Review
Cell Biology
Lori A. Passmore, Jeff Coller
Summary: Recent studies have shown that poly(A) tails play a complex role in the cytoplasm, including promoting translation and controlling mRNA stability through deadenylation. The length of poly(A) tails is correlated with translation rate and mRNA lifespan, indicating a significant role in gene regulation.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2022)
Article
Biology
Ipsita Basu, Biswajit Gorai, Thyageshwar Chandran, Prabal K. Maiti, Tanweer Hussain
Summary: Accurate and high-speed scanning and selection of the correct start codon are important events in protein synthesis. Molecular dynamics simulations and energy calculations suggest that the ribosomal 48S pre-initiation complex (PIC) may reject most non-AUG codons, with initiation factor eIF1 playing a crucial role. This study provides insights into the scanning process and the involvement of initiation factors in codon-anticodon-ribosome network stability.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Soushi Kobayashi, Akira Kaji, Hideko Kaji
Summary: Eukaryotic elongation factor 3 (eEF3) stimulates the release of mRNA from puromycin-treated polysomes. When eEF3 is partially removed from the crude extract, a UAA stop codon readthrough occurs, leading to an increase in the downstream ORF product. eEF3 enhances the release of luciferase from polysomes by eukaryotic release factor (eRF)1 and eRF3. These findings suggest that eEF3 assists eRFs in performing normal protein synthesis termination in yeast.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2023)
Review
Biochemistry & Molecular Biology
Qiushuang Wu, Ariel A. Bazzini
Summary: Messenger RNA (mRNA) stability and translational efficiency play crucial roles in protein production. Recent studies have shown that ribosomes, in addition to protein synthesis, also control mRNA stability in a codon-dependent manner known as codon optimality. Codons have a significant impact on mRNA stability and provide cis-regulatory information beyond their encoding amino acids. The molecular mechanism of codon optimality is still not fully understood, but it appears that the translation elongation rate triggers mRNA decay, where transfer RNAs may serve as master gene regulators influencing mRNA stability. This article discusses the findings of codon optimality and gene regulation related to codon composition in different eukaryotic species.
ANNUAL REVIEW OF BIOCHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Ivaylo P. Ivanov, James A. Saba, Chen-Ming Fan, Ji Wang, Andrew E. Firth, Chune Cao, Rachel Green, Thomas E. Dever
Summary: Start site selection in eukaryotes is influenced by the context nucleotides flanking the AUG codon and by levels of translation initiation factors. We found that some Hox genes initiate in suboptimal context and contain conserved uORFs. Analysis of CAGE-seq data revealed that the 5' leaders of Hox mRNAs are shorter than reported and lack proposed IRES elements. We showed that uORFs inhibit Hox reporter expression and start codon selection stringency can be altered by overexpressing translation initiation factors or modifying ribosome homeostasis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Sayanur Rahaman, Simone Faravelli, Sylvia Voegeli, Attila Becskei
Summary: The stability gain of mRNA in yeast depends on the mRNA coding sequence length. Codon optimality affects mRNA stability and polysome propensity above a threshold length. The untranslated regions (UTR) can tune this threshold length and some UTRs can destabilize mRNAs without reducing translation, which is important for controlling the oscillatory expression of cell cycle genes.
Article
Multidisciplinary Sciences
Michael R. Lawson, Laura N. Lessen, Jinfan Wang, Arjun Prabhakar, Nicholas C. Corsepius, Rachel Green, Joseph D. Puglisi
Summary: Through single-molecule fluorescence assays, researchers found that in the termination process of yeast translation, the two release factors eRF1 and eRF3 bind together to rapidly recognize stop codons and induce termination through a tightly regulated, multistep process that resembles transfer RNA selection during translation elongation.
Article
Biochemistry & Molecular Biology
Ronit Nir, Thomas Philipp Hoernes, Hiromi Muramatsu, Klaus Faserl, Katalin Kariko, Matthias David Erlacher, Aldema Sas-Chen, Schraga Schwartz
Summary: RNA can be modified post-transcriptionally with various modifications, including pseudouridine (psi), which has been found in mRNA molecules. This study investigates the possibility of snoRNA-guided pseudouridylation of mRNA targets and provides insights into the factors affecting the efficiency of this modification. The study also explores the potential therapeutic application of pseudouridylation in suppressing translational termination.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Genetics & Heredity
Na L. Gao, Zilong He, Qianhui Zhu, Puzi Jiang, Songnian Hu, Wei-Hua Chen
Summary: There is a universal GC gradient in eukaryotic genes, starting from the 25th codon, and especially pronounced at nonsynonymous sites, resulting in cheaper amino acid selection. High expression genes show a weakened GC gradient, suggesting a conserved selective constraint at the translation start to increase GC contents at nonsynonymous sites.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Yavuz T. Durmaz, Alankrit Shatadal, Kyle Friend
Summary: Messenger RNA translation and the presence of certain codons can affect mRNA stability and protein folding, with ribosomes playing a role in mRNA decay and ribosomal collisions potentially promoting mRNA decay and protein misfolding.
