1
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Soul J, Carlsson E, Hofmann SR, Russ S, Hawkes J, Schulze F, Sergon M, Pablik J, Abraham S, Hedrich CM. Tissue gene expression profiles and communication networks inform candidate blood biomarker identification in psoriasis and atopic dermatitis. Clin Immunol 2024; 265:110283. [PMID: 38880200 DOI: 10.1016/j.clim.2024.110283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 05/24/2024] [Accepted: 06/10/2024] [Indexed: 06/18/2024]
Abstract
Overlapping clinical and pathomechanistic features can complicate the diagnosis and treatment of inflammatory skin diseases, including psoriasis and atopic dermatitis (AD). Spatial transcriptomics allows the identification of disease- and cell-specific molecular signatures that may advance biomarker development and future treatments. This study identified transcriptional signatures in keratinocytes and sub-basal CD4+ and CD8+ T lymphocytes from patients with psoriasis and AD. In silico prediction of ligand:receptor interactions delivered key signalling pathways (interferon, effector T cells, stroma cell and matrix biology, neuronal development, etc.). Targeted validation of selected transcripts, including CCL22, RELB, and JUND, in peripheral blood T cells suggests the chosen approach as a promising tool also in other inflammatory diseases. Psoriasis and AD are characterized by transcriptional dysregulation in T cells and keratinocytes that may be targeted therapeutically. Spatial transcriptomics is a valuable tool in the search for molecular signatures that can be used as biomarkers and/or therapeutic targets.
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Affiliation(s)
- J Soul
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - E Carlsson
- Department of Women's & Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - S R Hofmann
- Department of Pediatrics, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - S Russ
- Department of Pediatrics, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - J Hawkes
- Department of Women's & Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - F Schulze
- Department of Pediatrics, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - M Sergon
- Institut of Pathology, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - J Pablik
- Institut of Pathology, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - S Abraham
- Department of Dermatology, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - C M Hedrich
- Department of Women's & Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom; Department of Paediatric Rheumatology, Alder Hey Children's NHS Foundation Trust Hospital, Liverpool, United Kingdom.
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2
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Hu Y, Lopez VA, Xu H, Pfister JP, Song B, Servage KA, Sakurai M, Jones BT, Mendell JT, Wang T, Wu J, Lambowitz AM, Tomchick DR, Pawłowski K, Tagliabracci VS. Biochemical and structural insights into a 5' to 3' RNA ligase reveal a potential role in tRNA ligation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590974. [PMID: 38712170 PMCID: PMC11071452 DOI: 10.1101/2024.04.24.590974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
ATP-grasp superfamily enzymes contain a hand-like ATP-binding fold and catalyze a variety of reactions using a similar catalytic mechanism. More than 30 protein families are categorized in this superfamily, and they are involved in a plethora of cellular processes and human diseases. Here we identify C12orf29 as an atypical ATP-grasp enzyme that ligates RNA. Human C12orf29 and its homologs auto-adenylate on an active site Lys residue as part of a reaction intermediate that specifically ligates RNA halves containing a 5'-phosphate and a 3'-hydroxyl. C12orf29 binds tRNA in cells and can ligate tRNA within the anticodon loop in vitro. Genetic depletion of c12orf29 in female mice alters global tRNA levels in brain. Furthermore, crystal structures of a C12orf29 homolog from Yasminevirus bound to nucleotides reveal a minimal and atypical RNA ligase fold with a unique active site architecture that participates in catalysis. Collectively, our results identify C12orf29 as an RNA ligase and suggest its involvement in tRNA biology.
