Article
Biotechnology & Applied Microbiology
Yide Huang, Ting Lin, Lingfang Lu, Fan Cai, Jie Lin, Yu'e Jiang, Yao Lin
Summary: A new codon pair optimization algorithm was introduced in this study, showing that codon optimization based on codon pair bias is more effective in enhancing protein expression levels in Pichia pastoris.
MICROBIAL CELL FACTORIES
(2021)
Article
Neurosciences
Rekha Khandia, Mohd. Saeed, Ahmed M. Alharbi, Ghulam Md. Ashraf, Nigel H. Greig, Mohammad Amjad Kamal
Summary: Codon usage analysis is important for molecular characterization and understanding gene evolution. This study investigated the association between gene length and various parameters related to codon usage. The findings showed a significant correlation between gene length and codon bias in neurodegeneration-associated genes. However, this association varied depending on the size of gene segments. The study also found that gene length was associated with nucleotide disproportion and codon choices. This analysis provides insights into gene expression and potential interventions in defective gene functioning in clinical settings.
FRONTIERS IN NEUROSCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Bo Xiong, Tie Wang, Shengjia Huang, Ling Liao, Xun Wang, Honghong Deng, Mingfei Zhang, Jiaxian He, Guochao Sun, Siya He, Zhihui Wang
Summary: This study analyzed the codon usage bias of 20 xyloglucan endotransglycosylase (XET) genes and found that most genes had weak codon usage bias, but some genes showed significant bias. Translational selection and base composition were identified as important factors affecting codon usage of XET genes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Sujatha Thankeswaran Parvathy, Varatharajalu Udayasuriyan, Vijaipal Bhadana
Summary: Codon usage bias is a common phenomenon observed in bacteria, plants, and animals, with consistent and characteristic patterns across different species and genes. The formation of codon bias is influenced by factors such as genome composition, gene expression levels, and gene length. Understanding codon usage bias can provide insights into phylogenetic relationships and gene evolution among organisms.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Multidisciplinary Sciences
Dominic Simm, Blagovesta Popova, Gerhard H. Braus, Stephan Waack, Martin Kollmar
Summary: The study analyzed the influence of a profiled codon usage adaptation approach on protein expression levels in the eukaryotic model organism Saccharomyces cerevisiae. Results showed that high levels of GFP expression and adaptation of toxic α Syn to endogenous low-level expression could be achieved using this approach. The new software for performing host-specific protein adaptations to commonly used model organisms is publicly available as a web-application.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Gun Li, Liang Zhang, Pei Xue
Summary: This study investigates the codon usage pattern of coding sequences in Mycobacterium tuberculosis and reveals the differences and characteristics of specific functional genes, providing new insights into the evolution of Mycobacterium tuberculosis and measures for prevention and control of tuberculosis from a gene engineering perspective.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemical Research Methods
Matthias Schmidt, Namil Lee, Chunjun Zhan, Jacob B. Roberts, Alberto A. Nava, Leah S. Keiser, Aaron A. Vilchez, Yan Chen, Christopher J. Petzold, Robert W. Haushalter, Lars M. Blank, Jay D. Keasling
Summary: In this study, the influence of 11 different codon variants on heterologous expression was analyzed. The best-performing codon variants resulted in a 50-fold increase in protein levels and successful synthesis of unnatural polyketides in different hosts. Additionally, an online tool for codon optimization was developed.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Abigail Leavitt LaBella, Dana A. Opulente, Jacob L. Steenwyk, Chris Todd Hittinger, Antonis Rokas
Summary: Reverse ecology involves inferring ecological information from patterns of genomic variation, with a focus on codon optimality. The study found a positive correlation between optimal codon usage in the galactose metabolism pathway and quantitative growth on galactose, as well as associations with human-associated and dairy-associated ecological niches in yeasts. This suggests that codon optimization can provide insights into the metabolic ecology of microbial eukaryotes, particularly for studying fungal dark matter species.
Article
Microbiology
Ethan T. Hillman, Elizabeth M. Frazier, Evan K. Shank, Adrian N. Ortiz-Velez, Jacob A. Englaender, Kevin Solomon
Summary: Anaerobic fungi have rich biosynthetic potential, but their biosynthetic pathways have limited success in model hosts like E. coli. This is due to the extreme AT bias in the genome of anaerobic fungi like P. indianae, which causes growth defects in E. coli. Codon optimization rescues growth and enables gene evaluation in otherwise difficult to express genes.
Review
Microbiology
Judit Gimenez-Roig, Estela Nunez-Manchon, Ramon Alemany, Eneko Villanueva, Cristina Fillat
Summary: Vaccination is the most effective method to prevent viral diseases, with recombinant vaccines being one of the most efficient strategies. Recombinant vaccines use safe viral vectors and transgenes to induce an immune response, playing a crucial role in preventing infections.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Jiajing Sheng, Xuan She, Xiaoyu Liu, Jia Wang, Zhongli Hu
Summary: This study systematically analyzed the codon usage patterns of Miscanthus plants and related species, revealing a preference for A/T bases and A/T-ending codons in the chloroplast genomes. The results suggested that the codon usage patterns are mainly influenced by natural selection, and Arabidopsis thaliana, Populus trichocarpa, and Saccharomyces cerevisiae could be considered as preferential exogenous expression receptors.
Article
Biotechnology & Applied Microbiology
Kunshan Liu, Yaqi Ouyang, Ru Lin, Chenyu Ge, Mian Zhou
Summary: Codon usage bias plays an important role in regulating gene expression levels, mRNA and protein stabilities in P. pastoris. Extreme codon optimization in genes with strong negative correlation between codon usage bias and protein structural disorder tendency may not be favored, and may affect protein structural conformation more severely in structural disordered proteins.
JOURNAL OF BIOTECHNOLOGY
(2022)
Article
Cell Biology
Parvin A. Barbhuiya, Arif Uddin, Supriyo Chakraborty
Summary: The study analyzed the codon usage patterns of mitochondrial ND genes in three amphibian groups, revealing differences in codon usage and significant variations in GC content among different groups. The results suggest that natural selection plays a predominant role in shaping codon usage bias of ND genes across orders.
JOURNAL OF CELLULAR PHYSIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Marion A. L. Picard, Fiona Leblay, Cecile Cassan, Anouk Willemsen, Josquin Daron, Frederique Bauffe, Mathilde Decourcelle, Antonin Demange, Ignacio G. Bravo
Summary: Differences in codon frequency have significant effects on transcription and translation efficiency, leading to phenotypic and functional differences. This study presents a multiscale analysis of synonymous codon recoding effects during heterologous gene expression and quantifies the impact of codon usage bias at different molecular and cellular levels. The results demonstrate that codon usage bias strongly influences molecular and cellular phenotype, affecting mRNA and protein levels, leading to reproducible phenotypic heterogeneity and trade-off between antibiotic resistance and heterologous expression burden. In human cells, codon usage bias modulates gene expression by altering mRNA availability and suitability for translation, resulting in protein level differences and functional phenotypic changes.
Article
Genetics & Heredity
Parvin A. Barbhuiya, Arif Uddin, Supriyo Chakraborty
Summary: The study revealed the existence of CUB in genes of amphibians, with the highest CUB in the order Caudata, the lowest in Anura, and an intermediate level in Gymnophiona.