Article
Microbiology
Rodrigo Campos-Silva, Gaetano D'Urso, Olivier Delalande, Emmanuel Giudice, Alexandre Jose Macedo, Reynald Gillet
Summary: Finding new antibiotics is crucial due to increasing multidrug resistance in microorganisms. Translation is a fundamental process that uses a significant amount of cellular energy, and the ribosome is a major target for antibiotics. Trans-translation is a quality control mechanism in bacteria that solves the problem of ribosomal stalling.
Article
Biochemistry & Molecular Biology
Gaetano D'Urso, Charlotte Guyomar, Sophie Chat, Emmanuel Giudice, Reynald Gillet
Summary: The bacterial trans-translation quality control system is responsible for rescuing stalled ribosomes on mRNA lacking a stop codon. This system involves the synergistic action of two partners, tmRNA and SmpB, to monitor and intervene in protein synthesis.
Article
Biochemistry & Molecular Biology
Marion Thepaut, Rodrigo Campos-Silva, Eva Renard, Frederique Barloy-Hubler, Eric Ennifar, Daniel Boujard, Reynald Gillet
Summary: Trans-translation is a major quality control system in bacteria for rescuing stalled ribosomes and is a promising target for novel antibiotic development. Various in vitro and in vivo systems have been created for evaluating trans-translational activity, but the focus of current work is on safe and easy in vitro evaluation specifically for pathogenic bacteria.
Article
Biochemistry & Molecular Biology
Pooja Srinivas, Kenneth C. Keiler, Christine M. Dunham
Summary: Bacteria use trans-translation to rescue stalled ribosomes and target incomplete proteins. New structural and biochemical data reveal important differences between trans-translation and traditional translation processes. These differences provide insights into the fundamental nature of trans-translation and guide the development of new antibiotics that specifically target bacteria.
Article
Multidisciplinary Sciences
Zachary D. Aron, Atousa Mehrani, Eric D. Hoffer, Kristie L. Connolly, Pooja Srinivas, Matthew C. Torhan, John N. Alumasa, Mynthia Cabrera, Divya Hosangadi, Jay S. Barbor, Steven C. Cardinale, Steven M. Kwasny, Lucas R. Morin, Michelle M. Butler, Timothy J. Opperman, Terry L. Bowlin, Ann Jerse, Scott M. Stagg, Christine M. Dunham, Kenneth C. Keiler
Summary: Bacterial ribosome rescue pathways are potential antibiotic targets that selectively inhibit the main ribosome rescue pathway trans-translation. Optimization of pharmacokinetic and antibiotic properties of acylaminooxadiazoles produced MBX-4132, effective in clearing multi-drug resistant Neisseria gonorrhoeae infection in mice. Structural analyses reveal a new mechanism for specific inhibition of trans-translation and a novel conformation within the bacterial ribosome critical for ribosome rescue pathways.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Neeraja Marathe, Ha An Nguyen, John N. Alumasa, Alexandra B. Kuzmishin Nagy, Michael Vazquez, Christine M. Dunham, Kenneth C. Keiler
Summary: This study reports a small molecule inhibitor called KKL-55 that specifically targets the interaction between EF-Tu and tmRNA, inhibiting bacterial translation without affecting normal translation. This discovery provides a potential avenue for developing new antibiotics to treat drug-resistant infections.
Article
Chemistry, Multidisciplinary
Adam Eordogh, Annabell Martin, Pablo Rivera-Fuentes
Summary: This study reports the development of functional probes that can operate at physiological pH and longer wavelengths compared to their predecessors. The probes are also compatible with HaloTag labeling, allowing for exceptionally long-term timelapse, single-molecule imaging of specific protein targets.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Microbiology
Joshua Stoll, Victor Zegarra, Gert Bange, Peter L. L. Graumann
Summary: Bacteria have nucleolus-like structures where ribosomal synthesis and maturation occur in close proximity at the cell poles, facilitating efficient ribosome maturation even under nutrient-deprived conditions.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Artyom A. Egorov, Gemma C. Atkinson
Summary: This article presents a tool for annotating conserved uORFs, which can predict functional ORFs in the upstream sequences of a user-defined protein or a set of protein homologs. It generates publication-quality figures with multiple sequence alignments, sequence logos, and locus annotation of the predicted conserved uORFs in graphical vector format.