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Affiliation(s)
- Yingjie Hu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Victor A. Lopez
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Hengyi Xu
- Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, Texas 78712, USA
| | - James P. Pfister
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Bing Song
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Kelly A. Servage
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Masahiro Sakurai
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Benjamin T. Jones
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Joshua T. Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Tao Wang
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, Texas 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children’s Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Alan M. Lambowitz
- Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Diana R. Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Vincent S. Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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3
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Moncan M, Rakhsh-Khorshid H, Eriksson LA, Samali A, Gorman AM. Insights into the structure and function of the RNA ligase RtcB. Cell Mol Life Sci 2023; 80:352. [PMID: 37935993 PMCID: PMC10630183 DOI: 10.1007/s00018-023-05001-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/19/2023] [Accepted: 10/11/2023] [Indexed: 11/09/2023]
Abstract
To be functional, some RNAs require a processing step involving splicing events. Each splicing event necessitates an RNA ligation step. RNA ligation is a process that can be achieved with various intermediaries such as self-catalysing RNAs, 5'-3' and 3'-5' RNA ligases. While several types of RNA ligation mechanisms occur in human, RtcB is the only 3'-5' RNA ligase identified in human cells to date. RtcB RNA ligation activity is well known to be essential for the splicing of XBP1, an essential transcription factor of the unfolded protein response; as well as for the maturation of specific intron-containing tRNAs. As such, RtcB is a core factor in protein synthesis and homeostasis. Taking advantage of the high homology between RtcB orthologues in archaea, bacteria and eukaryotes, this review will provide an introduction to the structure of RtcB and the mechanism of 3'-5' RNA ligation. This analysis is followed by a description of the mechanisms regulating RtcB activity and localisation, its known partners and its various functions from bacteria to human with a specific focus on human cancer.
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Affiliation(s)
- Matthieu Moncan
- Apoptosis Research Centre, University of Galway, Galway, Ireland
- School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | - Hassan Rakhsh-Khorshid
- Apoptosis Research Centre, University of Galway, Galway, Ireland
- School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30, Göteborg, Sweden
| | - Afshin Samali
- Apoptosis Research Centre, University of Galway, Galway, Ireland
- School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
- CÚRAM SFI Research Centre for Medical Devices, University of Galway, Galway, Ireland
| | - Adrienne M Gorman
- Apoptosis Research Centre, University of Galway, Galway, Ireland.
- School of Biological and Chemical Sciences, University of Galway, Galway, Ireland.
- CÚRAM SFI Research Centre for Medical Devices, University of Galway, Galway, Ireland.
- Biomedical Sciences, Upper Newcastle, University of Galway, Galway, H91 W2TY, Ireland.
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4
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Santos MFA, Pessoa JC. Interaction of Vanadium Complexes with Proteins: Revisiting the Reported Structures in the Protein Data Bank (PDB) since 2015. Molecules 2023; 28:6538. [PMID: 37764313 PMCID: PMC10536487 DOI: 10.3390/molecules28186538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The structural determination and characterization of molecules, namely proteins and enzymes, is crucial to gaining a better understanding of their role in different chemical and biological processes. The continuous technical developments in the experimental and computational resources of X-ray diffraction (XRD) and, more recently, cryogenic Electron Microscopy (cryo-EM) led to an enormous growth in the number of structures deposited in the Protein Data Bank (PDB). Bioinorganic chemistry arose as a relevant discipline in biology and therapeutics, with a massive number of studies reporting the effects of metal complexes on biological systems, with vanadium complexes being one of the relevant systems addressed. In this review, we focus on the interactions of vanadium compounds (VCs) with proteins. Several types of binding are established between VCs and proteins/enzymes. Considering that the V-species that bind may differ from those initially added, the mentioned structural techniques are pivotal to clarifying the nature and variety of interactions of VCs with proteins and to proposing the mechanisms involved either in enzymatic inhibition or catalysis. As such, we provide an account of the available structural information of VCs bound to proteins obtained by both XRD and/or cryo-EM, mainly exploring the more recent structures, particularly those containing organic-based vanadium complexes.
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Affiliation(s)
- Marino F. A. Santos
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Centro de Química Estrutural, Departamento de Engenharia Química, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - João Costa Pessoa
- Centro de Química Estrutural, Departamento de Engenharia Química, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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5
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Hayne CK, Sekulovski S, Hurtig JE, Stanley RE, Trowitzsch S, van Hoof A. New insights into RNA processing by the eukaryotic tRNA splicing endonuclease. J Biol Chem 2023; 299:105138. [PMID: 37544645 PMCID: PMC10485636 DOI: 10.1016/j.jbc.2023.105138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/27/2023] [Accepted: 07/29/2023] [Indexed: 08/08/2023] Open
Abstract
Through its role in intron cleavage, tRNA splicing endonuclease (TSEN) plays a critical function in the maturation of intron-containing pre-tRNAs. The catalytic mechanism and core requirement for this process is conserved between archaea and eukaryotes, but for decades, it has been known that eukaryotic TSENs have evolved additional modes of RNA recognition, which have remained poorly understood. Recent research identified new roles for eukaryotic TSEN, including processing or degradation of additional RNA substrates, and determined the first structures of pre-tRNA-bound human TSEN complexes. These recent discoveries have changed our understanding of how the eukaryotic TSEN targets and recognizes substrates. Here, we review these recent discoveries, their implications, and the new questions raised by these findings.
