Article
Biochemistry & Molecular Biology
Bandigi Narsimulu, Rahila Qureshi, Pranay Jakkula, Priti Singh, Mohammed Arifuddin, Insaf Ahmed Qureshi
Summary: In this study, the authors purified and characterized seryl tRNA synthetase (LdSerRS) and its mutants in Leishmania donovani. The purified LdSerRS showed high enzymatic activity and a higher content of alpha helices in secondary structure. A mutation in the ATP binding residues resulted in a reduced affinity for cofactor without significant alteration in secondary structure. The researchers identified Comp 5l as a specific inhibitor for leishmanial SerRS, which showed low potency towards purified HsSerRS. Structural analysis revealed the binding of Comp 5l into the cofactor binding site of LdSerRS with high affinity. The study provides a promising approach for developing specific therapeutics targeting leishmanial SerRS.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemical Research Methods
Qunfeng Zhang, Wenlong Zheng, Zhongdi Song, Qiang Zhang, Lirong Yang, Jianping Wu, Jianping Lin, Gang Xu, Haoran Yu
Summary: This study developed machine learning models to predict the substrate specificity of PylRS for novel NCAAs. The models showed high accuracy and provided a framework for expanding the substrate scope of PylRS variants and developing machine learning models for other PylRS variants.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Han-Kai Jiang, Nicole L. Ambrose, Christina Z. Chung, Yane-Shih Wang, Dieter Soll, Jeffery M. Tharp
Summary: Synthetic biology tools have been developed to control gene expression at the transcription level, but few methods exist for regulating gene expression at the translational level. In this study, split orthogonal aminoacyl-tRNA synthetases (o-aaRS) were designed to control gene translation in bacteria and mammalian cells. These split o-aaRSs function as genetically encoded AND gates, where stop codon suppression is controlled by two distinct molecular inputs. Additionally, they can be used as versatile biosensors to detect protein-protein interactions involved in cancer and SARS-CoV-2 infection.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Ya Chun Yu, Jung Min Han, Sunghoon Kim
Summary: Aminoacyl-tRNA synthetases play essential roles in protein synthesis and recent studies have revealed their previously unknown biological functions beyond catalytic roles. Sensing intracellular nutrients is crucial for cell physiology, and certain types of ARSs may be involved in sensing and signaling their cognate amino acids within cells.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
(2021)
Article
Microbiology
Zhiwei Gan, Xueping Zhang, Mengke Li, Xing Li, Xinlei Zhang, Chenkai Wang, Yazhong Xiao, Juanjuan Liu, Zemin Fang
Summary: In this study, a seryl-tRNA synthetase, ThserRS, was identified as a negative regulator of laccase lacA transcription in Trametes hirsuta AH28-2 under exposure to copper ion. ThserRS was shown to bind to the promoter of lacA and decrease its transcription and LacA activity.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemistry & Molecular Biology
Valentina Evic, Ruzica Soic, Marko Mocibob, Mario Kekez, Josef Houser, Michaela Wimmerova, Dubravka Matkovic-Calogovic, Ita Gruic-Sovulj, Ivana Kekez, Jasmina Rokov-Plavec
Summary: A unique disulfide bond involving cysteines that are conserved in all green plants has been identified in the crystal structure of Arabidopsis cytosolic seryl-tRNA synthetase. Both cysteines are important for protein stability, but with opposite effects, and their microenvironment may promote disulfide bond formation under oxidizing conditions. The presence of the disulfide bond may enable the protein to function under oxidative stress conditions, benefiting efficient plant stress response.
Article
Biochemistry & Molecular Biology
Haolin Zhang, Xuemei Gong, Qianqian Zhao, Takahito Mukai, Oscar Vargas-Rodriguez, Huiming Zhang, Yuxing Zhang, Paul Wassel, Kazuaki Amikura, Julie Maupin-Furlow, Yan Ren, Xun Xu, Yuri Wolf, Kira S. Makarova, Eugene Koonin, Yue Shen, Dieter Soll, Xian Fu
Summary: This study identified two mutually orthogonal PyIRS/tRNA(Pyl) pairs in a halophilic methanogen,and demonstrated that they can simultaneously decode different codons for the incorporation of distinct non-canonical amino acids.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biophysics
Xue Sun, Qinggang Li, Yu Wang, Wenjuan Zhou, Yanmei Guo, Jiuzhou Chen, Ping Zheng, Jibin Sun, Yanhe Ma
Summary: In this study, a new strategy for constructing whole-cell biosensors based on aminoacyl-tRNA synthetases (aaRSs) was proposed. By engineering aaRSs, the biosensors showed specificity and potential for developing sensors for various amino acids.
