bims-tricox 2022-08-28 papers

bims-tricox

Biomed News

on Translation, ribosomes and COX

Issue of 2022–08–28
eight papers selected by
Yash Verma, University of Delhi South Campus

Mutational Analyses of the Cysteine-Rich Domain of Yvh1, a Protein Required for Translational Competency in Yeast.
Wide mutational analysis to ascertain the functional roles of eL33 in ribosome biogenesis and translation initiation.
Ribosome profiling enhances understanding of mycobacterial translation.
Engineering Ribosomes to Alleviate Abiotic Stress in Plants: A Perspective.
Internal Ribosome Entry Site (IRES)-Mediated Translation and Its Potential for Novel mRNA-Based Therapy Development.
Duplicated ribosomal protein paralogs promote alternative translation and drug resistance.
Rbp95 binds to 25S rRNA helix H95 and cooperates with the Npa1 complex during early pre-60S particle maturation.
Ribosomes: The New Role of Ribosomal Proteins as Natural Antimicrobials.

Biology (Basel). 2022 Aug 22. pii: 1246. [Epub ahead of print]11(8):

Mutational Analyses of the Cysteine-Rich Domain of Yvh1, a Protein Required for Translational Competency in Yeast.

Hannah Zang, Robert Shackelford, Alice Bewley, Alexander E Beeser.

  Ribosome assembly is a complex biological process facilitated by >200 trans-acting factors (TAFs) that function as scaffolds, place-holders or complex remodelers to promote efficient and directional ribosomal subunit assembly but are not themselves part of functional ribosomes. One such yeast TAF is encoded by Mrt4 which assembles onto pre-60S complexes in the nuclear compartment and remains bound to pre-60S complexes as they are exported into the cytoplasm. There, Mrt4 is displaced from pre-60S complexes facilitating the subsequent addition of the ribosomal stalk complex (P0/P1/P2). Ribosomal stalk proteins interact with translational GTPases (trGTPase) which facilitate and control protein synthesis on the ribosome. The rRNA-binding domain of Mrt4 is structurally similar to P0, with both proteins binding to the same interface of pre-60S subunits in a mutually exclusive manner; the addition of the ribosomal stalk therefore requires the displacement of Mrt4 from pre-60S subunits. Mrt4 removal requires the C-terminal cysteine-rich domain (CRD) of the dual-specificity phosphatase Yvh1. Unlike many other TAFs, yeast lacking Yvh1 are viable but retain Mrt4 on cytoplasmic pre-60S complexes precluding ribosomal stalk addition. Although Yvh1's role in Mrt4 removal is well established, how Yvh1 accomplishes this is largely unknown. Here, we report an unbiased genetic screen to isolate Yvh1 variants that fail to displace Mrt4 from pre-60S ribosomes. Bioorthogonal non-canonical amino acid tagging (BONCAT) approaches demonstrate that these YVH1 loss-of-function variants also display defects in nascent protein production. The further characterization of one LOF variant, Yvh1F283L, establishes it as an expression-dependent, dominant-negative variant capable of interfering with endogenous Yvh1 function, and we describe how this Yvh1 variant can be used as a novel probe to better understand ribosome maturation and potentially ribosome heterogeneity in eukaryotes.

Keywords:  Mrt4; Yvh1; nascent protein translation; ribosome maturation

DOI:  https://doi.org/10.3390/biology11081246
Curr Genet. 2022 Aug 22.

Wide mutational analysis to ascertain the functional roles of eL33 in ribosome biogenesis and translation initiation.

Pilar Martín-Marcos, Álvaro Gil-Hernández, Mercedes Tamame.

  An extensive mutational analysis of RPL33A, encoding the yeast ribosomal protein L33A (eL33) allowed us to identify several novel rpl33a mutants with different translational phenotypes. Most of the rpl33a mutants are defective in the processing of 35S and 27S pre-rRNA precursors and the production of mature rRNAs, exhibiting reductions in the amounts of ribosomal subunits and altered polysome profiles. Some of the rpl33a mutants exhibit a Gcd- phenotype of constitutive derepression of GCN4 translation and strong slow growth phenotypes at several temperatures. Interestingly, some of the later mutants also show a detectable increase in the UUG/AUG translation initiation ratio that can be suppressed by eIF1 overexpression, suggesting a requirement for eL33 and a correct 60S/40S subunit ratio for the proper recognition of the AUG start codon. In addition to producing differential reductions in the rates of pre-rRNA maturation and perhaps in r-protein assembly, most of the point rpl33a mutations alter specific molecular interactions of eL33 with the rRNAs and other r-proteins in the 60S structure. Thus, rpl33a mutations cause distinctive effects on the abundance and/or functionality of 60S subunits, leading to more or less pronounced defects in the rates and fidelity of mRNA translation.