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Affiliation(s)
- Cassandra K Hayne
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.
| | - Samoil Sekulovski
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jennifer E Hurtig
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas, USA
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National, Institutes of Health, Research Triangle Park, North Carolina, USA.
| | - Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main, Germany.
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas, USA.
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6
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Abstract
The study of eukaryotic tRNA processing has given rise to an explosion of new information and insights in the last several years. We now have unprecedented knowledge of each step in the tRNA processing pathway, revealing unexpected twists in biochemical pathways, multiple new connections with regulatory pathways, and numerous biological effects of defects in processing steps that have profound consequences throughout eukaryotes, leading to growth phenotypes in the yeast Saccharomyces cerevisiae and to neurological and other disorders in humans. This review highlights seminal new results within the pathways that comprise the life of a tRNA, from its birth after transcription until its death by decay. We focus on new findings and revelations in each step of the pathway including the end-processing and splicing steps, many of the numerous modifications throughout the main body and anticodon loop of tRNA that are so crucial for tRNA function, the intricate tRNA trafficking pathways, and the quality control decay pathways, as well as the biogenesis and biology of tRNA-derived fragments. We also describe the many interactions of these pathways with signaling and other pathways in the cell.
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Affiliation(s)
- Eric M Phizicky
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Anita K Hopper
- Department of Molecular Genetics and Center for RNA Biology, Ohio State University, Columbus, Ohio 43235, USA
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7
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Abstract
RNA ligases are present across all forms of life. While enzymatic RNA ligation between 5'-PO4 and 3'-OH termini is prevalent in viruses, fungi, and plants, such RNA ligases are yet to be identified in vertebrates. Here, using a nucleotide-based chemical probe targeting human AMPylated proteome, we have enriched and identified the hitherto uncharacterised human protein chromosome 12 open reading frame 29 (C12orf29) as a human enzyme promoting RNA ligation between 5'-PO4 and 3'-OH termini. C12orf29 catalyses ATP-dependent RNA ligation via a three-step mechanism, involving tandem auto- and RNA AMPylation. Knock-out of C12ORF29 gene impedes the cellular resilience to oxidative stress featuring concurrent RNA degradation, which suggests a role of C12orf29 in maintaining RNA integrity. These data provide the groundwork for establishing a human RNA repair pathway.
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8
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Sekulovski S, Trowitzsch S. What connects splicing of transfer RNA precursor molecules with pontocerebellar hypoplasia? Bioessays 2023; 45:e2200130. [PMID: 36517085 DOI: 10.1002/bies.202200130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 01/19/2023]
Abstract
Transfer RNAs (tRNAs) represent the most abundant class of RNA molecules in the cell and are key players during protein synthesis and cellular homeostasis. Aberrations in the extensive tRNA biogenesis pathways lead to severe neurological disorders in humans. Mutations in the tRNA splicing endonuclease (TSEN) and its associated RNA kinase cleavage factor polyribonucleotide kinase subunit 1 (CLP1) cause pontocerebellar hypoplasia (PCH), a heterogeneous group of neurodegenerative disorders, that manifest as underdevelopment of specific brain regions typically accompanied by microcephaly, profound motor impairments, and child mortality. Recently, we demonstrated that mutations leading to specific PCH subtypes destabilize TSEN in vitro and cause imbalances of immature to mature tRNA ratios in patient-derived cells. However, how tRNA processing defects translate to disease on a systems level has not been understood. Recent findings suggested that other cellular processes may be affected by mutations in TSEN/CLP1 and obscure the molecular mechanisms of PCH emergence. Here, we review PCH disease models linked to the TSEN/CLP1 machinery and discuss future directions to study neuropathogenesis.
