Article
Multidisciplinary Sciences
Peizhen Yang, Ericka Havecker, Matthew Bauer, Carl Diehl, Bill Hendrix, Paul Hoffer, Timothy Boyle, John Bradley, Amy Caruano-Yzermans, Jill Deikman
Summary: RNA-based products in pharmaceutical and agricultural fields utilize RNA interference for targeted reduction of gene expression. This study investigates the efficacy of topically-applied siRNA duplexes in silencing specific genes, with findings suggesting flexibility in the 5' nucleotide requirement and similar thermodynamic rules across different plant and animal species.
Article
Biochemistry & Molecular Biology
Yuji Fujimoto, Hiro-oki Iwakawa
Summary: Many organisms produce secondary siRNAs to regulate biological processes, and plants have evolved various pathways for secondary siRNA production. The critical step is the production of double-stranded RNAs by RNA-dependent RNA polymerases. This article reviews recent advances in secondary siRNA production triggered by microRNAs and invasive nucleic acids, focusing on factors, events, and RNA/DNA elements that promote or inhibit the early steps of biogenesis.
JOURNAL OF BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Francisco Vazquez Prol, Joan Marquez-Molins, Ismael Rodrigo, Maria Pilar Lopez-Gresa, Jose Maria Belles, Gustavo Gomez, Vicente Pallas, Purificacion Lison
Summary: In this study, a new plasmid was designed for efficient and reproducible inoculation of infectious viroid clones using both in vitro and agro-inoculation methods. The results showed more severe symptoms in plants agro-inoculated with viroid clones. Viroid accumulation and form proportions were host and inoculation method-dependent, not correlating with symptoms. Ribosomal stress was identified as a novel signature of the pathogenesis of nuclear-replicating viroids in tomato plants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Yuriki Sakurai, Kyungmin Baeg, Andy Y. W. Lam, Keisuke Shoji, Yukihide Tomari, Hiro-oki Iwakawa
Summary: This study uncovers the molecular mechanisms underlying the production of secondary siRNAs in plants, and highlights the impact of the integrity of different small RNA binding sites on RDR6.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Plant Sciences
Neeti Sanan-Mishra, A. Abdul Kader Jailani, Bikash Mandal, Sunil K. Mukherjee
Summary: RNA silencing involves both transitive and systemic small RNAs, including secondary sRNAs. Double-stranded RNAs trigger systemic silencing pathways to negatively regulate gene expression. Secondary siRNAs play a substantial role in gene silencing, especially in antiviral defense.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
He Zichan, Jiao Linfei, Wang Jinliang, Shen Zhiqiang, Cong Yimei, Li Shu
Summary: The deficiency of the essential trace element selenium can lead to cell apoptosis, and miR-294 and HSPs play important roles in this process. Activation of the mitochondrial apoptosis pathway significantly enhances apoptosis of cerebellar cells in Se-deficient pigs. These findings enrich our understanding of the biological effects of Se deficiency.
BIOLOGICAL TRACE ELEMENT RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Hiro-Oki Iwakawa, Yukihide Tomari
Summary: Small RNAs regulate gene expression at the transcriptional and post-transcriptional levels by forming RISC complex and repressing target genes through mRNA cleavage, degradation, and translational repression. Various factors fine-tune RISC activity and stability, including guide-target RNA complementarity, recruitment of protein partners, and post-translational modifications of RISC itself.
Article
Biochemistry & Molecular Biology
Shirui Chen, Wei Liu, Masahiro Naganuma, Yukihide Tomari, Hiro-Oki Iwakawa
Summary: Monocot DCL3 and DCL5 exhibit distinct substrate preferences, which are determined by mutations in their PAZ domains.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Plant Sciences
Ayaka Yoshihisa, Satomi Yoshimura, Motoki Shimizu, Sayaka Sato, Shogo Matsuno, Akira Mine, Koji Yamaguchi, Tsutomu Kawasaki
Summary: In this study, the researchers discovered that OsERF101 is a transcription factor that interacts with Xa1, and it can regulate the recognition of TAL effectors by Xa1 and act as a positive regulator of Xa1-mediated immunity. Additionally, OsERF101 negatively regulates another Xa1-mediated immune pathway.
