Article
Multidisciplinary Sciences
Ling Yuan, Yaoyao Han, Jiazheng Zhao, Yixiao Zhang, Yadong Sun
Summary: The removal of introns from transfer RNA precursors is vital for tRNA maturation and functionality. In this study, the researchers present the cryo-EM structure of an active human tRNA splicing endonuclease complex bound to an intron-containing pre-tRNA. They uncover the molecular mechanism for eukaryotic pre-tRNA recognition and cleavage, as well as the evolutionary relationship between archaeal and eukaryotic TSENs.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Giuseppe D. Tocchini-Valentini, Glauco P. Tocchini-Valentini
Summary: A homodimeric tRNA endonuclease from the euryarchaeota Ferroplasma acidarmanus has been characterized, showing the ability to cleave BHB substrates at low temperatures and create proteins with new functionalities through domain recombination.
Article
Genetics & Heredity
Jennifer E. Hurtig, Ambro van Hoof
Summary: Through yeast genetics, it is discovered that TSEN not only participates in tRNA splicing but also has other functions, including degradation of a subset of mRNA encoding mitochondrial proteins and an unknown essential function. Overexpression of SEN54 can suppress sen2 mutants, indicating its general suppressive effect on sen2, regardless of tRNA-dependent or tRNA-independent functions. Mutations in the intron-debranching enzyme Dbr1 can also serve as tRNA splicing-independent suppressors. These findings provide insights into the essential function(s) of TSEN.
Article
Multidisciplinary Sciences
Jennifer E. Hurtig, Michelle A. Steiger, Vinay K. Nagarajan, Tao Li, Ti-Chun Chao, Kuang-Lei Tsai, Ambro van Hoof
Summary: Recent studies show that yeast TSEN cleaves a specific subset of mRNAs encoding mitochondrial proteins, with cleavage sites determined by sequence. The development of the comPARE bioinformatic approach enables the identification of these mRNA target sites more effectively.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Samoil Sekulovski, Pascal Devant, Silvia Panizza, Tasos Gogakos, Anda Pitiriciu, Katharina Heitmeier, Ewan Phillip Ramsay, Marie Barth, Carla Schmidt, Thomas Tuschl, Frank Baas, Stefan Weitzer, Javier Martinez, Simon Trowitzsch
Summary: Mutations within subunits of the tRNA splicing endonuclease complex are associated with pontocerebellar hypoplasia, and modulation of TSEN stability may contribute to the disease phenotype.
NATURE COMMUNICATIONS
(2021)
Review
Biochemistry & Molecular Biology
Xuemei Wang, Jingyi Wang, Simin Li, Congming Lu, Na Sui
Summary: RNA splicing is a process of removing introns and joining exons together in pre-mRNA. Chloroplast introns have lost their self-splicing ability and now rely on nuclear-encoded splicing factors. These splicing factors may form ribonucleoprotein particles to facilitate intron splicing. Although some chloroplast intron splicing factors have been identified, their precise roles in the splicing process remain unclear.
Article
Biotechnology & Applied Microbiology
Julianne K. David, Sean K. Maden, Mary A. Wood, Reid F. Thompson, Abhinav Nellore
Summary: Short-read tools for detecting intron retention have poor performance and often result in false positives and false negatives, calling into question the completeness and validity of putatively retained introns called by commonly used methods.
Article
Biochemistry & Molecular Biology
Zheng-Shan He, Andan Zhu, Jun-Bo Yang, Weishu Fan, De-Zhu Li
Summary: By utilizing different sequencing technologies such as PacBio, Iso-seq, and Illumina, combined with direct evidence, the chloroplast and mitochondrial genomes of N. 'Joey Tomocik' were assembled and analyzed in this study. Multiple intermediates during intron-splicing were observed, along with their interplay with RNA editing. Additionally, similar features were found in RNA editing sites in both organelles, suggesting a common evolutionary origin and shared editing machinery.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Qiqi Chen, Pan Shen, Ralph Bock, Shengchun Li, Jiang Zhang
Summary: A global survey of plastid gene expression during fruit ripening in kiwifruit reveals cis-elements that can potentially trigger high-level transgene expression in edible tissues, providing valuable resources for analyzing plastid gene expression and future efforts to engineer the plastid genome of kiwifruit.
PLANT CELL REPORTS
(2022)
Article
Biotechnology & Applied Microbiology
Claudio Lorenzi, Sylvain Barriere, Katharina Arnold, Reini F. Luco, Andrew J. Oldfield, William Ritchie
Summary: IRFinder-S is a specialized suite of tools for analyzing and exploring intron retention events in multiple samples, with a focus on accurately identifying true events, facilitating result sharing between labs, integrating a dynamic database for sample exploration and comparison, and providing a tested method for detecting differential levels of intron retention.
Article
Biochemistry & Molecular Biology
Yan-Zhuo Yang, Shuo Ding, Xin-Yuan Liu, Chunhui Xu, Feng Sun, Bao-Cai Tan
Summary: Mutations in maize DEAD-box RNA helicase 48 (ZmRH48) impair mitochondrial intron splicing, complex biosynthesis, and seed development. ZmRH48 deficiency reduces splicing efficiency of multiple introns, leading to lower levels of mitochondrial complexes and defective kernel formation. ZmRH48 interacts with PPR-SMR1, SPR2, and other proteins to facilitate intron splicing.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Wen-Qing Yang, Qing-Ping Xiong, Jian-Yang Ge, Hao Li, Wen-Yu Zhu, Yan Nie, Xiuying Lin, Daizhu Lv, Jing Li, Huan Lin, Ru-Juan Liu
Summary: The study revealed that THUMPD3 and TRMT112 are involved in tRNA m(2)G6 modification in human cells, impacting global protein synthesis and growth, especially with high expression levels in the testis.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Lei Qi, Huan Liu, Jian Gao, Kai Deng, Xiaoyan Wang, Xiuzhu Dong, Jie Li
Summary: This study investigates the pathways of rRNA maturation in Methanococcus maripaludis, a representative archaeon lacking known 3'-5' exonucleases. The results demonstrate that endonucleolytic processing, particularly at the 10-nt A/U-rich motifs, plays an essential role in the pre-rRNA maturation of M. maripaludis, indicating diverse pathways of rRNA maturation in archaeal species.
Article
Biochemistry & Molecular Biology
Martina Hager, Marie-Theres Poehler, Franziska Reinhardt, Karolin Wellner, Jessica Huebner, Heike Betat, Sonja Prohaska, Mario Moerl
Summary: CCA addition is a unique and highly accurate reaction in tRNA maturation. While the mechanism is well-known, it is still a mystery why bacterial and eukaryotic enzymes exhibit low tRNA substrate affinity but efficiently catalyze the reaction. Through the reconstruction and characterization of an ancestral enzyme from Gammaproteobacteria, researchers discovered that the ancestral enzyme has higher tRNA affinity and lower catalytic efficiency compared to the modern enzyme from Escherichia coli. They also found that the modern enzyme increased polymerization efficiency by reducing binding affinity to tRNA. This puzzling weak substrate interaction represents a distinct activity enhancement in the evolution of CCA-adding enzymes.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Review
Biochemistry & Molecular Biology
Nayef Jarrous, Dhivakar Mani, Aravind Ramanathan
Summary: The article discusses the coordination of transcription and processing of RNA in eukaryotes as a basic principle of gene expression regulation. It presents a model of high molecular weight initiation complexes of human RNA polymerase III on tRNA genes, highlighting their role in co-transcriptional processing of tRNA precursors to mature forms.
