Article
Multidisciplinary Sciences
Phillip C. Burke, Heungwon Park, Arvind Rasi Subramaniam
Summary: By measuring the effects of thousands of coding sequence motifs on mRNA levels in human cells, the authors identify nascent peptides with a combination of extended beta-strand structures and bulky, positively charged sequences that reduce mRNA levels by slowing translation.
NATURE COMMUNICATIONS
(2022)
Review
Biochemistry & Molecular Biology
Markus Hopfler, Ramanujan S. Hegde
Summary: Cells regulate mRNA processing, localization, and stability to ensure accurate gene expression. Recent discoveries have uncovered co-translational mechanisms that modulate mRNA translation, localization, processing, and stability. These mechanisms operate by recognizing the nascent protein and directing mRNA fate, allowing cells to dynamically regulate their transcriptomes in response to cellular changes.
Article
Biochemistry & Molecular Biology
Shota Tomomatsu, Atsuya Watanabe, Petr Tesina, Satoshi Hashimoto, Ken Ikeuchi, Sihan Li, Yoshitaka Matsuo, Roland Beckmann, Toshifumi Inada
Summary: Ribosome collisions trigger the ribosome-associated quality control (RQC) and lead to the degradation of mRNA called no-go decay (NGD) through endonucleolytic cleavage. In yeast, NGD can occur in two modes, either coupled to RQC (NGD(RQC+)) or uncoupled from RQC (NGD(RQC-)), depending on the mechanism of substrate recognition by Cue2 endonuclease. The study found that the ubiquitin binding activity of Cue2 is necessary for NGD(RQC-) but not for NGD(RQC+), and it involves the first two N-terminal Cue domains of Cue2. Additionally, Trp122 of Cue2 plays a crucial role in NGD(RQC+), while Mbf1 prevents ribosomal frameshifting induced by rare codon staller.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Yuhei Chadani, Nobuyuki Sugata, Tatsuya Niwa, Yosuke Ito, Shintaro Iwasaki, Hideki Taguchi
Summary: Translation elongation is essential for organisms to produce their proteomes, but there is a risk of elongation abortion due to sequences like intrinsic ribosome destabilization (IRD) sequences. Most potential IRD sequences in the middle of open reading frames remain hidden and do not interrupt translation, as the nascent polypeptide itself acts as a bridge in the ribosome, protecting it from dissociation. This inherent ability of nascent polypeptide products ensures elongation continuity.
Review
Biochemistry & Molecular Biology
Peng-yue Zhao, Ren-qi Yao, Zi-cheng Zhang, Sheng-yu Zhu, Yu-xuan Li, Chao Ren, Xiao-hui Du, Yong-ming Yao
Summary: Protein homeostasis is crucial for various life activities, and ribosomes, as the main apparatus of protein translation, play an essential role in maintaining protein homeostasis. However, malfunction of ribosomes can lead to the excessive production and accumulation of aberrant proteins, causing harmful effects on cellular fate and even cell death. Ribosomopathies are a group of diseases characterized by abnormalities in ribosomal compositions and functions, and cells have evolved ribosome quality control mechanisms to regulate the quantity and quality of ribosomes.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Zhi Wang, Peng Ge, Xiao-Long Zhou, Kun-Ming Shui, Huichao Geng, Jie Yang, Jia-Yu Chen, Jin Wang
Summary: nASAP is a user-friendly web server that provides practical quality evaluation and comprehensive analysis of nascent RNA datasets. It offers customized analysis modules for quality assessment, quantification analysis, pausing analysis, and network analysis, making it extremely useful in various fields.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Zhi Wang, Peng Ge, Xiao-Long Zhou, Kun-Ming Shui, Huichao Geng, Jie Yang, Jia-Yu Chen, Jin Wang
Summary: nASAP is a user-friendly and high-performance platform for processing nascent RNA data, providing functions such as quality assessment, quantification analysis, pausing analysis, and network analysis. It will play an important role in basic and advanced analysis of nascent RNA data.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Cell Biology
Yoshitaka Matsuo, Toshifumi Inada
Summary: The study finds that Hel2 preferentially binds to pre-engaged secretory ribosome-nascent chain complexes, especially under signal recognition particle (SRP) deficient conditions. Deletion of Hel2 exacerbates mitochondrial defects caused by insufficient SRP, leading to mistargeting of secretory proteins into mitochondria. These insights shed light on risk management in the secretory pathway for maintaining cellular protein homeostasis.
