Article
Biotechnology & Applied Microbiology
Jiacheng Hu, Yu Sun, Boshu Li, Zhen Liu, Zhiwei Wang, Qiang Gao, Mengyue Guo, Guanwen Liu, Kevin Tianmeng Zhao, Caixia Gao
Summary: CyDENT is a CRISPR-free modular base editing tool with strand selectivity. It utilizes TALEs fused with a FokI nickase, a single-strand-specific cytidine deaminase, and an exonuclease to achieve efficient base editing in nuclear, mitochondrial, and chloroplast genomes.
NATURE BIOTECHNOLOGY
(2023)
Review
Genetics & Heredity
Junjie Tan, Joachim Forner, Daniel Karcher, Ralph Bock
Summary: Genome editing has revolutionized biological research, with CRISPR/Cas-based editing being the preferred technology due to its simplicity and flexibility. Fusion of Cas nucleases with large protein domains allows for combination of DNA recognition properties with new enzymatic activities. Base editors and prime editors, produced by fusion with nucleoside deaminase or reverse transcriptase domains, induce site-specific alterations of a few nucleotides without generating double-strand breaks. Protein-only genome editing reagents based on transcription activator-like effectors have expanded base editing to chloroplast and mitochondrial genomes. This review summarizes current base editing methods for nuclear and organellar genomes, highlighting advances in precision, specificity, and efficiency, as well as discussing limitations and future challenges. In addition, applications in agricultural biotechnology and gene therapy are briefly overviewed.
TRENDS IN GENETICS
(2022)
Article
Plant Sciences
Aidi Zhang, Yuhong Xiong, Jing Fang, Kangchen Liu, Huixiang Peng, Xiujun Zhang
Summary: MORF genes play important roles in regulating plant immunity, especially against biotic and abiotic stresses. By studying the genome-wide analysis of peach MORF genes and the regulatory role of RNA editing in plant immunity, this research provides a foundation for further analysis of MORF gene functions and breeding new cultivars with high resistance.
Article
Plant Sciences
Yuhong Xiong, Jing Fang, Xiaohan Jiang, Tengfei Wang, Kangchen Liu, Huixiang Peng, Xiujun Zhang, Aidi Zhang
Summary: In this study, ten MORF genes were identified in the kiwifruit genome, and their genomic structures and chromosomal locations were analyzed. Based on RNA-seq data, tissue-specific patterns of MORF gene expression and chloroplast RNA editing were found. Differential expression and editing profiles were observed between resistant and susceptible kiwifruits after pathogen infection.
Review
Cell Biology
Jin-Soo Kim, Jia Chen
Summary: Mitochondria and chloroplasts are organelles that have their own genomes and targeted editing of these organelles' DNA can have therapeutic, agricultural and environmental potential. Recent advancements in protein-only base editors have enabled targeted organellar DNA editing in living cells. This review discusses the programmable deaminases developed for base editing and the precision and efficiency limitations of these tools.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2023)
Article
Plant Sciences
Yunlong Wang, Yihua Wang, Yulong Ren, Erchao Duan, Xiaopin Zhu, Yuanyuan Hao, Jianping Zhu, Rongbo Chen, Jie Lei, Xuan Teng, Yuanyan Zhang, Di Wang, Xin Zhang, Xiuping Guo, Ling Jiang, Shijia Liu, Yunlu Tian, Xi Liu, Liangming Chen, Haiyang Wang, Jianmin Wan
Summary: Thioredoxins regulate various biological processes in plant chloroplasts, and a mutation in the thioredoxin z gene can lead to a white panicle 2 mutant in rice, affecting the regulatory mechanism of chloroplast RNA editing factors.
Article
Plant Sciences
Jinyan Li, Keru Wang, Yongfang Yang, Yao Lu, Kaicheng Cui, Yajing Ji, Liqun Ma, Ke Cheng, Oren Ostersetzer-Biran, Feng Li, Guiqin Qu, Benzhong Zhu, Daqi Fu, Yunbo Luo, Hongliang Zhu
Summary: This study provides evidence for the role of SlRIP1b in RNA editing of mitochondrial transcripts in tomato plants. SlRIP1b affects C-U editing of numerous mitochondrial pre-RNA transcripts, particularly altering RNA editing of various cytochrome c maturation-related genes. Mutants of SlRIP1b exhibit abnormal carpel development and fruit development defects.