Keywords:  GCN4; Ribosome; Translation; Yeast; eL33; rRNA processing

DOI:  https://doi.org/10.1007/s00294-022-01251-1
Front Microbiol. 2022 ;13 976550

Ribosome profiling enhances understanding of mycobacterial translation.

Elizabeth B Sawyer, Teresa Cortes.

  A recent addition to the -omics toolkit, ribosome profiling, enables researchers to gain insight into the process and regulation of translation by mapping fragments of mRNA protected from nuclease digestion by ribosome binding. In this review, we discuss how ribosome profiling applied to mycobacteria has led to discoveries about translational regulation. Using case studies, we show that the traditional view of "canonical" translation mechanisms needs expanding to encompass features of mycobacterial translation that are more widespread than previously recognized. We also discuss the limitations of the method and potential future developments that could yield further insight into the fundamental biology of this important human pathogen.

Keywords:  Mycobacterium tuberculosis; non-canonical translation; omics; ribosome profiling; translation initiation

DOI:  https://doi.org/10.3389/fmicb.2022.976550
Plants (Basel). 2022 Aug 12. pii: 2097. [Epub ahead of print]11(16):

Engineering Ribosomes to Alleviate Abiotic Stress in Plants: A Perspective.

Leticia Dias-Fields, Katarzyna P Adamala.

  As the centerpiece of the biomass production process, ribosome activity is highly coordinated with environmental cues. Findings revealing ribosome subgroups responsive to adverse conditions suggest this tight coordination may be grounded in the induction of variant ribosome compositions and the differential translation outcomes they might produce. In this perspective, we go through the literature linking ribosome heterogeneity to plants' abiotic stress response. Once unraveled, this crosstalk may serve as the foundation of novel strategies to custom cultivars tolerant to challenging environments without the yield penalty.

Keywords:  abiotic stress; genetic engineering; perspective; plant ribosome; ribosome heterogeneity; stress tolerance; synthetic biology

DOI:  https://doi.org/10.3390/plants11162097
Biomedicines. 2022 Aug 02. pii: 1865. [Epub ahead of print]10(8):

Internal Ribosome Entry Site (IRES)-Mediated Translation and Its Potential for Novel mRNA-Based Therapy Development.

Rita Marques, Rafaela Lacerda, Luísa Romão.

  Many conditions can benefit from RNA-based therapies, namely, those targeting internal ribosome entry sites (IRESs) and their regulatory proteins, the IRES trans-acting factors (ITAFs). IRES-mediated translation is an alternative mechanism of translation initiation, known for maintaining protein synthesis when canonical translation is impaired. During a stress response, it contributes to cell reprogramming and adaptation to the new environment. The relationship between IRESs and ITAFs with tumorigenesis and resistance to therapy has been studied in recent years, proposing new therapeutic targets and treatments. In addition, IRES-dependent translation initiation dysregulation is also related to neurological and cardiovascular diseases, muscular atrophies, or other syndromes. The participation of these structures in the development of such pathologies has been studied, yet to a far lesser extent than in cancer. Strategies involving the disruption of IRES-ITAF interactions or the modification of ITAF expression levels may be used with great impact in the development of new therapeutics. In this review, we aim to comprehend the current data on groups of human pathologies associated with IRES and/or ITAF dysregulation and their application in the designing of new therapeutic approaches using them as targets or tools. Thus, we wish to summarise the evidence in the field hoping to open new promising lines of investigation toward personalised treatments.

Keywords:  IRES trans-acting factors; IRES-based multicistronic vectors; RNA-based therapies; antisense oligonucleotides; internal ribosome entry sites

DOI:  https://doi.org/10.3390/biomedicines10081865
Nat Commun. 2022 Aug 23. 13(1): 4938

Duplicated ribosomal protein paralogs promote alternative translation and drug resistance.

Mustafa Malik Ghulam, Mathieu Catala, Gaspard Reulet, Michelle S Scott, Sherif Abou Elela.

