Review
Chemistry, Multidisciplinary
Sebastian M. Castillo-Hair, Georg Seelig
Summary: Over the past two years, mRNA therapeutics and vaccines have rapidly made a transition from concept to real-world impact. While some aspects have been optimized for decades, the selection and design of noncoding sequences controlling translation efficiency have received less attention. Model-driven design is proposed as a promising alternative to provide unprecedented control over untranslated region function.
ACCOUNTS OF CHEMICAL RESEARCH
(2022)
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.
Review
Cell Biology
Marianne Mercer, Seoyeon Jang, Chunyang Ni, Michael Buszczak
Summary: Regulation of mRNA translation is crucial for germ cell development and function across species, involving specific RNA binding proteins. These proteins are conserved and play similar roles in germ cells of various species, highlighting the importance of understanding the mechanisms controlling mRNA translation in germ cells.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Xiaoyu Yang, Bo Song, Jie Cui, Lina Wang, Shuoshuo Wang, Linlin Luo, Lei Gao, Beixin Mo, Yu Yu, Lin Liu
Summary: This study reveals that translational reprogramming plays an important role in rice's response to salt stress, with the salt-tolerant cultivar SR86 adopting a more flexible translational adaptive strategy compared to the salt-sensitive cultivar NB. The differences in translational dynamics under salt stress between NB and SR86 may be due to their varying levels of ribosome stalling.
Review
Oncology
Albrecht Stenzinger, Arndt Vogel, Ulrich Lehmann, Angela Lamarca, Paul Hofman, Luigi Terracciano, Nicola Normanno
Summary: Cholangiocarcinomas are a heterogeneous group of tumors with distinct genomic alterations. Next-generation sequencing is a powerful tool for identifying gene variants and guiding personalized treatment for patients with cholangiocarcinomas. Understanding the use of NGS in molecular profiling is crucial for healthcare professionals to optimize treatment outcomes.
CANCER TREATMENT REVIEWS
(2024)
Article
Health Care Sciences & Services
Antonio Juan Ribelles, Pablo Gargallo, Pablo Berlanga, Vanessa Segura, Yania Yanez, Barbara Juan, Marta Salom, Margarita Llavador, Jaime Font de Mora, Victoria Castel, Adela Canete
Summary: The study analyzed 70 pediatric sarcoma patients and detected 30 pathogenic mutations in 18 different genes through histopathological analysis and NGS testing. Targeted treatment was implemented in 6 patients, leading to a disease control rate of 78%, demonstrating feasibility of personalized therapy for pediatric sarcomas.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Review
Microbiology
Elizabeth B. B. Sawyer, Teresa Cortes
Summary: Ribosome profiling, a recent addition to the -omics toolkit, provides insights into the process and regulation of translation. In the case of mycobacteria, this method has led to new discoveries about translational regulation and expanded our understanding of canonical translation mechanisms.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Pauline Francois, Hugo Arbes, Stephane Demais, Agnes Baudin-Baillieu, Olivier Namy
Summary: Ribosome profiling, a powerful tool for studying translation regulation, suffers from a lack of standardization in the bioinformatics part, hindering result reproducibility. A unique tool has been proposed to standardize the general steps of RiboSeq analysis, aiming to unify bioinformatics pipelines for translation research.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Tomoya Fujita, Takeshi Yokoyama, Mikako Shirouzu, Hideki Taguchi, Takuhiro Ito, Shintaro Iwasaki
Summary: This study investigated ribosome pause sites in Escherichia coli using different ribosome profiling strategies, revealing remarkable differences compared to eukaryotes. The identified pause sites were biochemically validated and provided a useful resource for ribosome stalling sites in bacteria.
Review
Biochemistry & Molecular Biology
Nikolay E. Shirokikh
Summary: During protein biosynthesis, ribosomes translate mRNA into amino acids, and various mRNA features can affect translation rates. Cell signaling pathways converge on mRNA control, and footprint analysis can reveal the locations and sizes of translational complexes, uncovering translation control mechanisms.
CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Tomoya Fujita, Takeshi Yokoyama, Mikako Shirouzu, Hideki Taguchi, Takuhiro Ito, Shintaro Iwasaki
Summary: In this study, ribosome pause sites in Escherichia coli were surveyed using monosome and disome profiling strategies. Compared to eukaryotes, ribosome collisions in bacteria showed remarkable differences, and the identified pause sites were biochemically validated and showed puromycin resistance.
Review
Biochemistry & Molecular Biology
Tatjana Huebner, Michael Steffens, Catharina Scholl
Summary: Currently, there is a lack of published information on the analytical validation of NGS applications targeting drug metabolizing enzymes, highlighting the need for a standardized reporting system. Establishing an appropriate analytical validation criteria for NGS-based qualitative tests for pharmacogenetic profiling is crucial for their implementation in clinical use.
MOLECULAR BIOLOGY REPORTS
(2023)
Article
Oncology
Hongsen Li, Liu Gong, Huanqing Cheng, Huina Wang, Xiaochen Zhang, Chuangzhou Rao, Zhangfa Song, Da Wang, Haizhou Lou, Feng Lou, Shanbo Cao, Hongming Pan, Yong Fang
Summary: This study investigated the molecular characterization of colorectal cancer with situs inversus totalis (SCRC), a rare condition. The results showed significant differences in mutated genes and mutational profiles between SCRC and non-SCRC patients. These findings contribute to personalized therapy and improved clinical management of SCRC patients.
FRONTIERS IN ONCOLOGY
(2022)
Review
Cell Biology
Christelle Morris, David Cluet, Emiliano P. Ricci
Summary: Eukaryotic gene expression is regulated by the translation and turnover of mRNAs, with the ribosome playing a central role in this process. The cell has evolved multiple translation-dependent mRNA surveillance pathways to handle specific problematic mRNAs. Current research focuses on translation features, genetic code complexity, and the emerging role of the ribosome as a regulatory hub.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2021)
Article
Microbiology
Victor Barrenechea, Maryhory Vargas-Reyes, Miguel Quiliano, Pohl Milon
Summary: The study revealed that Tig has a stronger stabilization effect on IF1 and can induce a faster compact conformation during translation initiation, leading to translation delay. Different tetracyclines inhibit protein translation initiation and elongation to different extents by affecting IF3 layout and retaining IF1.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Maya Galili, Tamir Tuller
BMC BIOINFORMATICS
(2020)
Article
Genetics & Heredity
Yoram Zarai, Zohar Zafrir, Bunpote Siridechadilok, Amporn Suphatrakul, Modi Roopin, Justin Julander, Tamir Tuller
Article
Biochemical Research Methods
Shaked Bergman, Alon Diament, Tamir Tuller
Article
Genetics & Heredity
Tal Gutman, Guy Goren, Omri Efroni, Tamir Tuller
Summary: Silent mutations have significant predictive power over cancer classification and survival prognosis, likely due to their impact on gene expression. Combining both non-silent and silent mutations can achieve the best classification and survival estimation results for various cancer types. It is recommended to integrate silent mutations into cancer research to fully understand the genomic landscape of cancer and its implications on cancer fitness.
NPJ GENOMIC MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Tamar Neumann, Tamir Tuller
Summary: This study developed a predictive model of small subunit (SSU) density based on TCP-seq data and analyzed the effect of transcript features on SSU scanning dynamics. The results showed that the AUG context indeed affects the movement of the SSU, strong folding may cause the detachment of the SSU from the mRNA, and several novel sequence motifs can affect the SSU scan.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Shir Bahiri Elitzur, Rachel Cohen-Kupiec, Dana Yacobi, Larissa Fine, Boaz Apt, Alon Diament, Tamir Tuller
Summary: The Shine-Dalgarno model indicates that translation initiation in bacteria is regulated by rRNA-mRNA interactions. These interactions not only affect the initiation phase of translation, but also influence all steps of the translation process, including pre-initiation, initiation, elongation, and termination. The study suggests that these interactions play a crucial role in shaping the evolution of transcripts in bacteria by impacting translation efficiency.
