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Sichen Shao, Jason Murray, Alan Brown, Jack Taunton, V Ramakrishnan, Ramanujan S Hegde
In eukaryotes, accurate protein synthesis relies on a family of translational GTPases that pair with specific decoding factors to decipher the mRNA code on ribosomes. We present structures of the mammalian ribosome engaged with decoding factor⋅GTPase complexes representing intermediates of translation elongation (aminoacyl-tRNA⋅eEF1A), termination (eRF1⋅eRF3), and ribosome rescue (Pelota⋅Hbs1l). Comparative analyses reveal that each decoding factor exploits the plasticity of the ribosomal decoding center to differentially remodel ribosomal proteins and rRNA...
November 17, 2016: Cell
A G Matveenko, M V Belousov, S A Bondarev, S E Moskalenko, G A Zhouravleva
Translation termination is an important step in gene expression. Its correct processing is governed by eRF1 (Sup45) and eRF3 (Sup35) proteins. In Saccharomyces cerevisiae, mutations in the corresponding genes, as well as Sup35 aggregation in [PSI^(+)] cells that propagate the prion form of Sup35 lead to inaccurate stop codon recognition and, consequently, nonsense suppression. The presence of stronger prion variants results in the more efficient suppression of nonsense mutations. Previously, we proposed a synthetic lethality test that enables the identification of genes that may influence either translation termination factors or [PSI^(+)] manifestation...
September 2016: Molekuliarnaia Biologiia
Christopher K Morrison, Tanya Arseneault, Amy Novinscak, Martin Filion
Phytophthora infestans causes late blight of potato, one of the most devastating diseases affecting potato production. Alternative approaches for controlling late blight are being increasingly sought due to increasing environmental concerns over the use of chemical pesticides and the increasing resistance of P. infestans to fungicides. Our research group has isolated a new strain of Pseudomonas fluorescens (LBUM636) of biocontrol interest producing the antibiotic phenazine-1-carboxylic acid (PCA). Wild-type LBUM636 was shown to significantly inhibit the growth of Phytophthora infestans in in vitro confrontational assays whereas its isogenic mutant (phzC-; not producing PCA) only slightly altered the pathogen's growth...
March 2017: Phytopathology
Andrew G Matveenko, Polina B Drozdova, Mikhail V Belousov, Svetlana E Moskalenko, Stanislav A Bondarev, Yury A Barbitoff, Anton A Nizhnikov, Galina A Zhouravleva
[PSI(+) ] is the prion form of the translation termination factor Sup35 (eRF3); [PSI(+) ] strains display nonsense suppression. Another prion-like element, [ISP(+) ], is linked to antisuppression in a specific background. Transcriptional regulator Sfp1 was shown to be responsible for [ISP(+) ] propagation. In this work, we identified SFP1 as a multicopy inducer of [PSI(+) ]-dependent lethality. Sfp1 is likely to up-regulate transcription of genes encoding release factors; however, its overproduction increases Sup35, but not Sup45 protein level...
December 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Alexandr Ivanov, Tatyana Mikhailova, Boris Eliseev, Lahari Yeramala, Elizaveta Sokolova, Denis Susorov, Alexey Shuvalov, Christiane Schaffitzel, Elena Alkalaeva
Poly(A)-binding protein (PABP) is a major component of the messenger RNA-protein complex. PABP is able to bind the poly(A) tail of mRNA, as well as translation initiation factor 4G and eukaryotic release factor 3a (eRF3a). PABP has been found to stimulate translation initiation and to inhibit nonsense-mediated mRNA decay. Using a reconstituted mammalian in vitro translation system, we show that PABP directly stimulates translation termination. PABP increases the efficiency of translation termination by recruitment of eRF3a and eRF1 to the ribosome...
September 19, 2016: Nucleic Acids Research
Wataru Horikawa, Kei Endo, Miki Wada, Koichi Ito
Ski7 functions as a cofactor in both normal mRNA turnover and non-stop mRNA decay (NSD) mRNA surveillance in budding yeast. The N-terminal region of Ski7 (Ski7N) interacts with the ski-complex and the exosome. The C-terminal region of Ski7 (Ski7C) binds guanine nucleotides and shares overall sequence and structural homology with the proteins of the translational GTPase superfamily, especially the tRNA/tRNA-mimic carrier protein subfamilies such as EF1α, eRF3, and Hbs1. Previous reports showed that Ski7N polypeptide functions adequately in vivo, while Ski7C, if any, only slightly...
2016: Scientific Reports
Xuhua Tang, Yiping Zhu, Stacey L Baker, Matthew W Bowler, Benjamin Jieming Chen, Chen Chen, J Robert Hogg, Stephen P Goff, Haiwei Song
Retroviral reverse transcriptase (RT) of Moloney murine leukemia virus (MoMLV) is expressed in the form of a large Gag-Pol precursor protein by suppression of translational termination in which the maximal efficiency of stop codon read-through depends on the interaction between MoMLV RT and peptidyl release factor 1 (eRF1). Here, we report the crystal structure of MoMLV RT in complex with eRF1. The MoMLV RT interacts with the C-terminal domain of eRF1 via its RNase H domain to sterically occlude the binding of peptidyl release factor 3 (eRF3) to eRF1...
