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Relevant bibliographies by topics / Stop codon read-through

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Academic literature on the topic 'Stop codon read-through'

Author: Grafiati

Published: 4 June 2021

Last updated: 10 February 2022

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Journal articles on the topic "Stop codon read-through"

1

Crawford, Daniel K., Iris Alroy, Neal Sharpe, Matthew M. Goddeeris, and Greg Williams. "ELX-02 Generates Protein via Premature Stop Codon Read-Through without Inducing Native Stop Codon Read-Through Proteins." Journal of Pharmacology and Experimental Therapeutics 374, no. 2 (May 6, 2020): 264–72. http://dx.doi.org/10.1124/jpet.120.265595.

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Kramarski, Lior, and Eyal Arbely. "Translational read-through promotes aggregation and shapes stop codon identity." Nucleic Acids Research 48, no. 7 (March 4, 2020): 3747–60. http://dx.doi.org/10.1093/nar/gkaa136.

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Abstract Faithful translation of genetic information depends on the ability of the translational machinery to decode stop codons as termination signals. Although termination of protein synthesis is highly efficient, errors in decoding of stop codons may lead to the synthesis of C-terminally extended proteins. It was found that in eukaryotes such elongated proteins do not accumulate in cells. However, the mechanism for sequestration of C-terminally extended proteins is still unknown. Here we show that 3′-UTR-encoded polypeptides promote aggregation of the C-terminally extended proteins, and targeting to lysosomes. We demonstrate that 3′-UTR-encoded polypeptides can promote different levels of protein aggregation, similar to random sequences. We also show that aggregation of endogenous proteins can be induced by aminoglycoside antibiotics that promote stop codon read-through, by UAG suppressor tRNA, or by knokcdown of release factor 1. Furthermore, we find correlation between the fidelity of termination signals, and the predicted propensity of downstream 3′-UTR-encoded polypeptides to form intrinsically disordered regions. Our data highlight a new quality control mechanism for elimination of C-terminally elongated proteins.

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Buck, Nicole E., Leonie Wood, Ruimei Hu, and Heidi L. Peters. "Stop codon read-through of a Methylmalonic aciduria mutation." Molecular Genetics and Metabolism 97, no. 4 (August 2009): 244–49. http://dx.doi.org/10.1016/j.ymgme.2009.04.004.

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Jaafar, Fauziah Mohd, Houssam Attoui, Philippe de Micco, and Xavier de Lamballerie. "Termination and read-through proteins encoded by genome segment 9 of Colorado tick fever virus." Journal of General Virology 85, no. 8 (August 1, 2004): 2237–44. http://dx.doi.org/10.1099/vir.0.80019-0.

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Genome segment 9 (Seg-9) of Colorado tick fever virus (CTFV) is 1884 bp long and contains a large open reading frame (ORF; 1845 nt in length overall), although a single in-frame stop codon (at nt 1052–1054) reduces the ORF coding capacity by approximately 40 %. However, analyses of highly conserved RNA sequences in the vicinity of the stop codon indicate that it belongs to a class of ‘leaky terminators’. The third nucleotide positions in codons situated both before and after the stop codon, shows the highest variability, suggesting that both regions are translated during virus replication. This also suggests that the stop signal is functionally leaky, allowing read-through translation to occur. Indeed, both the truncated ‘termination’ protein and the full-length ‘read-through’ protein (VP9 and VP9′, respectively) were detected in CTFV-infected cells, in cells transfected with a plasmid expressing only Seg-9 protein products, and in the in vitro translation products from undenatured Seg-9 ssRNA. The ratios of full-length and truncated proteins generated suggest that read-through may be down-regulated by other viral proteins. Western blot analysis of infected cells and purified CTFV showed that VP9 is a structural component of the virion, while VP9′ is a non-structural protein.

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Shalev, Moran, and Timor Baasov. "When proteins start to make sense: fine-tuning of aminoglycosides for PTC suppression therapy." MedChemComm 5, no. 8 (2014): 1092–105. http://dx.doi.org/10.1039/c4md00081a.

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Manjunath, Lekha E., Anumeha Singh, Sarthak Sahoo, Ashutosh Mishra, Jinsha Padmarajan, Chaithanya G. Basavaraju, and Sandeep M. Eswarappa. "Stop codon read-through of mammalian MTCH2 leading to an unstable isoform regulates mitochondrial membrane potential." Journal of Biological Chemistry 295, no. 50 (October 7, 2020): 17009–26. http://dx.doi.org/10.1074/jbc.ra120.014253.