Review
Pharmacology & Pharmacy
Luisa D. Burgers, Robert Fuerst
Summary: This review highlights the importance of eukaryotic protein synthesis, the role of natural products in research and drug development, and the interactions of bacterial-, marine- and plant-derived compounds with mRNA translation. It emphasizes the diversity of natural products in targeting different steps of translation and their potential as drug leads.
PHARMACOLOGICAL RESEARCH
(2021)
Article
Immunology
Xuhua Xia
Summary: The design of Pfizer/BioNTech and Moderna mRNA vaccines involves various optimizations such as enhancing translation efficiency and improving mRNA stability. Different optimizations may conflict with each other, requiring compromises to be made.
Article
Biotechnology & Applied Microbiology
Xavier Hernandez-Alias, Hannah Benisty, Leandro G. Radusky, Luis Serrano, Martin H. Schaefer
Summary: The study reveals tissue-specific codon preferences and their impact on protein synthesis. A machine learning model identifies clusters of tissues with different codon usage patterns. The developed algorithm, CUSTOM, optimizes protein production by suggesting synonymous codon design. This research has implications in gene design and biotechnological applications.
Review
Genetics & Heredity
Elva Vidya, Thomas F. Duchaine
Summary: This review discusses the regulation of the decapping process, including the roles and assembly of decapping co-factors, the functional convergence of decapping machineries with other RNA-protein complexes, and the models of decapping activation. The complexity of decapping regulation has been revealed through studies, but there are still important gaps to be filled.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Paul Powell, Usha Bhardwaj, Dixie Goss
Summary: This study identifies secondary structures that selectively interact with eIF3 and explores its role in translation initiation of BYDV. The findings propose a new model for BYDV translation initiation and expand the known functionality of eIF3.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Ekaterina A. Trifonova, Alexandra I. Klimenko, Zakhar S. Mustafin, Sergey A. Lashin, Alex V. Kochetov
Summary: Autism spectrum disorder (ASD) and autoimmune disorders (AID) share genetic heterogeneity and heritability, with a portion of genes related to the mTOR signaling pathway. This suggests that some cases of ASD and AID may involve a common abnormal pathway.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Agriculture, Multidisciplinary
A. Kochetov, A. Y. Pronozin, N. Shatskaya, D. A. Afonnikov, O. S. Afanasenko
Summary: Viroids, a class of molecules of great interest to researchers in phytopathology and molecular evolution, can be transmitted vertically through microspores and macrospores. The highly structured genomic RNA of PSTVd is prone to errors during replication, and infection induces immune responses in host plants. Disease symptoms may be caused by RNA-interference affecting important cellular regulatory factors.
VAVILOVSKII ZHURNAL GENETIKI I SELEKTSII
(2021)
Review
Agriculture, Multidisciplinary
A. Kochetov, T. A. Gavrilenko, O. S. Afanasenko
Summary: This review discusses the molecular mechanisms of plant resistance to cyst and gall nematodes and the potential of introducing resistance genes (R-genes) from related species as well as utilizing host-induced gene silencing (HIGS) for nematode biocontrol. Several recent studies have demonstrated the effectiveness of HIGS against sedentary nematodes, providing a promising approach for sustainable plant protection.
VAVILOVSKII ZHURNAL GENETIKI I SELEKTSII
(2021)
Article
Plant Sciences
S. M. Ibragimova, M. A. Genaev, A. Kochetov, D. A. Afonnikov
Summary: Proline, an amino acid, is important for stress resistance and development in plants. Genetically modified tobacco plants with reduced proline dehydrogenase activity and increased proline content show greater resistance to various stressors and have differences in leaf pubescence compared to control plants. Automated analysis reveals increased trichome numbers but decreased trichome length in transgenic plants.
BIOLOGIA PLANTARUM
(2022)
Review
Biochemistry & Molecular Biology
Ekaterina A. Trifonova, Zakhar S. Mustafin, Sergey A. Lashin, Alex V. Kochetov
Summary: This review analyzes the connection between mTOR signaling and maternal autoantibody-related autism spectrum disorder (ASD) and autoimmune neuropsychiatric disorders. It emphasizes the need for subtyping ASD based on pathogenic mechanisms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Agronomy
Alex V. Kochetov, Dmitry A. Afonnikov, Nikolay Shmakov, Gennady V. Vasiliev, Olga Y. Antonova, Natalja V. Shatskaya, Anastasiya Y. Glagoleva, Salmaz M. Ibragimova, Aleksander Khiutti, Olga S. Afanasenko, Tatjana A. Gavrilenko
Summary: The research evaluated the expression of NLR genes in three potato cultivars, showing induction of RB/Rpi-blb1/Rpi-sto1 transcript in resistant cultivars after infection with Phytophthora infestans. The discovery of novel NLR genes may facilitate the identification of new efficient resistance genes.
