Article
Multidisciplinary Sciences
Zhou Yin, Jeremy G. Bird, Jason T. Kaelber, Bryce E. Nickels, Richard H. Ebright
Summary: The article investigates the mechanism of action of Q proteins in transcription in Lambdoid bacteriophage. The results show that Q proteins form a nozzle-like structure to prevent pause and termination of RNA polymerase during transcription. Compared to previous studies, this research reveals the structural and functional differences of Q proteins in different bacteriophages.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Simona Cugusi, Richard Mitter, Gavin P. Kelly, Jane Walker, Zhong Han, Paola Pisano, Michael Wierer, Aengus Stewart, Jesper Q. Svejstrup
Summary: The heat shock response not only affects rapid induction of HS genes, but also alters various phases of the transcription cycle and triggers a new RNA splicing mechanism. This leads to the production of new short mRNAs that accumulate in the nucleus, causing significant reconfiguration of the human transcriptome.
Article
Genetics & Heredity
Andrew M. Clarke, Abigail K. Huffines, Yvonne J. K. Edwards, Chad M. Petit, David A. Schneider
Summary: Saccharomyces cerevisiae has approximately 200 copies of the 35S rDNA gene, transcribed by RNA polymerase I (Pol I) with the A12.2 subunit playing a crucial role. Investigating Pol I occupancy changes in the 35S gene and IGS in an rpa12 Delta strain, we found that the A12.2 subunit is important for transcription elongation and termination.
Article
Multidisciplinary Sciences
Chirangini Pukhrambam, Vadim Molodtsov, Mahdi Kooshkbaghi, Ammar Tareen, Hoa Vu, Kyle S. Skalenko, Min Su, Zhou Yin, Jared T. Winkelman, Justin B. Kinney, Richard H. Ebright, Bryce E. Nickels
Summary: In sigma-dependent transcriptional pausing, the presence or absence of GreB determines whether the paused state involves backtracking or scrunched by 2-4 base pairs or 2-3 base pairs respectively. The consensus sequence T(-3)N(-2)Y(-1)G(+1) is associated with pausing in both initial transcription and transcription elongation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Marc Morgan, Ramin Shiekhattar, Ali Shilatifard, Shannon M. Lauberth
Summary: The past decade has brought about a revolution in our understanding of regulatory noncoding RNAs (ncRNAs), including the recently identified downstream-of-gene (DoG)-containing transcripts that are produced through widespread transcriptional readthrough. The discovery of DoGs has paved the way for future research to explore the mechanisms behind readthrough transcription, RNA processing, and the cellular functions of these unique transcripts.
Article
Oncology
Ruth Q. Jacobs, Kaila B. Fuller, Stephanie L. Cooper, Zachariah Carter, Marikki Laiho, Aaron L. Lucius, David A. Schneider
Summary: This study evaluates the specificity of the compound BMH-21 on transcription by Pols I, II, and III. The results show that Pol I is more sensitive to inhibition by BMH-21 compared to Pols II and III. These findings support the ongoing development of BMH-21 and its derivatives as potential therapeutic agents.
Review
Genetics & Heredity
Rachel McNamar, Katrina Rothblum, Lawrence Rothblum
Summary: Pol I is responsible for transcribing ribosomal DNA genes in eukaryotes, and abnormalities in its activity are linked to cancer and genetic diseases. Studies show differences in Pol I transcription between yeast and mammals, which may affect the function and regulation of PAFs.
Article
Genetics & Heredity
Abigail K. Huffines, Yvonne J. K. Edwards, David A. Schneider
Summary: The RNA polymerase (Pol) I transcription defect caused by the deletion of Spt4 protein may affect the transcription elongation process. The complex formed by Spt4 and Spt5 promotes Pol I processivity, enhancing transcription elongation through G-rich regions of ribosomal DNA.
Article
Cell Biology
Jia Fei, Jun Xu, Ziwei Li, Kevin Xu, Dong Wang, George A. Kassavetis, James T. Kadonaga
Summary: NDF is a transcription elongation factor that binds to Pol II and enhances gene expression elongation by a different mechanism than TFIIS.
