bims-tricox Biomed News
on Translation, ribosomes and COX
Issue of 2023‒03‒05
six papers selected by
Yash Verma
University of Delhi South Campus
  1. rRNA methylation by Spb1 regulates the GTPase activity of Nog2 during 60S ribosomal subunit assembly.
  2. The multifaceted mitochondrial OXA insertase.
  3. Near-physiological in vitro assembly of 50S ribosomes involves parallel pathways.
  4. At the Crossroad of Nucleotide Dynamics and Protein Synthesis in Bacteria.
  5. The translating bacterial ribosome at 1.55 Å resolution generated by cryo-EM imaging services.
  6. Metabolic engineering of saccharomyces cerevisiae for glycerol utilization.
  1. Nat Commun. 2023 Mar 02. 14(1): 1207
    rRNA methylation by Spb1 regulates the GTPase activity of Nog2 during 60S ribosomal subunit assembly.
    Kamil Sekulski, Victor Emmanuel Cruz, Christine S Weirich, Jan P Erzberger.
      Biogenesis of the large ribosomal (60S) subunit involves the assembly of three rRNAs and 46 proteins, a process requiring approximately 70 ribosome biogenesis factors (RBFs) that bind and release the pre-60S at specific steps along the assembly pathway. The methyltransferase Spb1 and the K-loop GTPase Nog2 are essential RBFs that engage the rRNA A-loop during sequential steps in 60S maturation. Spb1 methylates the A-loop nucleotide G2922 and a catalytically deficient mutant strain (spb1D52A) has a severe 60S biogenesis defect. However, the assembly function of this modification is currently unknown. Here, we present cryo-EM reconstructions that reveal that unmethylated G2922 leads to the premature activation of Nog2 GTPase activity and capture a Nog2-GDP-AlF4- transition state structure that implicates the direct involvement of unmodified G2922 in Nog2 GTPase activation. Genetic suppressors and in vivo imaging indicate that premature GTP hydrolysis prevents the efficient binding of Nog2 to early nucleoplasmic 60S intermediates. We propose that G2922 methylation levels regulate Nog2 recruitment to the pre-60S near the nucleolar/nucleoplasmic phase boundary, forming a kinetic checkpoint to regulate 60S production. Our approach and findings provide a template to study the GTPase cycles and regulatory factor interactions of the other K-loop GTPases involved in ribosome assembly.
    DOI:  https://doi.org/10.1038/s41467-023-36867-5
  2. Trends Cell Biol. 2023 Feb 28. pii: S0962-8924(23)00020-X. [Epub ahead of print]
    The multifaceted mitochondrial OXA insertase.
    Bettina Homberg, Peter Rehling, Luis Daniel Cruz-Zaragoza.
      Most mitochondrial proteins are synthesized in the cytosol and transported into mitochondria by protein translocases. Yet, mitochondria contain their own genome and gene expression system, which generates proteins that are inserted in the inner membrane by the oxidase assembly (OXA) insertase. OXA contributes to targeting proteins from both genetic origins. Recent data provides insights into how OXA cooperates with the mitochondrial ribosome during synthesis of mitochondrial-encoded proteins. A picture of OXA emerges in which it coordinates insertion of OXPHOS core subunits and their assembly into protein complexes but also participates in the biogenesis of select imported proteins. These functions position the OXA as a multifunctional protein insertase that facilitates protein transport, assembly, and stability at the inner membrane.
    Keywords:  mitochondria; oxidase assembly; oxidative phosphorylation; protein translocation; ribosomes
    DOI:  https://doi.org/10.1016/j.tcb.2023.02.001
  3. Nucleic Acids Res. 2023 Mar 02. pii: gkad082. [Epub ahead of print]
    Near-physiological in vitro assembly of 50S ribosomes involves parallel pathways.
    Xiyu Dong, Lili K Doerfel, Kai Sheng, Jessica N Rabuck-Gibbons, Anna M Popova, Dmitry Lyumkis, James R Williamson.
