Article
Genetics & Heredity
Thalia H. Sass, Alexander E. Ferrazzoli, Susan T. Lovett
Summary: The transcription factor RpoS controls various genes important for stress tolerance in Escherichia coli. IraD promotes the stability of RpoS by inhibiting RssB, a protein involved in degradation. DNA damage induces iraD expression independently of the SOS response. Both iraD and rpoS are required for tolerance to DNA damaging treatments in the log phase of growth.
Article
Nanoscience & Nanotechnology
Wenqiang Li, Xia Wang, Jiaming Liu, Shuai Li, Nan Li, Huizhu Hu
Summary: Introducing rotational degree of control into conventional optical tweezers offers new possibilities in physics, optical manipulation, and life science. Previous rotational schemes relied on microsphere anisotropy, limiting their applications. This study demonstrates the first experimental realization of orbiting a homogeneous microsphere using angular momentum in a transversely rotating optical trap. This method enables the exploration of orbital-translational coupling and the creation of an ultra-stable micro-gyroscope.
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.
Article
Multidisciplinary Sciences
Surajit Chatterjee, Adrien Chauvier, Shiba S. Dandpat, Irina Artsimovitch, Nils G. Walter
Summary: In bacteria, the interaction between RNA polymerase and ribosome regulates gene expression through transcription-translation coupling. This coupling is mainly achieved by RNA polymerase promoting the binding of the ribosomal 30S subunit to antagonize ribosome binding site occlusion induced by a riboswitch, thereby facilitating translation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Plant Sciences
Xiaojing Liu, Fengfeng Du, Linhe Sun, Jinfeng Li, Shaozhou Chen, Naiwei Li, Yajun Chang, Jian Cui, Wen Chen, Dongrui Yao
Summary: In this study, it was found that the natural mutant 'Da Sajin' in lotus may have originated from a red-flowered ancestor. Partial loss of anthocyanin pigments in white petals may result from metabolic disorder caused by light destruction. The translational and post-translational regulatory network plays an important role in anthocyanin metabolism in lotus.
Review
Cell Biology
James A. Saba, Kifayathullah Liakath-Ali, Rachel Green, Fiona M. Watt
Summary: Stem cells are characterized by their ability to self-renew and differentiate into different cell types, and recent studies have shown that their behavior is closely tied to the regulation of protein synthesis by the ribosome. Understanding how translation mechanisms control stem cell function, including pluripotency and differentiation, may provide insights into mechanisms of tumorigenesis.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2021)
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)
Article
Microbiology
Amelia R. Silva-Rohwer, Kiara Held, Helen Yakhnin, Paul Babitzke, Viveka Vadyvaloo
Summary: Mutations in c-di-GMP biosynthesis drove the evolution of Y. pestis to be transmitted by fleas. The biofilm-mediated blockage of the flea foregut, dependent on c-di-GMP, allows regurgitative transmission of Y. pestis by fleabite. The diguanylate cyclases HmsT and HmsD, which synthesize c-di-GMP, play significant roles in transmission.
JOURNAL OF BACTERIOLOGY
(2023)
Article
Microbiology
Heidi A. Butz, Alexandra R. Mey, Ashley L. Ciosek, Alexander A. Crofts, Bryan W. Davies, Shelley M. Payne
Summary: CsrA is a critical posttranscriptional global regulator in Vibrio cholerae, controlling 22% of the bacterial transcriptome involving various cellular processes. Through RNA coimmunoprecipitation experiments, it was found that CsrA binds to multiple mRNAs encoding regulatory proteins, including major sigma factors. Additionally, CsrA directly binds to virulence gene transcripts, positively regulating the production of important virulence factors.
Review
Physiology
Alexandra Balvey, Mercedes Fernandez
Summary: Chronic liver disease is a major threat to public health globally, with obesity and aging population being the main drivers of its increasing incidence. Liver transplantation remains the only curative treatment, but is hindered by high costs and organ scarcity. Therefore, new strategies are urgently needed to prevent and reverse chronic liver disease.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Computer Science, Interdisciplinary Applications
Alexandros N. Nordas, Bassam A. Izzuddin
Summary: This paper presents an original and systematic methodology for surface coupling in the modeling of large-scale metal structures, which allows for the coupling of different element types and different levels of discretization detail. It also addresses domain partitioning problems involving computationally heterogeneous partitions. Numerical examples are provided to demonstrate the accuracy, versatility, and computational benefits of the developed methodology.
COMPUTERS & STRUCTURES
(2022)
Article
Multidisciplinary Sciences
Cheng Chen, Xiaobing Zhang, Yisha Wang, Xinyu Chen, Wenjie Chen, Songsong Dan, Shiqi She, Weiwei Hu, Jie Dai, Jianwen Hu, Qingyi Cao, Qianyu Liu, Yinghua Huang, Baoming Qin, Bo Kang, Ying-Jie Wang
Summary: RNA processing and translation are identified as the most differentially regulated processes between naive and primed human embryonic stem cells (hESCs) through quantitative proteomics, phosphoproteomics, and acetylproteomics analyses. Naive hESCs have a more compact proteome and can translate selective mRNAs through both eIF4E-dependent and eIF4E-independent/eIF4A2-dependent pathways. These findings contribute to a better understanding of the potential of naive hESCs and the optimization of conditions for clinical applications.
