bims-tricox Biomed News
on Translation, ribosomes and COX
Issue of 2022–06–26
seven papers selected by
Yash Verma, University of Delhi South Campus
  1. eIF5B and eIF1A reorient initiator tRNA to allow ribosomal subunit joining.
  2. Structural basis of Tom20 and Tom22 cytosolic domains as the human TOM complex receptors.
  3. Druggable differences: Targeting mechanistic differences between trans-translation and translation for selective antibiotic action.
  4. Orchestrating ribosomal RNA folding during ribosome assembly.
  5. Additional principles that govern the release of pre-ribosomes from the nucleolus into the nucleoplasm in yeast.
  6. Coordination of metal center biogenesis in human cytochrome c oxidase.
  7. Ribosome biogenesis and the cellular energy economy.
  1. Nature. 2022 Jun 22.
    eIF5B and eIF1A reorient initiator tRNA to allow ribosomal subunit joining.
    Christopher P Lapointe, Rosslyn Grosely, Masaaki Sokabe, Carlos Alvarado, Jinfan Wang, Elizabeth Montabana, Nancy Villa, Byung-Sik Shin, Thomas E Dever, Christopher S Fraser, Israel S Fernández, Joseph D Puglisi.
      Translation initiation defines the identity and quantity of a synthesized protein. The process is dysregulated in many human diseases1,2. A key commitment step is when the ribosomal subunits join at a translation start site on a messenger RNA to form a functional ribosome. Here, we combined single-molecule spectroscopy and structural methods using an in vitro reconstituted system to examine how the human ribosomal subunits join. Single-molecule fluorescence revealed when the universally conserved eukaryotic initiation factors eIF1A and eIF5B associate with and depart from initiation complexes. Guided by single-molecule dynamics, we visualized initiation complexes that contained both eIF1A and eIF5B using single-particle cryo-electron microscopy. The resulting structure revealed how eukaryote-specific contacts between the two proteins remodel the initiation complex to orient the initiator aminoacyl-tRNA in a conformation compatible with ribosomal subunit joining. Collectively, our findings provide a quantitative and architectural framework for the molecular choreography orchestrated by eIF1A and eIF5B during translation initiation in humans.
    DOI:  https://doi.org/10.1038/s41586-022-04858-z
  2. Proc Natl Acad Sci U S A. 2022 Jun 28. 119(26): e2200158119
    Structural basis of Tom20 and Tom22 cytosolic domains as the human TOM complex receptors.
    Jiayue Su, Desheng Liu, Fan Yang, Mei-Qing Zuo, Chang Li, Meng-Qiu Dong, Shan Sun, Sen-Fang Sui.
      Mitochondrial preproteins synthesized in cytosol are imported into mitochondria by a multisubunit translocase of the outer membrane (TOM) complex. Functioned as the receptor, the TOM complex components, Tom 20, Tom22, and Tom70, recognize the presequence and further guide the protein translocation. Their deficiency has been linked with neurodegenerative diseases and cardiac pathology. Although several structures of the TOM complex have been reported by cryoelectron microscopy (cryo-EM), how Tom22 and Tom20 function as TOM receptors remains elusive. Here we determined the structure of TOM core complex at 2.53 Å and captured the structure of the TOM complex containing Tom22 and Tom20 cytosolic domains at 3.74 Å. Structural analysis indicates that Tom20 and Tom22 share a similar three-helix bundle structural feature in the cytosolic domain. Further structure-guided biochemical analysis reveals that the Tom22 cytosolic domain is responsible for binding to the presequence, and the helix H1 is critical for this binding. Altogether, our results provide insights into the functional mechanism of the TOM complex recognizing and transferring preproteins across the mitochondrial membrane.
    Keywords:  TOM complex; Tom20; Tom22; cryo-EM; mitochondria
    DOI:  https://doi.org/10.1073/pnas.2200158119
  3. Bioessays. 2022 Jun 19. e2200046
    Druggable differences: Targeting mechanistic differences between trans-translation and translation for selective antibiotic action.
    Pooja Srinivas, Kenneth C Keiler, Christine M Dunham.
      Bacteria use trans-translation to rescue stalled ribosomes and target incomplete proteins for proteolysis. Despite similarities between tRNAs and transfer-messenger RNA (tmRNA), the key molecule for trans-translation, new structural and biochemical data show important differences between translation and trans-translation at most steps of the pathways. tmRNA and its binding partner, SmpB, bind in the A site of the ribosome but do not trigger the same movements of nucleotides in the rRNA that are required for codon recognition by tRNA. tmRNA-SmpB moves from the A site to the P site of the ribosome without subunit rotation to generate hybrid states, and moves from the P site to a site outside the ribosome instead of to the E site. During catalysis, transpeptidation to tmRNA appears to require the ribosomal protein bL27, which is dispensable for translation, suggesting that this protein may be conserved in bacteria due to trans-translation. These differences provide insights into the fundamental nature of trans-translation, and provide targets for new antibiotics that may have decrease cross-reactivity with eukaryotic ribosomes.
    Keywords:  antibiotics; protein synthesis; ribosome; tRNA; tmRNA; trans-translation; translation
    DOI:  https://doi.org/10.1002/bies.202200046
  4. Bioessays. 2022 Jun 25. e2200066
    Orchestrating ribosomal RNA folding during ribosome assembly.
    Michaela Oborská-Oplová, Stefan Gerhardy, Vikram Govind Panse.