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Stop codon read-through (SCR) is a process of continuation of translation beyond a stop codon. This phenomenon, which occurs only in certain mRNAs under specific conditions, leads to a longer isoform with properties different from that of the canonical isoform. MTCH2, which encodes a mitochondrial protein that regulates mitochondrial metabolism, was selected as a potential read-through candidate based on evolutionary conservation observed in the proximal region of its 3′ UTR. Here, we demonstrate translational read-through across two evolutionarily conserved, in-frame stop codons of MTCH2 using luminescence- and fluorescence-based assays, and by analyzing ribosome-profiling and mass spectrometry (MS) data. This phenomenon generates two isoforms, MTCH2x and MTCH2xx (single- and double-SCR products, respectively), in addition to the canonical isoform MTCH2, from the same mRNA. Our experiments revealed that a cis-acting 12-nucleotide sequence in the proximal 3′ UTR of MTCH2 is the necessary signal for SCR. Functional characterization showed that MTCH2 and MTCH2x were localized to mitochondria with a long t1/2 (>36 h). However, MTCH2xx was found predominantly in the cytoplasm. This mislocalization and its unique C terminus led to increased degradation, as shown by greatly reduced t1/2 (<1 h). MTCH2 read-through–deficient cells, generated using CRISPR-Cas9, showed increased MTCH2 expression and, consistent with this, decreased mitochondrial membrane potential. Thus, double-SCR of MTCH2 regulates its own expression levels contributing toward the maintenance of normal mitochondrial membrane potential.

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Xu, Lijun, Yanrong Hao, Cui Li, Quan Shen, Baofeng Chai, Wei Wang, and Aihua Liang. "Identification of amino acids responsible for stop codon recognition for polypeptide chain release factor." Biochemistry and Cell Biology 91, no. 3 (June 2013): 155–64. http://dx.doi.org/10.1139/bcb-2012-0091.

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One factor involved in eukaryotic translation termination is class 1 release factor in eukaryotes (eRF1), which functions to decode stop codons. Variant code species, such as ciliates, frequently exhibit altered stop codon recognition. Studies revealed that some class-specific residues in the eRF1 N-terminal domain are responsible for stop codon reassignment in ciliates. Here, we investigated the effects on stop codon recognition of chimeric eRF1s containing the N-terminal domain of Euplotes octocarinatus and Blepharisma japonicum eRF1 fused to Saccharomyces cerevisiae M and C domains using dual luciferase read-through assays. Mutation of class-specific residues in different eRF1 classes was also studied to identify key residues and motifs involved in stop codon decoding. As expected, our results demonstrate that 3 pockets within the eRF1 N-terminal domain were involved in decoding stop codon nucleotides. However, allocation of residues to each pocket was revalued. Our data suggest that hydrophobic and class-specific surface residues participate in different functions: modulation of pocket conformation and interaction with stop codon nucleotides, respectively. Residues conserved across all eRF1s determine the relative orientation of the 3 pockets according to stop codon nucleotides. However, quantitative analysis of variant ciliate and yeast eRF1 point mutants did not reveal any correlation between evolutionary conservation of class-specific residues and termination-related functional specificity and was limited in elucidating a detailed mechanism for ciliate stop codon reassignment. Thus, based on isolation of suppressor tRNAs from Euplotes and Tetrahymena, we propose that stop codon reassignment in ciliates may be controlled by cooperation between eRF1 and suppressor tRNAs.

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Brooks, Doug A., Viv J. Muller, and John J. Hopwood. "Stop-codon read-through for patients affected by a lysosomal storage disorder." Trends in Molecular Medicine 12, no. 8 (August 2006): 367–73. http://dx.doi.org/10.1016/j.molmed.2006.06.001.

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Bradley, Michael E., Sviatoslav Bagriantsev, Namitha Vishveshwara, and Susan W. Liebman. "Guanidine reduces stop codon read-through caused by missense mutations inSUP35 orSUP45." Yeast 20, no. 7 (2003): 625–32. http://dx.doi.org/10.1002/yea.985.

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Ogawa, Atsushi, Masayoshi Hayami, Shinsuke Sando, and Yasuhiro Aoyama. "A Concept for Selection of Codon-Suppressor tRNAs Based on Read-Through Ribosome Display in anIn VitroCompartmentalized Cell-Free Translation System." Journal of Nucleic Acids 2012 (2012): 1–7. http://dx.doi.org/10.1155/2012/538129.

