Article
Multidisciplinary Sciences
Matthew E. Cockman, Yoichiro Sugimoto, Hamish B. Pegg, Norma Masson, Eidarus Salah, Anthony Tumber, Helen R. Flynn, Joanna M. Kirkpatrick, Christopher J. Schofield, Peter J. Ratcliffe
Summary: JMJD6 is a 2-oxoglutarate-dependent dioxygenase involved in various cellular processes. Through mass spectrometry analysis, we identified 150 lysine hydroxylation sites on 48 protein substrates catalyzed by JMJD6, including 19 hydroxylation sites on BRD4. Most of these substrates are associated with membraneless organelle formation, suggesting a potential role for JMJD6 in regulating subcellular partitioning in response to stress.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Joanna Bonnici, Razanne Oueini, Eidarus Salah, Catrine Johansson, Christopher J. J. Schofield, Akane Kawamura
Summary: We found that the catalytic domains of all human KDM5s, KDM4E, and to a lesser extent KDM4A/D, exhibit both lysine demethylase (KDM) and arginine demethylase (RDM) activities on histone peptides. Ras GTPase-activating protein-binding protein 1 peptides are substrates for KDM5C/D RDM. This study highlights the potential of JmjC-KDMs to catalyze reactions beyond N-epsilon-methyllysine demethylation. Although limited to peptide fragments, our results provide guidance for biological studies investigating JmjC functions.
Review
Biochemistry & Molecular Biology
Sierra L. L. Love, Joseph D. D. Emerson, Kazunori Koide, Aaron A. A. Hoskins
Summary: Pre-mRNA splicing is a crucial step in human gene expression, carried out by a macromolecular machine known as the spliceosome. Mutations in this machinery can lead to various human diseases. This review provides an overview of the main features of the pre-mRNA splicing machinery in humans and how changes in its components' function can result in diseases ranging from blindness to cancers. The article also discusses drugs that interact with the spliceosome to alter splicing outcomes and speculates on future treatments for spliceosomopathies.
Article
Multidisciplinary Sciences
Praveen Kumar Kathare, Ruijiao Xin, Abirama Sundari Ganesan, Viviana M. June, Anireddy S. N. Reddy, Enamul Huq
Summary: Light signals have significant effects on the physiology, growth, and development of plants. SWAP1, an RNA-binding splicing factor, regulates light-regulated alternative splicing by interacting with other splicing factors and photoactivated phyB.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Changshou Wang, Lin Xu, Chen Du, Hao Yun, Keyun Wang, Hui Liu, Mingliang Ye, Jing Fan, Yu Zhou, Hong Cheng
Summary: CDK11 is a potential druggable target for cancer therapy, as it plays important roles in phosphorylating transcription and splicing factors and facilitating cell cycle progression in cancer cells. This study reveals that CDK11 forms a tight complex with cyclins L1/L2 and SAP30BP, and that SAP30BP is a critical activator of CDK11, regulating global pre-mRNA splicing.
Review
Biology
Miroslava Kretova, Tomas Selicky, Ingrid Cipakova, Lubos Cipak
Summary: Pre-mRNA splicing is a crucial process in eukaryotic cells to generate mature messenger RNAs for protein synthesis. The splicing process involves the removal of non-coding regions (introns) and joining of coding regions (exons) in pre-mRNAs. The spliceosome, composed of various proteins and factors, carries out the specific steps of splicing. Recent studies have revealed that post-translational modifications of splicing factors play significant roles in the regulation of pre-mRNA splicing, including phosphorylation, acetylation, methylation, ubiquitination, and sumoylation.
Article
Biochemistry & Molecular Biology
Hyun-Ji Park, Hae-Myeong Jung, Areum Lee, Seung-Hee Jo, Hyo-Jun Lee, Hyun-Soon Kim, Choon-Kyun Jung, Sung-Ran Min, Hye-Sun Cho
Summary: OsFKBP20-1b is SUMOylated under stress conditions in rice, leading to enhanced protein stability and interaction with OsSUMO1 and OsSUMO2. The low SUMOylation level of 5KR_OsFKBP20-1b results in inadequate association with U snRNAs in response to heat stress, affecting RNA processing.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Dan Nie, Xin Tang, Haijun Deng, Xiaojun Yang, Junji Tao, Fengli Xu, Yi Liu, Kang Wu, Kai Wang, Zhechuan Mei, Ailong Huang, Ni Tang
Summary: SLC27A5 plays a noncanonical role in inhibiting the progression of hepatocellular carcinoma (HCC) by regulating mRNA splicing and suppressing the PI3K/AKT pathway. The interaction between SLC27A5 and IGF2BP3 modulates the expression of the PIP4K2A-S isoform, which is a potential marker for diagnosing and predicting the prognosis of HCC. IGF2BP3 RNA decoy is a promising therapy for HCC patients with SLC27A5 deficiency.
