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Biochemistry & Molecular Biology
Lydia Hadjeras, Marie Bouvier, Isabelle Canal, Leonora Poljak, Quentin Morin-Ogier, Carine Froment, Odile Burlet-Schlitz, Lina Hamouche, Laurence Girbal, Muriel Cocaign-Bousquet, Agamemnon J. Carpousis
Summary: RNA processing and degradation are important for the regulation of gene expression. In bacteria, RNA degradosomes are multienzyme complexes that process and degrade RNA. The localization of RNA degradosomes to the bacterial inner cytoplasmic membrane plays a role in ribosome assembly and prevents wasteful degradation of rRNA precursors.
Article
Biochemistry & Molecular Biology
Tom Dendooven, Dhriti Sinha, Alzbeta Roeselova, Todd A. Cameron, Nicholas R. De Lay, Ben F. Luisi, Katarzyna J. Bandyra
Summary: Polynucleotide phosphorylase (PNPase) is an ancient exoribonuclease that is conserved in evolution and found in diverse species. It can act as an RNA degrading enzyme and as a chaperone for small regulatory RNAs, with pleiotropic consequences for gene regulation. Structures of the ternary assembly formed by PNPase, the RNA chaperone Hfq, and sRNA show how PNPase is repurposed to protect sRNAs from ribonucleases and facilitate regulatory actions on target genes.
Article
Biochemistry & Molecular Biology
Su-Juan Liu, Gui-Ming Lin, Yu-Qi Yuan, Wenli Chen, Ju-Yuan Zhang, Cheng-Cai Zhang
Summary: A protein called RebA was found to interact with RNase E in cyanobacteria and suppress its cleavage activity for substrates. The absence or overproduction of RebA had an impact on bacterial cell morphology, which was dependent on their physical interaction with RNase E.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Paula Clemente, Javier Calvo-Garrido, Sarah F. Pearce, Florian A. Schober, Megumi Shigematsu, Stefan J. Siira, Isabelle Laine, Henrik Spahr, Christian Steinmetzger, Katja Petzold, Yohei Kirino, Rolf Wibom, Oliver Rackham, Aleksandra Filipovska, Joanna Rorbach, Christoph Freyer, Anna Wredenberg
Summary: Using Drosophila and mouse models, this study demonstrates that non-canonical RNA processing in mammalian mitochondria results in the formation of 3' phosphates, which are hydrolyzed by the phosphatase activity of the carbon catabolite repressor 4 domain-containing family member ANGEL2. The findings also suggest the involvement of the FAST kinase domain-containing protein family in the generation of these 3' phosphates.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Rabia Ladjouzi, Matthieu Duban, Anca Lucau-Danila, Djamel Drider
Summary: This study investigated the role of polynucleotide phosphorylase (PNPase) in the biology of Enterococcus faecalis 14. By obtaining a mutant strain deficient in PNPase synthesis, the researchers found that differentially expressed genes, altered cell envelope ultrastructure, enhanced adhesion capacity on eukaryotic cells, and increased proteolytic activity were observed in the delta pnpA mutant compared to the wild-type strain. These findings suggest that PNPase may directly or indirectly control various biological functions in E. faecalis 14.
Article
Multidisciplinary Sciences
Zhiheng Yang, Wenzhe Liu, Lihua Zhao, Dongbao Yin, Jianfei Feng, Lidong Li, Xuefeng Guo
Summary: We propose a reliable in-situ single-PNPase-molecule dynamic electrical detector based on silicon nanowire field-effect transistors with ultra-high temporal resolution. These devices can realize real-time and label-free monitoring of RNA analog degradation with single-base resolution, and achieve approximately 80% accuracy in RNA nucleoside sequencing in a single testing process. This proof-of-concept provides a foundation for the development of high-throughput detection technologies for mechanistic exploration and single-molecule sequencing in a Complementary Metal Oxide Semiconductor (CMOS)-compatible environment.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Nimmy Francis, Malaya R. Behera, Kathiresan Natarajan, Rakesh S. Laishram
Summary: RNA 39-end polyadenylation plays a role in stress response in Escherichia coli. The poly(A) polymerase I (PAPI) is involved in this process, and its activity is inhibited by tyrosine phosphorylation at residue Y202, which is enhanced during stress. The bacterial tyrosine kinase Wzc phosphorylates PAPI-Y202, and its mutation renders cells more sensitive to stress. This phosphorylation-dependent stress tolerance mechanism operates independently of the primary stress regulator RpoS.
