Specialization from synthesis: How ribosome diversity can customize protein function

It was thought that the proteins produced by ribosomes were dictated only by the sequences of the mRNAs they translated, however it is becoming apparent that subpopulations of ribosomes can have unique properties that influence the functions of the proteins they produce. Ribosomes have been engineered to discriminate between different mRNA templates or with unique decoding properties, and many new applications of unnatural ribosomes can be foreseen. In natural systems ribosomes with alternate protein and RNA composition have been shown to selectively translate specific mRNAs. As more is learned about ribosome structure and the mechanisms of translation, new opportunities to engineer ribosomes for applications in biotechnology and synthetic biology can be developed and new examples of ribosome‐mediated regulation of translation are likely to emerge in nature.

• Publication year

  2013

• Venue

  FEBS Letters

• Publication date

  2013-04-17

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1016/j.febslet.2013.02.032PMID 23485824
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Engineered rRNA enhances the efficiency of selenocysteine incorporation during translation.

  2013influential reference
• Crystal structure of the 80S yeast ribosome.

  2012cited by this paper
• Non-canonical translation in RNA viruses

  2012cited by this paper
• Structural insights into eukaryotic ribosomes and the initiation of translation.

  2012cited by this paper
• A mechanistic overview of translation initiation in eukaryotes

  2012cited by this paper
• The human mitochondrial transcriptome and the RNA‐binding proteins that regulate its expression

  2012cited by this paper
• Selective translation during stress in Escherichia coli.

  2012cited by this paper
• Specialized ribosomes: a new frontier in gene regulation and organismal biology

  2012cited by this paper
• C7orf30 specifically associates with the large subunit of the mitochondrial ribosome and is involved in translation

  2012cited by this paper
• Molecular mechanisms of pathology and treatment in Diamond Blackfan Anaemia

  2012cited by this paper
• Structural Diversity in Bacterial Ribosomes: Mycobacterial 70S Ribosome Structure Reveals Novel Features

  2012cited by this paper
• Expanding the genetic code of Drosophila melanogaster.

  2012cited by this paper
• MRPS27 is a pentatricopeptide repeat domain protein required for the translation of mitochondrially encoded proteins

  2012cited by this paper
• Kinetic control of translation initiation in bacteria

  2012cited by this paper
• Selenocysteine Insertion Sequence (SECIS)-binding Protein 2 Alters Conformational Dynamics of Residues Involved in tRNA Accommodation in 80 S Ribosomes*

  2012cited by this paper
• A ribosome-specialized translation initiation pathway is required for cap-dependent translation of vesicular stomatitis virus mRNAs

  2012cited by this paper
• Mechanism of protein biosynthesis in mammalian mitochondria.

  2012cited by this paper
• Oxygenase-catalyzed ribosome hydroxylation occurs in prokaryotes and humans.

  2012cited by this paper
• Quality control in tRNA charging

  2012cited by this paper
• The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria

  2012cited by this paper
• Establishing Rps6 hemizygous mice as a model for studying how ribosomal protein haploinsufficiency impairs erythropoiesis.

  2012cited by this paper
• Structural aspects of mitochondrial translational apparatus.

  2012cited by this paper
• C7orf30 is necessary for biogenesis of the large subunit of the mitochondrial ribosome

  2012cited by this paper
• Atomic structures of the eukaryotic ribosome.

  2012cited by this paper
• One core, two shells: bacterial and eukaryotic ribosomes

  2012cited by this paper
• Designer proteins: applications of genetic code expansion in cell biology

  2012cited by this paper
• Ribosomal deficiencies in Diamond-Blackfan anemia impair translation of transcripts essential for differentiation of murine and human erythroblasts.

  2012cited by this paper
• Crystal Structure of the Eukaryotic 60S Ribosomal Subunit in Complex with Initiation Factor 6

  2011cited by this paper
• Trans‐splicing

  2011cited by this paper
• The structure of the eukaryotic ribosome at 3.0 A resolution. This entry contains proteins of the 40S subunit, ribosome A

  2011cited by this paper
• tRNA mimicry in translation termination and beyond

  2011cited by this paper
• The structure of the eukaryotic ribosome at 3.0 angstrom resolution.

  2011cited by this paper
• The Crystal Structure of the Signal Recognition Particle in Complex with Its Receptor

  2011cited by this paper
• Translation initiation: variations in the mechanism can be anticipated

  2011cited by this paper
• Selective translation of leaderless mRNAs by specialized ribosomes generated by MazF in Escherichia coli.

