Review
Physiology
Natalie Krahn, Dieter Soell, Oscar Vargas-Rodriguez
Summary: The evolution of aminoacyl-tRNA synthetase (aaRS) families is complex and has led to the emergence of unique characteristics and aaRS-like proteins. Recent studies have revealed widespread aaRS gene duplication and phylogenetic diversity, but only a fraction of these duplications have been characterized. Investigation of unexplored aaRS genomic duplications may uncover exciting biological processes, new drug targets, important bioactive molecules, and tools for synthetic biology applications.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Multidisciplinary Sciences
Oscar Vargas-Rodriguez, Ahmed H. Badran, Kyle S. Hoffman, Manyun Chen, Ana Crnkovi, Yousong Ding, Jonathan R. Krieger, Eric Westhof, Dieter Soll, Sergey Melnikov
Summary: Misincorporation of amino acids due to mistranslation is an emerging paradigm in microbial studies, with many pathogens deliberately altering their genetic code to aid in invasion or immune evasion. This study identifies a unique tRNA synthetase/tRNA pair in plant pathogens that allows for the mistranslation of specific codons, leading to the creation of a hidden proteome diversity. This finding highlights the mechanism by which important plant pathogens can alter the identity of their sense codons for their benefit.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemical Research Methods
Jessica T. Stieglitz, James A. Van Deventer
Summary: This study developed a yeast display-based platform to screen for previously undiscovered variants of aminoacyl-tRNA synthetases (aaRSs). The findings expand the options for genetic code manipulation in yeast and have important implications for the fundamental properties and evolvability of aaRSs. Access to diverse orthogonal translation systems is invaluable for applications in chemical biology, synthetic biology, and protein engineering.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemical Research Methods
Jessica T. Stieglitz, James A. Van Deventer
Summary: Protein expression with genetically encoded noncanonical amino acids (ncAAs) has various applications, but the lack of orthogonal translation systems (OTSs) limits their use. This study uses yeast display and flow cytometry to screen libraries of aaRSs for incorporating new ncAAs, improving existing aaRSs, and creating highly selective OTSs. The discovery of previously unknown aaRS variants significantly increases the available options for genetic code manipulation in yeast.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jessica M. Warren, Amanda K. Broz, Ana Martinez-Hottovy, Christian Elowsky, Alan C. Christensen, Daniel B. Sloan
Summary: The number of tRNAs encoded in plant mitochondrial genomes varies considerably. The loss of bacterial-like mitochondrial tRNA genes necessitates the import of nuclear-encoded counterparts with little sequence similarity. The evolution of aaRS subcellular localization in Sileneae reveals differing constraints on tRNA/aaRS interactions and alternative coevolutionary paths for maintaining organellar translation in plant cells.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Erika A. DeBenedictis, Gavriela D. Carver, Christina Z. Chung, Dieter Soll, Ahmed H. Badran
Summary: The authors demonstrate the discovery and evolution of quadruplet-decoding tRNAs, enabling four independent decoding events in a single protein in living cells. By developing a new evolution strategy, they significantly improve the translation efficiency of quadruplet codons and showcase the multiplexed decoding of up to four unique quadruplet codons in a protein.
NATURE COMMUNICATIONS
(2021)
Letter
Immunology
Yoshinao Muro, Yuta Yamashita, Haruka Koizumi, Mariko Ogawa-Momohara, Takuya Takeichi, Teruyuki Mitsuma, Masashi Akiyama
Summary: Anti-aminoacyl-tRNA synthetase (anti-ARS) antibodies are helpful in identifying inflammatory myopathy patients. In a study with Japanese patients, autoantibodies against CysARS and ValARS were found in the serum of two dermatomyositis patients. One patient showed features of anti-synthetase syndrome, while the other did not. Further research is needed to explore the clinical differences among different anti-ARS antibodies.
AUTOIMMUNITY REVIEWS
(2022)
Article
Oncology
Krishnendu Khan, Valentin Gogonea, Paul L. Fox
Summary: Aminoacyl-tRNA synthetases (AARS) are important enzymes in mammalian cells that play a key role in protein translation. Recent studies have found that they exist in the cytoplasmic multi-tRNA synthetase complex (MSC) and have non-canonical functions in addition to their role in protein translation. These findings have the potential to be new therapeutic targets for cancer and other diseases.