Article
Cell Biology
Haroon Butt, Jeremie Bazin, Kasavajhala V. S. K. Prasad, Nourelislam Awad, Martin Crespi, Anireddy S. N. Reddy, Magdy M. Mahfouz
Summary: Abiotic stresses have significant impacts on plant growth, development, and crop productivity. The plant-specific splicing factor RS33 plays an important role in regulating pre-mRNA splicing and abiotic stress responses in rice.
Article
Immunology
Elena Putscher, Michael Hecker, Brit Fitzner, Nina Boxberger, Margit Schwartz, Dirk Koczan, Peter Lorenz, Uwe Klaus Zettl
Summary: This study found that genetic variants from MS risk loci affect pre-mRNA splicing. These findings substantiate the role of alternative splicing events in the genetics of MS. Further research on how disease-causing genetic variants modify the interactions between splicing regulatory sequence elements and RNA-binding proteins can help deepen our understanding of the genetic susceptibility to MS.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Kazashi Kato, Rina Udagawa, Yuki Hayashi, Masayoshi Maki, Makiko Yanagida, Sae Higashiura, Reina Yagishita, Haruka Shimamoto, Keiji Kimura
Summary: This study demonstrates the mitotic functions of SF3B14 in controlling mitotic chromosome behavior by regulating the pre-mRNA splicing of TUBGCP6. SF3B14 depletion leads to prolonged mitosis and various mitotic defects, suggesting its crucial role in mitotic processes. Although predominantly localized in the nucleoplasm during interphase, SF3B14 does not colocalize with specific mitotic structures during mitosis, indicating a potential indirect regulation mechanism.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Mingtian Deng, Baobao Chen, Zifei Liu, Yongjie Wan, Dongxu Li, Yingnan Yang, Feng Wang
Summary: YBX1 plays important roles in maternal mRNA decay, alternative splicing, and transcriptional activity during early embryogenesis. These findings broaden our understanding of YBX1 functions.
CELL AND BIOSCIENCE
(2022)
Article
Microbiology
Stefanie Lawrinowitz, Jacob M. Wurlitzer, Dieter Weiss, Hans-Dieter Arndt, Erika Kothe, Markus Gressler, Dirk Hoffmeister
Summary: A dual-level regulatory mechanism connecting light with the production of ink-blue pentacyclic natural products, corticin pigments, in the Terana caerulea mushroom is described. Light selectively induces the expression of the corA gene encoding the first described mushroom polyporic acid synthetase. Additionally, light is necessary for the proper splicing of corA pre-mRNA.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biochemistry & Molecular Biology
Kazuhiro Maeta, Manal Farea, Hisahide Nishio, Masafumi Matsuo
Summary: This study identified a novel antisense oligonucleotide called KMM001 that inhibits the maturation of myostatin mRNA, resulting in decreased myostatin protein levels. KMM001 also inhibits SMAD-mediated myostatin signaling and promotes human myoblast proliferation. These findings suggest that KMM001 has potential therapeutic applications for muscle-wasting conditions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Genetics & Heredity
Zhongjing Su, Dongyang Huang
Summary: Alternative splicing plays a critical role in the regulation of immune cell development and immune activity, with aberrant splicing leading to abnormal immune responses. This review summarizes recent discoveries on immune-associated alternative splice variants, clinical disorders, and regulatory mechanisms.
Article
Biochemistry & Molecular Biology
Benjamin G. G. Saward, Thomas M. M. Leissing, Ian J. J. Clifton, Anthony Tumber, Christopher M. M. Timperley, Richard J. J. Hopkinson, Christopher J. J. Schofield
Summary: Transient receptor potential (TRP) channels play important roles in environmental sensing in animals. TRPA1 is responsible for sensing AITC and other electrophilic irritants, while TRPV3 is involved in skin maintenance. This study reports on the catalysis of asparaginyl hydroxylation of the ankyrin repeat domains (ARDs) of TRPA1 and TRPV3 by FIH. The results confirm previous findings on TRPV3 hydroxylation and identify a specific sequence in TRPA1 that undergoes hydroxylation. Structural studies reveal similarities and differences in the binding modes of TRPA1 and TRPV3 to FIH.
