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Stop codon readthrough

Manuel Miras, W Allen Miller, Verónica Truniger, Miguel A Aranda
Viral protein synthesis is completely dependent upon the host cell's translational machinery. Canonical translation of host mRNAs depends on structural elements such as the 5' cap structure and/or the 3' poly(A) tail of the mRNAs. Although many viral mRNAs are devoid of one or both of these structures, they can still translate efficiently using non-canonical mechanisms. Here, we review the tools utilized by positive-sense single-stranded (+ss) RNA plant viruses to initiate non-canonical translation, focusing on cis-acting sequences present in viral mRNAs...
2017: Frontiers in Plant Science
Julia Hofhuis, Severin Dieterle, Rosemol George, Fabian Schueren, Sven Thoms
Translational readthrough, the decoding of stop codons as sense codons, leads to C-terminal extension of proteins which may lead to the formation of protein isoforms with distinct properties from the original protein. Two proteins have recently been identified that are targeted to the peroxisome via hidden peroxisomal targeting signals in their readthrough extensions. This noninduced basal translational readthrough can be distinguished from pharmacological induction of readthrough by aminoglycosides or other small molecules, which can be used for the treatment of diseases caused by premature stop (termination) codons (PTCs)...
2017: Methods in Molecular Biology
Natalie E Baggett, Yan Zhang, Carol A Gross
Terminating protein translation accurately and efficiently is critical for both protein fidelity and ribosome recycling for continued translation. The three bacterial release factors (RFs) play key roles: RF1 and 2 recognize stop codons and terminate translation; and RF3 promotes disassociation of bound release factors. Probing release factors mutations with reporter constructs containing programmed frameshifting sequences or premature stop codons had revealed a propensity for readthrough or frameshifting at these specific sites, but their effects on translation genome-wide have not been examined...
March 2017: PLoS Genetics
Alessio Branchini, Mattia Ferrarese, Matteo Campioni, Giancarlo Castaman, Rosella Mari, Francesco Bernardi, Mirko Pinotti
Drug-induced readthrough over premature stop codons (PTCs) is a potentially attractive therapy for genetic disorders but a wide outcome variability has been observed. Through expression studies we investigated the responsiveness to the readthrough-inducing drug geneticin of eleven rationally-selected factor IX (FIX) nonsense mutations, present in 70% (324/469) of Hemophilia B (HB) patients with PTCs. Among the predicted readthrough-permissive TGA variants, only two (p.W240X, p.R384X) responded with a remarkable rescue of FIX activity...
February 14, 2017: Blood
Andrea M Reinig, Sara Mirzaei, Daniel J Berlau
Duchenne muscular dystrophy (DMD) is a genetic neuromuscular disease that primarily affects young males. Patients with DMD are unable to produce dystrophin, a crucial protein found in myocytes, leading to a loss of muscle support and integrity. Corticosteroids are the standard supportive treatment for DMD; however, there is a high demand to expand the number of safe, effective pharmacologic options. Recently a surge of new therapeutics for DMD is offering hope to patients. A variety of these new medications, such as stop codon readthrough agents, exon-skipping agents, and utrophin modulators, aim to replace dystrophin in myocytes...
February 2, 2017: Pharmacotherapy
Westley J Friesen, Christopher R Trotta, Yuki Tomizawa, Jin Zhuo, Briana Johnson, Jairo Sierra, Bijoyita Roy, Marla Weetall, Jean Hedrick, Josephine Sheedy, James Takasugi, Young-Choon Moon, Suresh Babu, Ramil Baiazitov, John D Leszyk, Thomas W Davis, Joseph M Colacino, Stuart W Peltz, Ellen M Welch
Nonsense mutations resulting in a premature stop codon in an open reading frame occur in critical tumor suppressor genes in a large number of the most common forms of cancers and are known to cause or contribute to the progression of disease. Low molecular weight compounds that induce readthrough of nonsense mutations offer a new means of treating patients with genetic disorders or cancers resulting from nonsense mutations. We have identified the nucleoside analog clitocine as a potent and efficacious suppressor of nonsense mutations...
April 2017: RNA
Tünde Nyikó, Andor Auber, Levente Szabadkai, Anna Benkovics, Mariann Auth, Zsuzsanna Mérai, Zoltán Kerényi, Andrea Dinnyés, Ferenc Nagy, Dániel Silhavy
When a ribosome reaches a stop codon, the eukaryotic Release Factor 1 (eRF1) binds to the A site of the ribosome and terminates translation. In yeasts and plants, both over- and underexpression of eRF1 lead to altered phenotype indicating that eRF1 expression should be strictly controlled. However, regulation of eRF1 level is still poorly understood. Here we show that expression of plant eRF1 is controlled by a complex negative autoregulatory circuit, which is based on the unique features of the 3΄untranslated region (3΄UTR) of the eRF1-1 transcript...
