Article
Biochemistry & Molecular Biology
Cecile Evrin, Albert Serra-Cardona, Shoufu Duan, Progya P. Mukherjee, Zhiguo Zhang, Karim P. M. Labib
Summary: In eukaryotes, the essential factor Spt5 plays a direct role in the process of re-deposition of nucleosomal histones during transcription. It contains an acidic amino terminal tail called Spt5N, which has a histone-binding motif that is essential for yeast cell viability.
Review
Biochemistry & Molecular Biology
Neha Singh, Mohd Asalam, Mohd Owais Ansari, Nadezhda S. Gerasimova, Vasily M. Studitsky, Md Sohail Akhtar
Summary: The epigenetic phenomenon plays a role in the phenotypic variation of organisms by regulating the transcription of protein coding genes. The carboxy terminal domain (CTD) of RNA Polymerase II is thought to bind different protein complexes involved in mRNA biogenesis and export. The epigenetic modifications of CTD mediate its interaction with chromatin and influence histone modifications.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
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)
Article
Plant Sciences
Simon Obermeyer, Richard Stoeckl, Tobias Schnekenburger, Christoph Moehle, Uwe Schwartz, Klaus D. Grasser
Summary: Transcript elongation by RNA polymerase II (RNAPII) plays a significant role in plant development and response to environmental cues. The heterohexameric polymerase-associated factor 1 complex (PAF1C) stabilizes RNAPII elongation complex and promotes efficient transcript synthesis. This study reveals distinct transcriptional responses of PAF1C subunit mutants ELF7 and CDC73 to high salt exposure, suggesting their (partial) specific functions.
FRONTIERS IN PLANT SCIENCE
(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
Biochemistry & Molecular Biology
Zhitai Hao, Vitaly Epshtein, Kelly H. Kim, Sergey Proshkin, Vladimir Svetlov, Venu Kamarthapu, Binod Bharati, Alexander Mironov, Thomas Walz, Evgeny Nudler
Summary: Rho is a crucial factor in transcription termination in bacteria, forming a pre-termination complex with RNAP and elongation factors to stabilize the process. RNA interacts with NusA before entering the central channel of Rho, highlighting the critical role of these interactions in termination. The study supports a mechanism where the formation of a persistent pre-termination complex is essential for the termination process.
Article
Biochemistry & Molecular Biology
Aiste Kasiliauskaite, Karel Kubicek, Tomas Klumpler, Martina Zanova, David Zapletal, Eliska Koutna, Jiri Novacek, Richard Stefl
Summary: This study visualized the architecture of Spt6 from Saccharomyces cerevisiae using cryo-electron microscopy and small-angle X-ray scattering, and found that the flexible N- and C-termini of Spt6 are critical for its function. The N-terminal region of Spt6 prevents its binding to Pol II CTD, Pol II CTD-linker, pre-formed intact nucleosomes and nucleosomal DNA. Additionally, Spt6 promotes nucleosome assembly in vitro through the cooperation between its intrinsically disordered and structured regions.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Junaid Akhtar, Yoan Renaud, Steffen Albrecht, Yad Ghavi-Helm, Jean-Yves Roignant, Marion Silies, Guillaume Junion
Summary: m(6)A RNA modification regulates RNAP II pausing in Drosophila cells, affecting pause release, Ser2P occupancy, and nascent RNA transcription. The m(6)A-mediated gene regulation adds another layer to the control of gene expression.
Article
Multidisciplinary Sciences
Amit K. Singh, Qingrong Chen, Cu Nguyen, Daoud Meerzaman, Dinah S. Singer
Summary: Cohesin plays a role in regulating alternative splicing by interacting with splicing factors and influencing splicing patterns. Mutations in cohesin are associated with distinct splicing patterns in acute myeloid leukemia, and cohesin interacts with another splicing regulator, BRD4, to generate unique splicing patterns. These findings provide insights into the role of cohesin in both normal and leukemic cells and its contribution to human disease.
