bims-tricox Biomed News
on Translation, ribosomes and COX
Issue of 2022‒07‒10
fourteen papers selected by
Yash Verma
University of Delhi South Campus


  1. Biochemistry (Mosc). 2022 Jun;87(6): 500-510
      Solving the structures of bacterial, archaeal, and eukaryotic ribosomes by crystallography and cryo-electron microscopy has given an impetus for studying intracellular regulatory proteins affecting various stages of protein translation. Among them are ribosome hibernation factors, which have been actively investigated during the last decade. These factors are involved in the regulation of protein biosynthesis under stressful conditions. The main role of hibernation factors is the reduction of energy consumption for protein biosynthesis and preservation of existing functional ribosomes from degradation, which increases cell survival under unfavorable conditions. Despite a broad interest in this topic, only a few articles have been published on the ribosomal silencing factor S (RsfS). According to the results of these studies, RsfS can be assigned to the group of hibernation factors. However, recent structural studies of the 50S ribosomal subunit maturation demonstrated that RsfS has the features inherent to biogenesis factors for example, ability to bind to the immature ribosomal subunit (similar to the RsfS mitochondrial ortholog MALSU1, mitochondrial assembly of ribosomal large subunit 1). In this review, we summarized the information on the function and structural features RsfS, as well as compared RsfS with MALSU1 in order to answer the emerging question on whether RsfS is a hibernation factor or a ribosome biogenesis factor. We believe that this review might promote future studies of the RsfS-involving molecular mechanisms, which so far remain completely unknown.
    Keywords:  RsfS; hibernation factor; ribosome; ribosome biogenesis factor
    DOI:  https://doi.org/10.1134/S0006297922060025
  2. Nucleic Acids Res. 2022 Jul 09. pii: gkac597. [Epub ahead of print]
      Translocation of messenger RNA (mRNA) and transfer RNA (tRNA) substrates through the ribosome during protein synthesis, an exemplar of directional molecular movement in biology, entails a complex interplay of conformational, compositional, and chemical changes. The molecular determinants of early translocation steps have been investigated rigorously. However, the elements enabling the ribosome to complete translocation and reset for subsequent protein synthesis reactions remain poorly understood. Here, we have combined molecular simulations with single-molecule fluorescence resonance energy transfer imaging to gain insights into the rate-limiting events of the translocation mechanism. We find that diffusive motions of the ribosomal small subunit head domain to hyper-swivelled positions, governed by universally conserved rRNA, can maneuver the mRNA and tRNAs to their fully translocated positions. Subsequent engagement of peptidyl-tRNA and disengagement of deacyl-tRNA from mRNA, within their respective small subunit binding sites, facilitate the ribosome resetting mechanism after translocation has occurred to enable protein synthesis to resume.
    DOI:  https://doi.org/10.1093/nar/gkac597
  3. J Biol Chem. 2022 Jun 29. pii: S0021-9258(22)00656-1. [Epub ahead of print] 102214
      Mitochondrial translation is a highly regulated process, and newly synthesized mitochondrial products must first associate with several nuclear-encoded auxiliary factors to form oxidative phosphorylation complexes. The output of mitochondrial products should therefore be in stoichiometric equilibrium with the nuclear-encoded products to prevent unnecessary energy expense or the accumulation of pro-oxidant assembly modules. In the mtDNA of Saccharomyces cerevisiae, COX1 encodes subunit 1 of the cytochrome c oxidase, and COB the central core of the cytochrome bc1 electron transfer complex; however, factors regulating the expression of these mitochondrial products are not well described. In this study, we identified Mrx9p as a new factor that controls COX1 and COB expression. We isolated MRX9 in a screen for mitochondrial factors that cause poor accumulation of newly synthesized Cox1p and compromised transition to the respiratory metabolism. Northern analyses indicated lower levels of COX1 and COB mature mRNAs accompanied by an accumulation of unprocessed transcripts in the presence of excess Mrx9p. Furthermore, in a strain devoid of mitochondrial introns, MRX9 overexpression did not affect COX1 and COB translation or respiratory adaptation, implying Mrx9p regulates processing of COX1 and COB RNAs. In addition, we found Mrx9p was localized in the mitochondrial inner membrane, facing the matrix, as a portion of it co-sedimented with mitoribosome subunits and its removal or overexpression altered Mss51p sedimentation. Finally, we showed accumulation of newly synthesized Cox1p in the absence of Mrx9p was diminished in cox14 null mutants. Taken together, these data indicate a regulatory role of Mrx9p in COX1 RNA processing.