  2011cited by this paper
• Ribosome-mediated specificity in Hox mRNA translation and vertebrate tissue patterning.

  2011cited by this paper
• Haploinsufficiency for ribosomal protein genes causes selective activation of p53 in human erythroid progenitor cells.

  2011cited by this paper
• Mice with ribosomal protein S19 deficiency develop bone marrow failure and symptoms like patients with Diamond-Blackfan anemia.

  2011cited by this paper
• Drosophila Ribosomal Protein Mutants Control Tissue Growth Non-Autonomously via Effects on the Prothoracic Gland and Ecdysone

  2011cited by this paper
• Expanding the Genetic Code of an Animal

  2011cited by this paper
• Crystal Structure of the Eukaryotic 40S Ribosomal Subunit in Complex with Initiation Factor 1

  2011cited by this paper
• S1 ribosomal protein and the interplay between translation and mRNA decay

  2011cited by this paper
• Functional specialization of ribosomes?

  2011cited by this paper
• Repeated parallel evolution of minimal rRNAs revealed from detailed comparative analysis.

  2011cited by this paper
• The human RPS4 paralogue on Yq11.223 encodes a structurally conserved ribosomal protein and is preferentially expressed during spermatogenesis

  2010cited by this paper
• Adding new chemistries to the genetic code.

  2010cited by this paper
• Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome

  2010cited by this paper
• A functional peptidyl-tRNA hydrolase, ICT1, has been recruited into the human mitochondrial ribosome

  2010cited by this paper
• Distinct genetic code expansion strategies for selenocysteine and pyrrolysine are reflected in different aminoacyl‐tRNA formation systems

  2010cited by this paper
• How mutations in tRNA distant from the anticodon affect the fidelity of decoding

  2010cited by this paper
• A transgenic mouse model demonstrates a dominant negative effect of a point mutation in the RPS19 gene associated with Diamond-Blackfan anemia.

  2010cited by this paper
• Threading the Needle: Getting Selenocysteine Into Proteins

  2010cited by this paper
• Dual functions of codons in the genetic code

  2010cited by this paper
• The role of L1 stalk-tRNA interaction in the ribosome elongation cycle.

  2010cited by this paper
• O-GlcNAc Cycling Enzymes Associate with the Translational Machinery and Modify Core Ribosomal Proteins

  2010cited by this paper
• Selenoproteins*

  2009cited by this paper
• Ribosomal protein L29/HIP deficiency delays osteogenesis and increases fragility of adult bone in mice

  2009cited by this paper
• Regulation and function of selenoproteins in human disease.

  2009cited by this paper
• Many ribosomal protein mutations are associated with growth impairment and tumor predisposition in zebrafish

  2009cited by this paper
• The many levels of control on bacterial selenoprotein synthesis.

  2009cited by this paper
• RPS25 is essential for translation initiation by the Dicistroviridae and hepatitis C viral IRESs.

  2009cited by this paper
• A role for the ribosome in development.

  2009cited by this paper
• Direct visualization of disulfide bonds through diselenide proxies using 77Se NMR spectroscopy.

  2009cited by this paper
• What recent ribosome structures have revealed about the mechanism of translation

  2009cited by this paper
• The labour pains of biochemical selenology: the history of selenoprotein biosynthesis.

  2009cited by this paper
• Escherichia coli MazF Leads to the Simultaneous Selective Synthesis of Both “Death Proteins” and “Survival Proteins”

  2009cited by this paper
• The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins

  2009cited by this paper
• Aminoacyl-tRNA synthesis and translational quality control.

  2009cited by this paper
• Structure of a mitochondrial ribosome with minimal RNA

  2009cited by this paper
• GTPase activation of elongation factor EF‐Tu by the ribosome during decoding

  2009cited by this paper
• An unexpected type of ribosomes induced by kasugamycin: a look into ancestral times of protein synthesis?

  2009cited by this paper
• Pentatricopeptide repeat domain protein 3 associates with the mitochondrial small ribosomal subunit and regulates translation

  2009cited by this paper
• Synthesis of orthogonal transcription-translation networks

  2009cited by this paper
• A mitochondrial protein compendium elucidates complex I disease biology.

  2008cited by this paper
• Specificity of the ribosomal A site for aminoacyl-tRNAs

  2008cited by this paper
• Building a Parallel Metabolism within the Cell.

