Article
Biochemistry & Molecular Biology
Yu-Chien Chen, Szu-Yu Tung, Chia-Wei Huang, Soo-Wah Gan, Bo-Chi Lin, Chia-Wei Chen, Zi-Qi Lin, Chin-Hung Sun
Summary: This study investigated the role of the topoisomerase Spo11 in the encystation process of Giardia lamblia. The findings indicate that Spo11 acts as a positive regulator in activating encystation, interacting with transcription factors involved in cwp gene expression for cyst formation. Disruption of the spo11 gene led to decreased cwp gene expression and cyst formation, highlighting the importance of Spo11 in regulating Giardia differentiation into cysts.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Zhenxing Zhang, Chao Chen, Fan Yang, Yi-Xin Zeng, Pengkai Sun, Ping Liu, Xinjian Li
Summary: A study has found that itaconate, an endogenous metabolite, functions as a lysosomal inducer in macrophages during bacterial infection. It activates the transcription factor TFEB by directly alkylating it, leading to increased lysosomal biogenesis and improved antibacterial ability. Inhibition of itaconate synthesis or expression of a mutant TFEB lacking alkylation impairs macrophage's antibacterial ability, while treatment with a cell-permeable itaconate derivative limits inflammation.
Article
Microbiology
Felix Grunberger, Robert Reichelt, Ingrid Waege, Verena Ned, Korbinian Bronner, Marcell Kaljanac, Nina Weber, Zubeir El Ahmad, Lena Knauss, M. Gregor Madej, Christine Ziegler, Dina Grohmann, Winfried Hausner
Summary: Although copper is essential for cellular life, higher concentrations can be toxic. The study analyzed the transcriptome response of Pyrococcus furiosus to increased copper levels and highlighted the crucial role of the copper-sensing regulator CopR in detoxification.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Microbiology
Alejandro Rodriguez-Gijon, Julia K. Nuy, Maliheh Mehrshad, Moritz Buck, Frederik Schulz, Tanja Woyke, Sarahi L. Garcia
Summary: Our understanding of the size of genomes in Archaea and Bacteria has been biased due to the dominance of cultivated microorganisms in laboratory settings. However, the recent efforts to study uncultivated microorganisms through the cataloging of Earth's microbiomes allow us to revise our perspective on genome size distribution. In our meta-analysis, we found that aquatic and host-associated microbial genomes have the smallest estimated sizes, followed by terrestrial microbial genomes and genomes from isolated microorganisms. The study also highlights the similarities in genome size between metagenomic assembled genomes and isolate genomes.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Ho-Chang Jeong, Siddharth Shukla, Wilson Chun Fok, Thao Ngoc Huynh, Luis Francisco Zirnberger Batista, Roy Parker
Summary: Mutations in the USB1 gene result in hematopoietic failure in patients with poikiloderma with neutropenia. The exact mechanism behind this condition has not been determined, as pre-mRNA splicing remains unaffected. In this study, human embryonic stem cells with the PN-associated mutation in USB1 were generated, and it was found that dysregulated microRNA levels contribute to the hematopoietic failure. Inhibition of PAPD5/7, enzymes responsible for adding 3'-end adenylated tails, rescued hematopoiesis in USB1 mutants, suggesting it as a potential therapy for PN.
Article
Biochemical Research Methods
Dongming Liang, Deirdre C. Tatomer, Jeremy E. Wilusz
Summary: Circular RNAs, generated from eukaryotic protein-coding genes during backsplicing of pre-mRNA, show promise as sensitive biomarkers and markers of readthrough transcription events in Drosophila and human cells. Depletion of transcription termination factors results in increased circular RNA output, suggesting potential for identifying cellular factors impacting transcription termination processes. Techniques utilizing plasmids to generate circular RNA downstream of genomic regions provide a generalizable method for studying RNA polymerase II transcription termination mechanisms.
