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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
Mei-Chun Cheng, Wen-Chieh Kuo, Yi-Ming Wang, Hsing-Yu Chen, Tsan-Piao Lin
Ethylene Response Factor 1 (ERF1) plays a crucial role in biotic and abiotic stress responses. Previous studies have shown that ERF1 regulates stress-responsive gene expression by binding to different cis-acting elements in response to various stress signals. ERF1 was also reported to be unstable in the dark, and it regulates hypocotyl elongation. Here, we elucidated the mechanism underlying degradation of ERF1. Yeast two-hybrid screening showed that UBIQUITIN-CONJUGATING ENZYME 18 (UBC18) interacted with ERF1...
October 27, 2016: New Phytologist
E Ortega, L Gutiérrez, M J Bernad, F Salmerón, I Juárez, D Vargas
The purpose of this study was to evaluate the pharmacokinetics of extended-release formulations (ERFs) of clindamycin with polymeric-based matrices. In a crossover study, 21 healthy adult dogs were randomly assigned (in groups of 7) to receive a single oral dose (20 mg/kg) of clindamycin without excipients (control) or an extended-release formulation containing clindamycin+Hydroxypropyl methylcellulose (HPMC)+poloxamer at a ratio of 1 : 0.04 : 0.5 (ERF1) or containing clindamycin+HPMC+acrylic acid polymer (AAP) at the same proportions (ERF2)...
September 14, 2016: Drug Research
Kristína Záhonová, Alexei Y Kostygov, Tereza Ševčíková, Vyacheslav Yurchenko, Marek Eliáš
A limited number of non-canonical genetic codes have been described in eukaryotic nuclear genomes. Most involve reassignment of one or two termination codons as sense ones [1-4], but no code variant is known that would have reassigned all three termination codons. Here, we describe such a variant that we discovered in a clade of trypanosomatids comprising nominal Blastocrithidia species. In these protists, UGA has been reassigned to encode tryptophan, while UAG and UAA (UAR) have become glutamate encoding. Strikingly, UAA and, less frequently, UAG also serve as bona fide termination codons...
September 12, 2016: Current Biology: CB
Md Kamrul Hasan, Congcong Liu, Fanan Wang, Golam Jalal Ahammed, Jie Zhou, Ming-Xing Xu, Jing-Quan Yu, Xiao-Jian Xia
Glutathione (GSH) plays a critical role in plant growth, development and responses to stress. However, the mechanism by which GSH regulates tolerance to cadmium (Cd) stress still remains unclear. Here we show that inhibition of GSH biosynthesis by buthionine sulfoximine (BSO) aggravated Cd toxicity by increasing accumulation of reactive oxygen species (ROS) and reducing contents of nitric oxide (NO) and S-nitrosothiol (SNO) in tomato roots. In contrast, exogenous GSH alleviated Cd toxicity by substantially minimizing ROS accumulation and increasing contents of NO and SNO, and activities of antioxidant enzymes that eventually reduced oxidative stress...
October 2016: Chemosphere
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
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
Jie-Li Mao, Zi-Qing Miao, Zhen Wang, Lin-Hui Yu, Xiao-Teng Cai, Cheng-Bin Xiang
[This corrects the article DOI: 10.1371/journal.pgen.1005760.].
May 2016: PLoS Genetics
Samatha Gunapati, Ram Naresh, Sanjay Ranjan, Deepti Nigam, Aradhana Hans, Praveen C Verma, Rekha Gadre, Uday V Pathre, Aniruddha P Sane, Vidhu A Sane
NAC proteins are plant-specific transcription factors that play essential roles in regulating development and responses to abiotic and biotic stresses. We show that over-expression of the cotton GhNAC2 under the CaMV35S promoter increases root growth in both Arabidopsis and cotton under unstressed conditions. Transgenic Arabidopsis plants also show improved root growth in presence of mannitol and NaCl while transgenic cotton expressing GhNAC2 show reduced leaf abscission and wilting upon water stress compared to control plants...
