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)
Article
Biochemistry & Molecular Biology
Clinton A. L. McFeely, Kara K. Dods, Shivam S. Patel, Matthew C. T. Hartman
Summary: Breaking codon degeneracy and introducing non-canonical amino acids offer numerous opportunities in synthetic biology. However, reliance on synthetic tRNAs lacking post-transcriptional modifications has limited the expansion of the genetic code. By developing a new fluorous method for tRNA capture, researchers have demonstrated the superiority of wild-type tRNA over synthetic counterparts in an in vitro translation system. Wild-type tRNAs are therefore enabling reagents for maximizing the reassignment potential of the genetic code.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Genetics & Heredity
Kenji Ikehara
Summary: The correspondence relations between codons and amino acids are determined by the genetic code, which is crucial for the life system composed of genes and proteins. This article discusses the origin and evolution of the genetic code, proposing the GNC-SNS primitive genetic code hypothesis. It explores the selection of four [GADV]-amino acids and four GNCs in the first genetic code, as well as the establishment of correspondence relations between them. The comprehensive analysis integrates theories on frozen-accident, coevolution, and adaptation to explain the origin of the genetic code.
Article
Chemistry, Multidisciplinary
Xue-Yuan Wu, Meng-Yin Li, Shao-Jun Yang, Jie Jiang, Yi-Lun Ying, Peng R. Chen, Yi-Tao Long
Summary: Conventional methods for protein nanopore engineering are limited by the 20 natural amino acids, which restricts the diversity of nanopores. To overcome this, we used the genetic code expansion technique to incorporate unnatural amino acids into aerolysin nanopores. Molecular dynamics simulations and single-molecule sensing experiments showed that the newly incorporated amino acids provided a favorable environment for target molecule interactions. This work provides a new framework for creating nanopores with unique sensing properties.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
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)
Review
Biochemistry & Molecular Biology
Olubodun Michael Lateef, Michael Olawale Akintubosun, Olamide Tosin Olaoba, Sunday Ocholi Samson, Malgorzata Adamczyk
Summary: The evolution of RNA translation process has been continued through synthetic biology, known as rational bioengineering, which enhances the properties and functionality of proteins. Genetic code expansion allows the incorporation of noncanonical amino acids (ncAAs) into proteins, increasing the range of applications. However, mediating factors reduce the efficiency of ncAA incorporation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(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
Riley M. Bednar, Subhashis Jana, Sahiti Kuppa, Rachel Franklin, Joseph Beckman, Edwin Antony, Richard B. Cooley, Ryan A. Mehl
Summary: The study presents a novel strategy named dual encoding and labeling (DEAL) for site-specific modification of proteins in vivo, enabling detailed investigation of protein function inside cells. This approach allows for multiple labeling reactions to occur simultaneously within a single protein, expanding the possibilities for protein engineering and characterization.
ACS CHEMICAL BIOLOGY
(2021)
Article
Mathematical & Computational Biology
Dino G. Salinas
Summary: This study provides a theoretical framework for evaluating the functional code robustness of genetic codes through calculating statistical parameters. By analyzing the error function distribution of completely random codes, general expressions for the average and standard deviation were obtained. These results can be used to discuss the advantages of natural selection in the creation of genetic codes.
ACTA BIOTHEORETICA
(2022)
Article
Biochemistry & Molecular Biology
Takuto Furuhashi, Kensaku Sakamoto, Akira Wada
Summary: This study developed a ribosome display technique for selecting peptide epitopes bound to monoclonal antibodies. By using genetic code expansion and photo-cross-linking reactions, low-affinity peptide epitopes can be efficiently identified. The results of this study contribute to the advancement of diverse peptide-based research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Nicole Hugouvieux-Cotte-Pattat, Monique Royer, Erwan Gueguen, Paul Le Guen, Roderich D. Suessmuth, Sylvie Reverchon, Stephane Cociancich
Summary: The Vfm quorum sensing system is important for the virulence of Dickeya bacteria, with a strain-specific polymorphism in the biosynthesis genes vfmO and vfmP potentially leading to the production of different analogues of the QS signal.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biology
E. Fimmel, M. Gumbel, M. Starman, L. Struengmann
Summary: Many theories suggest genetic code has always evolved to increase supply of amino acids encoded, with control mechanisms to prevent non-functional proteins. Efforts to expand genetic codes are relevant in biotechnology such as drug synthesis, and research on optimizing genetic codes for robustness is ongoing. Incorporating single point mutation weights into models can enhance understanding of genetic code robustness and potential for encoding new amino acids.