BIOSENSORS & BIOELECTRONICS
(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
Takumi Yokosawa, Keisuke Wakasugi
Summary: The study shows that Trp-deficient condition is critical for Trp uptake, not only in cells with added TrpRS protein but also in TrpRS-overexpressing cells. Tryptophanyl-AMP production by TrpRS is essential for high-affinity Trp uptake.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Hongjia Liu, Xue Gong, Hui Deng, Jinjuan Tan, Yanqing Sun, Fang Wang, Wenjuan Wu, Zhongjing Zhou, Rumeng Xu, Haiyan He, Clive Lo
Summary: Aminoacyl tRNA synthetases play a crucial role in protein translation by attaching specific amino acids to tRNAs. However, their functions in regulating plant growth and development are still not well understood. In this study, we identified a rice mutant, ylc3, which exhibited reduced chlorophyll content, altered thylakoid structure, and increased levels of certain amino acids under low temperature conditions. We found that YLC3 encodes an aspartyl-tRNA synthetase localized in the cytosol and mitochondria. Proteomics analysis revealed that thylakoid proteins were down-regulated in the mutant, while proteins involved in amino acid metabolism and protein synthesis were up-regulated, particularly key enzymes that convert aspartate to asparagine. Furthermore, we observed accumulation of uncharged tRNA-Asp and phosphorylation of the translation initiation factor eIF2 alpha in the mutant, suggesting that YLC3 regulates amino acid metabolism and chloroplast thylakoid development through modulation of protein synthesis.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Kommireddy Vasu, Iyappan Ramachandiran, Fulvia Terenzi, Debjit Khan, Arnab China, Krishnendu Khan, Aayushi Chechi, Camelia Baleanu-Gogonea, Valentin Gogonea, Paul L. Fox
Summary: The study reveals the critical role of the ZBD in determining the activity of ProRS and the stability of GluProRS, with disruptions of the ZBD leading to a reduction in GluProRS canonical function.
Article
Biochemistry & Molecular Biology
Jin-Tao Wang, Jing-Bo Zhou, Xue-Ling Mao, Li Zhou, Meirong Chen, Wenhua Zhang, En-Duo Wang, Xiao-Long Zhou
Summary: This study reveals the crucial role of t(6)A modification in tRNA(Ile) aminoacylation and codon decoding, as well as the commonality and diversity in substrate recognition by eukaryotic KEOPS.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Zhongqiang Wang, Hayden Matthews, Guozhong Deng, Xiaojian Zhou, Yongzheng Chen
Summary: Using thermodynamic techniques, it was found that the non-proteinogenic amino acids m-fluorotyrosine and 2,4-dihydroxyphenylalanine exhibited higher binding affinity to the tyrosyl-tRNA synthetase from Escherichia coli than to that from human cytosol.
AUSTRALIAN JOURNAL OF CHEMISTRY
(2021)
Article
Microbiology
Takahito Mukai, Ana Crnkovic, Takuya Umehara, Natalia N. Ivanova, Nikos C. Kyrpides, Dieter Soll
Article
Biochemistry & Molecular Biology
Ana Crnkovic, Mirela Cavuzic, Vlatka Godinic-Mikulcic, Gregor Anderluh, Ivana Weygand-Durasevic, Ita Gruic-Sovulj
Review
Biochemistry & Molecular Biology
Oscar Vargas-Rodriguez, Anastasia Sevostyanova, Dieter Soll, Ana Crnkovic
CURRENT OPINION IN CHEMICAL BIOLOGY
(2018)
Article
Biochemistry & Molecular Biology
Xian Fu, Ana Crnkovic, Anastasia Sevostyanova, Dieter Soll
Review
Genetics & Heredity
Kyle S. Hoffman, Ana Crnkovic, Dieter Soll
Review
Biochemistry & Molecular Biology
Ana Crnkovic, Oscar Vargas-Rodriguez, Dieter Soell
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2019)
Review
Biology
Ana Crnkovic, Marija Srnko, Gregor Anderluh
Summary: Nanopore-based sensing is a powerful technique that allows for the detection of diverse molecules, sequencing of nucleic acids, and analysis of enzymatic reactions. Protein-based nanopores selected from natural sources offer rapid, label-free detection and are easily produced and manipulated with standard techniques. The range of analytes can be expanded by using externally added adapter molecules.