Article
Chemistry, Physical
Mizuki Takenaka, Sachi Takenaka, Tatjana Barthel, Brody Frink, Sascha Haag, Daniil Verbitskiy, Bastian Oldenkott, Mareike Schallenberg-Rudinger, Christian G. Feiler, Manfred S. Weiss, Gottfried J. Palm, Gert Weber
Summary: RNA editosomes selectively deaminate cytidines to uridines to restore protein functionality in plant organellar transcripts; DYW domains contain a cytidine deaminase fold and a C-terminal DYW motif, regulated by a gated zinc shutter in the deaminase fold.
Article
Genetics & Heredity
Yuxin Zhao, Ruoshi Gao, Zhen Zhao, Shunkai Hu, Rui Han, Anburaj Jeyaraj, Emmanuel Arkorful, Xinghui Li, Xuan Chen
Summary: This study identified RNA editing sites in chloroplast genes of tea plants and analyzed their characteristics, structures, and specificity. Differential editing efficiency was observed among different tea varieties, and genes related to albinism were identified. These findings lay the foundation for further understanding the role of chloroplast RNA editing in the process of tea leaf albinism.
Review
Biochemistry & Molecular Biology
Ian Small, Joanna Melonek, Alexandra-Viola Bohne, Joerg Nickelsen, Christian Schmitz-Linneweber
Summary: Plant organellar RNA metabolism is regulated by numerous nucleus-encoded RNA-binding proteins (RBPs) that control RNA stability, processing, and degradation. These post-transcriptional processes are critical for the production of essential components in chloroplasts and mitochondria, which are necessary for organellar biogenesis and plant survival. While many organellar RBPs have been identified, our understanding of their mechanisms and kinetics in fulfilling their functions remains incomplete. This review provides a comprehensive summary of plant organellar RNA metabolism, focusing on the mechanistic aspects and kinetics of RBP functions.
Article
Multidisciplinary Sciences
Julia P. Schessner, Vincent Albrecht, Alexandra K. Davies, Pavel Sinitcyn, Georg H. H. Borner
Summary: The Dynamic Organellar Maps (DOMs) approach combines cell fractionation and shotgun-proteomics to analyze protein subcellular localization. By using data-independent acquisition (DIA) mass spectrometry, DIA-DOMs achieve deeper coverage and improve precision and reproducibility compared to previous methods. A software tool called DOM-ABC is introduced for analyzing profiling data. DIA-DOMs are applied to identify subcellular localization changes in HeLa cells, revealing cycles of Golgi proteins through endosomes. This workflow offers a superior label-free spatial proteomics approach for systematic phenotype discovery.
NATURE COMMUNICATIONS
(2023)
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)
Review
Immunology
Cassandra R. Harapas, Elina Idiiatullina, Mahmoud Al-Azab, Katja Hrovat-Schaale, Thomas Reygaerts, Annemarie Steiner, Pawat Laohamonthonkul, Sophia Davidson, Chien-Hsiung Yu, Lee Booty, Seth L. Masters
Summary: This review highlights the relationship between intracellular organelle damage and activation of the innate immune system. Understanding organellar homeostasis is crucial for identifying new innate immune pathways, and therapeutic strategies that target organellar homeostasis breakdown pathways could be beneficial for infection and chronic inflammatory diseases.
NATURE REVIEWS IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Francis A. Acquah, Blaine H. M. Mooers
Summary: Targeting the U-helix structure can lead to the development of safer and more efficient drugs for treating trypanosome infections, as this RNA editing pathway is absent in humans.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Plant Sciences
Mamoru Sugita
Summary: Pentatricopeptide repeat (PPR) proteins, a type of helical repeat protein, are widely found in eukaryotes, especially flowering plants. They play crucial roles in RNA metabolism during gene expression in the plastids and mitochondria. Physcomitrium patens, an early land plant, has numerous PPR genes, but their functions are largely unknown. Through reverse-genetics, the functions of 22 PPR proteins have been identified in mRNA processing, stabilization, splicing, and editing. This review discusses the PPR gene family in P. patens and its functions, highlighting similarities, and diversity in comparison to flowering plants and their roles in post-transcriptional regulation of organellar gene expression.