Article
Chemistry, Multidisciplinary
Chinthakunta Narendra Reddy, Ramasubbu Sankararamakrishnan
Summary: Viruses have evolved strategies to prevent apoptosis of infected cells, with proteins like A179L and BHRF1 showing favorable interactions with BH3-like peptides. The design of specific BH3-mimetic inhibitors for vBcl-2 homologues must also consider long-range interactions and nonhotspot residues.
Article
Agriculture, Multidisciplinary
I. Totsky, I. Rozanova, A. D. Safonova, A. S. Batov, Yu A. Gureeva, E. K. Khlestkina, A. Kochetov
Summary: The study screened the GenAgro potato collection using diagnostic PCR markers linked to nematode and wart resistance, finding that only the 57R marker showed high correlation with resistance and a diagnostic efficiency of 86.11%. The other markers did not show significant correlation with resistance and were not recommended for use in identifying resistant samples.
VAVILOVSKII ZHURNAL GENETIKI I SELEKTSII
(2021)
Review
Genetics & Heredity
T. S. Golubeva, V. A. Cherenko, O. I. Sinitsyna, A. V. Kochetov
Summary: This article reviews the basic knowledge and research progress on the interaction between potato and Phytophthora infestans, covering genetic resistance, chemical approaches, and promising methods for reducing the pathogenicity of late blight.
RUSSIAN JOURNAL OF GENETICS
(2022)
Article
Biochemistry & Molecular Biology
C. Narendra Reddy, Ramasubbu Sankararamakrishnan
Summary: Many steps in programmed cell death are conserved across different species. Proteins involved in apoptosis in Caenorhabditis elegans are homologous to those in mammals. This study models the ternary complex of CED-9, CED-4, and EGL-1 and performs molecular dynamics simulations to understand the dynamics and interactions involved in CED-4a's dissociation from CED-9.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Dmitry I. Karetnikov, Gennady V. Vasiliev, Stepan V. Toshchakov, Nikolay A. Shmakov, Mikhail A. Genaev, Mikhail A. Nesterov, Salmaz M. Ibragimova, Daniil A. Rybakov, Tatjana A. Gavrilenko, Elena A. Salina, Maxim V. Patrushev, Alex V. Kochetov, Dmitry A. Afonnikov
Summary: By comparing the genomic sequences of potato cultivars from Russia and South America, we found that the Russian potatoes have a more homogeneous genome with smaller copy number variations and deletion size compared to the South American ones. We identified genes related to immune/abiotic stress response, transport, tuberization, and photoperiod control. Additionally, we discovered a novel gene similar to Arabidopsis poly(ADP-ribose) glycohydrolase (PARG) that may play a role in circadian rhythm control and contribute to the acclimatization processes of Russian potato cultivars.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Agronomy
Alex V. Kochetov, Nikolay Shmakov, Dmitry A. Afonnikov, Gennady V. Vasiliev, Natalja V. Shatskaya, Anastasiya A. Egorova, Nina V. Mironenko, Nina M. Lashina, Alexander V. Khiutti, Olga S. Afanasenko
Summary: Potato spindle tuber viroid (PSTVd) is a small circular RNA that causes diseases in important crops like tomato and potato. The severity of symptoms varies depending on different factors. The molecular mechanisms behind the development of specific disease phenotypes are not well understood.
Article
Mathematical & Computational Biology
Rachana Dande, Ramasubbu Sankararamakrishnan
Summary: Aquaporins and aquaglyceroporins are important protein channels involved in transporting water and other neutral solutes. Single-nucleotide polymorphisms (SNPs) in these proteins have been found to be associated with specific human diseases. The study systematically analyzed the pattern of missense substitutions in 2798 SNPs in 13 human AQPs and found that some substitutions can disrupt the structure and function of the proteins. The researchers developed a database, dbAQP-SNP, to provide information on these SNPs in human AQPs.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)
Article
Agriculture, Multidisciplinary
A. A. Egorova, S. Gerasimova, A. V. Kochetov
Summary: Ornithine aminotransferase (OAT) is involved in connecting the urea cycle, proline cycle, and polyamine biosynthesis pathway in plants. The transcriptional regulation of the OAT gene is found to be associated with developmental processes and regulated by auxin and cytokinins.
VAVILOVSKII ZHURNAL GENETIKI I SELEKTSII
(2022)
Review
Agriculture, Multidisciplinary
T. S. Frolova, V. A. Cherenko, O. Sinitsyna, A. Kochetov
Summary: Phytophthora infestans is a major oomycete pathogen affecting crops in the Solanaceae family, particularly potatoes, leading to late blight. Studies on the interaction mechanisms between these crops and the pathogen have important implications for both fundamental knowledge and practical applications in agriculture.
VAVILOVSKII ZHURNAL GENETIKI I SELEKTSII
(2021)