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Affiliation(s)
- Samoil Sekulovski
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany
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9
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Austin S, Mekis R, Mohammed SEM, Scalise M, Wang W, Galluccio M, Pfeiffer C, Borovec T, Parapatics K, Vitko D, Dinhopl N, Demaurex N, Bennett KL, Indiveri C, Nowikovsky K. TMBIM5 is the Ca 2+ /H + antiporter of mammalian mitochondria. EMBO Rep 2022; 23:e54978. [PMID: 36321428 PMCID: PMC9724676 DOI: 10.15252/embr.202254978] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 09/07/2022] [Accepted: 10/07/2022] [Indexed: 11/25/2022] Open
Abstract
Mitochondrial Ca2+ ions are crucial regulators of bioenergetics and cell death pathways. Mitochondrial Ca2+ content and cytosolic Ca2+ homeostasis strictly depend on Ca2+ transporters. In recent decades, the major players responsible for mitochondrial Ca2+ uptake and release have been identified, except the mitochondrial Ca2+ /H+ exchanger (CHE). Originally identified as the mitochondrial K+ /H+ exchanger, LETM1 was also considered as a candidate for the mitochondrial CHE. Defining the mitochondrial interactome of LETM1, we identify TMBIM5/MICS1, the only mitochondrial member of the TMBIM family, and validate the physical interaction of TMBIM5 and LETM1. Cell-based and cell-free biochemical assays demonstrate the absence or greatly reduced Na+ -independent mitochondrial Ca2+ release in TMBIM5 knockout or pH-sensing site mutants, respectively, and pH-dependent Ca2+ transport by recombinant TMBIM5. Taken together, we demonstrate that TMBIM5, but not LETM1, is the long-sought mitochondrial CHE, involved in setting and regulating the mitochondrial proton gradient. This finding provides the final piece of the puzzle of mitochondrial Ca2+ transporters and opens the door to exploring its importance in health and disease, and to developing drugs modulating Ca2+ exchange.
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Affiliation(s)
- Shane Austin
- Department of Internal Medicine I and Comprehensive Cancer CenterMedical University of ViennaViennaAustria
- Present address:
Department of Biological & Chemical SciencesThe University of the West Indies, Cave Hill CampusCave HillBarbados
| | - Ronald Mekis
- Department of Internal Medicine I and Comprehensive Cancer CenterMedical University of ViennaViennaAustria
- Department of Biomedical Sciences, Institute of Physiology, Pathophysiology and BiophysicsUniversity of Veterinary Medicine ViennaViennaAustria
| | - Sami E M Mohammed
- Department of Biomedical Sciences, Institute of Physiology, Pathophysiology and BiophysicsUniversity of Veterinary Medicine ViennaViennaAustria
| | - Mariafrancesca Scalise
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular BiotechnologyUniversity of CalabriaArcavacata di RendeItaly
| | - Wen‐An Wang
- Department of Cell Physiology & MetabolismUniversity of GenevaGenevaSwitzerland
| | - Michele Galluccio
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular BiotechnologyUniversity of CalabriaArcavacata di RendeItaly
| | - Christina Pfeiffer
- Department of Internal Medicine I and Comprehensive Cancer CenterMedical University of ViennaViennaAustria
| | - Tamara Borovec
- Department of Internal Medicine I and Comprehensive Cancer CenterMedical University of ViennaViennaAustria
- Department of Biomedical Sciences, Institute of Physiology, Pathophysiology and BiophysicsUniversity of Veterinary Medicine ViennaViennaAustria
| | - Katja Parapatics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Dijana Vitko
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Nora Dinhopl
- Department of Pathobiology, Institute of PathologyUniversity of Veterinary MedicineViennaAustria
| | - Nicolas Demaurex
- Department of Cell Physiology & MetabolismUniversity of GenevaGenevaSwitzerland
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Cesare Indiveri
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular BiotechnologyUniversity of CalabriaArcavacata di RendeItaly
- CNR Institute of BiomembranesBioenergetics and Molecular Biotechnologies (IBIOM)BariItaly
| | - Karin Nowikovsky
- Department of Internal Medicine I and Comprehensive Cancer CenterMedical University of ViennaViennaAustria
- Department of Biomedical Sciences, Institute of Physiology, Pathophysiology and BiophysicsUniversity of Veterinary Medicine ViennaViennaAustria
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10
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ANGEL2 phosphatase activity is required for non-canonical mitochondrial RNA processing. Nat Commun 2022; 13:5750. [PMID: 36180430 PMCID: PMC9525292 DOI: 10.1038/s41467-022-33368-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 09/14/2022] [Indexed: 11/18/2022] Open
Abstract
Canonical RNA processing in mammalian mitochondria is defined by tRNAs acting as recognition sites for nucleases to release flanking transcripts. The relevant factors, their structures, and mechanism are well described, but not all mitochondrial transcripts are punctuated by tRNAs, and their mode of processing has remained unsolved. Using Drosophila and mouse models, we demonstrate that non-canonical processing results in the formation of 3′ phosphates, and that phosphatase activity by the carbon catabolite repressor 4 domain-containing family member ANGEL2 is required for their hydrolysis. Furthermore, our data suggest that members of the FAST kinase domain-containing protein family are responsible for these 3′ phosphates. Our results therefore propose a mechanism for non-canonical RNA processing in metazoan mitochondria, by identifying the role of ANGEL2. A subset of mitochondrial transcripts is not flanked by tRNAs and thus does not conform to the canonical mode of processing. Here, Clemente et al. demonstrate that phosphatase activity of ANGEL2 is required for correct processing of these transcripts.
