Article
Biology
Kevin E. W. Namitz, Tongyin Zheng, Ashley J. Canning, Nilda L. Alicea-Velazquez, Carlos A. Castaneda, Michael S. Cosgrove, Steven D. Hanes
Summary: Researchers identified a bivalent interaction between yeast Ess1 and CTD peptides of RNA polymerase II, suggesting an anchored mechanism of isomerization. The study raised the possibility of eukaryotic parvulin-class prolyl isomerases gaining broader substrate specificity during evolution by acquiring a flexible linker for a more dynamic binding mode.
COMMUNICATIONS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Sandra Schilbach, Haibo Wang, Christian Dienemann, Patrick Cramer
Summary: This study presents an atomic model for the yeast preinitiation complex (PIC) with core mediator, revealing the molecular details of RNA polymerase II (Pol II) transcription initiation. The structure of the mediator middle module was optimized, and the missing subunit Med1 was identified. The study found that the flexible C-terminal repeat domain (CTD) of Pol II forms defined interactions with the mediator head and middle modules, as well as other regions of the mediator. The binding mode between the yeast mediator and Pol II differs from the human counterpart.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Biochemistry & Molecular Biology
Daniela Simcikova, Sara Gelles-Watnick, Karla M. Neugebauer
Summary: Biomolecular condensates (BMCs) play a role in cellular functions through protein-protein, protein-RNA, and RNA-RNA interactions. Tudor domain-containing proteins, like SMN, contribute to BMC formation by binding to DMA modifications on protein ligands. SMN's absence causes SMA, and the identity of its DMA ligands is largely unknown, posing questions about its function. DMA modification can also affect protein interactions and localization. However, the lack of direct DMA detection methods hinders the understanding of Tudor-DMA interactions in cells.
TRENDS IN BIOCHEMICAL SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Kushol Gupta, Audrey Allen, Carolina Giraldo, Grant Eilers, Robert Sharp, Young Hwang, Hemma Murali, Katrina Cruz, Paul Janmey, Frederic Bushman, Gregory D. Van Duyne
Summary: The study reveals that the IN aggregates induced by ALLINIs exhibit weak three-dimensional gel characteristics with a fractal-like nature. Their formation is influenced by the host factor LEDGF/p75 and ex vivo resistance substitutions.
Review
Biochemistry & Molecular Biology
Mengdi Li, Danhui Ma, Zhijie Chang
Summary: CREPT and p15RS are RPRD proteins that regulate cell proliferation and tumorigenesis, with opposite functions. Aberrant expression of both proteins is found in cancers. They both interact with RNA polymerase II, but CREPT also plays a key role in DNA damage repair.
Article
Biochemistry & Molecular Biology
Kelsey S. Whinn, Zhi-Qiang Xu, Slobodan Jergic, Nischal Sharma, Lisanne M. Spenkelink, Nicholas E. Dixon, Antoine M. van Oijen, Harshad Ghodke
Summary: The accessory helicase Rep in Escherichia coli removes DNA-binding proteins that act as roadblocks to the replication fork, ensuring the smooth progress of genome duplication.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Xiawei Huang, Hongmiao Hu, Alexandre Webster, Fan Zou, Jiamu Du, Katalin Fejes Toth, Alexei A. Aravin, Sisi Li, Dinshaw J. Patek, Ravi Sachidanandam
Summary: PIWI proteins use piRNAs to repress transposons and protect genomic integrity of gametes, ensuring fertility. Post-translational modification of Aub with sDMA is essential for piRNA biogenesis and transposon silencing. Krimper facilitates piRNA generation through its Tudor domains that bind Aub and Ago3 in different modification and piRNA-loading states.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Rawad Hodeify, Maya Dib, Ethel Alcantara-Adap, Raphael Courjaret, Nancy Nader, Cleo Z. Reyes, Ayat S. Hammad, Satanay Hubrack, Fang Yu, Khaled Machaca
Summary: This study elucidates the regulation of Orai1 endocytosis during meiosis by the C-terminal structure, specifically through a region called the C-terminus Internalization Handle (CIH). The strength of intersubunit coiled coil (CC) domains controls access to CIH and ultimately affects Orai1 internalization. The findings suggest that Orai1 endocytosis requires both the N-terminal caveolin binding motif (CBM) and the C-terminal CIH, with access to CIH being influenced by the strength of intersubunit C-terminal CC.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Linyu Zuo, Guanwei Zhang, Matthew Massett, Jun Cheng, Zicong Guo, Liang Wang, Yifei Gao, Ru Li, Xu Huang, Pilong Li, Zhi Qi
Summary: FUS/EWS/TAF15 (FET) fusion oncoproteins, containing low complexity domain, form biomolecular condensates that recruit RNA polymerase II, promoting gene transcription. Through the development of a single-molecule assay, a causal relationship between the formation of condensates on DNA and gene transcription is supported, along with the identification of a threshold number of fusion-binding DNA elements required for the formation of FET protein condensates.