Correction
Biochemistry & Molecular Biology
Valerie Cognat, Geoffrey Morelle, Cyrille Megel, Stephanie Lalande, Jean Molinier, Timothee Vincent, Ian Small, Anne-Marie Duchene, Laurence Marechal-Drouard
NUCLEIC ACIDS RESEARCH
(2020)
Article
Multidisciplinary Sciences
Joanna Melonek, Jorge Duarte, Jerome Martin, Laurent Beuf, Alain Murigneux, Pierrick Varenne, Jordi Comadran, Sebastien Specel, Sylvain Levadoux, Kalia Bernath-Levin, Francois Torney, Jean-Philippe Pichon, Pascual Perez, Ian Small
Summary: Researchers have identified candidate genes Rf1 and Rf3 that can restore fertility in wheat plants carrying Triticum timopheevii-type cytoplasmic male sterility. This discovery is a significant step towards developing hybrid wheat varieties based on the CMS-Rf system.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Bernard Gutmann, Michael Millman, Lilian Vincis Pereira Sanglard, Ian Small, Catherine Colas des Francs-Small
Summary: In Arabidopsis thaliana, there are numerous C-to-U RNA editing events in the mitochondria and chloroplasts, with specificity provided by PPR proteins. The study identified MEF100 as essential for editing at specific sites in Arabidopsis mitochondria, affecting Complex I activity and leading to physiological consequences. Loss of the necessity for MEF100 editing results in divergence in the MEF100 binding site.
Article
Genetics & Heredity
M. Timothy Rabanus-Wallace, Bernd Hackauf, Martin Mascher, Thomas Lux, Thomas Wicker, Heidrun Gundlach, Mariana Baez, Andreas Houben, Klaus F. X. Mayer, Liangliang Guo, Jesse Poland, Curtis J. Pozniak, Sean Walkowiak, Joanna Melonek, Coraline R. Praz, Mona Schreiber, Hikmet Budak, Matthias Heuberger, Burkhard Steuernagel, Brande Wulff, Andreas Boerner, Brook Byrns, Jana Cizkova, D. Brian Fowler, Allan Fritz, Axel Himmelbach, Gemy Kaithakottil, Jens Keilwagen, Beat Keller, David Konkin, Jamie Larsen, Qiang Li, Beata Myskow, Sudharsan Padmarasu, Nidhi Rawat, Ugur Sesiz, Sezgi Biyiklioglu-Kaya, Andy Sharpe, Hana Simkova, Ian Small, David Swarbreck, Helena Toegelova, Natalia Tsvetkova, Anatoly V. Voylokov, Jan Vrana, Eva Bauer, Hanna Bolibok-Bragoszewska, Jaroslav Dolezel, Anthony Hall, Jizeng Jia, Viktor Korzun, Andre Laroche, Xue-Feng Ma, Frank Ordon, Hakan Ozkan, Monika Rakoczy-Trojanowska, Uwe Scholz, Alan H. Schulman, Dorthe Siekmann, Stefan Stojalowski, Vijay K. Tiwari, Manuel Spannagl, Nils Stein
Summary: Rye is a climate-resilient cereal crop used for hybrid breeding to improve wheat varieties, possessing necessary genes for hybridization. Research shows cultivated rye is genetically linked to wild relatives, offering potential applications in disease resistance, low-temperature tolerance, and more.
Article
Biology
Santana Royan, Bernard Gutmann, Catherine Colas des Francs-Small, Suvi Honkanen, Jason Schmidberger, Ashley Soet, Yueming Kelly Sun, Lilian Vincis Pereira Sanglard, Charles S. Bond, Ian Small
Summary: RNA editing in plants is carried out by PPR proteins, and a synthetic editing factor using PPR motifs has been successfully designed and demonstrated high specificity. This study paves the way for the design and application of programmable RNA editing factors based on plant PPR proteins.
COMMUNICATIONS BIOLOGY
(2021)
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)
Review
Plant Sciences
Joanna Melonek, Ian Small
Summary: Recent breakthroughs in sequencing data have revealed unexpected expansions in gene families related to restoring fertility in certain species, which will greatly benefit the development of hybrid production strategies in wheat and related species.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Article
Plant Sciences
Suvi Honkanen, Ian Small
Summary: The pentatricopeptide repeat protein GUN1 is an ancient protein that evolved within the streptophyte algal ancestors of land plants. It is highly conserved among land plants and plays a key role in chloroplast gene expression and retrograde signaling.
