Review
Biochemistry & Molecular Biology
Guus Gijsbertus Hubert van den Akker, Federico Zacchini, Bas Adrianus Catharina Housmans, Laura van der Vloet, Marjolein Maria Johanna Caron, Lorenzo Montanaro, Tim Johannes Maria Welting
Summary: Bicistronic reporter assays are crucial for transgene expression and understanding of internal ribosomal entry site translation. Analysis of literature revealed methodological variability in experiment and data presentation. Adherence to recommended practices can enhance transparency and reproducibility of bicistronic reporter studies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Jack D. Godfrey, Daniel Hejazi, Xiaofei Du, Cenfu Wei, Eshaan Rao, Christopher M. Gomez
Summary: The HER2/neu signaling pathway is frequently mutated in human cancer and targeting this pathway is effective in treatment. However, cancer cells often develop resistance. This study shows that smaller c-terminal fragments (CTFs) of the HER2 protein, generated through internal translation, are a cause of resistance. Understanding this mechanism could lead to new therapeutic interventions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Hong-Jiang Wang, Yan Guo, Meng-Jiao He, Zhong-Yu Liu, Qing Ye, Xing-Yao Huang, Yong-Qiang Deng, Xiao-Feng Li, Cheng-Feng Qin
Summary: Yellow fever (YF) is a highly contagious disease that poses a significant threat to human health. The current live attenuated vaccine, 17D, is considered the most efficient vaccine for YF control. However, 17D can cause adverse events such as neurotropic and viscerotropic diseases. Therefore, the development of a safer YF vaccine is urgently needed. In this study, a bicistronic YFV, named 17D-IRES, was generated using an IRES strategy. 17D-IRES showed effective replication and genetic stability in vitro, and significantly decreased neurovirulence and viscerotropism in vivo. Importantly, 17D-IRES induced strong immune responses and provided full protection against lethal YFV challenge. This study suggests that 17D-IRES could be a promising vaccine candidate against YF, and the IRES-based technology platform holds potential for developing attenuated vaccines against emerging viruses.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Baojun Wu, Murray P. Cox
Summary: Bicistronic transcripts have been reported in eukaryotes, including unicellular yeasts, and they can be divided into highly and lowly expressed categories, each with distinct features that influence translation.
Review
Microbiology
Sahibzada Waheed Abdullah, Jin'en Wu, Xuefei Wang, Huichen Guo, Shiqi Sun
Summary: This review discusses the various types of IRESs found in Picornaviridae and the past and present discoveries regarding ITAFs and their mechanism of action. It also summarizes the importance of herbal extracts, drugs, and chemicals in controlling picornavirus translation and replication. The movement of ITAFs from the nucleus to viral replication factories is also discussed.
Article
Biochemistry & Molecular Biology
Chia-Rui Shen, Ya-Shan Chen, Yih-Shiou Hwang, Hsi-Jien Chen, Chao-Lin Liu
Summary: The study demonstrated that the translation efficiency mediated by IRES is lower when the target gene is downstream, leading to reduced protein production. Additionally, a significantly decreased level of protein production was observed when an upstream cistron was present.
BIOMEDICAL JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Kangkang Niu, Xiaojuan Zhang, Qisheng Song, Qili Feng
Summary: This study demonstrates that RBM4 promotes mRNA translation of the VEGFA gene by binding to the G4 structure in the IRES.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Geon-Woo Kim, Aleem Siddiqui
Summary: The m(6)A modification of the HCV RNA genome plays a crucial role in IRES-dependent translation, with the m(6)A reader protein YTHDC2 being essential for recognizing and supporting HCV translation initiation. This study highlights the functional significance of m(6)A modification and YTHDC2 in HCV IRES-dependent translation initiation, providing potential therapeutic targets for interfering with the infectious process.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Medicine, Research & Experimental
Shaoyi Cai, Fuhua Peng, Heng Tang, Liping Zhou, Zhiyou Chen, Penghan Wu, Yueling Ou, Liang Tao, Qin Wang
Summary: Five new N-terminal-truncated Cx32 isoforms were identified, generated by cap-independent internal translation through internal ribosome entry sites (IRESs) in the coding sequence of GJB1 mRNA. Among them, GJB1-13k inhibited proliferation, promoted apoptosis, and limited cell cycle progression in GBM cells by inhibiting global mRNA translation. TSR3 was found to directly interact with GJB1-13k. It is suggested that overexpression of GJB1-13k in GBM cells with low TSR3 expression or combined targeting of GJB1-13k and TSR3 in GBM cells with high TSR3 expression could be a potential therapeutic strategy for GBM.
BIOMEDICINE & PHARMACOTHERAPY
(2023)
Article
Genetics & Heredity
Bianca R. Grosz, John Svaren, Gonzalo Perez-Siles, Garth A. Nicholson, Marina L. Kennerson
Summary: This study assessed the IRES activity of the human GJB1 5' UTR and found no significant differences in expression levels between the wild-type UTR and the UTR with the c.-103C > T mutation, suggesting an alternate pathogenic mechanism for this non-coding mutation.
