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
Multidisciplinary Sciences
Tea Lenarcic, Moritz Niemann, David J. F. Ramrath, Salvatore Calderaro, Timo Fluegel, Martin Saurer, Marc Leibundgut, Daniel Boehringer, Celine Prange, Elke K. Horn, Andre Schneider, Nenad Ban
Summary: This study investigates the assembly of the mitochondrial small subunit (mt-SSU) and identifies several assembly factors that interact with specific regions of rRNA to ensure proper assembly. The researchers use cryoelectron microscopy to determine the structures of assembly intermediates and propose a stepwise assembly process involving ribosomal protein and assembly factor exchange.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Hanna Kratzat, Timur Mackens-Kiani, Michael Ameismeier, Mia Potocnjak, Jingdong Cheng, Estelle Dacheux, Abdelkader Namane, Otto Berninghausen, Franz Herzog, Micheline Fromont-Racine, Thomas Becker, Roland Beckmann
Summary: In eukaryotic translation, the termination and ribosome recycling phases are linked to the initiation of a new round of translation by factors such as ABCE1 and eIF3j. Cryo-EM analysis of native yeast and human ABCE1-containing pre-initiation complexes revealed their association with 43S and 48S initiation phases, showcasing a novel hybrid conformation and interaction network. This study provides valuable insights into the structural and functional roles of ABCE1 and eIF3j in translation initiation.
Article
Biochemistry & Molecular Biology
A. Carolin Seefeldt, Javier Aguirre Rivera, Magnus Johansson
Summary: This study investigated the impact of erythromycin on protein synthesis in live bacterial cells by tracking tRNAs. The results showed that erythromycin significantly prolonged the dwell time of tRNA on ribosomes but occurred less frequently, highlighting the complexity of its effect on protein synthesis.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Review
Microbiology
Lorenzo Eugenio Leiva, Victor Zegarra, Gert Bange, Michael Ibba
Summary: Nucleotides are essential for biological processes in the cell, playing key roles in molecular biology and regulating metabolic pathways. They are dynamic, interact with each other, and provide feedback to the cell's metabolic state, adapting to environmental and growth challenges. Intracellular nucleotides fine-tune the activity of RNA polymerase, synthesis of tRNAs, mRNA translation, and assembly of ribosomes involved in protein synthesis. The ribosome acts as a molecular hub where nucleotides encounter and regulate the cell's state.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2023)
Review
Cell Biology
Yudi Liu, Jiuwei Cui, Andrew R. Hoffman, Ji-Fan Hu
Summary: Protein translation is a critical regulatory event involved in various physiological and pathological processes. The eukaryotic translation initiation factor 4G2 (eIF4G2) is important for cap-independent translation initiation via internal ribosome entry sites (IRESs), but recent findings suggest that it plays a role in other translation initiation pathways as well. This review summarizes the role of eIF4G2 in different translation initiation events and its involvement in apoptosis, cell survival, cell differentiation, and embryonic development.
CELL PROLIFERATION
(2023)
Article
Biochemistry & Molecular Biology
Yuki Kito, Akinobu Matsumoto, Kazuya Ichihara, Chisa Shiraishi, Ronghao Tang, Atsushi Hatano, Masaki Matsumoto, Peixun Han, Shintaro Iwasaki, Keiichi Nakayama
Summary: Translation begins with the binding of the eIF4F complex to the 5' mRNA cap, followed by scanning ribosomes searching for the start codon in the 5' untranslated region. This study shows that the ASC-1 complex (ASCC) associates with scanning ribosomes to regulate translation initiation. Knockdown of ASCC3, a subunit of ASCC, impairs the loading and scanning dynamics of the 43S preinitiation complex, leading to reduced translation efficiency. These findings demonstrate that ASCC not only promotes dissociation of colliding 80S ribosomes but also facilitates efficient translation initiation by scanning ribosomes.
Article
Biotechnology & Applied Microbiology
Soma Jana, Partha P. Datta
Summary: The study found that the pI values of translation factors are related to the translation event, where initiation factors are mainly basic, while elongation and release factors are strictly acidic. Among all translation factors, initiation factor 2 (IF2) and ribosome recycling factor (RRF) showed variable pI values that are linked to the order of phylogeny.
