bims-tricox Biomed News
on Translation, ribosomes and COX
Issue of 2022‒06‒19
seven papers selected by
Yash Verma
University of Delhi South Campus
  1. CG7630 is the Drosophila melanogaster homolog of the cytochrome c oxidase subunit COX7B.
  2. Role of aIF5B in archaeal translation initiation.
  3. Compact IF2 allows initiator tRNA accommodation into the P site and gates the ribosome to elongation.
  4. Ribosome profiling reveals multiple roles of SecA in cotranslational protein export.
  5. Structure of the mammalian ribosome as it decodes the selenocysteine UGA codon.
  6. Folding and Evolution of a Repeat Protein on the Ribosome.
  7. Structural insights into assembly of transcription preinitiation complex.
  1. EMBO Rep. 2022 Jun 14. e54825
    CG7630 is the Drosophila melanogaster homolog of the cytochrome c oxidase subunit COX7B.
    Michele Brischigliaro, Alfredo Cabrera-Orefice, Mattia Sturlese, Dei M Elurbe, Elena Frigo, Erika Fernandez-Vizarra, Stefano Moro, Martijn A Huynen, Susanne Arnold, Carlo Viscomi, Massimo Zeviani.
      The mitochondrial respiratory chain (MRC) is composed of four multiheteromeric enzyme complexes. According to the endosymbiotic origin of mitochondria, eukaryotic MRC derives from ancestral proteobacterial respiratory structures consisting of a minimal set of complexes formed by a few subunits associated with redox prosthetic groups. These enzymes, which are the "core" redox centers of respiration, acquired additional subunits, and increased their complexity throughout evolution. Cytochrome c oxidase (COX), the terminal component of MRC, has a highly interspecific heterogeneous composition. Mammalian COX consists of 14 different polypeptides, of which COX7B is considered the evolutionarily youngest subunit. We applied proteomic, biochemical, and genetic approaches to investigate the COX composition in the invertebrate model Drosophila melanogaster. We identified and characterized a novel subunit which is widely different in amino acid sequence, but similar in secondary and tertiary structures to COX7B, and provided evidence that this object is in fact replacing the latter subunit in virtually all protostome invertebrates. These results demonstrate that although individual structures may differ the composition of COX is functionally conserved between vertebrate and invertebrate species.
    Keywords:   D. melanogaster ; COX7B; cytochrome c oxidase; mitochondria; respiratory chain
    DOI:  https://doi.org/10.15252/embr.202254825
  2. Nucleic Acids Res. 2022 Jun 13. pii: gkac490. [Epub ahead of print]
    Role of aIF5B in archaeal translation initiation.
    Ramy Kazan, Gabrielle Bourgeois, Christine Lazennec-Schurdevin, Eric Larquet, Yves Mechulam, Pierre-Damien Coureux, Emmanuelle Schmitt.
      In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. In eukaryotes, the role of eIF5B in ribosomal subunit joining is established and structural data showing eIF5B bound to the full ribosome were obtained. To achieve its function, eIF5B collaborates with eIF1A. However, structural data illustrating how these two factors interact on the small ribosomal subunit have long been awaited. The role of the archaeal counterparts, aIF5B and aIF1A, remains to be extensively addressed. Here, we study the late steps of Pyrococcus abyssi translation initiation. Using in vitro reconstituted initiation complexes and light scattering, we show that aIF5B bound to GTP accelerates subunit joining without the need for GTP hydrolysis. We report the crystallographic structures of aIF5B bound to GDP and GTP and analyze domain movements associated to these two nucleotide states. Finally, we present the cryo-EM structure of an initiation complex containing 30S bound to mRNA, Met-tRNAiMet, aIF5B and aIF1A at 2.7 Å resolution. Structural data shows how archaeal 5B and 1A factors cooperate to induce a conformation of the initiator tRNA favorable to subunit joining. Archaeal and eukaryotic features of late steps of translation initiation are discussed.
    DOI:  https://doi.org/10.1093/nar/gkac490
  3. Nat Commun. 2022 Jun 13. 13(1): 3388
    Compact IF2 allows initiator tRNA accommodation into the P site and gates the ribosome to elongation.
    Ritwika S Basu, Michael B Sherman, Matthieu G Gagnon.
      During translation initiation, initiation factor 2 (IF2) holds initiator transfer RNA (fMet-tRNAifMet) in a specific orientation in the peptidyl (P) site of the ribosome. Upon subunit joining IF2 hydrolyzes GTP and, concomitant with inorganic phosphate (Pi) release, changes conformation facilitating fMet-tRNAifMet accommodation into the P site and transition of the 70 S ribosome initiation complex (70S-IC) to an elongation-competent ribosome. The mechanism by which IF2 separates from initiator tRNA at the end of translation initiation remains elusive. Here, we report cryo-electron microscopy (cryo-EM) structures of the 70S-IC from Pseudomonas aeruginosa bound to compact IF2-GDP and initiator tRNA. Relative to GTP-bound IF2, rotation of the switch 2 α-helix in the G-domain bound to GDP unlocks a cascade of large-domain movements in IF2 that propagate to the distal tRNA-binding domain C2. The C2-domain relocates 35 angstroms away from tRNA, explaining how IF2 makes way for fMet-tRNAifMet accommodation into the P site. Our findings provide the basis by which IF2 gates the ribosome to the elongation phase.