Ribosomes are often seen as monolithic machines produced from uniformly regulated genes. However, in yeast most ribosomal proteins come from duplicated genes. Here, we demonstrate that gene duplication may serve as a stress-adaptation mechanism modulating the global proteome through the differential expression of ribosomal protein paralogs. Our data indicate that the yeast paralog pair of the ribosomal protein L7/uL30 produces two differentially acetylated proteins. Under normal conditions most ribosomes incorporate the hypo-acetylated major form favoring the translation of genes with short open reading frames. Exposure to drugs, on the other hand, increases the production of ribosomes carrying the hyper-acetylated minor paralog that increases translation of long open reading frames. Many of these paralog-dependent genes encode cell wall proteins that could promote tolerance to drugs as their translation increases after exposure to drugs. Together our data suggest a mechanism of translation control that functions through a differential use of near-identical ribosomal protein isoforms.

DOI: https://doi.org/10.1038/s41467-022-32717-y
Nucleic Acids Res. 2022 Aug 26. pii: gkac724. [Epub ahead of print]

Rbp95 binds to 25S rRNA helix H95 and cooperates with the Npa1 complex during early pre-60S particle maturation.

Priya Bhutada, Sébastien Favre, Mariam Jaafar, Jutta Hafner, Laura Liesinger, Stefan Unterweger, Karin Bischof, Barbara Darnhofer, Devanarayanan Siva Sankar, Gerald Rechberger, Raghida Abou Merhi, Simon Lebaron, Ruth Birner-Gruenberger, Dieter Kressler, Anthony K Henras, Brigitte Pertschy.

Eukaryotic ribosome synthesis involves more than 200 assembly factors, which promote ribosomal RNA (rRNA) processing, modification and folding, and assembly of ribosomal proteins. The formation and maturation of the earliest pre-60S particles requires structural remodeling by the Npa1 complex, but is otherwise still poorly understood. Here, we introduce Rbp95 (Ycr016w), a constituent of early pre-60S particles, as a novel ribosome assembly factor. We show that Rbp95 is both genetically and physically linked to most Npa1 complex members and to ribosomal protein Rpl3. We demonstrate that Rbp95 is an RNA-binding protein containing two independent RNA-interacting domains. In vivo, Rbp95 associates with helix H95 in the 3' region of the 25S rRNA, in close proximity to the binding sites of Npa1 and Rpl3. Additionally, Rbp95 interacts with several snoRNAs. The absence of Rbp95 results in alterations in the protein composition of early pre-60S particles. Moreover, combined mutation of Rbp95 and Npa1 complex members leads to a delay in the maturation of early pre-60S particles. We propose that Rbp95 acts together with the Npa1 complex during early pre-60S maturation, potentially by promoting pre-rRNA folding events within pre-60S particles.

DOI: https://doi.org/10.1093/nar/gkac724
Int J Mol Sci. 2022 Aug 14. pii: 9123. [Epub ahead of print]23(16):

Ribosomes: The New Role of Ribosomal Proteins as Natural Antimicrobials.

Jessica J Hurtado-Rios, Ulises Carrasco-Navarro, Julio Cesar Almanza-Pérez, Edith Ponce-Alquicira.

  Moonlighting proteins are those capable of performing more than one biochemical or biophysical function within the same polypeptide chain. They have been a recent focus of research due to their potential applications in the health, pharmacological, and nutritional sciences. Among them, some ribosomal proteins involved in assembly and protein translation have also shown other functionalities, including inhibiting infectious bacteria, viruses, parasites, fungi, and tumor cells. Therefore, they may be considered antimicrobial peptides (AMPs). However, information regarding the mechanism of action of ribosomal proteins as AMPs is not yet fully understood. Researchers have suggested that the antimicrobial activity of ribosomal proteins may be associated with an increase in intracellular reactive oxidative species (ROS) in target cells, which, in turn, could affect membrane integrity and cause their inactivation and death. Moreover, the global overuse of antibiotics has resulted in an increase in pathogenic bacteria resistant to common antibiotics. Therefore, AMPs such as ribosomal proteins may have potential applications in the pharmaceutical and food industries in the place of antibiotics. This article provides an overview of the potential roles of ribosomes and AMP ribosomal proteins in conjunction with their potential applications.

Keywords:  antimicrobial peptides; moonlighting protein; ribosomal protein; ribosome

DOI:  https://doi.org/10.3390/ijms23169123