Article
Biochemistry & Molecular Biology
Alfredo Berzal-Herranz, Beatriz Berzal-Herranz, Sara Esther Ramos-Lorente, Cristina Romero-Lopez
Summary: This study provides evidence that West Nile virus promotes a cap-independent translation initiation mechanism in mammalian and insect cells, and suggests that its 3' UTR is involved in fine-tuned translation regulation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Sarah Takallou, Nathalie Puchacz, Danielle Allard, Kamaledin B. Said, Mohammad Reza Nokhbeh, Bahram Samanfar, Ashkan Golshani
Summary: Despite the similarity in translation initiation goals, translation initiation is phylogenetically diverse. The finding of the ability of Plautia stali intestine virus (PSIV) Internal Ribosome Entry Site (IRES) to initiate translation in E. coli challenged the idea that translation signals for prokaryotes and eukaryotes are distinct. This study investigates the features of PSIV IRES and its ability to mediate prokaryotic translation initiation, revealing that certain IRESs may also initiate E. coli translation and that the structural integrity of PSIV IRES is less critical in prokaryotes compared to eukaryotes, with two regions of complementarity to 16S ribosomal RNA playing a key role.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Ekaterina S. Komarova, Anna N. Slesarchuk, Maria P. Rubtsova, Ilya A. Osterman, Alexey E. Tupikin, Dmitry Pyshnyi, Olga A. Dontsova, Marsel R. Kabilov, Petr Sergiev
Summary: Flow-seq is a method that combines fluorescently activated cell sorting and next-generation sequencing to deduce a large amount of data about translation efficiency from a single experiment. It has been demonstrated that a variable length 5'-UTR library can be created and analyzed with Flow-seq, and the influence of RNA secondary structure and Shine-Dalgarno sequences on translation efficiency is smaller for natural 5'-UTRs compared to randomized libraries.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Zuben P. Brown, Irina S. Abaeva, Swastik De, Christopher U. T. Hellen, Tatyana Pestova, Joachim Frank
Summary: This study presents cryo-EM structures of hepatitis C virus IRES initiation complexes, revealing the dynamic network of 40S/IRES contacts and the conformational changes during the transition from eIF2- to eIF5B-containing 48S complexes, providing important insights into the process of subunit joining.
Article
Biochemistry & Molecular Biology
Guowei Geng, Chengming Yu, Xuefeng Yuan
Summary: This study found that the IRES activity of RNA2 in wheat yellow mosaic virus varies. Through analysis of RNA structure and mutagenesis, it was found that certain structural elements in the LYJN isolate synergistically ensure higher IRES activity. Additionally, both the HC and LYJN isolates have conserved structural elements that ensure basic IRES activity. This study reveals a novel evolution pattern of IRES, regulating IRES activity by altering the number of eIF4E-binding sites.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2024)
Article
Biochemistry & Molecular Biology
Joseph D. Coolon, Kraig R. Stevenson, C. Joel McManus, Bing Yang, Brenton R. Graveley, Patricia J. Wittkopp
MOLECULAR BIOLOGY AND EVOLUTION
(2015)
Review
Biochemistry & Molecular Biology
Joel McManus, Zhe Cheng, Christine Vogel
MOLECULAR BIOSYSTEMS
(2015)
Article
Biochemical Research Methods
Hao Wang, Joel McManus, Carl Kingsford
Editorial Material
Primary Health Care
Roger Jones
BRITISH JOURNAL OF GENERAL PRACTICE
(2016)
Article
Biochemistry & Molecular Biology
Yizhu Lin, Brigitte F. Schmidt, Marcel P. Bruchez, C. Joel McManus
NUCLEIC ACIDS RESEARCH
(2018)
Article
Biochemistry & Molecular Biology
C. Joel McManus, Gemma E. May, Pieter Spealman, Alan Shteyman
Article
Biochemistry & Molecular Biology
C. Joel McManus, Joseph D. Coolon, Jodi Eipper-Mains, Patricia J. Wittkopp, Brenton R. Graveley
Article
Microbiology
Manning Y. Huang, Carol A. Woolford, Gemma May, C. Joel McManus, Aaron P. Mitchell
Article
Biochemistry & Molecular Biology
Yizhu Lin, Gemma E. May, Hunter Kready, Lauren Nazzaro, Mao Mao, Pieter Spealman, Yehuda Creeger, C. Joel McManus
NUCLEIC ACIDS RESEARCH
(2019)
Review
Cell Biology
Christina Akirtava, Charles Joel McManus
Summary: Eukaryotic gene expression is tightly regulated during translation of mRNA to protein, with mRNA 5' transcript leader (TL) sequences playing a fundamental role. Under different conditions, TLcis-regulatory elements and trans-acting factors control translation initiation, providing insights into the mechanisms of translation regulation.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2021)
Article
Genetics & Heredity
Salini Konikkat, Michelle R. Scribner, Rory Eutsey, N. Luisa Hiller, Vaughn S. Cooper, Joel McManus
Summary: The antibiotic azithromycin alters the gene expression and intragenic 3' end formation in Pseudomonas aeruginosa, contributing to impaired biofilm growth and quorum sensing while upregulating genes associated with persistence. This study provides insights into the molecular mechanisms underlying the response of P. aeruginosa to antibiotics and potential new therapeutic strategies.
Article
Biology
Gemma E. May, Christina Akirtava, Matthew Agar-Johnson, Jelena Micic, John Woolford, Joel McManus
Summary: This study quantified thousands of yeast uORFs and found that AUG uORFs are generally strong repressors, while non-AUG uORFs have relatively weak impacts on gene expression. Machine learning regression modeling revealed that both uORF sequences and locations predict their effect on gene expression.