June 22, 2016: Nature Communications
Natalia Shcherbik, Tatiana A Chernova, Yury O Chernoff, Dimitri G Pestov
Cotranslational degradation of polypeptide nascent chains plays a critical role in quality control of protein synthesis and the rescue of stalled ribosomes. In eukaryotes, ribosome stalling triggers release of 60S subunits with attached nascent polypeptides, which undergo ubiquitination by the E3 ligase Ltn1 and proteasomal degradation facilitated by the ATPase Cdc48. However, the identity of factors acting upstream in this process is less clear. Here, we examined how the canonical release factors Sup45-Sup35 (eRF1-eRF3) and their paralogs Dom34-Hbs1 affect the total population of ubiquitinated nascent chains associated with yeast ribosomes...
August 19, 2016: Nucleic Acids Research
Yury O Chernoff, Denis A Kiktev
Chaperones of the diverse ubiquitous Hsp70 family are involved in the regulation of ordered self-perpetuating protein aggregates (amyloids and prions), implicated in both devastating diseases and protein-based inheritance. Yeast ribosome-associated chaperone complex (RAC), composed of the Hsp40 protein Zuo1 and non-canonical Hsp70 protein Ssz1, mediates association of the Hsp70 chaperone Ssb with translating ribosomes. Ssb participates in co-translational protein folding, regulation of premature translation termination, and ribosome biogenesis...
November 2016: Current Genetics
Soumaya Jerbi, Béatrice Jolles, Tahar Bouceba, Olivier Jean-Jean
The eukaryotic release factor 3 (eRF3) has been involved in the control of mRNA degradation through its association with the cytoplasmic Poly(A) Binding Protein, PABP. In mammals, eRF3 N-terminal domain contains two overlapping PAM2 motifs which specifically recognize the MLLE domain of PABP. In humans, eRF3a/GSPT1 gene contains a stable GGC repeat encoding a repeat of glycine residues in eRF3a N-terminus. There are five known eRF3a/GSPT1 alleles in the human population, encoding 7, 9, 10, 11 and 12 glycines...
2016: RNA Biology
Petra Beznosková, Stanislava Gunišová, Leoš Shivaya Valášek
The molecular mechanism of stop codon recognition by the release factor eRF1 in complex with eRF3 has been described in great detail; however, our understanding of what determines the difference in termination efficiencies among various stop codon tetranucleotides and how near-cognate (nc) tRNAs recode stop codons during programmed readthrough in Saccharomyces cerevisiae is still poor. Here, we show that UGA-C as the only tetranucleotide of all four possible combinations dramatically exacerbated the readthrough phenotype of the stop codon recognition-deficient mutants in eRF1...
March 2016: RNA
Andrés López-Perrote, Raquel Castaño, Roberto Melero, Teresa Zamarro, Hitomi Kurosawa, Tetsuo Ohnishi, Akiko Uchiyama, Kyoko Aoyagi, Gretel Buchwald, Naoyuki Kataoka, Akio Yamashita, Oscar Llorca
Nonsense-mediated mRNA decay (NMD) is an mRNA degradation pathway that regulates gene expression and mRNA quality. A complex network of macromolecular interactions regulates NMD initiation, which is only partially understood. According to prevailing models, NMD begins by the assembly of the SURF (SMG1-UPF1-eRF1-eRF3) complex at the ribosome, followed by UPF1 activation by additional factors such as UPF2 and UPF3. Elucidating the interactions between NMD factors is essential to comprehend NMD, and here we demonstrate biochemically and structurally the interaction between human UPF2 and eukaryotic release factor 3 (eRF3)...
February 29, 2016: Nucleic Acids Research
Saifeng Cheng, Dao-Xiu Zhou, Yu Zhao
Roots are essential organs for anchoring plants, exploring and exploiting soil resources, and establishing plant-microorganisms communities in vascular plants. Rice has a complex root system architecture consisting of several root types, including primary roots, lateral roots, and crown roots. Crown roots constitute the major part of the rice root system and play important roles during the growing period. Recently, we have refined a mechanism that involves ERF3/WOX11 interaction is required to regulate the expression of genes in the cytokinin signaling pathway during the different stages of crown roots development in rice...