    DOI:  https://doi.org/10.1038/s41467-022-31129-2
  4. Nat Commun. 2022 Jun 13. 13(1): 3393
    Ribosome profiling reveals multiple roles of SecA in cotranslational protein export.
    Zikun Zhu, Shuai Wang, Shu-Ou Shan.
      SecA, an ATPase known to posttranslationally translocate secretory proteins across the bacterial plasma membrane, also binds ribosomes, but the role of SecA's ribosome interaction has been unclear. Here, we used a combination of ribosome profiling methods to investigate the cotranslational actions of SecA. Our data reveal the widespread accumulation of large periplasmic loops of inner membrane proteins in the cytoplasm during their cotranslational translocation, which are specifically recognized and resolved by SecA in coordination with the proton motive force (PMF). Furthermore, SecA associates with 25% of secretory proteins with highly hydrophobic signal sequences at an early stage of translation and mediates their cotranslational transport. In contrast, the chaperone trigger factor (TF) delays SecA engagement on secretory proteins with weakly hydrophobic signal sequences, thus enforcing a posttranslational mode of their translocation. Our results elucidate the principles of SecA-driven cotranslational protein translocation and reveal a hierarchical network of protein export pathways in bacteria.
    DOI:  https://doi.org/10.1038/s41467-022-31061-5
  5. Science. 2022 Jun 17. 376(6599): 1338-1343
    Structure of the mammalian ribosome as it decodes the selenocysteine UGA codon.
    Tarek Hilal, Benjamin Y Killam, Milica Grozdanović, Malgorzata Dobosz-Bartoszek, Justus Loerke, Jörg Bürger, Thorsten Mielke, Paul R Copeland, Miljan Simonović, Christian M T Spahn.
      The elongation of eukaryotic selenoproteins relies on a poorly understood process of interpreting in-frame UGA stop codons as selenocysteine (Sec). We used cryo-electron microscopy to visualize Sec UGA recoding in mammals. A complex between the noncoding Sec-insertion sequence (SECIS), SECIS-binding protein 2 (SBP2), and 40S ribosomal subunit enables Sec-specific elongation factor eEFSec to deliver Sec. eEFSec and SBP2 do not interact directly but rather deploy their carboxyl-terminal domains to engage with the opposite ends of the SECIS. By using its Lys-rich and carboxyl-terminal segments, the ribosomal protein eS31 simultaneously interacts with Sec-specific transfer RNA (tRNASec) and SBP2, which further stabilizes the assembly. eEFSec is indiscriminate toward l-serine and facilitates its misincorporation at Sec UGA codons. Our results support a fundamentally distinct mechanism of Sec UGA recoding in eukaryotes from that in bacteria.
    DOI:  https://doi.org/10.1126/science.abg3875
  6. Front Mol Biosci. 2022 ;9 851038
    Folding and Evolution of a Repeat Protein on the Ribosome.
    José Alberto León-González, Perline Flatet, María Soledad Juárez-Ramírez, José Arcadio Farías-Rico.
      Life on earth is the result of the work of proteins, the cellular nanomachines that fold into elaborated 3D structures to perform their functions. The ribosome synthesizes all the proteins of the biosphere, and many of them begin to fold during translation in a process known as cotranslational folding. In this work we discuss current advances of this field and provide computational and experimental data that highlight the role of ribosome in the evolution of protein structures. First, we used the sequence of the Ankyrin domain from the Drosophila Notch receptor to launch a deep sequence-based search. With this strategy, we found a conserved 33-residue motif shared by different protein folds. Then, to see how the vectorial addition of the motif would generate a full structure we measured the folding on the ribosome of the Ankyrin repeat protein. Not only the on-ribosome folding data is in full agreement with classical in vitro biophysical measurements but also it provides experimental evidence on how folded proteins could have evolved by duplication and fusion of smaller fragments in the RNA world. Overall, we discuss how the ribosomal exit tunnel could be conceptualized as an active site that is under evolutionary pressure to influence protein folding.
    Keywords:  cotranslational; evolution; folding; protein; ribosome
    DOI:  https://doi.org/10.3389/fmolb.2022.851038
  7. Curr Opin Struct Biol. 2022 Jun 11. pii: S0959-440X(22)00083-5. [Epub ahead of print]75 102404
    Structural insights into assembly of transcription preinitiation complex.
    Xizi Chen, Yanhui Xu.
      RNA polymerase II (Pol II)-mediated transcription in eukaryotic cells starts with assembly of preinitiation complex (PIC) on core promoter, a DNA sequence of ∼100 base pairs. The transcription PIC consists of Pol II and general transcription factors TFIID, TFIIA, TFIIB, TFIIF, TFIIE, and TFIIH. Previous structural studies focused on PIC assembled on TATA box promoters with TFIID replaced by its subunit, TATA box-binding protein (TBP). However, the megadalton TFIID complex is essential for promoter recognition, TBP loading onto promoter, and PIC assembly for almost all Pol II-mediated transcription, especially on the TATA-less promoters, which account for ∼85% of core promoters of human coding genes. The functions of TFIID could not be replaced by TBP. The recent breakthrough in structure determination of TFIID-based PIC complexes in different assembly stages revealed mechanistic insights into PIC assembly on TATA box and TATA-less promotes and provided a framework for further investigation of transcription initiation.
    DOI:  https://doi.org/10.1016/j.sbi.2022.102404
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