    Keywords:  Saccharomyces cerevisiae; intron processing; mitochondrial translation
    DOI:  https://doi.org/10.1016/j.jbc.2022.102214
  4. Methods Mol Biol. 2022 ;2533 99-126
      The process of eukaryotic ribosome assembly stretches across the nucleolus, the nucleoplasm and the cytoplasm, and therefore relies on efficient nucleocytoplasmic transport. In yeast, the import machinery delivers ~140,000 ribosomal proteins every minute to the nucleus for ribosome assembly. At the same time, the export machinery facilitates translocation of ~2000 pre-ribosomal particles every minute through ~200 nuclear pore complexes (NPC) into the cytoplasm. Eukaryotic ribosome assembly also requires >200 conserved assembly factors, which transiently associate with pre-ribosomal particles. Their site(s) of action on maturing pre-ribosomes are beginning to be elucidated. In this chapter, we outline protocols that enable rapid biochemical isolation of pre-ribosomal particles for single particle cryo-electron microscopy (cryo-EM) and in vitro reconstitution of nuclear transport processes. We discuss cell-biological and genetic approaches to investigate how the ribosome assembly and the nucleocytoplasmic transport machineries collaborate to produce functional ribosomes.
    Keywords:  Budding Yeast; Nuclear Export; Nuclear Import; Ribosome Assembly; preribosome structure
    DOI:  https://doi.org/10.1007/978-1-0716-2501-9_7
  5. Methods Mol Biol. 2022 ;2533 217-228
      Protein synthesis in eukaryotes is carried out by 80S ribosomes with the help of many specific translation factors. Translation comprises four major steps: initiation, elongation, termination, and ribosome recycling. In this review, we provide a comprehensive list of translation factors required for protein synthesis in yeast and higher eukaryotes and summarize the mechanisms of each individual phase of eukaryotic translation.
    Keywords:  Ribosome; Translation; Yeast; mRNA; tRNA
    DOI:  https://doi.org/10.1007/978-1-0716-2501-9_13
  6. Methods Mol Biol. 2022 ;2533 71-80
      Technical advances have pushed the resolution limit of single-particle cryo-electron microscopy (cryo-EM) throughout the past decade and made the technique accessible to a wide range of samples. Among them, multisubunit DNA-dependent RNA polymerases (Pols) are a prominent example. This review aims at briefly summarizing the architecture and structural adaptations of Pol I, highlighting the importance of cryo-electron microscopy in determining the structures of transcription complexes.
    Keywords:  Cryo-electron microscopy; Pre-rRNA transcription; RNA polymerase I
    DOI:  https://doi.org/10.1007/978-1-0716-2501-9_5
  7. Methods Mol Biol. 2022 ;2533 259-280
      Protein synthesis is an essential and highly regulated cellular process. To facilitate the understanding of eukaryotic translation, we have assembled an in vitro translation system from yeast using purified components to recapitulate the initiation and elongation phases of protein synthesis. Here, we describe methods to express and purify the components of the translation system and the assays for their functional characterization.
    Keywords:  Ribosome; Translation; Yeast; mRNA; tRNA
    DOI:  https://doi.org/10.1007/978-1-0716-2501-9_16
  8. Methods Mol Biol. 2022 ;2533 81-96
      Recent technological progress revealed new prospects of high-resolution structure determination of macromolecular complexes using cryo-electron microscopy (cryo-EM) . In the field of RNA polymerase (Pol) I research, a number of cryo-EM studies contributed to understanding the highly specialized mechanisms underlying the transcription of ribosomal RNA genes . Despite a broad applicability of the cryo-EM method itself, preparation of samples for high-resolution data collection can be challenging. Here, we describe strategies for the purification and stabilization of Pol I complexes, exemplarily considering advantages and disadvantages of the methodology. We further provide an easy-to-implement protocol for the coating of EM-grids with self-made carbon support films. In sum, we present an efficient workflow for cryo-grid preparation and optimization, including early stage cryo-EM screening that can be adapted to a wide range of soluble samples for high-resolution structure determination .
