Review
Cell Biology
Inna Aphasizheva, Ruslan Aphasizhev
Summary: Trypanosoma brucei, a unicellular parasite, causes a range of diseases in African human and animal populations, posing a threat to public health and impacting the economy in sub-Saharan Africa. The organism is characterized by a single mitochondrion containing a kinetoplast nucleoid, which consists of densely packed DNA molecules called kinetoplast DNA (kDNA). The kDNA network includes maxicircles encoding rRNAs and proteins, as well as minicircles bearing gRNA genes.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2021)
Article
Microbiology
Joseph T. Smith Jr, Brianna Tylec, Arunasalam Naguleswaran, Isabel Roditi, Laurie K. Read
Summary: This study reveals the importance of mitochondrial mRNA editing in the developmental regulation of Trypanosoma brucei. The researchers found that temperature reduction and depletion of the differentiation-repressive kinase RDK1 can affect the metabolism of Trypanosoma brucei by altering the editing of mitochondrial cytochrome mRNAs.
Article
Plant Sciences
Chung-Shien Wu, Shu-Miaw Chaw
Summary: By characterizing mitochondrial and plastid genomes, RNA editing sites, and PPR proteins, we unveiled the evolution of mitochondrial RNA editing in gymnosperms. Our analyses revealed efficient non-synonymous editing and showed an increase in U-ending codons in gymnosperm mitochondria due to synonymous editing. We also found lineage-specific duplications in PLS-class PPR proteins, which likely contribute to accumulated RNA editing sites in gymnosperms.
Article
Multidisciplinary Sciences
Huaxia Shi, Ying Xu, Na Tian, Ming Yang, Fu-Sen Liang
Summary: The authors develop a chemically inducible and reversible RNA m6A modification editing platform that allows temporal control at specific sites of individual RNA transcripts.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Hong Zhang, Parker Murphy, Jason Yu, Sukyeong Lee, Francis T. F. Tsai, Ambro van Hoof, Jiqiang Ling
Summary: Aminoacyl-tRNA synthetases (aaRSs), essential enzymes for protein synthesis, can cause neurological disorders when mutated. This study investigates the mechanism behind these mutations and found that combined defects in aminoacylation and editing result in severe proteotoxicity. The results show that aminoacylation deficiency predisposes cells to proteotoxic stress and impairs ribosome-associated quality control.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Di Wu, Monique Pedroza, Jonathan Chang, Jurrien Dean
Summary: During oocyte development in mice, transcripts accumulate in the growth phase and are subsequently degraded during maturation. In this study, the researchers identified a small cohort of mRNAs that are polyadenylated after terminal uridylation in GV oocytes. They found that DIS3L2 ribonuclease plays a critical role in degrading uridylated transcripts and maintaining the stability of the transcriptome, as demonstrated by oocyte-specific Dis3l2 knockout mice. The study also revealed the impact of DIS3L2 depletion on oocyte development, leading to female infertility.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Lorenzo Gallicchio, Gonzalo H. Olivares, Cameron W. Berry, Margaret T. Fuller
Summary: Alternative cleavage and polyadenylation (APA) is a co-transcriptional RNA processing process that greatly affects gene expression. APA occurs naturally during development and cellular differentiation, and changes in APA are associated with pathological states. The understanding of APA regulation and its impact on gene expression is still incomplete.
Article
Biochemistry & Molecular Biology
Maria Maldonado, Kaitlyn Madison Abe, James Anthony Letts
Summary: This study uses the structures of plant respiratory complexes to analyze the impact of RNA editing on amino acid changes, providing a molecular explanation for the phenotypes of RNA editing mutants. The research bridges the gap between sequence and phenotype and offers a framework for further analysis of RNA editing mutants in plant mitochondria and chloroplasts.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Jason Carnes, Suzanne M. Mcdermott, Kenneth Stuart
Summary: RNA editing in Trypanosoma brucei generates mature mitochondrial mRNAs through extensive uridine insertion and deletion at specific editing sites (ESs) guided by RNA molecules (gRNAs). This process involves three different RNA Editing Catalytic Complexes (RECCs) that each have a unique endonuclease and share 12 common proteins. The study shows that the endonucleases remain associated with their common RECC proteins during editing, and the stoichiometry of the RECCs can be altered by changes in expression levels. The findings suggest that consecutive insertion and deletion ESs are edited non-processively by successive engagement and disengagement of the RECCs.
MOLECULAR AND BIOCHEMICAL PARASITOLOGY
(2023)
Article
Multidisciplinary Sciences
Issei Nakazato, Miki Okuno, Chang Zhou, Takehiko Itoh, Nobuhiro Tsutsumi, Mizuki Takenaka, Shin-Ichi Arimura
Summary: In addition to their role in respiration, mitochondria in land plants contain important genes whose functions and regulations are not fully understood. Until recently, it has been challenging to analyze and improve these genes due to the lack of methods for stably modifying plant mitochondrial genomes. However, the use of mitochondria-targeting transcription activator-like effector nucleases (mitoTALENs) has provided a breakthrough in gene disruption without causing major changes in genome structure. This study demonstrates the successful use of mitochondria-targeting TALEN-based cytidine deaminase to substitute targeted base pairs in plant mitochondrial genomes, highlighting the potential for precise genetic modifications in plants.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Plant Sciences
Jiaying Zhu, Changhao Li, Xu Peng, Xiuren Zhang
Summary: RNA secondary structure (RSS) is crucial in various biological processes, including RNA processing, transportation, and translation, as well as plant responses to environmental variations. At the molecular level, RSS is correlated with splicing, protein synthesis, and miRNA biogenesis.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Parasitology
Suzanne M. McDermott, Vy Pham, Isaac Lewis, Maxwell Tracy, Kenneth Stuart
Summary: mt-LAF3 is essential for normal expression of mitochondrial mRNAs and rRNAs in Trypanosoma brucei, but its PUS catalytic activity is not required for these functions. Instead, it acts as a mitochondrial RNA-stabilizing scaffold.
