Inhibition of post-termination ribosome recycling at premature termination codons in UPF1 ATPase mutants by Lucas D Serdar, DaJuan L Whiteside, Sarah L Nock, David McGrath, Kristian E Baker

“…Recognition and rapid degradation of mRNA harboring premature translation termination codons (PTCs) serves to protect cells from accumulating non-functional and potentially toxic truncated polypeptides. …”
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INVESTIGATION OF RELATION BETWEEN CODON 27 BETA-2 ADRENERGIC RECEPTOR POLYMORPHYSMS WITH BREAST CANCER by Etem Akbaş, Ertuğrul Seyrek, Hicran Mutluhan Şenli, Nazan Eras Erdoğan, İlter Helvacı

“…In our study, ADRB2 gene codon 27 Gln27 􀃆Glu polymorhpysm does not appear to be a significant risk factor in etiology of breast. …”
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Highly Predictive Reprogramming of tRNA Modifications Is Linked to Selective Expression of Codon-Biased Genes by Begley, Thomas J., Li, Fugen, Chan, Clement T. Y., Deng, Wenjun, DeMott, Michael S, Babu, I. Ramesh, Dedon, Peter C

“…Here, we demonstrate a coordinated translational stress response system involving stress-specific reprogramming of tRNA wobble modifications that leads to selective translation of codon-biased mRNAs representing different classes of critical response proteins. …”
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Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon by Khan, Yousuf A, Jungreis, Irwin, Wright, James C, Mudge, Jonathan M, Choudhary, Jyoti S, Firth, Andrew E, Kellis, Manolis

“…Ribosome profiling data revealed that ORF-Y is translated and that initiation likely occurs at a CUG codon. Inspection of an alignment of mammalian sequences containing ORF-Y revealed that the CUG codon has a strong initiation context and that a well-conserved predicted RNA stem-loop begins 14 nucleotides downstream. …”
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tRNA-modifying enzyme mutations induce codon-specific mistranslation and protein aggregation in yeast by Tavares, Joana F, Davis, Nick K, Poim, Ana, Reis, Andreia, Kellner, Stefanie, Sousa, Inês, Soares, Ana R, Moura, Gabriela MR, Dedon, Peter C, Santos, Manuel

“…Increased rates of amino acid misincorporation were also detected in these strains at protein sites that specifically mapped to the codons sites that are decoded by the hypomodified tRNAs, demonstrating that U34 tRNA modifications safeguard the proteome from translational errors, protein misfolding and proteotoxic stress.…”
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Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins by Chan, Tsz Yan Clement, Pang, Yan Ling Joy, Deng, Wenjun, Indrakanti, Ramesh Babu, Dyavaiah, Madhu, Begley, Thomas J., Dedon, Peter C.

“…In yeast exposed to hydrogen peroxide, there is a Trm4 methyltransferase-dependent increase in the proportion of tRNA[superscript Leu(CAA)] containing m[superscript 5]C at the wobble position, which causes selective translation of mRNA from genes enriched in the TTG codon. Of these genes, oxidative stress increases protein expression from the TTG-enriched ribosomal protein gene RPL22A, but not its unenriched paralogue. …”
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Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag. by Carlson, J, Brumme, Z, Rousseau, C, Brumme, C, Matthews, P, Kadie, C, Mullins, J, Walker, B, Harrigan, P, Goulder, P, Heckerman, D

“…The resulting phylogenetic dependency network is dense, containing 149 associations between HLA alleles and HIV codons and 1386 associations among HIV codons. These associations include the complete reconstruction of several recently defined escape and compensatory mutation pathways and agree with emerging data on patterns of epitope targeting. …”

A homozygous variant disrupting the PIGH start‐codon is associated with developmental delay, epilepsy, and microcephaly by Pagnamenta, A, Murakami, Y, Anzilotti, C, Titheradge, H, Oates, A, Morton, J, DDD Study, Kinoshita, T, Kini, U, Taylor, J

