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Special Issue "Progress and Expansion of Ribosome Research"

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Protein Functional and Structural Biology Team, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
Interests: structure and function of the ribosome; tRNA; protein synthesis; RNA-protein interaction; X-ray crystallographic study; cryo-EM structural analysis

Special Issue Information

Dear Colleagues,

Ribosome is the machinery responsible for one of the fundamental biological activities, protein synthesis, and research to elucidate its function and structure has progressed along with the development of new technologies and drugs. In addition, the study of ribosome biosynthesis itself consists of so many processes from gene replication and transcription to protein synthesis and folding, that elucidating these processes is equivalent to unraveling the regulation of cellular functions. Recently, new aspects of ribosomes concerning to human diseases and cellular functions, including various RNAs and nuclei, begin to emerge through advanced approaches in genetics, biochemistry, cell biology, and structural biology, as well as new techniques such as single molecule measurement and observation. As an international networking venue, this special issue welcomes submissions of papers that present the latest results, findings, and innovations broadly related to ribosome research.

Dr. Chie Takemoto
Guest Editor

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Keywords

ribosome biogenesis, ribosomal protein, rRNA, nucleus: rDNA, transcription, RNA processing/modification, assembly factor
protein synthesis, protein folding/localization/modification, quality control: ribozyme, tRNA, mRNA, translational factor, chaperone, ubiquitination
ribosomopathy, metabolism: antibiotics, drug, cell cycle, phosphorylation, nuclease, protease
molecular mechanism, structural analysis, structural dynamics: ribosome profiling, single-molecule analysis, NMR, cryoEM, AFM, X-ray crystallography

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Research

Open AccessArticle

Crystal Structure of Pyrrolysyl-tRNA Synthetase from a Methanogenic Archaeon ISO4-G1 and Its Structure-Based Engineering for Highly-Productive Cell-Free Genetic Code Expansion with Non-Canonical Amino Acids

and

Int. J. Mol. Sci. 2023, 24(7), 6256; https://doi.org/10.3390/ijms24076256 - 26 Mar 2023

Viewed by 1288

Abstract

Pairs of pyrrolysyl-tRNA synthetase (PylRS) and tRNA^Pyl from Methanosarcina mazei and Methanosarcina barkeri are widely used for site-specific incorporations of non-canonical amino acids into proteins (genetic code expansion). Previously, we achieved full productivity of cell-free protein synthesis for bulky non-canonical amino acids, including N^ε-((((E)-cyclooct-2-en-1-yl)oxy)carbonyl)-L-lysine (TCO*Lys), by using Methanomethylophilus alvus PylRS with structure-based mutations in and around the amino acid binding pocket (first-layer and second-layer mutations, respectively). Recently, the PylRS·tRNA^Pyl pair from a methanogenic archaeon ISO4-G1 was used for genetic code expansion. In the present study, we determined the crystal structure of the methanogenic archaeon ISO4-G1 PylRS (ISO4-G1 PylRS) and compared it with those of structure-known PylRSs. Based on the ISO4-G1 PylRS structure, we attempted the site-specific incorporation of N^ε-(p-ethynylbenzyloxycarbonyl)-L-lysine (pEtZLys) into proteins, but it was much less efficient than that of TCO*Lys with M. alvus PylRS mutants. Thus, the first-layer mutations (Y125A and M128L) of ISO4-G1 PylRS, with no additional second-layer mutations, increased the protein productivity with pEtZLys up to 57 ± 8% of that with TCO*Lys at high enzyme concentrations in the cell-free protein synthesis. Full article

(This article belongs to the Special Issue Progress and Expansion of Ribosome Research)

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Open AccessArticle

Mutation at the Site of Hydroxylation in the Ribosomal Protein uL15 (RPL27a) Causes Specific Changes in the Repertoire of mRNAs Translated in Mammalian Cells

Elizaveta A. Zolotenkova

Alexander V. Gopanenko

Alexey E. Tupikin

Marsel R. Kabilov

and

Alexey A. Malygin

Int. J. Mol. Sci. 2023, 24(7), 6173; https://doi.org/10.3390/ijms24076173 - 24 Mar 2023

Cited by 1 | Viewed by 683

Abstract

Ribosomal protein uL15 (RPL27a) carries a specific modification, hydroxylation, at the His39 residue, which neighbors the CCA terminus of the E-site-bound tRNA at the mammalian ribosome. Under hypoxia, the level of hydroxylation of this protein decreases. We transiently transfected HEK293T cells with constructs expressing wild-type uL15 or mutated uL15 (His39Ala) incapable of hydroxylation, and demonstrated that ribosomes containing both proteins are competent in translation. By applying RNA-seq to the total cellular and polysome-associated mRNAs, we identified differentially expressed genes (DEGs) in cells containing exogenous uL15 or its mutant form. Analyzing mRNA features of up- and down-regulated DEGs, we found an increase in the level of more abundant mRNAs and shorter CDSs in cells with uL15 mutant for both translated and total cellular mRNAs. The level of longer and rarer mRNAs, on the contrary, decreased. Our data show how ribosome heterogeneity can change the composition of the translatome and transcriptome, depending on the properties of the translated mRNAs. Full article

(This article belongs to the Special Issue Progress and Expansion of Ribosome Research)

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Special Issue "Progress and Expansion of Ribosome Research"

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