TRANSLATIONAL ONCOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Siqi Wu, Li Zheng, Zhoufei Hei, Jing-Bo Zhou, Guang Li, Peifeng Li, Jiayuan Wang, Hamid Ali, Xiao-Long Zhou, Jing Wang, Pengfei Fang
Summary: The structures of human Lysyl-tRNA synthetases (LysRSs) are more dynamic than those from single-celled organisms. Without the presence of MSC scaffold proteins, human LysRS can exist independently from the multi-tRNA synthetase complex (MSC). The interaction with the scaffold protein AIMP2 stabilizes the closed conformation of LysRS and protects its essential aminoacylation activity under stressed conditions. Deleting AIMP2 from human cells leads to slow cell growth in nutrient deficient mediums. These results suggest that the evolutionary emergence of the MSC in metazoan might be to protect the aminoacyl-tRNA synthetase components from being modified or recruited for use in other cellular pathways.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Review
Genetics & Heredity
Tamara L. Hendrickson, Whitney N. Wood, Udumbara M. Rathnayake
Summary: The selection of the twenty amino acids in the standard genetic code and the fixation of aminoacyl-tRNA synthetases (aaRSs) before LUCA were influenced by the chemical reactivity of amino acid side chains. Some amino acid properties delayed or prohibited the emergence of corresponding aaRSs, playing critical roles in defining the amino acids in the genetic code.
Article
Multidisciplinary Sciences
Krishnendu Khan, Briana Long, Valentin Gogonea, Gauravi M. Deshpande, Kommireddy Vasu, Paul L. Fox
Summary: Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes in the translation process that ligate amino acids to their corresponding transfer RNAs (tRNAs). In mammalian cells, these enzymes, along with AIMPs proteins, form a large multi-tRNA synthetase complex (MSC), whose assembly mechanism and function are still unclear. This study reveals the importance of cotranslational interactions, particularly involving AIMPs proteins, in the assembly process of the MSC. Interestingly, these cotranslational interactions sometimes involve more than two proteins, suggesting a diverse pathway for the ordered assembly of small subcomplexes into larger complexes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Immunology
Angeles S. Galindo-Feria, Antonella Notarnicola, Ingrid E. Lundberg, Begum Horuluoglu
Summary: Anti-synthetase syndrome is an autoimmune disease characterized by the presence of autoantibodies targeting aminoacyl t-RNA synthetases along with various clinical features. This review summarizes the functions of aaRSs, their autoantigenic properties, and their association with ASSD.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Swadha Gupta, Jaykumar Jani, Jigneshkumar Vijayasurya, Jigneshkumar Mochi, Saba Tabasum, Akash Sabarwal, Anju Pappachan
Summary: Aminoacyl-tRNA synthetases (AaRSs) play essential roles in translating genetic information and have diverse functions in cellular activities such as transcription, apoptosis, angiogenesis, inflammation, and cancer. Their multifunctionality suggests their potential as therapeutic targets.
Article
Genetics & Heredity
Takahito Mukai, Kazuaki Amikura, Xian Fu, Dieter Soell, Ana Crnkovic
Summary: This study provides a comprehensive bioinformatic analysis of the diversity of indirect cysteine encoding systems. The results shed new light on the variations in SepRS and SepCysS enzymes, adaptation to lifestyle and habitat, and provide new information on the evolution of the genetic code.
FRONTIERS IN GENETICS
(2022)
Review
Biochemistry & Molecular Biology
Sooin Kim, Hanbin Yi, Yurie T. Kim, Hyun Soo Lee
Summary: The expansion of the genetic code in synthetic biology has been a fascinating area of research. In the past two decades, significant progress has been made in engineering various components involved in protein synthesis, such as tRNA/aminoacyl-tRNA synthetase, new codons, ribosomes, and elongation factor Tu. Efforts to improve the technology of genetic code expansion have also been made through the biosynthesis and enhanced uptake of non-canonical amino acids.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Adit Naor, Neta Altman-Price, Shannon M. Soucy, Anna G. Green, Yulia Mitiagin, Israela Turgeman-Grott, Noam Davidovich, Johann Peter Gogarten, Uri Gophna
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2016)
Article
Microbiology
Samantha M. Gromek, Andrea M. Suria, Matthew S. Fullmer, Jillian L. Garcia, Johann Peter Gogarten, Spencer V. Nyholm, Marcy J. Balunas
FRONTIERS IN MICROBIOLOGY
(2016)
Article
Biochemistry & Molecular Biology