Article
Multidisciplinary Sciences
Ryan A. Herold, Raphael Reinbold, Christopher J. Schofield, Fraser A. Armstrong
Summary: Electrochemical studies reveal that nanoconfinement significantly increases the efficiency of enzyme-catalyzed cascade reactions. By using a nanoporous conducting indium tin oxide film and entrapping Isocitrate dehydrogenase 1 (IDH1), the complete electrochemical oxidation of isocitrate to 2-oxoglutarate is achieved using only the NADP(H) cofactor carried into the electrode pores. The results demonstrate the power of nanoconfinement in facilitating multistep enzyme catalysis and provide insights into the role of nicotinamide cofactors as redox carriers.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Vildan A. Turkmen, Jordi C. J. Hintzen, Anthony Tumber, Laust Moesgaard, Eidarus Salah, Jacob Kongsted, Christopher J. Schofield, Jasmin Mecinovic
Summary: Non-haem Fe(ii) and 2-oxoglutarate (2OG) dependent oxygenases catalyze oxidation of proteins, and this study focuses on the substrate selectivity and inhibition of human ribosomal oxygenases (ROX) MINA53 and NO66. The results show that MINA53 and NO66 have narrow substrate selectivity compared to other human JmjC hydroxylases. Inhibition assays also suggest that the activities of MINA53/NO66 might be regulated in vivo by competition with non-oxidized proteins/peptides.
RSC CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Medicinal
Shuang Liu, Martine Abboud, Victor Mikhailov, Xiao Liu, Raphael Reinbold, Christopher J. Schofield
Summary: This study reported the binding and inhibition studies of 13 IDH1/2 variant inhibitors on wild-type IDH1 and its cancer-associated variant, IDH1 R132H. Interestingly, all the variant inhibitors were able to bind wild-type IDH1 despite not inhibiting it or only weakly inhibiting it. The selectivity of the IDH1 R132H variant over wild-type IDH1 is not primarily related to the affinities of the inhibitors for the resting forms of the enzymes. The independent binding of Mg2+ and 2-oxoglutarate to the IDH1 variant makes it more susceptible to allosteric inhibition compared to the tighter binding of the isocitrate-Mg2+ complex substrate to wild-type IDH1. The results highlight that binding affinity does not necessarily correlate with inhibition selectivity and have implications for interpreting inhibitor screening results with IDH and related enzymes.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Tehmina Bharucha, Bevin Gangadharan, Abhinav Kumar, Ashleigh C. Myall, Nazli Ayhan, Boris Pastorino, Anisone Chanthongthip, Manivanh Vongsouvath, Mayfong Mayxay, Onanong Sengvilaipaseuth, Ooyanong Phonemixay, Sayaphet Rattanavong, Darragh P. O'Brien, Iolanda Vendrell, Roman Fischer, Benedikt Kessler, Lance Turtle, Xavier de Lamballerie, Audrey Dubot-Peres, Paul N. Newton, Nicole Zitzmann, SEAe Consortium
Summary: A diagnostic signature consisting of nine proteins for Japanese encephalitis was developed using liquid chromatography and tandem mass spectrometry techniques. The accuracy of the signature was tested and validated, showing 82% accuracy. Further research and validation can help refine the signature for rapid diagnosis of Japanese encephalitis.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Plant Sciences
Daniela J. Sueldo, Alice Godson, Farnusch Kaschani, Daniel Krahn, Till Kessenbrock, Pierre Buscaill, Christopher J. Schofield, Markus Kaiser, Renier A. L. van Der Hoorn
Summary: This study reports the dynamics of extracellular hydrolases in Nicotiana benthamiana upon infection with Pseudomonas syringae. The activity of 82 hydrolases, mostly serine hydrolases, increases during infection, while the activity of 60 hydrolases, mostly glycosidases and cysteine proteases, is suppressed. The study also reveals the antibacterial activity of NbPR3 and its essential active site substitution.
Article
Multidisciplinary Sciences
Larissa Dietz, Cara J. Ellison, Carlos Riechmann, C. Keith Cassidy, F. Daniel Felfoldi, Adan Pinto-Fernandez, Benedikt M. Kessler, Paul R. Elliott
Summary: Certain members of the inhibitor of apoptosis (IAP) family, including BIRC6, regulate cell death by inhibiting caspases, while SMAC antagonizes IAPs and promotes cell death. BIRC6 directly inhibits caspase-3 and-7 and ubiquitinates caspase-3,-7, and-9, working with noncanonical E1, UBA6. SMAC suppresses both mechanisms by competitively displacing caspases.