    Keywords:  Grid preparation; Negative staining; Plunge freezing; Preparation of transcription complexes; RNA polymerase I; Single-particle cryo-electron microscopy
    DOI:  https://doi.org/10.1007/978-1-0716-2501-9_6
  9. Methods Mol Biol. 2022 ;2533 3-22
      Ribosomes are universally conserved ribonucleoprotein complexes involved in the decoding of the genetic information contained in messenger RNAs into proteins. Accordingly, ribosome biogenesis is a fundamental cellular process required for functional ribosome homeostasis and to preserve satisfactory gene expression capability.Although the ribosome is universally conserved, its biogenesis shows an intriguing degree of variability across the tree of life . These differences also raise yet unresolved questions. Among them are (a) what are, if existing, the remaining ancestral common principles of ribosome biogenesis ; (b) what are the molecular impacts of the evolution history and how did they contribute to (re)shape the ribosome biogenesis pathway across the tree of life ; (c) what is the extent of functional divergence and/or convergence (functional mimicry), and in the latter case (if existing) what is the molecular basis; (d) considering the universal ribosome conservation, what is the capability of functional plasticity and cellular adaptation of the ribosome biogenesis pathway?In this review, we provide a brief overview of ribosome biogenesis across the tree of life and try to illustrate some potential and/or emerging answers to these unresolved questions.
    Keywords:  Adaptation; Archaea; Bacteria; Comparative biology; Eukaryotes; Evolution; Maturation; RNA modifications; Ribosome assembly; Ribosome biogenesis; Tree of life; rRNA
    DOI:  https://doi.org/10.1007/978-1-0716-2501-9_1
  10. Genes Dis. 2022 May;9(3): 731-740
      The CRISPR/Cas9 system, originally derived from the prokaryotic adaptive immune system, has been developed as efficient genome editing tools. It enables precise gene manipulation on chromosomal DNA through the specific binding of programmable sgRNA to target DNA, and the Cas9 protein, which has endonuclease activity, will cut a double strand break at specific locus. However, Cas9 is a foreign protein in mammalian cells, and the potential risks associated with its introduction into mammalian cells are not fully understood. In this study, we performed pull-down and mass spectrometry (MS) analysis of Streptococcus pyogenes Cas9 (SpyCas9) interacting proteins in HEK293T cells and showed that the majority of Cas9-associated proteins identified by MS were localized in the nucleolus. Interestingly, we further discovered that the Cas9 protein contains a sequence encoding a nucleolus detention signal (NoDS). Compared with wild-type (WT) Cas9, NoDS-mutated variants of Cas9 (mCas9) are less stable, although their gene editing activity is minimally affected. Overexpression of WT Cas9, but not mCas9, causes general effects on transcription and protein translation in the host cell. Overall, identification of NoDS in Cas9 will improve the understanding of Cas9's biological function in vivo, and the removal of NoDS in Cas9 may enhance its safety for future clinical use.
    Keywords:  CRISPR/Cas9; Gene editing; Global transcription; Nucleolus detention signal; Translation
    DOI:  https://doi.org/10.1016/j.gendis.2020.09.003
  11. Heliyon. 2022 Jul;8(7): e09820
      Understanding how cells grow and adapt under various nutrient conditions is pivotal in the study of biological stoichiometry. Recent studies provide empirical evidence that cells use multiple strategies to maintain an optimal protein production rate under different nutrient conditions. Mathematical models can provide a solid theoretical foundation that can explain experimental observations and generate testable hypotheses to further our understanding of the growth process. In this study, we generalize a modeling framework that centers on the translation process and study its asymptotic behaviors to validate algebraic manipulations involving the steady states. Using experimental results on the growth of E. coli under C-, N-, and P-limited environments, we simulate the expected quantitative measurements to show the feasibility of using the model to explain empirical evidence. Our results support the findings that cells employ multiple strategies to maintain a similar protein production rate across different nutrient limitations. Moreover, we find that the previous study underestimates the significance of certain biological rates, such as the binding rate of ribosomes to mRNA and the transition rate between different ribosomal stages. Furthermore, our simulation shows that the strategies used by cells under C- and P-limitations result in a faster overall growth dynamics than under N-limitation. In conclusion, the general modeling framework provides a valuable platform to study cell growth under different nutrient supply conditions, which also allows straightforward extensions to the coupling of transcription, translation, and energetics to deepen our understanding of the growth process.