Article
Multidisciplinary Sciences
Raphael V. Gayet, Katherine Ilia, Shiva Razavi, Nathaniel D. Tippens, Makoto A. Lalwani, Kehan Zhang, Jack X. Chen, Jonathan C. Chen, Jose Vargas-Asencio, James J. Collins
Summary: The researchers have developed a programmable RNA sensor called DART VADAR, which can convert target hybridization into a translational output, amplifying endogenous ADAR editing through positive feedback. This system has a high dynamic range and a small genetic footprint, making it suitable for controlling transgene expression in response to pre-defined transcriptional cues.
NATURE COMMUNICATIONS
(2023)
Review
Multidisciplinary Sciences
Ji Min Lee, Henrik M. Hammaren, Mikhail M. Savitski, Sung Hee Baek
Summary: Post-translational modifications (PTMs) on specific amino acids control the stability of target proteins. These PTM-regulated degrons act as signals for protein degradation or stabilization. This review summarizes the current knowledge of PTM-mediated protein stability regulation to enhance the identification of novel drug targets.
NATURE COMMUNICATIONS
(2023)
Review
Biochemistry & Molecular Biology
Matthew J. Payea, Carlos Anerillas, Ravi Tharakan, Myriam Gorospe
Summary: Senescence is a state of long-term cell cycle arrest caused by sublethal damage, leading to metabolic activity, production of inflammatory proteins, and inhibition of ribosome biogenesis. The translation process in senescent cells shows a paradoxical pattern with global repression triggered by DNA damage and selective increase in translation of specific proteins.
MOLECULAR AND CELLULAR BIOLOGY
(2021)
Article
Microbiology
Archana Pannuri, Christopher A. Vakulskas, Tesfalem Zere, Louise C. McGibbon, Adrianne N. Edwards, Dimitris Georgellis, Paul Babitzke, Tony Romeo
JOURNAL OF BACTERIOLOGY
(2016)
Article
Biochemistry & Molecular Biology
Alexander V. Yakhnin, Katsuhiko S. Murakami, Paul Babitzke
JOURNAL OF BIOLOGICAL CHEMISTRY
(2016)
Article
Biochemistry & Molecular Biology
Christopher A. Vakulskas, Yuanyuan Leng, Hazuki Abe, Takumi Amaki, Akihiro Okayama, Paul Babitzke, Kazushi Suzuki, Tony Romeo
NUCLEIC ACIDS RESEARCH
(2016)
Article
Microbiology
Helen Yakhnin, Robert Aichele, Sarah E. Ades, Tony Romeo, Paul Babitzke
JOURNAL OF BACTERIOLOGY
(2017)
Article
Microbiology
Smarajit Mondal, Alexander V. Yakhnin, Paul Babitzke
JOURNAL OF BACTERIOLOGY
(2017)
Editorial Material
Microbiology
Paul Babitzke, Michael O'Connor
JOURNAL OF BACTERIOLOGY
(2017)
Article
Biochemistry & Molecular Biology
David Mitchell, Laura E. Ritchey, Hongmarn Park, Paul Babitzke, Sarah M. Assmann, Philip C. Bevilacqua
Article
Multidisciplinary Sciences
Anastasia H. Potts, Christopher A. Vakulskas, Archana Pannuri, Helen Yakhnin, Paul Babitzke, Tony Romeo
NATURE COMMUNICATIONS
(2017)
Article
Multidisciplinary Sciences
Anastasia H. Potts, Yuanyuan Leng, Paul Babitzke, Tony Romeo
SCIENTIFIC REPORTS
(2018)
Article
Biochemistry & Molecular Biology
David Mitchell, Andrew J. Renda, Catherine A. Douds, Paul Babitzke, Sarah M. Assmann, Philip C. Bevilacqua
Review
Microbiology
Paul Babitzke, Ying-Jung Lai, Andrew J. Renda, Tony Romeo
ANNUAL REVIEW OF MICROBIOLOGY, VOL 73
(2019)
Article
Microbiology
Christine Pourciau, Archana Pannuri, Anastasia Potts, Helen Yakhnin, Paul Babitzke, Tony Romeo
Article
Microbiology
Helen Yakhnin, Alexander V. Yakhnin, Brandon L. Mouery, Zachary F. Mandell, Catherine Karbasiafshar, Mikhail Kashlev, Paul Babitzke
Article
Microbiology
Tony Romeo, Paul Babitzke
MICROBIOLOGY SPECTRUM
(2018)