2016: Scientific Reports
Wanhong Liu, Huanyan Wang, Yupei Chen, Shunqin Zhu, Min Chen, Xiaozhong Lan, Guoping Chen, Zhihua Liao
Previous publications reported that the artemisinin level was increased in Artemisia annua following a night-frost period. However, the molecular mechanism was not clear. In this study, we found that exogenous jasmonate effectively enhanced the freezing tolerance of A. annua. The jasmonate biosynthetic genes (LOX1, LOX2, AOC and JAR1) were induced by cold stress, leading to an increase in endogenous jasmonate in cold-treated A. annua. Increased endogenous jasmonate enhanced the expression of three jasmonate-responsive transcription factors, ERF1, ERF2, and ORA, all of which were reported to transcriptionally activate the expression of artemisinin biosynthetic genes, such as ADS, CYP71AV1, DBR2 and ALDH1...
March 14, 2016: Biotechnology and Applied Biochemistry
Denis Kusevic, Srikanth Kudithipudi, Albert Jeltsch
Bacterial HEMK2 homologs initially had been proposed to be involved in heme biogenesis or to function as adenine DNA methyltransferase. Later it was shown that this family of enzymes has protein glutamine methyltransferase activity, and they methylate the glutamine residue in the GGQ motif of ribosomal translation termination factors. The murine HEMK2 enzyme methylates Gln(185) of the eukaryotic translation termination factor eRF1. We have employed peptide array libraries to investigate the peptide sequence recognition specificity of murine HEMK2...
March 18, 2016: Journal of Biological Chemistry
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
Jie-Li Mao, Zi-Qing Miao, Zhen Wang, Lin-Hui Yu, Xiao-Teng Cai, Cheng-Bin Xiang
The gaseous phytohormone ethylene participates in the regulation of root growth and development in Arabidopsis. It is known that root growth inhibition by ethylene involves auxin, which is partially mediated by the action of the WEAK ETHYLENE INSENSITIVE2/ANTHRANILATE SYNTHASE α1 (WEI2/ASA1), encoding a rate-limiting enzyme in tryptophan (Trp) biosynthesis, from which auxin is derived. However, the molecular mechanism by which ethylene decreases root growth via ASA1 is not understood. Here we report that the ethylene-responsive AP2 transcription factor, ETHYLENE RESPONSE FACTOR1 (ERF1), plays an important role in primary root elongation of Arabidopsis...
January 2016: PLoS Genetics
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
Shubhadra Pillay, Yan Li, Leo E Wong, Konstantin Pervushin
Eukarya translation termination requires the stop codon recognizing protein eRF1. In contrast to the multiple proteins required for translation termination in Bacteria, eRF1 retains the ability to recognize all three of the stop codons. The details of the mechanism that eRF1 uses to recognize stop codons has remained elusive. This study describes the structural effects of mutations in the eRF1 N-domain that have previously been shown to alter stop codon recognition specificity. Here, we propose a model of eRF1 binding to the pre-translation termination ribosomal complex that is based in part on our solution NMR structures of the wild-type and mutant eRF1 N-domains...
2016: Scientific Reports
Pin-Yao Huang, Jérémy Catinot, Laurent Zimmerli
Pathogen attack leads to transcriptional changes and metabolic modifications allowing the establishment of appropriate plant defences. Transcription factors (TFs) are key players in plant innate immunity. Notably, ethylene response factor (ERF) TFs are integrators of hormonal pathways and are directly responsible for the transcriptional regulation of several jasmonate (JA)/ethylene (ET)-responsive defence genes. Transcriptional activation or repression by ERFs is achieved through the binding to JA/ET-responsive gene promoters...
March 2016: Journal of Experimental Botany
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
Fei-Yian Yoong, Laurel K O'Brien, Maria Jose Truco, Heqiang Huo, Rebecca Sideman, Ryan Hayes, Richard W Michelmore, Kent J Bradford
Seeds of most lettuce (Lactuca sativa) cultivars are susceptible to thermoinhibition, or failure to germinate at temperatures above approximately 28°C, creating problems for crop establishment in the field. Identifying genes controlling thermoinhibition would enable the development of cultivars lacking this trait and, therefore, being less sensitive to high temperatures during planting. Seeds of a primitive accession (PI251246) of lettuce exhibited high-temperature germination capacity up to 33°C. Screening a recombinant inbred line population developed from PI215246 and cv Salinas identified a major quantitative trait locus (Htg9...
January 2016: Plant Physiology
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