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Here is presented a concept forin vitroselection of suppressor tRNAs. It uses a pool of dsDNA templates in compartmentalized water-in-oil micelles. The template contains a transcription/translation trigger, an amber stop codon, and another transcription trigger for the anticodon- or anticodon loop-randomized gene for tRNASer. Upon transcription are generated two types of RNAs, a tRNA and a translatable mRNA (mRNA-tRNA). When the tRNA suppresses the stop codon (UAG) of the mRNA, the full-length protein obtained upon translation remains attached to the mRNA (read-through ribosome display) that contains the sequence of the tRNA. In this way, the active suppressor tRNAs can be selected (amplified) and their sequences read out. The enriched anticodon (CUA) was complementary to the UAG stop codon and the enriched anticodon-loop was the same as that in the natural tRNASer.

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Dissertations / Theses on the topic "Stop codon read-through"

1

George, Rosemol [Verfasser], Jutta [Akademischer Betreuer] Gärtner, Peter [Gutachter] Schu, and Markus [Gutachter] Bohnsack. "Lactate dehydrogenase is C-terminally extended by stop codon read-through which targets this isoform into the peroxisomes / Rosemol George. Betreuer: Jutta Gärtner. Gutachter: Peter Schu ; Markus Bohnsack." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2016. http://d-nb.info/1111883440/34.

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Wei, Yulong. "The Roles of Stop Codons and 3’ Flanking Base in Bacterial Translation Termination Efficiency." Thesis, Université d'Ottawa / University of Ottawa, 2016. http://hdl.handle.net/10393/35529.

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Understanding translation efficiency is crucial to pharmaceutical companies that have invested substantial time and effort in engineering bacteria to produce recombinant proteins. While translation initiation and elongation have been studied intensively, much remains obscure in the subprocess of translation termination. We aim to understand how stop codons and the first 3’ flanking (+4) base affect translation termination efficiency. In chapter two, we hypothesized that stop codon usage of UAG and UGA is dependent on the abundance of their respective decoders, RF1 and RF2. We predicted and observed that bacterial species with high relative proportions of RF1 uses UAG more, and vice versa for UGA. In addition, the usage of UGA, not UAG, is always avoided in highly expressed genes. Thus, we argued against the claim made by a recent study that UAG is a minor stop codon in bacteria. The claim is incorrect because UAG does not meet the two criteria of a minor codon: i) it is most avoided in highly expressed genes, and ii) it corresponds to the least abundant decoder. Interestingly, we found that the proportion of RF2 decreases rapidly towards zero in species with high AT contents; this explains why UGA is reassigned to a sense codon in bacterial lineages with high AT content. In chapter three, we examined the role of the first downstream (+4) base Uracil in bacterial translation termination. The +4U is associated with a decrease in stop codon read-through in bacteria and yeast. We hypothesized that i) +4U enhances the termination efficiency of stop signals, and ii) +4U may serve to prevent stop codon misreading by near cognate tRNAs (nc_tRNAs). We predicted that i) +4U is preferred in highly expressed genes (HEGs) than lowly expressed genes (LEGs), and ii) +4U usage increases with the frequency of stop codon nc_tRNAs. We found +4U consistently over-represented in HEGs in contrast to LEGs; however, +4U usage in HEGs decreases in GC-rich species where most stop codons are UGA and UAG. In addition, +4U usage increases significantly with UAA usage in the known highly expressed ribosomal protein genes. These results suggest that +4U is a strong stop signal enhancer for UAA, not UAG or UGA. Furthermore, in HEGs, +4U usage also increases significantly with the abundance of UAA nc_tRNAs, suggesting that +4U increases UAA termination efficiency presumably by reducing misreading of UAA by nc_tRNAs.

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George, Rosemol. "Lactate dehydrogenase is C-terminally extended by stop codon read-through which targets this isoform into the peroxisomes." Doctoral thesis, 2016. http://hdl.handle.net/11858/00-1735-0000-0028-87FA-4.

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4

"Investigation on the Read-through Phenomenon of Pre-mature Stop Codons." 2017. http://repository.lib.cuhk.edu.hk/en/item/cuhk-1292327.

