1
|
Taguchi A, Nakashima R, Nishino K. Structural Basis of Nucleotide Selectivity in Pyruvate Kinase. J Mol Biol 2024; 436:168708. [PMID: 39009072 DOI: 10.1016/j.jmb.2024.168708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/17/2024]
Abstract
Nucleoside triphosphates are indispensable in numerous biological processes, with enzymes involved in their biogenesis playing pivotal roles in cell proliferation. Pyruvate kinase (PYK), commonly regarded as the terminal glycolytic enzyme that generates ATP in tandem with pyruvate, is also capable of synthesizing a wide range of nucleoside triphosphates from their diphosphate precursors. Despite their substrate promiscuity, some PYKs show preference towards specific nucleotides, suggesting an underlying mechanism for differentiating nucleotide bases. However, the thorough characterization of this mechanism has been hindered by the paucity of nucleotide-bound PYK structures. Here, we present crystal structures of Streptococcus pneumoniae PYK in complex with four different nucleotides. These structures facilitate direct comparison of the protein-nucleotide interactions and offer structural insights into its pronounced selectivity for GTP synthesis. Notably, this selectivity is dependent on a sequence motif in the nucleotide recognition site that is widely present among prokaryotic PYKs, particularly in Firmicutes species. We show that pneumococcal cell growth is significantly impaired when expressing a PYK variant with compromised GTP and UTP synthesis activity, underscoring the importance of PYK in maintaining nucleotide homeostasis. Our findings collectively advance our understanding of PYK biochemistry and prokaryotic metabolism.
Collapse
Affiliation(s)
- Atsushi Taguchi
- SANKEN, Osaka University, Ibaraki, Osaka 567-0047, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan.
| | | | - Kunihiko Nishino
- SANKEN, Osaka University, Ibaraki, Osaka 567-0047, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka 565-0871, Japan.
| |
Collapse
|
2
|
Meena JK, Wang JH, Neill NJ, Keough D, Putluri N, Katsonis P, Koire AM, Lee H, Bowling EA, Tyagi S, Orellana M, Dominguez-Vidaña R, Li H, Eagle K, Danan C, Chung HC, Yang AD, Wu W, Kurley SJ, Ho BM, Zoeller JR, Olson CM, Meerbrey KL, Lichtarge O, Sreekumar A, Dacso CC, Guddat LW, Rejman D, Hocková D, Janeba Z, Simon LM, Lin CY, Pillon MC, Westbrook TF. MYC Induces Oncogenic Stress through RNA Decay and Ribonucleotide Catabolism in Breast Cancer. Cancer Discov 2024; 14:1699-1716. [PMID: 39193992 DOI: 10.1158/2159-8290.cd-22-0649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/12/2023] [Accepted: 05/06/2024] [Indexed: 08/29/2024]
Abstract
Upregulation of MYC is a hallmark of cancer, wherein MYC drives oncogenic gene expression and elevates total RNA synthesis across cancer cell transcriptomes. Although this transcriptional anabolism fuels cancer growth and survival, the consequences and metabolic stresses induced by excess cellular RNA are poorly understood. Herein, we discover that RNA degradation and downstream ribonucleotide catabolism is a novel mechanism of MYC-induced cancer cell death. Combining genetics and metabolomics, we find that MYC increases RNA decay through the cytoplasmic exosome, resulting in the accumulation of cytotoxic RNA catabolites and reactive oxygen species. Notably, tumor-derived exosome mutations abrogate MYC-induced cell death, suggesting excess RNA decay may be toxic to human cancers. In agreement, purine salvage acts as a compensatory pathway that mitigates MYC-induced ribonucleotide catabolism, and inhibitors of purine salvage impair MYC+ tumor progression. Together, these data suggest that MYC-induced RNA decay is an oncogenic stress that can be exploited therapeutically. Significance: MYC is the most common oncogenic driver of poor-prognosis cancers but has been recalcitrant to therapeutic inhibition. We discovered a new vulnerability in MYC+ cancer where MYC induces cell death through excess RNA decay. Therapeutics that exacerbate downstream ribonucleotide catabolism provide a therapeutically tractable approach to TNBC (Triple-negative Breast Cancer) and other MYC-driven cancers.
Collapse
Affiliation(s)
- Jitendra K Meena
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
| | - Jarey H Wang
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas
| | - Nicholas J Neill
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Dianne Keough
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Nagireddy Putluri
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Amanda M Koire
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Hyemin Lee
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Elizabeth A Bowling
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
| | - Siddhartha Tyagi
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
| | - Mayra Orellana
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
| | - Rocio Dominguez-Vidaña
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
| | - Heyuan Li
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
| | - Kenneth Eagle
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Charles Danan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Hsiang-Ching Chung
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
| | - Andrew D Yang
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas
| | - William Wu
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas
| | - Sarah J Kurley
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
| | - Brian M Ho
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas
| | - Joseph R Zoeller
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas
| | - Calla M Olson
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
| | - Kristen L Meerbrey
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Arun Sreekumar
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Clifford C Dacso
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Luke W Guddat
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Dominik Rejman
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Dana Hocková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Zlatko Janeba
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Lukas M Simon
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas
| | - Charles Y Lin
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Monica C Pillon
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
| | - Thomas F Westbrook
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| |
Collapse
|
3
|
Aubuchon LN, Verma P. Endogenous base damage as a driver of genomic instability in homologous recombination-deficient cancers. DNA Repair (Amst) 2024; 141:103736. [PMID: 39096699 DOI: 10.1016/j.dnarep.2024.103736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 07/18/2024] [Accepted: 07/22/2024] [Indexed: 08/05/2024]
Abstract
Homologous recombination (HR) is a high-fidelity DNA double-strand break (DSB) repair pathway. Both familial and somatic loss of function mutation(s) in various HR genes predispose to a variety of cancer types, underscoring the importance of error-free repair of DSBs in human physiology. While environmental sources of DSBs have been known, more recent studies have begun to uncover the role of endogenous base damage in leading to these breaks. Base damage repair intermediates often consist of single-strand breaks, which if left unrepaired, can lead to DSBs as the replication fork encounters these lesions. This review summarizes various sources of endogenous base damage and how these lesions are repaired. We highlight how conversion of base repair intermediates, particularly those with 5'or 3' blocked ends, to DSBs can be a predominant source of genomic instability in HR-deficient cancers. We also discuss how endogenous base damage and ensuing DSBs can be exploited to enhance the efficacy of Poly (ADP-ribose) polymerase inhibitors (PARPi), that are widely used in the clinics for the regimen of HR-deficient cancers.
Collapse
Affiliation(s)
- Lindsey N Aubuchon
- Division of Oncology, Department of Medicine, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Cancer Biology Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Priyanka Verma
- Division of Oncology, Department of Medicine, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Cancer Biology Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA.
| |
Collapse
|
4
|
Thomas RC, Zaksauskaite R, Al-Kandari NY, Hyde AC, Abugable AA, El-Khamisy SF, van Eeden FJ. Second generation lethality in RNAseH2a knockout zebrafish. Nucleic Acids Res 2024:gkae725. [PMID: 39217460 DOI: 10.1093/nar/gkae725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 07/31/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024] Open
Abstract
Removal of ribonucleotides from DNA by RNaseH2 is essential for genome stability, and its impacted function causes the neurodegenerative disease, Aicardi Goutières Syndrome. We have created a zebrafish rnaseh2a mutant to model this process. Surprisingly, RNaseH2a knockouts show little phenotypic abnormality at adulthood in the first generation, unlike mouse knockout models, which are early embryonic lethal. However, the second generation offspring show reduced development, increased ribonucleotide incorporation and upregulation of key inflammatory markers, resulting in both maternal and paternal embryonic lethality. Thus, neither fathers or mothers can generate viable offspring even when crossed to wild-type partners. Despite their survival, rnaseh2a-/- adults show an accumulation of ribonucleotides in both the brain and testes that is not present in early development. Our data suggest that homozygotes possess RNaseH2 independent compensatory mechanisms that are inactive or overwhelmed by the inherited ribonucleotides in their offspring, or that zebrafish have a yet unknown tolerance mechanism. Additionally, we identify ribodysgenesis, the rapid removal of rNMPs and subsequently lethal fragmentation of DNA as responsible for maternal and paternal embryonic lethality.
Collapse
Affiliation(s)
- Ruth C Thomas
- Bateson Centre, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- Healthy Lifespan Institute, Sheffield Institute for Neuroscience, University of Sheffield, Sheffield S10 2TN, UK
| | - Ringaile Zaksauskaite
- Bateson Centre, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- Healthy Lifespan Institute, Sheffield Institute for Neuroscience, University of Sheffield, Sheffield S10 2TN, UK
| | - Norah Y Al-Kandari
- Bateson Centre, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- Healthy Lifespan Institute, Sheffield Institute for Neuroscience, University of Sheffield, Sheffield S10 2TN, UK
| | - Anne Cathrine Hyde
- Bateson Centre, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- Healthy Lifespan Institute, Sheffield Institute for Neuroscience, University of Sheffield, Sheffield S10 2TN, UK
| | - Arwa A Abugable
- Healthy Lifespan Institute, Sheffield Institute for Neuroscience, University of Sheffield, Sheffield S10 2TN, UK
| | - Sherif F El-Khamisy
- Bateson Centre, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- Healthy Lifespan Institute, Sheffield Institute for Neuroscience, University of Sheffield, Sheffield S10 2TN, UK
- The Institute of Cancer Therapeutics, University of Bradford, BD7 1DP, UK
| | - Freek J van Eeden
- Bateson Centre, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- Healthy Lifespan Institute, Sheffield Institute for Neuroscience, University of Sheffield, Sheffield S10 2TN, UK
| |
Collapse
|
5
|
Stabile J, Fürstenau CR. Platelets isolation and ectonucleotidase assay: Revealing functional aspects of the communication between the vasculature and the immune system. J Immunol Methods 2024; 533:113746. [PMID: 39181235 DOI: 10.1016/j.jim.2024.113746] [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: 02/10/2024] [Revised: 08/17/2024] [Accepted: 08/19/2024] [Indexed: 08/27/2024]
Abstract
Platelets are enucleated fragments of cells with a diversity of internal granules. They are responsible for functions related to hemostasis, coagulation, and inflammation. The activation of these processes depends on a cascade coordinated by cytokines, chemokines, and components of purinergic signaling, such as ATP, ADP, and adenosine. Platelets express distinct components of the purinergic system: P2X1, P2Y1, PY12, and P2Y14 receptors; and the ectonucleotidases NTPDase, NPP, and 5NTE (ecto-5'-nucleotidase). Except for P2Y14, which has not yet exhibited a known function, all other components relate to the biological processes mentioned before. Platelets are known to display specific responses to microorganisms, being capable of recognizing pathogen-associated molecular patterns (PAMPs), engulfing certain classes of viruses, and participating in NETosis. Platelet function dysregulation implicates various pathophysiological processes, including cardiovascular diseases (CVDs) and infections. In COVID-19 patients, platelets exhibit altered purinergic signaling and increased activation, contributing to inflammation. Excessive platelet activation can lead to complications from thrombosis, which can affect the circulation of vital organs. Therefore, controlling the activation is necessary to end the inflammatory process and restore homeostasis. Ectonucleotidases, capable of hydrolyzing ATP, ADP, and AMP, are of fundamental importance in activating platelets, promising pharmacological targets for clinical use as cardiovascular protective drugs. In this review, we revisit platelet biology, the purinergic receptors and ectonucleotidases on their surface, and their importance in platelet activity. Additionally, we describe methods for isolating platelets in humans and murine, as well as the main techniques for detecting the activity of ectonucleotidases in platelets. Considering the multitude of functions revealed by platelets and their potential use as potent bioreactors able to secrete and present molecules involved in the communication of the vasculature with the immune system, it is crucial to deeply understand platelet biology and purinergic signaling participation to contribute to the developing of therapeutic strategies in diseases of the cardiovascular, inflammatory, and immune systems.
Collapse
Affiliation(s)
- Jeferson Stabile
- Laboratory of Vascular Biochemistry, Center for Natural and Human Sciences, Federal University of ABC, Santo André, SP, Brazil
| | - Cristina Ribas Fürstenau
- Laboratory of Vascular Biochemistry, Center for Natural and Human Sciences, Federal University of ABC, Santo André, SP, Brazil.
| |
Collapse
|
6
|
Hinrichs R, Graumann PL. Visual Evidence for the Recruitment of Four Enzymes with RNase Activity to the Bacillus subtilis Replication Forks. Cells 2024; 13:1381. [PMID: 39195267 DOI: 10.3390/cells13161381] [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: 07/22/2024] [Revised: 08/14/2024] [Accepted: 08/15/2024] [Indexed: 08/29/2024] Open
Abstract
Removal of RNA/DNA hybrids for the maturation of Okazaki fragments on the lagging strand, or due to misincorporation of ribonucleotides by DNA polymerases, is essential for all types of cells. In prokaryotic cells such as Escherichia coli, DNA polymerase 1 and RNase HI are supposed to remove RNA from Okazaki fragments, but many bacteria lack HI-type RNases, such as Bacillus subtilis. Previous work has demonstrated in vitro that four proteins are able to remove RNA from RNA/DNA hybrids, but their actual contribution to DNA replication is unclear. We have studied the dynamics of DNA polymerase A (similar to Pol 1), 5'->3' exonuclease ExoR, and the two endoribonucleases RNase HII and HIII in B. subtilis using single-molecule tracking. We found that all four enzymes show a localization pattern similar to that of replicative DNA helicase. By scoring the distance of tracks to replication forks, we found that all four enzymes are enriched at DNA replication centers. After inducing UV damage, RNase HIII was even more strongly recruited to the replication forks, and PolA showed a more static behavior, indicative of longer binding events, whereas RNase HII and ExoR showed no response. Inhibition of replication by 6(p hydroxyphenylazo)-uracil (HPUra) demonstrated that both RNase HII and RNase HIII are directly involved in the replication. We found that the absence of ExoR increases the likelihood of RNase HIII at the forks, indicating that substrate availability rather than direct protein interactions may be a major driver for the recruitment of RNases to the lagging strands. Thus, B. subtilis replication forks appear to be an intermediate between E. coli type and eukaryotic replication forks and employ a multitude of RNases, rather than any dedicated enzyme for RNA/DNA hybrid removal.
