Article
Biochemistry & Molecular Biology
Yonathan Goldtzvik, Neeladri Sen, Su Datt Lam, Christine Orengo
Summary: Proteins play a crucial role in cellular function, and their diversification within an organism can be achieved through post-translational modifications, alternative splicing, and gene duplication. This review focuses on recent advancements in understanding these mechanisms and their impact on protein structure and function, with illustrative examples provided.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Review
Developmental Biology
Chunyang Ni, Michael Buszczak
Summary: This review discusses different developmental disorders that are linked with disruptions in ribosome production and function. It highlights the diversity in ribosome production and protein synthesis among different cells and tissues, and how changes in protein synthesis can impact cell fate decisions. The review also touches upon ribosome heterogeneity in stress responses and development. These discussions emphasize the importance of considering both ribosome levels and functional specialization in the context of development and disease.
Review
Biochemistry & Molecular Biology
Yoshitaka Matsuo, Toshifumi Inada
Summary: Genetic mutations, mRNA processing errors, and lack of charged tRNAs can slow down or inhibit translating ribosomes. Monitoring systems are in place to detect and dispose of incomplete nascent chains and aberrant translation products to prevent accumulation and maintain protein homeostasis. Yeast models have been instrumental in uncovering the molecular mechanisms of these co-translational quality control systems.
Review
Cell Biology
Arantxa Martinez-Ferriz, Alejandro Ferrando, Alihamze Fathinajafabadi, Rosa Farras
Summary: This review focuses on the role of ubiquitination in cellular gene expression, both at the pre-translational level and co-translational level. By regulating ubiquitination, a balance between protein synthesis and degradation can be achieved, and it also plays a role in mRNA protection and translation recovery after stress removal.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Sarah C. Miller, Clinton C. MacDonald, Morgana K. Kellogg, Zemfira N. Karamysheva, Andrey L. Karamyshev
Summary: Ribosomal heterogeneity exists within and between cells, and exhibits specific changes in response to developmental stages and environmental stimuli. These changes regulate the translation of specific groups of genes by altering ribosomal affinity for certain mRNAs or the folding of nascent polypeptides. The identification of specialized ribosomes relies on evidence such as different ribosomal protein composition or modifications to RNA and/or protein, resulting in physiologically relevant changes in translation. In this review, we summarize ribosomal heterogeneity and specialization in mammals and discuss their implications in several human diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Evan M. Zhao, Angelo S. Mao, Helena de Puig, Kehan Zhang, Nathaniel D. Tippens, Xiao Tan, F. Ann Ran, Isaac Han, Peter Q. Nguyen, Emma J. Chory, Tiffany Y. Hua, Pradeep Ramesh, David B. Thompson, Crystal Yuri Oh, Eric S. Zigon, Max A. English, James J. Collins
Summary: The use of eukaryotic toehold switches (eToeholds) allows for efficient induction of gene translation in eukaryotic cells, capable of distinguishing the presence of RNA transcripts under various circumstances. Through optimization of RNA annealing, up to 16-fold induction of transgene expression was achieved.
NATURE BIOTECHNOLOGY
(2022)
Review
Cell Biology
Bingwei Lu
Summary: Translational control plays a crucial role in protein synthesis, affecting the rate and composition of protein production. It is particularly important for cells under stress and in disease conditions. While much is known about translational control at the initiation step, problems during the elongation and termination steps can lead to ribosome stalling and collision, triggering ribosome-associated quality control mechanisms.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Sezen Meydan, Nicholas R. Guydosh
Summary: This article discusses the distribution of mRNAs and the machinery that translates them in the cytoplasm, as well as the functions and mechanisms of localized gene expression. Quality control (QC) pathways play a crucial role in detecting abnormal translation events, but their impact on local translation is still unclear. Some QC pathways have been found to be enriched near specific organelles, but the extent of localized activity is largely unknown.
Article
Biotechnology & Applied Microbiology
Xiaoyu Yang, Bo Song, Jie Cui, Lina Wang, Shuoshuo Wang, Linlin Luo, Lei Gao, Beixin Mo, Yu Yu, Lin Liu
Summary: This study reveals that translational reprogramming plays an important role in rice's response to salt stress, with the salt-tolerant cultivar SR86 adopting a more flexible translational adaptive strategy compared to the salt-sensitive cultivar NB. The differences in translational dynamics under salt stress between NB and SR86 may be due to their varying levels of ribosome stalling.