      Construction of the eukaryotic ribosome is a complex process in which a nascent ribosomal RNA (rRNA) emerging from RNA Polymerase I hierarchically folds into a native three-dimensional structure. Modular assembly of individual RNA domains through interactions with ribosomal proteins and a myriad of assembly factors permit efficient disentanglement of the error-prone RNA folding process. Following these dynamic events, long-range tertiary interactions are orchestrated to compact rRNA. A combination of genetic, biochemical, and structural studies is now providing clues into how a nascent rRNA is transformed into a functional ribosome with high precision. With this essay, we aim to draw attention to the poorly understood process of establishing correct RNA tertiary contacts during ribosome formation.
    Keywords:  RNA folding; RNA-binding proteins; co-transcriptional ribosome assembly; low temperature; modular rRNA compaction
    DOI:  https://doi.org/10.1002/bies.202200066
  5. Nucleic Acids Res. 2022 Jun 23. pii: gkac430. [Epub ahead of print]
    Additional principles that govern the release of pre-ribosomes from the nucleolus into the nucleoplasm in yeast.
    Amber J LaPeruta, Jelena Micic, John L Woolford.
      During eukaryotic ribosome biogenesis, pre-ribosomes travel from the nucleolus, where assembly is initiated, to the nucleoplasm and then are exported to the cytoplasm, where assembly concludes. Although nuclear export of pre-ribosomes has been extensively investigated, the release of pre-ribosomes from the nucleolus is an understudied phenomenon. Initial data indicate that unfolded rRNA interacts in trans with nucleolar components and that, when rRNA folds due to ribosomal protein (RP) binding, the number of trans interactions drops below the threshold necessary for nucleolar retention. To validate and expand on this idea, we performed a bioinformatic analysis of the protein components of the Saccharomyces cerevisiae ribosome assembly pathway. We found that ribosome biogenesis factors (RiBi factors) contain significantly more predicted trans interacting regions than RPs. We also analyzed cryo-EM structures of ribosome assembly intermediates to determine how nucleolar pre-ribosomes differ from post-nucleolar pre-ribosomes, specifically the capacity of RPs, RiBi factors, and rRNA components to interact in trans. We observed a significant decrease in the theoretical trans-interacting capability of pre-ribosomes between nucleolar and post-nucleolar stages of assembly due to the release of RiBi factors from particles and the folding of rRNA. Here, we provide a mechanism for the release of pre-ribosomes from the nucleolus.
    DOI:  https://doi.org/10.1093/nar/gkac430
  6. Nat Commun. 2022 Jun 24. 13(1): 3615
    Coordination of metal center biogenesis in human cytochrome c oxidase.
    Eva Nývltová, Jonathan V Dietz, Javier Seravalli, Oleh Khalimonchuk, Antoni Barrientos.
      Mitochondrial cytochrome c oxidase (CcO) or respiratory chain complex IV is a heme aa3-copper oxygen reductase containing metal centers essential for holo-complex biogenesis and enzymatic function that are assembled by subunit-specific metallochaperones. The enzyme has two copper sites located in the catalytic core subunits. The COX1 subunit harbors the CuB site that tightly associates with heme a3 while the COX2 subunit contains the binuclear CuA site. Here, we report that in human cells the CcO copper chaperones form macromolecular assemblies and cooperate with several twin CX9C proteins to control heme a biosynthesis and coordinate copper transfer sequentially to the CuA and CuB sites. These data on CcO illustrate a mechanism that regulates the biogenesis of macromolecular enzymatic assemblies with several catalytic metal redox centers and prevents the accumulation of cytotoxic reactive assembly intermediates.
    DOI:  https://doi.org/10.1038/s41467-022-31413-1
  7. Curr Biol. 2022 Jun 20. pii: S0960-9822(22)00719-9. [Epub ahead of print]32(12): R611-R617
    Ribosome biogenesis and the cellular energy economy.
    David Shore, Benjamin Albert.
      Cell growth relies upon the ability to produce new proteins, which requires energy and chemical precursors, and an adequate supply of the molecular machines for protein synthesis - ribosomes. Although not widely appreciated, ribosomes are remarkably abundant in all cells. For example, in a rapidly growing yeast cell there are ∼2-4 x 105 ribosomes, produced and exported to the cytoplasm at a rate of ∼2,000-4,000 per minute, with ribosomal proteins making up ∼50% of total cellular protein number and ∼30% of cellular protein mass. Even in a typical human cell ribosomal proteins constitute ∼4-6% of total protein mass, and ribosomes are present at ∼107 per cell. We begin this primer by exploring the tight relationship between ribosome production and cell growth, which has important implications not just for the cell's global protein expression profile and maximum growth rate, but also for the molecular composition of the ribosome itself. We then discuss how and to what extent the expression of the RNA and protein components of ribosomes is fine-tuned to match the cell's needs and minimise waste. Finally, we highlight the importance of coordinated ribosomal RNA (rRNA) and ribosomal protein expression in eukaryotes and explore how defects in this process are associated with proteotoxicity and disease. A central underlying question addressed throughout is whether regulation of ribosome biogenesis has evolved to optimise energy efficiency or is instead (or in addition) driven by other goals, such as maximising cell growth rate, promoting adaptation to changing environmental conditions, or maintaining the stability of the cellular proteome.
    DOI:  https://doi.org/10.1016/j.cub.2022.04.083
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