Collapse
Affiliation(s)
- Rebecca Hinrichs
- Centre for Synthetic Microbiology (SYNMIKRO), Philipps Universität Marburg, Karl-von-Frisch-Str. 14, 35043 Marburg, Germany
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg, Germany
| | - Peter L Graumann
- Centre for Synthetic Microbiology (SYNMIKRO), Philipps Universität Marburg, Karl-von-Frisch-Str. 14, 35043 Marburg, Germany
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg, Germany
| |
Collapse
|
7
|
Potapov V, Krudup S, Maguire S, Unlu I, Guan S, Buss JA, Smail BA, van Eeuwen T, Taylor MS, Burns KH, Ong JL, Trachman RJ. Discrete measurements of RNA polymerase and reverse transcriptase fidelity reveal evolutionary tuning. RNA (NEW YORK, N.Y.) 2024; 30:1246-1258. [PMID: 38942481 PMCID: PMC11331410 DOI: 10.1261/rna.080002.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 06/05/2024] [Indexed: 06/30/2024]
Abstract
Direct methods for determining the fidelity of DNA polymerases are robust, with relatively little sample manipulation before sequencing. In contrast, methods for measuring RNA polymerase and reverse transcriptase fidelities are complicated by additional preparation steps that introduce ambiguity and error. Here, we describe a sequencing method, termed Roll-Seq, for simultaneously determining the individual fidelities of RNA polymerases and reverse transcriptases (RT) using Pacific Biosciences single molecule real-time sequencing. By using reverse transcriptases with high rolling-circle activity, Roll-Seq generates long concatemeric cDNA from a circular RNA template. To discern the origin of a mutation, errors are recorded and determined to occur within a single concatemer (reverse transcriptase error) or all concatemers (RNA polymerase error) over the cDNA strand. We used Roll-Seq to measure the fidelities of T7 RNA polymerases, a Group II intron-encoded RT (Induro), and two LINE RTs (Fasciolopsis buski R2-RT and human LINE-1). Substitution rates for Induro and R2-RT are the same for cDNA and second-strand synthesis while LINE-1 has 2.5-fold lower fidelity when performing second-strand synthesis. Deletion and insertion rates increase for all RTs during second-strand synthesis. In addition, we find that a structured RNA template impacts fidelity for both RNA polymerase and RT. The accuracy and precision of Roll-Seq enable this method to be applied as a complementary analysis to structural and mechanistic characterization of RNA polymerases and reverse transcriptases or as a screening method for RNAP and RT fidelity.
Collapse
Affiliation(s)
| | - Stanislas Krudup
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
- École Supérieure de Biotechnologie de Strasbourg, 67400 Strasbourg, France
| | - Sean Maguire
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Irem Unlu
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Shengxi Guan
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Jackson A Buss
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Benedict A Smail
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Trevor van Eeuwen
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
| | - Martin S Taylor
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Kathleen H Burns
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Jennifer L Ong
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | | |
Collapse
|
8
|
Shand EL, Sweeney K, Sundling KE, McClean MN, Brow DA. Live-cell analysis of IMPDH protein levels during yeast colony growth provides insights into the regulation of GTP synthesis. mBio 2024; 15:e0102124. [PMID: 38940616 PMCID: PMC11323793 DOI: 10.1128/mbio.01021-24] [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: 04/10/2024] [Accepted: 05/24/2024] [Indexed: 06/29/2024] Open
Abstract
The purine nucleotides ATP and GTP are made from the common precursor inosine monophosphate (IMP). Maintaining the correct balance of these nucleotides for optimal cell growth is controlled in part by the enzyme IMP dehydrogenase (IMPDH), which catalyzes the first dedicated step of GTP biosynthesis. The regulation of IMPDH mRNA and protein levels in the yeast S. cerevisiae grown in liquid culture has been studied in some detail, but regulation of IMPDH protein under conditions of cellular crowding on a solid substrate has not been examined. Here, we report real-time, live-cell analysis of the accumulation of the Imd2 isoform of IMPDH in yeast cells forming a monolayer colony in a microfluidic device over a 50-hour time course. We observe two distinct phases of increased Imd2 accumulation: a guanine-insensitive phase early in outgrowth and a guanine-sensitive phase later, when cells become crowded. We show that the IMPDH inhibitor mycophenolic acid enhances both phases of increase. Deletion of a transcription attenuator upstream of the mRNA start site that decreases Imd2 mRNA synthesis in the presence of high GTP increases the baseline level of Imd2 protein 10-fold and abolishes guanine-sensitive but not guanine-insensitive induction. Our results suggest that at least two mechanisms of yeast Imd2 regulation exist, the known GTP-dependent attenuation of RNA polymerase II elongation and a GTP concentration-independent pathway that may be controlled by cell growth state. Live-cell analysis of IMPDH protein levels in a growing yeast colony confirms a known mechanism of regulation and provides evidence for an additional mode of regulation. IMPORTANCE This study used live-cell microscopy to track changes in the level of a key enzyme in GTP nucleotide biosynthesis, inosine monophosphate dehydrogenase (IMPDH), during growth of a brewers yeast colony over 2 days in a microfluidic device. The results show that feedback regulation via transcription attenuation allows cells to adapt to nutrient limitation in the crowded environs of a yeast colony. They also identify a novel mode of regulation of IMPDH level that is not driven by guanine nucleotide availability.
Collapse
Affiliation(s)
- Erica L. Shand
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Kieran Sweeney
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kaitlin E. Sundling
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Megan N. McClean
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
- University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - David A. Brow
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| |
Collapse
|
9
|
Aplin C, Zielinski KA, Pabit S, Ogunribido D, Katt WP, Pollack L, Cerione RA, Milano SK. Distinct conformational states enable transglutaminase 2 to promote cancer cell survival versus cell death. Commun Biol 2024; 7:982. [PMID: 39134806 PMCID: PMC11319651 DOI: 10.1038/s42003-024-06672-x] [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: 11/20/2023] [Accepted: 08/02/2024] [Indexed: 08/15/2024] Open
Abstract
Transglutaminase 2 (TG2) is a GTP-binding, protein-crosslinking enzyme that has been investigated as a therapeutic target for Celiac disease, neurological disorders, and aggressive cancers. TG2 has been suggested to adopt two conformational states that regulate its functions: a GTP-bound, closed conformation, and a calcium-bound, crosslinking-active open conformation. TG2 mutants that constitutively adopt an open conformation are cytotoxic to cancer cells. Thus, small molecules that bind and stabilize the open conformation of TG2 could offer a new therapeutic strategy. Here, we investigate TG2, using static and time-resolved small-angle X-ray scattering (SAXS) and single-particle cryoelectron microscopy (cryo-EM), to determine the conformational states responsible for conferring its biological effects. We also describe a newly developed TG2 inhibitor, LM11, that potently kills glioblastoma cells and use SAXS to investigate how LM11 affects the conformational states of TG2. Using SAXS and cryo-EM, we show that guanine nucleotides bind and stabilize a monomeric closed conformation while calcium binds to an open state that can form higher order oligomers. SAXS analysis suggests how a TG2 mutant that constitutively adopts the open state binds nucleotides through an alternative mechanism to wildtype TG2. Furthermore, we use time resolved SAXS to show that LM11 increases the ability of calcium to bind and stabilize an open conformation, which is not reversible by guanine nucleotides and is cytotoxic to cancer cells. Taken together, our findings demonstrate that the conformational dynamics of TG2 are more complex than previously suggested and highlight how conformational stabilization of TG2 by LM11 maintains TG2 in a cytotoxic conformational state.
Collapse
Affiliation(s)
- Cody Aplin
- Department of Chemistry and Chemical Biology, Cornell University, 14853, Ithaca, NY, USA
- Department of Molecular Medicine, Cornell University, 14853, Ithaca, NY, USA
| | - Kara A Zielinski
- School of Applied and Engineering Physics, Cornell University, 14853, Ithaca, NY, USA
| | - Suzette Pabit
- School of Applied and Engineering Physics, Cornell University, 14853, Ithaca, NY, USA
| | - Deborah Ogunribido
- Department of Chemistry and Chemical Biology, Cornell University, 14853, Ithaca, NY, USA
| | - William P Katt
- Department of Molecular Medicine, Cornell University, 14853, Ithaca, NY, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, 14853, Ithaca, NY, USA
| | - Richard A Cerione
- Department of Chemistry and Chemical Biology, Cornell University, 14853, Ithaca, NY, USA.
- Department of Molecular Medicine, Cornell University, 14853, Ithaca, NY, USA.
| | - Shawn K Milano
- Department of Chemistry and Chemical Biology, Cornell University, 14853, Ithaca, NY, USA
- Department of Molecular Medicine, Cornell University, 14853, Ithaca, NY, USA
| |
Collapse
|
10
|
Sahoo A, Gupta S, Das G, Ghosh A, Bagale SS, Sinha S, Gore KR. 2'- O-Alkyl- N 3-Methyluridine Functionalized Passenger Strand Improves RNAi Activity by Modulating the Thermal Stability. ACS Med Chem Lett 2024; 15:1250-1259. [PMID: 39140063 PMCID: PMC11318005 DOI: 10.1021/acsmedchemlett.4c00140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/25/2024] [Accepted: 07/01/2024] [Indexed: 08/15/2024] Open
Abstract
Herein, we have demonstrated that the siRNA activity could be enhanced by incorporating the guide strand in the RISC complex through thermodynamic asymmetry caused by m3U-based destabilizing modifications. A nuclease stability study revealed that 2'-OMe-m3U and 2'-OEt-m3U modifications slightly improved the half-lives of siRNA strands in human serum. In the in vitro gene silencing assay, 2'-OMe-m3U modification at the 3'-overhang and cleavage site of the passenger strand in anti-renilla and anti-Bcl-2 siRNA duplexes were well-tolerated and exhibited improved gene silencing activity. However, gene silencing activity was attenuated when these modifications were incorporated at position 3 in the seed region of the antisense strand. The molecular modeling studies using these modifications at the seed region with the MID domain of hAGO2 explained that the 2'-alkoxy group makes steric interactions with the amino acid residues of the hAGO2 protein.
Collapse
Affiliation(s)
- Avijit Sahoo
- Department
of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Shalini Gupta
- School
of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Gourav Das
- Department
of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Atanu Ghosh
- School
of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | | | - Surajit Sinha
- School
of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Kiran R. Gore
- Department
of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| |
Collapse
|
11
|
Mangrum MM, Vogel AK, Wagner AS, King AE, Miao J, Zhou Y, Phillips EK, Peters BM, Reynolds TB. Disruption to de novo uridine biosynthesis alters β-1,3-glucan masking in Candida albicans. mSphere 2024:e0028724. [PMID: 39115319 DOI: 10.1128/msphere.00287-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 05/21/2024] [Indexed: 08/18/2024] Open
Abstract
The uridine derivatives UDP-glucose and UDP-N-acetylglucosamine are important for cell wall construction as they are the precursors for the synthesis of β-1,3-glucan and chitin, respectively. Previous studies have demonstrated attenuated virulence of uridine auxotrophs in mice, which has been attributed to insufficient uridine levels for growth in the host. We have discovered that uridine deprivation in the uridine auxotroph ura3ΔΔ disrupts cell wall architecture by increasing surface mannans, exposing β-1,3-glucan and chitin, and decreasing UDP-sugar levels. Cell wall architecture and UDP-sugars can be rescued with uridine supplementation. The cell wall architectural disruptions in the ura3ΔΔ mutant also impact immune activation since the mutant elicited greater TNFα secretion from RAW264.7 macrophages than wild type. To determine if cell wall defects contributed to decreased virulence in the ura3ΔΔ mutant, we used a murine model of systemic infection. Mice infected with the ura3ΔΔ mutant exhibited increased survival and reduced kidney fungal burden compared with mice infected with wild type. However, suppression of the immune response with cyclophosphamide did not rescue virulence in mice infected with the ura3ΔΔ mutant, indicating the attenuation in virulence of uridine auxotrophs can be attributed to decreased growth in the host but not increased exposure of β-1,3-glucan. Moreover, the ura3ΔΔ mutant is unable to grow on ex vivo kidney agar, which demonstrates its inability to colonize the kidneys due to poor growth. Thus, although uridine auxotrophy elicits changes to cell wall architecture that increase the exposure of immunogenic polymers, metabolic fitness costs more strongly drive the observed virulence attenuation.IMPORTANCECandida albicans is a common cause of bloodstream infections (candidemia). Treatment of these bloodstream infections is made difficult because of increasing antifungal resistance and drug toxicity. Thus, new tactics are needed for antifungal drug development, with immunotherapy being of particular interest. The cell wall of C. albicans is composed of highly immunogenic polymers, particularly β-1,3-glucan. However, β-1,3-glucan is naturally masked by an outer layer of mannoproteins, which hampers the detection of the fungus by the host immune system. Alteration in cell wall components has been shown to increase β-1,3-glucan exposure; however, it is unknown how the inability to synthesize precursors to cell wall components affects unmasking. Here, we demonstrate how cell wall architecture is altered in response to a deficit in precursors for cell wall synthesis and how uridine is a crucial component of these precursors.