Article
Biochemical Research Methods
Itamar Menuhin-Gruman, Matan Arbel, Niv Amitay, Karin Sionov, Doron Naki, Itai Katzir, Omer Edgar, Shaked Bergman, Tamir Tuller
Summary: Modern synthetic biology relies on stable genetic constructs, but maintenance requires cell energy and natural selection can lead to loss of construct functionality. The ESO software tool automates the design of evolutionarily stable constructs while considering host organism characteristics to balance stability and gene expression.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemical Research Methods
David Shallom, Danny Naiger, Shlomo Weiss, Tamir Tuller
Summary: In recent years, intracellular biophysical simulations have been increasingly used in both basic scientific research and synthetic biology. These simulations are time-consuming due to the complex networks of interactions between millions of components, and running them on parallel computers is not easy. This study presents a novel approach using dedicated hardware to address this issue, focusing specifically on simulating mRNA translation at a much faster rate than software solutions.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biology
Liyam Chitayat Levi, Ido Rippin, Moran Ben Tulila, Rotem Galron, Tamir Tuller
Summary: The development of computational biology methodologies has provided a comprehensive understanding of the complexity of microbiomes and their impact on the environment. However, current microbiome engineering techniques neglect the interactions between genetic information and bacterial populations. In this study, a generic computational method was developed to automatically tune gene expression in microbiomes based on user preferences. The method has been validated through computational and experimental tools.
Article
Biotechnology & Applied Microbiology
Arup Panda, Tamir Tuller
Summary: The environment may impact the codon and amino acid choice of microbial communities, and samples from similar environmental niches show similar codon and amino acid distribution compared to samples from other habitats. Factors like GC content, functional or taxonomic abundance cannot fully explain the trends observed at the codon or amino acid level, implying a direct environmental influence on them.
NPJ BIOFILMS AND MICROBIOMES
(2023)
Review
Biotechnology & Applied Microbiology
Matan Arbel-Groissman, Itamar Menuhin-Gruman, Doron Naki, Shaked Bergman, Tamir Tuller
Summary: Evolutionary stability of synthetic constructs made of heterologous genes is a major challenge in synthetic biology, and the available tools to address this challenge are discussed in this review.
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Rami Katz, Elad Attias, Tamir Tuller, Michael Margaliot
Summary: Research has shown that mRNAs compete for shared resources during translation, which can significantly impact the global dynamics of translation in the cell when resources are scarce. By modeling this competition using a network approach, it was found that adding a new mRNA has a complex effect on total protein production, with diminishing marginal utility as the number of mRNAs increases, leading to saturation of total protein production rate to a limiting value.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2022)
Article
Biochemistry & Molecular Biology
Stav Carmel Ezra, Tamir Tuller
Summary: This study investigates the translation initiation process in chloroplasts and develops computational models to understand and model translation regulation. The folding energy of rRNA and mRNA is found to correlate with codon usage and protein levels. Additionally, the presence of various structural elements in chloroplast transcripts is reported.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Sophie Vinokour, Tamir Tuller
Summary: The study demonstrates the use of generic algorithms to introduce silent mutations for optimizing or reducing ribosomal traffic jams during mRNA translation. The cost of these algorithms includes factors such as computational time and the number of mutations introduced, enriching the methods for translation engineering.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Review
Biochemistry & Molecular Biology
Shir Bahiri-Elitzur, Tamir Tuller
Summary: Codon usage bias refers to the differing frequencies of synonymous codons in genes and organisms, believed to be a balance between mutational biases and natural selection. Various codon usage bias indices have been developed to estimate the fitness of coding sequences to different phenomena, with applications in biomedical fields. Despite the differences in aims, many indices tend to correlate, highlighting the importance of continuously developing new indices to capture additional aspects of gene expression steps.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)