Article
Biochemistry & Molecular Biology
Natsuko Izumi, Keisuke Shoji, Takashi Kiuchi, Susumu Katsuma, Yukihide Tomari
Summary: The PIWI-interacting RNA (piRNA) pathway is a protection mechanism against transposons in animal germ cells. Gtsf1 and Gtsf1L promote endonuclease activity of PIWI proteins and bind to specific PIWI proteins, facilitating piRNA amplification.
Article
Plant Sciences
Momoko Takagi, Kei Hotamori, Keigo Naito, Sumire Matsukawa, Mayumi Egusa, Yoko Nishizawa, Yuri Kanno, Mitsunori Seo, Shinsuke Ifuku, Akira Mine, Hironori Kaminaka
Summary: Chitin, a known elicitor of disease resistance in plants, can induce systemic resistance against fungal pathogen Bipolaris oryzae in rice when supplemented in soils. Transcriptome analysis revealed genes related to cell-wall biogenesis and cytokinin signaling in the development of chitin-induced systemic response.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Yuki Kito, Akinobu Matsumoto, Kazuya Ichihara, Chisa Shiraishi, Ronghao Tang, Atsushi Hatano, Masaki Matsumoto, Peixun Han, Shintaro Iwasaki, Keiichi Nakayama
Summary: Translation begins with the binding of the eIF4F complex to the 5' mRNA cap, followed by scanning ribosomes searching for the start codon in the 5' untranslated region. This study shows that the ASC-1 complex (ASCC) associates with scanning ribosomes to regulate translation initiation. Knockdown of ASCC3, a subunit of ASCC, impairs the loading and scanning dynamics of the 43S preinitiation complex, leading to reduced translation efficiency. These findings demonstrate that ASCC not only promotes dissociation of colliding 80S ribosomes but also facilitates efficient translation initiation by scanning ribosomes.
Article
Plant Sciences
Momoko Takagi, Rikako Hirata, Yusuke Aihara, Yuki Hayashi, Miya Mizutani-Aihara, Eigo Ando, Megumi Yoshimura-Kono, Masakazu Tomiyama, Toshinori Kinoshita, Akira Mine, Yosuke Toda
Summary: This paper proposes an image analysis pipeline that can automatically quantify the stomatal aperture of Arabidopsis thaliana leaves. By combining a YOLO X-based stomatal detection submodule and a U-Net-based pore segmentation submodule, high-precision detection and segmentation of stomata and pores are achieved. In addition, a portable imaging device is designed for easy acquisition of stomatal images on-site. Utilizing this device and the optimized models, it is possible to replace manual measurement of stomatal response to pathogen inoculation, accelerating research on stomatal biology of model dicots.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Multidisciplinary Sciences
Chisa Shiraishi, Akinobu Matsumoto, Kazuya Ichihara, Taishi Yamamoto, Takeshi Yokoyama, Taisuke Mizoo, Atsushi Hatano, Masaki Matsumoto, Yoshikazu Tanaka, Eriko Matsuura-Suzuki, Shintaro Iwasaki, Shouji Matsushima, Hiroyuki Tsutsui, Keiichi I. Nakayama
Summary: This study reveals that the RPL3L-encoded ribosomal protein specifically expressed in heart and skeletal muscle affects translation elongation dynamics, and its deficiency impairs cardiac contractility in mice. The results provide insights into the mechanisms and physiological relevance of tissue-specific translational regulation.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Asuteka Nagao, Yui Nakanishi, Yutaro Yamaguchi, Yoshifumi Mishina, Minami Karoji, Takafumi Toya, Tomoya Fujita, Shintaro Iwasaki, Kenjyo Miyauchi, Yuriko Sakaguchi, Tsutomu Suzuki
Summary: The researchers established a highly sensitive method to profile pep-tRNAs using mass spectrometry, and detected a large number of nascent peptides from pep-tRNAs in Escherichia coli pth(ts) strain. Molecular mass analysis revealed that about 20% of the peptides had single amino-acid substitutions in the N-terminal sequences. Further analysis showed that most of the substitutions occurred at the C-terminal drop-off site, and the miscoded pep-tRNAs rarely participated in the next round of elongation but dissociated from the ribosome. These findings suggest that pep-tRNA drop-off is an active mechanism for the ribosome to reject miscoded pep-tRNAs in early elongation and contribute to quality control of protein synthesis.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Takahito Miyake, Yuichi Inoue, Xinyan Shao, Takehito Seta, Yuto Aoki, Khanh Tien Nguyen Pham, Yuichi Shichino, Junko Sasaki, Takehiko Sasaki, Masahito Ikawa, Yoshiaki Yamaguchi, Hitoshi Okamura, Shintaro Iwasaki, Masao Doi
Summary: Body temperature in homeothermic animals fluctuates within a physiological range and serves as a systemic signal for circadian clock-regulated physiology. The upstream open reading frame (uORF) of the core clock gene Per2 acts as a regulatory module for temperature-dependent circadian clock entrainment.