Article
Biochemistry & Molecular Biology
Christina Z. Chung, Natalie Krahn, Ana Crnkovic, Dieter Soll
Summary: The presence of selenocysteine in a protein provides unique properties and makes the production of recombinant selenoproteins desirable. This study presents a versatile strategy using intein-containing reporters to screen for evolved components of a translation system yielding increased selenoprotein amounts. The results obtained with intein-containing reporters are comparable to the Sec incorporation levels determined by mass spectrometry.
JOURNAL OF MOLECULAR BIOLOGY
(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
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)
Article
Biochemistry & Molecular Biology
Arjun Prabhakar, Natalie Krahn, Jingji Zhang, Oscar Vargas-Rodriguez, Miri Krupkin, Ziao Fu, Francisco J. Acosta-Reyes, Xueliang Ge, Junhong Choi, Ana Crnkovic, Mans Ehrenberg, Elisabetta Viani Puglisi, Dieter Soll, Joseph Puglisi
Summary: Ribosomes are flexible in accepting diverse aminoacyl-tRNA substrates, which is critical for using orthogonal translation systems for genetic code expansion. In this study, the researchers investigated the translation of allo-tRNA(UTu1) on the ribosome and identified a tertiary interaction preventing translocation. By disrupting this interaction through a single-nucleotide mutation, they relieved the translation roadblock and optimized translation.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Biology
Bjoern M. von Reumont, Gregor Anderluh, Agostinho Antunes, Naira Ayvazyan, Dimitris Beis, Figen Caliskan, Ana Crnkovic, Maik Damm, Sebastien Dutertre, Lars Ellgaard, Goran Gajski, Hannah German, Beata Halassy, Benjamin-Florian Hempel, Tim Hucho, Nasit Igci, Maria P. Ikonomopoulou, Izhar Karbat, Maria Klapa, Ivan Koludarov, Jeroen Kool, Tim Lueddecke, Riadh Ben Mansour, Maria Vittoria Modica, Yehu Moran, Ayse Nalbantsoy, Maria Eugenia Pachon Ibanez, Alexios Panagiotopoulos, Eitan Reuveny, Javier Sanchez Cespedes, Andy Sombke, Joachim M. Surm, Eivind A. B. Undheim, Aida Verdes, Giulia Zancolli
Summary: Venoms have evolved multiple times in different animal groups, with their components known as toxins being highly effective biochemical weapons. However, there are still many unanswered questions regarding the evolution of venom arsenals, and these questions have received little attention outside of certain animal groups. The study of venomous animals and their toxins has provided inspiration for translational research, and recent technological advancements have greatly improved venom research. Understanding the genomics and modifications of toxins is important in understanding their evolution and functions during different stages of development. Advanced imaging techniques and computer tomography also provide insights into the distribution and function of toxins in the venom system. The knowledge gained from studying venomous animals contributes to the identification and synthesis of venom compounds, which have potential benefits in various fields such as agriculture, pharmaceuticals, therapeutics, and diagnostics.
Meeting Abstract
Biochemistry & Molecular Biology
A. Crnkovic, G. Solinc, M. Srnko, M. Podobnik, G. Anderluh
Review
Biochemistry & Molecular Biology
Noah M. Reynolds, Oscar Vargas-Rodriguez, Dieter Soll, Ana Crnkovic
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2017)
Article
Biology
Takahito Mukai, Noah M. Reynolds, Ana Crnkovic, Dieter Soell