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11
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Hayne CK, Lewis TA, Stanley RE. Recent insights into the structure, function, and regulation of the eukaryotic transfer RNA splicing endonuclease complex. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1717. [PMID: 35156311 PMCID: PMC9465713 DOI: 10.1002/wrna.1717] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 04/30/2023]
Abstract
The splicing of transfer RNA (tRNA) introns is a critical step of tRNA maturation, for intron-containing tRNAs. In eukaryotes, tRNA splicing is a multi-step process that relies on several RNA processing enzymes to facilitate intron removal and exon ligation. Splicing is initiated by the tRNA splicing endonuclease (TSEN) complex which catalyzes the excision of the intron through its two nuclease subunits. Mutations in all four subunits of the TSEN complex are linked to a family of neurodegenerative and neurodevelopmental diseases known as pontocerebellar hypoplasia (PCH). Recent studies provide molecular insights into the structure, function, and regulation of the eukaryotic TSEN complex and are beginning to illuminate how mutations in the TSEN complex lead to neurodegenerative disease. Using new advancements in the prediction of protein structure, we created a three-dimensional model of the human TSEN complex. We review functions of the TSEN complex beyond tRNA splicing by highlighting recently identified substrates of the eukaryotic TSEN complex and discuss mechanisms for the regulation of tRNA splicing, by enzymes that modify cleaved tRNA exons and introns. Finally, we review recent biochemical and animal models that have worked to address the mechanisms that drive PCH and synthesize these studies with previous studies to try to better understand PCH pathogenesis. This article is categorized under: RNA Processing > tRNA Processing RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition.
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Affiliation(s)
- Cassandra K Hayne
- Department of Health and Human Services, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Tanae A Lewis
- Department of Chemistry, North Carolina Agricultural and Technical State University, Greensboro, North Carolina, USA
| | - Robin E Stanley
- Department of Health and Human Services, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
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12
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Gerber JL, Köhler S, Peschek J. Eukaryotic tRNA splicing - one goal, two strategies, many players. Biol Chem 2022; 403:765-778. [PMID: 35621519 DOI: 10.1515/hsz-2021-0402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 05/10/2022] [Indexed: 12/28/2022]
Abstract
Transfer RNAs (tRNAs) are transcribed as precursor molecules that undergo several maturation steps before becoming functional for protein synthesis. One such processing mechanism is the enzyme-catalysed splicing of intron-containing pre-tRNAs. Eukaryotic tRNA splicing is an essential process since intron-containing tRNAs cannot fulfil their canonical function at the ribosome. Splicing of pre-tRNAs occurs in two steps: The introns are first excised by a tRNA-splicing endonuclease and the exons are subsequently sealed by an RNA ligase. An intriguing complexity has emerged from newly identified tRNA splicing factors and their interplay with other RNA processing pathways during the past few years. This review summarises our current understanding of eukaryotic tRNA splicing and the underlying enzyme machinery. We highlight recent structural advances and how they have shaped our mechanistic understanding of tRNA splicing in eukaryotic cells. A special focus lies on biochemically distinct strategies for exon-exon ligation in fungi versus metazoans.