Collapse
Affiliation(s)
- Mikayla M Mangrum
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Amanda K Vogel
- Integrated Program in Biomedical Sciences, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Andrew S Wagner
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Ainsley E King
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Jian Miao
- Pharmaceutical Sciences Program, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Yue Zhou
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Elise K Phillips
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Brian M Peters
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee, USA
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Todd B Reynolds
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| |
Collapse
|
12
|
Sartori-Maldonado R, Montaser H, Soppa I, Eurola S, Juutila J, Balaz M, Puttonen H, Otonkoski T, Saarimäki-Vire J, Wartiovaara K. Thymidylate synthase disruption to limit cell proliferation in cell therapies. Mol Ther 2024; 32:2535-2548. [PMID: 38867450 DOI: 10.1016/j.ymthe.2024.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/10/2024] [Accepted: 06/10/2024] [Indexed: 06/14/2024] Open
Abstract
Stem and progenitor cells hold great promise for regenerative medicine and gene therapy approaches. However, transplantation of living cells entails a fundamental risk of unwanted growth, potentially exacerbated by CRISPR-Cas9 or other genetic manipulations. Here, we describe a safety system to control cell proliferation while allowing robust and efficient cell manufacture, without any added genetic elements. Inactivating TYMS, a key nucleotide metabolism enzyme, in several cell lines resulted in cells that proliferate only when supplemented with exogenous thymidine. Under supplementation, TYMS-/--pluripotent stem cells proliferate, produce teratomas, and successfully differentiate into potentially therapeutic cell types such as pancreatic β cells. Our results suggest that supplementation with exogenous thymidine affects stem cell proliferation, but not the function of stem cell-derived cells. After differentiation, postmitotic cells do not require thymidine in vitro or in vivo, as shown by the production of functional human insulin in mice up to 5 months after implantation of stem cell-derived pancreatic tissue.
Collapse
Affiliation(s)
- Rocio Sartori-Maldonado
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Hossam Montaser
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Inkeri Soppa
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Solja Eurola
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Juhana Juutila
- Faculty of Biological and Environmental Sciences University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
| | - Melanie Balaz
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Henri Puttonen
- Department of Pathology, Helsinki University Hospital, 00290 Helsinki, Finland
| | - Timo Otonkoski
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; Children's Hospital, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Jonna Saarimäki-Vire
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Kirmo Wartiovaara
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; Clinical Genetics, Helsinki University Hospital, 00290 Helsinki, Finland.
| |
Collapse
|
13
|
Bagdadi N, Wu J, Delaroche J, Serre L, Delphin C, De Andrade M, Carcel M, Nawabi H, Pinson B, Vérin C, Couté Y, Gory-Fauré S, Andrieux A, Stoppin-Mellet V, Arnal I. Stable GDP-tubulin islands rescue dynamic microtubules. J Cell Biol 2024; 223:e202307074. [PMID: 38758215 PMCID: PMC11101955 DOI: 10.1083/jcb.202307074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 02/26/2024] [Accepted: 05/04/2024] [Indexed: 05/18/2024] Open
Abstract
Microtubules are dynamic polymers that interconvert between phases of growth and shrinkage, yet they provide structural stability to cells. Growth involves hydrolysis of GTP-tubulin to GDP-tubulin, which releases energy that is stored within the microtubule lattice and destabilizes it; a GTP cap at microtubule ends is thought to prevent GDP subunits from rapidly dissociating and causing catastrophe. Here, using in vitro reconstitution assays, we show that GDP-tubulin, usually considered inactive, can itself assemble into microtubules, preferentially at the minus end, and promote persistent growth. GDP-tubulin-assembled microtubules are highly stable, displaying no detectable spontaneous shrinkage. Strikingly, islands of GDP-tubulin within dynamic microtubules stop shrinkage events and promote rescues. Microtubules thus possess an intrinsic capacity for stability, independent of accessory proteins. This finding provides novel mechanisms to explain microtubule dynamics.
Collapse
Affiliation(s)
- Nassiba Bagdadi
- Université Grenoble Alpes, INSERM, U1216, CNRS, CEA, Grenoble Institut Neurosciences (GIN), Grenoble, France
| | - Juliette Wu
- Université Grenoble Alpes, INSERM, U1216, CNRS, CEA, Grenoble Institut Neurosciences (GIN), Grenoble, France
| | - Julie Delaroche
- Université Grenoble Alpes, INSERM, U1216, CNRS, CEA, Grenoble Institut Neurosciences (GIN), Grenoble, France
| | - Laurence Serre
- Université Grenoble Alpes, INSERM, U1216, CNRS, CEA, Grenoble Institut Neurosciences (GIN), Grenoble, France
| | - Christian Delphin
- Université Grenoble Alpes, INSERM, U1216, CNRS, CEA, Grenoble Institut Neurosciences (GIN), Grenoble, France
| | - Manon De Andrade
- Université Grenoble Alpes, INSERM, U1216, CNRS, CEA, Grenoble Institut Neurosciences (GIN), Grenoble, France
| | - Marion Carcel
- Université Grenoble Alpes, INSERM, U1216, CNRS, CEA, Grenoble Institut Neurosciences (GIN), Grenoble, France
| | - Homaira Nawabi
- Université Grenoble Alpes, INSERM, U1216, CNRS, CEA, Grenoble Institut Neurosciences (GIN), Grenoble, France
| | - Benoît Pinson
- Metabolic Analyses Service, TBMCore—Université de Bordeaux—CNRS UAR 3427—INSERM US005, Bordeaux, France
| | - Claire Vérin
- Université Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, FR2048, Grenoble, France
| | - Yohann Couté
- Université Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, FR2048, Grenoble, France
| | - Sylvie Gory-Fauré
- Université Grenoble Alpes, INSERM, U1216, CNRS, CEA, Grenoble Institut Neurosciences (GIN), Grenoble, France
| | - Annie Andrieux
- Université Grenoble Alpes, INSERM, U1216, CNRS, CEA, Grenoble Institut Neurosciences (GIN), Grenoble, France
| | - Virginie Stoppin-Mellet
- Université Grenoble Alpes, INSERM, U1216, CNRS, CEA, Grenoble Institut Neurosciences (GIN), Grenoble, France
| | - Isabelle Arnal
- Université Grenoble Alpes, INSERM, U1216, CNRS, CEA, Grenoble Institut Neurosciences (GIN), Grenoble, France
| |
Collapse
|
14
|
Hofer A. How tumors hijack macrophages for immune evasion. NATURE CANCER 2024; 5:1134-1135. [PMID: 39152226 DOI: 10.1038/s43018-024-00808-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/19/2024]
Affiliation(s)
- Anders Hofer
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.
| |
Collapse
|
15
|
Lin MG, Yen CY, Shen YY, Huang YS, Ng IW, Barillà D, Sun YJ, Hsiao CD. Unraveling the structure and function of a novel SegC protein interacting with the SegAB chromosome segregation complex in Archaea. Nucleic Acids Res 2024:gkae660. [PMID: 39077943 DOI: 10.1093/nar/gkae660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 07/10/2024] [Accepted: 07/18/2024] [Indexed: 07/31/2024] Open
Abstract
Genome segregation is a fundamental process that preserves the genetic integrity of all organisms, but the mechanisms driving genome segregation in archaea remain enigmatic. This study delved into the unknown function of SegC (SSO0033), a novel protein thought to be involved in chromosome segregation in archaea. Using fluorescence polarization DNA binding assays, we discovered the ability of SegC to bind DNA without any sequence preference. Furthermore, we determined the crystal structure of SegC at 2.8 Å resolution, revealing the multimeric configuration and forming a large positively charged surface that can bind DNA. SegC has a tertiary structure folding similar to those of the ThDP-binding fold superfamily, but SegC shares only 5-15% sequence identity with those proteins. Unexpectedly, we found that SegC has nucleotide triphosphatase (NTPase) activity. We also determined the SegC-ADP complex structure, identifying the NTP binding pocket and relative SegC residues involved in the interaction. Interestingly, images from negative-stain electron microscopy revealed that SegC forms filamentous structures in the presence of DNA and NTPs. Further, more uniform and larger SegC-filaments are observed, when SegA-ATP was added. Notably, the introduction of SegB disrupts these oligomers, with ATP being essential for regulating filament formation. These findings provide insights into the functional and structural role of SegC in archaeal chromosome segregation.
Collapse
Affiliation(s)
- Min-Guan Lin
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Cheng-Yi Yen
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Yo-You Shen
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Sung Huang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Irene W Ng
- Department of Biology, University of York, Wentworth Way, YorkYO10 5DD, UK
| | - Daniela Barillà
- Department of Biology, University of York, Wentworth Way, YorkYO10 5DD, UK
| | - Yuh-Ju Sun
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Chwan-Deng Hsiao
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| |
Collapse
|
16
|
Ogino M, Green TJ, Ogino T. The complete pathway for co-transcriptional mRNA maturation within a large protein of a non-segmented negative-strand RNA virus. Nucleic Acids Res 2024:gkae659. [PMID: 39077935 DOI: 10.1093/nar/gkae659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/09/2024] [Accepted: 07/17/2024] [Indexed: 07/31/2024] Open
Abstract
Non-segmented negative-strand (NNS) RNA viruses, such as rabies, Nipah and Ebola, produce 5'-capped and 3'-polyadenylated mRNAs resembling higher eukaryotic mRNAs. Here, we developed a transcription elongation-coupled pre-mRNA capping system for vesicular stomatitis virus (VSV, a prototypic NNS RNA virus). Using this system, we demonstrate that the single-polypeptide RNA-dependent RNA polymerase (RdRp) large protein (L) catalyzes all pre-mRNA modifications co-transcriptionally in the following order: (i) 5'-capping (polyribonucleotidylation of GDP) to form a GpppA cap core structure, (ii) 2'-O-methylation of GpppA into GpppAm, (iii) guanine-N7-methylation of GpppAm into m7GpppAm (cap 1), (iv) 3'-polyadenylation to yield a poly(A) tail. The GDP polyribonucleotidyltransferase (PRNTase) domain of L generated capped pre-mRNAs of 18 nucleotides or longer via the formation of covalent enzyme-pre-mRNA intermediates. The single methyltransferase domain of L sequentially methylated the cap structure only when pre-mRNAs of 40 nucleotides or longer were associated with elongation complexes. These results suggest that the formation of pre-mRNA closed loop structures in elongation complexes via the RdRp and PRNTase domains followed by the RdRp and MTase domains on the same polypeptide is required for the cap 1 formation during transcription. Taken together, our findings indicate that NNS RNA virus L acts as an all-in-one viral mRNA assembly machinery.
Collapse
Affiliation(s)
- Minako Ogino
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA
| | - Todd J Green
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Tomoaki Ogino
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA
| |
Collapse
|
17
|
Yon WJ, Ha T, Zheng Y, Pedersen RTA. A tubulin-binding protein that preferentially binds to GDP-tubulin and promotes GTP exchange. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.09.539990. [PMID: 37214866 PMCID: PMC10197657 DOI: 10.1101/2023.05.09.539990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
α- and β-tubulin form heterodimers, with GTPase activity, that assemble into microtubules. Like other GTPases, the nucleotide-bound state of tubulin heterodimers controls whether the molecules are in a biologically active or inactive state. While α-tubulin in the heterodimer is constitutively bound to GTP, β-tubulin can be bound to either GDP (GDP-tubulin) or GTP (GTP-tubulin). GTP-tubulin hydrolyzes its GTP to GDP following assembly into a microtubule and, upon disassembly, must exchange its bound GDP for GTP to participate in subsequent microtubule polymerization. Tubulin dimers have been shown to exhibit rapid intrinsic nucleotide exchange in vitro, leading to a commonly accepted belief that a tubulin guanine nucleotide exchange factor (GEF) may be unnecessary in cells. Here, we use quantitative binding assays to show that BuGZ, a spindle assembly factor, binds tightly to GDP-tubulin, less tightly to GTP-tubulin, and weakly to microtubules. We further show that BuGZ promotes the incorporation of GTP into tubulin using a nucleotide exchange assay. The discovery of a tubulin GEF suggests a mechanism that may aid rapid microtubule assembly dynamics in cells.
Collapse
Affiliation(s)
- Wesley J Yon
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
- Cell, Molecular, Developmental Biology, and Biophysics Program, Johns Hopkins University, Baltimore, MD, USA
| | - Taekjip Ha
- Cell, Molecular, Developmental Biology, and Biophysics Program, Johns Hopkins University, Baltimore, MD, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Yixian Zheng
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
- Cell, Molecular, Developmental Biology, and Biophysics Program, Johns Hopkins University, Baltimore, MD, USA
| | - Ross T A Pedersen
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| |
Collapse
|
18
|
Tran DH, Kim D, Kesavan R, Brown H, Dey T, Soflaee MH, Vu HS, Tasdogan A, Guo J, Bezwada D, Al Saad H, Cai F, Solmonson A, Rion H, Chabatya R, Merchant S, Manales NJ, Tcheuyap VT, Mulkey M, Mathews TP, Brugarolas J, Morrison SJ, Zhu H, DeBerardinis RJ, Hoxhaj G. De novo and salvage purine synthesis pathways across tissues and tumors. Cell 2024; 187:3602-3618.e20. [PMID: 38823389 PMCID: PMC11246224 DOI: 10.1016/j.cell.2024.05.011] [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: 04/05/2023] [Revised: 03/16/2024] [Accepted: 05/03/2024] [Indexed: 06/03/2024]
Abstract
Purine nucleotides are vital for RNA and DNA synthesis, signaling, metabolism, and energy homeostasis. To synthesize purines, cells use two principal routes: the de novo and salvage pathways. Traditionally, it is believed that proliferating cells predominantly rely on de novo synthesis, whereas differentiated tissues favor the salvage pathway. Unexpectedly, we find that adenine and inosine are the most effective circulating precursors for supplying purine nucleotides to tissues and tumors, while hypoxanthine is rapidly catabolized and poorly salvaged in vivo. Quantitative metabolic analysis demonstrates comparative contribution from de novo synthesis and salvage pathways in maintaining purine nucleotide pools in tumors. Notably, feeding mice nucleotides accelerates tumor growth, while inhibiting purine salvage slows down tumor progression, revealing a crucial role of the salvage pathway in tumor metabolism. These findings provide fundamental insights into how normal tissues and tumors maintain purine nucleotides and highlight the significance of purine salvage in cancer.