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)
Article
Biochemistry & Molecular Biology
Jose Garcia-Martinez, Maria E. Perez-Martinez, Jose E. Perez-Ortin, Paula Alepuz
Summary: This study demonstrates the crucial role of Xrn1 in the transcriptional response of yeast cells to osmotic stress, showing that a lack of Xrn1 results in significantly lower transcriptional induction of upregulated genes, despite similar high levels of their transcripts due to parallel mRNA stabilization. In addition, Xrn1 seems to be directly involved in the formation of a competent elongation complex, recruiting to stress-upregulated genes in parallel with the RNAPII complex.
Article
Multidisciplinary Sciences
Tyler K. Fenstermaker, Svetlana Petruk, Sina K. Kovermann, Hugh W. Brock, Alexander Mazo
Summary: During DNA replication, the transcriptional machinery is believed to dissociate from DNA. However, our study shows that immediately after replication, Pol II, together with other general transcription proteins and immature RNA, re-associates with active genes on both leading and lagging strands of nascent DNA, and rapidly resumes transcription. This suggests that epigenetic marks may not be required for the recruitment of Pol II to newly synthesized DNA during the transition from replication to transcription.
Article
Medicine, Research & Experimental
Shane D. Falcinelli, Jackson J. Peterson, Anne-Marie W. Turner, David Irlbeck, Jenna Read, Samuel L. M. Raines, Katherine S. James, Cameron Sutton, Anthony Sanchez, Ann Emery, Gavin Sampey, Robert Ferris, Brigitte Allard, Simon Ghofrani, Jennifer L. Kirchherr, Caroline Baker, JoAnn D. Kuruc, Cynthia L. Gay, Lindsey I. James, Guoxin Wu, Paul Zuck, Inmaculada Rioja, Rebecca C. Furze, Rab K. Prinjha, Bonnie J. Howell, Ronald Swanstrom, Edward P. Browne, Brian D. Strahl, Richard M. Dunham, Nancie M. Archin, David M. Margolis
Summary: This study demonstrates the synergy in latent reservoir activation when using inhibitor of apoptosis protein (IAP) antagonists in combination with bromodomain and extraterminal domain protein inhibitors (BETi). It also highlights the importance of HIV transcriptional elongation and splicing as barriers to latent HIV protein expression, providing a rationale for further exploration of IAPi+BETi in animal models of HIV latency.
JOURNAL OF CLINICAL INVESTIGATION
(2022)
Article
Multidisciplinary Sciences
Lara Djakovic, Thomas Hennig, Katharina Reinisch, Andrea Milic, Adam W. Whisnant, Katharina Wolf, Elena Weiss, Tobias Haas, Arnhild Grothey, Christopher S. Juerges, Michael Kluge, Elmar Wolf, Florian Erhard, Caroline C. Friedel, Lars Doelken
Summary: HSV-1 infection disrupts transcription termination by RNA Polymerase II and leads to increased chromatin accessibility downstream of genes. The immediate-early protein ICP22 of HSV-1 is found to induce open chromatin downstream of genes when transcription termination is disrupted, accompanied by histone loss downstream of affected genes.
NATURE COMMUNICATIONS
(2023)
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.
Article
Microbiology
Natalia Voskoboynikova, Maria Karlova, Rainer Kurre, Armen Y. Mulkidjanian, Konstantin Shaitan, Olga S. Sokolova, Heinz-Juergen Steinhoff, Juergen J. Heinisch
Summary: In this study, Wsc1 was purified by trapping in water-soluble polymer-stabilized lipid nanoparticles, allowing for its extraction from yeast plasma membrane without denaturation. The structure of Wsc1 was characterized, providing new prospects for in vitro studies of yeast plasma proteins and potentially other fungi, including plant and human pathogens.
