Article
Biology
Yekaterina Shulgina, Sean R. Eddy
Summary: The genetic code, once thought to be a 'frozen accident,' has been found to evolve to some extent through the discovery of alternative genetic codes. The development of a computational method called Codetta allowed the prediction of amino acid decoding from nucleotide sequence data. By analyzing over 250,000 bacterial and archaeal genome sequences, five new codon reassignments for arginine were discovered, with evolutionary forces like low GC content driving these changes. The study demonstrates the utility of Codetta in understanding how genetic codes evolve and ensuring accuracy in protein databases.
Article
Microbiology
Veronika Kivenson, Blair G. Paul, David L. Valentine
Summary: Marine benthic environments can be influenced by anthropogenic and localized events, affecting microbial community composition that may only become evident decades later. Marine sediments are home to diverse taxa and can provide insights into unique evolutionary strategies. Genetic code expansion in abundant Deltaproteobacteria found in deep-sea industrial waste dump sites enhances their metabolic versatility, potentially impacting microbial interactions with ocean-dumped wastes.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Leon-Samuel Icking, Andreas Martin Riedlberger, Fabian Krause, Jonas Widder, Anne Smedegaard Frederiksen, Fabian Stockert, Michael Spaedt, Nikita Edel, Daniel Armbruster, Giada Forlani, Selene Franchini, Paulina Kaas, Buesra Merve Kirpat Konak, Fabrice Krier, Maiwenn Lefebvre, Daniel Mazraeh, Jeremy Ranniger, Johanna Gerstenecker, Pia Gescher, Karsten Voigt, Pavel Salavei, Nicole Gensch, Barbara Di Ventura, Mehmet Ali Oeztuerk
Summary: The incorporation of non-canonical amino acids (ncAAs) into proteins is a powerful technique used in various research fields. iNClusive, a manually curated repository, provides organized information on ncAAs successfully incorporated into target proteins.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Wenbing Chen, Yupeng Geng, Bing Zhang, Ying Yan, Fangqing Zhao, Miao Miao
Summary: By sequencing seven representative ciliate genomes, we discovered two previously undescribed genetic codes, highlighting the prevalence of bifunctional stop codons in ciliates. Evolutionary genomic analyses revealed that the gain or loss of reassigned stop codons in ciliates is influenced by their living environment, eukaryotic release factor 1, and suppressor tRNAs. This study provides new insights into the functional diversity and evolutionary history of stop codons in eukaryotic organisms.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Review
Microbiology
Federica De Lise, Andrea Strazzulli, Roberta Iacono, Nicola Curci, Mauro Di Fenza, Luisa Maurelli, Marco Moracci, Beatrice Cobucci-Ponzano
Summary: Genetic code decoding is no longer considered universal and immutable, but rather flexible. In Archaea, translational recoding has been extensively studied to regulate the decoding of selenocysteine and pyrrolysine, but further events in other species remain to be explored. The study of recoding episodes in Archaea is urgently needed.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Microbiology
Kexin Meng, Christina Z. Chung, Dieter Soell, Natalie Krahn
Summary: This review discusses the diverse genetic code systems of archaea, detailing the associated biochemical elements and molecular mechanisms. Archaea possess unique genetic code systems that can encode rare amino acids and utilize alternative pathways to synthesize and incorporate canonical amino acids.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Wil Biddle, David G. Schwark, Margaret A. Schmitt, John D. Fisk
Summary: The low efficiency and heterogeneous protein mixtures produced in sense codon reassignment pose challenges for improving the efficiency of this process. This study presents a fluorescence-based screening method to enhance the incorporation of noncanonical amino acids (ncAAs) in response to a specific sense codon, and further demonstrates the successful transplantation of mutations to another ncAA incorporation system. The described workflow provides a generalizable approach for tailoring orthogonal machinery to activate diverse ncAAs for any sense codon target.
FRONTIERS IN CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Pawel Blazej, Konrad Pawlak, Dorota Mackiewicz, Pawel Mackiewicz
Summary: This study investigates the evolutionary mechanisms of codon block structure in the genetic code through computer simulations. The results demonstrate that the reading system similar to that present in the standard genetic code (SGC) quickly dominates during evolution and possesses similar characteristics to the SGC.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Konrad Pawlak, Pawel Blazej, Dorota Mackiewicz, Pawel Mackiewicz
Summary: Synonymous codon usage is influenced by mutations and selection at both the nucleotide and amino acid levels. The proposed mutation-selection model demonstrates that the selection of amino acids based on physicochemical properties can result in biases in codon usage. Alternative genetic codes tend to exhibit greater codon bias than the standard genetic code, and the mutational pressures on cytosine and guanine content further affect usage bias. The study emphasizes the importance of considering amino acid selection in understanding codon usage patterns.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Kuba Nowak, Pawel Blazej, Malgorzata Wnetrzak, Dorota Mackiewicz, Pawel Mackiewicz
Summary: Reprogramming the standard genetic code to incorporate non-canonical amino acids offers new possibilities for medicine, industry, and biotechnology. Various methods of code engineering are available to store new genetic information and produce proteins with novel properties. The study provides a theoretical background for optimal genetic code expansion, discussing the robustness of the new coding system and the analysis of optimal codon sets using graph theory.