LIFE SCIENCE ALLIANCE
(2023)
Article
Biochemical Research Methods
Daniel P. Cetnar, Howard M. Salis
Summary: mRNA degradation is a complex process that affects gene expression levels. Through a synthetic biology approach, this study identified factors affecting mRNA stability in bacterial operons, such as the impact of long single-stranded RNA in 5' UTR and translation rates on mRNA levels. The research also developed biophysical models and design rules to control mRNA stability, facilitating the automated design of engineered genetic systems with specific functionalities.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Microbiology
Shivani Chhabra, Zachary F. Mandell, Bo Liu, Paul Babitzke, David H. Bechhofer
Summary: This study mapped the 3' ends of mRNA decay intermediates in strains lacking the major 3' exoribonuclease PNPase or the RNA helicase CshA, confirming the primary role of PNPase in mRNA turnover and suggesting the involvement of one or more unknown RNases.
Article
Biochemistry & Molecular Biology
Chaitanya Jain
Summary: Oligoribonuclease (Orn) from Escherichia coli (E. coli) is an essential ribonuclease that converts short RNA molecules (NanoRNAs) to mono-nucleotides. In this study, it was found that Orn can suppress the growth defects caused by the absence of two other RNases, poly-nucleotide phosphorylase and RNase PH. Further analyses showed that even with a small increase in expression, Orn can carry out molecular reactions normally performed by RNase T and RNase PH, and can fully digest single-stranded RNAs in various structural contexts. These findings provide new insights into Orn function and its role in E. coli RNA metabolism.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Microbiology
Patricia Apura, Victor de Lorenzo, Cecilia M. Arraiano, Esteban Martinez-Garcia, Sandra C. Viegas
Summary: The study revealed that different ribonucleases play specific roles in the physiology and environmental adaptation of the soil bacterium Pseudomonas putida KT2440. The absence of each ribonuclease led to distinct effects on growth, motility, and morphology of the organism, indicating species-specific regulatory functions and post-transcriptional adaptation mechanisms utilized by P. putida in facing hostile environments.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Xiaoying He, Yan Li, Yehui Tao, Xuelian Qi, Ruiqi Ma, Honghua Jia, Ming Yan, Kequan Chen, Ning Hao
Summary: Sucrose phosphorylase (SPase, EC2.4.1.7) is an important enzyme for producing glycosylated compounds. In this study, an attempt was made to extracellularly express a recombinant SPase from Thermobacillus sp. in E. coli, but the enzyme was unexpectedly produced outside the cells. Truncation experiments showed that both termini of the enzyme are crucial for protein folding and enzymatic activity.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biochemistry & Molecular Biology
Shakti Ingle, Shivani Chhabra, Denise Laspina, Elizabeth Salvo, Bo Liu, David H. Bechhofer
Summary: PNPase is the major mRNA decay activity in Bacillus subtilis, and its processivity can be affected by RNA secondary structure, which is thought to be overcome by the helicase activity of CshA. A color screen for mRNA decay in B. subtilis revealed a significant correlation between internal stem-loop structure strength and PNPase processivity, which is hindered in the absence of CshA. Other RNA helicases in B. subtilis were found not to play a role in mRNA decay.
Article
Biochemistry & Molecular Biology
Xuefeng Zhu, Xie Xie, Hrishikesh Das, Benedict G. Tan, Yonghong Shi, Ali Al-Behadili, Bradley Peter, Elisa Motori, Sebastian Valenzuela, Viktor Posse, Claes M. Gustafsson, B. Martin Haellberg, Maria Falkenberg
Summary: The non-coding RNA molecule 7S RNA regulates mitochondrial transcription in mammalian cells by inducing POLRMT dimerization, which prevents transcription initiation.
Article
Biochemistry & Molecular Biology
Joshua A. Sommers, Lorin N. Loftus, Martin P. Jones III, Rebecca A. Lee, Caitlin E. Haren, Adaira J. Dumm, Robert M. Brosh Jr
Summary: This study characterized the catalytic functions and properties of the helicase protein Nsp13 of SARS-CoV-2. It was found that Nsp13 exhibits functional cooperativity and has a preference for single-stranded DNA. The study also revealed the regulatory role of Mg2+ concentration in the catalytic functions of Nsp13.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Marianne Jaeger, Astrid Hubert, Rajinikanth Gogiraju, Magdalena L. Bochenek, Thomas Muenzel, Katrin Schaefer
ANTIOXIDANTS & REDOX SIGNALING
(2019)
Article
Biochemistry & Molecular Biology
Anna Chao Kaberdina, Olatz Ruiz-Larrabeiti, Sue Lin-Chao, Vladimir R. Kaberdin
MOLECULAR GENETICS AND GENOMICS
(2019)
