A new and updated resource for codon usage tables

Athey, John; Alexaki, Aikaterini; Osipova, Ekaterina; Rostovtsev, Alexandre; Santana-Quintero, Luis V.; Katneni, Upendra; Simonyan, Vahan; Kimchi-Sarfaty, Chava

doi:10.1186/s12859-017-1793-7

Title: A new and updated resource for codon usage tables

Journal Article · Sat Sep 02 00:00:00 EDT 2017 · BMC Bioinformatics

DOI:https://doi.org/10.1186/s12859-017-1793-7· OSTI ID:1626765

Athey, John ^[1]; Alexaki, Aikaterini ^[1]; Osipova, Ekaterina ^[2]; Rostovtsev, Alexandre ^[2]; Santana-Quintero, Luis V. ^[2]; Katneni, Upendra ^[1]; Simonyan, Vahan ^[2];

^[1]

U.S. Food and Drug Administration (FDA), Silver Spring, MD (United States). Center for Biologics Evaluation and Research. Office of Tissue and Advanced Therapies. Division of Plasma Protein Therapeutics
U.S. Food and Drug Administration (FDA), Silver Spring, MD (United States). Center for Biologics Evaluation and Research. High Performance Integrated Environment

Background: Due to the degeneracy of the genetic code, most amino acids can be encoded by multiple synonymous codons. Synonymous codons naturally occur with different frequencies in different organisms. The choice of codons may affect protein expression, structure, and function. Recombinant gene technologies commonly take advantage of the former effect by implementing a technique termed codon optimization, in which codons are replaced with synonymous ones in order to increase protein expression. This technique relies on the accurate knowledge of codon usage frequencies. Accurately quantifying codon usage bias for different organisms is useful not only for codon optimization, but also for evolutionary and translation studies: phylogenetic relations of organisms, and host-pathogen co-evolution relationships, may be explored through their codon usage similarities. Furthermore, codon usage has been shown to affect protein structure and function through interfering with translation kinetics, and cotranslational protein folding. Results: Despite the obvious need for accurate codon usage tables, currently available resources are either limited in scope, encompassing only organisms from specific domains of life, or greatly outdated. Taking advantage of the exponential growth of GenBank and the creation of NCBI’s RefSeq database, we have developed a new database, the High-performance Integrated Virtual Environment-Codon Usage Tables (HIVE-CUTs), to present and analyse codon usage tables for every organism with publicly available sequencing data. Compared to existing databases, this new database is more comprehensive, addresses concerns that limited the accuracy of earlier databases, and provides several new functionalities, such as the ability to view and compare codon usage between individual organisms and across taxonomical clades, through graphical representation or through commonly used indices. In addition, it is being routinely updated to keep up with the continuous flow of new data in GenBank and RefSeq. Conclusion: Given the impact of codon usage bias on recombinant gene technologies, this database will facilitate effective development and review of recombinant drug products and will be instrumental in a wide area of biological research. The database is available at hive.biochemistry.gwu.edu/review/codon.

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Research Organization:: Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: SC0014664

OSTI ID:: 1626765

Journal Information:: BMC Bioinformatics, Vol. 18, Issue 1; ISSN 1471-2105

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Journal Article · Wed Jul 31 00:00:00 EDT 2019 · PLoS Genetics · OSTI ID:1626765

LaBella, Abigail L.; Opulente, Dana A.; Steenwyk, Jacob L.; +3 more

Effects of codon optimization on coagulation factor IX translation and structure: Implications for protein and gene therapies

Journal Article · Tue Oct 29 00:00:00 EDT 2019 · Scientific Reports · OSTI ID:1626765

Alexaki, Aikaterini; Hettiarachchi, Gaya K.; Athey, John C.; +20 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Biochemistry & Molecular Biology
Biotechnology & Applied Microbiology
Mathematical & Computational Biology
Codon usage bias
Codon optimization
Recombinant protein therapeutics
Translational kinetics

Additional file 2: of A new and updated resource for codon usage tables Athey, John; Alexaki, Aikaterini; Osipova, Ekaterina https://doi.org/10.6084/m9.figshare.c.3870538_d2 The current record is supplemented by this text	text	January 2017
Additional file 1: of A new and updated resource for codon usage tables Athey, John; Alexaki, Aikaterini; Osipova, Ekaterina https://doi.org/10.6084/m9.figshare.c.3870538_d1 The current record is supplemented by this text	text	January 2017
Additional file 3: of A new and updated resource for codon usage tables Athey, John; Alexaki, Aikaterini; Osipova, Ekaterina https://doi.org/10.6084/m9.figshare.c.3870538_d3 The current record is supplemented by this text	text	January 2017
Additional file 2: of A new and updated resource for codon usage tables Athey, John; Alexaki, Aikaterini; Osipova, Ekaterina https://doi.org/10.6084/m9.figshare.c.3870538_d2.v1 The current record is supplemented by this text	text	January 2017
Additional file 1: of A new and updated resource for codon usage tables Athey, John; Alexaki, Aikaterini; Osipova, Ekaterina https://doi.org/10.6084/m9.figshare.c.3870538_d1.v1 The current record is supplemented by this text	text	January 2017
Additional file 3: of A new and updated resource for codon usage tables Athey, John; Alexaki, Aikaterini; Osipova, Ekaterina https://doi.org/10.6084/m9.figshare.c.3870538_d3.v1 The current record is supplemented by this text	text	January 2017
A new and updated resource for codon usage tables Athey, John; Alexaki, Aikaterini; Osipova, Ekaterina https://doi.org/10.6084/m9.figshare.c.3870538.v1 The current record is supplemented by this collection	collection	January 2017
A new and updated resource for codon usage tables Athey, John; Alexaki, Aikaterini; Osipova, Ekaterina https://doi.org/10.6084/M9.FIGSHARE.C.3870538 The current record is supplemented by this collection	collection	January 2017