“…Truncation of PIGH protein was consistent with the utilization of an in‐frame start‐site at codon 63. In summary, we describe siblings harboring a homozygous c.1A > T variant resulting in defective GPI‐anchor biogenesis and highlight the importance of exploring low‐coverage variants within autozygous regions.…”

mRNA quality control: an ancient machinery recognizes and degrades mRNAs with nonsense codons. by Behm-Ansmant, I, Kashima, I, Rehwinkel, J, Saulière, J, Wittkopp, N, Izaurralde, E

“…Nonsense-mediated mRNA decay (NMD) is an mRNA surveillance pathway which ensures the rapid degradation of mRNAs containing premature translation termination codons (PTCs or nonsense codons), thereby preventing the accumulation of truncated and potentially harmful proteins. …”

Screening for codon 249 p53 mutation in lung cancer associated with domestic radon exposure. by Lo, Y, Darby, S, Noakes, L, Whitley, E, Silcocks, P, Fleming, K, Bell, J

Differential bicodon usage in lowly and highly abundant proteins by Luis A. Diambra

Subjects: “…Synonymous codon usage…”
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Analysis of Codon Usage Patterns in <i>Giardia duodenalis</i> Based on Transcriptome Data from <i>Giardia</i>DB by Xin Li, Xiaocen Wang, Pengtao Gong, Nan Zhang, Xichen Zhang, Jianhua Li

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Ten Plastomes of <i>Crassula</i> (Crassulaceae) and Phylogenetic Implications by Hengwu Ding, Shiyun Han, Yuanxin Ye, De Bi, Sijia Zhang, Ran Yi, Jinming Gao, Jianke Yang, Longhua Wu, Xianzhao Kan

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Genetic characterization of intramuscular myxomas by William John Hatchett, Marta Brunetti, Kristin Andersen, Maren Randi Tandsæther, Ingvild Lobmaier, Marius Lund-Iversen, Thomas Lien-Dahl, Francesca Micci, Ioannis Panagopoulos

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GroEL dependency affects codon usage—support for a critical role of misfolding in gene evolution by Tobias Warnecke, Laurence D Hurst

Subjects: “…codon bias…”
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Heterologous Expression and Catalytic Properties of Codon-Optimized Small-Sized Bromelain from MD2 Pineapple by Rafida Razali, Fikran Aranda Fahrudin, Vijay Kumar Subbiah, Kazufumi Takano, Cahyo Budiman

“…Accordingly, the gene encoding MD2-SBro was firstly optimized in its codon profile, synthesized, and inserted into the pGS-21a vector. …”
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Conflicting selection pressures on synonymous codon use in yeast suggest selection on mRNA secondary structures by Stoletzki Nina

“…I look at protein coding yeast sequences and use optimal codons and synonymous substitutions to test for structural constraints. …”
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Statistical analysis of synonymous and stop codons in pseudo-random and real sequences as a function of GC content by Valentin Wesp, Günter Theißen, Stefan Schuster

“…Here, we calculate, for such sequences and for all 25 known genetic codes, the frequency of each amino acid and stop codon based on their set of codons and as a function of GC content. …”
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Meta-Analysis Results on the Association Between TP53 Codon 72 Polymorphism With the Susceptibility to Oral Cancer by Ying-Mei Lin, Jun Shao, Xiao-Hong Yin, CaiCai Huang, Xiao-Wei Jia, Ya-Di Yuan, Chang-Jing Wu, En-Ming Zhen, Zhong-Xiong Yao, Xian-Tao Zeng, Rui-Hua Liu

Subjects: “…TP53 codon 72…”
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Evolutionary Signatures Governing the Codon Usage Bias in Coronaviruses and Their Implications for Viruses Infecting Various Bat Species by Naveen Kumar, Rahul Kaushik, Chandana Tennakoon, Vladimir N. Uversky, Anamika Mishra, Richa Sood, Pratiksha Srivastava, Meghna Tripathi, Kam Y. J. Zhang, Sandeep Bhatia

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