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有一件對於研究生物學的學術人士最正常的事情是當核糖體負責翻譯識別任何三種終止密碼子，一個釋放因子結合核酶和釋放的同時結束翻譯的增長的肽鏈上。但是最令人驚奇的是居然會有實驗發現，這種終止密碼子的終止進程也有可能會被提前抑制，而且被翻譯成氨基酸。在另一方面，無意義抑制傳送核糖核酸被發現及被證明能夠蛋白翻譯過程中把特殊氨基酸摻入正在增長的肽鏈上。第21 種氨基酸，硒半胱胺酸，是這些能被摻入的修飾氨基酸中的其中一個，它是專門通過無意義抑制傳送核糖核酸識別UGA 終止密碼子進行。除了這個發現外，第22種氨基酸吡咯賴胺酸，也已被證明能利用無意義抑制傳送核糖核酸和傳送核糖核酸合成酶來直接摻入正在增長的肽鏈上的。在這裡，我提出一頂名為蛋白質翻譯修改新機制，在這當中預先已被共價修飾的氨基酸會被直接在翻譯過程中納入肽鏈。另外，作為組蛋白這樣一個如此高程度修飾的蛋白質，能有其中一種組蛋白修飾的可能性，是以這裹所提出的特殊機制去實現？所以為了驗證這一個假設，重組熒光素酶蛋白的質體被選為報告的載體。然後，執行熒光素酶活性測定和蛋白質印跡以證明經轉染的C2C12 小鼠成肌細胞系能在體外展示讀通現象。為了更深層次的去探討讀通現象，我們已經拜託了劍橋大學的一個研究小組分享一個傳送核糖核酸合成酶的質體和自行購買了一個立即可用的已修飾氨基酸，乙酰基賴氨酸。這兩種元素能分別在轉染的階段被加入，看看它們分別在讀通現象中能獨立呈現的效果。這項研究的結論是，在C2C12 這已經證明讀通現象的細胞系中，加入乙酰賴氨酸可以在UGA 和UAA 終止密碼子中上調讀通現象，不過加入傳送核糖核酸合成酶只能在UGA 終止密碼子中上調通讀現象密碼而已。
It is the most sensible thing for everybody studying Biology – when ribosome which is responsible for translation recognizes any of the three stop codons, a release factor binds to the ribozyme and releases the growing peptide chain ending translation at the same time. It is surprising to all scientists to find out that this termination progress could possibly be suppressed pre-maturely and translated into amino acids. On the other hand, non-sense suppressor tRNAs have been discovered and proven to be capable to incorporate special amino acids into the growing peptide chains during protein translation. The 21st amino acid, selenocysteine, is one of these incorporating modified amino acids and it is specifically carried by non-sense suppressor tRNA recognizing UGA stop codon. Apart from that, direct incorporation of pyrrolysine, the 22nd amino acid, was demonstrated making use of non-sense suppressor tRNA and tRNA synthetase. Here, I am proposing a novel mechanism called Protein Translating Modification, in which previously modified amino acids are incorporated into peptide chains directly during translation. In addition, as histone protein is such a heavily modified protein (predominantly at its N-terminal regions), is there a possibility for histone modifications of such “post-translational modifications” to be achieved by this mechanism? So in order to test the hypothesis, a recombinant luciferase-histone plasmid is constructed as reporter vector. Then, luciferase activity assay and Western Blotting will be performed to demonstrate the in vitro read-through phenomenon in the transfected C2C12 mouse myoblast cell lines. To look into the details of the read-through phenomenon, a tRNA amino-acyl synthetase bearing plasmid has been obtained from a research team (Professor Jason Chin) of the University of Cambridge and the immediately available modified (labelled) amino acids, acetyl-lysine, have also been purchased and/or synthesized. These two components could be added separately during transfection stage to see what are their separate effects contributing to the read-through phenomenon. The conclusion for this study is that in C2C12 this already demonstrating read-through phenomenon cell line, the addition of acetyl-lysine could up-regulate the read-through phenomenon in ochre and amber stop codons while the addition of the tRNA synthetase could only up-regulate the read-through phenomenon in amber stop codon only.
Wong Wai Hung.
Thesis M.Phil. Chinese University of Hong Kong 2017.
Includes bibliographical references (leaves ).
Abstracts also in Chinese.
Title from PDF title page (viewed on …).
Detailed summary in vernacular field only.

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Book chapters on the topic "Stop codon read-through"

1

Atkins, J. F., K. Herbst, M. O’Connor, T. M. F. Tuohy, R. B. Weiss, N. M. Wills, and R. F. Gesteland. "Mutants of tRNA, Ribosomes and mRNA Affecting Frameshifting, Hopping or Stop Codon Read-Through." In The Translational Apparatus, 371–74. Boston, MA: Springer US, 1993. http://dx.doi.org/10.1007/978-1-4615-2407-6_35.

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Kamei, Makoto, Karissa Kasperski, Maria Fuller, Emma J. Parkinson-Lawrence, Litsa Karageorgos, Valery Belakhov, Timor Baasov, John J. Hopwood, and Doug A. Brooks. "Aminoglycoside-Induced Premature Stop Codon Read-Through of Mucopolysaccharidosis Type I Patient Q70X and W402X Mutations in Cultured Cells." In JIMD Reports, 139–47. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/8904_2013_270.

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