Article
Biochemistry & Molecular Biology
Caillan Crowe-McAuliffe, Hiraku Takada, Victoriia Murina, Christine Polte, Sergo Kasvandik, Tanel Tenson, Zoya Ignatova, Gemma C. Atkinson, Daniel N. Wilson, Vasili Hauryliuk
Summary: In all branches of life, stalled translation intermediates are recognized and processed by ribosome-associated quality control pathways. The process involves splitting of stalled ribosomes and targeting incomplete proteins for degradation by NEMF family proteins. Structural analysis reveals the mechanism of C-terminal tailing in Bacillus subtilis, mediated by NEMF protein RqcH and RqcP, in synthesizing polypeptides in the absence of mRNA or the small subunit.
Article
Multidisciplinary Sciences
Surajit Chatterjee, Adrien Chauvier, Shiba S. Dandpat, Irina Artsimovitch, Nils G. Walter
Summary: In bacteria, the interaction between RNA polymerase and ribosome regulates gene expression through transcription-translation coupling. This coupling is mainly achieved by RNA polymerase promoting the binding of the ribosomal 30S subunit to antagonize ribosome binding site occlusion induced by a riboswitch, thereby facilitating translation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Yuichiro Mishima, Peixun Han, Kota Ishibashi, Seisuke Kimura, Shintaro Iwasaki
Summary: The control of mRNA stability is crucial for regulating gene expression patterns. Recent studies have found that the composition of codons in the open reading frame affects mRNA stability in various organisms. Experimental analyses are needed to clarify the effects of codons on mRNA stability and the pathways of cotranslational mRNA decay.
Article
Biochemistry & Molecular Biology
Xiongwen Cao, Alexandra Khitun, Cecelia M. Harold, Carson J. Bryant, Shu-Jian Zheng, Susan J. Baserga, Sarah A. Slavoff
Summary: This study discovered unannotated alt-proteins that play important roles in DNA damage stress and cell cycle regulation. One of these alt-proteins, MINAS-60, was found to negatively regulate assembly of the pre-60S ribosomal subunit. Depletion of MINAS-60 increases cytoplasmic 60S ribosomal subunit, leading to upregulated protein synthesis and cell proliferation.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Business
Xiaohui Shi, Feng Li, Pattarin Chumnumpan
Summary: This study explores the emergence and development of innovation platforms in nascent industries, using the example of the U.K.'s TRTG industry. Four key capabilities – innovation leverage, market exploration, quality control, and appropriation – are identified as crucial for successful platform development. The article also discusses how firms can redefine their boundaries to deploy these capabilities effectively.
JOURNAL OF MANAGEMENT
(2021)
Review
Pharmacology & Pharmacy
Byoungjae Kong, Yelee Kim, Eun Hye Kim, Jung Soo Suk, Yoosoo Yang
Summary: Messenger RNA (mRNA) has emerged as a powerful tool for treating various human diseases, especially malignant tumors. The successful use of mRNA vaccines during the COVID-19 pandemic highlights its potential in cancer immunotherapy. This review provides a comprehensive overview of the current state and prospects of mRNA-based therapeutics, including various delivery and therapeutic strategies.
ADVANCED DRUG DELIVERY REVIEWS
(2023)
Article
Biochemistry & Molecular Biology
Haoran Duan, Siqiong Zhang, Yoram Zarai, Rupert Ollinger, Yanmeng Wu, Li Sun, Cheng Hu, Yaohui He, Guiyou Tian, Roland Rad, Xiangquan Kong, Yabin Cheng, Tamir Tuller, Dieter A. Wolf
Summary: eIF3k and eIF3l play an important role in maintaining translational capacity during cellular stress by regulating ribosome synthesis.
