Article
Plant Sciences
V. Miguel Palomar, Sarah Jaksich, Sho Fujii, Jan Kucinski, Andrzej T. Wierzbicki
Summary: In this study, the genome-wide pattern of plastid-encoded RNA polymerase (PEP) binding to chloroplast DNA was investigated using plastid chromatin immunoprecipitation-sequencing (ptChIP-seq) method. The results showed that PEP has a complex DNA binding pattern with preferential association at genes encoding rRNA, tRNA, and a subset of photosynthetic proteins in mature Arabidopsis thaliana chloroplasts. Sigma factors SIG2 and SIG6 were found to have effects on PEP binding to a subset of tRNA genes and throughout the rest of the genome. PEP binding was commonly enriched on gene promoters, around transcription start sites, and the levels of PEP binding to DNA were correlated with levels of RNA accumulation.
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
Multidisciplinary Sciences
Dingwei He, Linlin You, Xiaoxian Wu, Jing Shi, Aijia Wen, Zhi Yan, Wenhui Mu, Chengli Fang, Yu Feng, Yu Zhang
Summary: This study investigates the mechanism of SutA's action on RNAP. Cryo-EM structures reveal how SutA assists RNAP in unwinding the promoter DNA. These findings are significant for understanding the function of SutA and the transcription regulation mechanism during bacterial infection.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Sijie Liu, Yu Hua, Jingna Wang, Lingyan Li, Junjie Yuan, Bo Zhang, Ziyang Wang, Jianguo Ji, Daochun Kong
Summary: Protection of 30 overhangs in DNA double-strand breaks (DSBs) repair is achieved through the transient formation of RNA-DNA hybrids, with RNA polymerase III (RNAPIII) responsible for synthesizing the RNA strand. CtIP and MRN nuclease activity are required for initiating RNAPIII-mediated RNA synthesis at DSBs. Reduced RNAPIII levels suppress homologous recombination (HR) and lead to genetic loss > 30 bp at DSBs.
Article
Chemistry, Multidisciplinary
Valentina Milasinovic, Kresimir Molcanov
Summary: The structural analysis of six new co-crystals revealed the presence of sandwich-like I-quinone-I- structures, with the competition between this motif and halogen bonding being described for the first time. The black color of the crystals indicates charge transfer from iodide to the quinoid ring, interpreted as n -> pi*. Intermolecular interactions were analyzed using Hirshfeld surfaces and Voronoi-Dirichlet polyhedra.
Article
Multidisciplinary Sciences
Ilona Christy Unarta, Siqin Cao, Shintaroh Kubo, Wei Wang, Peter Pak-Hang Cheung, Xin Gao, Shoji Takada, Xuhui Huang
Summary: The study elucidated the dynamics of Thermus aquaticus holoenzyme's gate opening using a quasi-Markov State Model, revealing the differential roles of beta-lobe and clamp in DNA loading and the mechanism by which Myxopyronin inhibits clamp opening. Additionally, a critical role of beta-lobe in DNA loading was uncovered, presenting an opportunity for the development of antibiotics targeting this region of RNAP. The study also demonstrated the potential of quasi-Markov State Models in studying biomolecular dynamics based on generalized master equation formalism.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biotechnology & Applied Microbiology
Ye Wang, Qingyang Li, Pingfang Tian, Tianwei Tan
Summary: This review highlights the potential of RNA polymerases in metabolic engineering and synthetic biology.
BIOTECHNOLOGY ADVANCES
(2022)
Review
Biochemistry & Molecular Biology
Sabina Kedzierska-Mieszkowska
Summary: This review aims to summarize the current understanding of the role of s factors in Leptospira interrogans, a highly invasive spirochaete responsible for leptospirosis. The disease has a significant impact on public health and the global economy. S factors are key regulators of gene expression in bacteria and play a crucial role in bacterial adaptative response to different environmental stimuli. The L. interrogans genome encodes a total of 14 s factors, including one housekeeping factor and three types of alternative factors. The characteristics and possible role of these factors in gene regulation and pathogen adaptability are discussed.
