Cryo-EM structure and rRNA modification sites of a plant ribosome

[EN] Protein synthesis in crop plants contributes to the balance of food and fuel on our planet, which influences human metabolic activity and lifespan. Protein synthesis can be regulated with respect to changing environmental cues via the deposition of chemical modifications into rRNA. Here, we present the structure of a plant ribosome from tomato and a quantitative mass spectrometry analysis of its rRNAs. The study reveals fine features of the ribosomal proteins and 71 plant-specific rRNA modifications, and it re-annotates 30 rRNA residues in the available sequence. At the protein level, isoAsp is found in position 137 of uS11, and a zinc finger previously believed to be universal is missing from eL34, suggesting a lower effect of zinc deficiency on protein synthesis in plants. At the rRNA level, the plant ribosome differs markedly from its human counterpart with respect to the spatial distribution of modifications. Thus, it represents an additional layer of gene expression regulation, highlighting the molecular signature of a plant ribosome. The results provide a reference model of a plant ribosome for structural studies and an accurate marker for molecular ecology.This work was supported by the Swedish Foundation for Strategic Research (ARC19:0051), the Knut and Alice Wallenberg Foundation (2018.0080), the EMBO Young Investigator Program, and a NASA award (80NSSC18K1139 to A.S.P.).Cottilli, P.; Itoh, Y.; Nobe, Y.; Petrov, AS.; Lisón, P.; Taoka, M.; Amunts, A. (2022). Cryo-EM structure and rRNA modification sites of a plant ribosome. Plant communications. 3(5):1-9. https://doi.org/10.1016/j.xplc.2022.100342193

Parameters of the Protein Energy Landscapes of Several Light-Harvesting Complexes Probed via Spectral Hole Growth Kinetics Measurements

44 Pag., 2 Tabl. The definitive version is available at: http://pubs.acs.org/journal/jpcbfkThe parameters of barrier distributions on the protein energy landscape in the excited electronic state of the pigment/protein system have been determined by means of spectral hole burning for the lowest-energy pigments of CP43 core antenna complex and CP29 minor antenna complex of spinach Photosystem II (PS II) as well as of trimeric and monomeric LHCII complexes transiently associated with the pea Photosystem I (PS I) pool. All of these complexes exhibit sixty to several hundred times lower spectral hole burning yields as compared with molecular glassy solids previously probed by means of the hole growth kinetics measurements. Therefore, the entities (groups of atoms), which participate in conformational changes in protein, appear to be significantly larger and heavier than those in molecular glasses. No evidence of a small (1 cm−1) spectral shift tier of the spectral diffusion dynamics has been observed. Therefore, our data most likely reflect the true barrier distributions of the intact protein and not those related to the interface or surrounding host. Possible applications of the barrier distributions as well as the assignments of low-energy states of CP29 and LHCII are discussed in light of the above results.Research at Concordia University is supported by NSERC and CFI. R.P. would like to thank Spanish MICINN (grant AGL2008-00377). M.S. acknowledges the contribution of the Photosynthetic Systems Program, Chemical Sciences, Geosciences, and Biosciences Division, Basic Energy Sciences, USDOE. J.P. and K.-D.I. gratefully acknowledge support from Deutsche Forschungsgemeinschaft (SFB 429, TP A1, and TP A3, respectively).Peer reviewe

Structural basis of mitochondrial membrane bending by the I-II-III2-IV2 supercomplex

Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane1. Here we show that a supercomplex containing all four respiratory chain components contributes to membrane curvature induction in ciliates. We report cryo-electron microscopy and cryo-tomography structures of the supercomplex that comprises 150 different proteins and 311 bound lipids, forming a stable 5.8-MDa assembly. Owing to subunit acquisition and extension, complex I associates with a complex IV dimer, generating a wedge-shaped gap that serves as a binding site for complex II. Together with a tilted complex III dimer association, it results in a curved membrane region. Using molecular dynamics simulations, we demonstrate that the divergent supercomplex actively contributes to the membrane curvature induction and tubulation of cristae. Our findings highlight how the evolution of protein subunits of respiratory complexes has led to the I-II-III2-IV2 supercomplex that contributes to the shaping of the bioenergetic membrane, thereby enabling its functional specialization