Collapse
Affiliation(s)
- Diem H Tran
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Dohun Kim
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Rushendhiran Kesavan
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Harrison Brown
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Trishna Dey
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Mona Hoseini Soflaee
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Hieu S Vu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Alpaslan Tasdogan
- Department of Dermatology, University Hospital Essen & German Cancer Consortium, Partner Site, Essen, Germany
| | - Jason Guo
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Divya Bezwada
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Houssam Al Saad
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Feng Cai
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Ashley Solmonson
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Halie Rion
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Rawand Chabatya
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Salma Merchant
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Nathan J Manales
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Vanina T Tcheuyap
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Megan Mulkey
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Thomas P Mathews
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - James Brugarolas
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sean J Morrison
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Hao Zhu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Gerta Hoxhaj
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.
| |
Collapse
|
19
|
Wang D, Sun D, Wang X, Peng X, Ji Y, Tang L, He Q, Chen D, Yang Y, Zhou X, Xiong B, Ai J. Remodeling tumor-associated macrophage for anti-cancer effects by rational design of irreversible inhibition of mitogen-activated protein kinase-activated protein kinase 2. MedComm (Beijing) 2024; 5:e634. [PMID: 38988492 PMCID: PMC11233931 DOI: 10.1002/mco2.634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 07/12/2024] Open
Abstract
Mitogen-activated protein kinase-activated protein kinase 2 (MK2) emerges as a pivotal target in developing anti-cancer therapies. The limitations of ATP-competitive inhibitors, due to insufficient potency and selectivity, underscore the urgent need for a covalent irreversible MK2 inhibitor. Our initial analyses of The Cancer Genome Atlas database revealed MK2's overexpression across various cancer types, especially those characterized by inflammation, linking it to poor prognosis and highlighting its significance. Investigating MK2's kinase domain led to the identification of a unique cysteine residue, enabling the creation of targeted covalent inhibitors. Compound 11 was developed, demonstrating robust MK2 inhibition (IC50 = 2.3 nM) and high selectivity. It binds irreversibly to MK2, achieving prolonged signal suppression and reducing pathological inflammatory cytokines in macrophages. Furthermore, compound 11 or MK2 knockdown can inhibit the tumor-promoting macrophage M2 phenotype in vitro and in vivo. In macrophage-rich tumor model, compound 11 notably slowed growth in a dose-dependent manner. These findings support MK2 as a promising anticancer target, especially relevant in cancers fueled by inflammation or dominated by macrophages, and provide compound 11 serving as an invaluable chemical tool for exploring MK2's functions.
Collapse
Affiliation(s)
- Danyi Wang
- State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiP. R. China
- School of PharmacyUniversity of Chinese Academy of SciencesBeijingP. R. China
| | - Deqiao Sun
- State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiP. R. China
- School of PharmacyUniversity of Chinese Academy of SciencesBeijingP. R. China
| | - Xiaoyan Wang
- School of PharmacyUniversity of Chinese Academy of SciencesBeijingP. R. China
| | - Xia Peng
- State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiP. R. China
- School of PharmacyUniversity of Chinese Academy of SciencesBeijingP. R. China
| | - Yinchun Ji
- State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiP. R. China
- School of PharmacyUniversity of Chinese Academy of SciencesBeijingP. R. China
| | - Lu Tang
- School of PharmacyUniversity of Chinese Academy of SciencesBeijingP. R. China
- State Key Laboratory of Chemical BiologyShanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiP. R. China
| | - Qichang He
- State Key Laboratory of Chemical BiologyShanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiP. R. China
| | - Danqi Chen
- School of PharmacyUniversity of Chinese Academy of SciencesBeijingP. R. China
- State Key Laboratory of Chemical BiologyShanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiP. R. China
| | - Ye Yang
- State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiP. R. China
- School of PharmacyUniversity of Chinese Academy of SciencesBeijingP. R. China
| | - Xuan Zhou
- State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiP. R. China
- School of PharmacyUniversity of Chinese Academy of SciencesBeijingP. R. China
| | - Bing Xiong
- School of PharmacyUniversity of Chinese Academy of SciencesBeijingP. R. China
- State Key Laboratory of Chemical BiologyShanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiP. R. China
| | - Jing Ai
- State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiP. R. China
- School of PharmacyUniversity of Chinese Academy of SciencesBeijingP. R. China
- Shandong Laboratory of Yantai Drug DiscoveryBohai Rim Advanced Research Institute for Drug DiscoveryYantaiP. R. China
| |
Collapse
|
20
|
Vanclooster P, Seghers S, Prenen H. State-of-the-art and upcoming trends in RAS-directed therapies in gastrointestinal malignancies. Curr Opin Oncol 2024; 36:313-319. [PMID: 38726828 DOI: 10.1097/cco.0000000000001042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
PURPOSE OF REVIEW Overall, the review underscores the evolving landscape of KRAS-targeted therapy and the potential for these approaches to improve outcomes for patients with gastrointestinal malignancies. It highlights the importance of ongoing research and clinical trials in advancing precision medicine strategies for KRAS-driven cancers. This review provides a comprehensive overview of the RAS signaling pathway and its significance in gastrointestinal malignancies. RECENT FINDINGS The introduction of KRAS inhibitor represents a significant advancement in the treatment landscape for KRAS-mutant cancers. In this review, we discuss upcoming trends in KRAS-targeted therapy, including the development of mutant-specific direct KRAS inhibitors like MRTX1133 and pan-RAS inhibitors such as RMC-6236. It also explores indirect RAS inhibitors targeting upstream and downstream components of the RAS pathway. Additionally, the review examines other upcoming strategies like combination therapies, such as CDK4/6 and ERK MAPK inhibitors, as well as adoptive cell therapy and cancer vaccines targeting KRAS-mutant cancers. SUMMARY Targeting RAS has become an important strategy in treating gastrointestinal cancer. These findings in this review underscore the importance of a multidisciplinary approach, integrating advances in molecular profiling, targeted therapy, immunotherapy, and clinical research to optimize treatment strategies for patients with KRAS-mutant gastrointestinal malignancies.
Collapse
Affiliation(s)
| | - Sofie Seghers
- Department of Oncology, Antwerp University Hospital, Edegem
- Center for Oncological Research (CORE)
| | - Hans Prenen
- Department of Oncology, Antwerp University Hospital, Edegem
- Center for Oncological Research (CORE)
- Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium
| |
Collapse
|
21
|
Yamada S, Mizukoshi T, Sato A, Sakakibara SI. Purinosomes and Purine Metabolism in Mammalian Neural Development: A Review. Acta Histochem Cytochem 2024; 57:89-100. [PMID: 38988694 PMCID: PMC11231565 DOI: 10.1267/ahc.24-00027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 05/19/2024] [Indexed: 07/12/2024] Open
Abstract
Neural stem/progenitor cells (NSPCs) in specific brain regions require precisely regulated metabolite production during critical development periods. Purines-vital components of DNA, RNA, and energy carriers like ATP and GTP-are crucial metabolites in brain development. Purine levels are tightly controlled through two pathways: de novo synthesis and salvage synthesis. Enzymes driving de novo pathway are assembled into a large multienzyme complex termed the "purinosome." Here, we review purine metabolism and purinosomes as spatiotemporal regulators of neural development. Notably, around postnatal day 0 (P0) during mouse cortical development, purine synthesis transitions from the de novo pathway to the salvage pathway. Inhibiting the de novo pathway affects mTORC1 pathway and leads to specific forebrain malformations. In this review, we also explore the importance of protein-protein interactions of a newly identified NSPC protein-NACHT and WD repeat domain-containing 1 (Nwd1)-in purinosome formation. Reduced Nwd1 expression disrupts purinosome formation, impacting NSPC proliferation and neuronal migration, resulting in periventricular heterotopia. Nwd1 interacts directly with phosphoribosylaminoimidazole-succinocarboxamide synthetase (PAICS), an enzyme involved in de novo purine synthesis. We anticipate this review will be valuable for researchers investigating neural development, purine metabolism, and protein-protein interactions.
Collapse
Affiliation(s)
- Seiya Yamada
- Laboratory for Molecular Neurobiology, Faculty of Human Sciences, Waseda University, Saitama, Japan
- Neuroscience Center, HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Tomoya Mizukoshi
- Laboratory for Molecular Neurobiology, Faculty of Human Sciences, Waseda University, Saitama, Japan
| | - Ayaka Sato
- Laboratory for Molecular Neurobiology, Faculty of Human Sciences, Waseda University, Saitama, Japan
| | - Shin-Ichi Sakakibara
- Laboratory for Molecular Neurobiology, Faculty of Human Sciences, Waseda University, Saitama, Japan
| |
Collapse
|
22
|
Kang YR, Jiao YT, Zhao CF, Zhang XW, Huang WH. Electroactive polymer tag modified nanosensors for enhanced intracellular ATP detection. Analyst 2024; 149:3530-3536. [PMID: 38757525 DOI: 10.1039/d4an00511b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
ATP plays a crucial role in cell energy supply, so the quantification of intracellular ATP levels is particularly important for understanding many physio-pathological processes. The intracellular quantification of this non-electroactive molecule can be realized using aptamer-modified nanoelectrodes, but is hindered by the limited quantity of modification and electroactive tags on the nanosized electrodes. Herein, we developed a simple but effective electrochemical signal amplification strategy for intracellular ATP detection, which replaces the regular ATP aptamer-linked ferrocene monomer with a polymer, thus greatly magnifying the amounts of electrochemical reporters linked to one chain of the aptamer and enhancing the signals. This ferrocene polymer-ATP aptamer was further immobilized onto Au nanowire electrodes (SiC@C@Au NWEs) to achieve accurate quantification of intracellular ATP in single cells, presenting high electrochemical signal output and high specificity. This work not only provides a powerful tool for quantifying intracellular ATP but also offers a simple and versatile strategy for electrochemical signal amplification in the detection of broader non-electroactive molecules involved in different kinds of intracellular physiological processes.
Collapse
Affiliation(s)
- Yi-Ran Kang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, Hubei Province, P. R. China.
| | - Yu-Ting Jiao
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, Hubei Province, P. R. China.
| | - Chen-Fei Zhao
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, Hubei Province, P. R. China.
| | - Xin-Wei Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, Hubei Province, P. R. China.
| | - Wei-Hua Huang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, Hubei Province, P. R. China.
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, P. R. China
| |
Collapse
|
23
|
Wang Y, Deng T, Liu X, Fang X, Mo Y, Xie N, Nie G, Zhang B, Fan X. Smart Nanoplatforms Responding to the Tumor Microenvironment for Precise Drug Delivery in Cancer Therapy. Int J Nanomedicine 2024; 19:6253-6277. [PMID: 38911497 PMCID: PMC11193972 DOI: 10.2147/ijn.s459710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/20/2024] [Indexed: 06/25/2024] Open
Abstract
The tumor microenvironment (TME) is a complex and dynamic entity, comprising stromal cells, immune cells, blood vessels and extracellular matrix, which is intimately associated with the occurrence and development of cancers, as well as their therapy. Utilizing the shared characteristics of tumors, such as an acidic environment, enzymes and hypoxia, researchers have developed a promising cancer therapy strategy known as responsive release of nano-loaded drugs, specifically targeted at tumor tissues or cells. In this comprehensive review, we provide an in-depth overview of the current fundamentals and state-of-the-art intelligent strategies of TME-responsive nanoplatforms, which include acidic pH, high GSH levels, high-level adenosine triphosphate, overexpressed enzymes, hypoxia and reductive environment. Additionally, we showcase the latest advancements in TME-responsive nanoparticles. In conclusion, we thoroughly examine the immediate challenges and prospects of TME-responsive nanopharmaceuticals, with the expectation that the progress of these targeted nanoformulations will enable the exploitation, overcoming or modulation of the TME, ultimately leading to significantly more effective cancer therapy.
