Review
Biochemistry & Molecular Biology
Vandana Yadav, Inayat Ullah Irshad, Hemant Kumar, Ajeet K. Sharma
Summary: This passage discusses the methods used to extract translation rate parameters from ribosome profiling data and their applications in deciphering the regulation of gene expression. The accurate rate parameters may provide new insights into the kinetic control of the process of gene expression.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemical Research Methods
Michaela Frye, Susanne Bornelov
Summary: CONCUR is a standalone tool written in Perl for codon usage analysis in ribosome profiling experiments. It estimates codon counts at the ribosome E-, P- and A-sites using aligned reads in BAM format, and is freely available on https://github.com/susbo/concur.
Article
Forestry
Yajun Zeng, Lianwen Shen, Shengqun Chen, Shuang Qu, Na Hou
Summary: This study analyzed the codon usage patterns of 26 Juglandaceae chloroplast genomes and found that chloroplast codons tend to exhibit conserved GC content and are primarily altered by natural selection.
Article
Biochemistry & Molecular Biology
Pedro do Couto Bordignon, Sebastian Pechmann
Summary: The translation of mRNAs into proteins by the ribosome is a crucial step in protein biosynthesis, tightly controlled to maintain cellular homeostasis. Ribosome profiling has provided insights into translation mechanisms, yet many aspects remain mysterious due to challenges in data interpretation. The study reveals programmed translational heterogeneity in genomic sequences, impacting cellular homeostasis and highlighting the complexity of translation regulation.
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)
Article
Biochemistry & Molecular Biology
Janaina Lima de Oliveira, Atahualpa Castillo Morales, Laurence D. Hurst, Araxi O. Urrutia, Christopher R. L. Thompson, Jason B. Wolf
Summary: Studies have found that synonymous codons are used at different frequencies due to the effects of neutral and selective forces. Selection in highly expressed genes remains to be extensively studied, with some evidence suggesting that certain factors do not impact codon preference.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Krishnamurthy Subramanian, Bryan Payne, Felix Feyertag, David Alvarez-Ponce
Summary: This is an online database that provides codon usage statistics for all species in RefSeq, allowing users to search for specific species or taxonomic groups and access relevant statistical tables.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Microbiology
J. L. Weissman, Marie Peras, Tyler P. Barnum, Jed A. Fuhrman
Summary: Trait inference from mixed-species microbial communities is a central problem in microbial ecology. The authors developed a tool, gRodon, for predicting the maximum growth rate of an organism based on its genomic data. This predictor can be applied to mixed-species communities to estimate the average community-wide maximum growth rate. The authors also provided an improved predictor for metagenomic data that corrects a persistent bias and showed the importance of data preprocessing for accurate predictions.
Article
Genetics & Heredity
Xin Li, Xiaocen Wang, Pengtao Gong, Nan Zhang, Xichen Zhang, Jianhua Li
Summary: This study systematically analyzed the codon usage pattern of Giardia duodenalis, revealing that mutational pressure and natural selection play important roles in shaping its codon usage bias. The study provides useful insights into the mechanisms behind Giardia duodenalis' codon usage bias formation.
Article
Engineering, Marine
Marc Krasovec, Dmitry A. Filatov
Summary: This study provides a comparative analysis of codon bias across multiple major phytoplankton groups. The results show that most groups have modest codon bias, with Haptophyta having the strongest bias and Chlorarachniophyta having the weakest bias. The optimal codons are typically GC-ending, but shifts to AT-ending codons were observed in Ochrophyta and Ciliophora. The study also highlights the modest codon bias in marine phytoplankton, which can be explained by the lower effective population sizes compared to the astronomically large census population sizes.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2022)
Review
Biophysics
Marina V. Rodnina
Summary: Faithful translation of messenger RNA (mRNA) into protein is crucial for maintaining protein homeostasis in cells. Recoding events, such as stop codon readthrough, frameshifting, and translational bypassing, allow intentional mistakes to be made during translation and produce alternative proteins. This review discusses the mechanisms of canonical decoding and tRNA-mRNA translocation, alternative pathways leading to recoding, and the connection between mRNA signals, ribosome dynamics, and recoding.
ANNUAL REVIEW OF BIOPHYSICS
(2023)
Article
Neurosciences
Rekha Khandia, Mohd. Saeed, Ahmed M. Alharbi, Ghulam Md. Ashraf, Nigel H. Greig, Mohammad Amjad Kamal
Summary: Codon usage analysis is important for molecular characterization and understanding gene evolution. This study investigated the association between gene length and various parameters related to codon usage. The findings showed a significant correlation between gene length and codon bias in neurodegeneration-associated genes. However, this association varied depending on the size of gene segments. The study also found that gene length was associated with nucleotide disproportion and codon choices. This analysis provides insights into gene expression and potential interventions in defective gene functioning in clinical settings.
FRONTIERS IN NEUROSCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Mackenzie M. Johnson, Adam J. Hockenberry, Matthew J. Mcguffie, Luiz Carlos Vieira, Claus O. Wilke
Summary: Variation in gene expression is closely associated with codon usage bias, especially under rapid growth conditions. Growth rate-dependent expression variation is an important constraint that influences the evolution of gene sequences in microorganisms.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Genetics & Heredity
Brian Dehlinger, Jared Jurss, Karson Lychuk, Catherine Putonti
Summary: The Codon Bias Database (CBDB) and the Dynamic Codon Biaser (DCB) are tools used to calculate codon usage bias in bacterial genomes, aiding in research on gene expression control, guiding protein structure, evolutionary studies, and phage-host predictions.
MICROBIAL GENOMICS
(2021)
Article
Virology
Irene Hoxie, John J. Dennehy
Summary: The reassortment of Rotavirus A (RVA) may generate new genome constellations with different segments showing varying degrees of co-segregation and host-species associations. The genetic diversity of all segments decreased dramatically around 2007, coinciding with the introduction of RVA vaccines. Additionally, codon usage patterns varied among segments, with some exhibiting higher adaptation to host genomes.
Review
Biochemistry & Molecular Biology
Shaked Bergman, Tamir Tuller
Article
Multidisciplinary Sciences
Yonatan Chemla, Michael Peeri, Mathias Luidor Heltberg, Jerry Eichler, Mogens Hogh Jensen, Tamir Tuller, Lital Alfonta
NATURE COMMUNICATIONS
(2020)
Article
Biochemical Research Methods
Shaked Bergman, Alon Diament, Tamir Tuller
Article
Genetics & Heredity
Arup Panda, Tamir Tuller
GENOMICS PROTEOMICS & BIOINFORMATICS
(2020)
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
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)