Article
Biochemistry & Molecular Biology
Juan C. C. Fontecilla-Camps
Summary: Examination of the genetic code reveals that amino acids coded by (A/U) codons have a wide range of functions and bind RNA, while those coded by (G/C) codons, except for Arg, do not. The preference for (A/U)-rich codons to be located at the GeCo half blocks suggests their specific determination. The lower affinity of cognate amino acids for their (G/C)-rich anticodons points to their late arrival to the GeCo. It is proposed that initially the code was composed of eight (A/U) codons, which were duplicated when G/C nucleotides were added to their wobble positions, and three new codons with G/C in their first position were incorporated. A combination of A/U and G/C nucleotides progressively generated the remaining codons.
Article
Multidisciplinary Sciences
Haruka Tsutsumi, Tomohiro Kuroda, Hiroyuki Kimura, Yuki Goto, Hiroaki Suga
Summary: Azoles are five-membered heterocycles found in peptidic natural products and synthetic peptiodomimetics. Here the authors demonstrate a posttranslational chemical modification method for in vitro ribosomal synthesis of peptides with exotic azole groups at specific positions.
NATURE COMMUNICATIONS
(2021)
Review
Chemistry, Multidisciplinary
Yuki Goto, Hiroaki Suga
Summary: The RaPID system has enabled rapid discovery of novel macrocyclic peptides with high affinity and specificity, suitable for various biochemical applications and drug development. The integration of the FIT system with mRNA display technology has expanded the structural diversity of peptides and allowed for the incorporation of exotic building blocks. The potential of these peptides as drug leads is demonstrated by their pharmacological activities in animal models and inhibition of intracellular proteins.
ACCOUNTS OF CHEMICAL RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Alexander A. Vinogradov, Masanobu Nagano, Yuki Goto, Hiroaki Suga
Summary: The study reports two strategies for direct access to diverse ED substrates, revealing that EDs are uniquely promiscuous enzymes capable of performing retro-Michael reaction and engaging in nonspecific hydrophobic interactions with substrates.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Alexander A. Vinogradov, Jun Shi Chang, Hiroyasu Onaka, Yuki Goto, Hiroaki Suga
Summary: This study reports an integrated platform for accurate profiling of substrate preferences for PTM enzymes. The platform combines mRNA display with next-generation sequencing for high-throughput data acquisition and utilizes deep learning for data analysis. The constructed deep learning models enable comprehensive analysis of enzymatic substrate preferences, quantification of fitness across sequence space, mapping of modification sites, and identification of important amino acids in the substrate. The study demonstrates the complexity of enzymatic preferences and highlights the potential of the developed platform for wider studies of PTM enzymes.
ACS CENTRAL SCIENCE
(2022)
Article
Biology
Taishi Kondo, Kazuhiro Matsuoka, Shun Umemoto, Tomoshige Fujino, Gosuke Hayashi, Yasumasa Iwatani, Hiroshi Murakami
Summary: In this study, affinity maturation of monobodies against SARS-CoV-2 spike protein and their neutralizing activity against several variants were reported. One monobody showed extremely high affinity and efficiently neutralized multiple variants. These monobodies could be useful for neutralizing current and future SARS-CoV-2 variants.
LIFE SCIENCE ALLIANCE
(2022)
Article
Chemistry, Multidisciplinary
Koki Nakatsu, Akimitsu Okamoto, Gosuke Hayashi, Hiroshi Murakami
Summary: This article reports a novel one-pot multi-segments ligation strategy using a specific formaldehyde scavenger to efficiently synthesize proteins by changing the pH values. By this method, mono-ubiquitinated histone H2A.Z was successfully synthesized.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Physical
Yuchen Zhang, Keisuke Hamada, Dinh Thanh Nguyen, Sumika Inoue, Masayuki Satake, Shunsuke Kobayashi, Chikako Okada, Kazuhiro Ogata, Masahiro Okada, Toru Sengoku, Yuki Goto, Hiroaki Suga
Summary: This study reports a new prenyltransferase, LimF, which geranylates the electron-deficient C2 atom of His imidazole and modifies diverse exotic peptides. Crystallographic analysis provides structural insights into the bifunctionality of LimF and its recognition of substrates. Moreover, the study shows the prenylation ability of LimF on various bioactive molecules containing an imidazole group.
