Study of Codon Usage Patterns and Influencing Factors in Rice Yellow Mottle Virus Based on Coding Sequence Data by Siddiq Ur Rahman, Sajid Nawaz, Sifat Ullah, Inayat Ur Rahman, Muhammad Inam Ul Haq, Muazzam Ali Khan, Abdullah Ahmed Al-Ghamdi, Fahad M. Al-Hemaid, Mohamed S. Elshikh, Reem M. Aljowaie, Wafa Ali Eltayb

Subjects: Get full text

Clues to tRNA Evolution from the Distribution of Class II tRNAs and Serine Codons in the Genetic Code by Harold S. Bernhardt

“…In the following, I propose that the class II tRNA structure of tRNASer and the arrangement of serine codons in the genetic code provide clues to the early evolution of tRNA and the genetic code. …”
Get full text

Structural insights into mRNA reading frame regulation by tRNA modification and slippery codon–anticodon pairing by Eric D Hoffer, Samuel Hong, S Sunita, Tatsuya Maehigashi, Ruben L Gonzalez Jnr, Paul C Whitford, Christine M Dunham

“…The absence of m1G37 in tRNAPro causes +1 frameshifting on polynucleotide, slippery codons. Here, we report structures of the bacterial ribosome containing tRNAPro bound to either cognate or slippery codons to determine how the m1G37 modification prevents mRNA frameshifting. …”
Get full text

Comprehensive mutagenesis maps the effect of all single-codon mutations in the AAV2 rep gene on AAV production by Nina K Jain, Pierce J Ogden, George M Church

“…To gain a comprehensive understanding of the Rep proteins and their mutational landscape, we assayed the effects of all 39,297 possible single-codon mutations to the AAV2 rep gene on AAV2 production. …”
Get full text

Viral proteins originated de novo by overprinting can be identified by codon usage: application to the "gene nursery" of Deltaretroviruses by Pavesi, A, Magiorkinis, G, Karlin, D

“…We assembled a reference set of overlapping genes for which we could reliably determine the ancestral frames, and found that their codon usage was significantly closer to that of the rest of the viral genome than the codon usage of de novo frames. …”

CTL Escape and Codon Covariation in Subtypes B and C p17 (Matrix) and p24 (Capsid) Proteins by Carlson, J, Brumme, Z, Rousseau, C, Brumme, C, Matthews, P, Kadie, C, Mullins, J, Walker, B, Harrigan, R, Goulder, P, Heckerman, D

Soluble expression and catalytic properties of codon-optimized recombinant bromelain from MD2 pineapple in Escherichia coli by Rafida Razali, Cahyo Budiman, Khairul Azfar Kamaruzaman, Vijay Kumar Subbiah

“…The gene encoding MD2Bro was codon-optimized, synthesized, and subsequently ligated into pET-32b(+) for further transformation into Escherichia coli BL21-CodonPlus(DE3). …”
Get full text
Get full text

EXPRESSION OF NUCLEOCAPSID VIRAL PROTEINS IN THE BACTERIAL SYSTEM OF Escherichia coli: THE INFLUENCE OF THE CODON COMPOSITION AND THE UNIFORMITY OF ITS DISTRIBUTION WITHIN GENE by E. G. Fomina, E. E. Grigorieva, V. V. Zverko, A. S. Vladyko

Subjects: Get full text

gtAI: an improved species-specific tRNA adaptation index using the genetic algorithm by Ali Mostafa Anwar, Saif M. Khodary, Eman Ali Ahmed, Eman Ali Ahmed, Aya Osama, Shahd Ezzeldin, Anthony Tanios, Sebaey Mahgoub, Sameh Magdeldin, Sameh Magdeldin

Subjects: “…codon usage…”
Get full text

A comprehensive analysis of Usutu virus (USUV) genomes revealed lineage-specific codon usage patterns and host adaptations by Jianglin Zhou, Yaling Xing, Zhe Zhou, Shengqi Wang

Subjects: “…codon usage…”
Get full text

National Prevalence of Caprine Prion Protein Genetic Variability at Codons 146, 211, and 222 in Goat Herds in the United States by Mohamed Zeineldin, Heather Cox-Struble, Patrick Camp, David Farrell, Randy Pritchard, Tyler C. Thacker, Kimberly Lehman

