Codon Usage Optimization in the Prokaryotic Tree of Life: How Synonymous Codons Are Differentially Selected in Sequence Domains with Different Expression Levels and Degrees of Conservation.

MBio
J. L. LopezAntonio Lagares

Abstract

Prokaryote genomes exhibit a wide range of GC contents and codon usages, both resulting from an interaction between mutational bias and natural selection. In order to investigate the basis underlying specific codon changes, we performed a comprehensive analysis of 29 different prokaryote families. The analysis of core gene sets with increasing ancestries in each family lineage revealed that the codon usages became progressively more adapted to the tRNA pools. While, as previously reported, highly expressed genes presented the most optimized codon usage, the singletons contained the less selectively favored codons. The results showed that usually codons with the highest translational adaptation were preferentially enriched. In agreement with previous reports, a C bias in 2- to 3-fold pyrimidine-ending codons, and a U bias in 4-fold codons occurred in all families, irrespective of the global genomic GC content. Furthermore, the U biases suggested that U3-mRNA-U34-tRNA interactions were responsible for a prominent codon optimization in both the most ancestral core and the highly expressed genes. A comparative analysis of sequences that encode conserved (cr) or variable (vr) translated products, with each one being under high (HEP)...Continue Reading

References

Feb 1, 1992·Journal of Molecular Evolution·N Sueoka
Dec 20, 1991·Journal of Molecular Biology·C MédigueA Danchin
Feb 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·S OsawaK Umesono
Apr 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·N Sueoka
Jan 10, 1981·Nucleic Acids Research·R GranthamR Mercier
Nov 1, 1993·Biochemical Society Transactions·P M SharpA T Lloyd
Apr 1, 1997·Journal of Molecular Evolution·J G Lawrence, H Ochman
Sep 2, 1998·Proceedings of the National Academy of Sciences of the United States of America·J O McInerney
Jul 23, 1999·Annals of the New York Academy of Sciences·J Mrázek, S Karlin
Aug 26, 2000·Journal of Bacteriology·S Karlin, J Mrázek
Jun 19, 2001·Trends in Biochemical Sciences·A P Gerber, W Keller
May 31, 2003·Proceedings of the National Academy of Sciences of the United States of America·Samuel KarlinJan Mrazek
Sep 4, 2003·Genome Biology·Vincent DaubinGuy Perrière
Apr 15, 1962·Proceedings of the National Academy of Sciences of the United States of America·N SUEOKA
Mar 3, 2004·Proceedings of the National Academy of Sciences of the United States of America·Swaine L ChenHarley H McAdams
Jun 3, 2004·Genome Research·Vincent Daubin, Howard Ochman
Sep 28, 2004·Nucleic Acids Research·Mario dos ReisLorenz Wernisch
Feb 25, 2005·Nucleic Acids Research·Paul M SharpR Elizabeth Sockett
Apr 1, 2005·PLoS Biology·Emmanuelle LeratNancy A Moran
Apr 27, 2005·Proceedings of the National Academy of Sciences of the United States of America·Howard OchmanVincent Daubin
Nov 15, 2006·Molecular Biology and Evolution·Nina Stoletzki, Adam Eyre-Walker
Dec 26, 2006·Journal of Molecular Biology·Paul F AgrisWilliam D Graham
May 8, 2007·Molecular Biology and Evolution·Ziheng Yang
May 22, 2009·BMC Bioinformatics·Jochen BlomAlexander Goesmann
Jul 14, 2009·PLoS Genetics·Ruth Hershberg, Dmitri A Petrov
Dec 19, 2009·Molecular Biology and Evolution·James J Davis, Gary J Olsen
Mar 24, 2010·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Paul M SharpKai Zeng
Apr 21, 2010·Molecular Biology and Evolution·Wenqi Ran, Paul G Higgs
Jun 30, 2010·PLoS Genetics·Fran SupekTomislav Smuc
Aug 4, 2010·Molecular Biology and Evolution·James J Davis, Gary J Olsen
Sep 15, 2010·PLoS Genetics·Falk HildebrandAdam Eyre-Walker
Sep 15, 2010·PLoS Genetics·Ruth Hershberg, Dmitri A Petrov
Apr 14, 2011·Molecular Systems Biology·Hila Gingold, Yitzhak Pilpel
Dec 1, 2011·Proceedings of the National Academy of Sciences of the United States of America·Katherine A KarbergJames J Davis
Apr 3, 2012·Cell·Eva Maria NovoaLluís Ribas de Pouplana
Aug 22, 2012·Proceedings of the National Academy of Sciences of the United States of America·Rahul RaghavanHoward Ochman
Jan 8, 2013·Nucleic Acids Research·Svetlana A ShabalinaAnna Kashina

❮ Previous
Next ❯

Citations

Oct 27, 2021·Microbial Genomics·Brian DehlingerCatherine Putonti

❮ Previous
Next ❯

Software Mentioned

Ggplot2
software
Factoextra
_ Modal
PAML suite
Inkskape
phytools R
Phylip
ng
tAI

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.