Article
Biochemistry & Molecular Biology
Maria Dolores Molina-Sanchez, Fernando Manuel Garcia-Rodriguez, Eduardo Andres-Leon, Nicolas Toro
Summary: In this study, we investigated the binding sites of RmInt1 in the Sinorhizobium meliloti genome using chromatin-immunoprecipitation coupled with next-generation sequencing. Our results showed that RmInt1 binding sites mainly cluster around the replication origin of each replicon in the S. meliloti genome. This study provides new evidence linking the mobility of group II introns to host DNA replication.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemical Research Methods
Ying Peng, Xiaoying Wei, Kun Yang
Summary: Histones catalyze DNA strand incision at AP sites and form reversible but long-lived DPCs at 3'-DNA termini within single-strand breaks. This study developed a chemical approach to synthesize stable and site-specific 3'-histone-DPCs and their repair by nucleases. The efficiency of DPC repair is influenced by the local protein environment, and previous DPC proteolysis facilitates the repair.
BIOCONJUGATE CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Dario Monachello, Marc Lauraine, Sandra Gillot, Francois Michel, Maria Costa
Summary: Mobile group II introns are retrotransposable elements that insert themselves into DNA target sites with the help of base-pairing interactions and the reverse transcriptase enzyme. A new base-pairing interaction named EBS2a-IBS2a has been identified, which is crucial for intron mobility by driving unwinding of the DNA duplex and is stabilized by the reverse transcriptase in a non-sequence-specific manner. This discovery has important implications for the biotechnological applications of group II introns in bacterial gene targeting.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Microbiology
Masahiro C. Miura, Shohei Nagata, Satoshi Tamaki, Masaru Tomita, Akio Kanai
Summary: This study developed a bioinformatic pipeline to systematically collect and analyze Group II introns (G2Is) in prokaryotes. The results showed the presence of G2Is in both bacteria and archaea, with their numbers defined almost at the phylum level. Furthermore, a comprehensive sequence analysis led to the identification of three new categories of intron-encoded proteins (IEPs), and it was observed that about 30% of IEPs are non-canonical. The study also analyzed the relationship between genomic signatures and the mechanism of G2I increases.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Chemistry, Inorganic & Nuclear
Takashi Nakamura, Satoru Watanabe
Summary: A hexanuclear palladium complex can have two different conformations, Alternate and Twisted, depending on the guests. Linear ditopic α,ω-diamines can be captured in three distinct cross-linking modes, and the length of the diamines can regulate the macrocyclic conformations. Heteroleptic site-selective bridging of two different diamines has also been achieved.
INORGANIC CHEMISTRY
(2023)
Article
Ecology
Felix LaRoche-Johnston, Catherine Prattico, Caroline Monat, Olivier Hinse, Benoit Cousineau
Summary: This study provides a comprehensive evolutionary history of a bacterial group II intron. It reveals that the Ll.LtrB homologs in Lactococci originated from a single lateral transfer event from Enterococcus faecalis. The study also demonstrates the dissemination of these introns in Lactococci through recurrent episodes of independent mobility events and lateral transfer.
Article
Biochemistry & Molecular Biology
Noemi Miltner, Gergo Kallo, Eva Csosz, Mario Miczi, Tibor Nagy, Mohamed Mahdi, Janos Andras Motyan, Jozsef Tozser
Summary: The main protease (Mpro) of SARS-CoV-2 is crucial for the virus's life cycle. Cleavage of viral polyproteins by Mpro is necessary for virus replication, and cleavage of host proteins may contribute to viral pathogenesis. Identification of host substrates and cleavage sites is important for understanding the enzyme's specificity and improving computational prediction methods.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Yihan Wan, Dimitrios G. Anastasakis, Joseph Rodriguez, Murali Palangat, Prabhakar Gudla, George Zaki, Mayank Tandon, Gianluca Pegoraro, Carson C. Chow, Markus Hafner, Daniel R. Larson
Summary: This study establishes a platform for observing the dynamics of RNA synthesis and processing at a single molecule level, revealing transcriptional bursting in all genes and significant kinetic variation in splicing within introns. The research also uncovers widespread stochastic recursive splicing within introns and proposes a unified theoretical model to explain these phenomena.
Article
Plant Sciences
Leila Feiz, Yukari Asakura, Linyong Mao, Susan R. Strickler, Zhangjun Fei, Margarita Rojas, Alice Barkan, David B. Stern
Summary: A new study shows that CRM Family Member1 (CFM1) facilitates the splicing of chloroplast introns in plants, particularly those not previously known to require CRM domain proteins. Deficiencies in these introns result in compromised chloroplast protein synthesis, leading to whole-plant chlorotic phenotypes.
Review
Genetics & Heredity
Ron Mizrahi, Sofia Shevtsov-Tal, Oren Ostersetzer-Biran
Summary: Mitochondria are organelles responsible for cellular energy production. Plant mitochondria have introns that play a significant role in protein splicing. These splicing processes are regulated by various protein factors and may be associated with cellular and environmental signals.