    Keywords:  Cell growth; Growth rate hypothesis; Inactive ribosomes; Mathematical analysis; Model formulation; Model validation; Translation dynamics
    DOI:  https://doi.org/10.1016/j.heliyon.2022.e09820
  12. Bio Protoc. 2022 May 05. 12(9): e4407
      Mammalian tissues are highly heterogenous and complex, posing a challenge in understanding the molecular mechanisms regulating protein expression within various tissues. Recent studies have shown that translation at the level of the ribosome is highly regulated, and can vary independently of gene expression observed at a transcriptome level, as well as between cell populations, contributing to the diversity of mammalian tissues. Earlier methods that analyzed gene expression at the level of translation, such as polysomal- or ribosomal-profiling, required large amounts of starting material to isolate enough RNA for analysis by microarray or RNA-sequencing. Thus, rare or less abundant cell types within tissues were not able to be properly studied with these methods. Translating ribosome affinity purification (TRAP) utilizes the incorporation of an eGFP-affinity tag on the large ribosome subunit, driven by expression of cell-type specific Cre-lox promoters, to allow for identification and capture of transcripts from actively translating ribosomes in a cell-specific manner. As a result, TRAP offers a unique opportunity to evaluate the entire mRNA translation profile within a specific cell type, and increase our understanding regarding the cellular complexity of mammalian tissues. Graphical abstract: Schematic demonstrating TRAP protocol for identifying ribosome-bound transcripts specifically within cerebellar Purkinje cells.
    Keywords:  Cell-specific translation; Protein synthesis; Translating ribosome affinity purification (TRAP)
    DOI:  https://doi.org/10.21769/BioProtoc.4407
  13. RNA Biol. 2022 Jan;19(1): 877-884
      Stress granules (SGs) are membrane-less condensates composed of RNA and protein that assemble in response to stress stimuli and disassemble when stress is lifted. Both assembly and disassembly are tightly controlled processes, yet, it remains elusive whether mRNAs in SGs completely recover for translation following stress relief. Using RNA-seq of translating fractions in human cell line, we found that higher fraction of the m6A-modified mRNAs recovered for translation compared to unmodified mRNAs, i.e. 95% vs 84%, respectively. Considering structural mRNA analysis, we found that the m6A modification enhances structuring at nucleotides in its close vicinity. Our results suggest that SG-sequestered mRNAs disassemble nearly completely from SGs and the m6A modification may display some advantage to the mRNAs in their recovery for translation likely by m6A-driven structural stabilization.
    Keywords:  deep sequencing; m6A modification; mRNA; mRNA structure; stress granules; translation
    DOI:  https://doi.org/10.1080/15476286.2022.2094137
  14. FEBS Open Bio. 2022 Jul 06.
      ABCE1 protein (Rli1 in S. cerevisiae) is a unique ribosome recycling factor which is composed of an N-terminal FeS cluster domain and two ATPase domains. Here, we report that heterologous expression of human ABCE1 in S. cerevisiae is unable to complement conditional knockout of ABCE1 (Rli1), at a typical experimental temperature of 30 °C. However, low but significant growth was observed at high temperature, 37°C. Considering the close interaction of ABCE1 with translation factors and ribosomal components, the observed temperature-dependent complementation may be attributed to heterologous co-functionality of ABCE1 with S. cerevisiae factor(s), and might reflect functional upregulation of human ABCE1 at its functional temperature.
    Keywords:  ABCE1; S. cerevisiae; heterologous functionality; ribosome recycling; temperature-dependency; translation
    DOI:  https://doi.org/10.1002/2211-5463.13463