Article
Cell Biology
Marjolein M. J. Caron, Maxime Eveque, Berta Cillero-Pastor, Ron M. A. Heeren, Bas Housmans, Kasper Derks, Andy Cremers, Mandy J. Peffers, Lodewijk W. van Rhijn, Guus van den Akker, Tim J. M. Welting
Summary: Sox9 plays an essential role in regulating ribosome biogenesis factors and ribosomal protein subunits during the early phase of chondrogenic differentiation, affecting translational capacity. Sox9 knockdown leads to decreased translation activity, while overexpression of Sox9 induces reciprocal effects.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Chao Sun, Andreas Nold, Claudia M. Fusco, Vidhya Rangaraju, Tatjana Tchumatchenko, Mike Heilemann, Erin M. Schuman
Summary: Neurons localize mRNAs and ribosomes in dendrites and axons for local protein synthesis to supply synapses. Study shows that ribosomes and nascent proteins positively correlate with synapse density and the amount of locally synthesized protein relates to spontaneous Ca2+ activity at synapses. Local and global plasticity result in a multifold increase in synaptic nascent protein with substantial heterogeneity between neighboring synapses.
Article
Microbiology
Daisuke Kurita, Hyouta Himeno
Summary: To maintain proteostasis, cells employ ribosome rescue systems to relieve stalled ribosomes on problematic mRNA. In Escherichia coli, there are at least three such systems to deal with ribosomes stalled on non-stop mRNA.
Article
Biochemistry & Molecular Biology
Zuben P. Brown, Irina S. Abaeva, Swastik De, Christopher U. T. Hellen, Tatyana Pestova, Joachim Frank
Summary: This study presents cryo-EM structures of hepatitis C virus IRES initiation complexes, revealing the dynamic network of 40S/IRES contacts and the conformational changes during the transition from eIF2- to eIF5B-containing 48S complexes, providing important insights into the process of subunit joining.
Article
Plant Sciences
Qiutao Xu, Yijie Wang, Yaping Yue, Zhengting Chen, Dao-Xiu Zhou, Yu Zhao
Summary: This article has been withdrawn due to an error, and the definitive version is published under DOI.
Article
Ecology
Tess E. Brewer, Andreas Wagner
Summary: Fast-growing bacteria encode fewer di-prolyl motifs compared to slow-growing ones, especially in highly expressed proteins. Many di-prolyl motifs are found in thermophiles and bacteria with complex, multicellular lifecycles.
Review
Biochemistry & Molecular Biology
Vandana Yadav, Inayat Ullah Irshad, Hemant Kumar, Ajeet K. Sharma
Summary: This passage discusses the methods used to extract translation rate parameters from ribosome profiling data and their applications in deciphering the regulation of gene expression. The accurate rate parameters may provide new insights into the kinetic control of the process of gene expression.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Cell Biology
Fatima Kamal, Xiaoye Liang, Kevin Manera, Tong-Tong Pei, Haeun Kim, Linh G. Lam, Alexander Pun, Steven J. Hersch, Tao G. Dong
Review
Cell Biology
Steven J. Hersch, Kevin Manera, Tao G. Dong
Article
Microbiology
Loreto Arias, Fabian Martinez, Daniela Gonzalez, Rodrigo Flores-Rios, Assaf Katz, Mario Tello, Sandra Moreira, Omar Orellana
Summary: Codon usage bias is found at organism and genome levels, with preferential codons mostly in genes encoding highly-expressed proteins. The role of rare codons in controlling the expression of lowly-expressed or temporarily-expressed proteins is still an open question, with potential impact on cell division.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Steven J. Hersch, Bojana Radan, Bushra Ilyas, Patrick Lavoie, William Wiley Navarre
Summary: Research shows that Salmonella diverges from E. coli in response to dicarboxylates, potentially due to adaptation to its virulent lifestyle. Understanding this divergence may reveal a novel aspect of the Salmonella virulence cycle.
JOURNAL OF BACTERIOLOGY
(2021)
Article
Infectious Diseases
Veronica Bravo, Assaf Katz, Lorena Porte, Thomas Weitzel, Carmen Varela, Narjol Gonzalez-Escalona, Carlos J. Blondel
Summary: This study conducted a comprehensive genome analysis of Campylobacter jejuni and Campylobacter coli strains from Chile, revealing underestimated incidence of campylobacteriosis in South America and highlighting the need for further genomic epidemiology studies in the region. The analysis identified high genetic diversity and widespread fluoroquinolone resistance, emphasizing the importance of understanding molecular epidemiology and antimicrobial resistance of this emerging pathogen in South American countries.