Article
Cell Biology
Cyriel Sebastiaan Olie, Adan Pinto-Fernandez, Andreas Damianou, Iolanda Vendrell, Hailiang Mei, Bianca den Hamer, Erik van der Wal, Jessica C. de Greef, Vered Raz, Benedikt M. Kessler
Summary: The ubiquitin proteasomal system plays a critical role in muscle physiology, but the function of deubiquitinating enzymes (DUBs) in muscle cells remains poorly understood. Through a genetic screen, we discovered that the depletion of USP18, a DUB, affects muscle cell differentiation. USP18 regulates differentiation initiation and maintenance independently of ISG15 and the ISG response. Alterations in gene networks and protein expression profiles were observed in the absence of USP18, leading to disrupted calcium homeostasis and reduced contractile force.
CELL DEATH & DISEASE
(2023)
Article
Chemistry, Multidisciplinary
Ryan A. Herold, Christopher J. Schofield, Fraser A. Armstrong
Summary: The study utilizes a nanoporous electrode material, the e-Leaf, to control enzyme cascades and gain detailed kinetic insight into an anti-cancer drug mechanism. The e-Leaf allows for the quantification of IDH1 R132H inhibition kinetics and reveals factors underlying inhibitor residence time. The study highlights the importance of this method in obtaining detailed kinetic and mechanistic information that is difficult to obtain using conventional techniques.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
David J. Fallon, Alex Phillipou, Christopher J. Schofield, David House, Nicholas C. O. Tomkinson, Jacob T. Bush
Summary: This article presents the development and optimization of a photoaffinity labelling (PAL) displacement assay. It uses a highly efficient PAL probe to assess the relative binding affinities of compounds to specific binding sites in multiple recombinant protein domains in tandem. The assay was validated using a test set of 264 compounds annotated with activity against the bromodomain and extra-terminal domain (BET) family in ChEMBL. The obtained pIC50 values correlated well with orthogonal TR-FRET data, highlighting the potential of this accessible PAL biochemical screening platform.
BIOCHEMICAL JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Lennart Brewitz, H. T. Henry Chan, Petra Lukacik, Claire Strain-Damerell, Martin A. Walsh, Fernanda Duarte, Christopher J. Schofield
Summary: This study investigates the DUB activity of PLpro and confirms its activity using mass spectrometry. The results suggest that the sequence and binding of substrates affect the catalysis of PLpro, and human proteins conjugated to ISG15 are better substrates. The study also implies the potential of using N epsilon-lysine-branched oligopeptides for substrate identification and monitoring catalysis by human DUBs.
BIOORGANIC & MEDICINAL CHEMISTRY
(2023)
Article
Pharmacology & Pharmacy
L. Leonie van Leeuwen, Mitchel J. R. Ruigrok, Benedikt M. Kessler, Henri G. D. Leuvenink, Peter Olinga
Summary: This study demonstrates the value of machine perfusion for administering antifibrotic drugs such as galunisertib and proves the effectiveness of ex vivo administration.
BRITISH JOURNAL OF PHARMACOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Hannah C. Scott, Simeon D. Draganov, Zhanru Yu, Benedikt M. Kessler, Adan Pinto-Fernandez
Summary: Bioactive lipids play important roles in cellular signaling events and are associated with human diseases. A liquid chromatography-dynamic multiple reaction monitoring-targeted mass spectrometry (LC-dMRM-MS) approach has been optimized for the analysis of eicosanoids and fatty acids in biological samples. By studying a cellular model of chronic myeloid leukemia (CML), it was found that immunomodulation by type I interferon (IFN-I) caused changes in the levels of specific lipids, potentially indicating their relevance in cancer inflammation and CML.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
William D. Figg Jr, Giorgia Fiorini, Rasheduzzaman Chowdhury, Yu Nakashima, Anthony Tumber, Michael A. McDonough, Christopher J. Schofield
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Elizabeth R. Dellar, Iolanda Vendrell, Kevin Talbot, Benedikt M. Kessler, Roman Fischer, Martin R. Turner, Alexander G. Thompson
Summary: This study used mass spectrometry with library-free data-independent acquisition to analyze the CSF proteome of ALS patients. It identified proteins correlated with clinical variables and strengthened the candidacy of CHIT1 and UCHL1 as biomarkers for ALS. The study also highlighted inflammatory and endoplasmic reticulum proteins as potential prognostic biomarkers.
JOURNAL OF NEUROCHEMISTRY
(2023)