Article
Chemistry, Multidisciplinary
Alexander A. Vinogradov, Yue Zhang, Keisuke Hamada, Jun Shi Chang, Chikako Okada, Hirotaka Nishimura, Naohiro Terasaka, Yuki Goto, Kazuhiro Ogata, Toru Sengoku, Hiroyasu Onaka, Hiroaki Suga
Summary: This study presents a new bioengineering approach for discovering pseudo-natural thiopeptides with favorable pharmacological properties, which was successfully utilized in affinity selection against TNIK kinase, resulting in the discovery of multiple candidate thiopeptides.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Tomohiro Kuroda, Yichao Huang, Soichiro Nishio, Yuki Goto, Hiroaki Suga
Summary: This study reports a new method for the in vitro synthesis of natural-product-like peptides bearing Hhc units. The method incorporates azide/hydroxy acids into the nascent peptide chain through genetic code reprogramming, allowing for the one-pot ribosomal synthesis of designer macrocycles with various Hhc units.
Article
Chemistry, Organic
Yue Zhang, Alexander A. Vinogradov, Jun Shi Chang, Yuki Goto, Hiroaki Suga
Summary: This article presents a strategy for synthesizing novel lactazole-like thiopeptides, including the preparation of central triheterocyclic amino acid and its use in solid-phase peptide synthesis, as well as a technique for preparing C-terminally functionalized thiopeptides for biological studies. The synthesis of 11 TNIK-inhibitor thiopeptides and 6 derivatives highlights the practicality of the developed protocols.
Article
Chemistry, Multidisciplinary
Takahiro Ono, Kazuhito V. Tabata, Yuki Goto, Yutaro Saito, Hiroaki Suga, Hiroyuki Noji, Jumpei Morimoto, Shinsuke Sando
Summary: Cyclic peptides that passively penetrate cell membranes are being actively researched in drug discovery. Common methods like PAMPA and Caco-2 assay have limitations in accurately measuring their permeability. A new lipid bilayer permeability assay was developed for label-free measurements of cyclic peptide permeability.
Article
Biochemistry & Molecular Biology
Sae Suzuki, Yuya Nakajima, Naoki Kamo, Akihisa Osakabe, Akimitsu Okamoto, Gosuke Hayashi, Hiroshi Murakami
Summary: This paper reports the use of thiocholine as a thiol catalyst in chemical protein synthesis. Thiocholine was found to be useful for NCL-based peptide ligation and metal-free desulfurization, with comparable efficiency to other alkyl thioesters. Importantly, thiocholine showed better reactivity as a thiol additive in desulfurization. The successful synthesis of two differently methylated histone H3 proteins was achieved via one-pot NCL and desulfurization with thiocholine.
Article
Chemistry, Multidisciplinary
Yuchen Zhang, Keisuke Hamada, Masayuki Satake, Toru Sengoku, Yuki Goto, Hiroaki Suga
Summary: Prenyltransferases in cyanobactin biosynthesis have been engineered to modify their prenylation modes, leading to the discovery of a novel farnesylation mode. The understanding of essential residues for farnesyl-binding pocket construction has allowed for the rational design of additional peptide alkylation biocatalysts.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Shun Umemoto, Taishi Kondo, Tomoshige Fujino, Gosuke Hayashi, Hiroshi Murakami
Summary: Extremely diverse libraries are essential for the selection of functional peptides or proteins, and mRNA display technology is a powerful tool for generating such libraries. The study examines the impact of mRNA sequences on protein/mRNA complex formation yield and demonstrates that N-terminal and C-terminal coding sequences have a significant influence. By utilizing specific C-terminal coding sequences, highly diverse libraries of monobodies and macrocyclic peptides were constructed. This research provides insights into the relationship between mRNA sequences and complex formation yield, facilitating the identification of functional peptides and proteins with therapeutic applications.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Taishi Kondo, Minori Eguchi, Seita Kito, Tomoshige Fujino, Gosuke Hayashi, Hiroshi Murakami
Summary: Researchers developed a cDNA TRAP display for rapid selection of antibody-like proteins in various conditions. By modifying the original puromycin linker, a monobody was covalently attached to the cDNA, and a proof-of-concept was demonstrated with the selection of an anti-EGFR1 monobody in a solution containing ribonuclease.
CHEMICAL COMMUNICATIONS
(2021)