Article
Biochemistry & Molecular Biology
Cassandra K. Hayne, Kevin John U. Butay, Zachary D. Stewart, Juno M. Krahn, Lalith Perera, Jason G. Williams, Robert M. Petrovitch, Leesa J. Deterding, A. Gregory Matera, Mario J. Borgnia, Robin E. Stanley
Summary: The authors used cryo-electron microscopy to investigate the recognition and processing of pre-tRNA by the human tRNA splicing endonuclease complex TSEN. They reported the structures of the TSEN-pre-tRNA complex, which reveal the overall architecture of the complex and the tRNA binding interfaces. These structures provide insights into the mechanism of pre-tRNA splicing and the neurodevelopmental disorders associated with mutations in the TSEN complex.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Chemistry, Physical
Runyou Ye, Maoshuai Zhu, Xufei Yan, Yang Long, Ying Xia, Xiangge Zhou
Summary: This study reveals a chelation-assisted palladium-catalyzed C=C bond cleavage reaction to form alkenyl nitrile, based on a formal group-exchange reaction. The isolated active Pd(II) complex and deuterium-labeled experiment confirm the necessity of the chelation group, proposing a plausible catalytic pathway.
Article
Multidisciplinary Sciences
Samoil Sekulovski, Pascal Devant, Silvia Panizza, Tasos Gogakos, Anda Pitiriciu, Katharina Heitmeier, Ewan Phillip Ramsay, Marie Barth, Carla Schmidt, Thomas Tuschl, Frank Baas, Stefan Weitzer, Javier Martinez, Simon Trowitzsch
Summary: Mutations within subunits of the tRNA splicing endonuclease complex are associated with pontocerebellar hypoplasia, and modulation of TSEN stability may contribute to the disease phenotype.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Kijun Kim, S. Chan Baek, Young-Yoon Lee, Carolien Bastiaanssen, Jeesoo Kim, Haedong Kim, V. Narry Kim
Summary: Only 758 pri-miRNAs are confidently processed by DROSHA, while the majority may be non-canonical or false entries. Analyses of the DROSHA-dependent pri-miRNAs show key cis-elements for processing, and widespread alternative processing and unproductive cleavage events were observed.
Article
Biochemical Research Methods
Yanping Long, Jinbu Jia, Weipeng Mo, Xianhao Jin, Jixian Zhai
Summary: The FLEP-seq method allows simultaneous detection of RNA polymerase II position, splicing status, polyadenylation site, and poly(A) tail length in plants. It enables calculation of cotranscriptional splicing kinetics and identification of polyadenylated transcripts with unspliced introns at specific positions posttranscriptionally.
Article
Biochemistry & Molecular Biology
Michele C. Erat, Emina Besic, Michael Oberhuber, Silke Johannsen, Roland K. O. Sigel
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY
(2018)
Article
Chemistry, Multidisciplinary
Eva Freisinger, Roland K. O. Sigel
Article
Biochemistry & Molecular Biology
Andrei Istrate, Silke Johannsen, Alena Istrate, Roland K. O. Sigel, Christian J. Leumann
NUCLEIC ACIDS RESEARCH
(2019)
Article
Chemistry, Multidisciplinary
Fabio D. Steffen, Richard Boerner, Eva Freisinger, Roland K. O. Sigel
Article
Multidisciplinary Sciences
Olivia P. Schmidt, Simon Jurt, Silke Johannsen, Ashkan Karimi, Roland K. O. Sigel, Nathan W. Luedtke
NATURE COMMUNICATIONS
(2019)
Article
Multidisciplinary Sciences
Fabio D. Steffen, Mokrane Khier, Danny Kowerko, Richard A. Cunha, Richard Boerner, Roland K. O. Sigel
NATURE COMMUNICATIONS
(2020)
Article
Biochemical Research Methods
Ulrike Anders, Maya Gulotti-Georgieva, Susann Zelger-Paulus, Fatima-Ezzahra Hibti, Chiraz Frydman, Detlev Suckau, Roland K. O. Sigel, Renato Zenobi
Summary: The study combined SPR imaging with MALDI MS to improve the identification of potential RNA binders, allowing for high-throughput analysis of complex mixtures. Results showed that in addition to Mss116, other proteins in crude yeast mitochondrial lysate may interact with the intronic RNA, suggesting that the folding and splicing of the intron may be regulated by multiple cofactors in vivo.
ANALYTICAL BIOCHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Stefan Gerhardy, Michaela Oborska-Oplova, Ludovic Gillet, Richard Boerner, Rob van Nues, Alexander Leitner, Erich Michel, Janusz J. Petkowski, Sander Granneman, Roland K. O. Sigel, Ruedi Aebersold, Vikram Govind Panse
Summary: This study reveals that yeast cells globally increase production of ribosome assembly machinery in response to low temperature. Puf6 binds to the nascent catalytic RNA-rich subunit interface within the 60S pre-ribosome, mimicking the role of Mg2+ to facilitate long-range tertiary contacts for compacting rRNA.
