Article
Cell Biology
Alejandro Collin, Araceli Gonzalez-Jimenez, Maria del Carmen Gonzalez-Jimenez, Manuel J. Alfonso, Olga Calvo
Summary: Saccharomyces cerevisiae Sub1 is a transcriptional stimulatory protein that shares homology with the ssDNA binding domain (ssDBD) of human PC4. This study reveals the key residues responsible for DNA-ScSub1 interaction in vivo, localized in the ssDBD, and demonstrates that the carboxyl-terminal (CT) region is required for transcription elongation. These findings indicate that Sub1 plays a dual role in transcription, participating in initiation through the ssDBD and in elongation through the CT region.
Article
Chemistry, Medicinal
Yuantao Fu, Yanzhi Zhang, Haiying Sun
Summary: Dysfunction of BET family proteins is associated with various human diseases, making them promising targets for drug development. Most current clinical BET inhibitors lack selectivity, but selective inhibitors targeting BD1 and BD2 are being developed to elucidate their distinct functions.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Zhenning Wang, Aixia Song, Hao Xu, Shibin Hu, Bolin Tao, Linna Peng, Jingwen Wang, Jiabei Li, Jiali Yu, Li Wang, Ze Li, Xizi Chen, Mengyun Wang, Yayun Chi, Jiong Wu, Yanhui Xu, Hai Zheng, Fei Xavier Chen
Summary: The transcription regulator PAF1 directly affects pausing and elongation during transcription, and also influences the deposition of epigenetic marks it controls. PAF1 degradation leads to the release of polymerase and a decline in histone modifications, which ultimately affects the production of transcriptional outputs.
Article
Biochemistry & Molecular Biology
Ruth Q. Jacobs, Zachariah M. Ingram, Aaron L. Lucius, David A. Schneider
Summary: Eukaryotes express three nuclear DNA-dependent RNA polymerases responsible for synthesizing all RNA required by the cell. Despite structural homology, these polymerases have functionally diverged to suit their distinct cellular roles. Direct comparison of their enzymatic properties is difficult due to disparate experimental conditions and techniques, but studies have revealed that Pol I is faster, less stable, and more error-prone than Pol II.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Thoma Itoh, Takashi Makino
Summary: Recent advancements in high throughput single cell RNA-seq have enabled the identification of functional compensation effects of gene perturbations through noise change, which can be measured quantitatively and captured in gene regulatory networks.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Bazile Ravoityte, Juliana Luksa, Ralf Erik Wellinger, Saulius Serva, Elena Serviene
Summary: This study analyzed the impact of L-A virus on gene expression in yeast hosts using high-throughput RNA sequencing data. It was found that the presence of L-A virus resulted in moderate alterations in gene expression, particularly in genes involved in ribosome biogenesis. Additionally, the transcriptional responses to L-A maintenance were similar to those induced by stress or nutrient availability. The study also identified yeast transcriptional regulators that modulate the levels of L-A dsRNA in cells.
Article
Biochemistry & Molecular Biology
Katelyn M. Green, Shannon L. Miller, Indranil Malik, Peter K. Todd
Summary: Repeat-associated non-AUG (RAN) translation of expanded repeat-mutation mRNA produces toxic peptides in neurons of patients suffering from neurodegenerative diseases. Cellular stressors that impair global translation do not inhibit RAN translation, suggesting a different mechanism. DENR, an alternative initiation factor, plays a significant role in RAN translation.
HUMAN MOLECULAR GENETICS
(2022)
Article
Multidisciplinary Sciences
Yosuke Ito, Yuhei Chadani, Tatsuya Niwa, Ayako Yamakawa, Kodai Machida, Hiroaki Imataka, Hideki Taguchi
Summary: The study reveals that nascent chains enriched in acidic amino acids destabilize the translating ribosome, eventually leading to stochastic premature termination in eukaryotes. Such risk of premature termination influences the amino acid distribution in the proteomes.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Bo Bae Lee, Hyeonju Woo, Min Kyung Lee, SeoJung Youn, Sumin Lee, Jae-Seok Roe, Soo Young Lee, TaeSoo Kim
Summary: Chromatin-based regulation of internal cryptic promoters is mediated by core promoter strength as well as transcription elongation factors.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Lukas Verhuelsdonk, Hans Georg Mannherz, Markus Napirei
Summary: The soluble nucleases of the DNase1 family play a crucial role in DNA and chromatin disposal during cell differentiation and death, and are involved in the suppression of anti-nuclear autoimmunity as well as thrombotic microangiopathies. Recombinant murine DNase1, DNase1-like 2, and DNase1-like 3 were expressed and purified using Pichia pastoris, allowing for the characterization of their specific activities and properties. The results suggest that the secretory DNase1 family members work together to achieve optimal DNA degradation and chromatin disposal under various biological conditions.
Article
Biotechnology & Applied Microbiology
Stephanie Rollero, Audrey Bloem, Jeanne Brand, Anne Ortiz-Julien, Carole Camarasa, Benoit Divol
Summary: This study investigated the impact of different nitrogen nutrition strategies on the production of carbon and sulphur volatile compounds by non-Saccharomyces yeasts in grape musts. The results showed specific metabolic signatures for each yeast strain in response to the nature of the nitrogen source, providing insights for modulating the aroma profile of wines produced with non-Saccharomyces species.