Article
Multidisciplinary Sciences
Yuzuru Itoh, Anas Khawaja, Ivan Laptev, Miriam Cipullo, Ilian Atanassov, Petr Sergiev, Joanna Rorbach, Alexey Amunts
Summary: This study reveals the sequential assembly mechanism of the small mitoribosomal subunit (SSU) using cryo-electron microscopy. The results demonstrate the role of auxiliary factors in promoting rRNA maturation and conformational changes, leading to the formation of the catalytic human mitoribosome.
Article
Multidisciplinary Sciences
Gillian Rexroad, John Paul Donohue, Laura Lancaster, Harry F. Noller
Summary: This study investigates the impact of GTP hydrolysis inhibition on the structural dynamics of the ribosome using ensemble FRET. The results show that blocking GTP hydrolysis slows both forward and reverse head rotation, and abolishes reverse head rotation. The study also reveals that the FRET pair used to monitor head rotation mainly reports on intersubunit rotation, and the signal from mRNA quenching correlates closely with reverse intersubunit rotation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Yan Zhang, Nikolay A. Aleksashin, Dorota Klepacki, Caleb Anderson, Nora Vazquez-Laslop, Carol A. Gross, Alexander S. Mankin
Summary: Kasugamycin (KSG) is a small ribosomal subunit-targeting antibiotic that interferes with translation in different stages. It inhibits protein synthesis by blocking the binding of canonical messenger RNA (mRNA) and initiator transfer RNA (tRNA) to the small ribosomal subunit. Even after the formation of the 70S initiation complex, KSG can still interfere with translation to a certain extent. However, it does not completely abolish translation and allows for the expression of certain proteins. The effectiveness of KSG depends on the nature of the mRNA residue preceding the start codon and is attenuated by translational coupling.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biology
Swati Gaikwad, Fardin Ghobakhlou, David J. Young, Jyothsna Visweswaraiah, Hongen Zhang, Alan G. Hinnebusch
Summary: The formation of the 43S preinitiation complex is a critical step in translation in eukaryotes. Studies show that when there is a limitation in 43S PIC assembly, strong mRNAs outcompete weak mRNAs during translation, leading to a reprograming in translational efficiencies.
Article
Biotechnology & Applied Microbiology
Christina Zuebert, Anna-Marie Ilic, Bojan Duduk, Michael Kube
Summary: The ribosomal rescue system in Acholeplasmataceae members is analyzed comprehensively in this study. The results show that these bacteria encode a ribosomal rescue system that depends on the tmRNA encoded by ssrA and the binding protein SmpB. The gene smpB exhibits conserved gene synteny, while the genomic context of ssrA is less conserved. The sequence variability of smpB can be used as a phylogenetic marker for Acholeplasmataceae.
MICROBIAL PHYSIOLOGY
(2022)
Article
Education, Scientific Disciplines
T. Nagarajan, N. Arul Muthu Kumaran, M. Hussain Munavar
Summary: Ribosomes stall at the 3' end of mRNAs lacking stop codons and pause on normal mRNAs during starvation, leading to ribosome deficiency. Bacteria use the tmRNA (a hybrid of tRNA and mRNA) in conjunction with the SmpB protein to rescue stalled ribosomes through the complex process of trans-translation. This review aims to discuss the role of trans-translation in regulating macromolecular processes in bacteria.
RESONANCE-JOURNAL OF SCIENCE EDUCATION
(2023)
Article
Biochemistry & Molecular Biology
Ryo Aoyama, Keiko Masuda, Masaru Shimojo, Takashi Kanamori, Takuya Ueda, Yoshihiro Shimizu
Summary: This study successfully reconstituted the 50S and 30S subunits of Escherichia coli ribosomes, as well as the 70S ribosomes, and demonstrated their ability to perform functional protein synthesis in vitro. This is a significant contribution to the field of ribosome engineering and the study of ribosome assembly processes.