Article
Biology
Mingming Chen, Naoyoshi Kumakura, Hironori Saito, Ryan Muller, Madoka Nishimoto, Mari Mito, Pamela Gan, Nicholas T. Ingolia, Ken Shirasu, Takuhiro Ito, Yuichi Shichino, Shintaro Iwasaki
Summary: A parasitic fungus has been found to overcome the toxicity of antimicrobial compounds produced by plants through a specific amino acid substitution. This study reveals the molecular mechanisms of fungal resistance against plant defense mechanisms.
Article
Multidisciplinary Sciences
Akira Yamashita, Yuichi Shichino, Kazuki Fujii, Yumie Koshidaka, Mayumi Adachi, Eri Sasagawa, Mari Mito, Shinichi Nakagawa, Shintaro Iwasaki, Keizo Takao, Nobuyuki Shiina
Summary: This study investigated the role of the prion-like domain (PrLD) in the RNA-binding protein NFAR2 in water immersion and restraint stress (WIRS). The findings suggest that PrLD is not necessary for the survival function of NFAR2, but is important for the response to WIRS. Additionally, PrLD is required for the nuclear localization of NFAR2, changes in mRNA expression and translation, and resistance to WIRS in fear-associated memory formation in the amygdala.
Article
Biochemistry & Molecular Biology
Yuji Fujimoto, Hiro-oki Iwakawa
Summary: Many organisms produce secondary siRNAs to regulate biological processes, and plants have evolved various pathways for secondary siRNA production. The critical step is the production of double-stranded RNAs by RNA-dependent RNA polymerases. This article reviews recent advances in secondary siRNA production triggered by microRNAs and invasive nucleic acids, focusing on factors, events, and RNA/DNA elements that promote or inhibit the early steps of biogenesis.
JOURNAL OF BIOCHEMISTRY
(2023)
Article
Biology
Eriko Matsuura-Suzuki, Hirotaka Toh, Shintaro Iwasaki
Summary: In vitro translation systems are important tools for studying translational regulation. This study presents a step-by-step protocol for a hybrid translation system that overcomes analytical hurdles in investigating the function of ribosomes in commercially available rabbit reticulocyte lysate (RRL). This protocol can be used to study the potency of heterologous ribosomes.
Article
Biology
Hironori Saito, Tatsuya Osaki, Yoshiho Ikeuchi, Shintaro Iwasaki
Summary: In addition to cytosolic protein synthesis, mitochondria also have a translation system tailored for mitochondrial genome-encoded mRNAs. The importance of mitochondrial protein synthesis is evidenced by the association with various diseases related to translation deficiencies in mitochondria. Although methods like labeling newly synthesized proteins and ribosome profiling have been used to monitor mitochondrial translation, measuring translation capacity in individual cells has been challenging. To address this issue, a method called mito-fluorescent noncanonical amino acid tagging (FUNCAT) fluorescence-activated cell sorting (FACS) has been developed recently, which allows the detection of mitochondrial translation in individual cells by labeling nascent peptides with a methionine analog and fluorophores.
