Article
Biochemistry & Molecular Biology
Mst. Ayesha Siddika, Hiroki Oi, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo, Shigeyoshi Matsumura, Yoshiya Ikawa
Summary: In this study, the construction of larger RNA assemblies based on ribozyme was achieved through the use of RNA oligomerization technology. The addition of specific interacting units enabled the assembly of ribozyme dimer, open-chain oligomers, and branched oligomers.
Article
Biochemistry & Molecular Biology
Mst. Ayesha Siddika, Takahiro Yamada, Risako Aoyama, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo, Shigeyoshi Matsumura, Yoshiya Ikawa
Summary: Naturally occurring ribozymes with a modular architecture can serve as promising platforms for constructing RNA nanostructures, as their modular redesign allows for oligomerization. These resulting RNA nanostructures can retain the catalytic function of the parent ribozyme, depending on their assembly. In this study, open-form oligomers of a bimolecular form of an RNase P ribozyme were designed and constructed, and analyzed biochemically and by atomic force microscopy (AFM).
Article
Biochemical Research Methods
Antoine Moniot, Yann Guermeur, Sjoerd Jacob de Vries, Isaure Chauvot de Beauchene
Summary: This article introduces a new pipeline for designing searchable databases on the 2D and 3D structures of protein-bound nucleic acids (NA), selecting context-specific NA structures, and creating corresponding fragment libraries. The strength of this pipeline lies in its modularity, allowing it to be adapted to various specific modeling problems.
Article
Plant Sciences
Nora Hartig, Kathrin M. Seibt, Tony Heitkam
Summary: Compared to mammalian counterparts, plant long interspersed nuclear elements (LINEs) exhibit high variability and split into numerous low-copy families. However, LINE families from the retrotransposable element (RTE) clade display stronger sequence conservation and have higher copy numbers. Understanding the cause of this RTE-typical property can shed light on the persistence of certain transposable elements in plant genomes. This study focuses on the detailed examination of RTE LINE structure, diversity, and evolution in plants, using the nightshade family as the ideal taxon due to its abundance, recent activity, and association with non-autonomous elements. Through bioinformatic, cytogenetic, and molecular approaches, the researchers identified 4029 full-length RTE LINEs in the Solanaceae family, with particular emphasis on the allotetraploid tobacco. They characterized a core group of 458 full-length LINEs, uncovered an integration event after polyploidization, and traced hybridization through the RTE LINE composition of parental genomes. Furthermore, they discovered the involvement of untranslated regions (UTRs) in the unique amplification and evolution patterns of RTE LINEs in plants, with conserved motifs found in the 3' UTR and a cycling process observed in the 5' UTR that rejuvenates the promoter sequences. This interplay between exchangeable promoters and conserved LINE bodies and 3' UTR allows RTE LINEs to persist and thrive in plant genomes.
Review
Cell Biology
Tao Wang, Xiaojun Li, Xiaojing Zhang, Qing Wang, Wenqian Liu, Xiaohong Lu, Shunli Gao, Zixi Liu, Mengshuang Liu, Lihong Gao, Wenna Zhang
Summary: A large number of RNA molecules have been found in the phloem of higher plants, where specific RNA motifs and structures facilitate their mobility, while RNA methylation, such as m5C, plays a crucial role in RNA transport. These studies provide a theoretical foundation for uncovering the mechanism of RNA transportation.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biology
Raeann Goering, Ankita Arora, Megan C. Pockalny, J. Matthew Taliaferro
Summary: RNA molecules are localized to specific subcellular regions through interactions between RNA regulatory elements and RNA binding proteins. The localization mechanisms are conserved across different cell types with different morphologies, indicating the presence of broadly similar mechanisms. In the study, it was found that mRNA encoding ribosomal proteins were strongly localized to the basal pole of human intestinal epithelial cells, and the same motifs were also sufficient to drive RNA localization to the neurites of mouse neuronal cells.