Collapse
Affiliation(s)
- Yujie Wang
- Shenzhen Key Laboratory of Nanozymes and Translational Cancer Research, Department of Otolaryngology, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, 518035, People’s Republic of China
| | - Tingting Deng
- Shenzhen Key Laboratory of Nanozymes and Translational Cancer Research, Department of Otolaryngology, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, 518035, People’s Republic of China
| | - Xi Liu
- Department of Nephrology, Shenzhen Longgang Central Hospital, Shenzhen, 518116, People’s Republic of China
| | - Xueyang Fang
- Shenzhen Key Laboratory of Nanozymes and Translational Cancer Research, Department of Otolaryngology, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, 518035, People’s Republic of China
| | - Yongpan Mo
- Department of Breast Surgery, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, 518035, People’s Republic of China
| | - Ni Xie
- The Bio-Bank of Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, Guangdong, 518035, People’s Republic of China
| | - Guohui Nie
- Shenzhen Key Laboratory of Nanozymes and Translational Cancer Research, Department of Otolaryngology, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, 518035, People’s Republic of China
| | - Bin Zhang
- Shenzhen Key Laboratory of Nanozymes and Translational Cancer Research, Department of Otolaryngology, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, 518035, People’s Republic of China
| | - Xiaoqin Fan
- Shenzhen Key Laboratory of Nanozymes and Translational Cancer Research, Department of Otolaryngology, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, 518035, People’s Republic of China
- The Bio-Bank of Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, Guangdong, 518035, People’s Republic of China
| |
Collapse
|
24
|
Umpierre AD, Li B, Ayasoufi K, Simon WL, Zhao S, Xie M, Thyen G, Hur B, Zheng J, Liang Y, Bosco DB, Maynes MA, Wu Z, Yu X, Sung J, Johnson AJ, Li Y, Wu LJ. Microglial P2Y 6 calcium signaling promotes phagocytosis and shapes neuroimmune responses in epileptogenesis. Neuron 2024; 112:1959-1977.e10. [PMID: 38614103 PMCID: PMC11189754 DOI: 10.1016/j.neuron.2024.03.017] [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: 06/29/2023] [Revised: 01/09/2024] [Accepted: 03/13/2024] [Indexed: 04/15/2024]
Abstract
Microglial calcium signaling is rare in a baseline state but strongly engaged during early epilepsy development. The mechanism(s) governing microglial calcium signaling are not known. By developing an in vivo uridine diphosphate (UDP) fluorescent sensor, GRABUDP1.0, we discovered that UDP release is a conserved response to seizures and excitotoxicity across brain regions. UDP can signal through the microglial-enriched P2Y6 receptor to increase calcium activity during epileptogenesis. P2Y6 calcium activity is associated with lysosome biogenesis and enhanced production of NF-κB-related cytokines. In the hippocampus, knockout of the P2Y6 receptor prevents microglia from fully engulfing neurons. Attenuating microglial calcium signaling through calcium extruder ("CalEx") expression recapitulates multiple features of P2Y6 knockout, including reduced lysosome biogenesis and phagocytic interactions. Ultimately, P2Y6 knockout mice retain more CA3 neurons and better cognitive task performance during epileptogenesis. Our results demonstrate that P2Y6 signaling impacts multiple aspects of myeloid cell immune function during epileptogenesis.
Collapse
Affiliation(s)
| | - Bohan Li
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing 100871, China
| | | | - Whitney L Simon
- Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Shunyi Zhao
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA; Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Manling Xie
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
| | - Grace Thyen
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
| | - Benjamin Hur
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA; Department of Surgery, Mayo Clinic, Rochester, MN 55905, USA
| | - Jiaying Zheng
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yue Liang
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
| | - Dale B Bosco
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
| | - Mark A Maynes
- Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhaofa Wu
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing 100871, China
| | - Xinzhu Yu
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jaeyun Sung
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA; Department of Surgery, Mayo Clinic, Rochester, MN 55905, USA
| | - Aaron J Johnson
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA; Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yulong Li
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing 100871, China.
| | - Long-Jun Wu
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA; Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA; Center for Neuroimmunology and Glial Biology, Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA.
| |
Collapse
|
25
|
Levesque S, Cosentino A, Verma A, Genovese P, Bauer DE. Enhancing prime editing in hematopoietic stem and progenitor cells by modulating nucleotide metabolism. Nat Biotechnol 2024:10.1038/s41587-024-02266-4. [PMID: 38806736 DOI: 10.1038/s41587-024-02266-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 04/26/2024] [Indexed: 05/30/2024]
Abstract
Therapeutic prime editing of hematopoietic stem and progenitor cells (HSPCs) holds great potential to remedy blood disorders. Quiescent cells have low nucleotide levels and resist retroviral infection, and it is possible that nucleotide metabolism could limit reverse transcription-mediated prime editing in HSPCs. We demonstrate that deoxynucleoside supplementation and Vpx-mediated degradation of SAMHD1 improve prime editing efficiency in HSPCs, especially when coupled with editing approaches that evade mismatch repair.
Collapse
Affiliation(s)
- Sébastien Levesque
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute, Cambridge, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Andrea Cosentino
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Milano-Bicocca University, Milan, Italy
| | - Archana Verma
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute, Cambridge, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Pietro Genovese
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute, Cambridge, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
- Broad Institute, Cambridge, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
26
|
Kennelly C, Tran P, Prindle A. Environmental purines decrease Pseudomonas aeruginosa biofilm formation by disrupting c-di-GMP metabolism. Cell Rep 2024; 43:114154. [PMID: 38669142 PMCID: PMC11197132 DOI: 10.1016/j.celrep.2024.114154] [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: 11/06/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Cyclic di-guanosine monophosphate (c-di-GMP) is a bacterial second messenger that governs the lifestyle switch between planktonic and biofilm states. While substantial investigation has focused on the proteins that produce and degrade c-di-GMP, less attention has been paid to the potential for metabolic control of c-di-GMP signaling. Here, we show that micromolar levels of specific environmental purines unexpectedly decrease c-di-GMP and biofilm formation in Pseudomonas aeruginosa. Using a fluorescent genetic reporter, we show that adenosine and inosine decrease c-di-GMP even when competing purines are present. We confirm genetically that purine salvage is required for c-di-GMP decrease. Furthermore, we find that (p)ppGpp prevents xanthosine and guanosine from producing an opposing c-di-GMP increase, reinforcing a salvage hierarchy that favors c-di-GMP decrease even at the expense of growth. We propose that purines can act as a cue for bacteria to shift their lifestyle away from the recalcitrant biofilm state via upstream metabolic control of c-di-GMP signaling.
Collapse
Affiliation(s)
- Corey Kennelly
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Peter Tran
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA; Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Arthur Prindle
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA; Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.
| |
Collapse
|
27
|
Gao S, Oden P, Ryan B, Yang H, Freudenthal B, Greenberg M. Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase β. Nucleic Acids Res 2024; 52:5392-5405. [PMID: 38634780 PMCID: PMC11109955 DOI: 10.1093/nar/gkae277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/28/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
N6-(2-deoxy-α,β-d-erythro-pentofuranosyl)-2,6-diamino-4-hydroxy-5-formamido-pyrimidine (Fapy•dG) is formed from a common intermediate and in comparable amounts to the well-studied mutagenic DNA lesion 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-OxodGuo). Fapy•dG preferentially gives rise to G → T transversions and G → A transitions. However, the molecular basis by which Fapy•dG is processed by DNA polymerases during this mutagenic process remains poorly understood. To address this we investigated how DNA polymerase β (Pol β), a model mammalian polymerase, bypasses a templating Fapy•dG, inserts Fapy•dGTP, and extends from Fapy•dG at the primer terminus. When Fapy•dG is present in the template, Pol β incorporates TMP less efficiently than either dCMP or dAMP. Kinetic analysis revealed that Fapy•dGTP is a poor substrate but is incorporated ∼3-times more efficiently opposite dA than dC. Extension from Fapy•dG at the 3'-terminus of a nascent primer is inefficient due to the primer terminus being poorly positioned for catalysis. Together these data indicate that mutagenic bypass of Fapy•dG is likely to be the source of the mutagenic effects of the lesion and not Fapy•dGTP. These experiments increase our understanding of the promutagenic effects of Fapy•dG.
Collapse
Affiliation(s)
- Shijun Gao
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Peyton N Oden
- Department of Biochemistry and Molecular Biology, and Department of Cancer Biology, University of Kansas Medical Center, KS City, KS 66160, USA
| | - Benjamin J Ryan
- Department of Biochemistry and Molecular Biology, and Department of Cancer Biology, University of Kansas Medical Center, KS City, KS 66160, USA
| | - Haozhe Yang
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, and Department of Cancer Biology, University of Kansas Medical Center, KS City, KS 66160, USA
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| |
Collapse
|
28
|
Marvin JS, Kokotos AC, Kumar M, Pulido C, Tkachuk AN, Yao JS, Brown TA, Ryan TA. iATPSnFR2: A high-dynamic-range fluorescent sensor for monitoring intracellular ATP. Proc Natl Acad Sci U S A 2024; 121:e2314604121. [PMID: 38748581 PMCID: PMC11126915 DOI: 10.1073/pnas.2314604121] [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: 08/24/2023] [Accepted: 04/10/2024] [Indexed: 05/27/2024] Open
Abstract
We developed a significantly improved genetically encoded quantitative adenosine triphosphate (ATP) sensor to provide real-time dynamics of ATP levels in subcellular compartments. iATPSnFR2 is a variant of iATPSnFR1, a previously developed sensor that has circularly permuted superfolder green fluorescent protein (GFP) inserted between the ATP-binding helices of the ε-subunit of a bacterial F0-F1 ATPase. Optimizing the linkers joining the two domains resulted in a ~fivefold to sixfold improvement in the dynamic range compared to the previous-generation sensor, with excellent discrimination against other analytes, and affinity variants varying from 4 µM to 500 µM. A chimeric version of this sensor fused to either the HaloTag protein or a suitable spectrally separated fluorescent protein provides an optional ratiometric readout allowing comparisons of ATP across cellular regions. Subcellular targeting the sensor to nerve terminals reveals previously uncharacterized single-synapse metabolic signatures, while targeting to the mitochondrial matrix allowed direct quantitative probing of oxidative phosphorylation dynamics.
Collapse
Affiliation(s)
| | - Alexandros C. Kokotos
- Department of Biochemistry, Weill Cornell Medicine, New York, NY10065
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Mukesh Kumar
- Department of Biochemistry, Weill Cornell Medicine, New York, NY10065
| | - Camila Pulido
- Department of Biochemistry, Weill Cornell Medicine, New York, NY10065
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | | | | | | | - Timothy A. Ryan
- HHMI, Ashburn, VA20147
- Department of Biochemistry, Weill Cornell Medicine, New York, NY10065
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| |
Collapse
|
29
|
Xu X, Chen Z, Bartman CR, Xing X, Olszewski K, Rabinowitz JD. One-carbon unit supplementation fuels purine synthesis in tumor-infiltrating T cells and augments checkpoint blockade. Cell Chem Biol 2024; 31:932-943.e8. [PMID: 38759619 DOI: 10.1016/j.chembiol.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/29/2024] [Accepted: 04/17/2024] [Indexed: 05/19/2024]
Abstract
Nucleotides perform important metabolic functions, carrying energy and feeding nucleic acid synthesis. Here, we use isotope tracing-mass spectrometry to quantitate contributions to purine nucleotides from salvage versus de novo synthesis. We further explore the impact of augmenting a key precursor for purine synthesis, one-carbon (1C) units. We show that tumors and tumor-infiltrating T cells (relative to splenic or lymph node T cells) synthesize purines de novo. Shortage of 1C units for T cell purine synthesis is accordingly a potential bottleneck for anti-tumor immunity. Supplementing 1C units by infusing formate drives formate assimilation into purines in tumor-infiltrating T cells. Orally administered methanol functions as a formate pro-drug, with deuteration enabling kinetic control of formate production. Safe doses of methanol raise formate levels and augment anti-PD-1 checkpoint blockade in MC38 tumors, tripling durable regressions. Thus, 1C deficiency can gate antitumor immunity and this metabolic checkpoint can be overcome with pharmacological 1C supplementation.
Collapse
Affiliation(s)
- Xincheng Xu
- Department of Chemistry, Princeton University, Princeton, NJ, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ, USA
| | - Zihong Chen
- Department of Chemistry, Princeton University, Princeton, NJ, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ, USA
| | - Caroline R Bartman
- Department of Chemistry, Princeton University, Princeton, NJ, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ, USA
| | - Xi Xing
- Department of Chemistry, Princeton University, Princeton, NJ, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ, USA
| | - Kellen Olszewski
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ, USA.
| | - Joshua D Rabinowitz
- Department of Chemistry, Princeton University, Princeton, NJ, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ, USA.
| |
Collapse
|
30
|
Wu S, Gabelli SB, Sohn J. The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS. Nat Commun 2024; 15:4012. [PMID: 38740774 PMCID: PMC11091121 DOI: 10.1038/s41467-024-48365-3] [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: 05/31/2023] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
cGAS activates innate immune responses against cytosolic double-stranded DNA. Here, by determining crystal structures of cGAS at various reaction stages, we report a unifying catalytic mechanism. apo-cGAS assumes an array of inactive conformations and binds NTPs nonproductively. Dimerization-coupled double-stranded DNA-binding then affixes the active site into a rigid lock for productive metal•substrate binding. A web-like network of protein•NTP, intra-NTP, and inter-NTP interactions ensures the stepwise synthesis of 2'-5'/3'-5'-linked cGAMP while discriminating against noncognate NTPs and off-pathway intermediates. One divalent metal is sufficient for productive substrate binding, and capturing the second divalent metal is tightly coupled to nucleotide and linkage specificities, a process which manganese is preferred over magnesium by 100-fold. Additionally, we elucidate how mouse cGAS achieves more stringent NTP and linkage specificities than human cGAS. Together, our results reveal that an adaptable, yet precise lock-and-key-like mechanism underpins cGAS catalysis.
Collapse
Affiliation(s)
- Shuai Wu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sandra B Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Discovery Chemistry, Merck Laboratories, West Point, PA, USA
| | - Jungsan Sohn
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
31
|
Ullah Khan S, Daniela Hernández-González K, Ali A, Shakeel Raza Rizvi S. Diabetes and the fabkin complex: A dual-edged sword. Biochem Pharmacol 2024; 223:116196. [PMID: 38588831 DOI: 10.1016/j.bcp.2024.116196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 03/27/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
The Fabkin complex, composed of FABP4, ADK, and NDPKs, emerges as a novel regulator of insulin-producing beta cells, offering promising prospects for diabetes treatment. Our approach, which combines literature review and database analysis, sets the stage for future research. These findings hold significant implications for both diabetes treatment and research, as they present potential therapeutic targets for personalized treatment, leading to enhanced patient outcomes and a deeper comprehension of the disease. The multifaceted role of the Fabkin complex in glucose metabolism, insulin resistance, anti-inflammation, beta cell proliferation, and vascular function underscores its therapeutic potential, reshaping diabetes management and propelling advancements in the field.