PLOS NEGLECTED TROPICAL DISEASES
(2021)
Article
Multidisciplinary Sciences
Kevin Manera, Florence Caro, Hao Li, Tong-Tong Pei, Steven J. Hersch, John J. Mekalanos, Tao G. Dong
Summary: The study reveals a quantity-sensing control mechanism of the T6SS, which down-regulates the expression of secreted components in the cytosol when T6SS is inactive. This Hcp-dependent sensing control allows organisms carrying T6SS to quickly adjust T6SS expression and prevent wasteful build-up of its major secreted components.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Microbiology
Steven J. Hersch, Linh Lam, Tao G. Dong
Summary: Genetic editing has been revolutionized by delivering Cre recombinase as a protein through engineered bacterial type six secretion system (T6SS). The versatile T6SS system can also deliver other exogenous effectors, like TseC, enhancing its efficacy against specific pathogens. This engineered system shows promise in microbiome manipulation and as a next-generation antimicrobial tool.
Article
Medicine, Research & Experimental
Sara Elgamal, Emanuele Cocucci, Ellen J. Sass, Xiaokui M. Mo, Angela R. Blissett, Edward P. Calomeni, Kerry A. Rogers, Jennifer A. Woyach, Seema A. Bhat, Natarajan Muthusamy, Amy J. Johnson, Karilyn T. Larkin, John C. Byrd
Summary: EVs play crucial roles in cancer, but studies on EVs show great variability. This research focused on isolating and characterizing EVs from CLL patient plasma and cell lines, identifying effective isolation methods and factors affecting results.
Article
Hematology
Eileen Y. Hu, Priscilla Do, Swagata Goswami, Jessica Nunes, Chi-ling Chiang, Sara Elgamal, Ann M. Ventura, Carolyn Cheney, Kevan Zapolnik, Erich Williams, Rajeswaran Mani, Frank Frissora, Xiaokui Mo, Lorenz Waldmeier, Roger R. Beerli, Haiyong Peng, Christoph Rader, Meixiao Long, Ulf Grawunder, John C. Byrd, Natarajan Muthusamy
Summary: This study presents a first-in-class anti-ROR1 antibody-drug conjugate that shows cytotoxicity to ROR1(+) malignant cells in vitro and extends survival in mouse models engrafted with human ROR1(+) leukemia. Combined treatment strategies with a BCL2 inhibitor further enhance the cytotoxic effects.
Article
Engineering, Chemical
Yuxuan Ren, Steven J. Hersch, Xiao He, Rufan Zhou, Tao G. Dong, Qingye Lu
Summary: This study successfully synthesized a lightweight and robust metal-organic framework/cellulose aerogel composite with good reusability and potential for wastewater treatment and antibacterial applications.
SEPARATION AND PURIFICATION TECHNOLOGY
(2022)
Article
Microbiology
Erin Oi-Yan Wong, Emma Joan Elizabeth Brownlie, Katharine Michelle Ng, Sornnujah Kathirgamanathan, Feiqiao Brian Yu, Bryan D. Merrill, Kerwyn Casey Huang, Alberto Martin, Carolina Tropini, William Wiley Navarre
Summary: The microbiota's role in animal physiology has been extensively studied in humans, but there is a lack of isolated lab mouse-associated bacteria. Gut inflammation affects commensal gut microbes and can lead to long-term changes in microbiota composition. To address this, the Collection of Inflammation-Associated Mouse Intestinal Bacteria (CIAMIB) was created, providing a diverse range of isolates, including many previously uncultivated species. This collection allows for the study of host-microbiota interactions.
Article
Gastroenterology & Hepatology
Emma J. E. Brownlie, Danica Chaharlangi, Erin Oi-Yan Wong, Deanna Kim, William Wiley Navarre
Summary: This study reveals that certain species of Lactobacillaceae can inhibit the growth of specific bacteria in the gut by acidifying the environment. It provides valuable insights into the interactions between Lactobacillaceae species and commensal intestinal bacteria.
Review
Microbiology
Lorenzo Eugenio Leiva, Assaf Katz
Summary: In bacteria, the translation of genetic information can begin through at least three different mechanisms. One of these mechanisms is leaderless initiation, which relies on the ability of 70S ribosomal particles to bind to AUG located at or near the 5' end of mRNAs to initiate translation. Unlike canonical translation, leaderless mRNAs lack a 5' untranslated region and a Shine-Dalgarno sequence, so the regulation of translation initiation is different for these mRNAs.
Article
Biochemical Research Methods
F. Talebni, D. Pushparajah, S. Chandrasekaran, S. J. Hersch, N. Nafissi, R. Slavcev
Summary: Gene therapy is a powerful treatment method, and non-viral gene therapy vectors have advantages in safety compared to viral vectors. Advanced purification and separation techniques are needed to maximize resolution in a scalable manner. The Prep Cell system showed effective separation and resolution of mini-DNA vectors, indicating its potential for mid-scale purification of DNA vectors for various research and clinical applications.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
(2023)