Article
Biochemistry & Molecular Biology
Jakob Trendel, Etienne Boileau, Marco Jochem, Christoph Dieterich, Jeroen Krijgsveld
Summary: Post-transcriptional gene regulation is achieved through the interaction between the transcriptome and RNA-binding proteins, and can dynamically respond to changes in cellular conditions. A method called PEPseq, using RNA sequencing, is established to monitor protein occupancy in a transcriptome-wide manner. It allows the investigation of changes in protein occupancy during translational stress and reveals an increase in protein interactions in specific mRNA coding regions. The PEPseq method serves as an unbiased discovery platform for studying post-transcriptional regulation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Wenzhu Li, Jing Zhang, Wenpeng Cheng, Yuze Li, Jinwen Feng, Jun Qin, Xiangwei He
Summary: This study suggests that there are functional differences among paralogous genes encoding ribosomal proteins, despite encoding the same ribosomal component, in the fission yeast S. pombe. The level of Rpl42p in actively translating ribosomes plays a crucial role in the phenotypic differences between mutant cells.
Article
Oncology
June Munro, Sarah L. L. Gillen, Louise Mitchell, Sarah Laing, Saadia A. A. Karim, Curtis J. J. Rink, Joseph A. A. Waldron, Martin Bushell
Summary: The study focuses on optimizing methods for accurate examination of translational control in primary mouse tissues in non-denaturing conditions. It is crucial to understand the process controlling gene expression at the level of translation as protein output can vary significantly between different mRNAs. Techniques such as polysome profiling and ribosome profiling are key in determining translation rates and should be utilized more in tissues and cancer models.
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
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.
Article
Biochemical Research Methods
Zachary Jansen, Sophia R. Reilly, Matan Lieber-Kotz, Andrew Z. Li, Qiyao Wei, Devon L. Kulhanek, Andrew R. Gilmour, Ross Thyer
Summary: Context independent gene expression is necessary for maintaining consistent and predictable behavior of genetic circuits. This study focuses on developing bicistronic translational control elements (BCDs) that leverage the helicase activity of translating ribosomes. The researchers have successfully developed a series of BCDs with varying strengths, allowing consistent expression levels across diverse sequence contexts and compatibility with modular cloning systems. They have also investigated the factors influencing translation of the leader peptide and demonstrated the flexibility and value of these BCDs in Rhodococcus species.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Hematology
Jan-Erik Messling, Karl Agger, Kasper L. Andersen, Kristina Kromer, Hanna M. Kuepper, Anders H. Lund, Kristian Helin
Summary: Novel therapies are urgently needed for the treatment of acute myeloid leukemia (AML). A study identified RIOK2 as a potential target for AML treatment, as its loss leads to decreased protein synthesis and apoptosis in leukemic cells.
Article
Biology
John R. P. Knight, Nikola Vlahov, David M. Gay, Rachel A. Ridgway, William James Faller, Christopher Proud, Giovanna R. Mallucci, Tobias von der Haar, Christopher Mark Smales, Anne E. Willis, Owen J. Sansom
Summary: The Rpl24(Bst) mutation suppresses tumorigenesis and proliferation in a colorectal cancer model with two common patient mutations, by inhibiting translation elongation through eEF2 phosphorylation. This study highlights translation elongation as a potential therapeutic target in CRC and other cancers where the Rpl24(Bst) mutation has a tumor suppressive effect in mouse models.
Article
Cell Biology
Matilda Rehn, Anne Wenzel, Anne-Katrine Frank, Mikkel Bruhn Schuster, Sachin Pundhir, Nanna Jorgensen, Kristoffer Vitting-Seerup, Ying Ge, Johan Jendholm, Magali Michaut, Erwin M. Schoof, Tanja Lyholm Jensen, Nicolas Rapin, Russell T. Sapio, Kasper Langebjerg Andersen, Anders H. Lund, Michele Solimena, Martin Holzenberger, Dimitri G. Pestov, Bo Torben Porse
Summary: Ribosomopathies are a range of disorders that affect protein synthesis and primarily impact hematopoietic stem cells and erythroid development. This study demonstrates that the deletion of poly-pyrimidine-tract-binding protein 1 (PTBP1) in the hematopoietic compartment leads to a condition resembling ribosomopathy. The loss of PTBP1 results in reduced HSC self-renewal, erythroid differentiation, and protein synthesis, along with defects in splicing and ribosome biogenesis.