Collapse
Affiliation(s)
- Safir Ullah Khan
- Department of Zoology, Wildlife & Fisheries, Faculty of sciences, Pir Mehr Ali Shah Arid Agriculture University, P.C. 46300, Rawalpindi, Pakistan
| | - Karla Daniela Hernández-González
- Facultad de Biología, Universidad Veracruzana, Circuito Gonzalo Aguirre Beltrán s/n, Zona Universitaria, C.P. 91000 Xalapa, Veracruz, México
| | - Amir Ali
- Nanoscience and Nanotechnology Program, Center for Research and Advanced Studies of the IPN, Mexico City, Mexico
| | - Syed Shakeel Raza Rizvi
- Department of Zoology, Wildlife & Fisheries, Faculty of sciences, Pir Mehr Ali Shah Arid Agriculture University, P.C. 46300, Rawalpindi, Pakistan.
| |
Collapse
|
32
|
Wen SL, Lang W, Li X, Cao QY. PEGylated AIEgens for dual sensing of ATP and H 2S and cancer cells photodynamic therapy. Talanta 2024; 271:125739. [PMID: 38309115 DOI: 10.1016/j.talanta.2024.125739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/12/2024] [Accepted: 01/30/2024] [Indexed: 02/05/2024]
Abstract
Fluorescent sensors have been widely applied for biosensing, but probes for both multiple analytes sensing and photodynamic therapy (PDT) effect are less reported. In this article, we reported three AIE-based probes anchored with different mass-weight polyethylene glycol (PEG) tails, i.e., TPE-PEG160, TPE-PEG350, and TPE-PEG750, for both adenosine-5'-triphosphate (ATP) and hydrogen sulfide (H2S) detection and also cancer cells photodynamic therapy. TPE-PEGns (n = 160, 350 and 750) contain the tetraphenylethylene-based fluorophore core, the pyridinium and amide anion binding sites, the H2S cleavable disulfide bond, and the hydrophilic PEG chain. They exhibit a good amphiphilic property and can self-assemble nona-aggregation with a moderated red emission in an aqueous solution. Importantly, the size of aggregation, photophysical property, sensing ability and photosensitivity of these amphiphilic probes can be controlled by tuning the PEG chain length. Moreover, the selected probe TPE-PEG160 has been successfully used to detect environmental H2S and image ATP levels in living cells, and TPE-PEG750 has been used for photodynamic therapy of tumor cells under light irradiation.
Collapse
Affiliation(s)
- Shi-Lian Wen
- College of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, PR China
| | - Wei Lang
- College of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, PR China
| | - Xue Li
- College of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, PR China
| | - Qian-Yong Cao
- College of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, PR China.
| |
Collapse
|
33
|
Papasergi-Scott MM, Pérez-Hernández G, Batebi H, Gao Y, Eskici G, Seven AB, Panova O, Hilger D, Casiraghi M, He F, Maul L, Gmeiner P, Kobilka BK, Hildebrand PW, Skiniotis G. Time-resolved cryo-EM of G-protein activation by a GPCR. Nature 2024; 629:1182-1191. [PMID: 38480881 DOI: 10.1038/s41586-024-07153-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 02/02/2024] [Indexed: 03/26/2024]
Abstract
G-protein-coupled receptors (GPCRs) activate heterotrimeric G proteins by stimulating guanine nucleotide exchange in the Gα subunit1. To visualize this mechanism, we developed a time-resolved cryo-EM approach that examines the progression of ensembles of pre-steady-state intermediates of a GPCR-G-protein complex. By monitoring the transitions of the stimulatory Gs protein in complex with the β2-adrenergic receptor at short sequential time points after GTP addition, we identified the conformational trajectory underlying G-protein activation and functional dissociation from the receptor. Twenty structures generated from sequential overlapping particle subsets along this trajectory, compared to control structures, provide a high-resolution description of the order of main events driving G-protein activation in response to GTP binding. Structural changes propagate from the nucleotide-binding pocket and extend through the GTPase domain, enacting alterations to Gα switch regions and the α5 helix that weaken the G-protein-receptor interface. Molecular dynamics simulations with late structures in the cryo-EM trajectory support that enhanced ordering of GTP on closure of the α-helical domain against the nucleotide-bound Ras-homology domain correlates with α5 helix destabilization and eventual dissociation of the G protein from the GPCR. These findings also highlight the potential of time-resolved cryo-EM as a tool for mechanistic dissection of GPCR signalling events.
Collapse
MESH Headings
- Humans
- Binding Sites
- Cryoelectron Microscopy
- GTP-Binding Protein alpha Subunits, Gs/chemistry
- GTP-Binding Protein alpha Subunits, Gs/drug effects
- GTP-Binding Protein alpha Subunits, Gs/metabolism
- GTP-Binding Protein alpha Subunits, Gs/ultrastructure
- Guanosine Triphosphate/metabolism
- Guanosine Triphosphate/pharmacology
- Models, Molecular
- Molecular Dynamics Simulation
- Protein Binding
- Receptors, Adrenergic, beta-2/metabolism
- Receptors, Adrenergic, beta-2/chemistry
- Receptors, Adrenergic, beta-2/ultrastructure
- Time Factors
- Enzyme Activation/drug effects
- Protein Domains
- Protein Structure, Secondary
- Signal Transduction/drug effects
Collapse
Affiliation(s)
- Makaía M Papasergi-Scott
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Guillermo Pérez-Hernández
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Hossein Batebi
- Institute of Medical Physics and Biophysics, Faculty of Medicine, Leipzig University, Leipzig, Germany
| | - Yang Gao
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Gözde Eskici
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Alpay B Seven
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ouliana Panova
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Hilger
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Institute of Pharmaceutical Chemistry, Philipps-University of Marburg, Marburg, Germany
| | - Marina Casiraghi
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Feng He
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Luis Maul
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter W Hildebrand
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
- Institute of Medical Physics and Biophysics, Faculty of Medicine, Leipzig University, Leipzig, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Georgios Skiniotis
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
34
|
Westarp S, Brandt F, Neumair L, Betz C, Dagane A, Kemper S, Jacob CR, Neubauer P, Kurreck A, Kaspar F. Nucleoside Phosphorylases make N7-xanthosine. Nat Commun 2024; 15:3625. [PMID: 38684649 PMCID: PMC11058261 DOI: 10.1038/s41467-024-47287-4] [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: 10/23/2023] [Accepted: 03/26/2024] [Indexed: 05/02/2024] Open
Abstract
Modern, highly evolved nucleoside-processing enzymes are known to exhibit perfect regioselectivity over the glycosylation of purine nucleobases at N9. We herein report an exception to this paradigm. Wild-type nucleoside phosphorylases also furnish N7-xanthosine, a "non-native" ribosylation regioisomer of xanthosine. This unusual nucleoside possesses several atypical physicochemical properties such as redshifted absorption spectra, a high equilibrium constant of phosphorolysis and low acidity. Ultimately, the biosynthesis of this previously unknown natural product illustrates how even highly evolved, essential enzymes from primary metabolism are imperfect catalysts.
Collapse
Affiliation(s)
- Sarah Westarp
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstrasse 76, 13355, Berlin, Germany
- BioNukleo GmbH, Ackerstraße 76, 13355, Berlin, Germany
| | - Felix Brandt
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106, Braunschweig, Germany
| | - Lena Neumair
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstrasse 76, 13355, Berlin, Germany
| | - Christina Betz
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstrasse 76, 13355, Berlin, Germany
| | - Amin Dagane
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstrasse 76, 13355, Berlin, Germany
| | - Sebastian Kemper
- Institute for Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106, Braunschweig, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstrasse 76, 13355, Berlin, Germany
| | - Anke Kurreck
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstrasse 76, 13355, Berlin, Germany.
- BioNukleo GmbH, Ackerstraße 76, 13355, Berlin, Germany.
| | - Felix Kaspar
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany.
| |
Collapse
|
35
|
Pytko KG, Dannenberg RL, Eckert KA, Hedglin M. Replication of [AT/TA] 25 Microsatellite Sequences by Human DNA Polymerase δ Holoenzymes Is Dependent on dNTP and RPA Levels. Biochemistry 2024; 63:969-983. [PMID: 38623046 DOI: 10.1021/acs.biochem.4c00006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Fragile sites are unstable genomic regions that are prone to breakage during stressed DNA replication. Several common fragile sites (CFS) contain A+T-rich regions including perfect [AT/TA] microsatellite repeats that may collapse into hairpins when in single-stranded DNA (ssDNA) form and coincide with chromosomal hotspots for breakage and rearrangements. While many factors contribute to CFS instability, evidence exists for replication stalling within [AT/TA] microsatellite repeats. Currently, it is unknown how stress causes replication stalling within [AT/TA] microsatellite repeats. To investigate this, we utilized FRET to characterize the structures of [AT/TA]25 sequences and also reconstituted lagging strand replication to characterize the progression of pol δ holoenzymes through A+T-rich sequences. The results indicate that [AT/TA]25 sequences adopt hairpins that are unwound by the major ssDNA-binding complex, RPA, and the progression of pol δ holoenzymes through A+T-rich sequences saturated with RPA is dependent on the template sequence and dNTP concentration. Importantly, the effects of RPA on the replication of [AT/TA]25 sequences are dependent on dNTP concentration, whereas the effects of RPA on the replication of A+T-rich, nonstructure-forming sequences are independent of dNTP concentration. Collectively, these results reveal complexities in lagging strand replication and provide novel insights into how [AT/TA] microsatellite repeats contribute to genome instability.
Collapse
Affiliation(s)
- Kara G Pytko
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Rachel L Dannenberg
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Kristin A Eckert
- Department of Pathology and Laboratory Medicine, The Jake Gittlen Laboratories for Cancer Research, Hershey, PA 17033, United States
| | - Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| |
Collapse
|
36
|
Liu T, Pyle AM. Highly Reactive Group I Introns Ubiquitous in Pathogenic Fungi. J Mol Biol 2024; 436:168513. [PMID: 38447889 DOI: 10.1016/j.jmb.2024.168513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/25/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024]
Abstract
Systemic fungal infections are a growing public health threat, and yet viable antifungal drug targets are limited as fungi share a similar proteome with humans. However, features of RNA metabolism and the noncoding transcriptomes in fungi are distinctive. For example, fungi harbor highly structured RNA elements that humans lack, such as self-splicing introns within key housekeeping genes in the mitochondria. However, the location and function of these mitochondrial riboregulatory elements has largely eluded characterization. Here we used an RNA-structure-based bioinformatics pipeline to identify the group I introns interrupting key mitochondrial genes in medically relevant fungi, revealing their fixation within a handful of genetic hotspots and their ubiquitous presence across divergent phylogenies of fungi, including all highest priority pathogens such as Candida albicans, Candida auris, Aspergillus fumigatus and Cryptococcus neoformans. We then biochemically characterized two representative introns from C. albicans and C. auris, demonstrating their exceptionally efficient splicing catalysis relative to previously-characterized group I introns. Indeed, the C. albicans mitochondrial intron displays extremely rapid catalytic turnover, even at ambient temperatures and physiological magnesium ion concentrations. Our results unmask a significant new set of players in the RNA metabolism of pathogenic fungi, suggesting a promising new type of antifungal drug target.
Collapse
Affiliation(s)
- Tianshuo Liu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA; Department of Chemistry, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.
| |
Collapse
|
37
|
Aspenström P. Miro GTPases at the Crossroads of Cytoskeletal Dynamics and Mitochondrial Trafficking. Cells 2024; 13:647. [PMID: 38607086 PMCID: PMC11012113 DOI: 10.3390/cells13070647] [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: 03/07/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/13/2024] Open
Abstract
Miro GTPases are key components in the machinery responsible for transporting mitochondria and peroxisomes along microtubules, and also play important roles in regulating calcium homeostasis and organizing contact sites between mitochondria and the endoplasmic reticulum. Moreover, Miro GTPases have been shown to interact with proteins that actively regulate cytoskeletal organization and dynamics, suggesting that these GTPases participate in organizing cytoskeletal functions and organelle transport. Derailed mitochondrial transport is associated with neuropathological conditions such as Parkinson's and Alzheimer's diseases. This review explores our recent understanding of the diverse roles of Miro GTPases under cytoskeletal control, both under normal conditions and during the course of human diseases such as neuropathological disorders.
Collapse
Affiliation(s)
- Pontus Aspenström
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology (IGP), Uppsala University, SE 751 85 Uppsala, Sweden
| |
Collapse
|
38
|
Pagba CV, Gupta AK, Dilsha K, Sadrpour P, Jakubec J, Prakash P, van der Hoeven D, Cho KJ, Gilbertson S, Gorfe AA. Biophysical and Biochemical Characterization of Structurally Diverse Small Molecule Hits for KRAS Inhibition. Chembiochem 2024; 25:e202300827. [PMID: 38349283 DOI: 10.1002/cbic.202300827] [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: 12/12/2023] [Revised: 02/12/2024] [Indexed: 03/08/2024]
Abstract
We describe six compounds as early hits for the development of direct inhibitors of KRAS, an important anticancer drug target. We show that these compounds bind to KRAS with affinities in the low micromolar range and exert different effects on its interactions with binding partners. Some of the compounds exhibit selective binding to the activated form of KRAS and inhibit signal transduction through both the MAPK or the phosphatidylinositide 3-kinase PI3K-protein kinase B (AKT) pathway in cells expressing mutant KRAS. Most inhibit intrinsic and/or SOS-mediated KRAS activation while others inhibit RAS-effector interaction. We propose these compounds as starting points for the development of non-covalent allosteric KRAS inhibitors.
