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Title: A new and updated resource for codon usage tables

Abstract

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available resources are either limited in scope, encompassing only organisms from specific domains of life, or greatly outdated.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), tomore » 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.« less

Authors:
 [1];  [1];  [2];  [2];  [2];  [1];  [2]; ORCiD logo [1]
  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
  2. U.S. Food and Drug Administration (FDA), Silver Spring, MD (United States). Center for Biologics Evaluation and Research. High Performance Integrated Environment
Publication Date:
Research Org.:
Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1626765
Grant/Contract Number:  
SC0014664
Resource Type:
Accepted Manuscript
Journal Name:
BMC Bioinformatics
Additional Journal Information:
Journal Volume: 18; Journal Issue: 1; Journal ID: ISSN 1471-2105
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Mathematical & Computational Biology; Codon usage bias; Codon optimization; Recombinant protein therapeutics; Translational kinetics

Citation Formats

Athey, John, Alexaki, Aikaterini, Osipova, Ekaterina, Rostovtsev, Alexandre, Santana-Quintero, Luis V., Katneni, Upendra, Simonyan, Vahan, and Kimchi-Sarfaty, Chava. A new and updated resource for codon usage tables. United States: N. p., 2017. Web. doi:10.1186/s12859-017-1793-7.
Athey, John, Alexaki, Aikaterini, Osipova, Ekaterina, Rostovtsev, Alexandre, Santana-Quintero, Luis V., Katneni, Upendra, Simonyan, Vahan, & Kimchi-Sarfaty, Chava. A new and updated resource for codon usage tables. United States. https://doi.org/10.1186/s12859-017-1793-7
Athey, John, Alexaki, Aikaterini, Osipova, Ekaterina, Rostovtsev, Alexandre, Santana-Quintero, Luis V., Katneni, Upendra, Simonyan, Vahan, and Kimchi-Sarfaty, Chava. Sat . "A new and updated resource for codon usage tables". United States. https://doi.org/10.1186/s12859-017-1793-7. https://www.osti.gov/servlets/purl/1626765.
@article{osti_1626765,
title = {A new and updated resource for codon usage tables},
author = {Athey, John and Alexaki, Aikaterini and Osipova, Ekaterina and Rostovtsev, Alexandre and Santana-Quintero, Luis V. and Katneni, Upendra and Simonyan, Vahan and Kimchi-Sarfaty, Chava},
abstractNote = {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.},
doi = {10.1186/s12859-017-1793-7},
journal = {BMC Bioinformatics},
number = 1,
volume = 18,
place = {United States},
year = {Sat Sep 02 00:00:00 EDT 2017},
month = {Sat Sep 02 00:00:00 EDT 2017}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Figures / Tables:

Table 1 Table 1: HIVE-CUT database size and statistics

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journal, September 2018

  • Regensdorff, Merle; Deckena, Marek; Stein, Maike
  • Journal of Phycology, Vol. 54, Issue 6
  • DOI: 10.1111/jpy.12781

Translational and transcriptional responses in human primary hepatocytes under hypoxia
journal, June 2019

  • Hettiarachchi, Gaya K.; Katneni, Upendra K.; Hunt, Ryan C.
  • American Journal of Physiology-Gastrointestinal and Liver Physiology, Vol. 316, Issue 6
  • DOI: 10.1152/ajpgi.00331.2018

DNA sequence symmetries from randomness: the origin of the Chargaff’s second parity rule
journal, April 2020

  • Fariselli, Piero; Taccioli, Cristian; Pagani, Luca
  • Briefings in Bioinformatics, Vol. 22, Issue 2
  • DOI: 10.1093/bib/bbaa041

Translational efficiency across healthy and tumor tissues is proliferation‐related
journal, March 2020

  • Hernandez‐Alias, Xavier; Benisty, Hannah; Schaefer, Martin H.
  • Molecular Systems Biology, Vol. 16, Issue 3
  • DOI: 10.15252/msb.20199275

Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum
journal, May 2020

  • Fernández, Rosa; Marcet-Houben, Marina; Legeai, Fabrice
  • Molecular Biology and Evolution, Vol. 37, Issue 9
  • DOI: 10.1093/molbev/msaa110

Splicing dysregulation contributes to the pathogenicity of several F9 exonic point variants
journal, June 2019

  • Katneni, Upendra K.; Liss, Aaron; Holcomb, David
  • Molecular Genetics & Genomic Medicine, Vol. 7, Issue 8
  • DOI: 10.1002/mgg3.840

Molecular dynamics simulations for genetic interpretation in protein coding regions: where we are, where to go and when
journal, December 2019

  • Galano-Frutos, Juan J.; García-Cebollada, Helena; Sancho, Javier
  • Briefings in Bioinformatics
  • DOI: 10.1093/bib/bbz146

Smoothing membrane protein structure determination by initial upstream stage improvements
journal, May 2019

  • Pedro, Augusto Quaresma; Queiroz, João António; Passarinha, Luís António
  • Applied Microbiology and Biotechnology, Vol. 103, Issue 14
  • DOI: 10.1007/s00253-019-09873-1

Resource conservation manifests in the genetic code
journal, November 2020


A Novel Marsupial Hepatitis A Virus Corroborates Complex Evolutionary Patterns Shaping the Genus Hepatovirus
journal, July 2018

  • de Oliveira Carneiro, Ianei; Sander, Anna-Lena; Silva, Namá
  • Journal of Virology, Vol. 92, Issue 13
  • DOI: 10.1128/jvi.00082-18

Codon Usage Bias Analysis of Citrus tristeza Virus: Higher Codon Adaptation to Citrus reticulata Host
journal, April 2019

  • Biswas, Kajal; Palchoudhury, Supratik; Chakraborty, Prosenjit
  • Viruses, Vol. 11, Issue 4
  • DOI: 10.3390/v11040331

Smoothing membrane protein structure determination by initial upstream stage improvements
journal, May 2019

  • Pedro, Augusto Quaresma; Queiroz, João António; Passarinha, Luís António
  • Applied Microbiology and Biotechnology, Vol. 103, Issue 14
  • DOI: 10.1007/s00253-019-09873-1

A case for a negative-strand coding sequence in a group of positive-sense RNA viruses.
text, January 2020

  • Dinan, Adam M.; Lukhovitskaya, Nina I.; Olendraite, Ingrida
  • Apollo - University of Cambridge Repository
  • DOI: 10.17863/cam.50796

Rare-variant pathogenicity triage and inclusion of synonymous variants improves analysis of disease associations of orphan G protein–coupled receptors
journal, October 2019

  • Dershem, Ridge; Metpally, Raghu P. R.; Jeffreys, Kirk
  • Journal of Biological Chemistry, Vol. 294, Issue 48
  • DOI: 10.1074/jbc.ra119.009253

Enhanced in vivo-imaging in medaka by optimized anaesthesia, fluorescent protein selection and removal of pigmentation
journal, March 2019


Multiparameter screening method for developing optimized red-fluorescent proteins
journal, January 2020


Machine Learning for detection of viral sequences in human metagenomic datasets
journal, September 2018


Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.