April 20, 2017: Nucleic Acids Research
Julia Hofhuis, Fabian Schueren, Christopher Nötzel, Thomas Lingner, Jutta Gärtner, Olaf Jahn, Sven Thoms
Translational readthrough gives rise to C-terminally extended proteins, thereby providing the cell with new protein isoforms. These may have different properties from the parental proteins if the extensions contain functional domains. While for most genes amino acid incorporation at the stop codon is far lower than 0.1%, about 4% of malate dehydrogenase (MDH1) is physiologically extended by translational readthrough and the actual ratio of MDH1x (extended protein) to 'normal' MDH1 is dependent on the cell type...
November 2016: Open Biology
Md Asiful Islam, Fahmida Alam, Mohammad Amjad Kamal, Siew Hua Gan, Kah Keng Wong, Teguh Haryo Sasongko
Nonsense mutations contribute to approximately 10-30% of the total human inherited diseases via disruption of protein translation. If any of the three termination codons (UGA, UAG and UAA) emerges prematurely [known as premature termination codon (PTC)] before the natural canonical stop codon, truncated non-functional proteins or proteins with deleterious loss or gain-of-function activities are synthesized, followed by the development of nonsense mutation-mediated diseases. In the past decade, PTC-associated diseases captured much attention in biomedical research, especially as molecular therapeutic targets via nonsense suppression (i...
November 22, 2016: Current Pharmaceutical Design
Georgios Kosmidis, Christiaan C Veerman, Simona Casini, Arie O Verkerk, Simone van de Pas, Milena Bellin, Arthur A M Wilde, Christine L Mummery, Connie R Bezzina
BACKGROUND: Several compounds have been reported to induce translational readthrough of premature stop codons resulting in the production of full-length protein by interfering with ribosomal proofreading. Here we examined the effect of 2 of these compounds, gentamicin and PTC124, in human-induced pluripotent stem cell (hiPSC)-derived cardiomyocytes bearing nonsense mutations in the sodium channel gene SCN5A, which are associated with conduction disease and potential lethal arrhythmias...
November 2016: Circulation. Arrhythmia and Electrophysiology
Kanghyun Lee, Ruchika Sharma, Om Kumar Shrestha, Craig A Bingman, Elizabeth A Craig
Ribosome-associated J protein-Hsp70 chaperones promote nascent-polypeptide folding and normal translational fidelity. The J protein Zuo1 is known to span the ribosomal subunits, but understanding of its function is limited. Here we present new structural and cross-linking data allowing more precise positioning of Saccharomyces cerevisiae Zuo1 near the 60S polypeptide-exit site and suggesting interactions of Zuo1 with the ribosomal protein eL31 and 25S rRNA helix 24. The junction between the 60S-interacting and subunit-spanning helices is a hinge that positions Zuo1 on the 40S yet accommodates subunit rotation...
November 2016: Nature Structural & Molecular Biology
Sujatha Jagannathan, Robert K Bradley
Genetic variants that disrupt protein-coding DNA are ubiquitous in the human population, with about 100 such loss-of-function variants per individual. While most loss-of-function variants are rare, a subset have risen to high frequency and occur in a homozygous state in healthy individuals. It is unknown why these common variants are well tolerated, even though some affect essential genes implicated in Mendelian disease. Here, we combine genomic, proteomic, and biochemical data to demonstrate that many common nonsense variants do not ablate protein production from their host genes...
December 2016: Genome Research
Irwin Jungreis, Clara S Chan, Robert M Waterhouse, Gabriel Fields, Michael F Lin, Manolis Kellis
Translational stop codon readthrough emerged as a major regulatory mechanism affecting hundreds of genes in animal genomes, based on recent comparative genomics and ribosomal profiling evidence, but its evolutionary properties remain unknown. Here, we leverage comparative genomic evidence across 21 Anopheles mosquitoes to systematically annotate readthrough genes in the malaria vector Anopheles gambiae, and to provide the first study of abundant readthrough evolution, by comparison with 20 Drosophila species...