GENES & DEVELOPMENT
(2022)
Review
Biochemistry & Molecular Biology
Tomasz W. Turowski, Magdalena Boguta
Summary: RNAPI and RNAPIII are multi-heterogenic protein complexes specialized in transcribing highly abundant non-coding RNAs, more complex than RNAPII synthesizing mRNAs. They share associated subcomplexes formed by specific subunits in yeast and establish an assembly platform co-translationally during the synthesis of the Rpb10 subunit.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Niko Linzer, Alexis Trumbull, Rukiye Nar, Matthew D. Gibbons, David T. Yu, John Strouboulis, Joerg Bungert
Summary: TFII-I, a key transcription factor, plays crucial roles in regulating Pol II transcription at the stages of initiation and elongation by interacting with various co-regulators and influencing transcription positively or negatively. Its expression changes are associated with a range of diseases and developmental processes, highlighting its important role in gene regulation.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Kai Zhou, Songkuan Zhuang, Fulong Liu, Yanheng Chen, You Li, Shihui Wang, Yuxuan Li, Huixin Wen, Xiaohua Lin, Jie Wang, Yue Huang, Cailing He, Nan Xu, Zongshu Li, Lang Xu, Zixuan Zhang, Lin-Feng Chen, Ruichuan Chen, Min Liu
Summary: P-TEFb modulates RNA polymerase II elongation through interaction with Brd4 and SEC. This study uncovers a novel mechanism for the reassembly of Cdk9 and CycT1 monomers on chromatin to form active P-TEFb.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Amr Elghondakly, Chih Hao Wu, Steven Klupt, Jonathan Goodson, Wade C. Winkler
Summary: Bacterial NusG interacts with RNA polymerase through its N-terminal domain, and its C-terminal domain forms dynamic interactions with various factors to affect transcription elongation. LoaP binds to a small RNA hairpin in the 50 leader region of its target operons with high affinity and specificity, expanding the repertoire of macromolecular interactions exhibited by NusG.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Nikoleta Giarimoglou, Adamantia Kouvela, Ioanna Patsi, Jinwei Zhang, Vassiliki Stamatopoulou, Constantinos Stathopoulos
Summary: The stem Sa in T-box riboswitches plays an important role in regulating transcription in Staphylococcus aureus, including antibiotic binding and discrimination of tRNA isoacceptors. Insertion of stem Sa in other bacteria leads to different transcriptional effects, providing insights into the regulatory mechanisms of T-box riboswitches.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Karla T. Falcon, Kristin E. N. Watt, Soma Dash, Ruonan Zhao, Daisuke Sakai, Emma L. Moore, Sharien Fitriasari, Melissa Childers, Mihaela E. Sardiu, Selene Swanson, Dai Tsuchiya, Jay Unruh, George Bugarinovic, Lin Li, Rita Shiang, Annita Achilleos, Jill Dixon, Michael J. Dixon, Paul A. Trainor
Summary: This study investigates the importance of ribosomal RNA (rRNA) transcription in craniofacial development and the implications of disruptions in this process. The researchers discovered that high expression of Pol I subunits in neuroepithelium and neural crest cells (NCCs) sustains elevated rRNA transcription, supporting the high levels of protein translation in these cells. However, disruptions in rRNA synthesis in NCCs can lead to p53 protein accumulation, NCC apoptosis, and craniofacial anomalies. Compound mutations in Pol I subunits further exacerbate these anomalies. Mechanistically, diminished rRNA synthesis causes an imbalance between rRNA and ribosomal proteins, affecting the binding of these proteins with Mdm2 and p53. This study highlights the critical role of rRNA transcription in craniofacial development and its specific sensitivities to disruptions in certain congenital craniofacial disorders.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Microbiology
Hiroyuki Okano, Rutger Hermsen, Terence Hwa
Summary: Bacteria grown on a mixture of carbon substrates exhibit two utilization patterns: hierarchical utilization (HU) and simultaneous utilization (SU). Recent studies have addressed various open questions from mechanistic, physiological, and ecological perspectives, shedding light on the behaviors and strategies adopted by cells in utilizing different carbon substrates.
CURRENT OPINION IN MICROBIOLOGY
(2021)
Article
Physics, Multidisciplinary
Gabriel Knotz, Ulrich Parlitz, Stefan Klumpp
Summary: The cell cycle has a significant impact on the dynamics of oscillatory gene circuits, leading to quasiperiodic motion and the formation of synchronization windows. The size of these windows is influenced by the timing of gene doubling and the location of the genes.
NEW JOURNAL OF PHYSICS
(2022)
Article
Multidisciplinary Sciences
Chenhao Wu, Rohan Balakrishnan, Nathan Braniff, Matteo Mori, Gabriel Manzanarez, Zhongge Zhang, Terence Hwa
Summary: Many cellular activities in bacteria are organized according to their growth rate. The accepted notion is that the growth rate is measured by ppGpp in bacterial physiology. Through quantitative experiments, it has been shown that the ppGpp pool responds inversely to the rate of translational elongation in Escherichia coli. In addition to its role in inhibiting ribosome biogenesis and activity, ppGpp forms a regulatory circuit that enables the cell to perceive and control its growth rate under different conditions. The linear growth law relating ribosome content and growth rate emerges as a consequence of maintaining a supply of ribosome reserves while preserving the elongation rate in slow growth conditions. Further analysis suggests that the elongation rate itself is detected by sensing the ratio of dwelling and translocating ribosomes, which collapses the complex dynamics of molecular processes into a physiological state of the whole cell.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Trang T. H. Nguyen, Emily J. Zakem, Ali Ebrahimi, Julia Schwartzman, Tolga Caglar, Kapil Amarnath, Uria Alcolombri, Francois J. Peaudecerf, Terence Hwa, Roman Stocker, Otto X. Cordero, Naomi M. Levine
Summary: Micro-scale microbial community dynamics significantly impact the fate of sinking particles in the ocean, playing a crucial role in global carbon cycling and future climate. By scaling-up essential features of particle-associated microbial dynamics, this study provides mechanistic insight into the contribution of microbes to the vertical carbon flux in the ocean.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Agnese Codutti, Mohammad A. Charsooghi, Elisa Cerda-Donate, Hubert M. Taieb, Tom Robinson, Damien Faivre, Stefan Klumpp, Raymond E. Goldstein
Summary: In this study, magnetically steerable microswimmers, specifically magnetotactic bacteria, were trapped in micrometer-sized microfluidic chambers and their motion was tracked and analyzed. The researchers observed a variety of different trajectories, depending on the chamber size and the strength of the magnetic field. Combining experimental observations with simulations, they explained the diversity of trajectories by the interplay between wall interactions and the magnetic torque. The study also highlighted the importance of single-cell tracking for understanding motility patterns and established a basis for analyzing and predicting microswimmer motility in more complex environments.