Review
Chemistry, Physical
Daniel Espiritu, Anna K. Gribkova, Shubhangi Gupta, Alexey K. Shaytan, Anna R. Panchenko
Summary: Cancer involves the interplay between the genome and epigenome at the cellular level, with nucleosomes playing a crucial role. Mutations, changes in expression, and slicing of histones can affect epigenetic dysregulation and carcinogenesis. The differential expression of histone variants and isoforms is linked to cancer phenotypes.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Multidisciplinary Sciences
Grigoriy A. Armeev, Anastasiia S. Kniazeva, Galina A. Komarova, Mikhail P. Kirpichnikov, Alexey K. Shaytan
Summary: Nucleosomes tightly wrap around 147 DNA base pairs with an octamer of histone proteins, and their dynamics enable DNA unwrapping and sliding. Molecular dynamics simulations revealed functional modes of nucleosome dynamics such as DNA breathing, unwrapping, twisting, and sliding. This study highlights the importance of nucleosomal DNA dynamics in chromatin conformational variability and the effects of chromatin modifications.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Kim Adameyko, Anton Burakov, Alexander D. Finoshin, Kirill Mikhailov, Oksana Kravchuk, Olga S. Kozlova, Nicolay G. Gornostaev, Alexander Cherkasov, Pavel A. Erokhov, Maria I. Indeykina, Anna E. Bugrova, Alexey S. Kononikhin, Andrey Moiseenko, Olga S. Sokolova, Artem N. Bonchuk, Irina Zhegalova, Anton A. Georgiev, Victor S. Mikhailov, Natalia E. Gogoleva, Guzel R. Gazizova, Elena Shagimardanova, Oleg A. Gusev, Yulia Lyupina
Summary: Ferritins are a conservative family of proteins found in all species, playing essential roles in resistance to redox stress, immune response, and cell differentiation. The study characterized ferritins in two cold-water sponges, revealing their regulation by cellular iron and oxygen levels, and their importance in various biological processes. Further research is needed to explore the function of atypical ferritins lacking iron-binding capacity in invertebrate species.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Food Science & Technology
Yulia Berezhnaya, Irina Bikaeva, Anastasiia Gachkovskaia, Artem Demidenko, Natalia Klimenko, Alexander Tyakht, Olesya Volokh, Dmitry Alexeev
Summary: The study compared cost-efficient and accurate methods for quantifying probiotics in dairy products, finding that cultivation-independent techniques had advantages over traditional cultivation-based ones. The evaluation of Lacticaseibacillus casei and rhamnosus levels in fermented dairy products with different starter cultures showed that formulations with Streptococcus and Lactobacillus had lower probiotic abundance compared to those containing Bifidobacterium in the starter culture.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Anatomy & Morphology
Dmitry Bagrov, Grigory S. Glukhov, Andrey Moiseenko, Maria G. Karlova, Daniil S. Litvinov, Petr A. Zaitsev, Liubov Kozlovskaya, Anna A. Shishova, Anastasia A. Kovpak, Yury Y. Ivin, Anastasia N. Piniaeva, Alexey S. Oksanich, Viktor P. Volok, Dmitry Osolodkin, Aydar A. Ishmukhametov, Alexey M. Egorov, Konstantin Shaitan, Mikhail P. Kirpichnikov, Olga S. Sokolova
Summary: This study characterized the beta-propiolactone inactivated SARS-CoV-2 virions using TEM and AFM, finding that samples prepared using SEC and IEC retained more spikes on the surface and the S proteins were in the pre-fusion conformation. Analytical TEM showed that the inactivated virions retained nucleic acid, demonstrating their potential as a vaccine candidate.
MICROSCOPY RESEARCH AND TECHNIQUE
(2022)
Article
Biochemical Research Methods
Anastasia Pechelyulko, Zhanna Andreeva-Kovalevskaya, Dmitriy Dmitriev, Viacheslav Lavrov, Yulia Massino, Alexey Nagel, Olga Segal, Olga S. Sokolova, Alexander Solonin, Yulia Tarakanova, Alexander Dmitriev
Summary: The study presents an optimized method for obtaining VLPs of recombinant HCV core protein expressed in yeast cells, which can be used for diagnostic test systems and vaccine engineering. The procedure involves in vitro self-assembly of HCcAg molecules into VLPs during protein purification, resulting in VLPs with around 90% purity.
PROTEIN EXPRESSION AND PURIFICATION
(2021)
Article
Virology
Anastasia S. Shchurova, Mikhail M. Shneider, Nikolay P. Arbatsky, Alexander S. Shashkov, Alexander O. Chizhov, Yuriy P. Skryabin, Yulia Mikhaylova, Olga S. Sokolova, Andrey A. Shelenkov, Konstantin A. Miroshnikov, Yuriy A. Knirel, Anastasia Popova
Summary: Acinetobacter baumannii is a significant nosocomial pathogen capable of producing structurally diverse capsular polysaccharides, which are targeted by bacteriophages encoding polysaccharide-degrading enzymes. A newly isolated myovirus, TaPaz, was found to infect A. baumannii strains with K47 capsular polysaccharide structure, containing genes for two tailspike depolymerases. One of these depolymerases was shown to specifically cleave the K47 CPS through a hydrolytic mechanism.