December 2016: Molecular Biology and Evolution
Alessio Branchini, Mattia Ferrarese, Silvia Lombardi, Rosella Mari, Francesco Bernardi, Mirko Pinotti
BACKGROUND: Whereas the rare homozygous nonsense mutations causing factor VII (FVII) deficiency may predict null conditions that are virtually incompatible with life, they can be associated with both life as well as appreciable differences in hemorrhagic symptoms. The misrecognition of premature stop codons (readthrough) may account for variable levels of functional full-length proteins. OBJECTIVES: To experimentally evaluate the basal and drug-induced levels of FVII produced by the homozygous p...
August 11, 2016: Journal of Thrombosis and Haemostasis: JTH
Fabian Schueren, Sven Thoms
Translational readthrough (TR) has come into renewed focus because systems biology approaches have identified the first human genes undergoing functional translational readthrough (FTR). FTR creates functional extensions to proteins by continuing translation of the mRNA downstream of the stop codon. Here we review recent developments in TR research with a focus on the identification of FTR in humans and the systems biology methods that have spurred these discoveries.
August 2016: PLoS Genetics
John VanNice, Steven T Gregory, Divya Kamath, Michael O'Connor
Ribosomal protein L19 is an essential ribosomal protein and is a component of bridge B8, one of the protein-RNA bridges linking the large and small ribosomal subunits. Bridge B8 also contributes to the accuracy of translation by affecting GTPase activation by ribosome-bound aminoacyl tRNA-EF-Tu•GTP ternary complexes. Previous work has identified a limited number of accuracy-altering alterations in protein L19 of Salmonella enterica and Thermus thermophilus. Here, we have targeted the Escherichia coli rplS gene encoding L19 for mutagenesis and have screened for mutants with altered levels of miscoding...
September 2016: Biochimie
Estienne Carl Swart, Valentina Serra, Giulio Petroni, Mariusz Nowacki
The prevailing view of the nuclear genetic code is that it is largely frozen and unambiguous. Flexibility in the nuclear genetic code has been demonstrated in ciliates that reassign standard stop codons to amino acids, resulting in seven variant genetic codes, including three previously undescribed ones reported here. Surprisingly, in two of these species, we find efficient translation of all 64 codons as standard amino acids and recognition of either one or all three stop codons. How, therefore, does the translation machinery interpret a "stop" codon? We provide evidence, based on ribosomal profiling and "stop" codon depletion shortly before coding sequence ends, that mRNA 3' ends may contribute to distinguishing stop from sense in a context-dependent manner...
July 28, 2016: Cell
Ivana Pibiri, Laura Lentini, Marco Tutone, Raffaella Melfi, Andrea Pace, Aldo Di Leonardo
Ataluren, also known as PTC124, is a 5-(fluorophenyl)-1,2,4-oxadiazolyl-benzoic acid suggested to suppress nonsense mutations by readthrough of premature stop codons in the mRNA. Potential interaction of PTC124 with mRNA has been recently studied by molecular dynamics simulations highlighting the importance of H-bonding and stacking π-π interactions. A series of non-acidic analogues of PTC124 were selected from a large database via a ligand-based virtual screening approach. Eight of them were synthesized and tested for their readthrough activity using the Fluc reporter harboring the UGA premature stop codon...
October 21, 2016: European Journal of Medicinal Chemistry
Joshua A Arribere, Elif S Cenik, Nimit Jain, Gaelen T Hess, Cameron H Lee, Michael C Bassik, Andrew Z Fire
A fraction of ribosomes engaged in translation will fail to terminate when reaching a stop codon, yielding nascent proteins inappropriately extended on their C termini. Although such extended proteins can interfere with normal cellular processes, known mechanisms of translational surveillance are insufficient to protect cells from potential dominant consequences. Here, through a combination of transgenics and CRISPR–Cas9 gene editing in Caenorhabditis elegans, we demonstrate a consistent ability of cells to block accumulation of C-terminal-extended proteins that result from failure to terminate at stop codons...
June 30, 2016: Nature
Janine Martitz, Peter Josef Hofmann, Jörg Johannes, Josef Köhrle, Lutz Schomburg, Kostja Renko
Aminoglycosides (AG) are oligosaccharide antibiotics that interfere with the small ribosomal subunit in aerobic, Gram-negative bacteria, causing pathogen-destructing error rates in their protein biosynthesis. Aminoglycosides also induce mRNA misinterpretation in eukaryotic cells, especially of the UGA (Opal)-stop codon, albeit to a lower extent. UGA recoding is essentially required for the incorporation of selenocysteine (Sec) into growing selenoproteins during translation. Selenocysteine incorporation requires the presence of a selenoprotein-specific stem-loop structure within the 3'-untranslated region of the mRNA, the so-called Sec-insertion sequence (SECIS) element...
September 2016: Journal of Trace Elements in Medicine and Biology
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