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Affiliation(s)
- Janina L Gerber
- Biochemistry Center (BZH), Heidelberg University, D-69120 Heidelberg, Germany
| | - Sandra Köhler
- Biochemistry Center (BZH), Heidelberg University, D-69120 Heidelberg, Germany
| | - Jirka Peschek
- Biochemistry Center (BZH), Heidelberg University, D-69120 Heidelberg, Germany
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13
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Han X, Li Y, Wang ZY, Liu LZ, Qiu JG, Liu BJ, Zhang CY. Label-free and sensitive detection of RNA demethylase FTO with primer generation rolling circle amplification. Chem Commun (Camb) 2022; 58:1565-1568. [PMID: 35014995 DOI: 10.1039/d1cc06493b] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We develop for the first time a label-free fluorescent method for sensitive detection of fat mass and obesity-associated protein (FTO) activity using MazF-mediated primer generation rolling circle amplification. This method is very simple with ultrahigh sensitivity and good specificity, and it can detect FTO activity at the single-cell level. Moreover, this method can be applied for the measurement of kinetic parameters and the screening of FTO inhibitors.
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Affiliation(s)
- Xiaoxia Han
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450000, China.
| | - Yueying Li
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
| | - Zi-Yue Wang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
| | - Ling-Zhi Liu
- Department of Oncology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jian-Ge Qiu
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450000, China.
| | - Bing-Jie Liu
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450000, China.
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
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14
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Welby E, Rehborg RJ, Harmelink M, Ebert AD. Assessment of cerebral spinal fluid biomarkers and microRNA-mediated disease mechanisms in spinal muscular atrophy patient samples. Hum Mol Genet 2021; 31:1830-1843. [PMID: 34919695 DOI: 10.1093/hmg/ddab365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/01/2021] [Accepted: 12/09/2021] [Indexed: 11/14/2022] Open
Abstract
Cerebral spinal fluid (CSF) is a promising biospecimen for the detection of central nervous system biomarkers to monitor therapeutic efficacy at the cellular level in neurological diseases. Spinal muscular atrophy (SMA) patients receiving intrathecal antisense oligonucleotide (nusinersen) therapy tend to show improved motor function, but the treatment effect on cellular health remains unknown. The objective of this study was to assess the potential of extracellular RNAs and microRNAs in SMA patient CSF as indicators of neuron and glial health following nusinersen treatment. Extracellular RNA analysis of CSF samples revealed ongoing cellular stress related to inflammation and glial differentiation, even after treatment administration. Downregulated microRNA expression associated with SMA-specific or general motor neuron dysfunction in animal and cellular models, tended to increase in nusinersen treated patient CSF samples and correlated with SMA Type 1 and 2 motor functioning improvements. However, miR-146a, known to be upregulated in SMA induced pluripotent stem cell (iPSC)-derived astrocytes, showed increased expression in nusinersen treated CSF samples. We then used mRNA sequencing and multi-electrode arrays to assess the transcriptional and functional effects of miR-146a on healthy and SMA iPSC-derived motor neurons. miR-146a treatment on iPSC-derived motor neurons led to a downregulation of extracellular matrix genes associated with synaptic perineuronal net and alterations in spontaneous electrophysiological activity. Together, this study suggests that extracellular RNAs and microRNAs may serve as useful biomarkers to monitor cellular health during nusinersen treatment. Moreover, these data highlight the importance of addressing astrocyte health and response to nusinersen in SMA pathogenesis and treatment strategies.