Amanda A. Dick, Timothy J. Harlow, J. Peter Gogarten
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2017)
Review
Biochemistry & Molecular Biology
Seila Omer, Timothy J. Harlow, Johann Peter Gogarten
TRENDS IN MICROBIOLOGY
(2017)
Article
Ecology
Jan F. Gogarten, T. Jonathan Davies, Jacquelynn Benjamino, J. Peter Gogarten, Joerg Grar, Alexander Mielke, Roger Mundry, Michael C. Nelson, Roman M. Wittig, Fabian H. Leendertz, Sebastien Calvignac-Spencer
Article
Genetics & Heredity
Matthew S. Fullmer, Matthew Ouellette, Artemis S. Louyakis, R. Thane Papke, Johann Peter Gogarten
Article
Multidisciplinary Sciences
Luiz Thiberio Rangel, Jeremiah Marden, Sophie Colston, Joao Carlos Setubal, Joerg Graf, Johann Peter Gogarten
Article
Microbiology
Mikhail G. Pyatibratov, Alexey S. Syutkin, Tessa E. F. Quax, Tatjana N. Melnik, R. Thane Papke, Johann Peter Gogarten, Igor I. Kireev, Alexey K. Surin, Sergei N. Beznosov, Anna V. Galeva, Oleg V. Fedorov
Article
Biochemistry & Molecular Biology
Lina Kloub, Sean Gosselin, Matthew Fullmer, Joerg Graf, Johann Peter Gogarten, Mukul S. Bansal
Summary: Horizontal gene transfer (HGT) is crucial for prokaryotic evolution, yet little is known about the scale of individual HGT events. A computational framework called HoMer is introduced to infer single-gene HGT events and potential multiple-gene transfers, aiding a better understanding of HGT and microbial evolution on a larger scale through systematic inference of HMGTs.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Evolutionary Biology
Yutian Feng, Uri Neri, Sean Gosselin, Artemis S. Louyakis, R. Thane Papke, Uri Gophna, Johann Peter Gogarten
Summary: Interest and controversy surrounding the evolutionary origins of extremely halophilic Archaea have increased due to the discovery of Nanohaloarchaea and Methanonatronarchaeia. Recent analyses show a shift in evolutionary placement of these groups, with Nanohaloarchaea outside of euryarchaeota and Methanonatronarchaeia near the base of Methanotecta. The study provides a robust taxonomic sampling and phylogenomic data to resolve conflicts and evaluate the monophyly of DPANN.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Evolutionary Biology
Luiz Thiberio Rangel, Shannon M. Soucy, Joao C. Setubal, Johann Peter Gogarten, Gregory P. Fournier
Summary: I-ES is a method for assessing shared evolution between gene families using a weighted orthogonal distance regression model applied to sequence distances, avoiding comparisons between gene tree topologies. It allows for many-to-many pairing of similarly evolving gene families and shows comparable accuracy to popular tree-based methods on simulated gene family data sets.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Evolutionary Biology
Sean Gosselin, Matthew S. Fullmer, Yutian Feng, Johann Peter Gogarten
Summary: Whole-genome comparisons based on average nucleotide identities and the genome-to-genome distance calculator have become important tools for rapidly classifying prokaryotic taxa. However, applying these methods to higher taxonomic units and phylogenetic inference has been challenging. Researchers propose a novel method that combines ANI and alignment fraction-based metrics to construct statistically supported phylogenies for archaeal and bacterial groups.
SYSTEMATIC BIOLOGY
(2022)
Review
Ecology
Isaiah Paolo A. Lee, Omar Tonsi Eldakar, J. Peter Gogarten, Cheryl P. Andam
Summary: Cooperation exists at all levels of biological organization, with bacteria cooperating by secreting beneficial molecules for the whole population. Recent findings show that mobile genetic elements promote bacterial cooperation through horizontal gene transfer (HGT), and cooperation can facilitate more frequent HGT. HGT itself can be considered as a form of cooperation and serves as an important enforcement mechanism in bacterial populations.
TRENDS IN ECOLOGY & EVOLUTION
(2022)
Article
Genetics & Heredity
Sophia P. Gosselin, Danielle R. Arsenault, Catherine A. Jennings, Johann Peter Gogarten
Summary: In this study, we discovered a protein family of methylases in actinophages that contains a putative intein and two unique insertion elements. We found that the distribution of these methylases is not conserved within phage clusters and varies across divergent phage groups. Furthermore, we observed evidence of long-distance horizontal gene transfer events involving the intein and ShiLan domain in the dispersed distribution of methylases.
Article
Microbiology
Yutian Feng, Artemis S. Louyakis, Andrea M. Makkay, Ray O. Guerrero, R. Thane Papke, J. Peter Gogarten
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2019)