“…The samples underwent DNA extraction, and the <i>PRNP</i> variants corresponding to codons 146, 211, and 222 were amplified and sequenced. …”
Get full text

Functional role of bacteriophage transfer RNAs: codon usage analysis of genomic sequences stored in the GENBANK/EMBL/DDBJ databases by T Kunisawa

Subjects: “…Codon usage…”
Get full text

Genetic features of bovine viral diarrhea virus subgenotype 1c in newborn calves at nucleotide and synonymous codon usages by Huihui Wang, Huihui Wang, Huihui Wang, Mengzhu Wang, Mengzhu Wang, Mengzhu Wang, Xili Feng, Xili Feng, Xili Feng, Yicong Li, Yicong Li, Yicong Li, Derong Zhang, Derong Zhang, Yan Cheng, Yan Cheng, Yan Cheng, Junlin Liu, Xiezhong Wang, Licheng Zhang, Hua La, Xiaoqian You, Zhongren Ma, Zhongren Ma, Jianhua Zhou, Jianhua Zhou

Subjects: Get full text

tRNA copy number and codon usage in the sea cucumber genome provide insights into adaptive translation for saponin biosynthesis by Chengzhang Liu, Jianbo Yuan, Xiaojun Zhang, Songjun Jin, Fuhua Li, Jianhai Xiang

“…We propose that coevolution between genomic tRNA content and codon usage of sea cucumbers facilitates their saponin synthesis and survival using food resources with low nutrient content.…”
Get full text

Cone Dystrophy Associated with a Novel Variant in the Terminal Codon of the <i>RPGR</i>-<i>ORF15</i> by Vlasta Hadalin, Maja Šuštar, Marija Volk, Aleš Maver, Jana Sajovic, Martina Jarc-Vidmar, Borut Peterlin, Marko Hawlina, Ana Fakin

“…We describe the phenotype associated with a novel variant in the terminal codon of the <i>RPGR^ORF15</i> c.3457T>A (Ter1153Lysext*38), which results in a C-terminal extension. …”
Get full text

Translational initiation factor eIF5 replaces eIF1 on the 40S ribosomal subunit to promote start-codon recognition by Jose Luis Llácer, Tanweer Hussain, Adesh K Saini, Jagpreet Singh Nanda, Sukhvir Kaur, Yuliya Gordiyenko, Rakesh Kumar, Alan G Hinnebusch, Jon R Lorsch, V Ramakrishnan

“…The present structure reveals the basis for a key role of eIF5 in start-codon selection.…”
Get full text

Insights into the Evolution and Host Adaptation of the Monkeypox Virus from a Codon Usage Perspective: Focus on the Ongoing 2022 Outbreak by Jianglin Zhou, Xuejun Wang, Zhe Zhou, Shengqi Wang

Subjects: Get full text

Chloroplasts evolved an additional layer of translational regulation based on non-AUG start codons for proteins with different turnover rates by Leelavathi Sadhu, Krishan Kumar, Saravanan Kumar, Abhishek Dass, Ranjana Pathak, Amit Bhardwaj, Pankaj Pandey, Nguyen Van Cuu, Bhupendra S. Rawat, Vanga Siva Reddy

“…However, the biological significance of such use of non-AUG codons is not fully understood. The present study was undertaken to unravel the significance of non-AUG start codons in vivo using the chloroplast genetic engineering approach. …”
Get full text

Manipulation of viral protein production using the PCNA of halovirus фCh1 via alternative start codon usage by Richard John Manning, Michael Tschurtschenthaler, Sonja Sabitzer, Angela Witte

“…Natrialba magadii, the only known host of фCh1, also encodes a putative PCNA of high sequence similarity, differing in the presence of an alternate GUG start codon 5′ of the AUG start codon resulting in a larger protein. …”
Get full text

Variabilidad genotipo fenotipo en encefalopatía neurogastrointestinal mitocondrial MNGIE por una mutación sin codón de parada by Blair Ortiz Giraldo, Diego Ferrnando Batero, Jorge Hernán Montoya, Juan Manuel Alfaro, Alejandra Wilches

Get full text