      Understanding the assembly principles of biological macromolecular complexes remains a significant challenge, due to the complexity of the systems and the difficulties in developing experimental approaches. As a ribonucleoprotein complex, the ribosome serves as a model system for the profiling of macromolecular complex assembly. In this work, we report an ensemble of large ribosomal subunit intermediate structures that accumulate during synthesis in a near-physiological and co-transcriptional in vitro reconstitution system. Thirteen pre-50S intermediate maps covering the entire assembly process were resolved using cryo-EM single-particle analysis and heterogeneous subclassification. Segmentation of the set of density maps reveals that the 50S ribosome intermediates assemble based on fourteen cooperative assembly blocks, including the smallest assembly core reported to date, which is composed of a 600-nucleotide-long folded rRNA and three ribosomal proteins. The cooperative blocks assemble onto the assembly core following defined dependencies, revealing the parallel pathways at both early and late assembly stages of the 50S subunit.
    DOI:  https://doi.org/10.1093/nar/gkad082
  4. Microbiol Mol Biol Rev. 2023 Feb 28. e0004422
    At the Crossroad of Nucleotide Dynamics and Protein Synthesis in Bacteria.
    Lorenzo Eugenio Leiva, Victor Zegarra, Gert Bange, Michael Ibba.
      Nucleotides are at the heart of the most essential biological processes in the cell, be it as key protagonists in the dogma of molecular biology or by regulating multiple metabolic pathways. The dynamic nature of nucleotides, the cross talk between them, and their constant feedback to and from the cell's metabolic state position them as a hallmark of adaption toward environmental and growth challenges. It has become increasingly clear how the activity of RNA polymerase, the synthesis and maintenance of tRNAs, mRNA translation at all stages, and the biogenesis and assembly of ribosomes are fine-tuned by the pools of intracellular nucleotides. With all aspects composing protein synthesis involved, the ribosome emerges as the molecular hub in which many of these nucleotides encounter each other and regulate the state of the cell. In this review, we aim to highlight intracellular nucleotides in bacteria as dynamic characters permanently cross talking with each other and ultimately regulating protein synthesis at various stages in which the ribosome is mainly the principal character.
    Keywords:  RNA; nucleotides; protein synthesis; ribosome; translation
    DOI:  https://doi.org/10.1128/mmbr.00044-22
  5. Nat Commun. 2023 Feb 25. 14(1): 1095
    The translating bacterial ribosome at 1.55 Å resolution generated by cryo-EM imaging services.
    Simon A Fromm, Kate M O'Connor, Michael Purdy, Pramod R Bhatt, Gary Loughran, John F Atkins, Ahmad Jomaa, Simone Mattei.
      Our understanding of protein synthesis has been conceptualised around the structure and function of the bacterial ribosome. This complex macromolecular machine is the target of important antimicrobial drugs, an integral line of defence against infectious diseases. Here, we describe how open access to cryo-electron microscopy facilities combined with bespoke user support enabled structural determination of the translating ribosome from Escherichia coli at 1.55 Å resolution. The obtained structures allow for direct determination of the rRNA sequence to identify ribosome polymorphism sites in the E. coli strain used in this study and enable interpretation of the ribosomal active and peripheral sites at unprecedented resolution. This includes scarcely populated chimeric hybrid states of the ribosome engaged in several tRNA translocation steps resolved at ~2 Å resolution. The current map not only improves our understanding of protein synthesis but also allows for more precise structure-based drug design of antibiotics to tackle rising bacterial resistance.
    DOI:  https://doi.org/10.1038/s41467-023-36742-3
  6. FEMS Yeast Res. 2023 Mar 03. pii: foad014. [Epub ahead of print]
    Metabolic engineering of saccharomyces cerevisiae for glycerol utilization.
    Ziqian Yu, Zhao Chang, Yinhua Lu, Han Xiao.
      Due to its wide availability, glycerol is considered as a promising alternative feedstock for microbial fermentation. As a model eukaryote, Saccharomyces cerevisiae is commonly adopted for bioproduction of various bulk and value-added chemicals, but it does not efficiently utilize glycerol. In this review, the metabolic pathway of glycerol and its regulation in S. cerevisiae are first introduced. Then, strategies, including metabolic engineering of the endogenous pathway, introduction of exogenous pathways, adaptive evolution, and reverse metabolic engineering are summarized for improving the glycerol utilization in S. cerevisiae. Finally, methods for further improving glycerol utilization by S. cerevisiae are proposed. This review provides insights for designing engineered S. cerevisiae for efficient utilization of glycerol.
    Keywords:   saccharomyces cerevisiae ; Adaptive evolution; Synthetic biology; glycerol; metabolic engineering
    DOI:  https://doi.org/10.1093/femsyr/foad014
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