Article
Biochemical Research Methods
Rose McDowell, Ian Small, Charles S. Bond
Summary: This review presents the latest understanding of RNA site recognition by PPR proteins and the progress made towards designing synthetic PPR proteins for RNA targeting. PPR proteins are considered ideal candidates for targeting and binding RNA transcripts due to their defined RNA binding code and modular structure.
Article
Genetics & Heredity
Alejandro A. Edera, Katharine A. Howell, Paul G. Nevill, Ian Small, M. Virginia Sanchez-Puerta
Summary: In angiosperms, the distribution of cox2i373 and cox2i691 introns in the mitochondrial cox2 gene varies. Frequent intron loss events influenced by localized retroprocessing are observed in cox2i691. The elongation of cox2i691 introns, especially in domain IV, is likely due to nuclear intracelular DNA transfer followed by incorporation into mitochondrial DNA. Surprisingly, cox2i691 is erroneously annotated as absent in public databases, but studies have shown its functionality through efficient cis-splicing.
Article
Plant Sciences
Corinne Best, Ron Mizrahi, Rana Edris, Hui Tang, Hagit Zer, Catherine Colas des Francs-Small, Omri M. Finkel, Hongliang Zhu, Ian D. Small, Oren Ostersetzer-Biran
Summary: Mitochondrial biogenesis relies on nuclearly encoded factors, which regulate the expression of the organellar-encoded genes. Pentatricopeptide repeat (PPR) proteins constitute a major gene family in angiosperms that are pivotal in many aspects of mitochondrial (mt)RNA metabolism (e.g. trimming, splicing, or stability). The loss-of-function allele of the MSP1 gene leads to seed abortion.
Review
Biochemistry & Molecular Biology
Ian Small, Joanna Melonek, Alexandra-Viola Bohne, Joerg Nickelsen, Christian Schmitz-Linneweber
Summary: Plant organellar RNA metabolism is regulated by numerous nucleus-encoded RNA-binding proteins (RBPs) that control RNA stability, processing, and degradation. These post-transcriptional processes are critical for the production of essential components in chloroplasts and mitochondria, which are necessary for organellar biogenesis and plant survival. While many organellar RBPs have been identified, our understanding of their mechanisms and kinetics in fulfilling their functions remains incomplete. This review provides a comprehensive summary of plant organellar RNA metabolism, focusing on the mechanistic aspects and kinetics of RBP functions.
Article
Biochemistry & Molecular Biology
Lilian Vincis Pereira Sanglard, Ian D. Small, Catherine Colas des Francs-Small, Abir U. Igamberdiev
Summary: Researchers created a library of redesigned PPR proteins, related to restorer-of-fertility proteins, and transformed them into plants to target mitochondrial transcripts. Testing 90 different variants in vivo showed a wide range of phenotypes. One specific variant from the library induced specific cleavage of atp1 transcripts, resulting in a phenotype characterized by slow growth and downward curled leaves, validating the use of this library as a source of mitochondrial "mutants". This study is a step towards developing specific RNA targeting tools using PPR proteins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Sang Dang Huynh, Joanna Melonek, Catherine Colas des Francs-Small, Charles S. Bond, Ian Small
Summary: Restorer-of-fertility (Rf) genes encode pentatricopeptide repeat (PPR) proteins that target mitochondria and bind to transcripts inducing cytoplasmic male sterility. A distinct domain called RfCTD is found in most Rf proteins and is associated with cleavage of mitochondrial RNA targets. Plant genera with bisexual flowers have higher numbers of RFL genes, suggesting their role in male fertility.
Article
Biochemical Research Methods
Kalia Bernath-Levin, Jason Schmidberger, Suvi Honkanen, Bernard Gutmann, Yueming Kelly Sun, Anuradha Pullakhandam, Catherine Colas des Francs-Small, Charles S. Bond, Ian Small
Summary: In this study, synthetic PPR proteins based on the S-type PPR motif found in plant organellar RNA editing factors were investigated. The results showed that these synthetic S-type PPR proteins are easy to design, capable of binding with high affinity and specificity, and functional under a wide range of conditions. The S-type PPR proteins outperformed the P-type PPR scaffold in many situations.