Collapse
Affiliation(s)
- Cynthia V Pagba
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
| | - Amit K Gupta
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
| | - Kasuni Dilsha
- Department of Chemistry, University of Houston, 3585 Cullen Blvd., Houston, TX 77204, USA
| | - Parisa Sadrpour
- Department of Biochemistry and Molecular Biology, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH 45435, USA
| | - Jacob Jakubec
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
| | - Priyanka Prakash
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
| | - Dharini van der Hoeven
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, 7500 Cambridge St., Houston, Texas, 77030, USA
| | - Kwang-Jin Cho
- Department of Biochemistry and Molecular Biology, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH 45435, USA
| | - Scott Gilbertson
- Department of Chemistry, University of Houston, 3585 Cullen Blvd., Houston, TX 77204, USA
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
- Biochemistry and Cell Biology Program & Therapeutics and Pharmacology Program, UTHealth MD Anderson Cancer Center Graduate School of Biomedical Sciences, Houston, 6431 Fannin St., Houston, Texas, 77030, USA
| |
Collapse
|
39
|
Ham D, Inoue A, Xu J, Du Y, Chung KY. Molecular mechanism of muscarinic acetylcholine receptor M3 interaction with Gq. Commun Biol 2024; 7:362. [PMID: 38521872 PMCID: PMC10960872 DOI: 10.1038/s42003-024-06056-1] [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: 06/06/2023] [Accepted: 03/15/2024] [Indexed: 03/25/2024] Open
Abstract
Muscarinic acetylcholine receptor M3 (M3) and its downstream effector Gq/11 are critical drug development targets due to their involvement in physiopathological processes. Although the structure of the M3-miniGq complex was recently published, the lack of information on the intracellular loop 3 (ICL3) of M3 and extensive modification of Gαq impedes the elucidation of the molecular mechanism of M3-Gq coupling under more physiological condition. Here, we describe the molecular mechanism underlying the dynamic interactions between full-length wild-type M3 and Gq using hydrogen-deuterium exchange mass spectrometry and NanoLuc Binary Technology-based cell systems. We propose a detailed analysis of M3-Gq coupling through examination of previously well-defined binding interfaces and neglected regions. Our findings suggest potential binding interfaces between M3 and Gq in pre-assembled and functionally active complexes. Furthermore, M3 ICL3 negatively affected M3-Gq coupling, and the Gαq AHD underwent unique conformational changes during M3-Gq coupling.
Collapse
Affiliation(s)
- Donghee Ham
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan.
| | - Jun Xu
- Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Yang Du
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, Shenzhen Futian Biomedical Innovation R&D Center, the Chinese University of Hong Kong, Shenzhen, 518172, Guangdong, China.
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea.
| |
Collapse
|
40
|
Zhou X, Huang S, Liu W, Shang L. Metal Ion-Regulated Fluorescent Sensor Array Based on Gold Nanoclusters for Physiological Phosphate Sensing. Anal Chem 2024; 96:4224-4231. [PMID: 38421217 DOI: 10.1021/acs.analchem.3c05582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The detection of physiological phosphates (PPs) is of great importance due to their essential roles in numerous biological processes, but the efficient detection of different PPs simultaneously remains challenging. In this work, we propose a fluorescence sensor array for detecting PPs based on metal-ion-regulated gold nanoclusters (AuNCs) via an indicator-displacement assay. Zn2+ and Eu3+ are selected to assemble with two different AuNCs, resulting in quenching or enhancing their fluorescence. Based on the competitive interaction of metal ions with AuNCs and PPs, the fluorescence of AuNCs will be recovered owing to the disassembly of AuNC-metal ion ensembles. Depending on different PPs' distinct fluorescence responses, a four-channel sensor array was established. The array not only exhibits good discrimination capability for eight kinds of PPs (i.e., ATP, ADP, AMP, GTP, CTP, UTP, PPi, and Pi) via linear discriminant analysis but also enables quantitative detection of single phosphate (e.g., ATP) in the presence of interfering PPs mixtures. Moreover, potential application of the present sensor array for the discrimination of different PPs in real samples (e.g., cell lysates and serum) was successfully demonstrated with a good performance. This work illustrates the great potential of a metal ion-regulated sensor array as a new and efficient sensing platform for differential sensing of phosphates as well as other disease-related biomolecules.
Collapse
Affiliation(s)
- Xiaomeng Zhou
- State Key Laboratory of Solidification Processing, School of Materials Science and Engineering, Northwestern Polytechnical University, Xi'an 710072, China
| | - Saijin Huang
- State Key Laboratory of Solidification Processing, School of Materials Science and Engineering, Northwestern Polytechnical University, Xi'an 710072, China
| | - Wenfeng Liu
- State Key Laboratory of Solidification Processing, School of Materials Science and Engineering, Northwestern Polytechnical University, Xi'an 710072, China
| | - Li Shang
- State Key Laboratory of Solidification Processing, School of Materials Science and Engineering, Northwestern Polytechnical University, Xi'an 710072, China
| |
Collapse
|
41
|
Gao S, Hou P, Oh J, Wang D, Greenberg MM. Molecular Mechanism of RNA Polymerase II Transcriptional Mutagenesis by the Epimerizable DNA Lesion, Fapy·dG. J Am Chem Soc 2024; 146:6274-6282. [PMID: 38393762 PMCID: PMC10932878 DOI: 10.1021/jacs.3c14476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Oxidative DNA lesions cause significant detrimental effects on a living species. Two major DNA lesions resulting from dG oxidation, 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-OxodGuo) and formamidopyrimidine (Fapy·dG), are produced from a common chemical intermediate. Fapy·dG is formed in comparable yields under oxygen-deficient conditions. Replicative bypass of Fapy·dG in human cells is more mutagenic than that of 8-OxodGuo. Despite the biological importance of transcriptional mutagenesis, there are no reports of the effects of Fapy·dG on RNA polymerase II (Pol II) activity. Here we perform comprehensive kinetic studies to investigate the impact of Fapy·dG on three key transcriptional fidelity checkpoint steps by Pol II: insertion, extension, and proofreading steps. The ratios of error-free versus error-prone incorporation opposite Fapy·dG are significantly reduced in comparison with undamaged dG. Similarly, Fapy·dG:A mispair is extended with comparable efficiency as that of the error-free, Fapy·dG:C base pair. The α- and β-configurational isomers of Fapy·dG have distinct effects on Pol II insertion and extension. Pol II can preferentially cleave error-prone products by proofreading. To further understand the structural basis of transcription processing of Fapy·dG, five different structures were solved, including Fapy·dG template-loading state (apo), error-free cytidine triphosphate (CTP) binding state (prechemistry), error-prone ATP binding state (prechemistry), error-free Fapy·dG:C product state (postchemistry), and error-prone Fapy·dG:A product state (postchemistry), revealing distinctive nucleotide binding and product states. Taken together, our study provides a comprehensive mechanistic framework for better understanding how Fapy·dG lesions impact transcription and subsequent pathological consequences.
Collapse
Affiliation(s)
- Shijun Gao
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Peini Hou
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
- Department of Regulatory Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, California 92093, United States
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| |
Collapse
|
42
|
Mostert D, Bubeneck WA, Rauh T, Kielkowski P, Itzen A, Jung K, Sieber SA. Pronucleotide Probes Reveal a Diverging Specificity for AMPylation vs UMPylation of Human and Bacterial Nucleotide Transferases. Biochemistry 2024; 63:651-659. [PMID: 38388156 PMCID: PMC10918828 DOI: 10.1021/acs.biochem.3c00568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/23/2024] [Accepted: 02/07/2024] [Indexed: 02/24/2024]
Abstract
AMPylation is a post-translational modification utilized by human and bacterial cells to modulate the activity and function of specific proteins. Major AMPylators such as human FICD and bacterial VopS have been studied extensively for their substrate and target scope in vitro. Recently, an AMP pronucleotide probe also facilitated the in situ analysis of AMPylation in living cells. Based on this technology, we here introduce a novel UMP pronucleotide probe and utilize it to profile uninfected and Vibrio parahaemolyticus infected human cells. Mass spectrometric analysis of labeled protein targets reveals an unexpected promiscuity of human nucleotide transferases with an almost identical target set of AMP- and UMPylated proteins. Vice versa, studies in cells infected by V. parahaemolyticus and its effector VopS revealed solely AMPylation of host enzymes, highlighting a so far unknown specificity of this transferase for ATP. Taken together, pronucleotide probes provide an unprecedented insight into the in situ activity profile of crucial nucleotide transferases, which can largely differ from their in vitro activity.
Collapse
Affiliation(s)
- Dietrich Mostert
- Center
for Functional Protein Assemblies (CPA), Department of Chemistry,
Chair of Organic Chemistry II, Technical
University of Munich, 85748 Garching, Germany
| | - Wilhelm Andrei Bubeneck
- Center
for Functional Protein Assemblies (CPA), Department of Chemistry,
Chair of Organic Chemistry II, Technical
University of Munich, 85748 Garching, Germany
| | - Theresa Rauh
- Center
for Functional Protein Assemblies (CPA), Department of Chemistry,
Chair of Organic Chemistry II, Technical
University of Munich, 85748 Garching, Germany
| | - Pavel Kielkowski
- Department
of Chemistry, Ludwig-Maximilians-Universität
München, 81377 München, Germany
| | - Aymelt Itzen
- Department
of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
| | - Kirsten Jung
- Department
of Biology I, Microbiology, Ludwig-Maximilians-Universität
München, 82152 Martinsried, Germany
| | - Stephan A. Sieber
- Center
for Functional Protein Assemblies (CPA), Department of Chemistry,
Chair of Organic Chemistry II, Technical
University of Munich, 85748 Garching, Germany
| |
Collapse
|
43
|
Cui H, Shi Q, Macarios CM, Schimmel P. Metabolic regulation of mRNA splicing. Trends Cell Biol 2024:S0962-8924(24)00025-4. [PMID: 38431493 DOI: 10.1016/j.tcb.2024.02.002] [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: 11/07/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 03/05/2024]
Abstract
Alternative mRNA splicing enables the diversification of the proteome from a static genome and confers plasticity and adaptiveness on cells. Although this is often explored in development, where hard-wired programs drive the differentiation and specialization, alternative mRNA splicing also offers a way for cells to react to sudden changes in outside stimuli such as small-molecule metabolites. Fluctuations in metabolite levels and availability in particular convey crucial information to which cells react and adapt. We summarize and highlight findings surrounding the metabolic regulation of mRNA splicing. We discuss the principles underlying the biochemistry and biophysical properties of mRNA splicing, and propose how these could intersect with metabolite levels. Further, we present examples in which metabolites directly influence RNA-binding proteins and splicing factors. We also discuss the interplay between alternative mRNA splicing and metabolite-responsive signaling pathways. We hope to inspire future research to obtain a holistic picture of alternative mRNA splicing in response to metabolic cues.
Collapse
Affiliation(s)
- Haissi Cui
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
| | - Qingyu Shi
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | | | - Paul Schimmel
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
44
|
Da J, Di X, Xie Y, Li J, Zhang L, Liu Y. Recent advances in nanomedicine for metabolism-targeted cancer therapy. Chem Commun (Camb) 2024; 60:2442-2461. [PMID: 38321983 DOI: 10.1039/d3cc05858a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Metabolism denotes the sum of biochemical reactions that maintain cellular function. Different from most normal differentiated cells, cancer cells adopt altered metabolic pathways to support malignant properties. Typically, almost all cancer cells need a large number of proteins, lipids, nucleotides, and energy in the form of ATP to support rapid division. Therefore, targeting tumour metabolism has been suggested as a generic and effective therapy strategy. With the rapid development of nanotechnology, nanomedicine promises to have a revolutionary impact on clinical cancer therapy due to many merits such as targeting, improved bioavailability, controllable drug release, and potentially personalized treatment compared to conventional drugs. This review comprehensively elucidates recent advances of nanomedicine in targeting important metabolites such as glucose, glutamine, lactate, cholesterol, and nucleotide for effective cancer therapy. Furthermore, the challenges and future development in this area are also discussed.
Collapse
Affiliation(s)
- Jun Da
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.
| | - XinJia Di
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.
| | - YuQi Xie
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.
| | - JiLi Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.
| | - LiLi Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.
| | - YanLan Liu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.
| |
Collapse
|
45
|
Tian L, Li Y, Shi Y. Dark and Dronc activation in Drosophila melanogaster. Proc Natl Acad Sci U S A 2024; 121:e2312784121. [PMID: 38381783 PMCID: PMC10907274 DOI: 10.1073/pnas.2312784121] [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: 07/26/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024] Open
Abstract
The onset of apoptosis is characterized by a cascade of caspase activation, where initiator caspases are activated by a multimeric adaptor complex known as the apoptosome. In Drosophila melanogaster, the initiator caspase Dronc undergoes autocatalytic activation in the presence of the Dark apoptosome. Despite rigorous investigations, the activation mechanism for Dronc remains elusive. Here, we report the cryo-EM structures of an auto-inhibited Dark monomer and a single-layered, multimeric Dark/Dronc complex. Our biochemical analysis suggests that the auto-inhibited Dark oligomerizes upon binding to Dronc, which is sufficient for the activation of both Dark and Dronc. In contrast, the previously observed double-ring Dark apoptosome may represent a non-functional or "off-pathway" conformation. These findings expand our understanding on the molecular mechanism of apoptosis in Drosophila.