NATURE COMMUNICATIONS
(2021)
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)
Review
Biochemistry & Molecular Biology
Keith J. Olsen, Sean J. Johnson
Summary: Mtr4, a Ski2-like RNA helicase, plays a central role in RNA surveillance and degradation pathways as an activator of the RNA exosome. Studies over the past 10 years have provided insight into the structure of Mtr4 and its interactions with protein and nucleic acid binding partners, showing its involvement in recruiting and presenting RNA substrates in a dynamic process. This review summarizes available Mtr4 structures and highlights gaps in current understanding.
BIOLOGICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Chaoyou Xue, Lucia Molnarova, Justin B. Steinfeld, Weixing Zhao, Chujian Ma, Mario Spirek, Kyle Kaniecki, Youngho Kwon, Ondrej Belan, Katerina Krejci, Simon J. Boulton, Patrick Sung, Eric C. Greene, Lumir Krejci
Summary: RECQ5 is identified as an ATP-dependent single-stranded DNA motor protein that can translocate on various nucleoprotein complexes and dismantle RAD51-ssDNA filaments. Protein-protein interaction with RAD51 is crucial for RECQ5's functions, but its substrate specificity and ability to remove certain mutant RAD51 proteins suggest a complex regulatory role in genome maintenance.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Daniel Moses, Vaibhav Mehta, Reza Salavati
Summary: Protozoans of the Trypanosoma and Leishmania species have a unique mitochondrial genome, the kinetoplast, which undergoes RNA editing through an enzyme cascade catalyzed by the RNA editing ligases KREL1 and KREL2. The carboxy-terminal domain (CTD) of KREL1 is involved in protein-protein interaction and dsRNA ligation activity, with the alpha H3 and KWKE motif playing important roles in these processes.
Article
Marine & Freshwater Biology
Zeyu Liu, Saisai Liu, Shiyang Guo, Wei Lu, Quanqi Zhang, Jie Cheng
Summary: This study identified 13 Tdrd family genes in economically important aquaculture fish and characterized the duplication and loss of certain Tdrd genes in teleost lineages. Codon based molecular evolution analysis suggested faster evolution of teleost Tdrd genes compared to mammals, potentially associated with the accelerated evolution of the piRNA pathway in teleost lineages. RNA-seq analysis showed dominant expression of teleost Tdrd genes in gonads, particularly highly expressed in testis, indicating their conserved function in gametogenesis and the piRNA pathway.
MARINE LIFE SCIENCE & TECHNOLOGY
(2022)
Article
Virology
Adeline Goulet, Christian Cambillau, Alain Roussel, Isabelle Imbert
Summary: Hepatitis E virus (HEV) is a major cause of acute viral hepatitis in humans globally, and it is now a global public health concern. The recent advancement in protein structure prediction software allows accurate prediction of the composition and structure of HEV replicases, which is important for producing stable and active proteins and conducting studies on structure, function, and inhibition.
Article
Biochemistry & Molecular Biology
Johannes Thoma, Bjorn M. Burmann
Article
Multidisciplinary Sciences
Guillaume Mas, Bjorn M. Burmann, Timothy Sharpe, Beatrice Claudi, Dirk Bumann, Sebastian Hiller
Review
Biochemistry & Molecular Biology
Johannes Thoma, Bjorn M. Burmann
Summary: Membrane proteins are evolved to reside in the hydrophobic lipid bilayers of cellular membranes, bridging different aqueous compartments separated by the membrane and dynamically interacting with their surrounding lipid environment. This interaction not only stabilizes membrane proteins, but also influences their folding, structure, and function.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Laura Troussicot, Bjorn M. Burmann, Mikael Molin
Summary: This review focuses on the structural studies and mechanisms underlying the chaperone function of 2-Cys PRDX systems, highlighting the coordination with other molecular chaperones. It also discusses the remarkable structural similarities between 2-Cys PRDXs, small HSPs, and J-domain-independent Hsp40 holdases in terms of their functions and dynamic equilibria.
