Identification of RNA editing sites in cotton (Gossypium hirsutum) chloroplasts and editing events that affect secondary and three-dimensional protein structures

Genetics and Molecular Research : GMR
Yuan JiangS X Yu

Abstract

RNA editing can alter individual nucleotides in primary transcripts, which can cause the amino acids encoded by edited RNA to deviate from the ones predicted from the DNA template. We investigated RNA editing sites of protein-coding genes from the chloroplast genome of cotton. Fifty-four editing sites were identified in 27 transcripts, which is the highest editing frequency found until now in angiosperms. All these editing sites were C-to-U conversion, biased toward ndh genes and U_A context. Examining published editotypes in various angiosperms, we found that RNA editing mostly converts amino acid from hydrophilic to hydrophobic and restores evolutionary conserved amino acids. Using bioinformatics to analyze the effect of editing events on protein secondary and three-dimensional structures, we found that 21 editing sites can affect protein secondary structures and seven editing sites can alter three-dimensional protein structures. These results imply that 24 editing sites in cotton chloroplast transcripts may play an important role in their protein structures and functions.

References

Jan 1, 1978·Biochemical Society Transactions·M J Sternberg, J M Thornton
Jan 1, 1993·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·M W Gray, P S Covello
Nov 18, 2000·The Journal of Biological Chemistry·Y SasakiY Nagano
Dec 29, 2000·Molecular & General Genetics : MGG·S CorneilleP Maliga
Aug 2, 2001·Plant & Cell Physiology·T M ReginaC Quagliariello
Oct 25, 2001·Journal of Molecular Evolution·T TsudzukiM Sugiura
Apr 25, 2003·Nucleic Acids Research·Masanori KugitaKoichi Yoshinaga
Jun 25, 2004·Bioscience, Biotechnology, and Biochemistry·Yukiko Sasaki, Yukio Nagano
Jul 9, 2004·Nucleic Acids Research·Andreas FiebigRalph Bock
Feb 9, 2006·Cellular and Molecular Life Sciences : CMLS·T Shikanai
Jul 11, 2006·Journal of Molecular Evolution·Sabine KahlauRalph Bock
May 8, 2007·Proceedings of the National Academy of Sciences of the United States of America·Kenji OkudaToshiharu Shikanai
Jul 29, 2008·The Plant Journal : for Cell and Molecular Biology·Anne-Laure Chateigner-BoutinPatricia León
May 19, 2009·Plant Physiology·Wenhe CaiLixin Zhang
Oct 23, 2009·The Plant Journal : for Cell and Molecular Biology·Kenji OkudaToshiharu Shikanai

❮ Previous
Next ❯

Citations

Jul 7, 2015·Journal of Proteome Research·George Sergeevich KrasnovElena Alexandrovna Ponomarenko

❮ Previous
Next ❯

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.