JOURNAL OF BIOCHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Tomoya Fujita, Takeshi Yokoyama, Mikako Shirouzu, Hideki Taguchi, Takuhiro Ito, Shintaro Iwasaki
Summary: In this study, ribosome pause sites in Escherichia coli were surveyed using monosome and disome profiling strategies. Compared to eukaryotes, ribosome collisions in bacteria showed remarkable differences, and the identified pause sites were biochemically validated and showed puromycin resistance.
Article
Biochemistry & Molecular Biology
Tatsuya Niwa, Yuhei Chadani, Hideki Taguchi
Summary: The Lon protease has been identified as the major protease involved in the degradation of obligate GroE substrates in GroE-depleted cells. Deletion of other major E. coli chaperones does not significantly affect the folding of these substrates, indicating that their folding is primarily dependent on GroE.
Review
Biochemistry & Molecular Biology
Shinobu Chiba, Keigo Fujiwara, Yuhei Chadani, Hideki Taguchi
Summary: Proteins with physiological functions have been found to interact with ribosomes and regulate gene expression during translation in both prokaryotes and eukaryotes. These regulatory nascent chains, also known as bacterial nascent chain-based mechanisms, can stall ribosomes and control translation arrest. Recent studies have shown that certain nascent chains can destabilize ribosomes and cause premature translation termination. This review highlights the importance of these bacterial mechanisms in regulating cellular functions.
JOURNAL OF BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Haruka Onodera, Tatsuya Niwa, Hideki Taguchi, Yuhei Chadani
Summary: This study reveals that excision of CP4-57 prophage in E. coli leads to the inactivation of tmRNA and switches the primary ribosome rescue pathway from trans-translation to ArfA/RF2. This switch not only rearranges the proteome landscape and phenotype of E. coli, but also provides a novel example of trans-translation-dependent regulation and redefines the physiological roles of prophage excision.
MOLECULAR MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Ayako Yamakawa, Tatsuya Niwa, Yuhei Chadani, Akinao Kobo, Hideki Taguchi
Summary: Life depends on proteins, and recent advances have shown that nascent chains (pep-tRNAs) directly participate in various cell functions. This study presents a new method called PETEOS to enrich pep-tRNAs and identify their polypeptide moieties. Using Escherichia coli as a model, around 800 proteins were identified, with a bias towards the N-termini, reflecting the population of nascent chains captured by PETEOS. This method can complement conventional approaches in investigating nascent chains in cells.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Yosuke Ito, Yuhei Chadani, Tatsuya Niwa, Ayako Yamakawa, Kodai Machida, Hiroaki Imataka, Hideki Taguchi
Summary: The study reveals that nascent chains enriched in acidic amino acids destabilize the translating ribosome, eventually leading to stochastic premature termination in eukaryotes. Such risk of premature termination influences the amino acid distribution in the proteomes.
NATURE COMMUNICATIONS
(2022)
Article
Oncology
Keiko Kasahara, Ryohei Narumi, Satoshi Nagayama, Keiko Masuda, Tsuyoshi Esaki, Kazutaka Obama, Takeshi Tomonaga, Yoshiharu Sakai, Yoshihiro Shimizu, Jun Adachi
Summary: This study performed a large-scale targeted proteomics analysis of plasma extracellular vesicles to identify novel subtypes of colorectal cancer (CRC) and important biomarker proteins associated with these subtypes. Liquid biopsy assessment with targeted proteomics analysis was proposed to be crucial for predicting CRC prognosis.
Article
Materials Science, Biomaterials
Yoshihiro Shimizu, Naoki Tanimura, Tomoaki Matsuura
Summary: ePURE_JSBML is a tool for constructing biologically relevant large-scale and detailed computational models based on a reconstituted cell-free protein synthesis system. Users can specify mRNA sequence, initial component concentration, and decoding rule. The tool utilizes Systems Biology Markup Language (SBML) using JSBML, a pure Java programming library, for model construction. It generates simulation files executable with Matlab, allowing various simulation experiments including the synthesis of proteins of a few hundred residues.