Review
Biochemistry & Molecular Biology
Jiantao Guo, Wei Niu
Summary: Noncanonical amino acid mutagenesis is a powerful tool for studying protein structure and function. Quadruplet codons have attracted attention for creating additional blank codons in noncanonical amino acid mutagenesis. This review discusses the methodologies and applications of quadruplet codon decoding in genetic code expansion both in vitro and in vivo.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Valappil Sisila, Mohan Indhu, Janani Radhakrishnan, Niraikulam Ayyadurai
Summary: Genetic code expansion allows the incorporation of noncoded amino acids (NCAAs) and unnatural amino acids (UNAAs) into engineered proteins, providing them with dedicated structure and function. This method has the potential to produce biomaterials with NCAAs/UNAAs that mimic natural matrix-cell interactions, which is important for tissue engineering. Codon suppression and reassignment globally introduce NCAAs/UNAAs, enabling the design of biomaterials with growth factor mimetics called catechols that modulate cell-matrix interactions. This protein engineering approach can lead to tunable biomaterials that are tissue-specific and compliant.
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Oncology
Abhijeet Pataskar, Jasmine Montenegro Navarro, Reuven Agami
Summary: ABPEPserver is an online database and analytical platform that visualizes a large-scale tumor proteomics analysis of Substitutant expression across eight tumor types sourced from the CPTAC database. It offers gene-association signature analysis of Substitutant peptides, comparison of enrichment between tumor and tumor-adjacent normal tissues, and a list of candidate peptides for immunotherapy design.
Article
Biochemistry & Molecular Biology
Li -Tao Guo, Kazuaki Amikura, Han -Kai Jiang, Takahito Mukai, Xian Fu, Yane-Shih Wang, Patrick O'Donoghue, Dieter Soell, Jeffery M. Tharp
Summary: The pyrrolysyl-tRNA synthetase (PylRS) is a major route to install noncanonical amino acids into proteins in living cells due to its tolerance for diverse amino acid substrates and orthogonality in multiple organisms. A novel class of PylRS enzymes was identified in a subset of methanogenic archaea, lacking the N-terminal tRNA-binding domain yet remaining active and orthogonal in bacteria and eukaryotes. Molecular phylogeny analysis revealed the coevolutionary history of PylRS and tRNAPyl, with the emergence of tRNAPyl sequences containing unique discriminator bases that may enable further genetic code expansion efforts.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Jeffery M. Tharp, Oscar Vargas-Rodriguez, Alanna Schepartz, Dieter Soll
Summary: In this study, a mutant tRNA was engineered to initiate translation at the UAU tyrosine codon efficiently. By utilizing a specific tRNA system, UAU was reassigned to selectively encode distinct ncAAs, showcasing the potential applications of this system. Additionally, a triply orthogonal system was developed to produce proteins containing three distinct ncAAs at defined sites, demonstrating the versatility and utility of the approach.
ACS CHEMICAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Vadim N. Gladyshev
Summary: Cells can naturally or be forced to transition to a state of significantly lower biological age, or rejuvenation. These processes may converge to the mid-embryonic state, 'ground zero', where it is possible to achieve a biological age lower than naturally through genome editing and prolonging the rejuvenation phase.
TRENDS IN MOLECULAR MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Maxim Gerashchenko, Zalan Peterfi, Sun Hee Yim, Vadim N. Gladyshev
Summary: The study developed a labeling-free method to measure organ- and celltype-specific translation elongation rates, and found significant differences in elongation rates among different mouse organs. Additionally, the study revealed that the elongation rate decreases with age, indicating tight regulation of translation at the level of elongation of nascent polypeptide chains.
NUCLEIC ACIDS RESEARCH
(2021)
Biographical-Item
Cell Biology
Michael Ristow, Chih-Hao Lee, Katrien De Bock, Vadim N. Gladyshev, Gokhan S. Hotamisligil, Brendan D. Manning
Article
Multidisciplinary Sciences
Adeline Augereau, Marco Mariotti, Melanie Pousse, Doria Filipponi, Frederick Libert, Benjamin Beck, Vera Gorbunova, Eric Gilson, Vadim N. Gladyshev
Summary: The study reveals that the naked mole rat TRF1 supports maximal glycolytic capacity under low oxygen, showing increased nuclear localization and association with telomeres, and protecting them from replicative stress. The evolutionary gain of metabolic function in naked mole rat TRF1 is attributed to specific amino acid changes in the protein's homodimerization domain, while it also accelerates telomere shortening. This evolutionary strategy highlights an adaptation of telomere biology for metabolic control in extreme environments.