2016: Plant Signaling & Behavior
Konstantin N Bulygin, Yulia S Bartuli, Alexey A Malygin, Dmitri M Graifer, Ludmila Yu Frolova, Galina G Karpova
Translation termination in eukaryotes is mediated by release factors: eRF1, which is responsible for stop codon recognition and peptidyl-tRNA hydrolysis, and GTPase eRF3, which stimulates peptide release. Here, we have utilized ribose-specific probes to investigate accessibility of rRNA backbone in complexes formed by association of mRNA- and tRNA-bound human ribosomes with eRF1•eRF3•GMPPNP, eRF1•eRF3•GTP, or eRF1 alone as compared with complexes where the A site is vacant or occupied by tRNA. Our data show which rRNA ribose moieties are protected from attack by the probes in the complexes with release factors and reveal the rRNA regions increasing their accessibility to the probes after the factors bind...
February 2016: RNA
Baofeng Chai, Cui Li, Jingfei Yu, Yanrong Hao, Ping Guo, Quan Shen
Two classes of polypeptide release factors (RFs) are responsible for maintaining accuracy in translation termination; however, their detailed mechanism of action and evolutionary history of these factors remain elusive. The structure and function of RFs vary in bacteria and eukaryotes, a fact that is suggestive of evolutionary changes in the translation termination system. Giardia lamblia (Diplomonada) and Trichomonas vaginalis (Parabasalia) are considered as early-diverged eukaryotes. The class II release factor, eRF3, of Giardia (Gl-eRF3) appears to have only one domain that corresponds to EF-1α and lacks the N-terminal domain, similar to that of eRF3 of other organisms...
July 2015: Molecular and Biochemical Parasitology
Yu Zhao, Saifeng Cheng, Yaling Song, Yulan Huang, Shaoli Zhou, Xiaoyun Liu, Dao-Xiu Zhou
Crown roots are the main components of the fibrous root system in rice (Oryza sativa). WOX11, a WUSCHEL-related homeobox gene specifically expressed in the emerging crown root meristem, is a key regulator in crown root development. However, the nature of WOX11 function in crown root development has remained elusive. Here, we identified a rice AP2/ERF protein, ERF3, which interacts with WOX11 and was expressed in crown root initials and during crown root growth. Functional analysis revealed that ERF3 was essential for crown root development and acts in auxin- and cytokinin-responsive gene expression...
September 2015: Plant Cell
Yoshifumi Hashimoto, Hiroto Inagaki, Shin-ichi Hoshino
The involvement of polypeptide chain-releasing factor eRF3 in translation termination and mRNA decay is well established. Moreover, the finding that the proteolytically processed isoform of eRF3 (p-eRF3) interacts with inhibitors of apoptosis proteins (IAPs) to activate caspase, implies that eRF3 is a cell death regulator. However, the protease(s) responsible for p-eRF3 production and how p-eRF3 regulates apoptosis remain unknown. Here, we show that calpain mediates p-eRF3 production in vitro and in living cells...
August 4, 2015: FEBS Letters
Alexandra Petrova, Denis Kiktev, Olga Askinazi, Svetlana Chabelskaya, Svetlana Moskalenko, Olga Zemlyanko, Galina Zhouravleva
Mutations in the essential genes SUP45 and SUP35, encoding yeast translation termination factors eRF1 and eRF3, respectively, lead to a wide range of phenotypes and affect various cell processes. In this work, we show that nonsense and missense mutations in the SUP45, but not the SUP35, gene abolish diploid pseudohyphal and haploid invasive growth. Missense mutations that change phosphorylation sites of Sup45 protein do not affect the ability of yeast strains to form pseudohyphae. Deletion of the C-terminal part of eRF1 did not lead to impairment of filamentation...
June 2015: FEMS Yeast Research
Mykola V Sopinskyy, Natalya A Vlasenko, Igor P Lisovskyy, Sergii O Zlobin, Zinoviia F Tsybrii, Lyudmyla I Veligura
The structural-phase transformations induced by air annealing of SiO x and SiO x  < Er,F > films were studied by the combined use of infrared spectroscopy and ellipsometry. The films were prepared using vacuum evaporation of SiO powder and co-evaporation of SiO and ErF3 powders. The annealing took place at moderate temperatures (750 and 1000 °C). It was found that the micro- and macrostructure of the annealed films is similar to the structure of the Si-SiO x nanocomposites obtained by annealing SiO x in vacuum or inert atmosphere and subjected to post-annealing in oxidizing atmosphere...
2015: Nanoscale Research Letters
Kazuki Saito, Koichi Ito
In eukaryotes, the tRNA-mimicking polypeptide-chain release factor, eRF1, decodes stop codons on the ribosome in a complex with eRF3; this complex exhibits striking structural similarity to the tRNA-eEF1A-GTP complex. Although amino acid residues or motifs of eRF1 that are critical for stop codon discrimination have been identified, the details of the molecular mechanisms involved in the function of the ribosomal decoding site remain obscure. Here, we report analyses of the position-123 amino acid of eRF1 (L123 in Saccharomyces cerevisiae eRF1), a residue that is phylogenetically conserved among species with canonical and variant genetic codes...
May 19, 2015: Nucleic Acids Research
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