Article
Virology
Olga Yu Timoshina, Mikhail M. Shneider, Peter Evseev, Anastasia S. Shchurova, Andrey A. Shelenkov, Yulia Mikhaylova, Olga S. Sokolova, Anastasia A. Kasimova, Nikolay P. Arbatsky, Andrey S. Dmitrenok, Yuriy A. Knirel, Konstantin A. Miroshnikov, Anastasia Popova
Summary: The study focused on a novel pathogenic bacteriophage Aristophanes which can affect the sugar polysaccharide structure of A.baumannii strains, belonging to a new genus of the subfamily Beijerinckvirinae of the family Autographiviridae.
Article
Cell Biology
Nadezhda S. Gerasimova, Olesya Volokh, Nikolay A. Pestov, Grigory A. Armeev, Mikhail P. Kirpichnikov, Alexey K. Shaytan, Olga S. Sokolova, Vasily M. Studitsky
Summary: Transcription by RNA polymerase II in chromatin involves the formation of small intranucleosomal DNA loops (i-loops) containing the enzyme, which are important for histone survival and transcription arrest during the transcription of damaged DNA. This study determined the structures of i-loops formed during transcription through nucleosomes with intact or damaged DNA using biochemical methods and electron microscopy. The results showed that i-loop formation is more efficient in the presence of single-strand DNA-binding proteins behind the transcribing enzyme, suggesting a potential role in transcription-coupled repair of hidden DNA damage in chromatin structure.
Article
Biochemistry & Molecular Biology
Olesya I. I. Volokh, Anastasia L. L. Sivkina, Andrey V. V. Moiseenko, Anna V. V. Popinako, Maria G. G. Karlova, Maria E. E. Valieva, Elena Y. Y. Kotova, Mikhail P. P. Kirpichnikov, Timothy Formosa, Vasily M. M. Studitsky, Olga S. S. Sokolova
Summary: In this study, the effects of curaxin CBL0137 on nucleosome unfolding by FACT were analyzed. It was found that curaxin can induce FACT-dependent nucleosome unfolding and trap FACT in the chromatin of cancer cells. The obtained models suggest novel mechanisms of nucleosome unfolding by FACT and c-trapping by curaxins.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Review
Crystallography
Y. G. Kacher, M. G. Karlova, G. S. Glukhov, H. Zhang, E. V. Zaklyazminskaya, G. Loussouarn, O. S. Sokolova
Summary: Membrane proteins, especially ion channels, became the focus of structural proteomics in the mid-20th century. Studies on ion channels involve diverse methods, including structural (such as X-ray crystallography, cryoelectron microscopy, and patch clamp) and functional approaches. The contribution of electrophysiological studies and molecular dynamics, along with advancements in X-ray crystallography and cryoelectron microscopy, have enabled the obtainment of atomic structure of ion channels.
CRYSTALLOGRAPHY REPORTS
(2021)
Article
Crystallography
I. S. Panina, A. A. Mamchur, I. A. Yaroshevich, D. V. Zlenko, E. B. Pichkur, S. S. Kudryavtseva, V. I. Muronetz, O. S. Sokolova, T. B. Stanishneva-Konovalova
Summary: The three-dimensional reconstruction of GroEL apo-form obtained by cryo-EM and MD calculations reveals a diverse mobility of the protein subunit domains, providing important insights into the mechanism of protein folding in the GroEL cavity.
CRYSTALLOGRAPHY REPORTS
(2021)
Meeting Abstract
Biochemistry & Molecular Biology
O. Volokh, A. Sivkina, M. Karlova, E. Kotova, V. Studitsky, O. S. Sokolova
Meeting Abstract
Biochemistry & Molecular Biology
Y. Kacher, M. Karlova, V. Rusinova, D. Abramochkin, E. Zaklyazminskaya, O. S. Sokolova