Article
Biochemistry & Molecular Biology
Ran Tian, Kai Han, Yuepan Geng, Chen Yang, Chengcheng Shi, Patrick Thomas, Coral Pearce, Kate Moffatt, Siming Ma, Shixia Xu, Guang Yang, Xuming Zhou, Vadim N. Gladyshev, Xin Liu, Diana O. Fisher, Lisa K. Chopin, Natalia O. Leiner, Andrew M. Baker, Guangyi Fan, Inge Seim
Summary: The 15 species of Antechinus exhibit a rare life-history strategy called semelparity, with males experiencing rapid aging during the breeding season. Genome research on these species provides insights into their genetic characteristics and aging mechanisms, aiding in the conservation of these unique animals.
MOLECULAR ECOLOGY RESOURCES
(2022)
Review
Cell Biology
Bohan Zhang, Alexandre Trapp, Csaba Kerepesi, Vadim N. Gladyshev
Summary: There are interventions proposed to reverse aging rather than just slow it down, but the criteria for achieving rejuvenation are still controversial. A key prerequisite for a rejuvenation intervention is a significant reduction in biological age, which can be assessed by biomarkers such as epigenetic clocks.
Review
Biochemistry & Molecular Biology
Petra A. Tsuji, Didac Santesmasses, Byeong J. Lee, Vadim N. Gladyshev, Dolph L. Hatfield
Summary: Selenium is an essential element in the diet and has many health benefits, such as preventing heart disease and cancer, supporting male reproduction, and boosting the immune system. It plays important roles in the molecular biology of organisms and its incorporation into proteins is a unique feature. Research has focused on selenium's role in cancer prevention and its potential involvement in various diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Artyom A. Egorov, Alexander Alexandrov, Valery N. Urakov, Desislava S. Makeeva, Roman O. Edakin, Artem S. Kushchenko, Vadim N. Gladyshev, Ivan Kulakovskiy, Sergey E. Dmitriev
Summary: The use of the standard G418-resistance cassette for producing knockout mutants in Saccharomyces cerevisiae has potential side effects on neighboring gene expression, affecting transcription efficiency and mRNA translation. Knockout can lead to changes in the transcription start site or alternative polyadenylation signals of neighboring genes, influencing their 5' and 3' UTRs. These events may explain the phenomenon of false genetic interactions due to neighboring gene effects.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Donghyun Kang, Jeeyeon Lee, Jisu Jung, Bradley A. Carlson, Moon Jong Chang, Chong Bum Chang, Seung-Baik Kang, Byung Cheon Lee, Vadim N. Gladyshev, Dolph L. Hatfield, Byeong Jae Lee, Jin-Hong Kim
Summary: Osteoarthritis is caused by the accumulation of oxidative stress. This study reveals that dysregulation of the selenium metabolic pathway disrupts redox homeostasis in chondrocytes, leading to the development of osteoarthritis. The downregulation of SEPHS1 impairs the synthesis of oxidoreductase selenoproteins, increases reactive oxygen species levels, and induces chondrocyte senescence.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Csaba Kerepesi, Margarita Meer, Julia Ablaeva, Vince G. Amoroso, Sang-Goo Lee, Bohan Zhang, Maxim Gerashchenko, Alexandre Trapp, Sun Hee Yim, Ake T. Lu, Morgan E. Levine, Andrei Seluanov, Steve Horvath, Thomas J. Park, Vera Gorbunova, Vadim N. Gladyshev
Summary: The study reveals that naked mole-rats, despite having no increased mortality with age, experience epigenetic aging. By conducting bisulfite sequencing on the blood of over 100 naked mole-rats, researchers observe age-related methylome remodeling and loss of methylome information, indicating the aging process. An epigenetic clock is developed to accurately predict the age of naked mole-rats. These animals age at a much slower rate than mice but faster than humans, consistent with their known maximum lifespans.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Quanwei Zhang, Gregory Tombline, Julia Ablaeva, Lei Zhang, Xuming Zhou, Zachary Smith, Yang Zhao, Alus M. Xiaoli, Zhen Wang, Jhih-Rong Lin, M. Reza Jabalameli, Joydeep Mitra, Nha Nguyen, Jan Vijg, Andrei Seluanov, Vadim N. Gladyshev, Vera Gorbunova, Zhengdong D. Zhang
Summary: The North American beaver has evolved genetic changes that likely contribute to its longevity and cancer resistance, such as enhanced ability to detoxify aldehydes, improved tumor suppression and DNA repair, and alterations in lipid metabolism. Unique gene duplications, positive selection signals, and changes in gene expression are observed in genes associated with tumor suppression and longevity in beavers, along with massive expansion of Aldh1a1 for aldehyde detoxification. These genetic adaptations may play a role in the beavers' longevity.
