Review
Plant Sciences
Volker Knoop
Summary: The genomes of plant cells' energy-converting organelles, chloroplasts and mitochondria, have errors that are corrected in RNA transcript copies. The function of genes in these organelles relies on site-specific cytidine-to-uridine (C-to-U) exchanges and additional reverse U-to-C exchanges. Research on these peculiar processes of plant RNA editing has been ongoing for over 30 years. Recent studies have provided insights into the biochemical machinery and the role of horizontal gene transfer in the acquisition and functional adaptation of plant RNA editing factors in other organisms.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Atsushi Sadamitsu, Yuya Inoue, Keiko Sakakibara, Hiromi Tsubota, Tomio Yamaguchi, Hironori Deguchi, Tomoaki Nishiyama, Masaki Shimamura
Summary: The complete chloroplast genome sequence of the moss Takakia lepidozioides has been reported, highlighting its evolutionary significance. This study reveals the dense RNA editing phenomenon and the largest gene collection in mosses from the evolutionary perspective. Interestingly, the Takakia moss retains the highest number of genes among all sequenced moss chloroplast genomes, providing insights into the genetic diversity and evolution of mosses.
PLANT MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yong Wang, Hao Li, Zi-Qin Huang, Bing Ma, Yan-Zhuo Yang, Zhi-Hui Xiu, Le Wang, Bao-Cai Tan
Summary: The PPR-E proteins recruit the trans deaminase PCW1 and bCCP1 to carry out RNA C-to-U editing, with assistance from the MORF1/8 proteins through protein-protein interactions. This process is essential for plant growth and development.
Article
Cell Biology
Riccardo Pecori, Isabel Chillon, Claudio Lo Giudice, Annette Arnold, Sandra Wuest, Marco Binder, Marco Marcia, Ernesto Picardi, Fotini Nina Papavasiliou
Summary: RNA editing is a modification of RNA molecules that can change their nucleotide sequence compared to the genome. In mammals, there are two types of RNA editing described: adenosine to inosine (A-to-I) and cytidine to uridine (C-to-U) editing. Recent advances in RNA sequencing technologies have allowed for the discovery of numerous editing sites, but validation of these sites is necessary due to potential errors in the methods used. Through validation, it was found that some editing events result from A-to-I editing on overlapping antisense RNAs transcribed from the same loci, which can be immunogenic and associated with autoimmune and immune-related diseases.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Biology
Alejandro A. Edera, Ian Small, Diego H. Milone, M. Virginia Sanchez-Puerta
Summary: A new method using deep convolutional neural network to predict plant mitochondrial C-to-U RNA editing events was introduced, which showed a significant improvement in predictive performance compared to traditional methods, indicating the potential importance for studying RNA regulation.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Biology
Zhan Gao, Wanyue Jiang, Yu Zhang, Liping Zhang, Mengmeng Yi, Haitao Wang, Zengyu Ma, Baozhen Qu, Xiaohan Ji, Hongan Long, Shicui Zhang
Summary: A study has identified an adenosine-to-inosine tRNA-editing deaminase, ADAT2, from amphioxus that can perform A-to-I editing of tRNA and convert C-to-U and A-to-I deamination of DNA when in complex with ADAT3. The study also reveals the key residues and binding sites involved in these activities. Furthermore, it suggests that ADAT2/3 is the only enzyme with both tRNA and DNA editing capabilities found in Metazoa.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Elena Lesch, Maximilian T. Schilling, Sarah Brenner, Yingying Yang, Oliver J. Gruss, Volker Knoop, Mareike Schallenberg-Ruedinger
Summary: RNA editing processes differ significantly between animals and plants, with plant PPR proteins playing a key role in plant organelle cytidine-to-uridine editing. It has been discovered that plant PPR editing factors can operate in the nucleo-cytosolic environment of humans and be re-engineered towards new targets.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Plant Sciences
Tanara P. Dalla Costa, Maria C. Silva, Amanda de Santana Lopes, Tulio Gomes Pacheco, Jose D. de Oliveira, Valter A. de Baura, Eduardo Balsanelli, Emanuel Maltempi de Souza, Fabio de Oliveira Pedrosa, Marcelo Rogalski
Summary: The plastome of Melocactus glaucescens exhibits unique rearrangements, IR expansion, and gene losses compared to other Cactaceae species. The study suggests tRNA import from the cytosol to the plastids in M. glaucescens and identifies high gene divergence and possible RNA-editing sites. The mapped SSRs in the plastome are helpful for assessing genetic diversity and conservation strategies.