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Affiliation(s)
- Emily Welby
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Rebecca J Rehborg
- Department of Neurology (Child Neurology), Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Matthew Harmelink
- Department of Neurology (Child Neurology), Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Allison D Ebert
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
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15
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Han Y, Ji L, Guan Y, Ma M, Li P, Xue Y, Zhang Y, Huang W, Gong Y, Jiang L, Wang X, Xie H, Zhou B, Wang J, Wang J, Han J, Deng Y, Yi X, Gao F, Huang J. An epigenomic landscape of cervical intraepithelial neoplasia and cervical cancer using single-base resolution methylome and hydroxymethylome. Clin Transl Med 2021; 11:e498. [PMID: 34323415 PMCID: PMC8288011 DOI: 10.1002/ctm2.498] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 06/22/2021] [Accepted: 06/27/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Cervical cancer (CC) is the second leading cause of cancer death among women worldwide. Epigenetic regulation of gene expression through DNA methylation and hydroxymethylation plays a pivotal role during tumorigenesis. In this study, to analyze the epigenomic landscape and identify potential biomarkers for CCs, we selected a series of samples from normal to cervical intra-epithelial neoplasia (CINs) to CCs and performed an integrative analysis of whole-genome bisulfite sequencing (WGBS-seq), oxidative WGBS, RNA-seq, and external histone modifications profiling data. RESULTS In the development and progression of CC, there were genome-wide hypo-methylation and hypo-hydroxymethylation, accompanied by local hyper-methylation and hyper-hydroxymethylation. Hydroxymethylation prefers to distribute in the CpG islands and CpG shores, as displayed a trend of gradual decline from health to CIN2, while a trend of increase from CIN3 to CC. The differentially methylated and hydroxymethylated region-associated genes both enriched in Hippo and other cancer-related signaling pathways that drive cervical carcinogenesis. Furthermore, we identified eight novel differentially methylated/hydroxymethylated-associated genes (DES, MAL, MTIF2, PIP5K1A, RPS6KA6, ANGEL2, MPP, and PAPSS2) significantly correlated with the overall survival of CC. In addition, no any correlation was observed between methylation or hydroxymethylation levels and somatic copy number variations in CINs and CCs. CONCLUSION Our current study systematically delineates the map of methylome and hydroxymethylome from CINs to CC, and some differentially methylated/hydroxymethylated-associated genes can be used as the potential epigenetic biomarkers in CC prognosis.
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Affiliation(s)
- Yingxin Han
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Centre for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | | | - Yanfang Guan
- Department of Computer Science and TechnologySchool of Electronic and Information EngineeringXi'an Jiao Tong UniversityXi'anChina
- GenePlus‐BeijingBeijingChina
| | | | | | - Yinge Xue
- Shanghai FLY Medical LaboratoryShanghaiChina
| | | | - Wanqiu Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Centre for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | | | - Li Jiang
- The Department of Obstetrics and GynecologyXinhua Hospital affiliated to Shanghai Jiao Tong UniversityShanghaiChina
| | - Xipeng Wang
- The Department of Obstetrics and GynecologyXinhua Hospital affiliated to Shanghai Jiao Tong UniversityShanghaiChina
| | - Hong Xie
- The Department of Obstetrics and GynecologyShenzhen People's HospitalShenzhenChina
| | - Boping Zhou
- The Department of Obstetrics and GynecologyShenzhen People's HospitalShenzhenChina
| | - Jiayin Wang
- Department of Computer Science and TechnologySchool of Electronic and Information EngineeringXi'an Jiao Tong UniversityXi'anChina
| | - Junwen Wang
- Genome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Jinghua Han
- Genome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Yuliang Deng
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Centre for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Xin Yi
- GenePlus‐BeijingBeijingChina
| | - Fei Gao
- Genome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
- Comparative Pediatrics and NutritionDepartment of Veterinary and Animal SciencesFaculty of Health and Medical SciencesUniversity of CopenhagenFrederiksbergDenmark
| | - Jian Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Centre for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
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16
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Yip MCJ, Shao S. Detecting and Rescuing Stalled Ribosomes. Trends Biochem Sci 2021; 46:731-743. [PMID: 33966939 DOI: 10.1016/j.tibs.2021.03.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/18/2021] [Accepted: 03/30/2021] [Indexed: 11/24/2022]
Abstract
Ribosomes that stall inappropriately during protein synthesis harbor proteotoxic components linked to cellular stress and neurodegenerative diseases. Molecular mechanisms that rescue stalled ribosomes must selectively detect rare aberrant translational complexes and process the heterogeneous components. Ribosome-associated quality control pathways eliminate problematic messenger RNAs and nascent proteins on stalled translational complexes. In addition, recent studies have uncovered general principles of stall recognition upstream of quality control pathways and fail-safe mechanisms that ensure nascent proteome integrity. Here, we discuss developments in our mechanistic understanding of the detection and rescue of stalled ribosomal complexes in eukaryotes.