Article
Multidisciplinary Sciences
Agnese Cristini, Michael Tellier, Flavia Constantinescu, Clelia Accalai, Laura Oana Albulescu, Robin Heiringhoff, Nicolas Bery, Olivier Sordet, Shona Murphy, Natalia Gromak
Summary: RNase H2 plays a key role in maintaining R-loop homeostasis, promoting transcription, and preventing R-loop-associated inflammation in humans.
NATURE COMMUNICATIONS
(2022)
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
Cell Biology
Alain R. Bonny, Karl Kochanowski, Maren Diether, Hana El-Samad
Summary: The growth slowdown in the hyperosmotic shock response plays a key role, accelerating adaptation by liquidating internal glycogen stores for the osmo-shock response. However, this faster adaptation also leads to increased sensitivity to subsequent osmotic stresses. Stress-induced growth slowdown acts as an arbiter to balance short-term adaptation with long-term robustness.
Article
Biochemistry & Molecular Biology
Jinfan Wang, Byung-Sik Shin, Carlos Alvarado, Joo-Ran Kim, Jonathan Bohlen, Thomas E. Dever, Joseph D. Puglisi
Summary: Through real-time single-molecule fluorescence spectroscopy, it has been found that the eukaryotic 43S preinitiation complex engages with mRNA through a slow, ATP-dependent process and proceeds to scan rapidly and directionally along the 5' untranslated region (5' UTR). Scanning ribosomes can traverse RNA secondary structures, but hairpin structures near the start codons drive them backward in the 5' direction, requiring rescanning.
Article
Biochemistry & Molecular Biology
Rafal Donczew, Steven Hahn
MOLECULAR AND CELLULAR BIOLOGY
(2018)
Article
Biochemistry & Molecular Biology
Derek Pacheco, Linda Warfield, Michelle Brajcich, Hannah Robbins, Jie Luo, Jeff Ranish, Steven Hahn
MOLECULAR AND CELLULAR BIOLOGY
(2018)
Article
Microbiology
Pawel Jaworski, Rafal Donczew, Thorsten Mielke, Christoph Weigel, Kerstin Stingl, Anna Zawilak-Pawlik
FRONTIERS IN MICROBIOLOGY
(2018)
Article
Microbiology
Malgorzata Plachetka, Dorota Zyla-Uklejewicz, Christoph Weigel, Rafal Donczew, Magdalena Donczew, Dagmara Jakimowicz, Anna Zawilak-Pawlik, Jolanta Zakrzewska-Czerwinska
Article
Biology
Rafal Donczew, Linda Warfield, Derek Pacheco, Ariel Erijman, Steven Hahn
Article
Biochemistry & Molecular Biology
Eric J. Tomko, Olivia Luyties, Jenna K. Rimel, Chi-Lin Tsai, Jill O. Fuss, James Fishburn, Steven Hahn, Susan E. Tsutakawa, Dylan J. Taatjes, Eric A. Galburt
Summary: The general transcription factor TFIIH contains three ATP-dependent catalytic activities and functions in nucleotide excision repair and Pol II transcription initiation. While the functions are conserved between metazoans and yeast, yeast TFIIH drives transcription start-site scanning. Human and yeast core-TFIIH complexes lack processive translocation, with the yeast kinase module aiding in robust transcription start-site scanning.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Lisa M. Tuttle, Derek Pacheco, Linda Warfield, Damien B. Wilburn, Steven Hahn, Rachel E. Klevit
Summary: The acidic activation domain (AD) of the yeast transcription factor Gal4 acts through binding to the Med15 subunit of the Mediator complex. The interaction between Gal4 and Med15 occurs through the same fuzzy binding mechanism as Gcn4 AD, indicating a common sequence-independent mechanism for AD-Mediator binding. Conversely, the structured binding partner Gal80 determines the type of protein-protein interaction for the intrinsically disordered protein Gal4 AD.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Pawel Jaworski, Dorota Zyla-Uklejewicz, Malgorzata Nowaczyk-Cieszewska, Rafal Donczew, Thorsten Mielke, Christoph Weigel, Anna Zawilak-Pawlik
Summary: This study reveals the structure of Helicobacter pylori oriC, with the DnaA trio being crucial for DNA unwinding and an observed interplay between DNA unwinding and DnaA binding during replication. This research also identifies a new class of ATP-DnaA boxes in oriC, suggesting a potential new regulatory pathway for orisome assembly in H. pylori.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Linda Warfield, Rafal Donczew, Lakshmi Mahendrawada, Steven Hahn
Summary: This study investigates the genome-wide roles of the mediator factor (MED) in transcription. Rapid depletion of the activator-binding domain (Tail) of MED reveals that it only regulates a small subset of genes. The study also classifies genes into tail-dependent and tail-independent categories and discusses their implications for MED, other coactivators, and transcriptional regulation mechanisms.
Article
Cell Biology
Jeremy A. Schofield, Steven Hahn
Summary: Through studying upstream activating sequences (UASs), core promoters, and other gene features, it was found that most UASs can broadly activate different types of promoters, while a few have strong promoter specificity. However, matching UASs and promoters from the same gene class is generally important for optimal expression. Additionally, sensitivity to MED Tail and SAGA depletion depends on the identity of UAS and core promoter, while dependence on TFIID primarily localizes to the promoter.