Mechanism of membrane-tethered mitochondrial protein synthesis

Mitochondrial ribosomes (mitoribosomes) are tethered to the mitochondrial inner membrane to facilitate the cotranslational membrane insertion of the synthesized proteins. We report cryo-electron microscopy structures of human mitoribosomes with nascent polypeptide, bound to the insertase oxidase assembly 1-like (OXA1L) through three distinct contact sites. OXA1L binding is correlated with a series of conformational changes in the mitoribosomal large subunit that catalyze the delivery of newly synthesized polypeptides. The mechanism relies on the folding of mL45 inside the exit tunnel, forming two specific constriction sites that would limit helix formation of the nascent chain. A gap is formed between the exit and the membrane, making the newly synthesized proteins accessible. Our data elucidate the basis by which mitoribosomes interact with the OXA1L insertase to couple protein synthesis and membrane delivery.Peer reviewe

ATP synthase hexamer assemblies shape cristae of Toxoplasma mitochondria

Mitochondrial ATP synthase plays a key role in inducing membrane curvature to establish cristae. In Apicomplexa causing diseases such as malaria and toxoplasmosis, an unusual cristae morphology has been observed, but its structural basis is unknown. Here, we report that the apicomplexan ATP synthase assembles into cyclic hexamers, essential to shape their distinct cristae. Cryo-EM was used to determine the structure of the hexamer, which is held together by interactions between parasite-specific subunits in the lumenal region. Overall, we identified 17 apicomplexan-specific subunits, and a minimal and nuclear-encoded subunit-a. The hexamer consists of three dimers with an extensive dimer interface that includes bound cardiolipins and the inhibitor IF1. Cryo-ET and subtomogram averaging revealed that hexamers arrange into ~20-megadalton pentagonal pyramids in the curved apical membrane regions. Knockout of the linker protein ATPTG11 resulted in the loss of pentagonal pyramids with concomitant aberrantly shaped cristae. Together, this demonstrates that the unique macromolecular arrangement is critical for the maintenance of cristae morphology in Apicomplexa

Structure of a mitochondrial ribosome with fragmented rRNA in complexwith membrane-targeting elements

Mitoibosomes of green alga belong to a diverged type with extreme fragmentation in rRNA andprotein material. We present a 2.9-Å resolution structure of an algal mitoribosome with reducedrRNA that is split in to 13 fragments. The architecture features a fragmentation pattern that hassimilarities with apicomplexan parasites. The unique phenomena of the rRNA include permutationand incorporation of a non-canonical and reduced mt-5S rRNA. On the protein level, elevenperipherally associated HEAT-repeat proteins involved in rRNA binding, and a specific trimer ofmL116 binds 3’ termini of three rRNA fragments. In the exit tunnel, mL128 constricts the path,and mL105 a homolog of a membrane targeting component mediates contacts with an innermembrane-bound insertase. Although overall protein content at the tunnel exit site of themitoribosome varies among eukaryotes, we find that the mechanisms of the constriction andmembrane tethering are shared between the algal and mammalian lineages. Therefore, our datareveals characteristics of fragmented rRNA an unexpected convergent evolution in the regulationof protein synthesis in mitochondria

Structure of a mitochondrial ribosome with fragmented rRNA in complexwith membrane-targeting elements

Mitoibosomes of green alga belong to a diverged type with extreme fragmentation in rRNA andprotein material. We present a 2.9-Å resolution structure of an algal mitoribosome with reducedrRNA that is split in to 13 fragments. The architecture features a fragmentation pattern that hassimilarities with apicomplexan parasites. The unique phenomena of the rRNA include permutationand incorporation of a non-canonical and reduced mt-5S rRNA. On the protein level, elevenperipherally associated HEAT-repeat proteins involved in rRNA binding, and a specific trimer ofmL116 binds 3’ termini of three rRNA fragments. In the exit tunnel, mL128 constricts the path,and mL105 a homolog of a membrane targeting component mediates contacts with an innermembrane-bound insertase. Although overall protein content at the tunnel exit site of themitoribosome varies among eukaryotes, we find that the mechanisms of the constriction andmembrane tethering are shared between the algal and mammalian lineages. Therefore, our datareveals characteristics of fragmented rRNA an unexpected convergent evolution in the regulationof protein synthesis in mitochondria