The effects of codon usage on the formation of secondary structures of nucleocapsid protein of peste des petits ruminants virus

Genes & Genomics
Xiao-Xia MaXue-Peng Cai

Abstract

The nucleocapsid (N) protein of peste des petits ruminants virus (PPRV) with a conserved amino acid usage pattern plays an important role in viral replication. The primary objective of this study was to estimate roles of synonymous codon usages of PPRV N gene and tRNA abundances of host in the formation of secondary structure of N protein. The potential effects of synonymous codon usages of N gene and tRNA abundances of host on shaping different folding units (α-helix, β-strand and the coil) in N protein were estimated, based on the information about the modeling secondary structure of PPRV N protein. The synonymous codon usage bias was found in different folding units in PPRV N protein. To better understand the role of translation speed caused by variant tRNA abundances in shaping the specific folding unit in N protein, we modeled the changing trends of tRNA abundance at the transition boundaries from one folding unit to another folding unit (β-strand → coil, coil → β-strand, α-helix → coil, coil → α-helix). The obvious fluctuations of tRNA abundance were identified at the two transition boundaries (β-strand → coil and coil → β-strand) in PPRV N protein. Our findings suggested that viral synonymous codon usage bias and cellula...Continue Reading

References

Mar 18, 2000·Biochemical and Biophysical Research Communications·S K GuptaT C Ghosh
Nov 5, 2003·Bioinformatics·A CarboneF Képès
Sep 21, 2004·IEEE Transactions on Nanobioscience·Wanjun GuZuhong Lu
Jan 31, 2008·BMC Bioinformatics·Pere PuigbòSantiago Garcia-Vallvé
Jul 16, 2008·Biotechnology Journal·Monica Marin
Aug 30, 2008·Journal of Molecular Biology·Chung-Jung TsaiRuth Nussinov
Sep 18, 2008·Biology Direct·Pere PuigbòSantiago Garcia-Vallve
Oct 17, 2008·PloS One·Thomas F Clarke, Patricia L Clark
Nov 11, 2008·Trends in Biochemical Sciences·Anton A Komar
Mar 28, 2009·Journal of the Royal Society, Interface·Mark WelchJeremy Minshull
Jun 6, 2009·Nature Structural & Molecular Biology·Günter KramerBernd Bukau
Nov 6, 2009·Molecular Systems Biology·Iris BahirMichal Linial
Sep 17, 2010·The Journal of General Virology·Ashley C BanyardGenevieve Libeau
Sep 18, 2010·Science·Ivana Weygand-Durasevic, Michael Ibba
Dec 12, 2012·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Jian-Hua ZhouYong-Sheng Liu
Mar 19, 2013·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Jian-hua ZhouYong-sheng Liu
Mar 10, 2015·Annual Review of Biophysics·Julie L Chaney, Patricia L Clark
Oct 8, 2015·Veterinary Microbiology·S ParidaA C Banyard
Apr 27, 2016·Advances in Virus Research·M D BaronG Libeau
Oct 13, 2016·Emerging Microbes & Infections·Azeem Mehmood ButtYigang Tong
Aug 23, 2017·ELife·Fanny PouyetMarie Sémon
Sep 1, 2017·Journal of Molecular Microbiology and Biotechnology·Darja Kanduc
Oct 12, 2017·Nature Reviews. Molecular Cell Biology·Gavin Hanson, Jeff Coller
Nov 2, 2017·Protein Science : a Publication of the Protein Society·Anabel RodriguezPatricia L Clark

❮ Previous
Next ❯

Related Concepts

Related Feeds

Cajal Bodies & Gems

Cajal bodies or coiled bodies are dense foci of coilin protein. Gemini of Cajal bodies, or gems, are microscopically similar to Cajal bodies. It is believed that Cajal bodies play important roles in RNA processing while gems assist the Cajal bodies. Find the latest research on Cajal bodies and gems here.

Related Papers

Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases
Jian-Hua ZhouYong-Sheng Liu
Zentralblatt für Veterinärmedizin. Reihe B. Journal of veterinary medicine. Series B
O A DurojaiyeC Smale
Emerging Infectious Diseases
Ahmed Salem El ArbiRenaud Lancelot
Emerging Infectious Diseases
Ashley C BanyardSatya Parida
© 2022 Meta ULC. All rights reserved