Correction
Biochemistry & Molecular Biology
Anna Chao Kaberdina, Olatz Ruiz-Larrabeiti, Sue Lin-Chao, Vladimir R. Kaberdin
MOLECULAR GENETICS AND GENOMICS
(2019)
Article
Cardiac & Cardiovascular Systems
Magdalena L. Bochenek, Christiane Leidinger, Nico S. Rosinus, Rajinikanth Gogiraju, Stefan Guth, Lukas Hobohm, Kerstin Jurk, Eckhard Mayer, Thomas Muenzel, Mareike Lankeit, Markus Bosmann, Stavros Konstantinides, Katrin Schaefer
CIRCULATION RESEARCH
(2020)
Article
Biochemistry & Molecular Biology
Ashok Kumar Madikonda, Akbarpasha Shaikh, Sonali Khanra, Harshita Yakkala, Sailu Yellaboina, Sue Lin-Chao, Dayananda Siddavattam
Article
Biochemistry & Molecular Biology
Eva Schuetz, Rajinikanth Gogiraju, Maria Pavlaki, Ioannis Drosos, George S. Georgiadis, Christos Argyriou, Amina Rim Ben Hallou, Fotios Konstantinou, Dimitrios Mikroulis, Rebecca Schueler, Magdalena L. Bochenek, Sogol Gachkar, Katja Buschmann, Mareike Lankeit, Susanne H. Karbach, Thomas Muenzel, Dimitrios Tziakas, Stavros Konstantinides, Katrin Schaefer
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Microbiology
Dharam Singh, Oleg N. Murashko, Sue Lin-Chao
JOURNAL OF BACTERIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Gunn-Guang Liou, Anna Chao Kaberdina, Wei-Syuan Wang, Vladimir R. Kaberdin, Sue Lin-Chao
Summary: By analyzing the physiology and gene expression of E. coli in low-oxygen environments, we identified genes involved in acid-stress adaptation, cell adhesion/biofilm formation, electron transport, oligopeptide transport, and anaerobic respiration/fermentation that are upregulated under microaerobic conditions. In contrast, genes involved in iron transport, aerobic respiration, and de novo nucleotide synthesis were downregulated. We also discovered and discussed the regulatory functions of differentially expressed noncoding small RNAs during microaerobic growth.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Medicine, Research & Experimental
Magdalena L. Bochenek, Rajinikanth Gogiraju, Stefanie Grossmann, Janina Krug, Jennifer Orth, Sabine Reyda, George S. Georgiadis, Henri M. Spronk, Stavros Konstantinides, Thomas Muenzel, John H. Griffin, Philipp Wild, Christine Espinola-Klein, Wolfram Ruf, Katrin Schaefer
Summary: The signaling between endothelial protein C receptor and protease activated receptor 1 plays a crucial role in ischemic reperfusion and neovascularization. This study highlights the connection between coagulation signaling, endothelial nitric oxide bioavailability, and angiogenesis.
Article
Hematology
Rajinikanth Gogiraju, Luisa Renner, Magdalena L. Bochenek, Konstantinos Zifkos, Michael Molitor, Sven Danckwardt, Philip Wenzel, Thomas Muenzel, Stavros Konstantinides, Katrin Schaefer
Summary: This study demonstrates the important role of erythrocyte ARG1 in controlling NO signaling and L-arginine metabolism in VSMCs, which ultimately influences the composition and calcification of atherosclerotic lesions.
ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY
(2022)
Article
Hematology
Rajinikanth Gogiraju, Sogol Gachkar, David Velmeden, Magdalena L. Bochenek, Konstantinos Zifkos, Astrid Hubert, Thomas Muenzel, Stefan Offermanns, Katrin Schaefer
Summary: Reduction of PTP1B in SMCs promotes adverse remodeling following vascular injury, including dedifferentiation, perivascular fibrosis, and collagen accumulation. This process involves a shift from SMAD2 to KLF4-regulated gene transcription driven by ERK1/2 phosphorylation.
THROMBOSIS AND HAEMOSTASIS
(2022)
Article
Multidisciplinary Sciences
Rajinikanth Gogiraju, Claudius Witzler, Fatemeh Shahneh, Astrid Hubert, Luisa Renner, Magdalena L. Bochenek, Konstantinos Zifkos, Christian Becker, Madhusudhan Thati, Katrin Schaefer
Summary: Obesity promotes endothelial dysfunction, and endothelial cells may actively contribute to the development of obesity and metabolic dysfunction. This study reveals the important role of endothelial leptin receptors in the transport of leptin into the brain and neuronal control of food intake, suggesting organ-specific changes in endothelial cell metabolism.
SCIENTIFIC REPORTS
(2023)
Article
Microbiology
Oleg N. Murashko, Kun-Hai Yeh, Chen-Hsin Albert Yu, Vladimir R. Kaberdin, Sue Lin-Chao
Summary: This study demonstrates that fluoride can impact gene expression posttranscriptionally by slowing down RNA degradation, thereby enhancing RNA stability and steady-state mRNA levels in E. coli.
MICROBIOLOGY SPECTRUM
(2023)
Review
Cardiac & Cardiovascular Systems
Rajinikanth Gogiraju, Magdalena L. Bochenek, Katrin Schaefer
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2019)
Article
Biochemistry & Molecular Biology
Jagannatham Naidu Bhupana, Bo-Tsang Huang, Gunn-Guang Liou, Marcus J. Calkins, Sue Lin-Chao