Article
Multidisciplinary Sciences
Maowu Luo, Lei Bao, Yan Chen, Yuanyuan Xue, Yong Wang, Bo Zhang, Chenliang Wang, Chase D. Corley, Jeffrey G. McDonald, Ashwani Kumar, Chao Xing, Yisheng Fang, Erik R. Nelson, Jennifer E. Wang, Yingfei Wang, Weibo Luo
Summary: The histone reader ZMYND8 is selectively expressed in breast cancer stem cells (BCSCs) and promotes breast tumor initiation through its epigenetic functions by regulating 27-HC metabolism, leading to the accumulation of 27-HC in BCSCs and activation of liver X receptor.
Article
Plant Sciences
Wenxing Chen, Qingyou Zheng, Jinwang Li, Ying Liu, Liqing Xu, Qinglin Zhang, Zhengrong Luo
Summary: The transcription factor DkMYB14 in persimmon fruit has been shown to have dual functions, acting as a repressor in proanthocyanidins (PAs) biosynthesis and as an activator in promoting insolubilization of PAs, ultimately leading to the elimination of astringency in the fruit.
Article
Biotechnology & Applied Microbiology
Sabrina Gfrerer, Dennis Winkler, Julia Novion Ducassou, Yohann Coute, Reinhard Rachel, Johannes Gescher
Summary: This study demonstrates the existence of an S-layer protein on the cytoplasmic membrane of Candidatus Micrarchaeum harzensis A_DKE, suggesting that the ability to form an S-layer may be a common trait among Micrarchaeota. The research also provides insights into the interaction between Micrarchaeota and their host organisms, shedding light on the limited metabolic capabilities shared by several DPANN archaea.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(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
Multidisciplinary Sciences
Senhao Zhang, Mohan B. Singh, Prem L. Bhalla
Summary: Soybean is a vital oilseed legume crop that relies on flowering for seed production, which is regulated by both environmental and endogenous factors. Certain FT homologs in soybean play roles in floral transition, with GmFT7 showing strong expression during this period.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Chang-Hyun Kim, Sang-Moo Park, Sun-jae Lee, Young-Dae Kim, Se-Hwan Jang, Seon-Min Woo, Taeg-Kyu Kwon, Zee-Yong Park, Ik-Joo Chung, Hye-Ran Kim, Chang-Duk Jun
Summary: NSrp70 is selectively expressed in developing thymocytes, highest at the DP stage. It regulates the cell cycle and survival of thymocytes by controlling the alternative processing of various RNA splicing factors. Knockout of NSrp70 in mice resulted in severe defects in T cell maturation and peripheral lymphopenia.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Cell Biology
Yuan Zhang, Yuling Chen, Zhao Zhang, Xiang Tao, Sha Xu, Xinyan Zhang, Tinatin Zurashvili, Zhouping Lu, Jose Ramon Bayascas, Liping Jin, Jianyuan Zhao, Xiangyu Zhou
Summary: The enzyme Acox2 is involved in bile acid synthesis and fatty acid degradation. Knockout mice for Acox2 spontaneously developed liver cancer with lymphocytic infiltrate. The study found that non-histone lysine crotonylation (Kcr) levels were decreased in the livers of Acox2(-/-) mice. The Kcr signals were concentrated in the nucleus of tumor cells but mostly located in the cytoplasm of normal liver cells. Further analysis revealed that downregulated Kcr sites were mainly located in mitochondrial and peroxisomal enzymes. Mutagenesis and analysis showed that a specific Kcr site might regulate TOP3B expression, leading to increased DNA damage.
CELL DEATH & DISEASE
(2022)
Article
Ecology
A. Rose, A. Padovan, K. Christian, J. van de Kamp, M. Kaestli, S. Tsoukalis, L. Bodrossy, K. Gibb
Summary: Research in the tropical savanna of northern Australia identified diverse microbial communities responsible for nitrogen cycling in a wastewater stabilization system, showing complex and dynamic responses to changing pond conditions.