INTERNATIONAL JOURNAL FOR PARASITOLOGY
(2023)
Article
Multidisciplinary Sciences
Ana Fiszbein, Michael McGurk, Ezequiel Calvo-Roitberg, GyeungYun Kim, Christopher B. Burge, Athma A. Pai
Summary: Messenger RNA isoform differences are mainly driven by alternative first, internal, and last exons. A recent study identified hybrid exons, which are enriched in long genes and genes involved in RNA splicing, and showed their usage varies considerably across human tissues. The HIT pipeline was developed to classify exons and reveal the common occurrence of hybrid exons in the human transcriptome.
Editorial Material
Cell Biology
Angelika B. Harbauer, Thomas L. Schwarz
Summary: In this study, the authors found that axonal mitophagy relies on local translation of Pink1 mRNA. The co-transport of Pink1 mRNA with mitochondria in neurons plays a crucial role in mitophagy in the distal parts of the cell. This finding contributes to our understanding of mitochondrial homeostasis in neurons.
Article
Biochemistry & Molecular Biology
Kyung W. W. Seo, Ralph E. E. Kleiner
Summary: In this study, the researchers developed TRIBE-ID, a strategy for quantifying RNA-protein interactions, and used it to study the interactions of G3BP1 and YBX1 under normal and oxidative stress conditions. They found that stress granule formation strengthened existing interactions and induced new RNA-protein binding events. Additionally, they discovered that G3BP1 stabilizes its targets independently of stress granule formation. This work provides a general approach for studying dynamic RNA-protein interactions in cellular contexts.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Inna Aphasizheva, Liye Zhang, Ruslan Aphasizhev
Article
Biochemistry & Molecular Biology
Takuma Suematsu, Liye Zhang, Inna Aphasizheva, Stefano Monti, Lan Huang, Qi Wang, Catherine E. Costello, Ruslan Aphasizhev
Article
Biochemistry & Molecular Biology
Inna Aphasizheva, Dmitri A. Maslov, Yu Qian, Lan Huang, Qi Wang, Catherine E. Costello, Ruslan Aphasizhev
MOLECULAR MICROBIOLOGY
(2016)
Article
Biochemistry & Molecular Biology
Lional Rajappa-Titu, Takuma Suematsu, Paola Munoz-Tello, Marius Long, Ozlem Demir, Kevin J. Cheng, Jason R. Stagno, Hartmut Luecke, Rommie E. Amaro, Inna Aphasizheva, Ruslan Aphasizhev, Stephane Thore
NUCLEIC ACIDS RESEARCH
(2016)
Review
Biochemistry & Molecular Biology
Ruslan Aphasizhev, Takuma Suematsu, Liye Zhang, Inna Aphasizheva
Review
Parasitology
Inna Aphasizheva, Ruslan Aphasizhev
TRENDS IN PARASITOLOGY
(2016)
Article
Multidisciplinary Sciences
Francois M. Sement, Takuma Suematsu, Liye Zhang, Tian Yu, Lan Huang, Inna Aphasizheva, Ruslan Aphasizhev
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2018)
Article
Multidisciplinary Sciences
Mikhail V. Mesitov, Tian Yu, Takuma Suematsu, Francois M. Sement, Liye Zhang, Clinton Yu, Lan Huang, Inna Aphasizheva
NATURE COMMUNICATIONS
(2019)
Article
Biochemistry & Molecular Biology
Inna Aphasizheva, Tian Yu, Takuma Suematsu, Qiushi Liu, Mikhail Mesitov, Clinton Yu, Lan Huang, Liye Zhang, Ruslan Aphasizhev
NUCLEIC ACIDS RESEARCH
(2020)
Review
Cell Biology
Inna Aphasizheva, Ruslan Aphasizhev
Summary: Trypanosoma brucei, a unicellular parasite, causes a range of diseases in African human and animal populations, posing a threat to public health and impacting the economy in sub-Saharan Africa. The organism is characterized by a single mitochondrion containing a kinetoplast nucleoid, which consists of densely packed DNA molecules called kinetoplast DNA (kDNA). The kDNA network includes maxicircles encoding rRNAs and proteins, as well as minicircles bearing gRNA genes.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2021)
Article
Biochemistry & Molecular Biology
Gabriel Silveira d'Almeida, Ananth Casius, Jeremy C. Henderson, Sebastian Knuesel, Ruslan Aphasizhev, Inna Aphasizheva, Aidan C. Manning, Todd M. Lowe, Juan D. Alfonzo
Summary: Following processing and modification, tRNAs in protein synthesis become functional adaptors. Eukaryotes have developed transport systems allowing tRNAs to move between nucleus and cytoplasm. In trypanosomes, all tRNAs are imported into the mitochondrion from the cytoplasm. Quality control mechanisms regulate tRNA(Tyr), the only tRNA with an intron, involving differential subcellular localization and retrograde nuclear transport.
Article
Biochemistry & Molecular Biology
Liye Zhang, Francois M. Sement, Takuma Suematsu, Tian Yu, Stefano Monti, Lan Huang, Ruslan Aphasizhev, Inna Aphasizheva