NATURE COMMUNICATIONS
(2021)
Review
Biochemistry & Molecular Biology
Astrid Sigel, Helmut Sigel, Roland K. O. Sigel
Summary: The coordination chemistry of nucleotides and their derivatives is crucial in the field of biological inorganic chemistry, as nucleotides play a direct or indirect role in all natural processes. Chemical modifications of nucleotides have led to the discovery of medically useful compounds, such as acyclic nucleoside phosphonates (ANPs), which exhibit antiviral activity. Among ANPs, diphosphorylated PMEA has been found to be a better substrate for polymerases compared to ATP due to its conformation, increased metal ion affinity, and the formation of a 5-membered chelate. Understanding the coordination chemistry of nucleotides and their derivatives can contribute to the development of new drugs and therapies.
Article
Chemistry, Multidisciplinary
Ryan M. L. McFadden, Daniel Szunyogh, Nicholas Bravo-Frank, Aris Chatzichristos, Martin H. Dehn, Derek Fujimoto, Attila Jancso, Silke Johannsen, Ildiko Kalomista, Victoria L. Karner, Robert F. Kiefl, Flemming H. Larsen, Jens Lassen, C. D. Philip Levy, Ruohong Li, Iain McKenzie, Hannah McPhee, Gerald D. Morris, Matthew R. Pearson, Stephan P. A. Sauer, Roland K. O. Sigel, Peter W. Thulstrup, W. Andrew MacFarlane, Lars Hemmingsen, Monika Stachura
Summary: We used beta-NMR to study the complexation of magnesium ions with ATP. We demonstrated that spin-polarized Mg-31 binds to ATP in solution before depolarizing. The observations of different complexes formed by Mg-31 provide valuable insights for using beta-NMR to study chemistry and biochemistry in solution.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Multidisciplinary Sciences
Markus Goetz, Anders Barth, Soren S-R Bohr, Richard Boerner, Jixin Chen, Thorben Cordes, Dorothy A. Erie, Christian Gebhardt, Melodie C. A. S. Hadzic, George L. Hamilton, Nikos S. Hatzakis, Thorsten Hugel, Lydia Kisley, Don C. Lamb, Carlos de Lannoy, Chelsea Mahn, Dushani Dunukara, Dick de Ridder, Hugo Sanabria, Julia Schimpf, Claus A. M. Seidel, Roland K. O. Sigel, Magnus Berg Sletfjerding, Johannes Thomsen, Leonie Vollmar, Simon Wanninger, Keith R. Weninger, Pengning Xu, Sonja Schmid
Summary: In this study, we compared the performance of 11 analysis tools in inferring kinetic rate constants from smFRET trajectories. The results highlight the current strengths and limitations in inferring kinetic information from smFRET data and provide recommendations for future developments.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Fabio Amadei, Maria Reichenbach, Sofia Gallo, Roland K. O. Sigel
Summary: The RNA structural elements called riboswitches play a critical role in regulating gene expression by responding to specific cellular metabolites. The folding pathway and structure of the moaA riboswitch from E. coli, which responds to the metabolite molybdenum cofactor (Moco), were investigated. The study revealed that low ion concentrations can induce a high degree of structure formation in the riboswitch, and Mg2+ facilitates the compaction of the riboswitch towards its active structure.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2023)
Article
Biochemical Research Methods
N. Schmid, S. Bruderer, F. Paruzzo, G. Fischetti, G. Toscano, D. Graf, M. Fey, A. Henrici, V. Ziebart, B. Heitmann, H. Grabner, J. D. Wegner, R. K. O. Sigel, D. Wilhelm
Summary: The analysis of nuclear magnetic resonance (NMR) spectra to detect peaks and characterize their parameters, often referred to as deconvolution, is a crucial step in the quantification, elucidation, and verification of the structure of molecular systems. We propose a robust, expert-level quality deep learning-based deconvolution algorithm for 1D experimental NMR spectra. Our algorithm demonstrates superior performance compared to expert results in challenging spectra.
JOURNAL OF MAGNETIC RESONANCE
(2023)
Article
Chemistry, Multidisciplinary
James S. Craig, Larry Melidis, Hugo D. Williams, Samuel J. Dettmer, Alexandra A. Heidecker, Philipp J. Altmann, Shengyang Guan, Callum Campbell, Douglas F. Browning, Roland K. O. Sigel, Silke Johannsen, Ross T. Egan, Brech Aikman, Angela Casini, Alexander Pothig, Michael J. Hannon
Summary: Holliday 4-way junctions are important for DNA processes. Metallo-supramolecular pillarplexes can interact with open DNA junction cavities. They can bind 3-way junctions but disrupt base pairing, while they can bind and increase binding sites of 4-way junctions. This offers possibilities for biological and synthetic nucleic acid nanostructures.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Editorial Material
Chemistry, Medicinal
Astrid Sigel, Helmut Sigel, Roland K. O. Sigel
ESSENTIAL METALS IN MEDICINE: THERAPEUTIC USE AND TOXICITY OF METAL IONS IN THE CLINIC
(2019)