Article
Biochemistry & Molecular Biology
Markus Baer, Anja Groth, Anders H. Lund, Katrine Sonne-Hansen
Article
Multidisciplinary Sciences
Kishor Gawade, Patrycja Plewka, Sophia J. Hafner, Anders H. Lund, Virginie Marchand, Yuri Motorin, Michal W. Szczesniak, Katarzyna D. Raczynska
Summary: FUS is a multifunctional protein involved in various aspects of RNA metabolism. Depletion of FUS leads to differential expression of snoRNAs, which guide the modification of rRNAs and snRNAs. Through our analysis, we observed hypermodification of rRNA species in cells with FUS knockout or FUS mutation related to ALS, suggesting a role of FUS in modulating rRNA modification and translation efficiency/fidelity. This study provides insights into a potential translation-related mechanism underlying ALS development and progression.
SCIENTIFIC REPORTS
(2023)
Review
Cell Biology
Wibke Groenewald, Anders H. H. Lund, David Michael Gay
Summary: It is well known that mutations in the WNT-signalling pathway are significant in cancer development. Understanding the role and occurrence of these mutations within the pathway is crucial for developing effective therapeutic strategies. Some cancers have mutations at the receptor level of the pathway, while others have mutations in the cytoplasmic segment, leading to ligand-dependent or ligand-independent pathway activation, respectively. This review explores the driving mutations in cancer and the available therapeutic interventions for each type of mutation, and also discusses a potential new therapeutic avenue targeting the translational apparatus downstream from WNT signalling.
Article
Cell Biology
Sophia J. Hafner, Martin D. Jansson, Kubra Altinel, Kasper L. Andersen, Zehra Abay-Norgaard, Patrice Menard, Martin Fontenas, Daniel M. Sorensen, David M. Gay, Frederic S. Arendrup, Disa Tehler, Nicolai Krogh, Henrik Nielsen, Matthew L. Kraushar, Agnete Kirkeby, Anders H. Lund
Summary: Translational regulation plays a crucial role in pluripotency maintenance and cell differentiation. This study reveals ribosome heterogeneity through rRNA 2'-O-methylation during early development and differentiation, indicating a direct role for ribosomes in regulating translation during cell fate acquisition.
DEVELOPMENTAL CELL
(2023)
Editorial Material
Biochemistry & Molecular Biology
Lien B. Lai, Venkat Gopalan, Martin D. Jansson, Qi Chen, Xudong Zhang, Maik Wolfram-Schauerte, Katharina Hofer
Summary: This article focuses on the importance of nucleic acids in biochemistry, specifically RNA, and discusses the generation of figures representing their structures. Several authors provide insights into the factors to consider when creating such figures, preferred software, and examples from their own research.
TRENDS IN BIOCHEMICAL SCIENCES
(2023)
Article
Endocrinology & Metabolism
Johan Vande Voorde, Rory T. Steven, Arafath K. Najumudeen, Catriona A. Ford, Alex Dexter, Ariadna Gonzalez-Fernandez, Chelsea J. Nikula, Yuchen Xiang, Lauren Ford, Stefania Maneta Stavrakaki, Kathryn Gilroy, Lucas B. Zeiger, Kathryn Pennel, Phimmada Hatthakarnkul, Efstathios A. Elia, Ammar Nasif, Teresa Murta, Eftychios Manoli, Sam Mason, Michael Gillespie, Tamsin R. M. Lannagan, Nikola Vlahov, Rachel A. Ridgway, Colin Nixon, Alexander Raven, Megan Mills, Dimitris Athineos, Georgios Kanellos, Craig Nourse, David M. Gay, Mark Hughes, Amy Burton, Bin Yan, Katherine Sellers, Vincen Wu, Kobe De Ridder, Engy Shokry, Alejandro Huerta Uribe, William Clark, Graeme Clark, Kristina Kirschner, Bernard Thienpont, Vivian S. W. Li, Oliver D. K. Maddocks, Simon T. Barry, Richard J. A. Goodwin, James Kinross, Joanne Edwards, Mariia O. Yuneva, David Sumpton, Zoltan Takats, Andrew D. Campbell, Josephine Bunch, Owen J. Sansom
Summary: In this study, the potential of untargeted metabolomics as a stratification tool for colorectal cancer (CRC) was investigated. The researchers presented a comprehensive pipeline to uncover metabolic vulnerabilities in CRC based on its genetic origin. Perturbations in methionine metabolism linked to APC deficiency were observed, and adenosylhomocysteinase was identified as an actionable therapeutic target.