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Affiliation(s)
- Matthew C J Yip
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Sichen Shao
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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17
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Kawamura T, Shigematsu M, Kirino Y. In vitro production and multiplex quantification of 2',3'-cyclic phosphate-containing 5'-tRNA half molecules. Methods 2021; 203:335-341. [PMID: 33962012 DOI: 10.1016/j.ymeth.2021.04.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/29/2022] Open
Abstract
RNA cleavages by many ribonucleases generate RNA molecules that contain a 2',3'-cyclic phosphate (cP) at their 3'-termini, and many cP-containing RNAs (cP-RNAs) are expressed as functional molecules in cells and tissues. 5'-tRNA half molecules are representative examples of functional cP-RNAs, playing important roles in various biological processes. We here show in vitro production of cP-containing 5'-tRNA half molecules that is able to prepare abundant synthetic cP-RNAs enough for functional analyses. Furthermore, we report a multiplex TaqMan RT-qPCR method which can simultaneously quantify multiple cP-containing 5'-tRNA half species. The method enabled us to efficiently quantify 5'-tRNA halves using samples with limited amounts, such as human plasma samples, revealing drastic enhancement of 5'-tRNA half levels at approximately 1,000-fold in patients infected with Mycobacterium tuberculosis. These in vitro production and multiplex quantification methods can be applied to any cP-RNAs, and they provide cost-effective, in-house techniques to accelerate expressional and functional characterizations of 5'-tRNA halves and other cP-RNAs.
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Affiliation(s)
- Takuya Kawamura
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Megumi Shigematsu
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA.
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18
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Jarrous N, Mani D, Ramanathan A. Coordination of transcription and processing of tRNA. FEBS J 2021; 289:3630-3641. [PMID: 33929081 DOI: 10.1111/febs.15904] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/02/2021] [Accepted: 04/28/2021] [Indexed: 12/17/2022]
Abstract
Coordination of transcription and processing of RNA is a basic principle in regulation of gene expression in eukaryotes. In the case of mRNA, coordination is primarily founded on a co-transcriptional processing mechanism by which a nascent precursor mRNA undergoes maturation via cleavage and modification by the transcription machinery. A similar mechanism controls the biosynthesis of rRNA. However, the coordination of transcription and processing of tRNA, a rather short transcript, remains unknown. Here, we present a model for high molecular weight initiation complexes of human RNA polymerase III that assemble on tRNA genes and process precursor transcripts to mature forms. These multifunctional initiation complexes may support co-transcriptional processing, such as the removal of the 5' leader of precursor tRNA by RNase P. Based on this model, maturation of tRNA is predetermined prior to transcription initiation.
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Affiliation(s)
- Nayef Jarrous
- Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Dhivakar Mani
- Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Aravind Ramanathan
- Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
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19
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Cristodero M, Brogli R, Joss O, Schimanski B, Schneider A, Polacek N. tRNA 3' shortening by LCCR4 as a response to stress in Trypanosoma brucei. Nucleic Acids Res 2021; 49:1647-1661. [PMID: 33406257 PMCID: PMC7897491 DOI: 10.1093/nar/gkaa1261] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 11/24/2020] [Accepted: 12/19/2020] [Indexed: 12/27/2022] Open
Abstract
Sensing of environmental cues is crucial for cell survival. To adapt to changes in their surroundings cells need to tightly control the repertoire of genes expressed at any time. Regulation of translation is key, especially in organisms in which transcription is hardly controlled, like Trypanosoma brucei. In this study, we describe the shortening of the bulk of the cellular tRNAs during stress at the expense of the conserved 3' CCA-tail. This tRNA shortening is specific for nutritional stress and renders tRNAs unsuitable substrates for translation. We uncovered the nuclease LCCR4 (Tb927.4.2430), a homologue of the conserved deadenylase Ccr4, as being responsible for tRNA trimming. Once optimal growth conditions are restored tRNAs are rapidly repaired by the trypanosome tRNA nucleotidyltransferase thus rendering the recycled tRNAs amenable for translation. This mechanism represents a fast and efficient way to repress translation during stress, allowing quick reactivation with a low energy input.
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Affiliation(s)
| | - Rebecca Brogli
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Oliver Joss
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Bernd Schimanski
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - André Schneider
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Norbert Polacek
- Correspondence may also be addressed to Norbert Polacek. Tel: +41 031 631 4320;
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