Collapse
Affiliation(s)
- Lu Tian
- Beijing Frontier Research Center for Biological Structures, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
| | - Yini Li
- Beijing Frontier Research Center for Biological Structures, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
| | - Yigong Shi
- Beijing Frontier Research Center for Biological Structures, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
- Westlake Laboratory of Life Sciences and Biomedicine, Westlake Institute for Advanced Study, Hangzhou310024, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou310024, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou310024, China
| |
Collapse
|
46
|
Miller WE, O'Connor CM. CMV-encoded GPCRs in infection, disease, and pathogenesis. Adv Virus Res 2024; 118:1-75. [PMID: 38461029 DOI: 10.1016/bs.aivir.2024.01.001] [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] [Indexed: 03/11/2024]
Abstract
G protein coupled receptors (GPCRs) are seven-transmembrane domain proteins that modulate cellular processes in response to external stimuli. These receptors represent the largest family of membrane proteins, and in mammals, their signaling regulates important physiological functions, such as vision, taste, and olfaction. Many organisms, including yeast, slime molds, and viruses encode GPCRs. Cytomegaloviruses (CMVs) are large, betaherpesviruses, that encode viral GPCRs (vGPCRs). Human CMV (HCMV) encodes four vGPCRs, including UL33, UL78, US27, and US28. Each of these vGPCRs, as well as their rodent and primate orthologues, have been investigated for their contributions to viral infection and disease. Herein, we discuss how the CMV vGPCRs function during lytic and latent infection, as well as our understanding of how they impact viral pathogenesis.
Collapse
Affiliation(s)
- William E Miller
- Department of Molecular and Cellular Bioscience, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Christine M O'Connor
- Infection Biology, Sheikha Fatima bint Mubarak Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States; Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland Clinic, Cleveland, OH, United States; Case Comprehensive Cancer Center, Cleveland, OH, United States.
| |
Collapse
|
47
|
Shannon A, Chazot A, Feracci M, Falcou C, Fattorini V, Selisko B, Good S, Moussa A, Sommadossi JP, Ferron F, Alvarez K, Canard B. An exonuclease-resistant chain-terminating nucleotide analogue targeting the SARS-CoV-2 replicase complex. Nucleic Acids Res 2024; 52:1325-1340. [PMID: 38096103 PMCID: PMC10853775 DOI: 10.1093/nar/gkad1194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/14/2023] [Accepted: 12/11/2023] [Indexed: 02/10/2024] Open
Abstract
Nucleotide analogues (NA) are currently employed for treatment of several viral diseases, including COVID-19. NA prodrugs are intracellularly activated to the 5'-triphosphate form. They are incorporated into the viral RNA by the viral polymerase (SARS-CoV-2 nsp12), terminating or corrupting RNA synthesis. For Coronaviruses, natural resistance to NAs is provided by a viral 3'-to-5' exonuclease heterodimer nsp14/nsp10, which can remove terminal analogues. Here, we show that the replacement of the α-phosphate of Bemnifosbuvir 5'-triphosphate form (AT-9010) by an α-thiophosphate renders it resistant to excision. The resulting α-thiotriphosphate, AT-9052, exists as two epimers (RP/SP). Through co-crystallization and activity assays, we show that the Sp isomer is preferentially used as a substrate by nucleotide diphosphate kinase (NDPK), and by SARS-CoV-2 nsp12, where its incorporation causes immediate chain-termination. The same -Sp isomer, once incorporated by nsp12, is also totally resistant to the excision by nsp10/nsp14 complex. However, unlike AT-9010, AT-9052-RP/SP no longer inhibits the N-terminal nucleotidylation domain of nsp12. We conclude that AT-9052-Sp exhibits a unique mechanism of action against SARS-CoV-2. Moreover, the thio modification provides a general approach to rescue existing NAs whose activity is hampered by coronavirus proofreading capacity.
Collapse
Affiliation(s)
- Ashleigh Shannon
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Aurélie Chazot
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Mikael Feracci
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Camille Falcou
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Véronique Fattorini
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Barbara Selisko
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Steven Good
- ATEA Pharmaceuticals, Inc., 225 Franklin St., Suite 2100, Boston, MA 02110, USA
| | - Adel Moussa
- ATEA Pharmaceuticals, Inc., 225 Franklin St., Suite 2100, Boston, MA 02110, USA
| | | | - François Ferron
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Karine Alvarez
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Bruno Canard
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| |
Collapse
|
48
|
Xu P, Yang T, Kundnani DL, Sun M, Marsili S, Gombolay A, Jeon Y, Newnam G, Balachander S, Bazzani V, Baccarani U, Park V, Tao S, Lori A, Schinazi R, Kim B, Pursell Z, Tell G, Vascotto C, Storici F. Light-strand bias and enriched zones of embedded ribonucleotides are associated with DNA replication and transcription in the human-mitochondrial genome. Nucleic Acids Res 2024; 52:1207-1225. [PMID: 38117983 PMCID: PMC10853789 DOI: 10.1093/nar/gkad1204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 11/30/2023] [Accepted: 12/05/2023] [Indexed: 12/22/2023] Open
Abstract
Abundant ribonucleoside-triphosphate (rNTP) incorporation into DNA by DNA polymerases in the form of ribonucleoside monophosphates (rNMPs) is a widespread phenomenon in nature, resulting in DNA-structural change and genome instability. The rNMP distribution, characteristics, hotspots and association with DNA metabolic processes in human mitochondrial DNA (hmtDNA) remain mostly unknown. Here, we utilize the ribose-seq technique to capture embedded rNMPs in hmtDNA of six different cell types. In most cell types, the rNMPs are preferentially embedded on the light strand of hmtDNA with a strong bias towards rCMPs; while in the liver-tissue cells, the rNMPs are predominately found on the heavy strand. We uncover common rNMP hotspots and conserved rNMP-enriched zones across the entire hmtDNA, including in the control region, which links the rNMP presence to the frequent hmtDNA replication-failure events. We show a strong correlation between coding-sequence size and rNMP-embedment frequency per nucleotide on the non-template, light strand in all cell types, supporting the presence of transient RNA-DNA hybrids preceding light-strand replication. Moreover, we detect rNMP-embedment patterns that are only partly conserved across the different cell types and are distinct from those found in yeast mtDNA. The study opens new research directions to understand the biology of hmtDNA and genomic rNMPs.
Collapse
Affiliation(s)
- Penghao Xu
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Taehwan Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Deepali L Kundnani
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Mo Sun
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Stefania Marsili
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Alli L Gombolay
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Youngkyu Jeon
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Gary Newnam
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Sathya Balachander
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Veronica Bazzani
- Department of Medicine, University of Udine, Udine 33100, Italy
- IMol Polish Academy of Sciences, Warsaw 02-247, Poland
| | - Umberto Baccarani
- Department of Medicine, University of Udine, Udine 33100, Italy
- General Surgery Clinic and Liver Transplant Center, University-Hospital of Udine, Udine 33100, Italy
| | - Vivian S Park
- Department of Biochemistry and Molecular Biology, Tulane Cancer Center, Tulane University of Medicine, New Orleans, LA 70118, USA
| | - Sijia Tao
- Center for ViroScience and Cure, Department of Pediatrics, Laboratory of Biochemical Pharmacology, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta 30322, GA, USA
| | - Adriana Lori
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta 30329, GA, USA
- Department of Population Science, American Cancer Society, Kennesaw 30144, GA, USA
| | - Raymond F Schinazi
- Center for ViroScience and Cure, Department of Pediatrics, Laboratory of Biochemical Pharmacology, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta 30322, GA, USA
| | - Baek Kim
- Center for ViroScience and Cure, Department of Pediatrics, Laboratory of Biochemical Pharmacology, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta 30322, GA, USA
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane Cancer Center, Tulane University of Medicine, New Orleans, LA 70118, USA
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Udine 33100, Italy
| | - Carlo Vascotto
- Department of Medicine, University of Udine, Udine 33100, Italy
- IMol Polish Academy of Sciences, Warsaw 02-247, Poland
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| |
Collapse
|
49
|
Aplin C, Zielinski KA, Pabit S, Ogunribido D, Katt WP, Pollack L, Cerione RA, Milano SK. Defining the conformational states that enable transglutaminase 2 to promote cancer cell survival versus cell death. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.04.578794. [PMID: 38370687 PMCID: PMC10871292 DOI: 10.1101/2024.02.04.578794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Transglutaminase 2 (TG2) is a GTP-binding/protein-crosslinking enzyme that has been investigated as a therapeutic target for Celiac disease, neurological disorders, and aggressive cancers. TG2 has been suggested to adopt two conformational states that regulate its functions: a GTP-bound, closed conformation, and a calcium-bound, crosslinking-active open conformation. TG2 mutants that constitutively adopt an open conformation are cytotoxic to cancer cells. Thus, small molecules that maintain the open conformation of TG2 could offer a new therapeutic strategy. Here, we investigate TG2, using static and time-resolved small-angle X-ray scattering (SAXS) and single-particle cryoelectron microscopy (cryo-EM), to determine the conformational states responsible for conferring its biological effects. We also describe a newly developed TG2 inhibitor, LM11, that potently kills glioblastoma cells and use SAXS to investigate how LM11 affects the conformational states of TG2. Using SAXS and cryo-EM, we show that guanine nucleotide-bound TG2 adopts a monomeric closed conformation while calcium-bound TG2 assumes an open conformational state that can form higher order oligomers. SAXS analysis also suggests how a TG2 mutant that constitutively adopts the open state binds nucleotides through an alternative mechanism to wildtype TG2. Furthermore, we use time-resolved SAXS to show that LM11 increases the ability of calcium to drive TG2 to an open conformation, which is not reversible by guanine nucleotides and is cytotoxic to cancer cells. Taken together, our findings demonstrate that the conformational dynamics of TG2 are more complex than previously suggested and highlight how conformational stabilization of TG2 by LM11 maintains TG2 in a cytotoxic conformational state.
Collapse
Affiliation(s)
- Cody Aplin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
| | - Kara A. Zielinski
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853
| | - Suzette Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853
| | - Deborah Ogunribido
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - William P. Katt
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853
| | - Richard A. Cerione
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
| | - Shawn K. Milano
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
| |
Collapse
|
50
|
Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sánchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Işik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, Riento K, Halls-Kass R, Augustin M, Lammens A, Jestel A, Upla P, Xibinaku K, Congreve S, Hennink M, Rogala KB, Schneider AM, Fairman JE, Christensen SM, Desrosiers B, Bisacchi GS, Saunders OL, Hafeez N, Miao W, Kapeller R, Zaller DM, Sali A, Weichenrieder O, Burns KH, Götte M, Rout MP, Arnold E, Greenbaum BD, Romero DL, LaCava J, Taylor MS. Structures, functions and adaptations of the human LINE-1 ORF2 protein. Nature 2024; 626:194-206. [PMID: 38096902 PMCID: PMC10830420 DOI: 10.1038/s41586-023-06947-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024]
Abstract
The LINE-1 (L1) retrotransposon is an ancient genetic parasite that has written around one-third of the human genome through a 'copy and paste' mechanism catalysed by its multifunctional enzyme, open reading frame 2 protein (ORF2p)1. ORF2p reverse transcriptase (RT) and endonuclease activities have been implicated in the pathophysiology of cancer2,3, autoimmunity4,5 and ageing6,7, making ORF2p a potential therapeutic target. However, a lack of structural and mechanistic knowledge has hampered efforts to rationally exploit it. We report structures of the human ORF2p 'core' (residues 238-1061, including the RT domain) by X-ray crystallography and cryo-electron microscopy in several conformational states. Our analyses identified two previously undescribed folded domains, extensive contacts to RNA templates and associated adaptations that contribute to unique aspects of the L1 replication cycle. Computed integrative structural models of full-length ORF2p show a dynamic closed-ring conformation that appears to open during retrotransposition. We characterize ORF2p RT inhibition and reveal its underlying structural basis. Imaging and biochemistry show that non-canonical cytosolic ORF2p RT activity can produce RNA:DNA hybrids, activating innate immune signalling through cGAS/STING and resulting in interferon production6-8. In contrast to retroviral RTs, L1 RT is efficiently primed by short RNAs and hairpins, which probably explains cytosolic priming. Other biochemical activities including processivity, DNA-directed polymerization, non-templated base addition and template switching together allow us to propose a revised L1 insertion model. Finally, our evolutionary analysis demonstrates structural conservation between ORF2p and other RNA- and DNA-dependent polymerases. We therefore provide key mechanistic insights into L1 polymerization and insertion, shed light on the evolutionary history of L1 and enable rational drug development targeting L1.
Collapse
Affiliation(s)
| | - Trevor van Eeuwen
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - David Hoyos
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arthur Zalevsky
- Department of Bioengineering and Therapeutic Sciences University of California, San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biology Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Egor P Tchesnokov
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | | | - Bryant D Miller
- Department of Pathology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Luciano H Di Stefano
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, The Netherlands
| | - Francesc Xavier Ruiz
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Matthew Hancock
- Department of Bioengineering and Therapeutic Sciences University of California, San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biology Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Esin Işik
- Department of Pathology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Carlos Mendez-Dorantes
- Department of Pathology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Thomas Walpole
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | - Charles Nichols
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | - Paul Wan
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | - Kirsi Riento
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | - Rowan Halls-Kass
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | | | - Alfred Lammens
- Proteros Biostructures GmbH, Martinsried, Planegg, Germany
| | - Anja Jestel
- Proteros Biostructures GmbH, Martinsried, Planegg, Germany
| | - Paula Upla
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - Kera Xibinaku
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | | | | | - Kacper B Rogala
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Anna M Schneider
- Structural Biology of Selfish RNA, Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | | | | | | | | | | | | | | | | | | | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences University of California, San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biology Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Oliver Weichenrieder
- Structural Biology of Selfish RNA, Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | - Kathleen H Burns
- Department of Pathology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada.
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA.
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA.
| | - Benjamin D Greenbaum
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA.
| | | | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA.
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, The Netherlands.
| | - Martin S Taylor
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|