Article
Microbiology
Zixiong Zhang, Ning Zhang, Saisai Guo, Qian Liu, Shujie Wang, Ao Zhang, Dongrong Yi, Jianyuan Zhao, Quanjie Li, Jing Wang, Yongxin Zhang, Ling Ma, Jiwei Ding, Shan Cen, Xiaoyu Li
Summary: In this study, it was found that the CCHC-type zinc-finger protein ZCCHC3 can repress LINE-1 retrotransposition, and this activity is closely related to its zinc-finger domain. Further studies showed that ZCCHC3 can post-transcriptionally diminish the LINE-1 RNA level. These findings demonstrate the significance of ZCCHC3 in the cellular control of LINE-1 replication.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Arianna Mangiavacchi, Peng Liu, Francesco Della Valle, Valerio Orlando
Summary: Retrotransposons are genetic elements present in eukaryotic genomes, with potentially harmful effects on genome stability but also regulatory and beneficial roles in non-pathological contexts. Studies have revealed the multifaceted activity of retrotransposable elements, highlighting their central role in early development and adult life.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Julita Gumna, Angelika Andrzejewska-Romanowska, David J. Garfinkel, Katarzyna Pachulska-Wieczorek
Summary: A universal feature of retroelement propagation is the formation of distinct nucleoprotein complexes mediated by the Gag capsid protein. Ty1 retrotransposon Gag protein from Saccharomyces cerevisiae lacks sequence homology with retroviral Gag, but is functionally related. Ty1 Gag binds with high affinity to different RNAs, with a preferential interaction observed with Ty1 RNA containing a packaging signal.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Xiaomin Ni, Andreas C. Joerger, Apirat Chaikuad, Stefan Knapp
Summary: FUBP-interacting repressor (FIR) is a suppressor of the proto-oncogene MYC's transcription, by binding to the far upstream element (FUSE) of the MYC promoter. Competition with FUSE-binding protein 1 (FUBP1) is a crucial mechanism for MYC transcriptional regulation.
Article
Chemistry, Multidisciplinary
Michaela Egger, Raphael Bereiter, Stefan Mair, Ronald Micura
Summary: Nucleolytic ribozymes utilize general acid-base catalysis to perform phosphodiester cleavage. However, the general base knockout study on pistol ribozymes challenges the common view that γ-catalysis critically depends on the N1 moiety. The overall catalysis of pistol ribozymes is made up by three catalytic factors (α, β, γ).
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Multidisciplinary Sciences
Max E. Wilkinson, Chris J. Frangieh, Rhiannon K. Macrae, Feng Zhang
Summary: Non-LTR retrotransposons or LINEs are a type of abundant eukaryotic transposons that insert into genomes through TPRT. The cryo-EM structure of the Bombyx mori R2 non-LTR retrotransposon initiating TPRT at its ribosomal DNA target is reported here. The target DNA sequence is unwound and recognized by an upstream motif, and the RT domain of the reverse transcriptase guides the retrotransposon RNA for reverse transcription. In vitro retargeting of R2 to non-native sequences using Cas9 suggests potential use as a reprogrammable RNA-based gene-insertion tool in the future.
Article
Biochemistry & Molecular Biology
Caterina Ciani, Anna Perez-Rafols, Isabelle Bonomo, Mariachiara Micaelli, Alfonso Esposito, Chiara Zucal, Romina Belli, Vito Giuseppe D'Agostino, Irene Bianconi, Vito Calderone, Linda Cerofolini, Orietta Massidda, Michael Bernard Whalen, Marco Fragai, Alessandro Provenzani
Summary: This study identified an RNA-binding protein, AB-Elavl, in the Gram-negative pathogen Acinetobacter baumannii. The protein contains a single RNA Recognition Motif (RRM) and exhibits structural similarities to the human HuR protein. Despite some differences in binding specificity and affinity, AB-Elavl can bind to AU-rich regions similar to HuR. This finding expands our understanding of RNA-binding proteins in A. baumannii and their potential role in antibiotic resistance.
Article
Biochemistry & Molecular Biology
Nikita S. Vassetzky, Olga R. Borodulina, Ilia G. Ustyantsev, Sergei A. Kosushkin, Dmitri A. Kramerov
Summary: This study thoroughly examines three subfamilies of the SINE family, detailing their distinctions based on relatively long indels. The age and activity of SINE subfamilies play a key role in their evolution, while the investigation of the shortest pol III transcription terminators reveals that functional terminators are more likely to be preserved in younger copies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Karin Broennimann, Inna Ricardo-Lax, Julia Adler, Eleftherios Michailidis, Ype P. de Jong, Nina Reuven, Yosef Shaul
Summary: Research has shown that hepatitis B virus (HBV) can promote RNR-R2 expression by a small conserved region within its transcript when infecting non-dividing cells, leading to an increase in dNTP levels. This demonstrates a non-coding function of HBV transcripts to support its propagation in non-cycling cells.