Article
Multidisciplinary Sciences
Abdulkhaleg Ibrahim, Christophe Papin, Kareem Mohideen-Abdul, Stephanie Le Gras, Isabelle Stoll, Christian Bronner, Stefan Dimitrov, Bruno P. Klaholz, Ali Hamiche
Summary: Studies have shown that MeCP2 is a microsatellite DNA binding protein that specifically recognizes 5hmC-modified CA repeat sequences, maintaining nucleosome-free regions in the genome. Dysfunction of MeCP2 may play a role in Rett syndrome.
Article
Biochemical Research Methods
Julie E. Walker, Thomas J. Santangelo
Review
Microbiology
Alexandra M. Gehring, Julie E. Walker, Thomas J. Santangelo
JOURNAL OF BACTERIOLOGY
(2016)
Article
Microbiology
Peng Wang, Zhuoteng Yu, Thomas J. Santangelo, John Olesik, Yufeng Wang, Ekaterina Heldwein, Xin Li
JOURNAL OF BACTERIOLOGY
(2017)
Article
Microbiology
Brett W. Burkhart, Lubomira Cubonova, Margaret R. Heider, Zvi Kelman, John N. Reeve, Thomas J. Santangelo
JOURNAL OF BACTERIOLOGY
(2017)
Article
Biochemistry & Molecular Biology
Margaret R. Heider, Brett W. Burkhart, Thomas J. Santangelo, Andrew F. Gardner
JOURNAL OF BIOLOGICAL CHEMISTRY
(2017)
Article
Multidisciplinary Sciences
Julie E. Walker, Olivia Luyties, Thomas J. Santangelo
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2017)
Article
Multidisciplinary Sciences
Francesca Mattiroli, Sudipta Bhattacharyya, Pamela N. Dyer, Alison E. White, Kathleen Sandman, Brett W. Burkhart, Kyle R. Byrne, Thomas Lee, Natalie G. Ahn, Thomas J. Santangelo, John N. Reeve, Karolin Luger
Article
Microbiology
Alexandra M. Gehring, David P. Astling, Rie Matsumi, Brett W. Burkhart, Zvi Kelman, John N. Reeve, Kenneth L. Jones, Thomas J. Santangelo
FRONTIERS IN MICROBIOLOGY
(2017)
Article
Biotechnology & Applied Microbiology
Michael Clayton Speed, Brett W. Burkhart, Jonathan W. Picking, Thomas J. Santangelo
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2018)
Review
Biochemistry & Molecular Biology
Craig J. Marshall, Thomas J. Santangelo
Article
Multidisciplinary Sciences
Craig J. Marshall, M. Zuhaib Qayyum, Julie E. Walker, Katsuhiko S. Murakami, Thomas J. Santangelo
Summary: Transcription termination is an important process in regulating gene expression, and the protein Eta has been identified as one of the factors involved in disrupting transcription elongation complexes. By studying the biochemical activities and crystal structure of Eta, researchers have gained insight into its role in transcription termination. The susceptibility of transcription elongation complexes to disruption by termination factors highlights the common features of transcription termination mechanisms.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Microbiology
Elizabeth A. Watts, Sandra C. Garrett, Ryan J. Catchpole, Landon M. Clark, Travis J. Sanders, Craig J. Marshall, Breanna R. Wenck, Robert L. Vickerman, Thomas J. Santangelo, Ryan Fuchs, Brett Robb, Sara Olson, Brenton R. Graveley, Michael P. Terns
Summary: The histones in Pyrococcus furiosus play a crucial role in directing the integration of CRISPR spacers, ensuring accurate integration at the 5' end of the CRISPR array. This co-evolution of CRISPR arrays with chromosomal DNA binding proteins highlights the widespread role of DNA binding and bending in facilitating spacer integration.
NATURE MICROBIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Breanna R. Wenck, Thomas J. Santangelo
TRANSCRIPTION-AUSTIN
(2020)
Article
Biochemistry & Molecular Biology
Alexandra M. Gehring, Thomas J. Santangelo
TRANSCRIPTION-AUSTIN
(2017)