Article
Multidisciplinary Sciences
Ruth M. Saecker, James Chen, Courtney E. Chiu, Brandon Malone, Johanna Sotiris, Mark Ebrahim, Laura Y. Yen, Edward T. Eng, Seth A. Darst
Summary: The initial step in gene expression requires opening the DNA duplex for RNA synthesis. Differences in DNA sequence and length upstream of the start site globally alter interactions between DNA and RNAP, impacting RPo lifetime and subsequent transcription steps. Limited sequence changes can trigger global alterations in the transcription bubble, modulating RPo lifetime and affecting the transcription cycle.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Linlin You, Expery O. Omollo, Chengzhi Yu, Rachel A. Mooney, Jing Shi, Liqiang Shen, Xiaoxian Wu, Aijia Wen, Dingwei He, Yuan Zeng, Yu Feng, Robert Landick, Yu Zhang
Summary: Efficient and accurate termination of gene transcription is essential for all living organisms. Both bacterial and eukaryotic RNA polymerases can terminate transcription through an independent factor pathway called intrinsic termination transcription. In this study, we used cryo-electron microscopy to analyze the structures of Escherichia coli transcription intrinsic termination complexes, which provide insights into the structural mechanism of bacterial termination and the pathway for RNA and DNA release relevant for all RNA polymerases.
Article
Biochemistry & Molecular Biology
Lucas Farnung, Moritz Ochmann, Gaurika Garg, Seychelle M. Vos, Patrick Cramer
Summary: During gene transcription, the presence of human elongation factors DSIF, PAF1 complex (PAF), RTF1, SPT6, and TFIIS facilitates efficient nucleosome passage by RNA polymerase II.
Article
Multidisciplinary Sciences
Linlin You, Expery O. Omollo, Chengzhi Yu, Rachel A. Mooney, Jing Shi, Liqiang Shen, Xiaoxian Wu, Aijia Wen, Dingwei He, Yuan Zeng, Yu Feng, Robert Landick, Yu Zhang
Summary: Efficient and accurate termination of gene transcription is crucial for all living organisms. This study uses cryo-electron microscopy to reveal the structural mechanism of bacterial intrinsic termination, where RNA polymerase pauses at terminator sequences, terminator RNA undergoes hairpin folding, and RNA polymerase rewinds the transcription bubble to release RNA and DNA. These findings provide insights into the pathway of factor-independent termination by all RNA polymerases.
Editorial Material
Biochemistry & Molecular Biology
Adam Osinski, Vincent S. Tagliabracci
Summary: The study elucidates the structural intricacies of the SARS-CoV-2 NiRAN domain and sheds light on its remarkable versatility in viral replication.
Article
Microbiology
Pascal Schmidt, David Brandt, Tobias Busche, Joern Kalinowski
Summary: A method called ROSE was developed for characterizing bacterial promoters genome-wide using in vitro transcription coupled to transcriptome sequencing. ROSE identified 3226 transcription start sites in E. coli K-12 MG1655 genomic DNA, with 2167 also identified in in vivo studies and 598 being new. In vivo experiments confirmed that ROSE could identify repressed promoters not detected in in vivo experiments. Therefore, ROSE is a complementary method to study bacterial transcriptional networks and can identify promoters not captured by in vivo transcriptome studies.
Article
Microbiology
Amy Switzer, Lynn Burchell, Panagiotis Mitsidis, Teresa Thurston, Sivaramesh Wigneshweraraj
Summary: The canonical function of sigma factor is to determine the gene specificity of RNA polymerase. Sigma(54) uniquely confers distinct functional and regulatory properties on RNAP in various bacterial species. The absence of sigma(54) in uropathogenic E. coli results in different colony sizes appearing at different times, suggesting a non-canonical function of sigma(54) in regulating genetic information flow.
JOURNAL OF BACTERIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)