Article
Evolutionary Biology
Rosa M. Pinto, Albert Bosch
Summary: Codon bias, a common phenomenon in all organisms, is influenced by mutation, drift, and selection. While selection for translation efficiency and accuracy is well recognized, fewer studies have explored the impact of translation rate control on codon usage. Experimental molecular evolution using RNA virus populations is a powerful tool in understanding the mechanisms behind codon bias. Furthermore, experimental studies are encouraged to define the role of selection in codon evolution, as most studies on virus codon usage rely on computational analyses.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Biotechnology & Applied Microbiology
Taolan Zhao, Yan-Ming Chen, Yu Li, Jia Wang, Siyu Chen, Ning Gao, Wenfeng Qian
Summary: The study revealed widespread ribosome collisions in cells, which are associated with slow ribosome release, slow peptide bond formation, and slow leaving of polylysine from the exit tunnel of ribosomes. Collisions occur more frequently in the gap regions between alpha-helices, where translational pauses can prevent interference with protein folding by downstream peptides. Paused or collided ribosomes are associated with specific chaperones, facilitating proper protein folding during translation.
Article
Biochemistry & Molecular Biology
Michal Perach, Zohar Zafrir, Tamir Tuller, Oded Lewinson
Summary: Due to genetic code redundancy, most amino acids are encoded by multiple synonymous codons, which are used unevenly in different organisms. Slow codons play important roles in regulating protein folding and function.
Article
Virology
Ben Berkhout, Formijn J. van Hemert
Summary: The human immunodeficiency virus (HIV) has an evolutionary tendency to accumulate A nucleotides in its RNA genome, but certain positions in the viral RNA lack A nucleotides due to local RNA structure requirements. These "noA" sites may play a significant role in the correct folding of the viral RNA.
Review
Biochemistry & Molecular Biology
Guenter Kramer, Ayala Shiber, Bernd Bukau
ANNUAL REVIEW OF BIOCHEMISTRY, VOL 88
(2019)
Article
Cell Biology
Anne Wentink, Carmen Nussbaum-Krammer, Bernd Bukau
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY
(2019)
Review
Microbiology
Axel Mogk, Carmen Ruger-Herreros, Bernd Bukau
ANNUAL REVIEW OF MICROBIOLOGY, VOL 73
(2019)
Review
Cell Biology
Rina Rosenzweig, Nadinath B. Nillegoda, Matthias P. Mayer, Bernd Bukau
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2019)
Article
Biology
Mohammed Jamshad, Timothy J. Knowles, Scott A. White, Douglas G. Ward, Fiyaz Mohammed, Kazi Fahmida Rahman, Max Wynne, Gareth W. Hughes, Guenter Kramer, Bernd Bukau, Damon Huber
Article
Cell & Tissue Engineering
Patricia Rusu, Chunxuan Shao, Anna Neuerburg, Azer Aylin Acikgoez, Yonghe Wu, Peng Zou, Prasad Phapale, Tchirupura S. Shankar, Kristina Doering, Steffen Dettling, Huiqin Koerkel-Qu, Goezde Bekki, Barbara Costa, Te Guo, Olga Friesen, Magdalena Schlotter, Mathias Heikenwalder, Darjus F. Tschaharganeh, Bernd Bukau, Guenter Kramer, Peter Angel, Christel Herold-Mende, Bernhard Radlwimmer, Hai-Kun Liu
Article
Multidisciplinary Sciences
Chi-ting Ho, Tomas Grousl, Oren Shatz, Areeb Jawed, Carmen Ruger-Herreros, Marije Semmelink, Regina Zahn, Karsten Richter, Bernd Bukau, Axel Mogk
NATURE COMMUNICATIONS
(2019)
Correction
Multidisciplinary Sciences
Anne S. Wentink, Nadinath B. Nillegoda, Jennifer Feufel, Gabriele Ubartaite, Carolyn P. Schneider, Paolo de los Rios, Janosch Hennig, Alessandro Barducci, Bernd Bukau
Summary: A correction to this paper has been published at https://doi.org/10.1038/s41586-020-03090-x.
Article
Multidisciplinary Sciences
Matilde Bertolini, Kai Fenzl, Ilia Kats, Florian Wruck, Frank Tippmann, Jaro Schmitt, Josef Johannes Auburger, Sander Tans, Bernd Bukau, Gunter Kramer
Summary: This study investigated whether newly synthesized proteins can form functional oligomers through co-co assembly. They found that this mechanism can lead to the co-assembly of hundreds of homomeric subunits in human cells, mainly mediated by N-terminal coiled coils among five major domain classes.
Article
Multidisciplinary Sciences
Ajeet K. Sharma, Johannes Venezian, Ayala Shiber, Guenter Kramer, Bernd Bukau, Edward P. O'Brien
Summary: A single cluster of nonoptimal codons in Saccharomyces cerevisiae can reduce a transcript's half-life, while the impact of multiple clusters remains unknown. A kinetic model predicts that inserting a second nonoptimal cluster near the 5' end can increase mRNA half-life, which was experimentally validated. The results suggest that codon usage bias has a more nuanced role in controlling cellular protein levels than previously thought.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Federico Cerullo, Sebastian Filbeck, Pratik Rajendra Patil, Hao-Chih Hung, Haifei Xu, Julia Vornberger, Florian W. Hofer, Jaro Schmitt, Guenter Kramer, Bernd Bukau, Kay Hofmann, Stefan Pfeffer, Claudio A. P. Joazeiro
Summary: This study uncovers the function of Bacillus subtilis MutS2, a member of the conserved MutS family, in translational quality control. MutS2 acts as a ribosome-binding protein and functions in sensing collisions between stalled and translating ribosomes. It promotes ribosomal subunit dissociation, ribosome recycling, and initiation of ribosome-associated protein quality control. These findings demonstrate the conserved role of ribosome collisions in mounting a complex response to translation interruption.
Article
Biochemistry & Molecular Biology
Joseph George Beton, Jim Monistrol, Anne Wentink, Erin C. Johnston, Anthony John Roberts, Bernd Gerhard Bukau, Bart W. Hoogenboom, Helen R. Saibil
Summary: Specific combinations of molecular chaperones in the human body can disassemble protein aggregates, which is important for combating disease-related fiber formation. This study reveals the mechanism of this disassembly process and the localization and activity of molecular chaperones on the fibers using techniques such as atomic force microscopy.
Article
Multidisciplinary Sciences
Ofrah Faust, Meital Abayev-Avraham, Anne S. Wentink, Michael Maurer, Nadinath B. Nillegoda, Nir London, Bernd Bukau, Rina Rosenzweig
Article
Multidisciplinary Sciences
Anne S. Wentink, Nadinath B. Nillegoda, Jennifer Feufel, Gabriele Ubartaite, Carolyn P. Schneider, Paolo De Los Rios, Janosch Hennig, Alessandro Barducci, Bernd Bukau
Article
Biochemistry & Molecular Biology
Michael Maurer, Daniela Linder, Kamila B. Franke, Jasmin Jaeger, Gabrielle Taylor, Felix Gloge, Sebastian Gremer, Laura Le Breton, Matthias P. Mayer, Eilika Weber-Ban, Marta Carroni, Bernd Bukau, Axel Mogk
CELL CHEMICAL BIOLOGY
(2019)