Article
Chemistry, Physical
Omar Munoz, Stefan Klumpp
Summary: This study proposes a model that extends the tug-of-war model by incorporating a mechanism of motor activation and inactivation. The model successfully explains some observations that are inconsistent with a simple tug-of-war scenario, including long unidirectional runs and a directional memory after unbinding from the filament.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Multidisciplinary Sciences
Tomoya Honda, Jonas Cremer, Leonardo Mancini, Zhongge Zhang, Teuta Pilizota, Terence Hwa
Summary: This study systematically investigates the coordination of motility gene expression with cellular physiology in bacteria. The results suggest that bacteria up-regulate the expression of motility genes at slow growth to compensate for reduction in cell size. This simple regulatory objective allows bacteria to maintain motility across a broad range of growth conditions, while minimizing biosynthetic and energetic demands. Additionally, the study reveals that larger cell size at fast growth is an efficient strategy to allocate cellular resources to biomass synthesis and growth, while maintaining processes such as motility that are only needed on a per-cell basis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Editorial Material
Biophysics
Stefan Klumpp
BIOPHYSICAL JOURNAL
(2023)
Review
Microbiology
Matthew Scott, Terence Hwa
Summary: This review describes how physiological constraints are sensed through metabolic fluxes and how flux-controlled regulation gives rise to simple empirical relations between protein levels and the rate of cell growth.
NATURE REVIEWS MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Rohan Balakrishnan, Matteo Mori, Igor Segota, Zhongge Zhang, Ruedi Aebersold, Christina Ludwig, Terence Hwa
Article
Microbiology
Chenhao Wu, Matteo Mori, Miriam Abele, Amir Banaei-Esfahani, Zhongge Zhang, Hiroyuki Okano, Ruedi Aebersold, Christina Ludwig, Terence Hwa
Summary: Bacterial fitness depends on their ability to adapt to changing environments. Escherichia coli, for example, primarily expresses protein synthesis machinery in rich growth medium and biosynthetic enzymes in minimal medium. By analysing timing of enzyme expression, quantitative proteomics has revealed a positive relation between onset time of enzyme synthesis and enzyme reserve in E. coli. A coarse-grained kinetic model based on proteomes has been developed to capture enzyme recovery kinetics and infer regulatory strategies underlying the gene expression program of E. coli.
NATURE MICROBIOLOGY
(2023)
Article
Microbiology
Arion Iffland-Stettner, Hiroyuki Okano, Matti Gralka, Ghita Guessous, Kapil Amarnath, Otto X. X. Cordero, Terence Hwa, Sebastian Bonhoeffer
Summary: A genome-scale metabolic model of V. splendidus 1A01 was reconstructed, offering solutions to the technical problems associated with model reconstruction for a marine bacterial strain like V. splendidus 1A01.
Article
Multidisciplinary Sciences
Matteo Mori, Chuankai Cheng, Brian R. Taylor, Hiroyuki Okano, Terence Hwa
Summary: This article presents a theoretical framework called FDM to quantify the contribution of each metabolic reaction to cellular functions. It highlights the importance of energy allocation in cell growth.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Ghita Guessous, Vadim Patsalo, Rohan Balakrishnan, Tolga caglar, James R. Williamson, Terence Hwa
Summary: Chitin-degrading bacteria have developed a mechanism of utilizing chitinases to sustain growth and dispersal, enabling them to explore new habitats without compromising their fitness on previously colonized ones.
NATURE MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Matteo Mori, Zhongge Zhang, Amir Banaei-Esfahani, Jean-Benoit Lalanne, Hiroyuki Okano, Ben C. Collins, Alexander Schmidt, Olga T. Schubert, Deok-Sun Lee, Gene-Wei Li, Ruedi Aebersold, Terence Hwa, Christina Ludwig
Summary: Accurate quantification of over 2,000 proteins in Escherichia coli under > 60 growth conditions using a new mass spectrometry workflow led to novel biological findings, providing valuable resources for systems biology and future multi-omics studies.
MOLECULAR SYSTEMS BIOLOGY
(2021)