Article
Chemistry, Multidisciplinary
Hao K. Shen, Kiyoshi Morishita, P. K. Hashim, Kou Okuro, Daiki Kashiwagi, Ayumi Kimura, Haruaki Yanagisawa, Masahide Kikkawa, Tatsuya Niwa, Hideki Taguchi, Takuzo Aida
Summary: Here, an ATP-responsive nanoparticle, (NP)-N-GroEL, was synthesized by DNA hybridization between a gold nanoparticle and GroEL protein. The (NP)-N-GroEL retained its machine-like function and could capture and release denatured green fluorescent protein in response to ATP. It exhibited significantly higher ATPase activity compared to its precursor (cys)GroEL and DNA-functionalized analogue. Furthermore, it was found that (NP)-N-GroEL could be extended to double-layered (GroEL)2 NP.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Miki Wada, Koichi Ito
Summary: The CGA codon is inefficiently decoded in Saccharomyces cerevisiae by wobble pairing with Arg-tRNA(ICG). The tRNA(Arg)(ICG) is edited post-transcriptionally from tRNA(Arg)(ACG) by the Tad2/Tad3 complex. Ribosome stalling caused by consecutive CGA codons leads to a reduction in protein product. Increasing the supply of tRNA(Arg)(ACG) genes that produce decoding Arg-tRNA(ICG) can enhance the product level, indicating that the reduction in product is mainly due to inefficient decoding and deficiency in tRNA supply. The ratio of mature tRNA(Arg)(ICG) to precursor tRNA(Arg)(ACG) is less than 30% and is responsive to the expression level of Tad2/Tad3.
Article
Biochemistry & Molecular Biology
Hiroshi Otsuka, Kei Endo, Miki Wada, Koichi Ito
Summary: Translation elongation is hindered by obstacles like rare codons or RNA structures, causing ribosomal stalling. Ribosome rescue pathways resolve persistent stalling states. The study identified the critical regions in ribosomal proteins S20 and Asc1 required for ribosome rescue, and revealed their interaction with the E3 ubiquitin ligase Hel2 and their crucial role at the collided ribosome interface.
Article
Biochemical Research Methods
Rena Matsumoto, Tatsuya Niwa, Yasuhiro Shimane, Yutetsu Kuruma, Hideki Taguchi, Takashi Kanamori
Summary: The study developed a cell-free method using a reconstituted cell-free protein synthesis system (PURE system) to perform N-terminal acetylation and myristoylation of nascent proteins in vitro. The proteins synthesized using the PURE system were successfully modified in the presence of modifying enzymes. The study also demonstrated protein myristoylation in giant vesicles, leading to partial localization to the membrane. The PURE-system-based strategy is useful for controlled synthesis of post-translationally modified proteins.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Kodai Fukumoto, Yuya Miyazono, Takuya Ueda, Yoshie Harada, Hisashi Tadakuma
Summary: Cellular transport systems are complex and efficient, and there is a need to design artificial transport systems using nanotechnology. However, the design principles have been difficult to establish due to the lack of understanding on how motor layout affects motile activity. In this study, a DNA origami platform was used to evaluate the effect of motor protein layout on transporter motility. The densely packed layout of kinesin motor protein was found to decrease the run length of the transporter, highlighting the importance of considering steric hindrance in transport system design.
NANOSCALE ADVANCES
(2023)
Article
Biochemistry & Molecular Biology
Tomoya Fujita, Takeshi Yokoyama, Mikako Shirouzu, Hideki Taguchi, Takuhiro Ito, Shintaro Iwasaki
Summary: This study investigated ribosome pause sites in Escherichia coli using different ribosome profiling strategies, revealing remarkable differences compared to eukaryotes. The identified pause sites were biochemically validated and provided a useful resource for ribosome stalling sites in bacteria.