Article
Clinical Neurology
Marzena Kurzawa-Akanbi, Seshu Tammireddy, Ivo Fabrik, Mary K. Doherty, Rachel Heap, Bjorn M. Burmann, Matthias Trost, John M. Lucocq, Anda Gherman, Graham Fairfoul, Preeti Singh, Florence Burte, Alison Green, Ian G. McKeith, Anetta Hartlova, Phillip D. Whitfield, Christopher M. Morris, Lina Gliaudelyte, Irena Matetko-Burmann
Summary: Mutations in glucocerebrosidase (GBA) are the most prevalent genetic risk factor for Lewy body disorders (LBD), characterized by altered sphingolipid metabolism in LBD regardless of GBA mutations. Extracellular vesicles (EV) derived from LBD cerebrospinal fluid and brain tissue are loaded with ceramides and neurodegeneration-linked proteins, capable of inducing aggregation of wild-type alpha-synuclein. This suggests abnormalities in ceramide metabolism are a feature of LBD and GBA mutations likely accelerate the pathological process in sporadic LBD.
ACTA NEUROPATHOLOGICA
(2021)
Article
Chemistry, Multidisciplinary
Dmitry M. Lesovoy, Panagiota S. Georgoulia, Tammo Diercks, Irena Matecko-Burmann, Bjorn M. Burmann, Eduard Bocharov, Wolfgang Bermel, Vladislav Y. Orekhov
Summary: This study introduces a sensitive and robust alternative method for rapid local assignment near affected signals in intrinsically disordered proteins (IDPs), based on FOcused SpectroscopY (FOSY) experiments using selective polarisation transfer (SPT). The efficiency of this method is demonstrated by identifying two phosphorylation sites of glycogen synthase kinase 3 beta (GSK3 beta) in human Tau40, an IDP of 441 residues, and revealing unprimed phosphorylation of Ser409. This approach may benefit NMR studies of post-translational modifications (PTMs) and hotspots in IDPs involved in molecular interactions.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Ashish A. Kawale, Bjorn M. Burmann
Summary: This study used solution NMR spectroscopy to analyze the dynamical properties of Tudor domains from four different bacterial proteins, revealing subtle differences in motions on different timescales and the importance of these dynamics in discerning domain functionalities.
Article
Multidisciplinary Sciences
Darius Sulskis, Johannes Thoma, Bjorn M. Burmann
Summary: This study analyzed the interaction and dynamics of the DegP PDZ domains, revealing an interdomain molecular lock that controls the interactions between the two PDZ domains, regulated by fine-tuned temperature-dependent protein dynamics. This lock may potentially be conserved in proteins with tandem PDZ domains.
Article
Chemistry, Multidisciplinary
Laura Troussicot, Alicia Vallet, Mikael Molin, Bjorn M. Burmann, Paul Schanda
Summary: Disulfide bond formation is crucial for protein structure and cell regulation. Peroxiredoxins eliminate reactive oxygen species through catalytic Cys oxidation and reduction. This study reveals that disulfide bond formation induces extensive conformational dynamics, including high molecular-weight oligomerization, which is driven by conflicts between reduction of mobility and favorable contacts.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Damasus C. Okeke, Jens Lidman, Irena Matecko-Burmann, Bjorn M. Burmann
Summary: To deal with the risk of stress-induced mutagenesis, cells employ Y-family DNA polymerases to repair DNA lesions and maintain genome integrity. In Escherichia coli, DNA polymerase IV, or DinB, is crucial for coping with these mutations through translesion DNA synthesis. However, important aspects of DinB's functional repertoire still remain elusive. This study used advanced solution NMR spectroscopy methods and biophysical characterization to elucidate the role of the Thumb domain in DinB's functional cycle, providing insights into its interaction with DNA and RNA polymerase.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Ashish A. Kawale, Bjorn M. Burmann
Summary: This protocol outlines the detailed steps for using solution NMR spectroscopy to understand the backbone dynamics of proteins at the amino acid level. It also demonstrates the application of the protocol on structurally analogous Tudor domains with disparate functionalities.