsid proteins. The protruding domains contain a putative catalytic site that is probably required for the entry of the virus into the host cell. In addition, parts of the DWV RNA genome interact with the inside of the virus capsid. Identifying the RNA binding and catalytic sites within the DWV virion offers prospects for the development of antiviral treatments.

Skubnik, K.; Novacek, J.; Füzik, T.; Pridal, A.; Paxton, R. J. & Plevka, P., Structure of deformed wing virus, a major honey bee pathogen, PNAS, 114, 3210-3215 (2017) DOI: 10.1073/pnas.1615695114

NMR structure shows how the CTD-interacting domain of Rtt103p recognizes threonine-4 phosphorylated CTD of RNA polymerase II (RNAPII).

Richard Štefl Research Group

Significance

Phosphorylation patterns of the C‐terminal domain (CTD) of largest subunit of RNApolymerase II (called the CTD code) orchestrate the recruitment of RNA processing and transcription factors. Recent studies showed that not only serines and tyrosines but also threonines of the CTD can be phosphorylated with a number of functional consequences, including the interaction with yeast transcription termination factor, Rtt103p. The solution structure of the Rtt103p CTD‐interacting domain (CID) bound to Thr4 phosphorylated CTD has been obtained by NMR. The structure reveals a direct recognition of the phospho‐Thr4 mark by Rtt103p CID and shows extensive interactions involving residues from three repeats of the CTD heptad. The structural data suggests that the recruitment of a CID‐containing CTD‐binding factor may be coded by more than one letter of the CTD code.

Jasnovidova, O.; Krejcikova, M.; Kubicek, K. & Stefl, R. Structural insight into recognition of phosphorylated threonine-4 of RNA polymerase II C-terminal domain by Rtt103p. Embo Reports 18, 906-913, doi:10.15252/embr.201643723 (2017).