Article
Biochemistry & Molecular Biology
Ruchika, Toshifumi Tsukahara
Summary: This study investigated U-to-C RNA editing in Arabidopsis tissues and its effects on mRNA stability, focusing on PPR proteins. The research showed that U-to-C RNA editing affects the stability of edited genes' mRNA and identified such editing in the nuclear PPR gene of 12-day-old seedlings. Additionally, the study explored the impact of U-to-C RNA editing on mRNA structure and stability using a transcription inhibitor.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Igor Zivkovic, Kate Ivkovic, Nevena Cvetesic, Aleksandra Marsavelski, Ita Gruic-Sovulj
Summary: AARS clears non-cognate amino acids to ensure faithful protein synthesis; evolutionary pressure did not shape editing site to optimize rates against fidelity threats; editing is shaped to protect cognate aminoacyl-tRNAs against hydrolysis.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Ruchika, Chisato Okudaira, Matomo Sakari, Toshifumi Tsukahara
Summary: The study identified U-to-C RNA editing events in nuclear genes of Arabidopsis through high-throughput RNA sequencing, confirming their presence and providing a basis for further research on the mechanism and functions of this unique post-transcriptional modification.
Article
Plant Sciences
Eriko Matsuo, Kounosuke Morita, Takuro Nakayama, Euki Yazaki, Chihiro Sarai, Kazuya Takahashi, Mitsunori Iwataki, Yuji Inagaki
Summary: Dinoflagellates have diverse plastids that originated from endosymbionts. In this study, the plastid genomes of three dinoflagellates were sequenced and compared, revealing features different from those of the pedinophycean green algae.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Oncology
Heming Wang, Sinuo Chen, Jiayi Wei, Guangqi Song, Yicheng Zhao
Summary: RNA editing, induced by ADAR, plays a crucial regulatory role in metazoans, affecting multiple cellular processes and functions. Despite the development of bioinformatics tools for identifying editing sites, the lack of widely accepted standards and challenges in tumor sample analysis still exist. Numerous editing sites have been reported in non-coding regions, impacting the biosynthesis of ncRNAs.
FRONTIERS IN ONCOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yuange Duan, Wanzhi Cai, Hu Li
Summary: The adaptiveness of nonsynonymous RNA editing in plants can be explained by the restorative effects of fixing unfavorable genomic mutations at the RNA level. The restorative hypothesis predicts that nonsynonymous editing sites are more frequent and have higher editing levels than synonymous sites, and that nonsynonymous edits are compensated by RNA editing on genomic sites with recent mutations. These predictions were confirmed in a study of chloroplast RNA editomes of 21 vascular plants, demonstrating the evolutionary significance of plant RNA editing.
Editorial Material
Biochemistry & Molecular Biology
Xiaoxin Pu, Qinwei Xu, Jinxiang Wang, Baoyi Liu
Summary: Recent studies have provided strong evidence that C-to-U RNA editing is the driving force behind SARS-CoV-2 evolution. However, there are concerns about the accuracy of the interpretation on C-to-U RNA editing. By re-analyzing the SARS-CoV-2 population data, it was found that the editing frequency on C-to-U sites did not perfectly correlate with the binding motif of the editing enzyme APOBEC, indicating potential false-positive sites or incomplete representation of the mutation rate. This work aims to enhance understanding of the molecular basis of SARS-CoV-2 mutation and guide future studies on its evolution.