  2008cited by this paper
• From one amino acid to another: tRNA-dependent amino acid biosynthesis

  2008cited by this paper
• An engineered selenocysteine defines a unique class of antibody derivatives

  2008cited by this paper
• The ribosomal protein genes and Minute loci of Drosophila melanogaster

  2007cited by this paper
• Functional specificity among ribosomal proteins regulates gene expression.

  2007cited by this paper
• The Ribosome Filter Redux

  2007cited by this paper
• Eukaryotic ribosomal protein RPS25 interacts with the conserved loop region in a dicistroviral intergenic internal ribosome entry site

  2007cited by this paper
• Structured mRNAs regulate translation initiation by binding to the platform of the ribosome.

  2007cited by this paper
• Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion

  2007cited by this paper
• Natural expansion of the genetic code.

  2007cited by this paper
• Genetic incorporation of unnatural amino acids into proteins in mammalian cells

  2007cited by this paper
• Intragenomic 16S rDNA Divergence in Haloarcula marismortui Is an Adaptation to Different Temperatures

  2007cited by this paper
• Germ Versus Soma Decisions: Lessons from Flies and Worms

  2007cited by this paper
• Reconstructing the evolution of the mitochondrial ribosomal proteome

  2007cited by this paper
• Functional epitopes at the ribosome subunit interface

  2006cited by this paper
• Impaired Control of IRES-Mediated Translation in X-Linked Dyskeratosis Congenita

  2006cited by this paper
• RNA synthetic biology

  2006cited by this paper
• Synthesizing cellular networks from evolved ribosome-mRNA pairs.

  2006cited by this paper
• Role of mitochondrial ribosome-dependent translation in germline formation in Drosophila embryos.

  2005cited by this paper
• Selenocysteine tRNA‐specific elongation factor SelB is a structural chimaera of elongation and initiation factors

  2005cited by this paper
• Genetic Analysis of RpL38 and RpL5, Two Minute Genes Located in the Centric Heterochromatin of Chromosome 2 of Drosophila melanogaster

  2005cited by this paper
• Ribosomal protein L30 is a component of the UGA-selenocysteine recoding machinery in eukaryotes

  2005cited by this paper
• Cellular logic with orthogonal ribosomes.

  2005cited by this paper
• The structure of the 80S ribosome from Trypanosoma cruzi reveals unique rRNA components.

  2005cited by this paper
• Initiation of Protein Synthesis in Bacteria

  2005cited by this paper

• Small Black Phosphorus Disrupts Vascular Development and Hematopoiesis in Zebrafish Larvae.

  2025cites this paper
• Interplay between codon usage and ribosome heterogeneity: A new layer of translational regulation.

  2025cites this paper
• Assessing Human Ribosomal DNA Variation and Its Association With Phenotypic Outcomes

  2025cites this paper
• Ribosome Specialization in Protozoa Parasites

  2023cites this paper
• Response mechanism of microbial community during anaerobic biotransformation of marine toxin domoic acid.

  2022cites this paper
• Shackled ribosomes unleashed

  2022cites this paper
• Ribosomopathies—A tree of pathologies with many roots and branches!

  2021cites this paper
• Ribosome diversity

  2021cites this paper
• Dynamic interplay between RPL3- and RPL3L-containing ribosomes modulates mitochondrial activity in the mammalian heart

  2021cites this paper
• Introduction to ribosome factory, origin, and evolution of translation

  2021cites this paper
• Translational activators and mitoribosomal isoforms cooperate to mediate mRNA-specific translation in Schizosaccharomyces pombe mitochondria

  2021cites this paper
• Transcriptomic analysis of the black tiger shrimp (Penaeus monodon) reveals insights into immune development in their early life stages

  2021cites this paper
• An age-downregulated ribosomal RpS28 protein variant regulates the muscle proteome

  2021cites this paper
• Orthogonal translation enables heterologous ribosome engineering in E. coli

  2021cites this paper
• A Time‐Resolved Cryo‐EM Study of Saccharomyces cerevisiae 80S Ribosome Protein Composition in Response to a Change in Carbon Source

  2020cites this paper
• The evolving role of ribosomes in the regulation of protein synthesis.