Article
Biology
Alaattin Kaya, Cheryl Zi Jin Phua, Mitchell Lee, Lu Wang, Alexander Tyshkovskiy, Siming Ma, Benjamin Barre, Weiqiang Liu, Benjamin R. Harrison, Xiaqing Zhao, Xuming Zhou, Brian M. Wasko, Theo K. Bammler, Daniel E. L. Promislow, Matt Kaeberlein, Vadim N. Gladyshev
Summary: This study explored replicative lifespan diversity among diverse wild yeast isolates, identifying genetic networks and novel genes, metabolites, and pathways associated with natural variation in lifespan. Furthermore, it revealed unique adaptations in long-lived strains to interconnected amino acid biosynthesis, glutamate metabolism, and mitochondrial function. Overall, the research demonstrates how gene-environment interactions shape cellular processes involved in phenotypic variation such as lifespan.
Article
Chemistry, Multidisciplinary
Hae Min Lee, Dong Wook Choi, Seahyun Kim, Aro Lee, Minseo Kim, Yeon Jin Roh, Young Ho Jo, Hwa Yeon Cho, Ho-Jae Lee, Seung-Rock Lee, Lionel Tarrago, Vadim N. Gladyshev, Ji Hyung Kim, Byung Cheon Lee
Summary: This study developed a biological sensor, tpMetROG, for quantifying oxidized methionine in target proteins, demonstrating its versatile application in various proteins.
Article
Multidisciplinary Sciences
Lei Zhang, Xiao Dong, Xiao Tian, Moonsook Lee, Julia Ablaeva, Denis Firsanov, Sang-Goo Lee, Alexander Y. Maslov, Vadim N. Gladyshev, Andrei Seluanov, Vera Gorbunova, Jan Vijg
Summary: Long-lived species demonstrate a higher capacity for accurate DNA damage repair, which may help slow down the aging process. The mutagen-induced mutation frequencies are inversely correlated with the maximum life span of different species, with the most significant difference observed between mice and other species.
Article
Cell Biology
Esther Meron, Maria Thaysen, Suzanne Angeli, Adam Antebi, Nir Barzilai, Joseph A. Baur, Simon Bekker-Jensen, Maria Birkisdottir, Evelyne Bischof, Jens Bruening, Anne Brunet, Abigail Buchwalter, Filipe Cabreiro, Shiqing Cai, Brian H. Chen, Maria Ermolaeva, Collin Y. Ewald, Luigi Ferrucci, Maria Carolina Florian, Kristen Fortney, Adam Freund, Anastasia Georgievskaya, Vadim N. Gladyshev, David Glass, Tyler Golato, Vera Gorbunova, Jan Hoejimakers, Riekelt H. Houtkooper, Sibylle Jager, Frank Jaksch, Georges Janssens, Martin Borch Jensen, Matt Kaeberlein, Gerard Karsenty, Peter de Keizer, Brian Kennedy, James L. Kirkland, Michael Kjaer, Guido Kroemer, Kai-Fu Lee, Jean-Marc Lemaitre, David Liaskos, Valter D. Longo, Yu-Xuan Lu, Michael R. MacArthur, Andrea B. Maier, Christina Manakanatas, Sarah J. Mitchell, Alexey Moskalev, Laura Niedernhofer, Ivan Ozerov, Linda Partridge, Emmanuelle Passegue, Michael A. Petr, James Peyer, Dina Radenkovic, Thomas A. Rando, Suresh Rattan, Christian G. Riedel, Lenhard Rudolph, Ruixue Ai, Manuel Serrano, Bjoern Schumacher, David A. Sinclair, Ryan Smith, Yousin Suh, Pam Taub, Alexandre Trapp, Anne-Ulrike Trendelenburg, Dario Riccardo Valenzano, Kris Verburgh, Eric Verdin, Jan Vijg, Rudi G. J. Westendorp, Alessandra Zonari, Daniela Bakula, Alex Zhavoronkov, Morten Scheibye-Knudsen
Summary: Aging is the biggest risk factor for most chronic diseases, attracting attention from industry and investors. This year's ARDD meeting featured presentations from 75 speakers and included a longevity workshop to discuss aging mechanisms and potential modifications.