  2020cites this paper
• Functional Analysis of the Ribosomal uL6 Protein of Saccharomyces cerevisiae

  2019cites this paper
• Affirmation of Distinctive Ribosomal Protein Paralog-Specific Ribosomes

  2019cites this paper
• Translatomics: The Global View of Translation

  2019cites this paper
• Prodrug approaches to reduce treprostinil toxicity

  2019cites this paper
• Mammalian mitochondrial translation - revealing consequences of divergent evolution.

  2019cites this paper
• The relative importance of ecological drivers of arbuscular mycorrhizal fungal distribution varies with taxon phylogenetic resolution.

  2019cites this paper
• Does functional specialization of ribosomes really exist?

  2019cites this paper
• Pimp My Ribosome: Ribosomal Protein Paralogs Specify Translational Control.

  2018cites this paper
• Correction: Specialized ribosomes and specific ribosomal protein paralogs control translation of mitochondrial proteins

  2018cites this paper
• Specialized ribosomes and specific ribosomal protein paralogs control translation of mitochondrial proteins

  2018cites this paper
• Transdifferentiation of human somatic cells by ribosome

  2018cites this paper
• The shape of the bacterial ribosome exit tunnel affects cotranslational protein folding

  2018cites this paper
• Implication de la protéine de biogenèse des ribosomes Rsl24d1 dans l'homéostasie de cellules souches embryonnaires murines

  2018cites this paper
• Unravelling gene regulation in the epidermis during differentiation

  2018cites this paper
• Size-variable zone in V3 region of 16S rRNA

  2017cites this paper
• Étude des facteurs de la biogenèse des ribosomes dans les progéniteurs neuraux de poisson zèbre

  2017cites this paper
• Alterations of the translation apparatus during aging and stress response.

  2017cites this paper
• Repurposing ribosomes for synthetic biology.

  2017cites this paper
• Analysis of Proteins, Protein Complexes, and Organellar Proteomes Using Sheathless Capillary Zone Electrophoresis - Native Mass Spectrometry

  2017cites this paper
• Synthetic chimeras with orthogonal ribosomal proteins increase translation yields by recruiting mRNA for translation as measured by profiling active ribosomes

  2016cites this paper
• The relationship between the nucleolus and cancer: Current evidence and emerging paradigms.

  2016cites this paper
• Sequence variation in nuclear ribosomal small subunit, internal transcribed spacer and large subunit regions of Rhizophagus irregularis and Gigaspora margarita is high and isolate‐dependent

  2016cites this paper
• Thinking beside the box: Should we care about the non-coding strand of the 16S rRNA gene?

  2016cites this paper
• Tma108, a putative M1 aminopeptidase, is a specific nascent chain-associated protein in Saccharomyces cerevisiae

  2016cites this paper
• Corrigendum: Methylation of ribosomal RNA by NSUN5 is a conserved mechanism modulating organismal lifespan

  2016cites this paper
• New tricks for an old dog: ribosome biogenesis contributes to stem cell homeostasis.

  2015cites this paper
• Translation initiation factor 3 families: what are their roles in regulating cyanobacterial and chloroplast gene expression?

  2015cites this paper
• Methylation of ribosomal RNA by NSUN5 is a conserved mechanism modulating organismal lifespan

  2015cites this paper
• Functional study of the role played by nucleolar proteins in the control of neural progenitor homeostasis using zebrafish as a model

  2015cites this paper
• GATA1 and PU.1 Bind to Ribosomal Protein Genes in Erythroid Cells: Implications for Ribosomopathies

  2015cites this paper
• Lyar, a cell growth-regulating zinc finger protein, was identified to be associated with cytoplasmic ribosomes in male germ and cancer cells

  2014cites this paper
• Supernumerary proteins of mitochondrial ribosomes.

  2014cites this paper
• Diverse diseases from a ubiquitous process: The ribosomopathy paradox

  2014cites this paper
• Mitochondrial protein synthesis: Figuring the fundamentals, complexities and complications, of mammalian mitochondrial translation

  2014cites this paper
• Mitoribosomal regulation of OXPHOS biogenesis in plants

  2014cites this paper
• Contrôle de l'expression des gènes ribosomaux chez la levure et l'homme

  2013cites this paper
• Specialized Yeast Ribosomes: A Customized Tool for Selective mRNA Translation

  2013cites this paper
• The many faces of proteins

  2013cites this paper
• Eukaryotic ribosome biogenesis at a glance

  2013cites this paper
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  year unknowncites this paper
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  year unknowncites this paper